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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

A CRISPR Approach to Treating Sickle Cell

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Unedited and edited sickle cells
Caption: Red blood cells from patient with sickle cell disease. The cells were differentiated from bone marrow with unedited and edited hematopoietic stem cells, and the red arrows show the sickled cells. Credit: Wu et al. Nature Medicine. March 25, 2019

Recently, CBS’s “60 Minutes” highlighted the story of Jennelle Stephenson, a brave young woman with sickle cell disease (SCD). Jennelle now appears potentially cured of this devastating condition, thanks to an experimental gene therapy being tested at the NIH Clinical Center in Bethesda, MD. As groundbreaking as this research may be, it’s among a variety of innovative strategies now being tried to cure SCD and other genetic diseases that have long seemed out of reach.

One particularly exciting approach involves using gene editing to increase levels of fetal hemoglobin (HbF) in the red blood cells of people with SCD. Shortly after birth, babies usually stop producing HbF, and switch over to the adult form of hemoglobin. But rare individuals continue to make high levels of HbF throughout their lives. This is referred to as hereditary persistence of fetal hemoglobin (HPFH). (My own postdoctoral research in the early 1980s discovered some of the naturally occurring DNA mutations that lead to this condition.)

Individuals with HPFH are entirely healthy. Strikingly, rare individuals with SCD who also have HPFH have an extremely mild version of sickle cell disease—essentially the presence of significant quantities of HbF provides protection against sickling. So, researchers have been exploring ways to boost HbF in everyone with SCD—and gene editing may provide an effective, long-lasting way to do this.

Clinical trials of this approach are already underway. And new findings reported in Nature Medicine show it may be possible to make the desired edits even more efficiently, raising the possibility that a single infusion of gene-edited cells might be able to cure SCD [1].

Sickle cell disease is caused by a specific point mutation in a gene that codes for the beta chain of hemoglobin. People with just one copy of this mutation have sickle cell trait and are generally healthy. But those who inherit two mutant copies of this gene suffer lifelong consequences of the presence of this abnormal protein. Their red blood cells—normally flexible and donut-shaped—assume the sickled shape that gives SCD its name. The sickled cells clump together and stick in small blood vessels, resulting in severe pain, anemia, stroke, pulmonary hypertension, organ failure, and far too often, early death.

Eleven years ago, a team led by Vijay Sankaran and Stuart Orkin at Boston Children’s Hospital and the Dana-Farber Cancer Institute discovered that a protein called BCL11A seemed to determine HbF levels [2]. Subsequent work showed the protein actually works as a master mediator of the switch from fetal to adult hemoglobin, which normally occurs shortly after birth.

Five years ago, Orkin and Daniel Bauer identified a specific enhancer of BCL11A expression that could be an attractive target for gene editing [3]. They could knock out the enhancer in the bone marrow, and BCL11A would not be produced, allowing HbF to stay switched on.

Because the BCL11A protein is required to turn off production of HbF in red cells. the researchers had another idea. They thought it might be possible to keep HbF on permanently by disrupting BCL11A in blood-forming hematopoietic stem cells (HSCs). The hope was that such a treatment might offer people with SCD a permanent supply of healthy red blood cells.

Fast-forward to the present, and researchers are now testing the ability of gene editing tools to cure the disease. A favorite editing system is CRISPR, which I’ve highlighted on my blog.

CRISPR is a highly precise gene-editing tool that relies on guide RNA molecules to direct a scissor-like Cas9 enzyme to just the right spot in the genome to correct the misspelling. The gene-editing treatment involves removing bone marrow from a patient, modifying the HSCs outside the body using CRISPR gene-editing tools, and then returning them back to the patient. Preclinical studies had shown that CRISPR can be effective in editing BCL11A to boost HbF production.

But questions lingered about the editing efficiency in HSCs versus more common, shorter-lived progenitor cells found in bone marrow samples. The efficiency greatly influences how long the edited cells might benefit patients. Bauer’s team saw room for improvement and, as the new study shows, they were right.

To produce lasting HbF production, it’s important to edit as many HSCs as possible. But it turns out that HSCs are more resistant to editing than other types of cells in bone marrow. With a series of adjustments to the gene-editing protocol, including use of an optimized version of the Cas9 protein, the researchers showed they could push the number of edited genes from about 80 percent to about 95 percent.

Their studies show that the most frequent Cas9 edits in HSCs are tiny insertions of a single DNA “letter.” With that slight edit to the BCL11A gene, HSCs reprogram themselves in a way that ensures long-term HbF production.

As a first test of their CRISPR-edited human HSCs, the researchers carried out the editing on HSCs derived from patients with SCD. Then they transferred the editing cells into immune-compromised mice. Four months later, the mice continued to produce red blood cells that produced high levels of HbF and resisted sickling. Bauer says they’re already taking steps to begin testing cells edited with their optimized protocol in a clinical trial.

What’s truly exciting is that the first U.S. human clinical trials of such a gene-editing approach for SCD are already underway, led by CRISPR Therapeutics/Vertex Pharmaceuticals and Sangamo Therapeutics/Sanofi. In January, CRISPR Therapeutics/Vertex Pharmaceuticals announced that the U.S. Food and Drug Administration (FDA) had granted Fast Track Designation for their CRISPR-based treatment called CTX001 [4].

In that recent “60 Minutes” segment, I dared to suggest that we now have what looks like a cure for SCD. As shown by this new work and the clinical trials underway, we in fact may soon have multiple different strategies to provide cures for this devastating disease. And if this can work for sickle cell, a similar strategy might work for other genetic conditions that currently lack any effective treatment.

References:

[1] Highly efficient therapeutic gene editing of human hematopoietic stem cells. Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement K, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE. Nat Med. 2019 Mar 25.

[2] Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Sankaran VG, Menne TF, Xu J, Akie TE, Lettre G, Van Handel B, Mikkola HK, Hirschhorn JN, Cantor AB, Orkin SH.Science. 2008 Dec 19;322(5909):1839-1842.

[3] An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH. Science. 2013 Oct 11;342(6155):253-257.

[4] CRISPR Therapeutics and Vertex Announce FDA Fast Track Designation for CTX001 for the Treatment of Sickle Cell Disease, CRISPR Therapeutics News Release, Jan. 4, 2019.

Links:

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)

Could Gene Therapy Cure Sickle Cell Anemia? (CBS News)

Daniel Bauer (Dana-Farber Cancer Institute, Boston)

Somatic Cell Genome Editing Program (Common Fund/NIH)

NIH Support: National Heart, Lung, and Blood Institute; National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases; National Institute of Diabetes and Digestive and Kidney Diseases


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