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Novartis uses a ‘dimmer switch’ medication to fine-tune gene therapy candidates
Reporter: Amandeep Kaur, BSc., MSc.
Using viral vectors, lipid nanoparticles, and other technologies, significant progress has been achieved in refining the delivery of gene treatments. However, modifications to the cargo itself are still needed to increase safety and efficacy by better controlling gene expression.
To that end, researchers at Children’s Hospital of Philadelphia (CHOP) have created a “dimmer switch” system that employs Novartis’ investigational Huntington’s disease medicine branaplam (LMI070) as a regulator to fine-tune the quantity of proteins generated from a gene therapy.
The investigational medicine branaplam was shown to fine-tune the expression of an erythropoietin gene therapy in mice by scientists from Children’s Hospital of Philadelphia and Novartis. (Novartis)
According to a new study published in Nature, the Xon system altered quantities of erythropoietin—which is used to treat anaemia associated with chronic renal disease—delivered to mice using viral vectors. The method has previously been licenced by Novartis, the maker of the Zolgensma gene therapy for spinal muscular atrophy.
The Xon system depends on a process known as “alternative splicing,” in which RNA is spliced to include or exclude specific exons of a gene, allowing the gene to code for multiple proteins. The team used branaplam, a small-molecule RNA-splicing modulator, for this platform. The medication was created to improve SMN2 gene splicing in order to cure spinal muscular atrophy. Novartis shifted its research to try the medication against Huntington’s disease after a trial failure.
A gene therapy’s payload remains dormant until oral branaplam is given, according to Xon. The medicine activates the expression of the therapy’s functional gene by causing it to splice in the desired way. Scientists from CHOP and the Novartis Institutes for BioMedical Research put the dimmer switch to the exam in an Epo gene therapy carried through adeno-associated viral vectors. The usage of branaplam increased mice Epo levels in the blood and hematocrit levels (the proportion of red blood cells to whole blood) by 60% to 70%, according to the researchers. The researchers fed the rodents branaplam again as their hematocrit decreased to baseline levels. The therapy reinduced Epo to levels similar to those seen in the initial studies, according to the researchers.
The researchers also demonstrated that the Xon system could be used to regulate progranulin expression, which is utilised to treat PGRN-deficient frontotemporal dementia and neuronal ceroid lipofuscinosis. The scientists emphasised that gene therapy requires a small treatment window to be both safe and effective.
In a statement, Beverly Davidson, Ph.D., the study’s senior author,said, “The dose of a medicine can define how high you want expression to be, and then the system can automatically ‘dim down’ at a pace corresponding to the half-life of the protein.”
“We may imagine scenarios in which a medication is used only once, such as to control the expression of foreign proteins required for gene editing, or only on a limited basis. Because the splicing modulators we examined are administered orally, compliance to control protein expression from viral vectors including Xon-based cassettes should be high.”
In gene-modifying medicines, scientists have tried a variety of approaches to alter gene expression. For example, methyl groups were utilised as a switch to turn on or off expression of genes in the gene-editing system CRISPR by a team of researchers from the Massachusetts Institute of Technology and the University of California, San Francisco.
Auxolytic, a biotech company founded by Stanford University academics, has described how knocking down a gene called UMPS could render T-cell therapies ineffective by depriving T cells of the nutrition uridine. Xon could also be tailored to work with cancer CAR-T cell therapy, according to the CHOP-Novartis researchers. The dimmer switch could help prevent cell depletion by halting CAR expression, according to the researchers. According to the researchers, such a tuneable switch could help CRISPR-based treatments by providing “a short burst” of production of CRISPR effector proteins to prevent undesirable off-target editing.
Genetic scissors: a tool for rewriting the code of life
Emmanuelle Charpentier and Jennifer A. Doudna have discovered one of gene technology’s sharpest tools: the CRISPR/Cas9 genetic scissors. Using these, researchers can change the DNA of animals, plants and microorganisms with extremely high precision. This technology has had a revolutionary impact on the life sciences, is contributing to new cancer therapies and may make the dream of curing inherited diseases come true.
Researchers need to modify genes in cells if they are to find out about life’s inner workings. This used to be time-consuming, difficult and sometimes impossible work. Using the CRISPR/Cas9 genetic scissors, it is now possible to change the code of life over the course of a few weeks.
“There is enormous power in this genetic tool, which affects us all. It has not only revolutionised basic science, but also resulted in innovative crops and will lead to ground-breaking new medical treatments,” says Claes Gustafsson, chair of the Nobel Committee for Chemistry.
As so often in science, the discovery of these genetic scissors was unexpected. During Emmanuelle Charpentier’s studies of Streptococcus pyogenes, one of the bacteria that cause the most harm to humanity, she discovered a previously unknown molecule, tracrRNA. Her work showed that tracrRNA is part of bacteria’s ancient immune system, CRISPR/Cas, that disarms viruses by cleaving their DNA.
Charpentier published her discovery in 2011. The same year, she initiated a collaboration with Jennifer Doudna, an experienced biochemist with vast knowledge of RNA. Together, they succeeded in recreating the bacteria’s genetic scissors in a test tube and simplifying the scissors’ molecular components so they were easier to use.
In an epoch-making experiment, they then reprogrammed the genetic scissors. In their natural form, the scissors recognise DNA from viruses, but Charpentier and Doudna proved that they could be controlled so that they can cut any DNA molecule at a predetermined site. Where the DNA is cut it is then easy to rewrite the code of life.
Since Charpentier and Doudna discovered the CRISPR/Cas9 genetic scissors in 2012 their use has exploded. This tool has contributed to many important discoveries in basic research, and plant researchers have been able to develop crops that withstand mould, pests and drought. In medicine, clinical trials of new cancer therapies are underway, and the dream of being able to cure inherited diseases is about to come true. These genetic scissors have taken the life sciences into a new epoch and, in many ways, are bringing the greatest benefit to humankind.
Emmanuelle Charpentier, born 1968 in Juvisy-sur-Orge, France. Ph.D. 1995 from Institut Pasteur, Paris, France. Director of the Max Planck Unit for the Science of Pathogens, Berlin, Germany.
Jennifer A. Doudna, born 1964 in Washington, D.C, USA. Ph.D. 1989 from Harvard Medical School, Boston, USA. Professor at the University of California, Berkeley, USA and Investigator, Howard Hughes Medical Institute.
Other Articles on the Nobel Prize in this Open Access Journal Include:
there have been many instances of off-target effects where genes, other than the selected target, are edited out. This ‘off-target’ issue has hampered much of the utility of CRISPR in gene-therapy and CART therapy
However, an article in Science by Jon Cohen explains a Nature paper’s finding of a new tool in the CRISPR arsenal called prime editing, meant to increase CRISPR specificity and precision editing capabilities.
Primeediting promises to be a cut above CRISPR Jon Cohen CRISPR, an extraordinarily powerful genome-editing tool invented in 2012, can still be clumsy. … Primeediting steers around shortcomings of both techniques by heavily modifying the Cas9 protein and the guide RNA. … ” Primeediting “well may become the way that disease-causing mutations are repaired,” he says.
The effort, led by Drs. David Liu and Andrew Anzalone at the Broad Institute (Cambridge, MA), relies on the modification of the Cas9 protein and guide RNA, so that there is only a nick in a single strand of the double helix. The canonical Cas9 cuts both strands of DNA, and so relies on an efficient gap repair activity of the cell. The second part, a new type of guide RNA called a pegRNA, contains an RNA template for a new DNA sequence to be added at the target location. This pegRNA-directed synthesis of the new template requires the attachment of a reverse transcriptase enzymes to the Cas9. So far Liu and his colleagues have tested the technology on over 175 human and rodent cell lines with great success. In addition, they had also corrected mutations which cause Tay Sachs disease, which previous CRISPR systems could not do. Liu claims that this technology could correct over 89% of pathogenic variants in human diseases.
A company Prime Medicine has been formed out of this effort.
As was announced, prime editing for human therapeutics will be jointly developed by both Prime Medicine and Beam Therapeutics, each focusing on different types of edits and distinct disease targets, which will help avoid redundancy and allow us to cover more disease territory overall. The companies will also share knowledge in prime editing as well as in accompanying technologies, such as delivery and manufacturing.
Reader of StatNews.: Can you please compare the pros and cons of prime editing versus base editing?
The first difference between base editing and prime editing is that base editing has been widely used for the past 3 1/2 years in organisms ranging from bacteria to plants to mice to primates. Addgene tells me that the DNA blueprints for base editors from our laboratory have been distributed more than 7,500 times to more than 1,000 researchers around the world, and more than 100 research papers from many different laboratories have been published using base editors to achieve desired gene edits for a wide variety of applications. While we are very excited about prime editing, it’s brand-new and there has only been one paper published thus far. So there’s much to do before we can know if prime editing will prove to be as general and robust as base editing has proven to be.
We directly compared prime editors and base editors in our study, and found that current base editors can offer higher editing efficiency and fewer indel byproducts than prime editors, while prime editors offer more targeting flexibility and greater editing precision. So when the desired edit is a transition point mutation (C to T, T to C, A to G, or G to A), and the target base is well-positioned for base editing (that is, a PAM sequence exists approximately 15 bases from the target site), then base editing can result in higher editing efficiencies and fewer byproducts. When the target base is not well-positioned for base editing, or when other “bystander” C or A bases are nearby that must not be edited, then prime editing offers major advantages since it does not require a precisely positioned PAM sequence and is a true “search-and-replace” editing capability, with no possibility of unwanted bystander editing at neighboring bases.
Of course, for classes of mutations other than the four types of point mutations that base editors can make, such as insertions, deletions, and the eight other kinds of point mutations, to our knowledge prime editing is currently the only approach that can make these mutations in human cells without requiring double-stranded DNA cuts or separate DNA templates.
Nucleases (such as the zinc-finger nucleases, TALE nucleases, and the original CRISPR-Cas9), base editors, and prime editors each have complementary strengths and weaknesses, just as scissors, pencils, and word processors each have unique and useful roles. All three classes of editing agents already have or will have roles in basic research and in applications such as human therapeutics and agriculture.
Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2,3,4,5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase, programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit. We performed more than 175 edits in human cells, including targeted insertions, deletions, and all 12 types of point mutation, without requiring double-strand breaks or donor DNA templates. We used prime editing in human cells to correct, efficiently and with few byproducts, the primary genetic causes of sickle cell disease (requiring a transversion in HBB) and Tay–Sachs disease (requiring a deletion in HEXA); to install a protective transversion in PRNP; and to insert various tags and epitopes precisely into target loci. Four human cell lines and primary post-mitotic mouse cortical neurons support prime editing with varying efficiencies. Prime editing shows higher or similar efficiency and fewer byproducts than homology-directed repair, has complementary strengths and weaknesses compared to base editing, and induces much lower off-target editing than Cas9 nuclease at known Cas9 off-target sites. Prime editing substantially expands the scope and capabilities of genome editing, and in principle could correct up to 89% of known genetic variants associated with human diseases.
From Anzolone et al. Nature 2019 Figure 1.
Prime editing strategy
Cas9 targets DNA using a guide RNA containing a spacer sequence that hybridizes to the target DNA site. We envisioned the generation of guide RNAs that both specify the DNA target and contain new genetic information that replaces target DNA nucleotides. To transfer information from these engineered guide RNAs to target DNA, we proposed that genomic DNA, nicked at the target site to expose a 3′-hydroxyl group, could be used to prime the reverse transcription of an edit-encoding extension on the engineered guide RNA (the pegRNA) directly into the target site (Fig. 1b, c, Supplementary Discussion).
These initial steps result in a branched intermediate with two redundant single-stranded DNA flaps: a 5′ flap that contains the unedited DNA sequence and a 3′ flap that contains the edited sequence copied from the pegRNA (Fig. 1c). Although hybridization of the perfectly complementary 5′ flap to the unedited strand is likely to be thermodynamically favoured, 5′ flaps are the preferred substrate for structure-specific endonucleases such as FEN122, which excises 5′ flaps generated during lagging-strand DNA synthesis and long-patch base excision repair. The redundant unedited DNA may also be removed by 5′ exonucleases such as EXO123.
The authors reasoned that preferential 5′ flap excision and 3′ flap ligation could drive the incorporation of the edited DNA strand, creating heteroduplex DNA containing one edited strand and one unedited strand (Fig. 1c).
DNA repair to resolve the heteroduplex by copying the information in the edited strand to the complementary strand would permanently install the edit (Fig. 1c).
They had hypothesized that nicking the non-edited DNA strand might bias DNA repair to preferentially replace the non-edited strand.
Results
The authors evaluated the eukaryotic cell DNA repair outcomes of 3′ flaps produced by pegRNA-programmed reverse transcription in vitro, and performed in vitro prime editing on reporter plasmids, then transformed the reaction products into yeast cells (Extended Data Fig. 2).
Reporter plasmids encoding EGFP and mCherry separated by a linker containing an in-frame stop codon, +1 frameshift, or −1 frameshift were constructed and when plasmids were edited in vitro with Cas9 nickase, RT, and 3′-extended pegRNAs encoding a transversion that corrects the premature stop codon, 37% of yeast transformants expressed both GFP and mCherry (Fig. 1f, Extended Data Fig. 2).
They fused a variant of M—MLV-RT (reverse transcriptase) to Cas9 with an extended linker and this M-MLV RT fused to the C terminus of Cas9(H840A) nickase was designated as PE1. This strategy allowed the authors to generate a cell line containing all the required components of the primer editing system. They constructed 19 variants of PE1 containing a variety of RT mutations to evaluate their editing efficiency in human cells
Generated a pentamutant RT incorporated into PE1 (Cas9(H840A)–M-MLV RT(D200N/L603W/T330P/T306K/W313F)) is hereafter referred to as prime editor 2 (PE2). These were more thermostable versions of RT with higher efficiency.
Optimized the guide (pegRNA) using a series of permutations and recommend starting with about 10–16 nt and testing shorter and longer RT templates during pegRNA optimization.
In the previous attempts (PE1 and PE2 systems), mismatch repair resolves the heteroduplex to give either edited or non-edited products. So they next developed an optimal editing system (PE3) to produce optimal nickase activity and found nicks positioned 3′ of the edit about 40–90 bp from the pegRNA-induced nick generally increased editing efficiency (averaging 41%) without excess indel formation (6.8% average indels for the sgRNA with the highest editing efficiency) (Fig. 3b).
The cell line used to finalize and validate the system was predominantly HEK293T immortalized cell line
Together, their findings establish that PE3 systems improve editing efficiencies about threefold compared with PE2, albeit with a higher range of indels than PE2. When it is possible to nick the non-edited strand with an sgRNA that requires editing before nicking, the PE3b system offers PE3-like editing levels while greatly reducing indel formation.
Off Target Effects: Strikingly, PE3 or PE2 with the same 16 pegRNAs containing these four target spacers resulted in detectable off-target editing at only 3 out of 16 off-target sites, with only 1 of 16 showing an off-target editing efficiency of 1% or more (Extended Data Fig. 6h). Average off-target prime editing for pegRNAs targeting HEK3, HEK4, EMX1, and FANCFat the top four known Cas9 off-target sites for each protospacer was <0.1%, <2.2 ± 5.2%, <0.1%, and <0.13 ± 0.11%, respectively (Extended Data Fig. 6h).
The PE3 system was very efficient at editing the most common mutation that causes Tay-Sachs disease, a 4-bp insertion in HEXA(HEXA1278+TATC).
References
Landrum, M. J. et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 44, D862–D868 (2016).
Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science337, 816–821 (2012).
Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements. Biotechnol. 36, 765–771 (2018).
Core member and chair of the faculty, Broad Institute of MIT and Harvard; director, Klarman Cell Observatory, Broad Institute of MIT and Harvard; professor of biology, MIT; investigator, Howard Hughes Medical Institute; founding co-chair, Human Cell Atlas.
millions of genome variants, tens of thousands of disease-associated genes, thousands of cell types and an almost unimaginable number of ways they can combine, we had to approximate a best starting point—choose one target, guess the cell, simplify the experiment.
In 2020, advances in polygenic risk scores, in understanding the cell and modules of action of genes through genome-wide association studies (GWAS), and in predicting the impact of combinations of interventions.
we need algorithms to make better computational predictions of experiments we have never performed in the lab or in clinical trials.
Human Cell Atlas and the International Common Disease Alliance—and in new experimental platforms: data platforms and algorithms. But we also need a broader ecosystem of partnerships in medicine that engages interaction between clinical experts and mathematicians, computer scientists and engineers
Feng Zhang, PhD
investigator, Howard Hughes Medical Institute; core member, Broad Institute of MIT and Harvard; James and Patricia Poitras Professor of Neuroscience, McGovern Institute for Brain Research, MIT.
fundamental shift in medicine away from treating symptoms of disease and toward treating disease at its genetic roots.
Gene therapy with clinical feasibility, improved delivery methods and the development of robust molecular technologies for gene editing in human cells, affordable genome sequencing has accelerated our ability to identify the genetic causes of disease.
1,000 clinical trials testing gene therapies are ongoing, and the pace of clinical development is likely to accelerate.
refine molecular technologies for gene editing, to push our understanding of gene function in health and disease forward, and to engage with all members of society
Elizabeth Jaffee, PhD
Dana and Albert “Cubby” Broccoli Professor of Oncology, Johns Hopkins School of Medicine; deputy director, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins.
a single blood test could inform individuals of the diseases they are at risk of (diabetes, cancer, heart disease, etc.) and that safe interventions will be available.
developing cancer vaccines. Vaccines targeting the causative agents of cervical and hepatocellular cancers have already proven to be effective. With these technologies and the wealth of data that will become available as precision medicine becomes more routine, new discoveries identifying the earliest genetic and inflammatory changes occurring within a cell as it transitions into a pre-cancer can be expected. With these discoveries, the opportunities to develop vaccine approaches preventing cancers development will grow.
shape how the culture of research will develop over the next 25 years, a culture that cares more about what is achieved than how it is achieved.
building a creative, inclusive and open research culture will unleash greater discoveries with greater impact.
John Nkengasong, PhD
Director, Africa Centres for Disease Control and Prevention.
To meet its health challenges by 2050, the continent will have to be innovative in order to leapfrog toward solutions in public health.
Precision medicine will need to take center stage in a new public health order— whereby a more precise and targeted approach to screening, diagnosis, treatment and, potentially, cure is based on each patient’s unique genetic and biologic make-up.
Eric Topol, MD
Executive vice-president, Scripps Research Institute; founder and director, Scripps Research Translational Institute.
In 2045, a planetary health infrastructure based on deep, longitudinal, multimodal human data, ideally collected from and accessible to as many as possible of the 9+ billion people projected to then inhabit the Earth.
enhanced capabilities to perform functions that are not feasible now.
AI machines’ ability to ingest and process biomedical text at scale—such as the corpus of the up-to-date medical literature—will be used routinely by physicians and patients.
the concept of a learning health system will be redefined by AI.
Linda Partridge, PhD
Professor, Max Planck Institute for Biology of Ageing.
Geroprotective drugs, which target the underlying molecular mechanisms of ageing, are coming over the scientific and clinical horizons, and may help to prevent the most intractable age-related disease, dementia.
Trevor Mundel, MD
President of Global Health, Bill & Melinda Gates Foundation.
finding new ways to share clinical data that are as open as possible and as closed as necessary.
moving beyond drug donations toward a new era of corporate social responsibility that encourages biotechnology and pharmaceutical companies to offer their best minds and their most promising platforms.
working with governments and multilateral organizations much earlier in the product life cycle to finance the introduction of new interventions and to ensure the sustainable development of the health systems that will deliver them.
deliver on the promise of global health equity.
Josep Tabernero, MD, PhD
Vall d’Hebron Institute of Oncology (VHIO); president, European Society for Medical Oncology (2018–2019).
genomic-driven analysis will continue to broaden the impact of personalized medicine in healthcare globally.
Precision medicine will continue to deliver its new paradigm in cancer care and reach more patients.
Immunotherapy will deliver on its promise to dismantle cancer’s armory across tumor types.
AI will help guide the development of individually matched
genetic patient screenings
the promise of liquid biopsy policing of disease?
Pardis Sabeti, PhD
Professor, Harvard University & Harvard T.H. Chan School of Public Health and Broad Institute of MIT and Harvard; investigator, Howard Hughes Medical Institute.
the development and integration of tools into an early-warning system embedded into healthcare systems around the world could revolutionize infectious disease detection and response.
But this will only happen with a commitment from the global community.
Els Toreele, PhD
Executive director, Médecins Sans Frontières Access Campaign
we need a paradigm shift such that medicines are no longer lucrative market commodities but are global public health goods—available to all those who need them.
This will require members of the scientific community to go beyond their role as researchers and actively engage in R&D policy reform mandating health research in the public interest and ensuring that the results of their work benefit many more people.
The global research community can lead the way toward public-interest driven health innovation, by undertaking collaborative open science and piloting not-for-profit R&D strategies that positively impact people’s lives globally.
Human gene editing continues to hold a major fascination within a biomedical and biopharmaceutical industries. It’s extraordinary potential is now being realized but important questions as to who will be the beneficiaries of such breakthrough technologies remained to be answered. The session will discuss whether gene editing technologies can alleviate some of the most challenging unmet medical needs. We will discuss how research advances often never reach minority communities and how diverse patient populations will gain access to such breakthrough technologies. It is widely recognize that there are patient voids in the population and we will explore how community health centers might fill this void to ensure that state-of-the-art technologies can reach the forgotten patient groups . We also will touch ethical questions surrounding germline editing and how such research and development could impact the community at large.
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Genome editing offers the potential of new and effective treatments for genetic diseases. As companies work to develop these treatments, regulators are focused on ensuring that any such products meet applicable safety and efficacy requirements. This panel will discuss how European Union and United States regulators are approaching therapeutic use of genome editing, issues in harmonization between these two – and other – jurisdictions, challenges faced by industry as regulatory positions evolve, and steps that organizations and companies can take to facilitate approval and continued efforts at harmonization.
CBER: because of the nature of these gene therapies, which are mainly orphan, there is expedited review. Since they started this division in 2015, they have received over 1500 applications.
Spark: Most of the issues were issues with the primary disease not the gene therapy so they had to make new endpoint tests so had talks with FDA before they entered phase III. There has been great collaboration with FDA, now they partnered with Novartis to get approval outside US. You should be willing to partner with EU pharmas to expedite the regulatory process outside US. In China the process is new and Brazil is behind on their gene therapy guidance. However there is the new issue of repeat testing of your manufacturing process, as manufacturing of gene therapies had been small scale before. However he notes that problems with expedited review is tough because you don’t have alot of time to get data together. They were lucky that they had already done a randomized trial.
Sidley Austin: EU regulatory you make application with advance therapy you don’t have a national option, the regulation body assesses a committee to see if has applicability. Then it goes to a safety committee. EU has been quicker to approve these advance therapies. Twenty five percent of their applications are gene therapies. Companies having issues with manufacturing. There can be issues when the final application is formalized after discussions as problems may arise between discussions, preliminary applications, and final applications.
Sarepta: They have a robust gene therapy program. Their lead is a therapy for DMD (Duchenne’s Muscular Dystrophy) where affected males die by 25. Japan and EU have different regulatory applications and although they are similar and data can be transferred there is more paperwork required by EU. The US uses an IND for application. Global feedback is very challenging, they have had multiple meetings around the world and takes a long time preparing a briefing package….. putting a strain on the small biotechs. No company wants to be either just EU centric or US centric they just want to get out to market as fast as possible.
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People with two copies of the Δ32 mutation died at rates 21 percent higher than those with one or no copies – application of CRISPR @Berkeley
Reporter: Aviva Lev-Ari, PhD, RN
2.1.3.3 People with two copies of the Δ32 mutation died at rates 21 percent higher than those with one or no copies – application of CRISPR @Berkeley, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
CCR5-∆32 is deleterious in the homozygous state in humans
We use the genotyping and death register information of 409,693 individuals of British ancestry to investigate fitness effects of the CCR5-∆32 mutation. We estimate a 21% increase in the all-cause mortality rate in individuals who are homozygous for the ∆32 allele. A deleterious effect of the ∆32/∆32 mutation is also independently supported by a significant deviation from the Hardy–Weinberg equilibrium (HWE) due to a deficiency of ∆32/∆32 individuals at the time of recruitment.
“Here is a functional protein that we know has an effect in the organism, and it is well-conserved among many different species, so it is likely that a mutation that destroys the protein is, on average, not good for you,” he said. “Otherwise, evolutionary mechanisms would have destroyed that protein a long time ago.”
In the UK Biobank data they found two lines of evidence to suggest that these days, CCR5 actually is a net negative. In the first analysis they tracked how long people survived after enrolling in the Biobank study. They found that between the ages of 41 and 78, people with two copies of the Δ32 mutation had significantly higher death rates. They also observed that far fewer people with two copies enrolled in the study than expected, which they interpreted to mean that these individuals were less likely to survive into middle age than the general population. “Something has removed people with two copies of the mutation, and the likely explanation is increased mortality,” says Nielsen.
A child was born missing a large chunk of DNA in its CCR5 gene. This gene coded for a receptor on the surface of immune cells useful for coordinating responses to invading pathogens. And this spontaneous deletion torpedoed CCR5 production—one copy shrunk the number of receptors on cells, two copies erased the receptor altogether.
Today, the Δ32 mutation occurs in about 10 percent of the population of Europe, in a decreasing gradient from north to south. Natural selection pushed it through the population about 100 times faster than if it were a neutral change to the genome. But with the invention of vaccines, and the eradication of diseases like smallpox over the last century, the mutation has become less useful. According to Nielsen and Wei’s analysis, it’s now downright detrimental.
Opportunities and Ethics of Editing Genomes: A CRISPR-Inspired Conversation, Prof. Jennifer Doudna’s Lecture at Stanford University, JANUARY 24, 2019 – 7:00PM TO 8:30PM, CEMEX AUDITORIUM, GRADUATE SCHOOL OF BUSINESS
Reporter: Aviva Lev-Ari, PhD, RN
2.1.4.2 Opportunities and Ethics of Editing Genomes: A CRISPR-Inspired Conversation, Prof. Jennifer Doudna’s Lecture at Stanford University, JANUARY 24, 2019 – 7:00PM TO 8:30PM, CEMEX AUDITORIUM, GRADUATE SCHOOL OF BUSINESS, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
Opportunities and Ethics of Editing Genomes: A CRISPR-Inspired Conversation
CENTER FOR BIOMEDICAL ETHICS, MCCOY FAMILY CENTER FOR ETHICS IN SOCIETY, CENTER FOR LAW AND BIOSCIENCES
Recent reports of the first babies to be born with CRISPR-edited genes have sparked widespread condemnation and calls for action. These concerns will be top of mind when world-renowned scientist Jennifer Doudna, co-inventor of CRISPR, speaks at Stanford on Thursday, Jan. 24, as part of the Arrow Lecture Series on Ethics and Leadership.
Doudna, a professor of chemistry and molecular and cell biology at U.C. Berkeley, rocked the research world in 2012 when she and her colleagues announced the invention of CRISPR-Cas9, a technology that uses an RNA-guided protein found in bacteria to edit an organism’s DNA quickly and inexpensively.
Following her lecture, Doudna will have an on-stage conversation with Political Science Professor Rob Reich, faculty director of the McCoy Family Center for Ethics in Society, and Kelly Ormond, a professor of genetics at Stanford’s School of Medicine and faculty member of the Stanford Center for Biomedical Ethics.
Doudna is the co-author with Sam Sternberg of “A Crack in Creation,” a personal account of her research and the societal and ethical implications of gene editing. Doudna has received many other honors including the Breakthrough Prize in Life Sciences and membership in the National Academy of Sciences, the National Academy of Medicine, the National Academy of Inventors and the American Academy of Arts and Sciences.
The Arrow Lecture Series, presented by the Center for Ethics in Society, honors the late Nobel Laureate Kenneth Arrow, the Joan Kenney Professor of Economics and Professor of Operations Research, Emeritus.
The McCoy Family Center for Ethics in Society is committed to bringing ethical reflection to bear on important social problems through research, teaching, and community engagement. Drawing on the established strengths of Stanford’s interdisciplinary faculty, the Center develops initiatives with ethical dimensions that relate to pressing public problems. A bridge to the undergraduate Stanford community, the Center houses the Undergraduate Program in Ethics in Society in addition to these current initiatives:
Public events, including the Tanner, Wesson, and Arrow lectures, and multi-year themed lecture series
The Hope House Scholars Program in which Stanford faculty, postdocs, or graduate students teach a course in the humanities to the residents of Hope House, a residential drug and alcohol treatment facility for women, many of whom have recently been incarcerated.
The Buzz blog which features the voices of Stanford students and freelance writers on happenings at the McCoy Center
Gene-editing Second International Summit in Hong Kong: George Church, “Let’s be quantitative before we start being accusatory”
Reporter: Aviva Lev-Ari, PhD, RN
2.1.4.3 Gene-editing Second International Summit in Hong Kong: George Church, “Let’s be quantitative before we start being accusatory”, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
UPDATED on 11/30/2018
Gene editing takes a foreboding leap forward
He Jiankui. Photo: Zhang Wei/Chinese News Service/VCG via Getty Images
China is temporarily suspending the work of scientists who claimed twins were born after being genetically edited as embryos.
Why it matters: The scientific consensus is that gene editing embryos at this stage of science is “irresponsible.” But, while this particular experiment has not been verified, the fact is the technology is available to researchers, so there’s a growing call for international limitations on its use.
ICYMI: Chinese scientist He Jiankui announced earlier this week that twins were born after he used the gene-editing tool CRISPR-Cas9 to cut the CCR5 gene that’s known to play a role in HIV infection.
He stirred even more dismay when he mentioned the possibility of a second pregnancy.
China currently bans human implantation of gene-edited embryos. Its Ministry of Science and Technology is investigating the claims, per Xinhua.
There are concerns about the safety, efficacy and possible mosaicism, where a person can contain genes in both its edited and unedited forms, from cutting genes.
Editing embryos raises an even bigger concern: The genetic changes and all the unknowns around them can be passed down to future generations.
Between the lines: Not everyone viewed it as a complete disaster. For instance, Harvard Medical School’s George Daley suggested that it may be time to reconsider the massive amounts of research done over the past several years and look for plausible methods of moving forward.
What to watch: Scientists are cautious about predicting what the impact will be, in part because the details of this claim are thin. However, the debate is heating up and one concern is it will dampen important research.
Medical ethicist Jonathan Moreno from the University of Pennsylvania says the situation reminds him of other times in history where there were tremors in the science world, like the death of 18-year-old Jesse Gelsinger in 1999 from a gene therapy trial that led to years of diminished research.
The bottom line: The alarm over what could be next is real. But scientists hope the current debate will promote consensus on firm limits and promote transparency.
Meanwhile, prominent geneticist George Church is one of the few scientists who seem to be looking on the bright side of He’s controversial claim. “Let’s be quantitative before we start being accusatory,” Church told Science. “As long as these are normal, healthy kids it’s going to be fine for the field and the family.”
The ethical red flags of genetically edited babies
Driving the news: Chinese scientist He Jiankui announced Sunday night that a pair of twin girls had been born from embryos he modified using the gene-editing tool known as CRISPR.
He hasn’t provided solid proof, but if it‘s true, it would be the first time the technology has been used to engineer a human.
What they’re saying: The inventors of CRISPR technology did not seem pleased with the development — one called for a moratorium on implantation edited embryos into potential mothers.
“I hope we will be more cautious in the next thing we try to do, and think more carefully about when you should use technology versus when you could use technology,” said Jessica Berg, a bioethicist at Case Western Reserve University.
Between the lines: Several specific factors in He’s work sent up ethical red flags.
Many scientists had assumed that, when this technology was first used in humans, it would edit out mutations tied to a single gene that were certain to cause a child pain and suffering once it was born — essentially, as a last resort.
But He used CRISPR to, as he put it, “close a door” that HIV could have one day traveled through. That has prompted some speculation that this project was more about testing the technology than serving an acute medical need.
“That should make us very uneasy about the whole situation,” Berg said. “Of all the things to have started with, it does make you a little suspicious about this particular choice.”
The intrigue: There’s a lot we still don’t know about He’s work, and that’s also contributing to an attitude of skepticism.
How many embryos did he edit and implant before these live births?
How will he know it worked? As the children age, they’ll likely have their blood drawn and those samples will be exposed to HIV in a lab, but researchers aren’t going to tell them to go out and have unprotected sex or use intravenous drugs — another reason HIV seems like an odd starting place for human gene editing.
How did this even happen? The university where He worked said he was on leave, and Chinese officials have said he’s under investigation. But gene editing is a pretty hard thing to freelance.
The other side: He defended his work in avideo message, saying, “I understand my work will be controversial but I believe families need this technology and I’m willing to take the criticism for them.”
“Their parents don’t want a designer baby, just a child who won’t suffer from a disease which medicine can now prevent,” He said.
Yes, but: Now that this threshold may have been crossed, attempts to create “designer babies” — within the limitations of what CRISPR can do — probably aren’t far off, some experts fear.
There are “likely to be places that are less regulated than others, where people are going to attempt to see what they can do,” Berg said. “I wouldn’t say everything in the world has changed now, but it’s certainly the next step.”
Jennifer Doudna and NPR science correspondent Joe Palca, several interviews
Reporter: Aviva Lev-Ari, PhD, RN
2.1.3.5 Jennifer Doudna and NPR science correspondent Joe Palca, several interviews, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair
The ethical red flags of genetically edited babies
Driving the news: Chinese scientist He Jiankui announced Sunday night that a pair of twin girls had been born from embryos he modified using the gene-editing tool known as CRISPR.
He hasn’t provided solid proof, but if it‘s true, it would be the first time the technology has been used to engineer a human.
What they’re saying: The inventors of CRISPR technology did not seem pleased with the development — one called for a moratorium on implantation edited embryos into potential mothers.
“I hope we will be more cautious in the next thing we try to do, and think more carefully about when you should use technology versus when you could use technology,” said Jessica Berg, a bioethicist at Case Western Reserve University.
Between the lines: Several specific factors in He’s work sent up ethical red flags.
Many scientists had assumed that, when this technology was first used in humans, it would edit out mutations tied to a single gene that were certain to cause a child pain and suffering once it was born — essentially, as a last resort.
But He used CRISPR to, as he put it, “close a door” that HIV could have one day traveled through. That has prompted some speculation that this project was more about testing the technology than serving an acute medical need.
“That should make us very uneasy about the whole situation,” Berg said. “Of all the things to have started with, it does make you a little suspicious about this particular choice.”
The intrigue: There’s a lot we still don’t know about He’s work, and that’s also contributing to an attitude of skepticism.
How many embryos did he edit and implant before these live births?
How will he know it worked? As the children age, they’ll likely have their blood drawn and those samples will be exposed to HIV in a lab, but researchers aren’t going to tell them to go out and have unprotected sex or use intravenous drugs — another reason HIV seems like an odd starting place for human gene editing.
How did this even happen? The university where He worked said he was on leave, and Chinese officials have said he’s under investigation. But gene editing is a pretty hard thing to freelance.
The other side: He defended his work in avideo message, saying, “I understand my work will be controversial but I believe families need this technology and I’m willing to take the criticism for them.”
“Their parents don’t want a designer baby, just a child who won’t suffer from a disease which medicine can now prevent,” He said.
Yes, but: Now that this threshold may have been crossed, attempts to create “designer babies” — within the limitations of what CRISPR can do — probably aren’t far off, some experts fear.
There are “likely to be places that are less regulated than others, where people are going to attempt to see what they can do,” Berg said. “I wouldn’t say everything in the world has changed now, but it’s certainly the next step.”
Doudna, who spoke at Harvard’s Science Center, explained the work that led to the development of CRISPR/Cas9 gene–editing technology, which was described in a paper in the journal Science in 2012. A sign of how quickly the techniques would be adopted by her scientific colleagues came within months.
Eventbrite – Science History Institute presents Jennifer A. Doudna, “CRISPR Biology and Biotechnology: the Future of Genome Editing” – Friday, November 16, 2018 at Science History Institute, Philadelphia, PA.
A pioneer of the Crispr gene–editing technology that’s taken Wall Street by storm says the field is probably five to 10 years away from having an approved therapy for patients.
BOOK BY JENNIFER DOUDNA AND SAMUEL STERNBERG HOUGHTON MIFFLIN HARCOURT, 2017 304 PP.; $28.00 (HARDCOVER) $14.99 (KINDLE) CRISPR is the basis of a genome editingtechnology—the latest breakthrough in the grand tradition that began over 400 generations ago when we started to grow wheat and rice instead of just picking its wild cousins.
The CRISPR-Cas9 geneediting technology was discovered in 2012 by campus professor of chemistry, molecular biology and biochemistry Jennifer Doudna and Emmanuelle Charpentier, director at the Max …
2 hours ago · The International Summit on Human Genome Editing begins here on Tuesday and many researchers, ethicists, and policymakers attending the meeting first learned of He’s claim through media reports.
Video of Conversation With Jennifer Doudna and NPR’s Joe Palca
Jennifer Doudna featured on NPR’s Morning Edition for her work on CRISPR/Cas9 — a tool for editing genes
October 13, 2014
Jennifer Doudna. Jennifer Doudna. Photo: Roy Kaltschmidt, Berkeley Lab Public Affairs
UC Berkeley’s Jennifer Doudna was featured on NPR’s Morning Edition for her work on CRISPR/Cas9 — a tool for editing genes. Jennifer Doudna and her colleagues showed that CRISPR/Cas9, can be used with great precision to selectively disable or add several genes at once in human cells, offering a potent new tool to understand and treat complex genetic diseases.
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