DNA
Revolutionizing Technology to Treat Genetic Diseases: The NIH TARGETED Challenge
Posted on by Lawrence Tabak, D.D.S., Ph.D. and Douglas M. Sheeley, Sc.D., NIH Common Fund
Recent scientific advances in the field of genome editing, which enables precise modifications to DNA, have greatly increased the potential to treat genetic diseases. Despite revolutionary progress in this area, treatment options remain limited. Several scientific challenges must be addressed before gene editing can be widely used in the clinic. For example, gene editing tools may cut in unintended areas in addition to the target site, and more research is necessary to understand how these errors affect patients.
Another key challenge is that many organs remain difficult to reach with gene therapies because we do not have adequate ways to deliver gene editing tools to all cells. While efficient delivery technologies exist for some targets, like liver cells, novel and specialized delivery methods designed for specific cell types and locations in the body are needed to ensure genome editing tools can reach sufficient numbers and types of somatic cells to modify DNA safely and effectively. Somatic cell gene therapies target non-reproductive cells, so the changes only affect the person who receives the gene therapy and are not passed down generation to generation.
To address these challenges, NIH launched the TARGETED (Targeted Genome Editor Delivery) Challenge, a multi-phase competition funded through the NIH Common Fund as part of the NIH Somatic Cell Genome Editing (SCGE) Program. SCGE was funded in 2018 to improve the efficacy and specificity of genome editing to help reduce the burden of common and rare diseases caused by genetic changes.
As part of the TARGETED Challenge, research teams will develop technologies for delivering genome editors to somatic cells. NIH will award up to $6 million in prize money across the challenge.
The Challenge is focused on finding delivery systems that can be programmed with biological or chemical tags that correspond to specific target cells and tissues. These tags would direct the delivery systems and the genome editing therapies to the target cells or tissues—like mail being delivered to different zip codes. Such programmable delivery systems would improve gene editing efficacy by targeting diseases at their source and would enhance safety by reducing undesired impacts on other tissues or cells. Ultimately, the development of safe and effective programmable delivery technologies for genome editors that are applicable to multiple diseases would help advance the application of gene editing therapies into the clinic.
The Challenge also is interested in gene editing delivery technologies that can cross the blood-brain barrier (BBB). The BBB protects the brain by blocking harmful substances from entering the fluid of the central nervous system. Unfortunately, it also blocks the uptake of many therapeutics, hindering treatments for brain diseases. While viruses are one of the few approaches that can be used as delivery systems to cross the BBB, they are expensive and difficult to make. Therefore, there is a pressing need for effective non-viral technologies to deliver genome editing machinery across the BBB to a substantial proportion of clinically relevant brain cell types. Such technologies could have broad implications for the treatment of many neurogenetic diseases.
Solutions to both target areas would not only provide proof-of-concept for the delivery of genome editing therapeutics, but they could be adapted to deliver other types of therapies to treat common and rare diseases in general.
The first phase of the Challenge began on May 15, 2023 and will run until October 5, 2023. More information about the Challenge is available on the TARGETED Genome Editor Delivery Challenge website.
Links:
“National Institutes of Health launch TARGETED Challenge,” NIH Common Fund, May 15, 2023
TARGETED Genome Editor Delivery Challenge (NIH Common Fund)
Somatic Cell Genome Editing Program (NIH Common Fund)
NIH Support: The SCGE program is led by the NIH Common Fund, the National Center for Advancing Translational Sciences (NCATS), and the National Institute of Neurological Disorders and Stroke (NINDS). The Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) Initiative and the National Heart, Lung, and Blood Institute (NHLBI) are also contributors to this Challenge.
All of Us: Release of Nearly 100,000 Whole Genome Sequences Sets Stage for New Discoveries
Posted on by Joshua Denny, M.D., M.S., and Lawrence Tabak, D.D.S., Ph.D.
Nearly four years ago, NIH opened national enrollment for the All of Us Research Program. This historic program is building a vital research community within the United States of at least 1 million participant partners from all backgrounds. Its unifying goal is to advance precision medicine, an emerging form of health care tailored specifically to the individual, not the average patient as is now often the case. As part of this historic effort, many participants have offered DNA samples for whole genome sequencing, which provides information about almost all of an individual’s genetic makeup.
Earlier this month, the All of Us Research Program hit an important milestone. We released the first set of nearly 100,000 whole genome sequences from our participant partners. The sequences are stored in the All of Us Researcher Workbench, a powerful, cloud-based analytics platform that makes these data broadly accessible to registered researchers.
The All of Us Research Program and its many participant partners are leading the way toward more equitable representation in medical research. About half of this new genomic information comes from people who self-identify with a racial or ethnic minority group. That’s extremely important because, until now, over 90 percent of participants in large genomic studies were of European descent. This lack of diversity has had huge impacts—deepening health disparities and hindering scientific discovery from fully benefiting everyone.
The Researcher Workbench also contains information from many of the participants’ electronic health records, Fitbit devices, and survey responses. Another neat feature is that the platform links to data from the U.S. Census Bureau’s American Community Survey to provide more details about the communities where participants live.
This unique and comprehensive combination of data will be key in transforming our understanding of health and disease. For example, given the vast amount of data and diversity in the Researcher Workbench, new diseases are undoubtedly waiting to be uncovered and defined. Many new genetic variants are also waiting to be identified that may better predict disease risk and response to treatment.
To speed up the discovery process, these data are being made available, both widely and wisely. To protect participants’ privacy, the program has removed all direct identifiers from the data and upholds strict requirements for researchers seeking access. Already, more than 1,500 scientists across the United States have gained access to the Researcher Workbench through their institutions after completing training and agreeing to the program’s strict rules for responsible use. Some of these researchers are already making discoveries that promote precision medicine, such as finding ways to predict how to best to prevent vision loss in patients with glaucoma.
Beyond making genomic data available for research, All of Us participants have the opportunity to receive their personal DNA results, at no cost to them. So far, the program has offered genetic ancestry and trait results to more than 100,000 participants. Plans are underway to begin sharing health-related DNA results on hereditary disease risk and medication-gene interactions later this year.
This first release of genomic data is a huge milestone for the program and for health research more broadly, but it’s also just the start. The program’s genome centers continue to generate the genomic data and process about 5,000 additional participant DNA samples every week.
The ultimate goal is to gather health data from at least 1 million or more people living in the United States, and there’s plenty of time to join the effort. Whether you would like to contribute your own DNA and health information, engage in research, or support the All of Us Research Program as a partner, it’s easy to get involved. By taking part in this historic program, you can help to build a better and more equitable future for health research and precision medicine.
Note: Joshua Denny, M.D., M.S., is the Chief Executive Officer of NIH’s All of Us Research Program.
Links:
All of Us Research Program (NIH)
Join All of Us (NIH)
DNA Base Editing May Treat Progeria, Study in Mice Shows
Posted on by Dr. Francis Collins
My good friend Sam Berns was born with a rare genetic condition that causes rapid premature aging. Though Sam passed away in his teens from complications of this condition, called Hutchinson-Gilford progeria syndrome, he’s remembered today for his truly positive outlook on life. Sam expressed it, in part, by his willingness to make adjustments that allowed him, in his words, to put things that he always wanted to do in the “can do” category.
In this same spirit on behalf of the several hundred kids worldwide with progeria and their families, a research collaboration, including my NIH lab, has now achieved a key technical advance to move non-heritable gene editing another step closer to the “can do” category to treat progeria. As published in the journal Nature, our team took advantage of new gene-editing tools to correct for the first time a single genetic misspelling responsible for progeria in a mouse model, with dramatically beneficial effects [1, 2]. This work also has implications for correcting similar single-base typos that cause other inherited genetic disorders.
The outcome of this work is incredibly gratifying for me. In 2003, my NIH lab discovered the DNA mutation that causes progeria. One seemingly small glitch—swapping a “T” in place of a “C” in a gene called lamin A (LMNA)—leads to the production of a toxic protein now known as progerin. Without treatment, children with progeria develop normally intellectually but age at an exceedingly rapid pace, usually dying prematurely from heart attacks or strokes in their early teens.
The discovery raised the possibility that correcting this single-letter typo might one day help or even cure children with progeria. But back then, we lacked the needed tools to edit DNA safely and precisely. To be honest, I didn’t think that would be possible in my lifetime. Now, thanks to advances in basic genomic research, including work that led to the 2020 Nobel Prize in Chemistry, that’s changed. In fact, there’s been substantial progress toward using gene-editing technologies, such as the CRISPR editing system, for treating or even curing a wide range of devastating genetic conditions, such as sickle cell disease and muscular dystrophy
It turns out that the original CRISPR system, as powerful as it is, works better at knocking out genes than correcting them. That’s what makes some more recently developed DNA editing agents and approaches so important. One of them, which was developed by David R. Liu, Broad Institute of MIT and Harvard, Cambridge, MA, and his lab members, is key to these latest findings on progeria, reported by a team including my lab in NIH’s National Human Genome Research Institute and Jonathan Brown, Vanderbilt University Medical Center, Nashville, TN.
The relatively new gene-editing system moves beyond knock-outs to knock-ins [3,4]. Here’s how it works: Instead of cutting DNA as CRISPR does, base editors directly convert one DNA letter to another by enzymatically changing one DNA base to become a different base. The result is much like the find-and-replace function used to fix a typo in a word processor. What’s more, the gene editor does this without cutting the DNA.
Our three labs (Liu, Brown, and Collins) first teamed up with the Progeria Research Foundation, Peabody, MA, to obtain skin cells from kids with progeria. In lab studies, we found that base editors, targeted by an appropriate RNA guide, could successfully correct the LMNA gene in those connective tissue cells. The treatment converted the mutation back to the normal gene sequence in an impressive 90 percent of the cells.
But would it work in a living animal? To get the answer, we delivered a single injection of the DNA-editing apparatus into nearly a dozen mice either three or 14 days after birth, which corresponds in maturation level roughly to a 1-year-old or 5-year-old human. To ensure the findings in mice would be as relevant as possible to a future treatment for use in humans, we took advantage of a mouse model of progeria developed in my NIH lab in which the mice carry two copies of the human LMNA gene variant that causes the condition. Those mice develop nearly all of the features of the human illness
In the live mice, the base-editing treatment successfully edited in the gene’s healthy DNA sequence in 20 to 60 percent of cells across many organs. Many cell types maintained the corrected DNA sequence for at least six months—in fact, the most vulnerable cells in large arteries actually showed an almost 100 percent correction at 6 months, apparently because the corrected cells had compensated for the uncorrected cells that had died out. What’s more, the lifespan of the treated animals increased from seven to almost 18 months. In healthy mice, that’s approximately the beginning of old age.
This is the second notable advance in therapeutics for progeria in just three months. Last November, based on preclinical work from my lab and clinical trials conducted by the Progeria Research Foundation in Boston, the Food and Drug Administration (FDA) approved the first treatment for the condition. It is a drug called Zokinvy, and works by reducing the accumulation of progerin [5]. With long-term treatment, the drug is capable of extending the life of kids with progeria by 2.5 years and sometimes more. But it is not a cure.
We are hopeful this gene editing work might eventually lead to a cure for progeria. But mice certainly aren’t humans, and there are still important steps that need to be completed before such a gene-editing treatment could be tried safely in people. In the meantime, base editors and other gene editing approaches keep getting better—with potential application to thousands of genetic diseases where we know the exact gene misspelling. As we look ahead to 2021, the dream envisioned all those years ago about fixing the tiny DNA typo responsible for progeria is now within our grasp and getting closer to landing in the “can do” category.
References:
[1] In vivo base editing rescues Hutchinson-Gilford Progeria Syndrome in mice. Koblan LW et al. Nature. 2021 Jan 6.
[2] Base editor repairs mutation found in the premature-ageing syndrome progeria. Vermeij WP, Hoeijmakers JHJ. Nature. 6 Jan 2021.
[3] Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Nature. 2016 May 19;533(7603):420-424.
[4] Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR. Nature. 2017 Nov 23;551(7681):464-471.
[5] FDA approves first treatment for Hutchinson-Gilford progeria syndrome and some progeroid laminopathies. Food and Drug Administration. 2020 Nov 20.
Links:
Progeria (Genetic and Rare Diseases Information Center/NIH)
What are Genome Editing and CRISPR-Cas9? (National Library of Medicine/NIH)
Somatic Cell Genome Editing Program (Common Fund/NIH)
David R. Liu (Harvard University, Cambridge, MA)
Collins Group (National Human Genome Research Institute/NIH)
Jonathan Brown (Vanderbilt University Medical Center, Nashville, TN)
NIH Support: National Human Genome Research Institute; National Center for Advancing Translational Sciences; National Institute of Biomedical Imaging and Bioengineering; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; Common Fund
All of Us: Partnering Together for the Future of Precision Medicine
Posted on by Dr. Francis Collins
Over the past year, it’s been so inspiring to watch tens of thousands of people across the country selflessly step forward for vaccine trials and other research studies to combat COVID-19. And they are not alone. Many generous folks are volunteering to take part in other types of NIH-funded research that will improve health all across the spectrum, including the more than 360,000 who’ve already enrolled in the pioneering All of Us Research Program.
Now in its second year, All of Us is building a research community of 1 million participant partners to help us learn more about how genetics, environment, and lifestyle interact to influence disease and affect health. So far, more than 80 percent of participants who have completed all the initial enrollment steps are Black, Latino, rural, or from other communities historically underrepresented in biomedical research.
This community will build a diverse foundation for precision medicine, in which care is tailored to the individual, not the average patient as is now often the case. What’s also paradigm shifting about All of Us is its core value of sharing information back with participants about themselves. It is all done responsibly through each participant’s personal All of Us online account and with an emphasis on protecting privacy.
All of Us participants share their health information in many ways, such as taking part in surveys, offering access to their electronic health records, and providing biosamples (blood, urine, and/or saliva). In fact, researchers recently began genotyping and sequencing the DNA in some of those biosamples, and then returning results from analyses to participants who’ve indicated they’d like to receive such information. This first phase of genotyping DNA analysis will provide insights into their genetic ancestry and four traits, including bitter taste perception and tolerance for lactose.
Results of a second sequencing phase of DNA analysis will likely be ready in the coming year. These personalized reports will give interested participants information about how their bodies are likely to react to certain medications and about whether they face an increased risk of developing certain health conditions, such as some types of cancer or heart disease. To help participants better understand the results, they can make a phone appointment with a genetic counselor who is affiliated with the program.
This week, I had the pleasure of delivering the keynote address at the All of Us Virtual Face-to-Face. This lively meeting was attended by a consortium of more than 2,000 All of Us senior staff, program leads with participating healthcare provider organizations and federally qualified health centers, All of Us-supported researchers, community partners, and the all-important participant ambassadors.
If you are interested in becoming part of the All of Us community, I welcome you—there’s plenty of time to get involved! To learn more, just go to Join All of Us.
Links:
All of Us Research Program (NIH)
Join All of Us (NIH)
Experts Conclude Heritable Human Genome Editing Not Ready for Clinical Applications
Posted on by Dr. Francis Collins
We stand at a critical juncture in the history of science. CRISPR and other innovative genome editing systems have given researchers the ability to make very precise changes in the sequence, or spelling, of the human DNA instruction book. If these tools are used to make non-heritable edits in only relevant tissues, they hold enormous potential to treat or even cure a wide range of devastating disorders, such as sickle cell disease, inherited neurologic conditions, and muscular dystrophy. But profound safety, ethical, and philosophical concerns surround the use of such technologies to make heritable changes in the human genome—changes that can be passed on to offspring and have consequences for future generations of humankind.
Such concerns are not hypothetical. Two years ago, a researcher in China took it upon himself to cross this ethical red line and conduct heritable genome editing experiments in human embryos with the aim of protecting the resulting babies against HIV infection. The medical justification was indefensible, the safety issues were inadequately considered, and the consent process was woefully inadequate. In response to this epic scientific calamity, NIH supported a call by prominent scientists for an international moratorium on human heritable, or germline, genome editing for clinical purposes.
Following on the heels of this unprecedented ethical breach, the U.S. National Academy of Sciences, U.S. National Academy of Medicine, and the U.K. Royal Society convened an international commission, sponsored by NIH, to conduct a comprehensive review of the clinical use of human germline genome editing. The 18-member panel, which represented 10 nations and four continents, included experts in genome editing technology; human genetics and genomics; psychology; reproductive, pediatric, and adult medicine; regulatory science; bioethics; and international law. Earlier this month, this commission issued its consensus study report, entitled Heritable Human Genome Editing [1].
The commission was designed to bring together thought leaders around the globe to engage in serious discussions about this highly controversial use of genome-editing technology. Among the concerns expressed by many of us was that if heritable genome editing were allowed to proceed without careful deliberation, the enormous potential of non-heritable genome editing for prevention and treatment of disease could become overshadowed by justifiable public outrage, fear, and disgust.
I’m gratified to say that in its new report, the expert panel closely examined the scientific and ethical issues, and concluded that heritable human genome editing is too technologically unreliable and unsafe to risk testing it for any clinical application in humans at the present time. The report cited the potential for unintended off-target DNA edits, which could have harmful health effects, such as cancer, later in life. Also noted was the risk of producing so-called mosaic embryos, in which the edits occur in only a subset of an embryo’s cells. This would make it very difficult for researchers to predict the clinical effects of heritable genome editing in human beings.
Among the many questions that the panel was asked to consider was: should society ever decide that heritable gene editing might be acceptable, what would be a viable framework for scientists, clinicians, and regulatory authorities to assess the potential clinical applications?
In response to that question, the experts replied: heritable gene editing, if ever permitted, should be limited initially to serious diseases that result from the mutation of one or both copies of a single gene. The first uses of these technologies should proceed incrementally and with extreme caution. Their potential medical benefits and harms should also be carefully evaluated before proceeding.
The commission went on to stress that before such an option could be on the table, all other viable reproductive possibilities to produce an embryo without a disease-causing alteration must be exhausted. That would essentially limit heritable gene editing to the exceedingly rare instance in which both parents have two copies of a recessive, disease-causing gene variant. Or another quite rare instance in which one parent has two copies of an altered gene for a dominant genetic disorder, such as Huntington’s disease.
Recognizing how unusual both scenarios would be, the commission held out the possibility that some would-be parents with less serious conditions might qualify if 25 percent or less of their embryos are free of the disease-causing gene variant. A possible example is familial hypercholesterolemia (FH), in which people carrying a mutation in the LDL receptor gene have unusually high levels of cholesterol in their blood. If both members of a couple are affected, only 25 percent of their biological children would be unaffected. FH can lead to early heart disease and death, but drug treatment is available and improving all the time, which makes this a less compelling example. Also, the commission again indicated that such individuals would need to have already traveled down all other possible reproductive avenues before considering heritable gene editing.
A thorny ethical question that was only briefly addressed in the commission’s report is the overall value to be attached to a couple’s desire to have a biological child. That desire is certainly understandable, although other options, such an adoption or in vitro fertilization with donor sperm, are available. This seems like a classic example of the tension between individual desires and societal concerns. Is the drive for a biological child in very high-risk situations such a compelling circumstance that it justifies asking society to start down a path towards modifying human germline DNA?
The commission recommended establishing an international scientific advisory board to monitor the rapidly evolving state of genome editing technologies. The board would serve as an access point for scientists, legislators, and the public to access credible information to weigh the latest progress against the concerns associated with clinical use of heritable human genome editing.
The National Academies/Royal Society report has been sent along to the World Health Organization (WHO), where it will serve as a resource for its expert advisory committee on human genome editing. The WHO committee is currently developing recommendations for appropriate governance mechanisms for both heritable and non-heritable human genome editing research and their clinical uses. That panel could issue its guidance later this year, which is sure to continue this very important conversation.
Reference:
[1] Heritable Human Genome Editing, Report Summary, National Academy of Sciences, September 2020.
Links:
“Heritable Genome Editing Not Yet Ready to Be Tried Safely and Effectively in Humans,” National Academies of Sciences, Engineering, and Medicine news release, Sep. 3, 2020.
International Commission on the Clinical Use of Human Germline Genome Editing (National Academies of Sciences, Engineering, and Medicine/Washington, D.C.)
Video: Report Release Webinar , International Commission on the Clinical Use of Human Germline Genome Editing (National Academies of Sciences, Engineering, and Medicine)
National Academy of Sciences (Washington, D.C.)
National Academy of Medicine (Washington, D.C.)
The Royal Society (London)
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