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.

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Genomes, Maps, And How They Affect You - IFLScience

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.

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Are Phages Overlooked Mediators of Health and Disease? - The Scientist

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.

Continue reading here:

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

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.

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The First Targeted Therapy For Lung Cancer Patients With The KRAS Gene MutationExtraordinary Results With Sotorasib - SurvivorNet