Category Archives: Transhuman News

All right, lets do this one last time. My name is CRISPR. I was made from a bacterial defense system, and for years Ive been the one and only gene editing wunderkind. Im pretty sure you know the rest. Im relatively cheap to make, easy to wield, and snip out genes pretty on target. Im going into clinical trials. Im reviving the entire field of gene therapy. Theres only one CRISPR. And youre looking at it.

Well, just as Spider-Man was way off, so is the idea of a single CRISPR to rule them all. This month, Dr. David Liu at the Broad Institute of MIT and Harvard in Cambridge, MA, introduced an upgrade that in theory may correct nearly 90 percent of all disease-causing genetic variations. Rather than simply deactivating a gene, CRISPR-based prime editing is a true search-and-replace editor for the human genome. With a single version, it can change individual DNA letters, delete letters, or insert blocks of new letters into the genome, with minimal damage to the DNA strand.

For now, prime editing has only been tested in cultured cells. But its efficacy is off the charts. Early experiments found it could correct single-letter misspellings in sickle cell disease, snip out four superfluous letters that underlie Tay-Sachs, and insert three missing letters to correct a genomic typo that leads to cystic fibrosis. In all, the tool worked remarkably well in over 175 edits in both human and mouse cells.

The excitement has been palpable, said Dr. Fyodor Urnov at the University of California, Berkeley, who was not involved in the research. I cant overstate the significance of this.

Given all of the existing CRISPR upgrades, why are scientists head over heels about prime editing?

CRISPR 1.0 generally refers to the classic version, which snips open the double helix to get rid of a certain gene. But as a tool, todays CRISPR is less like genetic scissors and more similar to a Swiss Army knife, one that scientists keep on improving. There are variants that, rather than destroying a gene, insert one or change one genetic letter to another, or ones that can target thousands of genetic spots at the same time. There are also spin-offs that hunt down RNAthe messenger that carries DNAs genetic code to the greater cellular universe, rather than the genetic code itself. Its truly a CRISPR multiverse out there.

Yet for all of CRISPRs upgrades, the tool has serious issues. For one, its very rough on the genome. Cas9, the protein scissor component of CRISPR, doesnt surgically cut out a gene. Rather, editing is in fact the cell detecting damage to the double helix, and trying its best to patch the broken strands back up. Just as scars form on our skin, this process can often introduce errors in the repairing processadding or missing a letter or two. Scientists often take advantage of this botched repair to destroy a gene that causes disease, or sneak in some additional code.

The problem? This process is basically genome vandalism, said Dr. George Church, a CRISPR pioneer at Harvard who wasnt involved in the new work. Its great when the repair goes according to plan; when it doesnt, the repair can introduce unwantedor downright dangerousmutations.

Lius idea for prime editing grew from his work on base editors. Here, the CRISPR machinery doesnt chop up the double helix. Rather, it uses the blood hound guide RNA to shuttle a new protein component to the target DNA sequence. This component then performs a single letter swap: C to T, or G to A.

Although considered much safer than traditional cut-and-glue CRISPR, base editors are limited in the number of genetic diseases they can treat. Its like editing on a broken keyboardsome misspellings just cant be fixed.

Prime editing circumvents these problems by heavily upgrading both components. The altered Cas9, for example, only snips a single strand of the double helix, rather than chomping through both. The new guide, pegRNA, both tethers the entire machinery to the target site, and encodes the desired edit.

Then comes the third component that magically ties everything together: a protein dubbed reverse transcriptase, which can make DNA sequences based on the blueprint in pegRNA, to insert into the nicked target site.

Still confused? Picture the DNA double helix as a laddertwo strands with connecting rungs in the middle. Prime editing cuts one strand using its neutered Cas9. This creates an opening for the other two components to insert a new gene into the severed spot; meanwhile, the original DNA sequence is snipped off. Now, rather than the original X, X (for example), the cell has X, Y.

The prime editor then performs a second snip at the opposing, non-edited strand. This alerts the cell of DNA damage, which it then tries to fixusing the new gene as a template. The end result is the cell goes from disease-causing X, X to normal, healthy Y, Y.

Several reasons.

One, because it doesnt cut both DNA strands, it doesnt immediately activate the cells repair system that is prone to errors. This means that scientists have far better control over the type of edit they want, and its no longer left to chance.

Two, prime is remarkably multi-purpose. Previously, the consensus among genome scientists was that a separate CRISPR tool was required for each specific type of edit: delete a gene, insert new DNA code, or DNA letter substitutions. In contrast, prime can achieve all three functions without additional modification. For experiments, it means less setup. For development into gene therapy, it means less overhead investment.

Three, prime editing can swap any of the DNA letters into any other, meaning it can now target an enormous amount of inherited diseases. For example, sickle cell disease, which causes oxygen-carrying blood cells to deform into sharp sickle-like shapes, requires changing a T into an A at a precise spot. Base editors cant do that. Prime editing can. Thats about 7,000 genetic disorders now amenable to gene therapy.

Four, prime editing also works in cells that no longer divide to renew themselves, such as neurons and muscle cells. Because these cells cant pass on their therapeutic DNA edit to daughter cells, to fix genetic deficits scientists have to be able to efficiently correct mutations in a large population. With prime editing, thats now possible.

Finally, prime editing can remove an exact number of letters from a given spot on the genome, at least up to 80. This allows scientists to precisely dictate the DNA sequences they want out, rather than relying on chance.

Early experiments with prime editing in cells show the tool is incredibly accurate. Off-target nicks were below 10 percent, and less than one-tenth of edited cells had unwanted changes to their genome, compared to up to 90 percent for first-gen CRISPR systems.

Nevertheless, the tool will have to go through rigorous testing before its widely accepted. Working in a few types of human cells is one thing; having it perform equally well inside a living body is something else completely. Most of primes tricks so far can be replicated using CRISPR 1.0, though at lower efficacy and with higher chances of off-target failures. Unlike prime editing, however, the original version has years of experience and plenty of clinical trials underwaycongenital blindness, sickle cell diseaseto back it up.

Whats more, prime is massive in terms of molecular tools. Getting it into cells will be a struggle. Getting it to the brain, which is protected by a dense wall of cells, will be even harder. To get the editor to their target, scientists will likely rely on gene therapy, itself a budding industry.

If CRISPR is like scissors, base editors are like a pencil. Then you can think of prime editors like a word processor, capable of precise search and replace, said Liu. All will have rolesThis is the beginning rather than the end.

Image Credit:petarg/Shutterstock.com

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Everything You Need to Know About Superstar CRISPR Prime Editing - Singularity Hub

Ask the average whiskey drinker to name the key ingredients in their favorite spirit, and theyll probably tell you which grains its made from. Of course, whats just as crucial to the final product as the grains its distilled from is the barreland the American-made barrels that both American distillers and many of their Scottish and Irish counterparts rely on are almost exclusively made from the noble white oak tree.

The whisk(e)y business is so reliant on this species that concerns are arising about what would happen if disease hit the species, something that gets increasingly likely as the climate changes. Thats why, not unlike the research we wrote about earlier this fall into drought resistance in barley, researchers from the University of Kentucky, University of Tennessee, Penn State, and the US Forest Service are partnering with Makers Mark and the Independent Stave Company to research the genome of the white oak.

This research is for the greater good of the industry and the entire Eastern forest, said Seth DeBolt, director of the University of Kentuckys James B. Beam Institute for Kentucky Spirits, in a prepared statement. Wed like to get a reference map for the white oak genome. Weve identified a tree at the Makers Mark Distillery on Star Hill Farm as a gorgeous representative specimen of the species.

This reference tree is hundreds of years oldwhite oak trees have been known to live four centuriesand researchers are collecting acorns and grafts from it. The team is approaching oak as an agricultural product, which, for the whiskey business, makes sense. They hope to identify some of the genetic variation that exists within the species.

The challenge here is to thoroughly understand a species, a really foundational, long-lived species that anchors the forest, said DeBolt. The goal is to answer questions such as: How does it live that long, in a single location? How does it maintain resistance to so many different diseases?

American white oak is a key ingredient in bourbon-making. The color, and much of the flavor, of bourbon come from white oak barrels, so its critically important that this precious natural resource be managed and preserved for generations to come, said Makers Marks Rob Samuels, chief distillery officer. At Makers Mark, were constantly stepping up our own environmental efforts, which have become a guiding principle for everything we do, and were proud to play a part in this research that will reach far beyond our home at Star Hill Farm and help this vital species thrive long into the future.

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The University of Kentucky is Researching the Genome of White Oak - The Whiskey Wash

A substantial proportion of oncologists in the United States are loath to broach the issue of cost if patients require genomic testing as part of their cancer care, a recent survey has found.

And whereas half of those surveyed did frequently bring up the issue of cost with their patients, approximately one quarter only sometimes raise the issue of cost if genomic testing was required, and the other quarter rarely or never discuss it, the same survey shows.

The survey involved 1220 oncologists who participated in the 2017 National Survey of Precision Medicine in Cancer Treatment.

This is a nationally representative survey of medical oncologists sponsored by the National Cancer Institute, National Human Genomic Research Institute, and the American Cancer Society, say the authors.

The results were published online November 1 in The Journal of the National Cancer Institute (JNCI)

"Use of genomic testing is increasing in the United States," note the authors. led by Robin Yabroff, PhD, an epidemiologist with the American Cancer Society.

More than 30 genomic tests associated with cancer drugs are now available in the US. Most often, these tests identify a genetic mutation and thus allow the use of a targeted agent instead of chemotherapy.

Testing can be expensive and not all tests and related treatments are covered by health insurance, the authors write, and even when those who have private health insurance can experience medical financial hardship.

"Oncologists may not be the providers best suited for all discussions about the expected costs of care," the authors acknowledge.

However, they can ensure that cost conversations do take place with someone from the medical team who is qualified to do so, they suggest.

The authors also point out that training materials and practice guides are available to help physicians overcome their discomfort about having discussions concerning the cost of care with patients as well as about how much genomic interventions may cost that patient.

"Even privately insured cancer survivors report problems paying medical bills, stress related to medical bills, or delaying or forgoing care because of cost," the authors warn.

"Thus, discussions about the expected costs of cancer care are important for all patients," they conclude.

These discussions can be difficult because of the nuances involved, suggests Richard Schilsky, MD, chief medical officer of the American Society of Clinical Oncology (ASCO), writing in an accompanying editorial.

"The biggest challenge may be explaining to a patient the nuances of context of use and clinical utility that define the true value of a tumor biomarker test. Patients need to know not just what the test will cost but how it will inform their care, impact their options, affect their outcomes and whether, in the long run, it might even guide them to better treatments and/or lower their overall costs of care," he explains.

Further research on how best to convey these complex issues in the course of a clinical encounter is desperately needed before we can effectively 'talk the talk' about tumor genomic testing," Schilsky concludes.

The findings are based on answers that were obtained to this question in the survey: 'In the past 12 months, when you or your staff discussed any form of genomic testing with your cancer patients or their families, how often did you discuss the likely costs of the testing and related treatment?'

Results showed that the frequency of cost discussions differed by the type of cancer that physicians treated.

For example, some 60.1% of oncologists who treated only solid tumors frequently discussed the cost of genomic testing with patients compared with 50.4% of those who treated both hematologic cancers and solid tumors, and 27.9% of oncologists who treated only hematologic cancers (P < .001)

In fact, oncologists who treated both solid and hematologic cancers were almost three times more likely to often have cost discussions with patients compared with oncologists who only treated hematologic malignancies (odds ratio [OR], 2.82).

Oncologists who only treated solid tumors were four times more likely to have frequent cost discussions (OR, 4.01) compared with those who only managed blood cancers, researchers add.

Oncologists who had graduated from medical school at least 15 years before taking the survey were also more likely to have frequent discussions about the cost of genomic testing and related treatment costs, compared with those who had graduated less than 15 years ago.

Just over half (54%) of physicians who had used next-generation sequencing gene panel tests in the past 12 months reported often discussing the cost of genomic testing compared with almost 38% of those who did not (P < .001), the authors add.

"Oncologists with formal training in genomic testing were more likely than those without this training to report discussing costs often," the investigators continue at 54.6% vs 44.1%, respectively (P =.001).

Similarly, oncologists who had electronic health record (EHR) alerts for genomic testing were at least twice as likely to have frequent cost discussions compared with oncologists who did not have EHR alerts (OR, 2.22).

Higher patient volumes also prompted more frequent discussions about genomic testing costs, as did a having a higher percentage of patients either insured by Medicaid, or who were self-pay or uninsured, as was practicing in lower income areas.

In 2009, the American Society of Clinical Oncology highlighted the important role that oncologists have in discussions about potential out-of-pocket costs that patients may incur in the course of their cancer care.

The Institute of Medicine later categorized these discussions as being a critical element in high-quality care.

The study authors have disclosed no relevant financial relationships.

JNCI. Published online November 1, 2019. Abstract, Editorial

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Cost of Genomic Tests Often Not Discussed With Patients - Medscape

Identification of melanoma-specific Dark Antigens to be presented at The Society for Immunotherapy of Cancer 34thAnnual Meeting (SITC)

LONDON, Nov. 6, 2019 /PRNewswire/ -- Ervaxx, a biotechnology company pioneering the use of Dark Antigens to developoff-the-shelf cancer vaccines and T-cell receptor-based immunotherapies, formally announces its launch following two years in incubation by SV Health Investors.

Ervaxx coincides its launch with the presentation of new research to identify novel melanoma-specific Dark Antigens by application of its novel EDAPT platform at The Society for Immunotherapy of Cancer 34th Annual Meeting (SITC) (9 November 2019, National Harbor, MD, USA). Details of the poster can be found below.

Ervaxx' founding idea is that the 'dark matter' of the human genome (i.e. the 98% of the genome that does not encode known proteins) contains antigen-coding sequences that are uniquely expressed by cancer cells and shared across patients. These sequences, which are normally silenced in healthy cells, represent a large potential repertoire of novel antigens that Ervaxx aims to develop as targets for new immunotherapies.

Ervaxx has developed its proprietary EDAPT platform to explore this new and expanding Dark Antigen repertoire, and to identify and assess its tumor-specific and immunogenic potential to combat cancer. EDAPT combines bioinformatics, transcriptomics, immunopeptidomics and state-of-the-art immunology to discover and validate novel Dark Antigens with which to deliver a pipeline of off-the-shelf tumor-specific therapeutic cancer vaccines and T cell receptor (TCR)-based therapies. The platform is built upon pioneering research from the company's founders at the Francis Crick Institute (London, UK) and developed by Ervaxx in partnership with other leading academic collaborators.

Initially, Ervaxx has focused on the discovery and development of off-the-shelf cancer vaccines based on Dark Antigens derived from endogenous retroviral (ERV) related DNA sequences where significant and compelling research by its founders has been conducted. Retroviral DNA is a component of genomic dark matter and makes up about 8% of the entire genome. Ervaxx and its collaborators have identified thousands of novel ERV-related sequences, with enriched expression in over 30 tumor types.

This work has been further advanced by Ervaxx, which is progressing its lead cancer vaccine programme targeting melanoma, for which highly immunogenic target antigens have been identified. The research being presented at SITC describes the application of EDAPT to identify over 2,000 potential melanoma-specific Dark Antigens encoded by the cancer genomes of melanoma patients using ERV markers to search for aberrantly expressed and highly immunogenic target antigens.

The presentation and tumor specificity of these Dark Antigens were validated, and immunogenicity and lack of central tolerance in normal donor CD8+ T-cells were also confirmed. Constructs encoding multiple Dark Antigens with high immunogenicity that are conserved across patients and across HLA subtypes have been selected to create a therapeutic, off-the-shelf cancer vaccine.

The company is utilizing the EDAPT platform to expand its discovery focus beyond ERV-related sequences and is also advancing into additional indications, including non-small cell lung cancer, ovarian cancer and other solid tumor indications with high unmet medical need.

Ervaxx has raised $17.5m in seed/Series A funding from SV Health Investors and a leading (undisclosed) global pharmaceutical company, with which it also has a strategic R&D partnership. The company is headquartered in London and operates R&D from its laboratory in the Bioescalator Building at Oxford University.

The company has established an experienced board of directors chaired by Houman Ashrafian (Ervaxx co-founder, Managing Partner at SV Health Investors) and including Kate Bingham (Managing Partner at SV Health Investors), Tim Edwards (Karus Therapeutics, AstronauTx, Storm Therapeutics and others); Veronique Birault (Director of Translation at the Francis Crick Institute) and Kevin Pojasek (Ervaxx President & CEO and Venture Partner at SV Health Investors).

Kevin Pojasek, CEO of Ervaxx, said:

"We are delighted to announce our formal launch today and to bring forward our exciting and innovative science. Our Dark Antigens have the potential to bring new and effective cancer treatments to patients by providing a completely new set of targets, which can be combined to maximise population coverage and immunogenic response. We believe we are the first company with an integrated platform designed to explore the dark matter of the genome for novel cancer targets. Our hope is that this pioneering approach will generate a new wave of effective immunotherapies for a wide range of cancers."

Houman Ashrafian, Chairperson and Co-founder of Ervaxx, added:

"The science behind Ervaxx is truly ground-breaking and opens up exciting possibilities for the development of new and multiple modalities of tumor-specific cancer therapies based on Dark Antigens. We are delighted with the progress the company has made during its incubation phase. An excellent team has been brought together with new R&D capabilities to rapidly drive the translation of this research into the clinic. We look forward to supporting its progress as a pioneer in this new cancer immunotherapy approach."

SITC Poster details

Abstract title: Discovery of immunogenic ERV-derived antigens as targets for melanoma immunotherapy

Abstract number:P680

Authors:Jupp, R. et al

Date/time:Saturday, 9 November, 07:00am - 08:30pm

About Ervaxx

Ervaxx is pioneering the use of Dark Antigens to deliver targeted off-the-shelf cancer vaccines and other immunotherapies for treating and preventing cancer. Ervaxx Dark Antigens derive from vast untapped expanses of genetic 'dark matter' beyond the normal coding regions of the genome, which are generally silenced in normal tissue but can become selectively activated in cancer.

Ervaxx' powerful, proprietary EDAPT platform has been developed to discover and validate Dark Antigens providing an in-depth assessment of candidate antigens on primary tumor cells along with their immunogenic potential. The EDAPT platform has identified proprietary antigens that map to multiple solid tumor types and generate robust, antigen-specific T-cell responses. Ervaxx is advancing a pipeline of off-the-shelf cancer vaccines and T cell receptor (TCR)-based therapies leveraging these insights into the role of Dark Antigens in cancer.

Ervaxx was co-founded by SV Health Investors and is based on pioneering research at the Francis Crick Institute (London, UK). The company has offices in London, UK and a laboratory in the Bioescalator Building at Oxford University, UK. Ervaxx also has a strategic partnership with a global pharmaceutical company.

For more information visit: http://www.ervaxx.com

Ervaxx, Dark Antigen and EDAPT are trademarks of Ervaxx Limited

FOR MORE INFORMATIONErvaxx LimitedKevin Pojasek, CEOTel: +44-(0)-1865618828Email: info@ervaxx.com

Citigate Dewe RogersonMark Swallow, Frazer Hall, Nathaniel DahanTel: +44-(0)-20-7638-9571Email: ervaxx@citigatedewerogerson.com

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Ervaxx Launches to Pioneer the Use of Dark Antigens for the Development of Off-the-Shelf Cancer Vaccines and T-cell Receptor-based Immunotherapies -...

ABBOTT PARK, Ill., Nov. 6, 2019 /PRNewswire/ -- Abbott (NYSE: ABT) announced today that a team of its scientists identified a new subtype of the human immunodeficiency virus (HIV), called HIV-1 Group M, subtype L.1 The findings, published today in the Journal of Acquired Immune Deficiency Syndromes (JAIDS), show the role next-generation genome sequencing is playing in helping researchers stay one step ahead of mutating viruses and avoiding new pandemics.

Since the beginning of the global AIDS pandemic, 75 million people have been infected with HIV and 37.9 million people today are living with the virus.2 Thanks to the work done by the global health community over the past few decades, the goal of ending the HIV pandemic is becoming feasible. Yet researchers must remain vigilant to monitor for new strains to make sure testing and treatments continue to work.

"In an increasingly connected world, we can no longer think of viruses being contained to one location," said Carole McArthur, Ph.D., M.D., professor in the departments of oral and craniofacial sciences, University of Missouri Kansas City, and one of the study authors. "This discovery reminds us that to end the HIV pandemic, we must continue to outthink this continuously changing virus and use the latest advancements in technology and resources to monitor its evolution."

This research marks the first time a new subtype of "Group M" HIV virus has been identified since guidelines for classifying new strains of HIV were established in 2000. Group M viruses are responsible for the global pandemic, which can be traced back to the Democratic Republic of Congo (DRC) in Sub-Saharan Africa.3,4

The science behind genetic sequencing to discover new viruses

To determine whether an unusual virus is in fact a new HIV subtype, three cases must be discovered independently.5 The first two samples of this subtype were discovered in DRC in the 1980s and the 1990s. The third, collected in 2001, was difficult to sequence at that time because of the amount of virus in the sample and the existing technology.

Today, next-generation sequencing technology allows researchers to build an entire genome at higher speeds and lower costs. In order to utilize this technology, Abbott scientists had to develop and apply new techniques to help narrow in on the virus portion of the sample to fully sequence and complete the genome.6

"Identifying new viruses such as this one is like searching for a needle in a haystack," said Mary Rodgers, Ph.D., a principal scientist and head of the Global Viral Surveillance Program, Diagnostics, Abbott, and one of the study authors. "By advancing our techniques and using next generation sequencing technology, we are pulling the needle out with a magnet. This scientific discovery can help us ensure we are stopping new pandemics in their tracks."

Twenty-five years of tracking mutating viruses around the world

As a leader in blood screening and infectious disease testing, Abbott created its Global Viral Surveillance Program 25 years ago to monitor HIV and hepatitis viruses and identify mutations to ensure the company's diagnostic tests remain up to date. As part of this research, Abbott scientists confirmed that its core and molecular laboratory diagnostic tests can detect this new HIV strain.

In partnership with blood centers, hospitals and academic institutions around the world, Abbott has collected more than 78,000 samples containing HIV and hepatitis viruses from 45 countries, identified and characterized more than 5,000 strains, and published 125 research papers to date to help the scientific community learn more about these viruses. The study published today, "Complete genome sequence of CG-0018a-01 establishes HIV-1 subtype L," is now available online.

To learn more about Abbott's virus hunting efforts, visit http://www.abbott.com/virushunters.

About Abbott:Abbott is a global healthcare leader that helps people live more fully at all stages of life. Our portfolio of life-changing technologies spans the spectrum of healthcare, with leading businesses and products in diagnostics, medical devices, nutritionals and branded generic medicines. Our 103,000 colleagues serve people in more than 160 countries.

Connect with us atwww.abbott.com, on LinkedIn at http://www.linkedin.com/company/abbott-/, on Facebook atwww.facebook.com/Abbottand on Twitter @AbbottNews and @AbbottGlobal.

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Abbott Announces Discovery of New Strain of HIV, Keeping Global Health Community a Step Ahead of the Virus - BioSpace