StemCell Therapy

What is a genome

A genome is a collective term for all the genetic material within an organism. In essence,the genome decides exactly what that organism will look and act like at birth one huge, expansive instruction manual that tellscells their duties. Every living thing has a genome, from bacteria to plants to humans, and they are all different in size with various combinations of genes inside.

The human genome packs in 30,000 genes, but this is just 1% of the total genetic material contained within. Quite frankly, its a mess in there much of the genetic material is duplicated DNA that (supposedly) does very little, and the vast majority of DNA simply doesnt code for anything(these sections are calledintrons). That isnt to say it does nothing. In fact,recent studieshave shown us that non-coding DNA is essential to controlling whether our genes get switched on or not. However, most of the time its the actual genes that are the important bit.

Studying the genome of humans and other organisms is vitalfor a number of reasons.Firstly, it helps us characterize each one before genomics, scientists simply grouped animals and plants by what they looked like, but research into their genes now allows for accuratecharacterization oforganismsinto specificgeneraand species.

In humans, genomic research has allowed researchers to understand the underlying causes of many complex diseases and find possible targets for treatment.Currently, the best tool to do thisisgenome-wide association studies (GWAS).

The idea behind GWAS is relatively intuitive simply take a group of people with the disease you wish to study, and compare their genomesfor common genetic variants that could predict the presence of that disease.These studies have illuminated a huge number of variants linked with higher disease prevalence while also helping researchers to understand the role each gene playsin the human body.Although powerful, GWAS studies are purely a starting point. Following a large-scale GWAS, researchers must thenanalyzeany variants that are highlighted in great depth, and many times such research will provide nothing of clinical relevance. However, itsstill our best way of identifying risk variants in genetic disease.

So,we know the genome is packed to the brim with genes that code for proteins, separated by large strings ofnon-coding DNA. However, when cells replicateearly in development they usually go throughchromosomal recombination, in which chromosomes trade regions of their genetic code between each other. This spreads genes to many different positions (called loci)throughout the genome. If we can make a map of these genes, we candiscover their function, how they are inherited, or target them with therapies.

Therefore, we want to create a genome map.There are two types of maps used in genomics: genetic maps and physical maps.

Physical mapsare relatively straightforward, in which genomic loci are mapped based on the physical distance between them, measured in base pairs.The most common way to create a physical map of a human genome is byfirst breaking the DNA sequence into many fragments, before using a variety of different techniques to identify how those pieces fit back together. By understanding which pieces overlapand reconstructing the shattered genome, scientists can gain a decently accurate map of where each gene lies.

Genetic mapsare slightly different,using specific marker regions within the DNA that are used as trackers. These mapsrequiresamples (usually saliva) from family members,which are then compared toidentifyhow much recombination has occurred that includes markers of interest. The principle is thatif two genes are close together on thechromosome, thenthey are more likely to travel together through the genome as it recombines. By using this data,scientists can get a rough idea of where specific genes lie on chromosomes. However, it is not as accurate as physical mapping andrelies heavilyon a decentpopulation size andthe number of genetic markers used.

A genome browser is any available database that allows a user to access and compare genomes in an intuitive way. When you map or sequence a genome, the data is prettymessy.Genomes are usually stored in huge files, calledFASTAfiles, that contain extensive strings of letters that would look foreign to most users. Genome browsers take this data and make it accessibleto scientists around the globe.

Many genome browsers are available online, containing bacterial, model organism, and human reference genomes.

Genomelinkis one of the latest examples of public access and analysis of genomes. The industry took off in recentyears, with the rapid rise of sites that provide ancestry and medical information based on genomic sequencing, includingAncestryand23andMe.These sites work by comparing genetic markers associated with different populations should you share specific regions of DNA that correspond with African populations, for example, you may have some relation to African ancestors. Each site uses its own markers, so information may vary between tests, and some have disputed the true accuracy of these tests, although advances in genomics have significantly improved them in recent years.

Genomelinkgoes further than most sites, claiming to provide information on a huge variety of genetic traits that a user may have. These include metabolism, sports performance, and even personality traits such as loneliness. Each trait isdrawn from genome correlation studies, with each taking a specific trait and comparing the genomes of each carrier of that trait.

However, although bothGenomelinkand other sites use up-to-date reference genomes and are usually relatively accurate, they should never be substituted for medical information. If you believe you carry a pathogenic genevariant, you should seek advice from a genomic counselor.

Originally posted here:
Genomes, Maps, And How They Affect You - IFLScience

SAN CARLOS, Calif., Feb. 1, 2021 /PRNewswire/ --Natera, Inc. (NASDAQ: NTRA), a pioneer and global leader in cfDNA testing, presented key results from its SMART study at the SMFM 41st Annual Pregnancy Meeting.1 The SMART study sets a new standard as the largest prospective NIPT study to date(N = 20,927 enrolled from 21 medical centers), and the only large-scale study to collect genetic outcomes in most of the subjects. The study includes the validation of a new artificial intelligence-based algorithm for Panoramacalled Panorama AI, which utilizes information from over 2 million cfDNA tests performed by Natera.

Key results related to the 22q11.2 microdeletion:

"This is the first prospective NIPT study in which genetic outcomes were confirmed in the vast majority of the patients enrolled, and provides a wealth of data about the real-world performance of NIPT across a diverse group of global centers and patients," said Mary Norton, MD, Professor, UCSF, and one of the Principal Investigators of SMART. "The findings related to high prevalence of 22q11.2 deletion syndrome, the limited ability of ultrasound to detect all cases prenatally, and the performance of NIPT in detection of these cases with high accuracy provide exciting data to inform discussions around testing for a broader set of conditions beyond common aneuploidies."

"The diagnostic odyssey related to 22q11.2 deletion syndrome is well documented, with median time to diagnosis of almost 5 years.6And in the meantime, a window of opportunity might be lost to intervene and impact outcomes. Delivery of a child with 22q11.2 deletion syndrome should be at a tertiary facility well-equipped to deal with short-term complications that are associated with the disorder.7 Depending on the issue at hand (e.g., cardiac, endocrine), appropriate interventions are warranted. For example, timely administration of neonatal calcium has been shown to correlate with preventing the intellectual decline commonly seen in affected children,"8,9 said Pe'er Dar, MD, Albert Einstein College of Medicine, Bronx NY, and one of the Principal Investigators of SMART. "With the ability to detect more accurately in combination with a low false positive rate, I believe that the findings of the SMART study provide professional societies with sufficient evidence to consider including screening for 22q11.2 deletions in routine prenatal genetic screening."

In 2020, Natera performed over 400,000 tests for the 22q11.2 microdeletion. Natera has established a CPT code and favorable pricing for microdeletion testing. Based on high prevalence and excellent performance in the study, Natera looks forward to engaging professional societies for routine testing of pregnancies for the 22q11.2 microdeletion, and will then pursue broader insurance coverage.

About Panorama

Panoramareveals a baby's risk for severe genetic disorders as early as nine weeks into pregnancy. The test uses a unique single-nucleotide polymorphism (SNP)-based technology to analyze fetal/placental DNA obtained through a blood draw from the mother. It is the only commercially available test that differentiates between maternal and fetal DNA to assess the risk of aneuploidies. The test also screens twin pregnancies for zygosity and fetal sex of each baby, and identifies risk for more genetic conditions in twin pregnancies than any other NIPT. Panorama is one of several genetic screening tests from Natera designed to help families on the path to parenthood. Natera has published 23 papers, studying over 1.3 million patients, since the launch of Panorama the largest body of evidence in the space today. Panorama has been developed and its performance characteristics determined by Natera, the CLIA-certified laboratory performing the test. The test has not been cleared or approved by the US Food and Drug Administration (FDA). CAP accredited, ISO 13485 certified, and CLIA certified.

About Natera

Naterais a pioneer and global leader in cell-free DNA testing from a simple blood draw. The mission of the company is to change the management of disease worldwide with a focus on women's health, oncology, and organ health. Natera operates ISO 13485-certified and CAP-accredited laboratories certified under the Clinical Laboratory Improvement Amendments (CLIA) in San Carlos, California and Austin, Texas. It offers proprietary genetic testing services to inform obstetricians, transplant physicians, oncologists, and cancer researchers, including biopharmaceutical companies, and genetic laboratories through its cloud-based software platform. For more information, visitnatera.com. Follow Natera onLinkedIn.

Forward-Looking Statements

All statements other than statements of historical facts contained in this press release are forward-looking statements and are not a representation that Natera's plans, estimates, or expectations will be achieved. These forward-looking statements represent Natera's expectations as of the date of this press release, and Natera disclaims any obligation to update the forward-looking statements. These forward-looking statements are subject to known and unknown risks and uncertainties that may cause actual results to differ materially, including with respect to our efforts to develop and commercialize new product offerings, our ability to successfully increase demand for and grow revenues for our product offerings, whether the results of clinical or other studies will support the use of our product offerings, our expectations of the reliability, accuracy and performance of our tests, or of the benefits of our tests and product offerings to patients, providers and payers. Additional risks and uncertainties are discussed in greater detail in "Risk Factors" in Natera's recent filings on Forms 10-K and 10-Q and in other filings Natera makes with the SEC from time to time. These documents are available atwww.natera.com/investorsandwww.sec.gov.

Contacts

Investor Relations: Mike Brophy, CFO, Natera, Inc., 510-826-2350

Media: Paul Greenland, VP of Corporate Marketing, Natera, Inc., [emailprotected]

References

SOURCE Natera, Inc.

Transforming Management of Genetic Disease

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SMART Study Finds 22q11.2 Microdeletion Prevalence Much Higher than Expected - PRNewswire

When microbiologist Breck Duerkop started his postdoc in 2009, he figured hed be focusing on bacteria. After all, hed joined the lab of microbiome researcher Lora Hooper at the University of Texas Southwestern Medical Center in Dallas to study host-pathogen interactions in the mammalian gut and was particularly interested in what causes some strains of normally harmless commensal bacteria, such as Enterococcusfaecalis, to become dangerous, gut-dominating pathogens. Hed decided to explore the issue by giving germ-free mice a multidrug-resistant strain of E. faecalis that sometimes causes life-threatening infections in hospital patients, and analyzing how these bacteria express their genes in the mouse intestine.

Not long into the project, Duerkop noticed something else going on: some of the genes being expressed in E. faecalis werent from the regular bacterial genome. Rather, they were from bacteriophages, bacteria-infecting viruses that, if they dont immediately hijack and kill the cells they infect, can sometimes incorporate their genetic material into the bacterial chromosome. These stowaway viruses, known as prophages while theyre in the bacterial chromosome, may lie dormant for multiple bacterial generations, until certain environmental or other factors trigger their reactivation, at which point they begin replicating and behaving like infectious agents once again. (See illustration below.) Duerkops data showed that the chromosome of the E. faecalis strain he was using contained seven of these prophages and that the bacteria were churning out virus particles with custom combinations of these prophage sequences during colonization of the mouse gut.

The presence of viruses in Duerkops E. faecalis strain wasnt all that surprising. Natural predators of bacteria, bacteriophages are the most abundant biological entities on the planet, and in many fields, researchers take their presence for granted. Nobody really was thinking about phages in the context of bacterial communities in animal hosts, Duerkop says. It would [have been] very easy to just look at it and say, Oh, there are some phage genes here. . . . Moving on. But he was curious about why E. faecalis would be copying and releasing them, rather than leaving the prophages asleep in its chromosome, while it was trying to establish itself in the mouse intestine.

Predation is just one type of phage-bacteria interaction taking place within the mammalian microbiome; many phages are capable of inserting their genomes into the bacterial chromosome.

Encouraged by Hooper, he put his original project on hold in order to dig deeper. To his surprise, he discovered that the E. faecalis strain, known as V583, seemed to be using its phages to gain a competitive advantage over related strains. Experiments with multiple E. faecalis strains in cell culture and in mice showed that the phage particles produced by the bacteria didnt harm other V583 cells, but infected and killed competing strains. Duerkop and his colleagues realized that, far from being background actors in the bacterial community, the phages are important for colonization behavior for this opportunistic pathogen.

The idea that a phage could play such a significant role in the development of the gut bacterial community was relatively novel when the team published its results in 2012. Since then, its been pretty well established that phages can shape the assembly of microbial communities in the intestine, and that can influence the outcome on the hosteither beneficially or detrimentally, says Duerkop, who now runs his own lab at the University of Colorado School of Medicine in Aurora. Theres evidence that phages help bacteria share genetic material with one another, too, and may even interact directly with the mammalian immune system, an idea that Duerkop says would have had you laughed out of a room of immunologists just a few years ago.

Around the time that Duerkop was working on E. faecalis in Dallas, University of Oxford postdoc Pauline Scanlan was studying Pseudomonas fluorescens, a bacterial species that is abundant in the natural environment and is generally harmless to humans, although its in the same genus as the important human pathogen Pseudomonas aeruginosa. Bacteria in this genus sometimes evolve whats known as a mucoid phenotypethat is, cells secrete large amounts of a compound called alginate, forming a protective goo around themselves. In P. aeruginosa, this goo can help the bacteria evade the mammalian immune system and antibiotics, and when it crops up, its not good news for the patient, Scanlan says. She was curious about what causes a non-mucoid bacterial population to evolve into a mucoid one and had found previous research suggesting that the presence of bacteriophages could play a role. Other studies documented high densities of phages in mucus samples from the lungs of some cystic fibrosis patients with P. aeruginosa infections.

Working in the lab of evolutionary biologist Angus Buckling (now at the University of Exeter), Scanlan grew a strain of P. fluorescenswith a phage called Phi2 that specifically infects and destroys this bacterium. Cells with the gummy mucoid coating, the researchers noted, were more resistant to phage infection than regular cells were. Whats more, over generations, bacterial populations were more likely to evolve the mucoid phenotypes in the presence of Phi2 than they were in its absence, indicating that the phenotype may arise in Pseudomonas as an adaptive response to phage attack. Scanlan, now at University College Cork (UCC) in Ireland, notes that more work is needed to extend the findings to a clinical setting, but the results hint that phages could in some cases be responsible for driving bacteria to adopt more virulent phenotypes.

Such a role for viruses in driving bacterial evolution fits well with phages reputation as the ultimate predators, says Colin Hill, a molecular microbiologist also at UCC who got his introduction to phages studying bacteria used in making fermented foods such as cheese. Hill notes an estimate commonly cited in the context of marine biologya field that explored phage-bacteria interactions long before human biology didthat phages kill up to 50 percent of the bacteria in any environment every 48 hours. The thing that any bacterium has on its mind most, if bacteria had minds, would be phage, Hill says, because its the thing most likely to kill them.

Several in vivo animal studies lend support to the idea that predatory phages help shape bacterial evolution and community composition in the mammalian microbiome. In 2019, for example, researchers at Harvard Medical School reported that phages not only directly affect the bacteria they infect in the mouse gut, but also influence the rest of the microbiome community via cascading effects on the chemical and biological composition of the gut. Observational studies hint at similar processes at work in the human gut. A few years ago, researchers at Washington University Medical School in St. Louis observed patterns of phage and bacterial population dynamics that resembledpredator-prey cycles in the guts of children younger than two years old: low bacterial densities at birth were followed by decreases in phages, after which the bacteria would rebound, and then the phages would follow suit. The team concluded that these cycles were likely a natural part of healthy microbiome development.

Although researchers are only just beginning to appreciate the importance of phages in microbiome dynamics, theyve already begun to explore links to human disease. Authors of one 2015 study reported that Crohns disease and ulcerative colitis patients showed elevated levels of certain phages, particularly within the viral order Caudovirales. They proposed that an altered virome could contribute to pathogenesis through predator-prey interactions between phages and their bacterial hosts. Other studies have explored possible phage-driven changes in the bacterial community in human diseases such as diabetes and certain cancers that are known to be associated with a disrupted microbiome. But the observational nature of human microbiome studies prevents conclusions about what drives whatchanges in virome composition could themselves be the result of disruptions to the bacterial community, for example.

Currently, researchers are exploring the possibility of using predatory phages as weapons against pathogenic bacteria, particularly those that present a serious threat to public health due to the evolution of resistance to multiple antibiotics. Its the principle that the enemy of my enemy is my friend, says Yale University virologist and evolutionary biologist Paul Turner. If we have a pathogen that is in your microbiome, can we go in and remove that bacterial pathogen by introducing a predatory phage, something that is cued to only destroy [that pathogen]? Although the strategy was first proposed more than a century ago, we and others are trying to update it, he adds. (See My Enemys Enemy below.)

Phages can interact with bacteria in two main ways. In the first, phages infect a bacterial cell and hijack that cells protein-making machinery to replicate themselves, after which the newly made virus particles lyse the bacterium and go on to infect more cells. In the second process, known as lysogeny, the viral genome is incorporated into the bacterial chromosome, becoming whats known as a prophage, and lies dormantpotentially for many generationsuntil certain biotic or abiotic factors in the bacterium or the environment induce it to excise itself from the chromosome and resume the cycle of viral replication, lysis, and infection of new cells.

Predation is just one type of phage-bacteria interaction taking place within the mammalian microbiome. Many phages are capable of inserting their genomes into the bacterial chromosome, a trick beyond the bounds of traditional predator-prey relationships in other kingdoms of life that adds complexity to the relationship between phages and bacteria, and consequently, to phages potential influences on human health.

This role for phages has long been of interest to Imperial College Londons Jos Penads. Over the last 15 years or so, he and colleagues have described various ways in which many phages help bacteria swap genetic material among cells. He likens phages to cars that bacteria use to transport cargo around and says that, in his opinion, it almost makes sense to view phages as an extension of bacteria rather than as independent entities. This is part of the bacterium, he says. Without phages, bacteria cannot really evolve. They are absolutely required.

With lateral [transduction] you can move huge parts of the bacterial chromosome.

Jos Penads, Imperial College London

In the simplest case, the genetic material being transported consists of viral genes in the genomes of so-called temperate phages, which spend at least part of their lifecycle stashed away in bacterial chromosomes as prophages. These phages are coming to be appreciated by microbiologists as an important driver of bacterial evolution in the human microbiome, notes Hill. The lack of practical and accurate virus detection methods makes it difficult to precisely characterize a lot of the phages resident in mammalian guts, but microbiologists estimate that up to 50 percent are temperate phages, and, more importantly for human health, that many of them may carry genes relevant to bacterial virulence. Researchers have long known, for example, that many toxins produced by bacteriaincluding Shiga toxin, made by some pathogenic E. coli strains, and cholera toxin, secreted by the cholera-causing bacterium Vibrio choleraeare in fact encoded by viral genes contained in the bacterial chromosome, and that infection by temperate phages that carry these genes may be able to turn a harmless bacterial population into one thats pathogenic.

Evidence from other studies points to phages as capable of transporting not just their own genomes, but bits of bacterial DNA as well. In the best-studied examples of this phenomenon, known as bacterial transduction, tiny chunks of the bacterial genome get packed up into viral particles instead of or alongside the phage genome, and are shuttled to other bacterial cells. In 2018, however, Penads and colleagues presented results showing that very large pieces of bacterial DNA can also be exchanged this way, in a process the team named lateral transduction. Not only does the discovery have implications for how researchers understand viral replication in infected cells, it shines light on a novel way for bacteria to share their genes. With lateral [transduction] you can move huge parts of the bacterial chromosome, says Penads. The team first observed the phenomenon in the important human pathogen Staphylococcus aureus, and is now looking for it in other taxa, he adds. Right now, for us, its important to show that its a general mechanism, with many bugs involved.

Although the research is still in the nascent stages, this mechanism could help explain findings from University of Barcelona microbiologist Maite Muniesa and others who have been studying whether phages transport antibiotic resistance genes between bacterial cells, and whether they can act as reservoirs for these genes in the natural environment. Early studies on this issue had proposed that, like many toxin genes, antibiotic resistance genes might be encoded in viral sequences and thus transported to bacteria with the rest of the viral genome. But the idea wasnt without controversya 2016 analysis of more than 1,100 phage genomes from various environments concluded that phage genomes only rarely include antibiotic resistance genes. That studys authors argued that prior reports of these genes in phage genomes were likely due to contamination, or to the difficulty of distinguishing viral sequences from bacterial ones.

Nevertheless, Muniesas team has published multiple reports of antibiotic resistance sequences in phage particles, including in samples of meat products from a Barcelonan fresh-food retailer, and more recently in seawater samplesnot only from the Mediterranean coastline but even off the coast of Antarctica, far from human populations that use antibiotics. We were pretty surprised that we found these particles in this area with low human influence, Muniesa says. Although her team hasnt determined whether the antibiotic resistance sequences are of phage or bacterial origin, she suspects they might be bacterial genes that ended up in phage particles during lateral transduction or some process like it. Bacteria are using these phage particles in a natural way to move [genes] between their brothers and sisters, lets say, she says. Its happening everywhere.

Duerkop cautions that its not yet clear how often phage-mediated transfer of antibiotic resistance genes occurs or how significant it is in the epidemiology of drug-resistant infections in people. Its not to say that antibiotic resistance cant be mediated through phage, he says. I just dont think its a major driver of antibiotic resistance.

Whatever its natural role, temperate phages ability to insert themselves into bacterial genomes could have applications in new antibacterial therapies. Viruses that insert pathogenicity-reducing genes or disrupt the normal expression of the bacterial chromosome could be used to hobble dangerous bacteria, for examplean approach that proved successful last year in mouse experiments with Bordetella bronchiseptica, a bacterium that often causes respiratory diseases in livestock. Using a phage from the order Siphoviridae, researchers found that infected B. bronchiseptica cells were substantially less virulent in mice than control cells were, likely because the viral genome had inserted itself in the middle of a gene that the bacterium needs to infect its host. Whats more, injecting mice with the phage before exposing them to B. bronchiseptica seemed to completely protect them from infection by the microbe, hinting at the possibility of using temperate phages as vaccines against some bacteria.

Bacteria-infecting viruses, or bacteriophages, may influence microbial communities in the mammalian gut in various ways, some of which are illustrated here. Through predation, phages can influence the abundance of specific bacterial taxa, with indirect effects on the rest of the community, and can drive the evolution of specific bacterial phenotypes. Phages can also incorporate their genomes into bacterial chromosomes, where the viral sequences lie dormant as prophages until reactivated. Researchers have found that phages interact directly with mammalian cells in the gut, too. These cross-kingdom interactions could affect the health of their eukaryotic hosts.

Despite growing interest in phages role in shuttling material among bacteria, some of the biggest recent developments in research on phages in the human gut have turned out not to involve bacteria at all. One of the key pieces of this particular puzzle was fitted by University of Utah microbiologist June Round and her colleagues, who as part of a phage therapy study a few years ago fed several types of Caudovirales phages to mice that were genetically predisposed to certain types of cancer and had been infected with a strain of E. coli known to increase that risk. The premise was pretty simplistic, recalls Round. It was just to identify a cocktail of phage that would target bacteria that we know drive chronic colorectal cancer.

The team was surprised to see that the phages, despite being viewed by most researchers as exclusively bacteria-attacking entities, prompted a substantial response from the mices immune systemsmammalian defenses that should, according to conventional wisdom, be indifferent to the war between bacteria and phages in the gut. Intrigued, the researchers tried adding their phage cocktail to mice that had had their gut bacteria completely wiped out with antibiotics. Still, they saw an immune response. It was then, Round says, that we realized that [the phages] were likely interacting with the immune system.

Exploring further, the team found that the phages were activating both innate and adaptive immune responses in mice. In rodents with colitis, the phages exacerbated inflammation. Turning their attention to people, the researchers isolated phages from ulcerative colitis patients with active disease, as well as from patients with disease in remission and from healthy controls, and showed that only viruses collected from patients with active disease stimulated immune cells in vitro. And when the team studied patients who received fecal microbiota transplantationan experimental treatment for ulcerative colitis that involves giving beneficial gut bacteria to a patient to try to alleviate inflammation and improve symptomsthe researchers found that a lower abundance of Caudovirales in a recipients intestine at the time of transplant correlated with treatment success.

Some of the biggest recent developments in research on phages in the human gut have turned out not to involve bacteria at all.

By the time the team published its results in 2019, a couple of other groups had also documented evidence of direct interactions between phages and host immune systems. Meanwhile, Duerkop, Hooper, and colleagues reported that mice with colitis tended to have specific bacteriophage communities, rich in Caudovirales, that developed in parallel with the disease. Many of the types of phage they identified in the intestines of those diseased mice also turned up in high abundance in samples taken from the guts of people with inflammatory bowel disease, the researchers noted in their paper, supporting a possible role for phages in the development of disease.

Round says that researchers are still unsure about exactly why these trans-kingdom interactions are happeningparticularly when it comes to host adaptive immune responses, which tend to be specific to a particular pathogen. She speculates that mammalian hosts might derive a benefit from destroying certain phages if those phages are carrying genes that could aid a bacterium with the potential to cause disease. Exactly how immune cells would detect what genes a phage is carrying isnt yet clear.

Meanwhile, hints of collaboration between eukaryotic cells and phages have cropped up in the work of several other labs. One recent study of a phage therapy against P. aeruginosa found that phages and immune cells seem to act in synergy to clear infections in mice. Other work has indicated that phages bind to glycoproteins presented by cells along the mucosal surfaces of the mammalian gut and may provide a protective barrier against bacterial pathogensa relationship that some microbiologists have argued represents an example of phage-animal symbiosis. Duerkop adds that theres evidence emerging to support the idea that phages in the mammalian intestine not only can be engulfed by certain eukaryotic cells, but also might slip out of the gut and into the bloodstream to make their way to other parts of the body, with as yet undiscovered consequences.

Whether these mechanisms can be exploited for therapeutic purposes remains to be seen, but Round notes that they do raise the possibility of unintended effects in some circumstances if researchers try to use phages to influence human health via the gut microbiome. At least in the type of chronic inflammatory diseases she and her team have been studying, we might just be making it worse by using phages to target disease-causing bacteria, she says, adding that all research groups studying such approaches should take into account potential knock-on effects. Considering phages multiple interactions, with both bacteria and animal cells, she says, its a lot more complex than what wed appreciated.

Bacteriophages ability to selectively target and kill specific bacterial strains has long been recognized as a possible basis for antimicrobial therapies. Proposed by researchers in Europe as early as 1919, phage therapy went on to be widely promoted in Germany, the USSR, and elsewhere before being overtaken worldwide by the soaring popularity of antibiotics in the 1940s. But the strategy has come back into fashion among many microbiologists, thanks to the growing public health problem of antibiotic resistance in bacterial pathogens and to the rapidly improving scientific understanding of phage-bacteria interactions.

Some of the latest approaches aim not only to target specific bacteria with phages, but also to avoid (or exploit) the seemingly inevitable evolution of phage resistance in those bacteria. One way researchers try to do this is by taking advantage of an evolutionary trade-off: bacterial strains that evolve adaptations to one therapy will often suffer reduced fitness when confronted with a second therapy, perhaps one that targets the same or similar pathways in a different way.

Yale University virologist and evolutionary biologist Paul Turner, for example, has studied how phages in the Myoviridae (a family in the order Caudovirales) can promote antibiotic sensitivity in the important human pathogen Pseudomonas aeruginosa. Turner and colleagues showed a few years ago that one such phage binds to a protein called OprM in the bacterial cell membrane, and that bacterial populations under attack from these phages will often evolve reduced production of OprM proteins as a way of avoiding infection. However, OprM also happens to be important for pumping antibiotics out of the cell, such that abnormal OprM levels can reduce bacterias abilityto survive antibiotic treatment in vitro.

A handful of groups have published case studies using this kind of approach, known as phage steering, in humans. A couple years ago, for example, Turner and colleagues reported that a post-surgery patients chronicP. aeruginosa infection cleared up after treatment with the OprM-binding phage and the antibiotic ceftazidime. Researchers at the University of California, San Diego, in partnership with California-based biotech AmpliPhi Biosciences (now Armata Pharmaceuticals), reportedsimilar successin a cystic fibrosis patient with a P. aeruginosa infection who was treated with a mixture of phages and with antibiotics. A Phase 1/2 trial for that therapy was greenlighted by the US Food and Drug Administration last October.

The complexity of the relationship between phages and bacteria, not to mention recently discovered interactions between phages and eukaryotic cells, has many researchers tempering optimism about phage therapy with caution. There might be off-target effects to this that we hadnt really thought about, says University of Colorado School of Medicine microbiologist Breck Duerkop. That said, thanks to research in the last few years, the black veil on phage therapy is, I believe, being lifted, he adds, which Im really excited about because I think they have a ton of potential to be used in biomedicine.

Read the original here:
Are Phages Overlooked Mediators of Health and Disease? - The Scientist

Arthur Allen and Liz Szabo, Kaiser Health NewsUse Our Content

It can be republished for free.

When getting vaccinated against covid-19, theres no sense being picky. You should take the first authorized vaccine thats offered, experts say.

The newest covid vaccine on the horizon, from Johnson & Johnson, is probably a little less effective at preventing sickness than the two shots already being administered around the United States, from Pfizer-BioNTech and Moderna. On Friday, Johnson & Johnson announced that, in a 45,000-person trial, its vaccine was about 66% effective at preventing moderate to severe covid illness. No one who received the vaccine was hospitalized with or died of the disease, according to the company, which said it expected to seek Food and Drug Administration authorization as early as this week. If the agency authorizes use of the vaccine, millions of doses could be shipped out of J&Js warehouses beginning in late February.

The J&J vaccine is similar to the shots from Moderna and Pfizer-BioNTech but uses a different strategy for transporting genetic code into human cells to stimulate immunity to the disease. The Moderna and Pfizer-BioNTech vaccines were found in trials last fall to be 94% effective against confirmed covid. They also prevented nearly all severe cases.

But the difference in those efficacy numbers may be deceptive. The vaccines were tested in different locations and at different phases of the pandemic. And J&J gave subjects in its trial only one dose of the vaccine, while Moderna and Pfizer have two-dose schedules, separated by 28 and 21 days, respectively. The bottom line, however, is that all three do a good job at preventing serious covid.

Its a bit like, do you want a Lamborghini or a Chevy to get to work? said Dr. Gregory Poland, director of the Mayo Clinics Vaccine Research Group. Ultimately, I just need to get to work. If a Chevy is available, sign me up.

So while expert panels may debate in the future about which vaccine is best for whom, from a personal and public health perspective, the best advice for now is to get whatever you can as soon as you can get it, because the sooner we all get vaccinated the better off we all are, said Dr. Norman Hearst, a family doctor and epidemiologist at the University of California-San Francisco.

Here are five reasons experts say you should take the J&J shot assuming the FDA authorizes it if its the one thats offered to you first:

1. All three vaccines protect against hospitalization and death.

Of the 10 cases of severe disease in the Pfizer trial, nine received a placebo, or fake vaccine, and none of the 30 severe cases in the Moderna trial occurred in people who got the true vaccine. Johnson & Johnson did not release specific numbers but said none of the vaccinated patients were hospitalized or died. The real goal is to keep people out of the hospital and the ICU and the morgue, said Dr. Paul Offit, director of the Vaccine Education Center at Childrens Hospital of Philadelphia. This vaccine will do that well.

2. The efficacy levels could be a case of apples and oranges.

The data that Moderna and Pfizer-BioNTech presented to the FDA for their vaccines came from large clinical trials that took place over the summer and early fall in the United States. At the time, none of the new variants of covid some of which may be better at evading the immune responses produced by vaccines were circulating here. In contrast, the J&J trial began in September and was put into the arms of people in South America, South Africa and the United States.

Newly widespread variants in Brazil and South Africa appear somewhat better at evading the vaccines defenses, and its possible a new variant in California where many J&J volunteers were enrolled may also have that trait. The J&J vaccine was 72% effective against moderate to severe covid in the U.S. part of the trial, compared with 57% in South Africa, where a more contagious mutant virus is the dominant strain. Another vaccine, made by the Maryland company Novavax, had 90% efficacy in a large British trial, but only about 50% in South Africa. The Moderna and Pfizer-BioNTech vaccines might not have gotten the same sparkling results had they been tested more recently or in South Africa.

This vaccine was tested in the pandemic here and now, said Dr. Dan Barouch, a Harvard Medical School professor whose lab at the Center for Virology and Vaccine Research at Beth Israel Deaconess Medical Center in Boston developed the J&J vaccine. The pandemic is a much more complex pandemic than it was several months ago.

Some of that difference in performance also could be attributable to different patient populations or disease conditions, and not just the mutant virus. A large percentage of South Africans carry the human immunodeficiency virus, or HIV. Chinese vaccines have performed wildly differently in countries where they were tested in recent months.

We dont know which vaccines are the Lamborghinis, Poland said, because these arent true head-to-head comparisons.

3. Speed is of the essence.

To stop the spread of covid, the mutation of the virus that causes it and the continued pummeling of the economy, we all need to be vaccinated as quickly as possible. The inadequate supply of vaccines has been felt acutely.

Dr. Virginia Banks 103-year-old mother is one of the few living Americans who were around for the countrys last great pandemic the 1918 influenza yet shes been unable to get a covid vaccination, said Banks, a physician with Northeast Ohio Infectious Disease Associates in Youngstown.

Patients cant be picky about which vaccine they accept, Banks said. People need to get vaccinated with the vaccines out today so we can get closer to herd immunity to slow the spread of the virus.

Banks has worked hard to promote covid vaccines to skeptical minority communities, frequently appearing on local TV news and making at least two presentations by Zoom each week. Blacks to date have been vaccinated against covid at much lower rates than whites.

Theres a downside to waiting, said Dr. William Schaffner, a professor of preventive medicine and health policy at Vanderbilt University Medical Center. Delaying vaccination carries serious risks, given that more than 3,800 Americans have been dying every day of covid.

4. The J&J vaccine appears to have some real advantages.

First, it seems to cause fewer serious side effects like the fever and malaise suffered by some Pfizer-BioNTech and Moderna vaccine recipients. High fever and dehydration are particular concerns in fragile elderly people who have one foot on the banana peel, said Dr. Kathryn Edwards, scientific director of the Vanderbilt Vaccine Research Program. The J&J vaccine may be a better vaccine for the infirm.

Many people may also prefer the J&J shot because its one and done, Schaffner said. Easier for administrators too: just one appointment to schedule.

5. The J&J vaccine is much easier to ship, store and administer.

While the Johnson & Johnson vaccine can be stored in regular refrigerators, the Pfizer-BioNTech vaccine must be kept long-term in ultra-cold freezers at temperatures between minus 112 degrees and minus 76 degrees Fahrenheit, according to the Centers for Disease Control and Prevention.

Both the Moderna and Pfizer-BioNTech vaccines must be used or discarded within six hours after the vial is opened. Vials of the J&J vaccine can be stored in a refrigerator and restored for later use if doses remain. Right now we have mass immunization clinics that are open but have no vaccine, said Offit. Here you have a single-dose regime with easy storage and handling.

A persons address not their personal preference may determine which vaccine they receive, said E. John Wherry, director of the Institute for Immunology at the University of Pennsylvanias Perelman School of Medicine. He pointed out that the Johnson & Johnson vaccine is a simpler choice for rural areas.

A vaccine doesnt have to be 95% effective to be an incredible leap forward, said Wherry. When we get to the point where we have choices about which vaccine to give, it will be a luxury to have to struggle with that question.

This story was produced by KHN, which publishes California Healthline, an editorially independent service of the California Health Care Foundation.

Kaiser Health News (KHN) is a national health policy news service. It is an editorially independent program of the Henry J. Kaiser Family Foundation which is not affiliated with Kaiser Permanente.

This story can be republished for free (details).

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When Your Chance for a Covid Shot Comes, Dont Worry About the Numbers - Kaiser Health News

New York, Feb. 01, 2021 (GLOBE NEWSWIRE) -- Reportlinker.com announces the release of the report "Global CRISPR Gene Editing Market: Focus on Products, Applications, End Users, Country Data (16 Countries), and Competitive Landscape - Analysis and Forecast, 2020-2030" - https://www.reportlinker.com/p06018975/?utm_source=GNW Application Agricultural, Biomedical (Gene Therapy, Drug Discovery, And Diagnostics), Industrial, and Other Applications [Genetically Modified Foods (GM Foods), Biofuel, And Animal (Livestock) Breeding] End-User - Academic Institutes and Research Centers, Biotechnology Companies, Contract Research Organizations (CROs), and Pharmaceutical and Biopharmaceutical Companies

Regional Segmentation

North America U.S., Canada Europe Germany, France, Italy, U.K., Spain, Switzerland, and Rest-of-Europe Asia-Pacific China, Japan, India, South Korea, Singapore, Australia, and Rest-of-Asia-Pacific (RoAPAC) Latin America Brazil, Mexico, and Rest-of-the-Latin America Rest-of-the-World

Growth Drivers

Prevalence of Genetic Disorders and Use of Genome Editing Government and Private Funding Technology Advancement in CRISPR Gene Editing

Market Restraints

CRISPR Gene Editing: Off Target Effects and Delivery Ethical Concerns and Implications with Respect to Human Genome Editing

Market Opportunities

Expanding Gene and Cell Therapy Area CRISPR Gene Editing Scope in Agriculture

Key Companies ProfiledAbcam, Inc., Applied StemCell, Inc., Agilent Technologies, Inc., Cellecta, Inc., CRISPR Therapeutics AG, Thermo Fisher Scientific, Inc., GeneCopoeia, Inc., GeneScript Biotech Corporation, Horizon Discovery Group PLC, Integrated DNA Technologies, Inc., Merck KGaA, New England Biolabs, Inc., Origene Technologies, Inc., Rockland Immunochemicals, Inc., Synthego Corporation, System Biosciences LLC, ToolGen, Inc., Takara Bio

Key Questions Answered in this Report: What is CRISPR gene editing? What is the timeline for the development of CRISPR technology? How did the CRISPR gene editing market evolve, and what is its scope in the future? What are the major market drivers, restraints, and opportunities in the global CRISPR gene editing market? What are the key developmental strategies that are being implemented by the key players to sustain this market? What is the patent landscape of this market? What will be the impact of patent expiry on this market? What is the impact of COVID-19 on this market? What are the guidelines implemented by different government bodies to regulate the approval of CRISPR products/therapies? How is CRISPR gene editing being utilized for the development of therapeutics? How will the investments by public and private companies and government organizations affect the global CRISPR gene editing market? What was the market size of the leading segments and sub-segments of the global CRISPR gene editing market in 2019? How will the industry evolve during the forecast period 2020-2030? What will be the growth rate of the CRISPR gene editing market during the forecast period? How will each of the segments of the global CRISPR gene editing market grow during the forecast period, and what will be the revenue generated by each of the segments by the end of 2030? Which product segment and application segment are expected to register the highest CAGR for the global CRISPR gene editing market? What are the major benefits of the implementation of CRISPR gene editing in different field of applications including biomedical research, agricultural research, industrial research, gene therapy, drug discovery, and diagnostics? What is the market size of the CRISPR gene editing market in different countries of the world? Which geographical region is expected to contribute to the highest sales of CRISPR gene editing market? What are the reimbursement scenario and regulatory structure for the CRISPR gene editing market in different regions? What are the key strategies incorporated by the players of global CRISPR gene editing market to sustain the competition and retain their supremacy?

Market OverviewThe development of genome engineering with potential applications proved to reflect a remarkable impact on the future of the healthcare and life science industry.The high efficiency of the CRISPR-Cas9 system has been demonstrated in various studies for genome editing, which resulted in significant investments within the field of genome engineering.

However, there are several limitations, which need consideration before clinical applications.Further, many researchers are working on the limitations of CRISPR gene editing technology for better results.

The potential of CRISPR gene editing to alter the human genome and modify the disease conditions is incredible but exists with ethical and social concerns. The global CRISPR gene editing market was valued at $846.2 million in 2019 and is expected to reach $10,825.1 million by 2030, registering a CAGR of 26.86% during the forecast.

The growth is attributed to the increasing demand in the food industry for better products with improved quality and nutrient enrichment and the pharmaceutical industry for targeted treatment for various diseases. Further, the continued significant investments by healthcare companies to meet the industry demand and growing prominence for the gene therapy procedures with less turnaround time are the prominent factors propelling the growth of the global CRISPR gene editing market.

Research organizations, pharmaceutical and biotechnology industries, and institutes are looking for more efficient genome editing technologies to increase the specificity and cost-effectiveness, also to reduce turnaround time and human errors.Further, the evolution of genome editing technologies has enabled wide range of applications in various fields, such as industrial biotech and agricultural research.

These advanced methods are simple, super-efficient, cost-effective, provide multiplexing, and high throughput capabilities. The increase in the geriatric population and increasing number of cancer cases, and genetic disorders across the globe are expected to translate into significantly higher demand for CRISPR gene editing market.

Furthermore, the companies are investing huge amounts in the research and development of CRISPR gene editing products, and gene therapies. The clinical trial landscape of various genetic and chronic diseases has been on the rise in recent years, and this will fuel the CRISPR gene editing market in the future.

Within the research report, the market is segmented based on product type, application, end-user, and region. Each of these segments covers the snapshot of the market over the projected years, the inclination of the market revenue, underlying patterns, and trends by using analytics on the primary and secondary data obtained.

Competitive LandscapeThe exponential rise in the application of precision medicine on a global level has created a buzz among companies to invest in the development of novel CRISPR gene editing. Due to the diverse product portfolio and intense market penetration, Merck KGaA, and Thermo Fisher Scientific Inc. have been the pioneers in this field and have been the major competitors in this market. The other major contributors of the market include companies such as Integrated DNA Technologies (IDT), Genscript Biotech Corporation, Takara Bio Inc, Agilent Technologies, Inc., and New England Biolabs, Inc.

Based on region, North America holds the largest share of CRISPR gene editing market due to substantial investments made by biotechnology and pharmaceutical companies, improved healthcare infrastructure, rise in per capita income, early availability of approved therapies, and availability of state-of-the-art research laboratories and institutions in the region. Apart from this, Asia-Pacific region is anticipated to grow at the fastest CAGR during the forecast period.

Countries Covered North America U.S. Canada Europe Germany Italy France Spain U.K. Switzerland Rest-of-Europe Asia-Pacific China India Australia South Korea Singapore Japan Rest-of-Asia-Pacific Latin America Brazil Mexico Rest-of-Latin America Rest-of-the-WordRead the full report: https://www.reportlinker.com/p06018975/?utm_source=GNW

About ReportlinkerReportLinker is an award-winning market research solution. Reportlinker finds and organizes the latest industry data so you get all the market research you need - instantly, in one place.

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Global CRISPR Gene Editing Market: Focus on Products, Applications, End Users, Country Data (16 Countries), and Competitive Landscape - Analysis and...

First Targeted Therapy For Lung Cancer With KRAS

For the first time, there may be an effective treatment option for people with lung cancer that contains a genetic mutation called KRAS. The results of a groundbreaking using a drug calledSotorasib have just been published in the highly-respected New England Journal of Medicine.

Dr. Roy Herbst, Chief of Medical Oncology at Yale tells SurvivorNet We are excited we have a drug that could work in these patients. The fact that tumors respond to this therapy is a big deal.

Lung cancer remains the leading cause of cancer death in the united states. The most common form of lung cancer, non-small cell lung cancer (NSCLC), has recently seen major advancements with new treatments such as immunotherapy and targeted therapies extending the lives of thousands of patients. However, despite these recent advancements little has been available to help patients who have lung cancer with a KRAS mutation. This mutation is found in approximately 10-12% of patients with NSCLC and any drug that can improve the outlook for these patients would be a game-changer for lung cancer.

Now we finally have targeted therapy options for these patients.

In patients who have advanced stage or metastatic NSCLC most patients will have their tumor tested for genetic abnormalities or biomarkers to help their doctors select what treatments are best. Some common biomarkers such as EGFR and PDL1 have medications that doctors can use to target the lung cancer and improve a patients survival and quality of life. Despite this, one biomarker that has never had a treatment is KRAS. KRAS is a mutation that occurs in some patients with NSCLC and is generally associated with poor outcomes. One reason this mutation is considered a bad risk factor is that unlike other mutations such as EGFR there has never been a drug approved to treat this type of lung cancer.

Fortunately, for patients, this may be changing soon. A new drug called Sotorasib that specifically targets the KRAS mutation recently showed positive results in the early phase CODEBREAK 100 study. Based on the results from the early phase study Sotorasib was granted Break Through Therapy Designation and the drug has been accepted into the Real-Time Oncology Pilot Review Program by the U.S. Food and Drug Administration (FDA). When discussing the trial, Dr. Velcheti, Director of the Thoracic Medical Oncology Program at NYU Langone says The CODEBREAK 100 trial represents the clinical validation of significant research efforts spanning decades. Now we finally have targeted therapy options for these patients.

Overall I am impressed with this drug. It is hard for the public to understand just how far drug development has come.

So what does this mean for patients? This means that the new drug targeting KRAS may soon be available for patients whose tumors harbor this mutation and who have not responded to other treatments.

Lung specialists from across the country were eager to speak with SurvivorNet regarding the exciting news. Dr. Brendon Stiles, Associate Professor of Cardiothoracic Surgery at Weill Cornell Medical Center tells SurvivorNet Overall I am impressed with this drug. It is hard for the public to understand just how far drug development has come. The KRAS mutation has long been considered undruggable, meaning if you have this mutation, there was not a medicine designed specifically to treat this type of cancer. The chance of responding to the new therapy is around 40%. Although, researches would prefer to see this percent be higher the results of the study give hope that future therapies may have even better outcomes. Dr. Herbst is also optimistic about the future of drugs targeting KRAS and thinks the results of this study opens up a whole new world for lung cancer. If you or a loved one have NSCLC with a KRAS mutation ask your doctor about what treatment options are best for you.

Learn more about SurvivorNet's rigorous medical review process.

Dr. Roy Herbst, Chief of Medical Oncology at Yale tells SurvivorNet We are excited we have a drug that could work in these patients. The fact that tumors respond to this therapy is a big deal.

Now we finally have targeted therapy options for these patients.

In patients who have advanced stage or metastatic NSCLC most patients will have their tumor tested for genetic abnormalities or biomarkers to help their doctors select what treatments are best. Some common biomarkers such as EGFR and PDL1 have medications that doctors can use to target the lung cancer and improve a patients survival and quality of life. Despite this, one biomarker that has never had a treatment is KRAS. KRAS is a mutation that occurs in some patients with NSCLC and is generally associated with poor outcomes. One reason this mutation is considered a bad risk factor is that unlike other mutations such as EGFR there has never been a drug approved to treat this type of lung cancer.

Fortunately, for patients, this may be changing soon. A new drug called Sotorasib that specifically targets the KRAS mutation recently showed positive results in the early phase CODEBREAK 100 study. Based on the results from the early phase study Sotorasib was granted Break Through Therapy Designation and the drug has been accepted into the Real-Time Oncology Pilot Review Program by the U.S. Food and Drug Administration (FDA). When discussing the trial, Dr. Velcheti, Director of the Thoracic Medical Oncology Program at NYU Langone says The CODEBREAK 100 trial represents the clinical validation of significant research efforts spanning decades. Now we finally have targeted therapy options for these patients.

Overall I am impressed with this drug. It is hard for the public to understand just how far drug development has come.

So what does this mean for patients? This means that the new drug targeting KRAS may soon be available for patients whose tumors harbor this mutation and who have not responded to other treatments.

Lung specialists from across the country were eager to speak with SurvivorNet regarding the exciting news. Dr. Brendon Stiles, Associate Professor of Cardiothoracic Surgery at Weill Cornell Medical Center tells SurvivorNet Overall I am impressed with this drug. It is hard for the public to understand just how far drug development has come. The KRAS mutation has long been considered undruggable, meaning if you have this mutation, there was not a medicine designed specifically to treat this type of cancer. The chance of responding to the new therapy is around 40%. Although, researches would prefer to see this percent be higher the results of the study give hope that future therapies may have even better outcomes. Dr. Herbst is also optimistic about the future of drugs targeting KRAS and thinks the results of this study opens up a whole new world for lung cancer. If you or a loved one have NSCLC with a KRAS mutation ask your doctor about what treatment options are best for you.

Learn more about SurvivorNet's rigorous medical review process.

Here is the original post:
The First Targeted Therapy For Lung Cancer Patients With The KRAS Gene MutationExtraordinary Results With Sotorasib - SurvivorNet

What is genetic testing?

Genetic testing is a type of medical test that looks for changes in your DNA. DNA is short for deoxyribonucleic acid. It contains the genetic instructions in all living things. Genetic tests analyze your cells or tissue to look for any changes in

Genetic testing may be done for many different reasons, including to

Genetic tests are often done on a blood or cheek swab sample. But they may also be done on samples of hair, saliva, skin, amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue. The sample is sent to a laboratory. There, a lab technician will use one of several different techniques to look for genetic changes.

The benefits of genetic testing include

The physical risks of the different types of genetic testing are small. But there can be emotional, social, or financial drawbacks:

The decision about whether to have genetic testing is complex. In addition to discussing the test with your health care provider, you can meet with a genetic counselor. Genetic counselors have specialized degrees and experience in genetics and counseling. They can help you understand the tests and weigh the risks and benefits. If you do get a test, they can explain the results and make sure that you have the support that you need.

Continued here:
Genetic Testing: MedlinePlus

What is a genetic disease?

A genetic disease is any disease caused by an abnormality in the genetic makeup of an individual. The genetic abnormality can range from minuscule to major -- from a discrete mutation in a single base in the DNA of a single gene to a gross chromosomal abnormality involving the addition or subtraction of an entire chromosome or set of chromosomes. Some people inherit genetic disorders from the parents, while acquired changes or mutations in a preexisting gene or group of genes cause other genetic diseases. Genetic mutations can occur either randomly or due to some environmental exposure.

What are the four types of genetic disorders (inherited)?

There are a number of different types of genetic disorders (inherited) and include:

The baby with Down syndrome has a hallmark appearance. However, every aspect of the appearance does not need to be present as the phenotype, the way the genes make the child look, can be markedly different for each patient. Common Down syndrome symptoms are:

7 single gene inheritance disorders

Single gene inheritance is also called Mendelian or monogenetic inheritance. Changes or mutations that occur in the DNA sequence of a single gene cause this type of inheritance. There are thousands of known single-gene disorders. These disorders are known as monogenetic disorders (disorders of a single gene).

Single-gene disorders have different patterns of genetic inheritance, including

Some examples of single-gene disorders include

7 common multifactorial genetic inheritance disorders

Multifactorial inheritance is also called complex or polygenic inheritance. Multifactorial inheritance disorders are caused by a combination of environmental factors and mutations in multiple genes. For example, different genes that influence breast cancer susceptibility have been found on chromosomes 6, 11, 13, 14, 15, 17, and 22. Some common chronic diseases are multifactorial disorders.

Examples of multifactorial inheritance include

Multifactorial inheritance also is associated with heritable traits such as fingerprint patterns, height, eye color, and skin color.

4 chromosomal abnormalities

Chromosomes, distinct structures made up of DNA and protein, are located in the nucleus of each cell. Because chromosomes are the carriers of the genetic material, abnormalities in chromosome number or structure can result in disease. Chromosomal abnormalities typically occur due to a problem with cell division.

For example, Down syndrome (sometimes referred to as "Down's syndrome") or trisomy 21 is a common genetic disorder that occurs when a person has three copies of chromosome 21. There are many other chromosomal abnormalities including:

Diseases may also occur because of chromosomal translocation in which portions of two chromosomes are exchanged.

3 mitochondrial genetic inheritance disorders

This type of genetic disorder is caused by mutations in the non-nuclear DNA of mitochondria. Mitochondria are small round or rod-like organelles that are involved in cellular respiration and found in the cytoplasm of plant and animal cells. Each mitochondrion may contain 5 to 10 circular pieces of DNA. Since egg cells, but not sperm cells, keep their mitochondria during fertilization, mitochondrial DNA is always inherited from the female parent.

Examples of mitochondrial disease include

What is the human genome?

The human genome is the entire "treasury of human inheritance." The sequence of the human genome obtained by the Human Genome Project, completed in April 2003, provides the first holistic view of our genetic heritage. The 46 human chromosomes (22 pairs of autosomal chromosomes and 2 sex chromosomes) between them house almost 3 billion base pairs of DNA that contains about 20,500 protein-coding genes. The coding regions make up less than 5% of the genome (the function of all the remaining DNA is not clear) and some chromosomes have a higher density of genes than others.

Most genetic diseases are the direct result of a mutation in one gene. However, one of the most difficult problems ahead is to further elucidate how genes contribute to diseases that have a complex pattern of inheritance, such as in the cases of diabetes, asthma, cancer, and mental illness. In all these cases, no one gene has the yes/no power to say whether a person will develop the disease or not. It is likely that more than one mutation is required before the disease is manifest, and a number of genes may each make a subtle contribution to a person's susceptibility to a disease; genes may also affect how a person reacts to environmental factors.

Medically Reviewed on 10/17/2019

References

United States. National Heart, Lung, and Blood Institute. "Cystic Fibrosis." <https://www.nhlbi.nih.gov/health-topics/cystic-fibrosis>.

United States. National Human Genome Research Institute. "Frequently Asked Questions About Genetic Disorders." <https://www.genome.gov/19016930/faq-about-genetic-disorders/>.

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21 Common Genetic Disorders: Types, Symptoms, Causes ...

Taught by the genetic counselor faculty of the University of South Carolina Genetic Counseling Program, this specially designed genetic counseling online course,Genetic Counseling: Career for the Future, is comprised of lectures from genetic counselors, readings from professional literature and practical activities to help broaden your understanding of the profession and prepare for graduate school.

Online course topics include genetic counseling as a health care profession,with an introduction to various arenas of genetic counseling including prenatal, pediatric, cancer and adult. You'll explore clinical, laboratory and research roles, the counselor-patient relationship, ethical issues and other hot topics, as well as strategies for preparing for graduate education.

Summer 2020 Session:June 8 - August 28Registration Deadline isJune 3

Fall 2020 Session:August 17 November 13Registration Deadline is August 12

Spring 2021 Session:January 11 April 2Registration Deadline is January6

Register Now!

Ourgenetic counseling online course is offered over a 12-week period with two to three hours of self-paced activity per week. Upon completion, youll receive a continuing education certificate to add to your resume. There are no prerequisites for the course. Designed as an in-depth exploration of genetic counseling, the course will demonstrate your commitment to genetic counselor education at the same time you become savvy about the profession and considerations for graduate school.

The Genetic Counseling Program strives to increase diversity among genetic counselors and promotes an inclusive learning environment. As part of our Diversity Recruitment Initiative, a limited number of discounted registration fees will be granted to individuals of underrepresented communities of color. Come learn with us!

One of my reasons for taking this course was to feel inspired every week and gain further insight into the field of genetic counseling as I prepare for applications, and that is definitely happening! I really appreciate the range of assignments and I think it's a good combination to help structure our learning.

The work load is just right. Everything we have done has made me more and more excited about working towards my career as a genetic counselor.

I can tell that you have put a lot of time and effort into making this course as informative, up-to-date, and engaging as an in-person class.

It's fun to communicate with so many people with different backgrounds. Everyone shares their different experiences and I am constantly learning.

I've enjoyed reading the articles and responding to others on the discussion board. The videos have been so insightful --hearing from genetic counselors, learning about their jobs, and what excites them has been very meaningful to me.

With all of the information being online, I can start and stop the work as I please and always find time to do the readings and activities for the week. I really enjoy that the fact that the information comes from such a variety of resources...especially resources that I would have never known about otherwise. All of the articles, websites and videos have been so informative and learning more information about the field has deepened my passion for genetic counseling!"

You may also be interested in theSummer Internship.

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Genetic Counseling Online Course - School of Medicine ...

Today marked some wheeling and dealing in the life sciences industry as several companies licensed products or invested in other companies. Heres a look.

Eli Lillyand Asahi Kasei Pharma Eli Lilly and Company inked a license agreement with Tokyos Asahi Kasei Pharma Corporation. In it, Lilly picks up exclusive rights to AK1780 from Asahi. The drug is an oral P2X7 receptor antagonist that recently finished a Phase I dosing study. P2X7 receptors are associated with neuroinflammation that drives chronic pain conditions.

Under the terms of the deal, Lilly will handle future global development and regulatory activities. Lilly is paying Asahi Kasei Pharma $20 million up front and the Japanese company is eligible for up to $210 million in development and regulatory milestones. Asahi Kasei will retain the rights to promote the drug in Japan and China, including Hong Kong and Macau. If it makes it to market, Asahi Kesei will also be eligible for up to $180 million in sales milestones and tiered royalties from the mid-single to low-double digits.

Lilly is committed to developing novel medicines that may provide relief for patients suffering with various pain conditions, said Mark Mintun, vice president of pain and neurodegeneration research at Lilly. We are pleased to license this molecule from Asahi Kasei Pharma, and look forward to developing it further as a potential treatment for neuroinflammatory pain conditions.

Artiva Biotherapeutics and Merck San Diego-based Artiva Biotherapeutics announced an exclusive global collaboration and license agreement with Merck to develop novel chimeric antigen receptor (CAR)-NK cell therapies against solid tumor-associated antigens. They will leverage Artivas off-the-shelf allogeneic NK cell manufacturing platform and its proprietary CAR-NK technology. At first, the collaboration will include two CAR-NK programs with an option for a third. None of them are currently part of Artivas current or planned pipeline. Artiva will develop the programs through the first GMP manufacturing campaign and to preparation for the Investigational New Drug (IND) application, where Merck will take over clinical and commercial development.

Merck is paying Artiva $30 million upfront for the first two programs and another $15 million if Merck chooses to go ahead with the third. Artiva will be up for development and commercial milestones up to $612 million per program and royalties on global sales. Merck also is ponying up research funding for each program.

Our NK platform has been developed to be truly off-the-shelf and we believe it will be further validated by this exclusive collaboration with Merck, as we work together to bring cell therapies to all patients who may benefit, said Peter Flynn, chief operating officer of Artiva.

NeuBase Therapeutics and Vera Therapeutics Pittsburgh-based NeuBase Therapeutics announced a binding agreement to acquire infrastructure, programs and intellectual property for several peptide-nucleic acid (PNA) scaffolds from Vera Therapeutics, formerly called TruCode Gene Repair. Vera is based in South San Francisco. On January 19, Vera announced its launch with a $80 million Series C financing led by Abingworth LLP and joined by Sofinnova Investments, Longitude Capital, Fidelity Management & Research Company, Surveyor Capital, Octagon Capital, Kliner Perkins, GV and Alexandria Venture Investments. Veras lead clinical candidate is atacicept, a novel B cell and plasma cell inhibitor being developed for patients with IgA nephropathy (IgAN).

The technology acquired by NeuBase has shown the ability to resolve disease in genetic models of several disease indications. NeuBase is focused on genetic medicine.

With this acquisition, we enhance our PATrOL platform, furthering our unique ability to directly engage and correct malfunctioning genes with exquisite precision to address the root causes of a wide variety of human diseases, said Dietrich A. Stephan, chief executive officer of NeuBase. These assets extend and refine our PATrOL platforms capabilities and accelerates, through our Company, to bring the rapidly growing genetic medicines industry toward a single high-impact focal point. We are committed to advancing our pipeline and candidates to the clinic and to exploiting the full potential of PNA technology to continue creating value for our shareholders and importantly, for patients.

Bio-Techne Corporation and Changzhou Eminence Biotechnology Co Minneapolis-based Bio-Techne Corporation announced an initial minority strategic equity investment in Chinas Changzhou Eminence Biotechnology Co. Eminence plans to use the financing to expand its manufacturing capacity and increase the service capabilities of its China-based GMP media production facility. Eminence, based in Changzhou City, Jiangsu, China, launched in 2016 and initially focused on manufacturing and selling best-in-class media to life science companies, including Chinese Hamster Ovary (CHO) cells and other serum-free media products and services. The company is currently finishing and scaling its GMP production facility, which it plans to complete by the end of this year.

With our protein analysis instruments and expanding GMP protein capabilities, Bio-Techne continues to expand its offering of products and tools critical for bioprocessing, said Chuck Kumeth, president and chief executive officer of Bio-Techne. Investing in Eminence not only gives Bio-Techne a foothold in providing additional products and services to support the critical needs of the rapidly growing Chinese biopharmaceutical industry, but also fits extremely well with our existing high-growth product portfolio in China. We look forward to working with the Eminence team.

Most Read Today

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4 New Life Sciences Licensing Deals and Investments to Watch - BioSpace

Dr. Li has over 30 years of experience in basic and applied biomedical research. She joins Neurophth from the University of Louisville School of Medicine, where she was a professor in the department of Ophthalmology and Visual Sciences for over 14 years. Her research focuses on the role of Hippo/YAP1 signaling pathway on different stages of ocular development, NF-kB/IKK2 inhibition of neovascularization, and gene discovery screening for eye diseases using mouse models.

Throughout her career, Dr. Li has contributed to more than 45 publications in journals including Investigative Ophthalmology & Visual Science (IOVS), Proceedings of the National Academy of Sciences of the United States of America(PNAS), Nature Review Immunology, and Science. She is currently the editorial board member of Scientific Reportsand Source Journal of Ophthalmology. Dr. Li holds a Ph.D. in cell biology from the Washington University in St. Louis and obtained both her Bachelor's and Master of Science degrees in Genetics from Beijing University.

"We are thrilled to have Dr. Li on our team, bringing over 3 decades of her diverse experience in basic and applied biomedical research," said Bin Li, M.D., Ph.D., Founder and Chairman of the Board of Neurophth. "Given her prior experience at Baylor College of Medicine mentored by Dr. Savio Woo, an internationally recognized expert in molecular human genetics and gene therapy, and Dr. Mark Kay, a leading researcher in the fields of AAV gene therapy and the current Head of Division of Human Gene Therapy at the Stanford University School of Medicine, Dr. Li has extensive knowledge in gene therapy for hepatic deficiencies, ocular diseases, and viral vector reconstruction."

"We are excited to have Qiutang join and expand our exceptional research and development team. She brings a wealth of experience in gene therapies for ocular diseases to Neurophth," said Alvin Luk, Ph.D., M.B.A., C.C.R.A., Chief Executive Officer at Neurophth. "Her deep understanding of viral vector design and animal models in the inhibition of neovascularization for ocular diseases, such as age-related macular degeneration and diabetic retinopathy, further bolsters our ability to deliver on our growing pipeline of clinical programs and platform capabilities."

"It has been captivating to watch the scale, scope, and speed with which Neurophth has successfully transformed itself into an innovative and diversified gene therapy company," said Dr. Li. "I look forward to being a part of Neurophth team as the company executes the next stage of its growth strategy and expands its pipeline of gene therapy candidates focused on ocular and non-ocular diseases, building a brighter future for patients worldwide."

About Neurophth

Neurophth is China's first gene therapy company in ophthalmic diseases.Headquartered in Wuhan with subsidiaries in Shanghai, Suzhou, and the U.S., Neurophth, a fully integrated company, is striving to discover and develop gene therapies for patients suffering from blindness and other eye diseases globally. Our AAV validated platform which has been published in Nature - Scientific Reports, Ophthalmology, and EBioMedicine, successfully delivered proof-of-concept data with investigational gene therapies in the retina. Our most advanced investigational candidate, NR082 (rAAV2-ND4), in development for the treatment ofND4-mutated LHON, has received orphan drug designations in theU.S. The pipeline also includesND1-mutated LHON, autosomal dominant optic atrophy, glaucoma, wAMD/DME, and other preclinical candidates. Neurophth has initiated the scaling up in-house process in single-use manufacturing technologies to support future commercial demand at the Suzhou facility. To learn more about us and our growing pipeline, visitwww.neurophth.com.

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http://www.neurophth.com

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Neurophth Therapeutics Further Expands Ocular Gene Therapy Expertise with Appointment of Qiutang Li, Ph.D., as Chief Scientific Officer - PRNewswire

Over the next 10 years, gene therapies are expected come into their own as a treatment option for a variety of diseases. So far, two such therapies have snagged regulatory approval, Novartis Zolgensma for spinal muscular atrophy, and Sparks Luxturna for a rare form of genetic blindness. More are waiting their turn.

Multiple companies are delving into gene therapy research with hopes of developing a one-time treatment for devastating genetic diseases. Gene therapies offer great reward in the form of treating various devastating diseases, but there are also significant risks. Over the past year, several clinical studies have been halted or scrapped due to safety concerns.

Bay Area-based Audentes Therapeutics had a temporary hold placed on the gene therapy under development for X-linked myotubular myopathy following reports of several patient deaths. That hold has since been lifted by the U.S. Food and Drug Administration. Uniqure also saw a hold placed on its hemophilia B trial after a patient in the study developed liver cancer. The hold was placed weeks after the company announced promising Phase III results at a conference in December.

Despite those risks, hundreds of millions of dollars in research dollars are being invested in gene therapies because of the potential near-curative capabilities the technology could offer. In December, life sciences giant Bayer launched a cell and gene therapy platform within its pharmaceutical division in order to become a leading company within a rapidly emerging and evolving field that offers the potential of life-saving therapies. Eli Lilly also dove into the field in December with the acquisition of Prevail Therapeutics. That deal was expected to extend Eli Lillys research efforts through the creation of a gene therapy program that will be anchored by Prevail's portfolio of clinical-stage and preclinical neuroscience assets.

This week, German scientists reported they were able to use gene therapy to help paralyzed mice run again. The researchers were able to genetically engineer a unique protein dubbed hyper-interleukin-6, which was then able to stimulate the regeneration of nerve cells in the visual system. A few weeks after the treatment, the injured animals were able to walk again.

Scientists in China announced the development of a gene therapy that could potentially reverse the effects of ageing. Initial research was conducted with mice, but if it is proven to be safe, human testing could begin. As Reuters reported, the method involved inactivating a gene called kat7 which the scientists found to be a key contributor to cellular ageing. Researchers used CRISPR/Cas9 to screen thousands of genes for those which were particularly strong drivers of cellular senescence, the term used to describe cellular ageing, Reuters said.

Earlier this month, a public-private partnership in Boston formed to open a new facility to boost advances in cell and gene therapies. This creation of this new facility is being helmed by Harvard University and the Massachusetts Institute of Technology. Those prestigious universities are partnering with industry members such as Fujifilm Diosynth Biotechnologies, Cytivia and Alexandria Real Estate Equities, as well as multiple research hospitals. Part of the goal of this new institute, which is still unnamed at this point, is to boost the supply of materials for research and early clinical studies, provide space for some research and also offer training in equipment used for gene therapies, The Harvard Gazette reported this week.

On Monday, Curadigm, a subsidiary of France-based Nanobiotix, forged a collaboration with Sanofi to assess if that companys Nanoprimer technology is a promising option to significantly improve gene therapy development. The goal of the project is to establish proof-of-concept for the Nanoprimer as a combination product that could improve treatment outcomes for gene therapy product candidates.

Many promising nucleic acid-based therapeutics administered intravenously are limited in their efficacy due to rapid clearance in the liver, which prevents these therapies from reaching the necessary accumulation in target tissues to generate their intended outcomes. Additionally, accumulation in the liver, rather than in the target tissues, can lead to dose-limiting hepatic toxicity, Nanobiotix said in its announcement. The Nanoprimer is designed to precisely and temporarily occupy therapeutic clearance pathways in the liver. Delivered intravenously, immediately prior to the recommended therapy, the technology acts to prevent rapid clearancethereby increasing bioavailability and subsequent accumulation of therapeutics in the targeted tissues.

The Nanoprimer is a combination product candidate that does not alter or modify the therapies it is paired with, which means if the research with Sanofi is successful, Curadigm could seek out other opportunities for its technology.

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Are Gene Therapies the Medicine of the Future? - BioSpace

Two different gene therapies have been used to mitigate a mechanism underlying development of sickle cell disease (SCD) and transfusion-dependent -thalassemia (TDT), and both have demonstrated clinical success in separate, concurrently published trials.

The hemoglobinopathies manifest after fetal hemoglobin synthesis is replaced by adult hemoglobin in individuals who have inherited a mutation in the hemoglobin subunit gene (HBB).Identifying factors in the conversion from fetal to adult hemoglobin synthesis, however, has provided potential targets for therapeutic intervention.

Gene therapy that can safely arrest or reduce the conversion offers the potential for a one-time treatment to obviate the need for lifetime transfusions and iron chelation for patients with TDT, and the pain management, transfusions and hydroxyurea administration for those with SCD.

Two groups of investigators have now reported in The New England Journal of Medicine that, using different gene therapy techniques that target the transcription factor, BCL11a, involved in the globin switching, they have improved clinical outcomes in patients with TDT and with SCD.

In an editorial in the issue featuring the 2 studies, Mark Walters, MD, Blood and Marrow Transplant Program, University of California, San Francisco-Benioff Children's Hospital, welcomed the breakthroughs.

"These trials herald a new generation of broadly applicable curative treatments for hemoglobinopathies," Walters wrote.

In one clinical trial with 2 patients, one with TDT and the other with SCD, Haydar Frangoul, MD, MS, Medical Director, Pediatric Hematology/Oncology, Sarah Cannon Center for Blood Cancer at the Children's Hospital at Tristar Centennial, and colleagues administered CRISPR-Cas9 gene edited hematopoietic stem and progenitor cells (HSPCs) with reduced BCL11A expression in the erythroid lineage.

The product, CTX001, had been shown in preclinical study to restore -globulin synthesis and reactivate production of fetal hemoglobin. Both patients underwent busulfan-induced myeloablation prior to receiving the treatment.

The investigators suggested that the CRISPR-Cas9-based gene-edited product could change the paradigm for patients with these conditions, if it was found to successfully and durably graft, produce no "off-target" editing products, and, importantly, improve clinical course.

"Recently approved therapies, including luspatercept and crizanlizumab, have reduced transfusion requirements in patients with TDT and the incidence of vaso-occlusive episodes in those with SCD, respectively, but neither treatment addressed the underlying cause of the disease nor fully ameliorates disease manifestations," Frangoul and colleagues wrote.

The investigators reported that both patients had "early, substantial, and sustained increases" in pancellularly distributed fetal hemoglobin levels during the 12-month study period. Further, the patients no longer required transfusions, and the patient with SCD no longer experienced vaso-occlusive episodes after the treatment.

In commentary accompanying the report, Harry Malech, MD, Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease (NIAID), National Institutes of Health (NIH), Bethesda, MD, described the investigators' application of the gene-editing technology as a "remarkable level of functional correction of the disease phenotype."

"With tangible results for their patients, Frangoul et al have provided a proof of principle of the emerging clinical potential for gene-editing treatments to ameliorate the burden of human disease," Malech pronounced.

In the other published trial, with 6 patients with SCD, Erica Esrick MD, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, and colleagues described results with infusion of gene-modified cells derived from lentivirus insertion of a gene that knocks down BCL11a by encoding an erythroid-specific, inhibitory short-hairpin RNA (shRNA).

The severity of SCD that qualified patients for enrollment included history of stroke (n = 3), frequent vaso-occlusive events (n = 2) and frequent episodes of priapism (1).Patients were followed for 2 years, and offered enrollment in a 13-year long-term follow-up study.The infusion of the experimental drug BCH-BB694, from the short hairpin RNA embedded within an endogeonous micro RNA scaffold (termed a shmiR vector), was initiated after myeloablation with busulfan.

Esrick and colleagues reported that, at median follow-up of 18 months (range, 7-29), all patients had engraftment and a robust and stable HbF induction broadly distributed in red cells.Clinical manifestations of SCD were reduced or absent during the follow-up period; with no patient having a vaso-occlusive crisis, acute chest syndrome, or stoke subsequent to the gene therapy infusion.Adverse events were consistent with effects of the preparative chemotherapy.

"The field of autologous gene therapies for hemoglobinopathies is advancing rapidly," Esrick and colleagues reported, "including lentiviral trials of gene addition in which the nonsickling hemoglobin is formed from an exogenous -globin or modified -globin gene."

Walters agreed that gene therapy is rapidly progressing, but expressed concern about the large gap that looms between laboratory bench and clinical bedside, particularly for this affected population.

"Access to and delivery of these highly technical therapies in patients with sickle cell disease will be challenging and probably limited to resource-rich nations, at least in the short term," Walters commented.

The studies, CRISPR-Cas9 Gene Editing for Sickle Cell Disease and -Thalassemia, as well as, Post-Transcriptional Genetic Silencing of BCL11A to Treat Sickle Cell Disease, were published online in The New England Journal of Medicine.

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Two Gene Therapies Fix Fault in Sickle Cell Disease and -thalassemia - MD Magazine

With the rising demand for cell and gene therapies, the need for manufacturing innovation has never been higher. A surge of deals and expansions in the last year is fuelling the push to truly make these therapies widely available and affordable.

Cell and gene therapies offer huge potential to treat a wide range of diseases including cancer, neurological, and genetic diseases. They have even shown promise to treat the symptoms of Covid-19.

The amount of academic and early-stage biotech research in this area has skyrocketed over the last few years. According to the Alliance for Regenerative Medicine, there are currently 1,220 ongoing clinical trials in this space, 152 of which are at phase III. Despite the global pandemic, investment in this area is also at a record high around the world, with the equivalent of 15.7B invested in 2020, a figure double that of 2019.

But research alone cannot get these complex treatments to patients. The sharp discrepancy between the high number of products in early-stage development and the still very small number that have made it onto the market, as well as their cost, speaks to the impact and importance of cost-effective and scalable manufacturing, Ryan Cawood, CEO of Oxgene (previously Oxford Genetics), told me. Oxgene is a UK biotech aiming to improve manufacturing for cell and gene therapies.

To meet this challenge, cell and gene therapy producers are exploding into motion. With 2021 only just getting started, weve seen manufacturing deals between Vigeneron and Daiichi Sankyo, Sirion Biotech and Cellectis, and Cevec and Biogen. The giant Thermo Fisher Scientific absorbed the Belgian viral vector producer Henogen for 724M. And CDMO heavyweights like Cognate BioServices and Polyplus Transfection have announced expansions to their manufacturing capacity.

Thedifficulties with manufacturing the recently approved Covid-19 mRNA vaccines in high enough quantities has really highlighted the importance of having a solid manufacturing strategy in place. This lesson applies equally to companies trying to take cell and gene therapies to market.

Stuck in the first generation

Despite the huge increase in development of cell and gene therapies over the past couple of years, manufacturing technology for these therapies is largely still at the first-generation stage. This can make scaling up a challenge.

Often cell and gene therapy manufacturing processes are highly manual stemming from the early academic or process development stage and, without adequate technology solutions available currently, these processes often remain this way through clinical trials and then into commercial manufacturing, said Jason Foster, CEO of Ori Biotech, a London- and New Jersey-based company focusing on cell and gene therapy manufacturing.

These first-generation processes cause manufacturing to be expensive, highly variable and low-throughput, which reduces the ability of patients to access these potentially life-saving therapies.

Another problem common to all bio-based therapeutics is that any product sourced from a live cell or a component of one is subject to a lot more variation than a simpler pharmaceutical product.

Most gene therapies are built on viruses found in nature. They have not evolved for very high productivity in a large-scale, animal component-free bioreactor, said Cawood.

The more complicated the biologic becomes, the more parts of it require optimization, and the more analytics you require.

According to Kevin Alessandri, the cofounder and CEO/CTO of the French company TreeFrog Therapeutics, there is also a lot of waste in cell therapy manufacturing.

Yields are impaired by high cell death at every passage, and genetic alterations inevitably arise, said Alessandri. When it comes to producing commercial batches to treat thousands of patients, scaling out 2D cell culture processes is far too expensive and poses batch-to-batch reproducibility issues.

While many in the industry are now turning to bioreactors to produce cells on a bigger scale, this is also not without problems. Impeller-induced shear stress is damaging the cells, thus negatively impacting cell viability and triggering undesired genetic mutations, explained Alessandri.

Taking manufacturing up a gear

What are companies in this space doing to make scaling up cell and gene therapies easier, quicker, and cheaper?

Ori Biotech raised24.8M in Series A funding in October last year to develop an automated and robotic manufacturing system to minimize the number of manual steps needed to produce a given cell or gene therapy. This speeds up the process as well as making it more accurate. Another advantage of the technology is that it can tailor the production capacity according to demand.

This is impossible to do in most current processes, which involve manual tube welding and transfers from flask to bag to bigger bag to bioreactor, said Foster, adding that this increases cost and variability while constraining throughput. Oris technology, in contrast, could take years off the production timeline and cut costs by as much as 80%.

London-based Synthace is one of several companies trying to improve advanced therapeutic manufacturing by developing software and computer systems to optimize the process, rather than industrial machinery.

Peter Crane, Corporate Strategy Manager for the company, said that in-depth data analysis and planning before starting the manufacturing process can make a big difference to outcomes, and that connected software can help make this task easier.

The best way to remove some of the risk associated with biomanufacturing of these products is to solve as many problems as possible before manufacturing.

In addition to making the process quicker, cheaper, and more accurate, computing tools can also help with quality control and tracking. In cell therapy manufacturing, especially autologous products, line of sight around electronic batch records, as well as the vein-to-vein supply chain, is incredibly important, emphasized Crane.

Another company specifically focusing on logistics and quality control is the Cardiff- and San Francisco-based TrakCel, which nailed deals with Ori Biotech in February and the UKs National Health Service in November.

The company TreeFrog Therapeutics works with cell encapsulation technology to improve quality and reduce waste, albeit from a more mechanical viewpoint. The company launched an industrial demonstration plant in June last year, followed by two co-development deals with undisclosed big pharma partners.

Encapsulated stem cells spontaneously self-organize in an in vivo-like 3D conformation promoting fast and homogeneous growth, as well as genomic stability, said Alessandri. The resulting 3D stem cell colony can then be differentiated in the capsule into functional microtissues ready for transplantation.

With our technology, which is based on high-throughput microfluidics capable of generating over 1,000 capsules per second, it becomes possible to expand and differentiate stem cells at a large scale, in industrial bioreactors, with best-in-class cell quality and reduced operating costs.

Oxgene has a focus on scaling up production for manufacturers. In September, the company launched a technology to scale up manufacturing of viral vector production with less contamination and a 40-fold improvement in yield compared to current methods. Oxgenes expertise with viral vectors also prompted a collaboration deal in April with the CDMO Fujifilm Diosynth Biotechnologies.

Innovation in new manufacturing technologies just hasnt kept pace with the level of discovery around genetic disease and potential avenues open to treat them, or even development of the viral vectors themselves, said Cawood. This is definitely changing though.

Enter the second generation of manufacturing

Cell and gene therapy manufacturing is definitely hot right now, boosted by increased needs from biotech and pharma companies developing Covid-19 vaccines and therapies, and by notable increases in investment.

Huge advances in gene and cell therapies over the last few years, such as the approval of the eye gene therapy Luxturna and the first CAR T-cell therapies, mean the demand for new manufacturing technologies has also increased exponentially.

A lot of very promising programs are now in the pipeline, and patients are waiting for their approval, said Alessandri. Industry urgently needs robust manufacturing technology, capable of serving millions of patients.

European biotechs are busy developing second-generation technologies to allow easier and cheaper scale up, producing higher quality products with less waste. They could start to phase out first-generation methods very soon.

The realm of cell manufacturing in industrial and food biotech is also likely to see big breakthroughs in the coming years. Earlier this month, for instance, the nutrition and health giant Royal DSM set up a lab in the Netherlands dedicated to applying artificial intelligence (AI) to the challenge of growing microbial strains at a commercial scale.

Rapid improvements in advanced computing options such as AI and machine learning technology, as well as robotics, are already having an effect on the industry, but this will only get bigger as time goes on.

Cover image from Elena Resko. Body text image from Shutterstock

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Cell and Gene Therapy Firms Gear up to Revolutionize Manufacturing - Labiotech.eu

Introduction

The arrival and prevalence of drug-resistant tuberculosis has become a major problem in global tuberculosis (TB) control. In 2019, it was estimated that there were 500,000 cases of rifampicin-resistant TB (RR-TB) worldwide, of which 78% were multidrug-resistant TB (MDR-TB), resistant to both isoniazid (INH) and rifampicin (RIF). China has a high burden of TB and RR/MDR-TB and accounts for 14% of global RR/MDR-TB cases.1 INH and RIF are the core first-line drugs in the treatment of TB, but treatment of RR/MDR-TB with these first-line regimens will have poor effect. It is important to quickly identify the results of drug susceptibility tests (DST) in patients, especially tests relating to INH and RIF, to enable appropriate drugs to be chosen based on DST profiles.

Detection of drug-resistant target gene mutation can help to detect drug resistance earlier than phenotypic DST. Molecular DST in MTB has been widely used in clinical work to evaluate resistance to INH and RIF. KatG and inhA gene mutations are the main mechanism of INH resistance in MTB.2 Gene inhA (including promoter and coding areas) is one of important molecular markers of INH resistance, and inhA is also the molecular basis of cross resistance to ethionamide (ETH) prothionamide (PTH),24 a group C drug recommended by the WHO for the treatment of MDR-TB.5 ETH/PTH and INH are activated by monooxygenase EthA and catalase-peroxidase KatG. The activated forms of the two drugs act on a common targetthe NADH-dependent enoyl-ACP reductase inhA (Rv1484) bindingwith a bactericidal effect that affects cell wall synthesis.2 ETH/PTH has obvious adverse reactions such as nausea and drug-induced liver injury,6 and care is needed when choosing this drug. However, due to the convenience and ease of oral administration, ETH/PTH is still recommended in MDR-TB treatment in China.6 Based on the correlation between ETH/PTH resistance and inhA, clinicians may refer to inhA gene detection to guide the use of ETH/PTH.3,4,7

A variety of reports suggest that mutations in the inhA gene in TB strains can predict ETH/PTH resistance, although some studies have also shown that clinical strains with inhA mutations are sensitive to ETH.3,4,7 MeltPro TB assay utilizes the real-time polymerase chain reaction (PCR) probe-based melting curve analysis technique8 to detect the common drug-resistant mutation sites of katG, inhA and rpoB genes in MTB and rapidly diagnose INH and RIF resistance. This technique is widely used in clinical work.9,10 In this study, we analyze the correlation between inhA mutation test results and phenotypic ETH susceptibility through MeltPro TB assay and evaluate whether the inhA test can be used to guide the clinical application of ETH where phenotypic DST results are unavailable.

In this retrospective study, patients undergoing treatment at Beijing Chest Hospital, Capital Medical University with positive MeltPro TB assay results for inhA and katG genes (mutated or not mutated) were screened from February 2015 to February 2016. Samples were tested for katG and inhA genes with culture and phenotypic DST and the dissociation curve method. Patients who met the following conditions were subsequently included in the analysis: cultured clinical specimens were positive for MTB; DST results were available for INH, RIF, Levofloxacin (Lfx), Amikacin (Am), Capreomycin (Cm), and ETH; and test results were positive for katG and inhA mutations. If two or more samples from the same patient were positive, the first sample was recorded. The basic information collected for each patient included their age, gender, disease diagnosis, initial treatment, and subsequent treatment.

The study was conducted in accordance with the Declaration of Helsinki (revised 2013). The study was approved by Beijing Chest Hospital, Capital Medical University (No.201986) and informed consent was obtained from all the patients.

Sample processing, culture, and drug susceptibility detection were conducted in accordance with the Laboratory Inspection Procedure of Tuberculosis Diagnosis.11 The clinical samples were treated and cultured on a modified LowensteinJensen culture medium (Zhuhai intkr Co. Ltd., China). Positive colonies were cultured for DST and strain identification using the LowensteinJensen proportion method. The critical concentration references were as follows: low-concentration INH 0.2 g/mL, high-concentration INH 1.0 g/mL, RIF 40 g/mL, Levofloxacin2 g/mL, Amikacin 30g/mL, Capreomycin 40 g/mL, and ETH 40g/mL. Growth (cultivation) at this concentration was defined as indicating drug resistance.3

An automatic DNA extraction machine (Zeesan Biotech, Xiamen, China) and a paramagnetic particle method were used to extract crude DNA (1 mL) from the decontaminated samples according to the MeltPro TB assay instructions. The amplification program was used to analyze the melting. The fluorescence signal intensity was collected on the LightCycler 480 System (Indianapolis Roche Group) in the FAM and TET channels, and the melting temperature TM value was obtained by identifying the peak of the melting.7,12 The detection sites of INH resistance included inhA94, inhA promoter region 17 ~ 8 mutation, and katG315 codon mutation. The katG and inhA mutation results were recorded.

Data collection was carried out using Excel 2007 and the statistical analysis employed SPSS 17.0 software. The count data were represented by rate (%), 2 TEST and Fishers exact test to compare the differences between the groups. The parameters of the continuous measurements were expressed as mean standard deviation and compared using a t-test. P < 0.05 indicated that a result was statistically significant.

A total of 704 clinical specimens were tested using the dissociation curve method and found to be positive for inhA and katG genes. Specimens of MeltPro TB assay detect negative, specimens without phenotypic DST results and repeated samples were removed. Following this, 382 patients were enrolled in the study. These patients included 283 (74.1%) cases of sputum, 58 (15.2%) cases of bronchial lavage fluid, 1(0.3%) case of cerebrospinal fluid, and 40 (10.5%) cases of sanious; 292 were initial treatment patients and 90 were re-treatment patients. And 28 (7.3%) cases were resistant to ETH. The proportion of re-treatment patients with resistance to ETH was higher than the proportion of initial treatment patients (P < 0.001; Table 1). In addition, 11.0% (42/382) were MDR-TB, 10.2% (39/382) were pre-extensively drug resistant tuberculosis (pre-XDR-TB); 4.2% (16/382) were extensively drug resistant tuberculosis (XDR-TB).

Table 1 Demographic and Clinical Characteristics of Patients

Of the 382 bacterial strains, 118 strains (30.9%) were resistant to INH. Among these INH resistant strains, 22.9% (27/118) were also resistant to ETH, and all of these strains were MDR-TB. Of the 118 INH-resistant strains, katG mutation accounted for 52.5% (62/118), inhA mutation accounted for 20.3% (24/118), and inhA+katG mutation accounted for 4.2% (5/118); strains with no mutation accounted for 22.9% (27/118). Of the 28 phenotypic ETH-resistant strains, 27 (96.4%) resistant to INH resistance. Of the same 28 strains, inhA mutation accounted for 42.9% (12/28). Of the 34 inhA mutant strains, 85.3% (29/34) had an inhA mutation without a katG mutation; among this group, 34.5% (10/29) showed low resistance to INH, 48.3% (14/29) showed high resistance to INH, and 13.8% (5/29) were sensitive to INH. The rates of ETH-resistance in low- and high-level INH-resistant strains showed no statistical differences (2 = 2.264; P = 0.132; Fishers test). The rate of single inhA mutations (without katG mutation) in strains with low INH-resistance was higher than the rate in strains with high INH-resistance (2 = 13.076; P < 0.001; Fishers test). All of 21 INH-resistant but non-MDR-TB strains were sensitive to ETH; four of these were inhA mutant strains. In addition, eight strains (four INH-resistant and four INH-sensitive) with single inhA mutation (without katG and rpoB mutations) were sensitive to ETH, and the patients carrying those eight strains were not initially treated with anti-TB drugs (Figure 1 and Table 2).

Table 2 Frequency of Ethionamide Resistance in Low-and High-Level Isoniazid Resistant and Isoniazid Susceptible Mycobacterium tuberculosis Isolates

Figure 1 Phenotypic DST results of ETH in MTB with inhA gene mutation enrolled in this study.

China has a high burden of TB and one of the highest incidences of MDR-TB in the world.13 Particularly in recent years, the incidence of DR-TB has been on the rise in China. Rifampicin (RIF) and isoniazid (INH) are the leading first-line anti-TB drugs, playing an important role in the treatment of TB. MDR-TB is widely regarded as an important factor in the failure of chemotherapy in treating TB. The resistance of genes to INH is more complicated, and is mainly caused by mutations in genes such as katG and inhA. Each mutation site has a certain correlation with drug resistance. ETH/PTH is a second-line drug treatment for TB, used mostly in MDR-TB and XDR-TB. According to data from domestic and overseas research, the majority of ETH/PTH-resistant strains also show INH resistance.10,14,15 In the present study, almost all ETH-resistant strains were also found to be resistant to both INH and RIF (96.4%), and the ETH-resistance rate in MDR-TB was 27.8%, which is consistent with our previous studies and similar data (20%24.8%) from TB treatment institutions in China.1619

The main molecular mechanisms underlying INH resistance are inhA and katG mutations, reported to account for 8%43% and 50%95% of drug-resistant strains, respectively.20 Tests for these two genetic mutations are used to diagnose the majority of instances of MTB resistance to INH. Mutations in the inhA gene are the molecular basis of cross resistance to ETH/PTH and INH. Therefore, the inhA gene can also aid in diagnosing ETH resistance. This study analyzed inhA and katG mutations and phenotypic INH and ETH susceptibility in clinical strains. Of the 118 INH-resistant strains analyzed, 56.7% (67/118) were katG mutations, and 24.5% (29/118) were inhA mutations. Of the 28 phenotypically ETH-resistant strains, inhA mutations accounted for 42.9%, which is consistent with previous reports.10,20 However, in this study, only 35.3% of the 34 inhA mutant strains were resistant to ETH, and only 42.9% of ETH-resistant strains had inhA mutations. A recent study in South Korea found that only 23 (67%) of 34 PTH-resistant strains had an inhA mutation, while data from a study in Guangzhou, China indicates that, of 46 PTH-resistant strains, 43.2% had an inhA promoter (12 strains were c-15t and 4 strains t-8c), and 6.2% had a coding gene mutation (all were S94A).10,21 The results of the present study show an inhA mutation rate in ETH-resistant strains (42.9%) similar to that in the study in China referenced above.

The question of whether inhA mutations can indicate phenotypic ETH resistance remains. Most previous research has focused on inhA mutations in INH- or ETH/PTH-resistant strains (mainly MDR-TB), while inhA mutations in sensitive strains have rarely been studied. There is a moderate level of evidence for an association between c-15t inhA promoter mutations and low-to-moderate INH resistance.22 This study shows that only 35.3% of 34 inhA mutant strains were resistant to ETH. The possible reasons for the inconsistency between inhA mutation and the ETH-resistant phenotype include the dissociation curve detection of mutant codons on inhA94 from 17 to 8 in the inhA promoter region. In addition, some positive mutations may be synonymous mutations and will not cause protein changes or ETH resistance.15,17,23 The ETH-resistant phenotype may have other regulatory mechanisms that cause strains with inhA mutations not to generate ETH resistance. This study also found that all strains with single inhA mutations (without katG or rpoB mutations) were sensitive to ETH. Taking the results of the present study in combination with those of other domestic studies, it can be argued that inhA mutations are not a reliable indicator of ETH resistance in China;17,24 the detection of inhA mutations is not necessarily a sign of resistance to ETH, and genotypic and phenotypic drug susceptibility must be detected simultaneously to guide clinical use of ETH.

Although inhA mutations have been shown to be associated with low INH resistance, this study shows that, of 29 inhA mutant strains, 48.3% (14/29), mainly INH- and RIF-resistant strains, had high INH resistance.2 InhA mutations were not a good indicator of low INH resistance. Other studies have also shown that inhA mutant (non-katG mutation) strains are highly resistant to INH, as are some strains combined with furA, oxyr-ahpc, or inhA double (c-15t combined with S94A or I194T) mutations.25 The data in this study were derived from clinical data, and no particular type of inhA mutation was specified. In addition, apart from inhA and katG315, no other INH-resistant genes were examined. Hence, the specific mechanism underlying the high drug resistance of nearly half of inhA remains unclear. Nonetheless, we found that the single inhA mutant strain (without katG and rpoB mutation) showed low-level resistance and susceptibility to INH, and these strains were sensitive to ETH. Hence, ETH and high-dose INH treatment may be effective for the majority of single inhA mutated INH-resistant strains.

However, this study has certain limitations. First, the present study is a summary of clinical data. Laboratory tests only reported whether or not the isolates had katG and inhA mutations; they did not provide detailed descriptions including the mutation sites. In addition, we did not discuss the mechanism of drug resistance in isolates where the inhA genotype and ETH-resistant phenotype were inconsistent. This will be the focus of further study, and we will evaluate the feasibility of using the targets identified by the melting curve analysis in the Chinese population. Third, the sample size was small, and all included patients came from the hospital where the author worked. The research findings may therefore contain some bias; however, they are still encouraging.

Although inhA mutations are associated with mechanisms of joint INH and ETH resistance, they may not be a reliable indicator of ETH resistance. In particular, TB strains with single inhA mutations (without katG or rpoB mutations) may remain sensitive to ETH. This is a preliminary study,future work is required to explore the mechanism of ETH resistance, to look for the reasons of inconsistency of phenotype and gene mutation.

We are particularly grateful to all the people who have given us help on our article.

There is no funding to report.

The authors declare that they have no competing interests.

1. World Health Organization. Global tuberculosis report. 2020.

2. Vilchze C, Jacobs JR. WR. Resistance to isoniazid and ethionamide in Mycobacterium tuberculosis: genes, mutations, and causalities. Microbiol Spectr. 2014;2(4):MGM22013. doi:10.1128/microbiolspec.MGM2-0014-2013

3. Vadwai V, Ajbani K, Jose M, et al. Can inhA mutation predict ethionamide resistance? Int J Tuberc Lung Dis. 2013;17(1):129130. doi:10.5588/ijtld.12.0511

4. Niehaus AJ, Mlisana K, Gandhi NR, Mathema B, Brust JC. High prevalence of inhA promoter mutations among patients with drug-resistant tuberculosis in KwaZulu-Natal, South Africa. PLoS One. 2015;10(9):e0135003. doi:10.1371/journal.pone.0135003

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10. Darban-Sarokhalil D, Nasiri MJ, Fooladi AA, Heidarieh P, Feizabadi MM. Rapid detection of rifampicin- and isoniazid-resistant Mycobacterium tuberculosis using TaqMan allelic discrimination. Osong Public Health Res Perspect. 2016;7(2):127130. doi:10.1016/j.phrp.2016.01.003

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13. Jou R, Lee WT, Kulagina EV, et al. Redefining MDR-TB: comparison of Mycobacterium tuberculosis clinical isolates from Russia and Taiwan. Infect Genet Evol. 2019;72:141146. doi:10.1016/j.meegid.2018.12.031

14. Morlock GP, Metchock B, Sikes D, Crawford JT, Cooksey RC. ethA, inhA, and katG loci of ethionamide-resistant clinical Mycobacterium tuberculosis isolates. Antimicrob Agents Chemother. 2003;47(12):37993805. doi:10.1128/AAC.47.12.3799-3805.2003

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[Full text] The Value of the inhA Mutation Detection in Predicting Ethionamide Res | IDR - Dove Medical Press

A research report on Regenerative Medicine Market features a succinct analysis on the latest market trends. The report also includes detailed abstracts about statistics, revenue forecasts and market valuation, which additionally highlights its status in the competitive landscape and growth trends accepted by major industry players.

Regenerative Medicine Market: Increased in bone and joint surgeries and increased prevalence of neurodegenerative, orthopedic, oncology, and genetic diseases are the key drivers for Global Regenerative Medicine Market.

Regenerative Medicine Market is valued at around USD 16148.16 Million in 2017 and expected to reach USD 74831.35 Million by 2024 with the CAGR of 22.27% over the forecast period.

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Regenerative Medicine market report published by the Brandessence Market Research and Consulting Pvt. Ltd. provides the detail information about regenerative medicine market from various aspects. This report consists of drivers, restrains, Opportunities which help the market to grow over the analysis period and recent trends which support the growth of market. This report consists of regional segmentation with of Product Type, application, therapy.

Regenerative medicines are those medicines which are used to repair, regenerate, and replace the tissues or organs damaged due to disease, injury or natural aging. Regenerative medicines are used in the treatment of various disorders such as orthopedic, neurodegenerative, oncology and others. These medicines help in the restoration of natural functioning of the organs and tissues. Regenerative medicines can also be used for the treatment of various chronic and genetic disorders, it also helps in the treatment of organ transplant which has reduced the rejection cases to a major extent.

There are various factors driving the growth of the regenerative medicine market, one of the major driving the growth of the market are increased prevalence of various chronic and genetic diseases over the period of time. Moreover, increase in technological advancement has also help in the development of effective and better therapies for the treatment of chronic disorders. Furthermore, the increased burden of these diseases has increased the demand of various effective medications which led to the increase in the regenerative medicine market. Increased research on stem cells has given a new direction to the regenerative medicines an expected to create various opportunities over the forecast period. However, high cost of treatment and stringent government regulations are expected to inhibit the growth of regenerative medicines over the forecast period.

Global regenerative medicines market report covers prominent players like Stryker Corporation, Cook Biotech Inc., Vericel Corporation, DePuy Synthes, Inc. Medtronic, Inc., Organogenesis Inc., Osiris Therapeutics, Inc., NuVasive, Inc., Acelity (KCI Concepts), Zimmer Holdings, Inc., Integra LifeSciences, C.R. Bard and others.

Regenerative Medicine Market Segmentation

By Product Type Cell-based products, Acellular products

By Application Orthopedic & Musculoskeletal Disorders, Cardiology, Dermatology, Diabetes, Central Nervous System Disorders, Others

By Therapy Cell therapy, Gene therapy, Tissue engineering, Immunotherapy

By Region

North America, US, Mexico, Chily, Canada, Europe, UK, France, Germany, Italy, Asia Pacific, China, South Korea, Japan, India, Southeast Asia, Latin America, Brazil, The Middle East and Africa, GCC, Africa, Rest of Middle East and Africa

Regenerative Medicine MarketKey Players

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US Regenerative Medicine Market by Trend Analysis, Gross Margin Analysis, Cost Structure Analysis and Forecast to 2027 KSU | The Sentinel Newspaper -...

January 29, 2021 I COVID-19 may become seasonal, severe infection associated with myeloid immune cells, potential Achilles heel of coronaviruses identified, melatonin synthesized in lungs could have protective effect, and plitidepsin outperforms remdesivir in preclinical trials. Plus: NSAID use during COVID-19 is time-dependent on its harm or benefit and NAU to test Allarity drug against Coronavirus Variant B117.

Research News

COVID-19 may be seasonal, like the flu, suggests a new paper published in Evolutionary Bioinformatics. Authors of the paper show that COVID-19 cases and mortality rates, among other epidemiological metrics, are significantly correlated with temperature and latitude across 221 countries. They also explain that our own immune systems could be partially responsible for the pattern of seasonality. For example, our immune response to the flu can be influenced by temperature and nutritional status, including vitamin D, a critical nutrient to our immune defenses. The researchers add that it is, however, too soon to say how seasonality and our immune systems interact in the case of COVID-19. DOI:10.1177/1176934321989695

SARS-CoV-2 independently entered Russia at least 67 times, primarily at the end of February and beginning of March 2020, according to a new study published in Nature Communications. Researchers of the study used 211 virus genomes, which were sequenced at Smorodintsev Research Institute of Influenza, and all genomes had been obtained from patients from 25 Russian regions during mid-March to April 2020. They determined that the vast majority of introductions came from European countries, and no cases of introduction from China were registered, which they attribute to the timely closure of borders with the country. Currently, nine local virus lineages are circulating in Russia, which are not present elsewhere in the world. DOI:10.1038/s41467-020-20880-z

Research led at Vanderbilt University Medical Center has discovered a proofreading exoribonuclease, called nsp14-ExoN, which can correct errors in the RNA sequence that occur during replication, when copies of a virus are generated. They believe that this may be the Achilles heel of the coronavirus, a finding that could help close the door on COVID-19 and possibly head off future pandemics. Using cutting-edge technologies and novel bioinformatics approaches, the researchers discovered that this ExoN also regulates the rate of recombination, which is the ability of the coronavirus to shuffle parts of its genome and even pull genetic material from other viral strains while it replicates in order to gain evolutionary advantage. These patterns of recombination are conserved across multiple coronaviruses, including SARS-CoV-2. They believe that the coronavirus ExoN is therefore a conserved, important target for inhibition and attenuation in the ongoing pandemic. This research is published in PLOS Pathogens. DOI:10.1371/journal.ppat.1009226

Also at Vanderbilt University Medical Center (VUMC), researchers have identified genetic factors that increase the risk for developing pneumonia to help identify patients with COVID-19 at greatest risk for this life-threatening complication. The researchers conducted genome-wide association studies (GWAS) of more than 85,000 patients whose genetic information is stored in VUMCs BioVU biobank. They identified nearly 9,000 cases of pneumonia in patients of European ancestry and 1,710 cases in patients of African ancestry. After further analysis, the research team linked the gene that causes cystic fibrosis (CF) and European ancestry and the mutation that causes sickle cell disease (SCD) in patients of African ancestry as the strongest pneumonia associations. After removing patients with CF and SCD, they then pinpointed a pneumonia-associated variation in a gene called R3HCC1L in patients of European ancestry, and one near a gene called UQCRFS1 in patients of African ancestry. They believe these findings could be applied to identifying patients with high risk of severe pneumonia to enable early interventions. They have published this work in the American Journal of Human Genetics. DOI:10.1016/j.ajhg.2020.12.010

Melatonin produced in the lungs acts as a barrier against SARS-CoV-2, blocking the expression of genes that encode proteins in cells serving as viral entry points, finds researchers at the University of So Paulo (USP). The hormone, therefore, prevents infection of these cells by the virus and inhibits the immune response so that the virus remains in the respiratory tract for a few days and then leaves the host, say the researchers. They used RNA sequencing data to quantify the level of expression of 212 COVID-19 signature genes in 288 samples from healthy human lungs. The researchers correlated these gene expression levels with a gene index that estimated the capacity of the lungs to synthesize melatonin (MEL-index). They then were able to determine that when the MEL-index was high, the entry points for the virus in the lungs were closed, and vice-versa. The research team suggests the potential for nasal administration of melatonin to prevent disease from developing in pre-symptomatic COVID-19 patients. This study is published in Melatonin Research. DOI:10.32794/mr11250090

In a new study, published in Cell Reports Medicine, La Jolla Institute for Immunology (LJI) researchers suggest that T cells can mount attacks against many SARS-CoV-2 targets, beyond the key sites on the viruss spike protein. They believe that by attacking the virus from many angles, the body is equipped to potentially recognize different SARS-CoV-2 variants. The researchers examined T cells from 100 people who had recovered from COVID-19 to take a closer look at the genetic sequence of the virus to separate the potential epitopes from the epitopes that these T cells would recognize. Their analysis revealed that not all parts of the virus induce the same strong immune response in everyone, and T cells can recognize dozens of epitopes on SARS-CoV-2 that vary from person to person. They determined that each study participant had the ability to recognize about 17 CD8+ T cell epitopes and 19 CD4+ T cell epitopes. DOI:10.1016/j.xcrm/2021/100202

John Hopkins Medicine researchers, in collaboration with Immunoscape, have published a complete profile of the response of T cells in people who have recovered from SARS-CoV-2 infection. The paper, published in The Journal of Clinical Investigation, better defines which T cells interact with which specific portion of the SARS-CoV-2 virus and how those interactions can provide long-lasting immunity against COVID-19. The researchers collected blood samples from 30 convalescent patients who had recovered from mild cases of COVID-19 and the Immunoscape team, a U.S.-Singapore biotechnology company, used its highly sensitive human leukocyte antigen (HLA)-SARS-CoV-2 tetramers to tag and identify the types of virus-recognizing CD8+ T cells. The researchers found that as levels of neutralizing antibodies increased in the convalescent plasma, so did the number of memory CD8+ T cells that recognized SARS-CoV-2 epitopes. They believe this means lasting protection against reinfection, and this knowledge will guide COVID-19 vaccine design to produce a strong immune response that could provide years of protection. DOI:10.1172/JCI145476

Severe COVID-19 patients have significantly elevated levels of a certain type of immune cell in their blood, call monocytic myeloid-derived suppressor cells (M-MDSC), according to a new study published in the Journal of Clinical Investigation. Karolinska Institutet researchers studied 147 patients with mild to fatal COVID-19 who were sampled repeatedly from blood and respiratory tract. These samples were then compared with patients who had influenza and healthy individuals. They found that the patients with severe COVID-19 had significantly higher levels of M-MDSCs in their blood when compared to milder cases and healthy participants. COVID-19 patients also had fewer T cells in their blood than healthy individuals that showed signs of impaired function. Additionally, their analysis revealed that the levels of M-MDSCs early in the course of infection seemed to reflect subsequent disease severity. DOI:10.1172/JCI44734

Researchers have engineered an antibody that effectively neutralizes SARS-CoV-2 and that also acts against multiple SARS-like viruses. Their antibody, ADG-2, was studied in mice. To engineer this broadly neutralizing antibody (bnAb), the researchers started with antibodies from the memory B cells of a 2003 SARS survivor that cross-neutralized multiple SARS-related viruses with modest potency. They then selectively engineered the binding affinities of several of these bnAbs, creating improvements in their abilities to bind the virus. The researchers then studied the engineered antibodies for SARS-CoV-2 neutralizing activity in mouse cell lines. ADG-2 was particularly effective. It showed broad binding activity to more than a dozen SARS-related coronaviruses. This research is published in Science. DOI:10.1126/science.abf4830

Plitidepsin has shown a potent efficacy against SARS-CoV-2 in preclinical trials, outperforming the antiviral remdesivir. These results, published in Science, show that in studies in human cells, plitidepsin demonstrated potent anti-SARS-CoV-2 activity: 27.5-fold more so than remdesivir as tested in the same cell line. In a model of human lung cells, plitidepsin greatly reduced viral replication. In further experiments involving both plitidepsin and remdesivir in vitro, the researchers suggest that plitidepsin has an additive effect with the approved drug and would be a potential candidate for a combined therapy. Authors of the research article believe that this promising treatment, which has limited clinical approval for the treatment of multiple myeloma, should be strongly considered for expanded clinical trials for the treatment of COVID-19. DOI:10.1126/science.abf4058

Oregon Health & Science University (OHSU) researchers have demonstrated that antibodies generated by the SARS-CoV-2 virus react to other strains of coronavirus and vice-versa. They determined, however, that antibodies generated by the 2003 SARS outbreak had only limited effectiveness in neutralizing SARS-CoV-2. The researchers believe that these findings have implications on both vaccine effectiveness and diagnosis of COVID-19. They believe that more work needs to be done to determine the lasting effectiveness of COVID-19 vaccine, given the speed of mutations. The team believes their study also suggests that efforts to accurately discern a previous COVID-19 infection, by analyzing antibodies in the blood, may be complicated by the presence of antibodies reacting to other strains of coronavirus including the common cold. This study is published in Cell Reports. DOI:10.1016/j.celrep.2021.108737

A new method to mapping viral mutations that escape leading clinical antibodies against COVID-19 has revealed mutations in the SARS-CoV-2 virus that allow it to evade treatments, including a single amino-acid mutation that fully escapes Regenerons antibody cocktail. University of Washington researchers and colleagues developed this scanning method to map how mutations to the receptor-binding domain (RBD) affect its recognition by antibodies. Their maps identified mutations that escape antibody binding, including a single mutation that escapes both antibodies in the Regeneron antibody cocktail. To further investigate, the team examined deep sequencing data from a persistently infected patient who was treated with the antibody cocktail at day 145 after diagnosis with COVID-19, and their analysis identified resistance mutations that arose in the patient. Furthermore, after they examined all human-derived SARS-CoV-2 sequences available as of mid-January 2021, the researchers report a substantial number of RBD mutations that escaped one or more of the antibodies that are in circulation. This paper is published in Science. DOI:10.1126/science.abf9302

Monash University researchers have discovered two new molecules that provide profound protection in experimental models of asthma, as well as protection from acute respiratory distress syndrome (ARDS) that is seen in some patients with severe COVID-19. In their study, originally designed to investigate how the immune system impacts gut bacteria, the researchers found that p-cresol sulfate (PCS), a gut bacteria by-product, led to a striking protection against asthma. They then determined that PCS was produced by enhanced bacterial metabolism of L-tyrosine, a well-known amino acid found in dietary supplements. The researchers saw significant protection against lung inflammation in mice given either L-tyrosine or PCS, as well as protection from ARDS. The researchers now aim to test one of the molecules in a clinical trial in asthmatics this year. These new findings are published in Nature Immunology. DOI:10.1038/s41590-020-00856-3

Non-steroidal anti-inflammatory drugs (NSAIDs) reduced both antibody and inflammatory responses to SARS-CoV-2 infection in mice, a new study finds that is published in the Journal of Virology. The authors of the study highlight that the timing of NSAID use during COVID-19 is important. They explain that NSAIDs anti-inflammatory activity could be detrimental early in SARS-CoV-2 infection because inflammation is usually helpful during this stage. This changes at later stages of COVID-19, particularly if the patient experiences intense inflammation known as cytokine storm. The researchers also note that a reduction in neutralizing antibodies caused by NSAIDs could be benign, or it might hinder the immune systems ability to fight the infection in its early stages. It could also reduce the magnitude or duration of protection from either natural infection or vaccination. DOI:10.1128/JVI.00014-21

Rhesus macaque monkeys infected with SARS-CoV-2 developed protective immune responses that could be reproduced with a vaccine, according to University of California, Davis (UC Davis) researchers. The team infected eight rhesus macaques at the California National Primate Research Center (CNPRC) with SARS-CoV-2 virus isolated from the first human patient treated at UC Davis, and they followed the immune responses in the monkeys over two weeks. The animals showed signs of lasting immunity and, most importantly, structures called germinal centers developed in the lymph nodes near the lungs. These germinal centers contained cells call T follicular helper (Tfh) cells. Germinal centers and Tfh cells are associated with generating plasma cells that remain in the body for many years to produce antibodies against pathogens the immune system has seen before, the researchers explain. They believe these results suggest that vaccines that induce this response will support immunity against COVID-19. This study is published in Nature Communications. DOI:10.1038/s41467-020-20642-x

Patients who have recovered from severe COVID-19 infection could be left with more protective T cells needed to fight reinfection, finds a team of researchers led at La Jolla Institute for Immunology (LJI). For their study, published in Science Immunology, the team analyzed CD8+ T cells from 39 COVID-19 patients and 10 individuals who had never been exposed to the virus. Of the COVID-19 patients, 17 had a mild case that did not require hospitalization, 13 had been hospitalized, and nine needed intensive care support. Surprisingly, the researchers saw weaker CD8+ T cell responses in patients with milder COVID-19 cases and saw the strongest CD8+ T cell responses in the patients who required hospitalization or intensive care. The team now hopes to study how T cells in tissues hit hardest by SARS-CoV-2, such as the lungs, react to the virus. They explain the importance of this as the memory T cells that provide long-term immunity need to live in the tissues. DOI:10.11260/sciimmunol.abe4782

In a new study published in Science Signaling, scientists discovered that SARS-CoV-2 may enter and replicate in human cells by exploiting newly identified sequences within cell receptors. They also suggest that these sequences could potentially serve as targets for new therapies against COVID-19. After analyzing the Eukaryotic Linear Motif database, the team of scientists discovered that ACE2 and various receptors contained several short linear motifs (SLiMs), or small amino acid sequences, that they predict plays a role in endocytosis and autophagy, or the entering of human cells and cellular housekeeping. The team determined that two SLiMs in ACE2 bound to endocytosis-related proteins, and one SLiM in the integrin beta-3 (3) bound to two proteins involved in autophagy. They believe that their prediction models could help identify similar SLiMs that assist with the replication of not only SARS-CoV-2, but other viruses that cause disease. DOI:10.1126/scisignal.abd0334

Ohio University researchers have published the first structural biology analysis of a section of the COVID-19 viral RNA called the stem-loop II motif, which they believe could be a potential target for anti-viral drugs to combat the virus. The research team identified this non-coding section of the RNA that is likely key to SARS-CoV-2 replication. Interestingly, they determined that the structural flexibility of this noncoding RNA motif differs by only a single nucleotide when compared to that in the early 2000s SARS-CoV outbreak, and the team also identified FDA-approved drugs that bind to the RNA motif and alter its flexibility. Since the structure and flexibility of noncoding RNA affects its function, the researchers suggest that it may be possible to develop antiviral drugs that specifically target this RNA motif to battle the virus. This research is published in Biochemical and Biophysical Research Communications. DOI:10.1016/j.bbrc.2021.01.013

Innate immunity may play a larger role in controlling SARS-CoV-2 viral load than adaptive immunity, according to a new study published in ACS Pharmacology & Translational Science. Researchers of the study developed a mathematical model that predicts viral load over time in organs that express the ACE2 receptor, which allows SARS-CoV-2 entry into human cells. They then used this model to simulate different conditions to determine this key role for innate immunity in controlling viral load. The researchers suggest the importance of starting antiviral or interferon therapy as soon as possible after the onset of COVID-19 symptoms. DOI:10.1021/acsptsci.0c00183

Industry News

Allarity Therapeutics in Denmark plans to further test the antiviral activity of stenoparib, its Poly ADP-Ribose Polymerase (PARP) inhibitor, against the B.1.1.7 variant of SARS-CoV-2. Stenoparib is a small molecule, targeting inhibitor of PARP, a key DNA damage repair enzyme active in tumors, which was originally developed by the pharmaceutical company Eisai. Results of previous pre-clinical studies for SARS-CoV-2 demonstrated that stenoparib inhibits SARS-CoV-2 as a single agent, and stenoparib in combination with remdesivir was active in inhibiting coronavirus in vitro. Allarity will now work with scientists at Northern Arizona Universitys Pathogen and Microbiome Institute (PMI) to test the similar ability of stenoparib to block the infection and replication of Coronavirus Variant B117. Press Release

Clear Labs announced the availability of the Clear Dx Whole Genome Sequencing (WGS), the first automated WGS solution that determines the complete RNA sequence of the SARS-CoV-2 genome in less than 24-hours with only minutes of hands-on time. The Clear Dx platform is powered by next generation sequencing (NGS), robotics and cloud-based analytics, and as a result, their WGS can more easily determine the nature of virus transmission by differentiating virus strains and monitoring mutations that lead to variants. In addition to WGS, the platform also features the Clear Dx SARS-CoV-2 Diagnostic Assay, which has received EUA, that allows labs to perform diagnostic screening and genomic surveillance simultaneously. Press Release

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Profile of T Cells, Broadly Neutralizing Antibodies, Anti-Viral Targets: COVID-19 Updates - Bio-IT World

BOSTON--(BUSINESS WIRE)--Vertex Pharmaceuticals Incorporated (Nasdaq: VRTX) today announced that the U.S. Food and Drug Administration (FDA) has accepted its supplemental New Drug Application (sNDA) to expand the use of TRIKAFTA (elexacaftor/tezacaftor/ivacaftor and ivacaftor) to include children ages 6 through 11 years old who have at least one F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene or a mutation in the CFTR gene that is responsive based on in vitro data. The FDA has granted Priority Review of the sNDA and assigned a Prescription Drug User Fee Act (PDUFA) target action date of June 8, 2021. The submission was supported by data from a global Phase 3 study of TRIKAFTA in children ages 6 through 11 years old with cystic fibrosis (CF) who have either two copies of the F508del mutation or one copy of the F508del mutation and one minimal function mutation.

If approved for this expanded use, we will have the opportunity to treat the underlying cause of the disease earlier in life with TRIKAFTA and potentially benefit approximately 1,500 additional children with CF, said Carmen Bozic, M.D., Executive Vice President and Chief Medical Officer at Vertex. Since our initial approval of TRIKAFTA in 2019, we have continued to work tirelessly to bring this medicine to those waiting as quickly as possible. We look forward to working with the Agency as they review the application over the course of the coming months.

Vertex plans to submit a Marketing Authorization Application (MAA) variation for the triple combination in the European Union in the first half of 2021 for children ages 6 through 11. Global regulatory filings in additional markets, including Canada and Australia, are planned in the coming months for this age group.

About Cystic Fibrosis

Cystic Fibrosis (CF) is a rare, life-shortening genetic disease affecting more than 80,000 people globally. CF is a progressive, multi-system disease that affects the lungs, liver, GI tract, sinuses, sweat glands, pancreas and reproductive tract. CF is caused by a defective and/or missing CFTR protein resulting from certain mutations in the CFTR gene. Children must inherit two defective CFTR genes one from each parent to have CF. While there are many different types of CFTR mutations that can cause the disease, the vast majority of all people with CF have at least one F508del mutation. These mutations, which can be determined by a genetic test, or genotyping test, lead to CF by creating non-working and/or too few CFTR proteins at the cell surface. The defective function and/or absence of CFTR protein results in poor flow of salt and water into and out of the cells in a number of organs. In the lungs, this leads to the buildup of abnormally thick, sticky mucus that can cause chronic lung infections and progressive lung damage in many patients that eventually leads to death. The median age of death is in the early 30s.

INDICATION AND IMPORTANT SAFETY INFORMATION FOR TRIKAFTA (elexacaftor/tezacaftor/ivacaftor and ivacaftor)

What is TRIKAFTA?

TRIKAFTA is a prescription medicine used for the treatment of cystic fibrosis (CF) in patients aged 12 years and older who have at least one copy of the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene or another mutation that is responsive to treatment with TRIKAFTA. Patients should talk to their doctor to learn if they have an indicated CF gene mutation. It is not known if TRIKAFTA is safe and effective in children under 12 years of age.

Patients should not take TRIKAFTA if they take certain medicines or herbal supplements, such as: the antibiotics rifampin or rifabutin; seizure medications such as phenobarbital, carbamazepine, or phenytoin; or St. Johns wort.

Before taking TRIKAFTA, patients should tell their doctor about all of their medical conditions, including if they: have kidney problems; have or have had liver problems; are pregnant or plan to become pregnant because it is not known if TRIKAFTA will harm an unborn baby; or are breastfeeding or planning to breastfeed because it is not known if TRIKAFTA passes into breast milk.

TRIKAFTA may affect the way other medicines work, and other medicines may affect how TRIKAFTA works. Therefore, the dose of TRIKAFTA may need to be adjusted when taken with certain medications. Patients should especially tell their doctor if they take antifungal medications such as ketoconazole, itraconazole, posaconazole, voriconazole, or fluconazole; or antibiotics such as telithromycin, clarithromycin, or erythromycin.

TRIKAFTA can cause dizziness in some people who take it. Patients should not drive a car, operate machinery, or do anything that needs them to be alert until they know how TRIKAFTA affects them.

Patients should avoid food or drink that contains grapefruit while they are taking TRIKAFTA.

TRIKAFTA can cause serious side effects, including:

High liver enzymes in the blood, which is a common side effect in people treated with TRIKAFTA. The patient's doctor will do blood tests to check their liver before they start TRIKAFTA, every 3 months during the first year of taking TRIKAFTA, and every year while taking TRIKAFTA. Patients should call their doctor right away if they have any of the following symptoms of liver problems: pain or discomfort in the upper right stomach (abdominal) area; yellowing of the skin or the white part of the eyes; loss of appetite; nausea or vomiting; dark, amber-colored urine.

Abnormality of the eye lens (cataract) in some children and adolescents treated with TRIKAFTA. If the patient is a child or adolescent, their doctor should perform eye examinations before and during treatment with TRIKAFTA to look for cataracts.

The most common side effects of TRIKAFTA include headache, diarrhea, upper respiratory tract infection (common cold) including stuffy and runny nose, stomach (abdominal) pain, inflamed sinuses, increase in liver enzymes, increase in a certain blood enzyme called creatine phosphokinase, rash, flu (influenza), and increase in blood bilirubin.

These are not all the possible side effects of TRIKAFTA. Please click the product link to see the full Prescribing Information for TRIKAFTA.

About Vertex

Vertex is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious diseases. The company has multiple approved medicines that treat the underlying cause of cystic fibrosis (CF) a rare, life-threatening genetic disease and has several ongoing clinical and research programs in CF. Beyond CF, Vertex has a robust pipeline of investigational small molecule medicines in other serious diseases where it has deep insight into causal human biology, including pain, alpha-1 antitrypsin deficiency and APOL1-mediated kidney diseases. In addition, Vertex has a rapidly expanding pipeline of genetic and cell therapies for diseases such as sickle cell disease, beta thalassemia, Duchenne muscular dystrophy and type 1 diabetes mellitus.

Founded in 1989 in Cambridge, Mass., Vertex's global headquarters is now located in Boston's Innovation District and its international headquarters is in London. Additionally, the company has research and development sites and commercial offices in North America, Europe, Australia and Latin America. Vertex is consistently recognized as one of the industry's top places to work, including 11 consecutive years on Science magazine's Top Employers list and a best place to work for LGBTQ equality by the Human Rights Campaign. For company updates and to learn more about Vertex's history of innovation, visit http://www.vrtx.com or follow us on Facebook, Twitter, LinkedIn, YouTube and Instagram.

Special Note Regarding Forward-Looking Statements

This press release contains forward-looking statements as defined in the Private Securities Litigation Reform Act of 1995, including, without limitation, statements made by Dr. Carmen Bozic in this press release, statements regarding our plans to submit an MAA in the EU and other global regulatory filings in additional markets, our expectations regarding the number of patients newly eligible for TRIKAFTA, and statements regarding the potential benefits of TRIKAFTA. While Vertex believes the forward-looking statements contained in this press release are accurate, these forward-looking statements represent the company's beliefs only as of the date of this press release and there are a number of risks and uncertainties that could cause actual events or results to differ materially from those expressed or implied by such forward-looking statements. Those risks and uncertainties include, among other things, that the sNDA to expand the use of TRIKAFTA to include children ages 6 through 11 could not be approved on a timely basis, or at all, that data from the company's development programs may not support registration or further development of its compounds due to safety, efficacy or other reasons, and other risks listed under the heading Risk Factors in Vertex's most recent annual report and subsequent quarterly reports filed with the Securities and Exchange Commission (SEC) and available through the company's website at http://www.vrtx.com and on the SECs website at http://www.sec.gov. You should not place undue reliance on these statements. Vertex disclaims any obligation to update the information contained in this press release as new information becomes available.

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Vertex Announces U.S. FDA Acceptance of Supplemental New Drug Application for TRIKAFTA (elexacaftor/tezacaftor/ivacaftor and ivacaftor) in Children...

When the French Emmanuelle Charpentier and the American Jennifer Doudna, won the Nobel Prize in Chemistry 2020, the award fell short compared to the importance of their contribution to the gene editing. These girls, yeah they discovered the black thread with their scissors CRISPR to alter and repair DNA, contributing to the health of living beings. A revolutionary technique, thanks to which mice with damage to the spinal cord They have walked again, hoping that one day it could be applied to humans.

Although it seems inspired by the Lucy movie, gene editing also known as biohacking, it is nothing other than correct and repair the cells of the DNA Or, insert the missing cells, which cause genetic diseases as simple as myopia to the diabetes. In addition, they have been shown to have an important benefit in other types of patients such as HIV. Being a new miracle in medicine.

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In a simple explanation, one of the theories of CRISPR, is that genetic diseases are due to damage or absence in the genomic sequence. What the experts do is all engineering work, repairing or inserting the genetic sequence. For example, some genetic diseases such as sclerosis, diabetes or muscular dystrophy are believed to be due toin the absence or damage de a gene X, while biohackers take care of repair it. It is truly fascinating.

However, gene editing therapies in humans are illegal in many countries, in addition to being a potentially controversial issue because it questions the objective of prolonging life and practically playing god. In fact, a group of UNESCO scientists requested the prohibition of any edition of the human germ line since they could lead to actions of baby design .

Twitter: @N_Neandertalien

However, a study of the Ruhr University, in Germany, revives the debate on the future of genetic medicine, by getting a group of hamsters with spinal cord damage to walk again dfter two to three weeks of receiving a new gene therapy, while there is a huge chance that this new treatment will have the same success in humans.

The scientists worked with mice with spinal damage and consequently lost all mobility on both legs. They first began by stimulating the nervous system to identify the damaged gene, after a series of studies, they developed the gene hyperinterleukin-6genetically modified and injected it into the sensory motor cortex and did what they could at the time: wait.

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Being an unpublished study, the consequences could have been diverse, but once the hyper-interleukin-6, achieved adapt to the genetic sequence, for the production of the protein within the cells. Lto protein, or hyperinterleukin-6 (hIL-6), acts assuming a key characteristic Disabling spinal cord injuries, which is damage to nerve fibers known as axons. What is special about our study is that the protein is not only used to stimulate nerve cellss that produce it themselves, but also takes it further (through the brain) , Gave DailyMail, Dr. Dietmar Fischer, who led the study.

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There is no miracle, everything is thanks to science and like all treatment, genetic editing would take time to show the first results. But, after a couple of weeks, the CRISPR worked its magic. All mice managed to recobrar movement body and not only that, Little time they all walked again.

Now the scientists will have to wait to analyze if the mice do not suffer from serious side effects, if so, they will take the next step to study if this gene-editing therapy can be applied in humans, which could save more than five million people in the world who suffer from partial or total paralysis.

It sounds spectacular, we know. But please dont try to play scientist. Gene editing may have grave consequences in humans, if it is practiced in a way experimental. While modified genes are not found in nature, they are designed specifically for genetic engineers with all the knowledge and within a laboratory. Better, if you are interested in the subject and you would like to enter the world of CRISPR, we recommend the Netflix documentary entitled Unnatural Selection

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The story of the hamster that walked again thanks to genetic editing - Explica

Introduction

Elizabethkingia anophelis (E. anophelis) is an aerobic, immotile, oxidase-positive, indole-positive, Gram-negative, non-fermenting bacillus, belonging to the genus Elizabethkingia and the family Flavobacteriaceae, which was first isolated from the midgut of the mosquito Anopheles gambiae in 2011.1 The first clinically significant E. anophelis infection was associated with a case of neonatal meningitis in Bangui, Central African Republic in 2011.2

Thereafter, within the genus Elizabethkingia, E. anophelis has emerged as a major nosocomial pathogen, which can cause severe pneumonia, meningitis, infections of the bloodstream, osteomyelitis, endocarditis, endophthalmitis, skin and soft tissue infection, urinary tract infection and abdominal infection.310,14,15 Whole genome sequencing (WGS) has recently uncovered a wide range of virulence factors contributing to the pathogenesis of E. anophelis, including products of the capsule, lipopolysaccharides, endopeptidases, lipid biosynthesis and metabolism, magnesium transport proteins, macrophage infectivity, heat shock proteins, catalase, peroxidases, superoxide dismutase, two-component regulatory system, and more.5,1820

Extensive research has shown that E. anophelis isolates are resistant to most -lactams, carbapenems and aminoglycosides.4,5,1417 The emergence of multidrug-resistant (MDR) bacterial pathogens is considered a potential public health hazard, they are widely detected in the environment and their transmission to humans is either by the food chain or via infected animals, poultry, and fish.2629 Furthermore, MDR bacterial pathogens often pose a therapeutic dilemma for clinicians and are therefore associated with a high mortality rate and poor prognosis.

Recently, the incidence of infections caused by the genus Elizabethkingia has increased continuously worldwide, especially those caused by E. anophelis species. A single-hospital study from South Korea reported that there was an increase in the prevalence of Elizabethkingia genus infections among hospitalized patients from 0.02 in 2009 to 0.88 in 2017.9 The first recorded outbreak of E. anophelis infection was from Singapore in 2012, in which three out of five patients died of septicemia.3 Furthermore, during 20142016, several outbreaks have occurred in the Midwestern United States, including Wisconsin, Illinois, and Michigan, in which the patient fatality rate related to E. anophelis infections ranged from 30.8% to 70%.58 Therefore, E. anophelis infection is regarded as profoundly serious and important and should be taken seriously by clinicians.

A recent study indicated that E. anophelis has been continuously misidentified as Elizabethkingia meningoseptica (E. meningoseptica) using conventional methods (API/ID32, Phoenix 100 ID/AST, Vitek 2 and Vitek MS).13 Therefore, most of the previously reported data regarding clinical characteristics, antimicrobial susceptibility patterns and carbapenem resistance mechanisms of E. anopheles, may be incorrect. To date, however, the susceptibility patterns of E. anophelis isolates have not been reported in Mainland China, especially with data collated using the more robust broth dilution method. Genome-wide analysis has revealed that this multidrug-resistant pathogen carries a class A serine--lactamase, CME, 2 metallo--lactamases, GOB and BlaB, in addition to numerous genes encoding for putative efflux pumps.5,1820 However, no studies have focused on the function of these putative efflux pumps in E. anophelis isolates. In addition, data reporting on risk factors associated with infection and mortality in E. anophelis infected patients may potentially help clinicians identify high-risk patients and help guide future therapeutic strategies.

The present study was therefore initiated to: (i) identify the risk factors associated with E. anophelis infection and in-hospital mortality, (ii) investigate the antimicrobial susceptibility patterns and carbapenem resistance mechanisms of E. anophelis isolates and (iii) characterize the function of -lactamases and putative efflux pumps expressed in E. anophelis isolates.

This study used the clinical microbiology database from a 3200-bed university-affiliated medical center (Chongqing, China) to retrospectively collect those strains that were identified as the genus Elizabethkingia between January 2015 and December 2019. Sampling and isolation of bacterial strains were a part of the routine hospital laboratory procedures and microbial identification was performed in the microbiology laboratory using the VITEK2 compact (bioMrieux, Inc., NC, USA) and the VITEK MS (bioMrieux, MO, USA) systems. All strains from the genus Elizabethkingia were stored at 80C in 15% glycerol until use. Complete 16S rRNA gene sequencing was used to reconfirm the identity of all isolates. The primers used for amplification and sequencing of the 16S rRNA gene are listed in Table S1 in Additional file 1. The sequences were assembled using SeqMan (DNAStar) and compared with publicly available sequences in the NCBI (http://www.ncbi.nlm.nih.gov) using the BLAST algorithm. Strains were considered to be accurately identified when a strain shared >99.0% 16S rRNA sequence with a type of strain in GenBank. The sequences of 16S rRNA were performed using ClustalW, and the phylogenetic trees were constructed in MEGA7 software using the Neighbor-Joining method.

Electronic medical records of the patients were collected retrospectively and we excluded subjects with the following characteristics: patients with polymicrobial infection and patients admitted for <48 hours. Only the first episode was considered for patients with more than one positive E. anophelis culture. To evaluate the risk factors associated with E. anophelis infection, controls were defined as randomly selected patients with non-E. anophelis infections during the same time (at a 3:1 ratio to the case group). Selected epidemiological, demographic, clinical, laboratory, treatment and outcome data were obtained from the electronic medical records. Empirically administering agents to isolates that were not susceptible was defined as inappropriate empirical antimicrobial therapy. Shock was defined as the coexistence of a systolic pressure of <90 mm Hg and organ dysfunction of the respiratory system, liver, or kidneys. Serum total protein content of <60 g/L or albumin content <25 g/L was the criteria used to define hypoproteinemia. Hypokalemia was diagnosed for a serum potassium level <3.5 mmol/L. Systemic steroid use was defined as oral or intravenous administration of at least 20 mg/day of a steroid (prednisone, hydrocortisone, methylprednisolone, or dexamethasone) within 1 month of infection. We defined anemia as a hemoglobin level of <130 g/L in men and <120 g/L in women according to the World Health Organization (WHO) guidelines. The primary clinical outcome was in-hospital mortality.

The reference broth microdilution method was used to evaluate the minimum inhibitory concentrations (MICs) of all antibiotics in E. anophelis and recombinant strains according to the Clinical and Laboratory Standards Institute (CLSI) M07-Ed11 (2019). The criterion suggested by the CLSI for other non-Enterobacteriaceae was used to determine the susceptibility of isolates to antibiotics except for ceftazidime/avibactam, aztreonam/avibactam, vancomycin, tigecycline, rifampicin, colistin and fosfomycin. The US Food and Drug Administration (FDA) Enterobacteriaceae criteria were used to interpret isolate susceptibility to tigecycline (resistant MIC 8 g/mL, susceptible MIC 2 g/mL and intermediate MIC = 4 g/mL). The MIC breakpoint applied to vancomycin and rifampicin was adapted from the CLSI criteria for Staphylococcus spp. A MIC of 16/4 g/mL was considered resistant for the combination of ceftazidime/avibactam and aztreonam/avibactam. MICs for colistin were interpreted at susceptible breakpoints of 2 g/mL and resistant breakpoints of >2g/mL according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) Enterobacteriaceae criteria. Likewise, for fosfomycin, we elected to use the susceptible breakpoint of 32 g/mL and resistant breakpoint of >32 g/mL based on EUCAST Enterobacteriaceae criteria. The reference strains Escherichia coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 27853) were used as negative controls and quality controls for antibiotic susceptibility testing.

The presence of the carbapenemase genes (blaKPC, blaIMP, blaVIM, blaNDM, blaBlaB, blaGOB and blaOXA-48-like) and extended-spectrum beta-lactamase (ESBL) genes (blaTEM, blaSHV, blaCME and blaCTX-M) were confirmed by touch-down PCR assays and sequencing. Touch-down PCR amplification was performed using a thermal cycler (Applied Biosystems VeritiPro PCR, CA, USA) under the following cycling conditions: Initial step of 95C for 3 min, followed by 8 cycles of 92C for 20 sec, with annealing temperatures starting at 68C for 20 sec (decreasing 2C/cycle), and with a final extension at 72C for 30 sec; this step was followed by 21 cycles of 92C for 20 sec, 55C for 20 sec, 72C for 30 sec, and finally, 72Cfor 5 min. DNA sequencing was performed using an Applied Biosystems 3730 DNA Analyzer.

We amplified the full-length coding sequences (CDSs) of the genes using specific primers flanked by restriction sites (EcoRI, XhoI or BamHI). These included genes encoding for blaCME, blaBlaB, blaGOB, CzcABC family efflux RND transporter, Efflux ABC transporter (ATP-binding protein), the MATE family of MDR efflux pumps, small multidrug resistance family (SMR) proteins and MFS-type transporter. Amplified PCR fragments were purified and cloned into the corresponding sites within the pET-28a plasmid and then electroporated into BL21 competent E. coli. Positive clones were verified by PCR and sequencing. The sets of primers used for amplification and sequencing of target genes are provided in Table S1 in Additional file 1.

The data were evaluated using SPSS statistical software (version 22.0, IBM). Data are presented as counts (proportions) for categorical variables. Direct comparisons between two groups were determined using the 2 test or Fishers exact test. Means ( standard deviation) were used to express normally distributed continuous variables and the median ( inter-quartile range) was calculated for non-normally distributed variables. Comparisons between two groups were conducted using Students t-test for normally distributed variables or a MannWhitney U-test for non-normally distributed variables. To evaluate independent risk factors for the infection and in-hospital mortality of E. anophelis isolates, we examined all plausible variables using a univariate analysis. Risk factors with a P value <0.1 as detected by the univariate analysis were included in a multivariate logistic-regression model with the enter method. Odds ratios (ORs) and 95% confidence intervals (CIs) were determined for each risk factor of infection and in-hospital mortality. A two-tailed P value <0.05 was considered statistically significant.

The Institutional Review Board and Ethics Committee of Chongqing Medical University approved this study (approval number: 2020703). The study was conducted in accordance with the Declaration of Helsinki. The collection of culture isolates and collation of anonymous clinical data was in accordance with the approved clinical practice guidelines. The need to give informed consent for this study was waived by the Institutional Review Board due to the nature of the retrospective analysis with no individual patient identifiers.

A total of 59 non duplicated Elizabethkingia isolates were collected from the clinical microbiology laboratory for microbial trait investigation. Full 16S rRNA gene sequencing was performed on 59 Elizabethkingia clinical strains. After comparison with available sequences in the NCBI using BLAST, 16S rRNA sequencing showed that 39 (69.6%) isolates were identified as Elizabethkingia anophelis R26. The phylogenetic tree based on 16S rRNA showed the genetic relationship among Elizabethkingia anophelis (Figure 1).

Figure 1 Phylogenetic tree showing the relationship of the 39 E. anophelis isolates using 16S rRNA gene sequence. Bootstrap support value above branches, the scale bar indicates the number of substitutions per site.

Of the E. anophelis isolates with a documented site of infection, 18 (46.2%) were from the respiratory tract, eight (20.5%) were from the urinary tract, six (15.4%) from blood, three (7.7%) from cerebrospinal fluid, and four were from peritoneal fluid, amniotic fluid, conjunctival sac, and the cornea (Table 5). From January 2015 to December 2019, 39 E. anophelis samples were isolated from 39 consecutive patients who were enrolled in the study. These patients consisted of 21 males (53.8%) and 18 females (46.2%) with a median age of 61.

Notably, chronic obstructive pulmonary disease was the most frequent comorbidity (76.9%), followed by anemia (66.7%). The empirical antibiotics used in the 39 patients included carbapenems (38.5%), -lactam/lactamase inhibitors (33.3%), -lactams (30.8%), teicoplanin (25.6%), levofloxacin (17.9%), aminoglycosides (17.9%), minocycline (12.8%) and antibiotics administered either alone or in combination (Table 5), and 84.6% of these empirical antibiotic therapies were deemed as inappropriate antibiotic use. Overall, the in-hospital mortality rate of patients with E. anophelis infection was 51.3%. Furthermore, -lactam/lactamase inhibitor antibiotics were used significantly more in patients who did not survive (P = 0.041).

Compared to the non-E. anophelis infection controls, the potential risk factors for the acquisition of E. anophelis infections are shown in Tables 1 and 2. Univariate analysis indicated that hypertension, cerebrovascular diseases, chronic obstructive pulmonary disease, renal diseases, surgery in the past 6 months, anemia, hypoproteinemia, and hypokalemia were significantly more frequent in patients with E. anophelis infections (P < 0.05). There was also a positive correlation between patient age and their likelihood of acquiring an E. anophelis infection (P < 0.05). In the multivariate analysis, coronary artery diseases (OR 5.81, 95% CI: 1.0930.93, P = 0.039), chronic obstructive pulmonary disease (OR 6.71, 95% CI: 1.5528.99, P = 0.011), surgery in the past 6 months (OR 18.04, 95% CI: 3.2998.87, P = 0.001), anemia (OR 6.72, 95% CI: 1.1240.42, P = 0.038) and systemic steroid use (OR 9.87, 95% CI: 1.3074.94, P = 0.027) were independent risk factors for the acquisition of an E. anophelis infection.

Table 1 Univariate Analysis of Clinical Features of Patients Infected with E. anophelis Isolates

Table 2 Multivariate Analysis of Clinical Features of Patients Infected with E. anophelis Isolates

Univariate and multivariate logistic-regression analysis results for the factors associated with in-hospital mortality are shown in Table 3. Univariate analysis showed that cerebrovascular disease (P = 0.035), chronic obstructive pulmonary disease (P = 0.020), nasogastric tube insertion (P = 0.008) and anemia (P = 0.002) were associated with a higher mortality rate. Using further multivariate analysis, anemia (OR 86.38, 95% CI: 1.425251.29; P = 0.033) was identified as the only independent risk factor for in-hospital mortality in patients with E. anophelis infections.

Table 3 Risk Factors Associated with In-Hospital Mortality

The susceptibility of the 39 E. anophelis isolates to the antimicrobial agents tested in this study is shown in Table 4. The isolates showed high in-vitro susceptibility towards minocycline (100%), and piperacillin/tazobactam (71.8%) but with lower in-vitro susceptibility towards levofloxacin (38.5%), ciprofloxacin (30.8%), rifampicin (20.5%), piperacillin (17.9%) and tigecycline (10.3%). The MIC50, MIC90 and MIC range for minocycline on the isolates were 0.5, 1, and 0.251 g/mL, respectively, whereas the MIC50, MIC90 and MIC range for piperacillin/tazobactam were 16, 32, and 464 g/mL, respectively. All isolates displayed resistance to vancomycin, ceftazidime, cefepime, aztreonam, ceftazidime/clavulanic acid, cefepime/clavulanic acid, colistin and fosfomycin according to the breakpoints used. It is worth noting that while all isolates produced the MBLs BlaB and GOB, aztreonam/avibactam could not further inhibit growth.

Table 4 Antimicrobial Susceptibilities of E. Anophelis Isolates Determined by the Broth Microdilution Method

PCR experiments were used to detect the presence of blaGOB and blaBlaB in 37 isolates, and blaCME -lactamase genes in 36 isolates from the original 39 E. anophelis isolates (Table 5 and Figure 2). Sequence alignments showed that E. anophelis strains harbored two types of the blaCME gene, blaCME-1 (n = 34) and blaCME-2 (n = 2), eight types of the blaBlaB gene, including blaBlaB-29 (17), blaBlaB-2 (7), blaBlaB-1 (5), blaBlaB-17 (3), blaBlaB-3 (1), blaBlaB-9 (1), blaBlaB-33 (1) and blaBlaB-34 (1), and eight types of the blaGOB gene, including blaGOB-38 (19), blaGOB-20 (8), blaGOB-32 (3), blaGOB-50 (3), blaGOB-39 (1), blaGOB-4 (1), blaGOB-40 (1) and blaGOB-45 (1). The most detected combination of -lactamases was CME-1 + BlaB-29 + GOB-38 (n = 17).

Table 5 Empirical Antimicrobial Therapy in Patients Infected with E. anophelis Isolates

Figure 2 (A) Electrophoretic pattern of BlaB gene (759 bp); M: 1002000 bp DNA ladder; Lanes 1, 2, 3, 5, 6, 7, 8, 9: positive E. anophelis strains; Lanes 4: negative E. anophelis strain. (B) Electrophoretic pattern of CME gene (912 bp); M: 1002000 bp DNA ladder; Lanes 1, 2, 3, 4, 6, 7, 8: positive E. anophelis strains; Lanes 5, 9: negative E. anophelis strains. (C) Electrophoretic pattern of GOB gene (885 bp); M: 1002000 bp DNA ladder; Lanes 1, 2, 4, 5, 7, 8, 9: positive E. anophelis strains; Lanes 3, 6: negative E. anophelis strains.

We also investigated the presence of other -lactamase genes, however, none of the 39 E. anophelis isolates harbored carbapenemase genes (blaKPC, blaIMP, blaVIM, blaNDM and blaOXA-48-like) or ESBL genes (blaTEM, blaSHV and blaCTX-M).

To further evaluate the function of -lactamases, the most prevalent forms of blaCME, blaBlaB and blaGOB genes from E. anophelis isolates were cloned into a pET28a(+) plasmid vector. We also amplified and cloned genes encoding putative efflux pump proteins including the CzcABC family efflux RND transporter, Efflux ABC transporter (ATP-binding protein), MATE family members of the MDR efflux pump, small multidrug resistance family (SMR) proteins and MFS-type transporter. These plasmids were transformed into BL21 (DE3) E.coli and the MICs of the common antibiotics were tested in the resultant strains. The strain transformed with pET-CME displayed an increased MIC for ampicillin, piperacillin, cefazolin, cefuroxime, ceftazidime, ceftriaxone and aztreonam when compared to the pET28a(+) vector construct. This suggests that the extended-spectrum serine--lactamase CME is functionally involved in cephalosporin and monobactam resistance (Table 6). The MIC for imipenem increased 32-fold (from 0.125 to 4 g/mL) in the presence of the pET-BlaB construct and 16-fold (from 0.125 to 2 g/mL) in the presence of the pET-GOB construct. This suggests that the MBLs BlaB and GOB, are responsible for increased imipenem resistance (Table 6). Along with the increase in imipenem resistance, the pET-BlaB and pET-GOB constructs also conferred an increased MIC for ampicillin, piperacillin, cefazolin, cefuroxime, and ceftazidime. This indicates that the MBLs BlaB and GOB can also degrade ampicillin, piperacillin, cefazolin, cefuroxime, and ceftazidime (Table 6). All the efflux pump transformants tested, including pET-ABC, pET-MFS, pET-MATE, pET-SMR and pET-RND did not result in increased MICs for any of the antibiotics tested (Table 6).

Table 6 The Antibiotic Susceptibilities of BL21 (DE3) E. coli Expressing CME, BlaB, GOB, Putative Efflux Proteins or the pET28a(+) Vector

Infection with E. anophelis in humans is increasing in many countries and there have been several reports of E. anophelis outbreaks in the community and nosocomial environment in Singapore and the Midwestern United States, including Wisconsin, Illinois, and Michigan.310 However, as suggested previously, E. anophelis is commonly misidentified as E. meningoseptica when using biochemical identification methodologies or automated identification systems in clinical settings. Therefore, data regarding the clinical features, clinical prognosis, and the antimicrobial susceptibility profiles of E. anophelis could be skewed. For these reasons, we have, for the first time identified the risk factors associated with the acquisition of E. anophelis and we have found that anemia is an independent risk factor for in-hospital mortality in patients with E. anophelis infections. Moreover, we demonstrate for the first time that various putative efflux pumps found in E. anophelis do not alter antimicrobial resistance and therefore, do not possess a drug efflux function. -Lactamases were commonly found in E. anophelis isolates and the MBLs BlaB and GOB, are responsible for carbapenem resistance, whereas the ESBL, CME is functionally involved in resistance to cephalosporins and monobactams.

In the present study, we initially explored risk factors associated with E. anophelis infection and using multivariate analysis, we found that coronary artery diseases, chronic obstructive pulmonary disease, surgery in the past 6 months, anemia and systemic steroid use were independently associated with E. anophelis infection. Previous studies have suggested that patients with E. anophelis infection could have greater underlying comorbidities and this study is the first to provide a statistical analysis to support this hypothesis.310 Moreover, surgery in the past 6 months, anemia and systemic steroid use are known to compromise the immune status of the patients. Therefore, these patients are more vulnerable to the acquisition of E. anophelis infection in the same hospital environment.

In previous reports, the case fatality rate of patients with E. anophelis infection ranged from 24% to 60% in different countries.414 In line with this, our study showed that the in-hospital mortality rate of patients with an E. anophelis infection was 51.3%. We, therefore, went on to explored the factors influencing this mortality. When compared with the only previous study investigating risk factors for mortality,10 our study demonstrated that anemia was the only independent predictor of mortality in patients infected with E. anophelis, a factor which has not been reported previously and these patients may present as anemic because of the hemolytic activity of E. anophelis. Several studies have reported that this bacterium can lyse erythrocytes to access essential nutrients (such as amino acids) using hemolysins and heme-degrading proteins.2022 This process may alter the host's physiological status and compromise the immune system, thereby worsening the patient prognosis with E. anophelis. Therefore, anemic patients with a confirmed E. anophelis infection should be considered as higher risk and should be given greater scrutiny and special care. Unexpectedly, inadequate antibiotic therapy was not associated with mortality, this is probably because of the small sample size of infected patients in our study.

Published information concerning the antimicrobial susceptibility patterns of E. anophelis, identified using reliable methods is limited. Studies from Singapore and Taiwan have demonstrated that E. anophelis was resistant to carbapenems, -lactams, -lactam/-lactam inhibitor and aminoglycosides.1416 However, previous research showed that the susceptibility of E. anophelis to fluoroquinolones, tigecycline, piperacillin, piperacillin-tazobactam and trimethoprim-sulfamethoxazole was variable.46,10,17 Using a disk diffusion or agar dilution test, studies from Hong Kong, South Korea and the USA reported the following susceptibilities of E. anophelis to ciprofloxacin (22%100%), levofloxacin (29%96%), piperacillin (41.1%100%), piperacillin-tazobactam (92%), vancomycin (0%100%) and trimethoprim-sulfamethoxazole (22%70.6%).4,5,17 However, when using the broth microdilution test, researchers from Taiwan and Singapore showed the following susceptibilities of E. anophelis to ciprofloxacin (1%21.5%), levofloxacin (16%78.5%), piperacillin (19.4%), piperacillin-tazobactam (30.6%92.4%), vancomycin (0%), tigecycline (5.1%26.4%), minocycline (97.5%100%) and trimethoprim-sulfamethoxazole (4%92.4%).1416 As shown above, there are huge discrepancies in the susceptibility levels of E. anophelis to ciprofloxacin, levofloxacin, piperacillin, and vancomycin when comparing the disk diffusion or agar dilution tests and the broth microdilution test. This suggests that the susceptibility of E. anophelis seen using the disk diffusion test or agar dilution test may be unreliable and inaccurate, as the broth microdilution test represents the gold-standard method for antimicrobial susceptibility testing.

There are also obvious differences in the susceptibility of E. anophelis to antibacterial agents when the standard broth microdilution test is used. A possible explanation for this inconsistency is that natural geographical differences cause variation in the susceptibility patterns observed in previous studies. It is therefore necessary to investigate the antimicrobial susceptibility of E. anophelis in local areas as a guide to antibiotic selection. Our study showed the following susceptibility of E. anophelis to various treatments: minocycline (100%), piperacillin-tazobactam (71.8%), levofloxacin (38.5%), ciprofloxacin (30.8%), piperacillin (17.9%), rifampicin (20.5%) and tigecycline (10.3%). All isolates displayed resistance to ceftazidime, cefepime, aztreonam, ceftazidime/clavulanic acid, cefepime/clavulanic acid, colistin and fosfomycin, according to the breakpoints used. Most of the antimicrobial susceptibility results in this study are consistent with those of previous studies performed using the broth microdilution test. These results suggest that antimicrobial therapy for E. anophelis should prioritize minocycline or piperacillin-tazobactam. However, in our study, patients in the non-survival group were treated with significantly more -lactam/lactamase inhibitor antibiotics as compared to the survival group (P = 0.041). This observation indicates that piperacillin-tazobactam is not an effective treatment for E. anophelis infections. This study was limited by the fact that antimicrobial susceptibility in-vitro does not equate to in-vivo clinical efficacy. Therefore, large prospective clinical trials are urgently needed to validate therapeutic recommendations.

In this study, we screened for the presence of carbapenemase genes (blaKPC, blaIMP, blaVIM, blaNDM, blaBlaB, blaGOB and blaOXA-48-like) and ESBL genes (blaTEM, blaSHV, blaCME and blaCTX-M) in all 39 E. anophelis isolates. No carbapenemase genes (blaKPC, blaIMP, blaVIM, blaNDM and blaOXA-48-like) or ESBL genes (blaTEM, blaSHV and blaCTX-M) were detected in any isolates. However, we identified 35 (89.7%) isolates co-harboring blaGOB, blaBlaB and blaCME -lactamase genes. The most detected combination of -lactamases was CME-1, BlaB-29, and GOB-38 (n = 17).

To further evaluate the function of -lactamases, recombinant strains harboring either blaCME, blaBlaB or blaGOB were constructed. The transformed strain expressing CMEs displayed an increased MIC for ampicillin, piperacillin, cefazolin, cefuroxime, ceftazidime, ceftriaxone and aztreonam as compared to the pET28a(+) vector construct. This suggests that the ESBL CME is functionally involved in resistance to cephalosporins and monobactams. The MIC for imipenem increased 32-fold (from 0.125 to 4 g/mL) in the presence of the BlaB-expressing construct and 16-fold (from 0.125 to 2 g/mL) in the presence of the GOB-expressing construct. This suggests that the metallo--lactamases BlaB and GOB are responsible for the observed carbapenem resistance.

Aztreonam/avibactam is a novel class of combinational -lactamase-inhibitor, designed to treat serious infections of metallo--lactamase (MBL)-producing Gram-negative bacteria, which is currently in Phase I clinical trials (NCT01689207). Aztreonam is relatively stable against MBL hydrolysis, however, it is easily inactivated by class A (eg, KPC), class C (eg, AmpC) and certain class D (eg, OXA-48) serine--lactamase enzymes.23 Avibactam potently inhibits class A, class C and certain class D serine--lactamase enzymes and displays a broader -lactamase inhibition profile than other -lactamase inhibitors.23 When in combination, aztreonam/avibactam is effective against isolates co-producing ESBLs and MBLs with porin loss/deficiency.24 However, it was quite unexpected that E. anophelis is resistant to aztreonam/avibactam according to our experimental results.

Genomic annotation of all Elizabethkingia spp. reveals that besides -lactamases, there are also numerous putative efflux pump proteins including CzcABC family efflux RND transporter, Efflux ABC transporter (ATP-binding protein), MATE family of MDR efflux pumps, small multidrug resistance family (SMR) proteins and MFS-type transporter. Interestingly, however, none of these transporters have been phenotypically characterized.5,1820 It was, therefore, critical to investigate the function of these putative efflux pumps. Our data showed that all recombinant efflux pump strains including pET-ABC, pET-MFS, pET-MATE, pET-SMR and pET-RND did not result in increased MICs for -lactam and non--lactam antibiotics. These results suggest that the putative efflux pump genes from E. anophelis are not responsible for antimicrobial drug resistance. Similarly, Schindler et al cloned and expressed 21 putative efflux pump genes in Staphylococcus aureus which had no effect on any of the antibiotics tested.25 In summary, we demonstrate for the first time that the various putative efflux pumps found in E. anophelis do not possess antimicrobial drug efflux function.

There were some limitations to our study; however, firstly, the small sample size from the single-center study prevented its translation to the wider population. However, the identification of both a carbapenem resistance mechanism and the susceptibility profile of the drug-resistant E. anophelis are of great clinical importance and warrant an urgent, wider, in-depth study. Secondly, no further investigation into the clonality of these isolates was performed, so that the possibility of infection outbreaks cannot be ruled out.

In conclusion, this study provided a detailed report of risk factors, antimicrobial susceptibility patterns and carbapenem resistance mechanisms in E. anophelis clinical isolates from one medical center in Southwest China. Our data showed that patients with anemia, coronary artery diseases, chronic obstructive pulmonary disease or patients who have received systemic steroids or surgery in the past 6 months are more likely to acquire an E. anophelis infection. Furthermore, patients with anemia have a worse prognosis and therefore require more attention and special care from clinicians. The collected clinical isolates exhibited remarkable multidrug resistance to colistin, fosfomycin, aztreonam/avibactam and tigecycline, which are all regarded as last-resort treatments for carbapenem-resistant Enterobacteriaceae, while minocycline is the most effective antibiotic against E. anophelis in-vitro. Mechanistic analysis revealed that carbapenem resistance is associated with the hydrolytic activity of the MBLs BlaB and GOB and is not associated with various putative efflux pumps expressed in E. anophelis. Future in-vivo and prospective clinical trials are urgently needed to determine optimal antimicrobial agent efficacies based on in-vitro drug susceptibility testing results and resistance mechanisms.

This study was supported by the Natural Science Foundation of Chongqing (No.cstc2019jcyj-msxmX0253). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

The authors report no conflicts of interest in this work.

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[Full text] MBLs, Rather Than Efflux Pumps, Led to Carbapenem Resistance in Fosfom | IDR - Dove Medical Press