CRISPR Conundrum: Pursuing Consensus on Human Germline Editing

2020-06-12T18:02:09-07:00 June 12th, 2020|Biology, Genetics|

By Daniel Erenstein, Neurobiology, Physiology, and Behavior, ‘21

Author’s Note: In November 2018, a scientist in China became the first person to claim that they had edited the genes of human embryos carried to term. Two twins, named with the pseudonyms Lulu and Nana, were born from these very controversial experiments. This news rapidly propelled the debate on human germline genome editing into the mainstream. My interest in this issue was inspired by my involvement with the Innovative Genomics Institute, located in Berkeley, CA. While attending Berkeley City College during the spring and fall semesters of 2019, I participated in the institute’s CRISPR journal club for undergraduates. Each week, we discussed the latest research from the field of CRISPR gene editing. I also took part in a conference, attended by leading geneticists, bioethicists, philosophers, professors of law and policy, science journalists, and other stakeholders, examining where the consensus, if any, lies on human germline genome editing. Discussions from this conference serve as a foundation for this submission to The Aggie Transcript.

 

New details have emerged in the ongoing controversy that kicked off in November of 2018 when a Chinese biophysicist claimed that, during in vitro fertilization, he had genetically edited two embryos that were later implanted into their mother. Twins, anonymously named Lulu and Nana, are believed to have been born as a result of these experiments. This announcement from He Jiankui in a presentation at the Second International Summit on Human Germline Editing in Hong Kong was largely met with swift condemnation from scientists and bioethicists [1, 2].

Late last year, excerpts of the unpublished research report were made public for the first time since He’s announcement, shedding light on his approach to edit resistance to human immunodeficiency virus, or HIV, into human genomes using CRISPR-Cas9 [3]. CRISPR, short for clustered regularly interspaced short palindromic repeats, are specific patterns in bacterial DNA. Normally, a bacterium that has survived an attack by a bacteriophagea virus that infects bacteria and depends on them in order to reproduce—will catalog bacteriophage DNA by incorporating these viral sequences into their own DNA library. This genetic archive of viral DNA, stored between the palindromic repeats of CRISPR, can be revisited as a reference when the bacterium faces future attacks, aiding in its immune response [4].

To respond effectively, bacteria will transcribe a complementary CRISPR RNA molecule from the existing CRISPR sequence. Using crRNAshort for CRISPR RNAas a guide, CRISPR-associated proteins play the part of a search engine, scanning the cell for any entering viral DNA that matches the crRNA sequence [5]. There are many subtypes of CRISPR-associated proteins [6], but Cas9 is one such type that acts as an enzyme by catalyzing double-stranded breaks in sequences complementary to the guide [7]. This immune system effectively defends against the DNA of invading bacteriophages, protecting the bacterium from succumbing to the virus [5]. 

A cell’s built-in mechanisms typically repair any double-stranded breaks in DNA via one of two processes: nonhomologous end-joining (NHEJ) or homology-directed repair (HDR) [8]. During NHEJ, base pairs might be unintentionally inserted or deleted, causing frameshift mutations called indels in the repaired DNA sequence. These mutations significantly affect the structure and function of any protein encoded by the sequence and can result in a completely nonfunctional gene product. NHEJ is frequently relied upon by gene editing researchers to “knock out” or inactivate certain genes. HDR is less efficient, but the process is often exploited by scientists to “knock in” genes or substitute DNA [9].

CRISPR is programmable, meaning that certain DNA sequences can be easily added to these sites, precisely altering the cell’s genetic code at specific locations. Jiankui He was not the first to use CRISPR to edit the genes of human embryos, but no one was known to have ever performed these experiments on viable embryos intended for a pregnancy. He and two of his colleagues have since been fined and sentenced to prison for falsifying ethical review documents and misinforming doctors, the state-run Chinese news agency Xinhua reported in December 2019 [10]. But He’s experiments supposedly yielded another birth during the second half of 2019 [11], confirmed by China in January [12], and Russian scientist Denis Rebrikov has since expressed strong interest in moving forward with human germline genome editing to explore a potential cure for deafness [13].

Despite what seems like overwhelming opposition to human germline genome editing, He’s work has even generated interest from self-described biohackers like Josiah Zayner, CEO of The ODIN, a company which produces do-it-yourself genetic engineering kits for use at home and in the classroom. 

“As long as the children He Jiankui engineered haven’t been harmed by the experiment, he is just a scientist who forged some documents to convince medical doctors to implant gene-edited embryos,” said Zayner in a STAT opinion reacting to news of He’s sentence [14]. “The 4-minute mile of human genetic engineering has been broken. It will happen again.”

Concerns abound, though, about the use of this technology to cure human diseases. And against the chilling backdrop of a global COVID-19 pandemic, fears run especially high about bad actors using CRISPR gene editing with malicious intent. 

A scientist or biohacker with basic lab know-how could conceivably buy DNA sequences and, using CRISPR, edit them to make an even more panic-inducing bacteria or virus,” said Neal Bear, a television producer and global health lecturer at Harvard Medical School, in a recent STAT opinion [15]. “What’s to stop a rogue scientist from using CRISPR to conjure up an even deadlier version of Ebola or a more transmissible SARS?” 

Into the unknown: understanding off-target effects

In his initial presentation, He said that he had targeted the C-C chemokine receptor type 5 (CCR5) gene, which codes for a receptor on white blood cells recognized by HIV during infection. His presentation suggested that gene editing introduced a known mutation named CCR5Δ32 that changes the receptor enough to at least partially inhibit recognition by HIV. The babies’ father was a carrier of HIV, so this editing was performed to supposedly protect the twins from future HIV infection [16]. 

He’s edits to the CCR5 gene—and human germline genome editing, in generalworry geneticists because the off-target effects of introducing artificial changes into the human gene pool are largely unknown. In a video posted on his lab’s YouTube channel [17], He claimed that follow-up sequencing of the twins’ genomes confirmed that “no gene was changed except the one to prevent HIV infection.”

Excerpts from the unpublished study indicate otherwise, according to an expert asked to comment on He’s research in MIT Technology Review, because any cells taken from the twins to run these sequencing tests were no longer part of the developing embryos [3].

“It is technically impossible to determine whether an edited embryo ‘did not show any off-target mutations’ without destroying that embryo by inspecting every one of its cells,” said Fyodor Urnov, professor of molecular and cell biology at UC Berkeley and gene-editing specialist [3]. “This is a key problem for the entirety of the embryo-editing field, one that the authors sweep under the rug here.”

Urnov’s comments raise concerns about “mosaicism” in the cells of Lulu and Nana—and any other future babies brought to term after germline genome editing during embryonic stages of development. In his experiments, He used preimplantation genetic diagnosis to verify gene editing. Even if the cells tested through this technique showed the intended mutation, though, there is a significant risk that the remaining cells in the embryo were left unedited or that unknown mutations with unforeseeable consequences were introduced [16].

While the CCR5Δ32 mutation has, indeed, been found to be associated with HIV resistance [18, 19], even individuals with both copies of CCR5Δ32 can still be infected with certain strains of HIV [20]. In addition, the CCR5Δ32 mutation is found almost exclusively in certain European populations and in very low frequencies elsewhere, including China [21, 22], amplifying the uncertain risk of introducing this particular mutation into Chinese individuals and the broader Chinese gene pool [16].

Perhaps most shocking to the scientific community is the revelation that He’s experiment did not actually edit the CCR5 gene as intended. In He’s November 2018 presentation, he discussed the rates of mutation via non-homologous end-joining but made no mention of the other repair mechanism, homology-directed repair, which would be used to “knock in” the intended mutation. This “[suggests] that He had no intention of generating the CCR5Δ32 allele,” wrote Haoyi Wang and Hui Yang in a PLoS Biology paper on He’s experiments [16].

Gauging the necessity of germline genome editing

The potential of CRISPR to revolutionize how we treat diseases like cystic fibrosis, sickle cell disease, and muscular dystrophy is frequently discussed in the news; just recently, clinical trials involving a gene-editing treatment for Leber congenital amaurosis, a rare genetic eye disorder, stirred enthusiasm, becoming the first treatment to directly edit DNA while it’s still in the body [23]. While this treatment edits somatic cells—cells that are not passed onto future generations during reproduction—there is increasing demand for the use of germline genome editing as well, even despite the reservations of scientists and bioethicists. 

This begs the question: how will society decide what types of genetic modifications are needed? In the case of He’s experiments, most agree that germline genome editing was an unnecessary strategy to protect against HIV. Assisted reproductive technology (ART), a technique that features washing the father’s sperm of excess seminal fluids before in vitro fertilization (IVF), was used in He’s experiments [3] and has already been established as an effective defense against HIV transmission [24]. Appropriately handling gametesanother word for sperm and egg cellsduring IVF is an additional method used to protect the embryo from viral transmission, according to Jeanne O’Brien, a reproductive endocrinologist at the Shady Grove Fertility Center [3].

“As for considering future immunity to HIV infection, simply avoiding potential risk of HIV exposure suffices for most people,” wrote Wang and Yang in their PLoS Biology paper [16]. “Therefore, editing early embryos does not provide benefits for the babies, while posing potentially serious risks on multiple fronts.”

One such unintended risk of He’s experiments might be increased susceptibility to West Nile virus, an infection thought to be prevented by unmutated copies of the CCR5 receptor [11]. 

In a paper that examines the societal and ethical impacts of human germline genome editing, published last year in The CRISPR Journal [25], authors Jodi Halpern, Sharon O’Hara, Kevin Doxzen, Lea Witkowsky, and Aleksa Owen add that “this mutation may increase vulnerability to other infections such as influenza, creating an undue burden on these offspring, [so] we would opt instead for safer ways to prevent HIV infection.”

The authors go on to propose the implementation of a Human Rights Impact Assessment. This assessment would evaluate germline editing treatments or policies using questions that weigh the benefits of an intervention against its possible risks or its potential to generate discrimination. The ultimate goal of such an assessment would be to “establish robust regulatory frameworks necessary for the global protection of human rights” [25].

Most acknowledge that there are several questions to answer before human germline genome editing should proceed: Should we do it? Which applications of the technology are ethical? How can we govern human germline genome editing? Who has the privilege of making these decisions?

Evaluating consensus on germline genome editing

In late October of last year, scientists, bioethicists, policymakers, patient advocates, and religious leaders gathered with members of the public in Berkeley for a discussion centered around some of these unanswered questions. One of the pioneers of CRISPR gene editing technologies, Jennifer Doudna, is a professor of biochemistry and molecular biology at UC Berkeley, and the Innovative Genomics Institute, which houses Doudna’s lab, organized this CRISPR Consensus? conference in collaboration with the Initiative on Science, Technology, and Human Identity at Arizona State University and the Keystone Policy Center. 

The goal of the conference was to generate conversation about where the consensus, if any, lies on human germline genome editing. One of the conference organizers, J. Benjamin Hurlbut, emphasized the role that bioethics—the study of ethical, social, and legal issues caused by biomedical technologies—should play in considerations of germline genome editing. 

He’s “aim was apparently to race ahead of his scientific competitors but also to reshape and speed up, as he put it, the ethical debate. But speed is surely not what we need in this case,” said Hurlbut, associate professor of biology and society at Arizona State University, at the conference [26].

Central to the debate surrounding consensus is the issue of stakeholders in decision-making about germline genome editing. Experts seem to be divided in their definitions of a stakeholder, with varying opinions about the communities that should be included in governance. They do agree, however, that these discussions are paramount to ensure beneficence and justice, tenets of bioethical thought, for those involved. 

An underlying reason for these concerns is that, should human germline genome editing become widely available in the future, the cost of these therapies might restrict access to certain privileged populations.

“I don’t think it’s far-fetched to say that there’s institutionalized racism that goes on around access to this technology, the democratization and self-governance of it,” said Keolu Fox, a UC San Diego scholar who studies the anthropology of natural selection from a genomics perspective. Fox focused his discussion on indigenous populations when addressing the issue of autonomy in governance of germline genome editing [26]. 

“If we don’t put indigenous people or vulnerable populations in the driver’s seat so that they can really think about the potential applications of this type of technology, self-governance, and how to create intellectual property that has a circular economy that goes back to their community,” Fox said, “that is continued colonialism in 2020.”

Indeed, marginalized communities have experienced the evil that genetics can be used to justify, and millions of lives have been lost throughout human history to ideologies emphasizing genetic purity like eugenics and Nazism. 

“We know that history with genetics is wrought with a lot of wrongdoings and also good intentions that can go wrong, and so there’s a community distrust [of germline editing],” said Billie Liangolou, a UC San Francisco (UCSF) Benioff Children’s Hospital genetic counselor, during a panel on stakeholders that included Fox. Liangolou works with expecting mothers, guiding them through the challenges associated with difficult genetic diagnoses during pregnancy [26].

Others agree that the communities affected most by human germline genome editing should be at the forefront of decision-making about this emerging technology. Sharon Begley, a senior science writer at STAT News, told the conference audience that a mother with a genetic disease once asked her if she could “just change my little drop of the human gene pool so that my children don’t have this terrible thing that I have” [26].

This question, frequently echoed throughout society by other prospective parents, reflects the present-day interest in human germline genome editing technologies, interest that will likely continue to grow as further research on human embryos continues.

In an opinion published by STAT News, Ethan Weiss, a cardiologist and associate professor of medicine at UCSF, acknowledges the concerns of parents faced with these decisions [27]. His daughter, Ruthie, has oculocutaneous albinism, a rare genetic disorder characterized by mutations in the OCA2 gene, which is involved in producing melanin. Necessary for normally functioning vision, melanin is a pigment found in the eyes [28].

Weiss and his partner “believe that had we learned our unborn child had oculocutaneous albinism, Ruthie would not be here today. She would have been filtered out as an embryo or terminated,” he said.

But, in the end, Weiss offers up a cautionary message to readers, encouraging people to “think hard” about the potential effects of human germline genome editing. 

“We know that Ruthie’s presence in this world makes it a better, kinder, more considerate, more patient, and more humane place,” Weiss said. “It is not hard, then, to see that these new technologies bring risk that the world will be less kind, less compassionate, and less patient when there are fewer children like Ruthie. And the kids who inevitably end up with oculocutaneous albinism or other rare diseases will be even less ‘normal’ than they are today.”

Weiss’ warning is underscored by disability rights scholars who say that treating genetic disorders with CRISPR or other germline editing technologies could lead to heightened focus on those who continue to live with these disabilities. In an interview with Katie Hasson of the Center for Genetics and Society, located in Berkeley, Jackie Leach Scully commented on the stigmatization that disabled people might face in a world where germline editing is regularly practiced [29].

“Since only a minority of disability is genetic, even if genome editing eventually becomes a safe and routine technology it won’t eradicate disability,” said Scully, professor of bioethics at the University of New South Wales in Australia. “The concern then would be about the social effects of [heritable genome editing] for people with non-genetic disabilities, and the context that such changes would create for them.” 

Others worry about how to define the boundary between the prevention of genetic diseases and the enhancement of desirable traits—and what this means for the decisions a germline editing governing body would have to make about people’s value in society. Emily Beitiks, associate director of the Paul K. Longmore Institute on Disability at San Francisco State University, is among the community of experts who have raised such concerns [30].

 “Knowing that these choices are being made in a deeply ableist culture,” said Beitiks in an article posted on the Center for Genetics and Society’s blog [30], “illustrates how hard it would be to draw lines about what genetic diseases ‘we’ agree to engineer out of the gene pool and which are allowed to stay.”

Religious leaders have also weighed in on the ethics of human germline genome editing. Father Joseph Tham, who has previously published work on what he calls “the secularization of bioethics,” presented his views on the role of religion in this debate about bioethics at the conference [26].

“Many people in the world belong to some kind of religious tradition, and I think it would be a shame if religion is not a part of this conversation,” said Tham, professor at Regina Apostolorum Pontifical University’s School of Bioethics.

Tham explained that the church already disapproves of IVF techniques, let alone human germline editing, “because in some way it deforms the whole sense of the human sexual act.”

Islamic perspectives on germline editing differ. In a paper published last year, Mohammed Ghaly, one of the conference panelists, discussed how the Islamic religious tradition informs perspectives on human genome editing in the Muslim world [31].

“The mainstream position among Muslim scholars is that before embryos are implanted in the uterus, they do not have the moral status of a human being,” said Ghaly, professor of Islam and biomedical ethics at Hamad Bin Khalifa University. “That is why the scholars find it unproblematic to use them for conducting research with the aim of producing beneficial knowledge.”

Where Muslim religious scholars draw the line, Ghaly says, is at the applications of human germline genome editing, not research about it. Issues regarding the safety and effectiveness of germline editing make its current use in viable human embryos largely untenable, according to the majority of religious scholars [31].

The unfolding, back-and-forth debate about who and how to design policies guiding human germline genome editing continues to rage on, but there is little doubt about consensus on one point. For a technology with effects as far-reaching as this one, time is of the essence.

 

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