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What A Year It Was for Science Advances!

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Science Breakthroughs of the Year 2020

At the close of every year, editors and writers at the journal Science review the progress that’s been made in all fields of science—from anthropology to zoology—to select the biggest advance of the past 12 months. In most cases, this Breakthrough of the Year is as tough to predict as the Oscar for Best Picture. Not in 2020. In a year filled with a multitude of challenges posed by the emergence of the deadly coronavirus disease 2019 (COVID-2019), the breakthrough was the development of the first vaccines to protect against this pandemic that’s already claimed the lives of more than 360,000 Americans.

In keeping with its annual tradition, Science also selected nine runner-up breakthroughs. This impressive list includes at least three areas that involved efforts supported by NIH: therapeutic applications of gene editing, basic research understanding HIV, and scientists speaking up for diversity. Here’s a quick rundown of all the pioneering advances in biomedical research, both NIH and non-NIH funded:

Shots of Hope. A lot of things happened in 2020 that were unprecedented. At the top of the list was the rapid development of COVID-19 vaccines. Public and private researchers accomplished in 10 months what normally takes about 8 years to produce two vaccines for public use, with more on the way in 2021. In my more than 25 years at NIH, I’ve never encountered such a willingness among researchers to set aside their other concerns and gather around the same table to get the job done fast, safely, and efficiently for the world.

It’s also pretty amazing that the first two conditionally approved vaccines from Pfizer and Moderna were found to be more than 90 percent effective at protecting people from infection with SARS-CoV-2, the coronavirus that causes COVID-19. Both are innovative messenger RNA (mRNA) vaccines, a new approach to vaccination.

For this type of vaccine, the centerpiece is a small, non-infectious snippet of mRNA that encodes the instructions to make the spike protein that crowns the outer surface of SARS-CoV-2. When the mRNA is injected into a shoulder muscle, cells there will follow the encoded instructions and temporarily make copies of this signature viral protein. As the immune system detects these copies, it spurs the production of antibodies and helps the body remember how to fend off SARS-CoV-2 should the real thing be encountered.

It also can’t be understated that both mRNA vaccines—one developed by Pfizer and the other by Moderna in conjunction with NIH’s National Institute of Allergy and Infectious Diseases—were rigorously evaluated in clinical trials. Detailed data were posted online and discussed in all-day meetings of an FDA Advisory Committee, open to the public. In fact, given the high stakes, the level of review probably was more scientifically rigorous than ever.

First CRISPR Cures: One of the most promising areas of research now underway involves gene editing. These tools, still relatively new, hold the potential to fix gene misspellings—and potentially cure—a wide range of genetic diseases that were once to be out of reach. Much of the research focus has centered on CRISPR/Cas9. This highly precise gene-editing system relies on guide RNA molecules to direct a scissor-like Cas9 enzyme to just the right spot in the genome to cut out or correct a disease-causing misspelling.

In late 2020, a team of researchers in the United States and Europe succeeded for the first time in using CRISPR to treat 10 people with sickle cell disease and transfusion-dependent beta thalassemia. As published in the New England Journal of Medicine, several months after this non-heritable treatment, all patients no longer needed frequent blood transfusions and are living pain free [1].

The researchers tested a one-time treatment in which they removed bone marrow from each patient, modified the blood-forming hematopoietic stem cells outside the body using CRISPR, and then reinfused them into the body. To prepare for receiving the corrected cells, patients were given toxic bone marrow ablation therapy, in order to make room for the corrected cells. The result: the modified stem cells were reprogrammed to switch back to making ample amounts of a healthy form of hemoglobin that their bodies produced in the womb. While the treatment is still risky, complex, and prohibitively expensive, this work is an impressive start for more breakthroughs to come using gene editing technologies. NIH, including its Somatic Cell Genome Editing program, continues to push the technology to accelerate progress and make gene editing cures for many disorders simpler and less toxic.

Scientists Speak Up for Diversity: The year 2020 will be remembered not only for COVID-19, but also for the very public and inescapable evidence of the persistence of racial discrimination in the United States. Triggered by the killing of George Floyd and other similar events, Americans were forced to come to grips with the fact that our society does not provide equal opportunity and justice for all. And that applies to the scientific community as well.

Science thrives in safe, diverse, and inclusive research environments. It suffers when racism and bigotry find a home to stifle diversity—and community for all—in the sciences. For the nation’s leading science institutions, there is a place and a calling to encourage diversity in the scientific workplace and provide the resources to let it flourish to everyone’s benefit.

For those of us at NIH, last year’s peaceful protests and hashtags were noticed and taken to heart. That’s one of the many reasons why we will continue to strengthen our commitment to building a culturally diverse, inclusive workplace. For example, we have established the NIH Equity Committee. It allows for the systematic tracking and evaluation of diversity and inclusion metrics for the intramural research program for each NIH institute and center. There is also the recently founded Distinguished Scholars Program, which aims to increase the diversity of tenure track investigators at NIH. Recently, NIH also announced that it will provide support to institutions to recruit diverse groups or “cohorts” of early-stage research faculty and prepare them to thrive as NIH-funded researchers.

AI Disentangles Protein Folding: Proteins, which are the workhorses of the cell, are made up of long, interconnected strings of amino acids that fold into a wide variety of 3D shapes. Understanding the precise shape of a protein facilitates efforts to figure out its function, its potential role in a disease, and even how to target it with therapies. To gain such understanding, researchers often try to predict a protein’s precise 3D chemical structure using basic principles of physics—including quantum mechanics. But while nature does this in real time zillions of times a day, computational approaches have not been able to do this—until now.

Of the roughly 170,000 proteins mapped so far, most have had their structures deciphered using powerful imaging techniques such as x-ray crystallography and cryo–electron microscopy (cryo-EM). But researchers estimate that there are at least 200 million proteins in nature, and, as amazing as these imaging techniques are, they are laborious, and it can take many months or years to solve 3D structure of a single protein. So, a breakthrough certainly was needed!

In 2020, researchers with the company Deep Mind, London, developed an artificial intelligence (AI) program that rapidly predicts most protein structures as accurately as x-ray crystallography and cryo-EM can map them [2]. The AI program, called AlphaFold, predicts a protein’s structure by computationally modeling the amino acid interactions that govern its 3D shape.

Getting there wasn’t easy. While a complete de novo calculation of protein structure still seemed out of reach, investigators reasoned that they could kick start the modeling if known structures were provided as a training set to the AI program. Utilizing a computer network built around 128 machine learning processors, the AlphaFold system was created by first focusing on the 170,000 proteins with known structures in a reiterative process called deep learning. The process, which is inspired by the way neural networks in the human brain process information, enables computers to look for patterns in large collections of data. In this case, AlphaFold learned to predict the underlying physical structure of a protein within a matter of days. This breakthrough has the potential to accelerate the fields of structural biology and protein research, fueling progress throughout the sciences.

How Elite Controllers Keep HIV at Bay: The term “elite controller” might make some people think of video game whizzes. But here, it refers to the less than 1 percent of people living with human immunodeficiency virus (HIV) who’ve somehow stayed healthy for years without taking antiretroviral drugs. In 2020, a team of NIH-supported researchers figured out why this is so.

In a study of 64 elite controllers, published in the journal Nature, the team discovered a link between their good health and where the virus has inserted itself in their genomes [3]. When a cell transcribes a gene where HIV has settled, this so-called “provirus,” can produce more virus to infect other cells. But if it settles in a part of a chromosome that rarely gets transcribed, sometimes called a gene desert, the provirus is stuck with no way to replicate. Although this discovery won’t cure HIV/AIDS, it points to a new direction for developing better treatment strategies.

In closing, 2020 presented more than its share of personal and social challenges. Among those challenges was a flood of misinformation about COVID-19 that confused and divided many communities and even families. That’s why the editors and writers at Science singled out “a second pandemic of misinformation” as its Breakdown of the Year. This divisiveness should concern all of us greatly, as COVID-19 cases continue to soar around the country and our healthcare gets stretched to the breaking point. I hope and pray that we will all find a way to come together, both in science and in society, as we move forward in 2021.

References:

[1] CRISPR-Cas9 gene editing for sickle cell disease and β-thalassemia. Frangoul H et al. N Engl J Med. 2020 Dec 5.

[2] ‘The game has changed.’ AI triumphs at protein folding. Service RF. Science. 04 Dec 2020.

[3] Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Jiang C et al. Nature. 2020 Sep;585(7824):261-267.

Links:

COVID-19 Research (NIH)

2020 Science Breakthrough of the Year (American Association for the Advancement of Science, Washington, D.C)


Experts Conclude Heritable Human Genome Editing Not Ready for Clinical Applications

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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)


Gene-Editing Advance Puts More Gene-Based Cures Within Reach

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Prime Editing
Caption: The prime editing system (left) contains three parts: two enzymes, Cas9 and reverse transcriptase, and an engineered guide RNA, pegRNA. Unlike regular CRISPR gene editing, prime editing nicks just one strand of the DNA molecule (right) and then uses RNA and reverse transcriptase to direct highly targeted changes to a cell’s DNA. Credit: Broad Institute of MIT and Harvard, Cambridge, MA.

There’s been tremendous excitement recently about the potential of CRISPR and related gene-editing technologies for treating or even curing sickle cell disease (SCD), muscular dystrophy, HIV, and a wide range of other devastating conditions. Now comes word of another remarkable advance—called “prime editing”—that may bring us even closer to reaching that goal.

As groundbreaking as CRISPR/Cas9 has been for editing specific genes, the system has its limitations. The initial version is best suited for making a double-stranded break in DNA, followed by error-prone repair. The outcome is generally to knock out the target. That’s great if eliminating the target is the desired goal. But what if the goal is to fix a mutation by editing it back to the normal sequence?

The new prime editing system, which was described recently by NIH-funded researchers in the journal Nature, is revolutionary because it offers much greater control for making a wide range of precisely targeted edits to the DNA code, which consists of the four “letters” (actually chemical bases) A, C, G, and T [1].

Already, in tests involving human cells grown in the lab, the researchers have used prime editing to correct genetic mutations that cause two inherited diseases: SCD, a painful, life-threatening blood disorder, and Tay-Sachs disease, a fatal neurological disorder. What’s more, they say the versatility of their new gene-editing system means it can, in principle, correct about 89 percent of the more than 75,000 known genetic variants associated with human diseases.

In standard CRISPR, a scissor-like enzyme called Cas9 is used to cut all the way through both strands of the DNA molecule’s double helix. That usually results in the cell’s DNA repair apparatus inserting or deleting DNA letters at the site. As a result, CRISPR is extremely useful for disrupting genes and inserting or removing large DNA segments. However, it is difficult to use this system to make more subtle corrections to DNA, such as swapping a letter T for an A.

To expand the gene-editing toolbox, a research team led by David R. Liu, Broad Institute of MIT and Harvard, Cambridge, MA, previously developed a class of editing agents called base editors [2,3]. Instead of cutting DNA, base editors directly convert one DNA letter to another. However, base editing has limitations, too. It works well for correcting four of the most common single letter mutations in DNA. But at least so far, base editors haven’t been able to make eight other single letter changes, or fix extra or missing DNA letters.

In contrast, the new prime editing system can precisely and efficiently swap any single letter of DNA for any other, and can make both deletions and insertions, at least up to a certain size. The system consists of a modified version of the Cas9 enzyme fused with another enzyme, called reverse transcriptase, and a specially engineered guide RNA, called pegRNA. The latter contains the desired gene edit and steers the needed editing apparatus to a specific site in a cell’s DNA.

Once at the site, the Cas9 nicks one strand of the double helix. Then, reverse transcriptase uses one DNA strand to “prime,” or initiate, the letter-by-letter transfer of new genetic information encoded in the pegRNA into the nicked spot, much like the search-and-replace function of word processing software. The process is then wrapped up when the prime editing system prompts the cell to remake the other DNA strand to match the new genetic information.

So far, in tests involving human cells grown in a lab dish, Liu and his colleagues have used prime editing to correct the most common mutation that causes SCD, converting a T to an A. They were also able to remove four DNA letters to correct the most common mutation underlying Tay-Sachs disease, a devastating condition that typically produces symptoms in children within the first year and leads to death by age four. The researchers also used their new system to insert new DNA segments up to 44 letters long and to remove segments at least 80 letters long.

Prime editing does have certain limitations. For example, 11 percent of known disease-causing variants result from changes in the number of gene copies, and it’s unclear if prime editing can insert or remove DNA that’s the size of full-length genes—which may contain up to 2.4 million letters.

It’s also worth noting that now-standard CRISPR editing and base editors have been tested far more thoroughly than prime editing in many different kinds of cells and animal models. These earlier editing technologies also may be more efficient for some purposes, so they will likely continue to play unique and useful roles in biomedicine.

As for prime editing, additional research is needed before we can consider launching human clinical trials. Among the areas that must be explored are this technology’s safety and efficacy in a wide range of cell types, and its potential for precisely and safely editing genes in targeted tissues within living animals and people.

Meanwhile, building on all these bold advances, efforts are already underway to accelerate the development of affordable, accessible gene-based cures for SCD and HIV on a global scale. Just last month, NIH and the Bill & Melinda Gates Foundation announced a collaboration that will invest at least $200 million over the next four years toward this goal. Last week, I had the chance to present this plan and discuss it with global health experts at the Grand Challenges meeting Addis Ababa, Ethiopia. The project is an unprecedented partnership designed to meet an unprecedented opportunity to address health conditions that once seemed out of reach but—as this new work helps to show—may now be within our grasp.

References:

[1] Search-and-replace genome editing without double-strand breaks or donor DNA. Anzalone AV, Randolph PB, Davis JR, Sousa AA, Koblan LW, Levy JM, Chen PJ, Wilson C, Newby GA, Raguram A, Liu DR. Nature. Online 2019 October 21. [Epub ahead of print]

[2] 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.

[3] 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.

Links:

Tay-Sachs Disease (Genetics Home Reference/National Library of Medicine/NIH)

Sickle Cell Disease (National Heart, Lung, and Blood Institute/NIH)

Cure Sickle Cell Initiative (NHLBI)

What are Genome Editing and CRISPR-Cas9? (National Library of Medicine/NIH)

Somatic Cell Genome Editing Program (Common Fund/NIH)

David R. Liu (Harvard, Cambridge, MA)

NIH Support: National Institute of Allergy and Infectious Diseases; National Human Genome Research Institute; National Institute for General Medical Sciences; National Institute of Biomedical Imaging and Bioengineering; National Center for Advancing Translational Sciences


Joining Forces Against Sickle Cell Disease and HIV Infection

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Gates Collaboration Telebriefing
The NIH and the Bill and Melinda Gates Foundation, Seattle, will invest at least $200 million over the next four years to develop affordable gene-based cures globally for sickle cell disease and HIV infection. The announcement of this timely collaboration was made during a late-morning telebriefing at NIH on October 23, 2019. Here, I met with two of my fellow participants on the call: Gary Gibbons (left), director of NIH’s Heart, Lung, and Blood Institute; and Trevor Mundel, (middle), president of the Gates Foundation’s global health efforts. Also joining the telebriefing remotely by phone were Tony Fauci, director of NIH’s National Institute of Allergy and Infectious Diseases; and Matishidiso Moeti, director of the World Health Organization’s Regional Office for Africa. Credit: NIH

Celebrating Be Best’s First Anniversary

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The NIH Director speaks at Be Best's First Anniversary in the White House Rose Garden
On May 7, 2019, I joined the President and First Lady in the White House Rose Garden to mark the first anniversary of the First Lady’s Be Best program. During my remarks, I recognized Amani (standing), who recently underwent a bone marrow transplant for sickle cell disease, and others from the NIH Children’s Inn. Credit: NIH

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