Hacking Darwin

by Jamie Metzl

  But as we increasingly master and grow comfortable with this technology, we’ll create a process with applications extending far beyond health care, which we’ll use to alter the genetics of ourselves and our children in increasingly significant ways.

  *An intense debate broke out among scientists after a 2017 study, later debunked and retracted, suggested that the off-target effects of CRISPR were greater than previously understood.

  *The difference between gene therapy and gene editing sometimes confuses people because the two processes are closely related. Genetic engineering and gene editing are tools used in gene therapies that also have far broader functionality. All gene therapy is genetic engineering, but not all genetic engineering is gene therapy.

  *Some nuclear genes influence mitochondrial function and vice versa.

  Chapter 6

  Rebuilding the Living World

  Death from exposure to the Ebola virus is excruciating.

  First, you feel extremely weak, with flu-like symptoms. As the virus starts infecting and then bursting your cells and blood vessels, you then experience uncontrolled nausea, diarrhea, vomiting, and headaches. Your cells hemorrhage, causing uncontrolled bleeding throughout your body. You then go into shock before you die a gruesome, bloody death, your vital fluids bursting out from every orifice of your body.

  Early Ebola outbreaks in the poorest parts of Africa saw death rates of up to 90 percent of those infected. The somewhat better health care provided during the 2014 Ebola outbreak in West Africa reduced the death rate to around 60 percent.

  The people most likely to be infected by Ebola are the family members and health-care providers caring for loved ones and patients already infected. Just being exposed to the saliva, vomit, urine, or stool of an Ebola victim is enough.

  But scientists who studied survivors of the 2014 Ebola outbreak in Guinea were surprised to come across a group of caretaker women who had been exposed but somehow seemed immune to the disease. Some of these women had contracted the virus at an earlier point and survived, possibly giving them immunity to later exposures. Others, however, possessed antibodies even though they hadn’t been exposed. What was happening? the scientists wondered. Could some of these women be genetically immune to Ebola?

  Researchers zeroed in on a gene that encodes a protein called Niemann-Pick Type C, or NPC, which the Ebola virus targets when attacking a host. Having nothing to do with Ebola, children inheriting two copies from their parents of the mutated version of this gene generally die from Niemann Pick Type C disease, a neurodegenerative disorder.

  Some single-gene diseases like Huntington’s disease and Marfan syndrome are dominant, which means that you’ll almost certainly get the disease if you inherit the gene and either of your parents is homozygous for the mutation. Others, like with sickle cell disease, Tay-Sachs, and Niemann-Pick Type C disease, are recessive disorders, which means you only get the disease if you inherit the gene from both parents. But just like recessive carriers of the sickle cell disease gene can have immunity from malaria, preliminary studies of these West African women suggested that people with only one mutated copy of the NPC gene may have increased resistance to the Ebola virus.

  We’ve already explored single-gene and other mutations that can cause disease. But just as there are some individual genetic mutations that can inflict harm, there are many more single-gene mutations that can do good.

  As the Ebola case shows, sometimes these can be the same genes that help us in one context but hurt us in another. Over the past decade, scientists have been searching to find more of the single gene mutations with outsize potentials to help us, at least in the context of the world we know today. Finding them, however, is a challenge.

  It’s much easier to identify an illness that presents itself with observable symptoms than to identify the absence of a disease among people who, but for a particular genetic mutation, might otherwise have it. But by finding outliers like the women with Ebola immunity and pouring through databases of hundreds of thousands, or even millions, of genomes and health records to find correlations between the presence of a rare variant gene and resistance to specific diseases, researchers are increasingly striking gold.

  David Altschuler, for example, while a researcher at the Broad Institute of Harvard and MIT, recruited a cohort of elderly and overweight people who were statistically at a high risk of developing type 2 diabetes but hadn’t. After sequencing the members of the group, to see how they might be genetically different from other people with the disease who were equally old and overweight, he came to believe that a single mutation in the SLC30A8 gene made his cohort 65 percent better able to regulate their insulin levels and less likely to get diabetes.1

  Another study found that 1 percent of Northern Europeans carried a mutation in their CCR-5 gene that makes them immune to HIV infection.2 Another elderly study found that about one in 650 people with mutations of their NPC1L1 gene had less than half the risk of a heart attack compared to people just like them but without the mutation.3

  Because making small changes to the human genome is easier and safer than making big ones, identifying single-gene mutations with significant potential positive impact raises the enticing possibility of gene editing these small mutations into ourselves or future children. Because our biology represents a delicate balancing act of priorities played out over billions of years, only a tiny number of genes are likely to have an impact large enough to make the benefit of adding or removing them outweigh the potential danger of making a change.

  But as the Ebola and other cases point out, it’s definitely worthwhile to look for them.

  According to Harvard’s George Church, a preliminary list of these rare single genes that could potentially be manipulated to give us special benefits might include:

  GENE IMPACT

  LRP5 Extra-strong bones

  MSTN Lean muscles

  SCN9A Insensitivity to pain

  ABCC11 Low odor production

  CCR5, FUT2 Virus resistance

  PCSK9 Low coronary disease

  APP Low Alzheimer’s

  GHR, GH Low cancer

  SLC30A8 Low type 2 diabetes

  IFIH1 Low type 1 diabetes

  Source: “A Conversation with George Church on Genomics & Germline Human Genetic Modification,” The Niche Knoepfler Lab Stem Cell Blog, March 9, 2015, https://ipscell.com/2015/03/georgechurchinterview/.

  Making small changes to genes like these isn’t our only path to effect these changes. Genes, as we’ve learned, are a set of instructions telling cells to make proteins that do things. Although it matters what the genes say, what the cells actually do is ultimately what’s important. So, even if we find a particular gene that does something we feel is good or bad, we wouldn’t necessarily need to change the gene in order to change its expression. In some cases, it might make more sense and be safer, easier, and cheaper to develop drugs that instruct the cells to do what we want, even if the “bad” mutation remains or the “good” mutation is never there.

  Even so, there will be some mutations, both cumulatively helpful and hurtful ones, where this type of treatment will not be possible. Like with mitochondrial disease, there might be a mutation that is seen as so harmful that some carriers would want to get rid of it for all future generations. Some parents might want to alter the germ line of their future children to make them immune to HIV, less likely to face cognitive decline as they age, or benefit from any other single-gene mutation that confirms a special advantage.

  When considering the possibility of having one or a small number of single-gene edits made to their preimplanted embryos, the first question parents will ask is whether this is safe. At present, the answer is no. CRISPR is still not a perfect technology. One of the largest concerns about the first generation of CRISPR gene-editing tools was their potential to cut the genome in places other than where the scientists intended.

  This type of off-target cutting has shown up most significantly in the gene editin
g of human cells. An important 2013 study examined off-target CRISPR edits in human cells and found that CRISPR edits for therapeutic applications would need to be significantly improved to be “used safely in the longer term for treatment of human diseases.”4 If these types of off-target mutations were always benign, any small change made by CRISPR editing human genes inside a person wouldn’t amount to much. But that is not the case. A CRISPR-induced mutation could also have the potential to become cancerous. That’s why regulators around the world have been justifiably cautious about authorizing the gene editing of humans.

  The Chinese research group that shocked the world by announcing its CRISPR-editing of the nonviable in human embryos in 2015, for example, reported abysmal accuracy levels. Of the eighty-six fertilized eggs injected with the CRISPR-Cas9 system designed to edit their genomes, only a few contained the desired genetic change. This ratio of attempts to successes is acceptable in plant, worm, fly, and mouse models, where the cost of mistakes tends to be lower but would be unthinkable for humans.5

  The path toward reaching a level of reliability, where CRISPR could be safely used inside humans, will not be linear. A high-profile 2018 study, for example, found that a single human gene, p53, blocked CRISPR edits in some human cells, as part of the body’s natural defense mechanism against dangerous mutations like cancer.6 One way around this would be to deactivate the p53 gene, but this would bring a new danger—increased cancer risk. Another 2018 study published in Nature Biotechnology found 20 percent more off-target DNA alterations than previously expected when making CRISPR-Cas9 edits in mice.7

  Scientists intent on addressing such concerns have focused on increasing the accuracy of CRISPR gene editing, with some dramatic success. They are discovering new enzymes that more precisely attach to or break the genome than CRISPR-Cas9. These new CRISPRs—with names like CRISPR-cpf1 (a.k.a. 12a), CRISPR-Cas3, CRISPR-13, CRISPR-CasX, and CRISPR-CasY—are proliferating. New AI algorithms are also being deployed to assess where CRISPR edits can most optimally be made.

  In 2017, researchers reported a new method for changing DNA and RNA nucleotide “letters”—the A’s, C’s, G’s, and T’s—without cutting the genome.8 The original CRISPR model required cutting across the twisting ladder of DNA; the modified process changes the genes without cutting the ladder at all.

  To do this, researchers tricked the DNA atoms to pair differently than they otherwise would. Remember that A’s pair with T’s and C’s with G’s; so, if the cell thinks an A is a C, for example, it will pair it with a G rather than a T. The gene and its expression change, but the uncertainty that arises from cutting DNA is avoided.

  This approach is particularly useful because an estimated 32,000 of the roughly 50,000 known changes in the human genome associated with diseases are caused by the swapping, deletion, or insertion of a single gene.9 Called an adenine base editor, or ABE, this new version of CRISPR works 34 to 68 percent of the time, with less than 0.1 percent of cells showing evidence of additional mistakes, a big improvement but still not ready to be deployed inside a human body.10 Chinese researchers reported in August 2018 that they had base edited the genomes to repair a mutation causing Marfan syndrome in sixteen out of eighteen viable preimplanted human embryos.11 Although none of these embryos were implanted due to legal and ethical considerations, it is clear where this technology is headed.

  Base-editing technology was then used to increase the precision and potentially the safety of gene editing even further through a process called CRISPR-SKIP. Editing a single base with this approach causes the cell to “skip over” and not “read” targeted strings of protein-coding genes. Preliminary indications suggest CRISPR-SKIP could be used to deactivate damage-causing mutations in the genome with far fewer off-target effects than many of the other CRISPR systems.12

  In addition to using CRISPR for gene editing, significant progress is also being made using CRISPR to edit the epigenetic marks orchestrating how genes function and the RNA guides that translate the genetic information into instructions for the cell.13 Together, these approaches will make altering genes and their expression more precise.

  Another big challenge to overcome to make the gene editing of preimplanted human embryos safe is the uneven spread of a genetic change across the cells, which scientists call mosaicism. Uneven distribution of a gene-edited mutation can lead to abnormal growth of the fetus and other serious problems. But this challenge, too, is being gradually addressed. Recent studies have shown that using CRISPR as soon as possible after fertilization and editing the sperm and egg cells prior to fertilization decrease the chances that cell mosaicism will occur.14

  After Shoukhrat Mitalipov and his team announced their new approaches for minimizing this potential problem,15 another group of superstar geneticists issued a statement the following month raising questions about the accuracy of this research. “It is essential that conclusions regarding the ability to correct a mutation in human embryos be fully supported,” Dieter Egli, George Church, and their colleagues wrote in a joint statement arguing that Mitalipov’s conclusions were far from proven. “Absent such data, the biomedical community and, critically, patients with disease-causing mutations interested in such research must be made aware that numerous challenges in gene correction remain.”16

  This debate among leading genetics researchers then ramped up a notch in August 2018, when Nature published, in the same issue, two scathing critiques of Mitalipov’s research as well as a long and detailed response from Mitalipov and thirty-one of his colleagues from around the world.17 Although all scientists would agree that our ability to precisely edit preimplanted human embryos is increasing, the debate is still raging about whether we are ready yet to use these technologies on human embryos intended to be implanted in a mother and taken to term.

  But, once again, the operative word in this last sentence is yet.

  If logic were our guide, people would start getting more comfortable with gene editing embryos once the error rate in gene editing matched the error rate of natural conception. As we’ve seen from the experience of self-driving cars, however, the reality is that a new technology like this needs to be much safer than nature for it to be adopted. At least for the technical process of making a very limited number of genome edits, this standard will be soon reached. If and when this happens, gene editing preimplanted embryos and eggs and/or sperm may be the only way for some parents carrying a subset of genetic disorders to have a biologically related child who would not inherit the disorder. These instances would include some Y chromosome defects, dominant monogenetic diseases like Huntington’s where one parent is homozygous, and recessive conditions where both parents are homozygous.18

  An extremely controversial first use of CRISPR to allegedly edit a single gene, CCR5, in the preimplanted embryos of a pair of twins to make them immune to HIV was announced by Chinese researchers in late November 2018. Although roundly condemned by many scientists and ethicists in China and around the world, this first-ever case of gene editing humans was a harbinger of where our genetically engineered future is heading.19

  But while increasing confidence with the use of IVF, embryo selection, and single-gene editing of preimplanted embryos seems all but inevitable, the prospect of editing more complex genetic traits remains significantly more remote.

  As we’ve seen, complex traits like height, intelligence, and personality are most often determined by the complex interaction of hundreds or even thousands of genes, all performing multiple functions and interacting with other body systems and the constantly changing environment around us.20 A group of Stanford researchers recently argued that most genetic diseases and traits are not just polygenic, influenced by multiple genes, but instead what they call omnigenic. This hypothesis argues that traits are influenced not just by the systemic contribution of the many “core genes,” the ones that now show up on genome-wide association studies, but also by a much larger network of peripheral genes that don’t.21 If true, this would make understandi
ng complex diseases and traits far more complicated than previously imagined.

  The more genes that influence a particular trait, the more difficult a computational task it becomes to fully understand the correlation between genetic patterns and certain gene expressions. The harder it is to understand the multiple functions each gene performs in the complex and interconnected ecosystem of the genome, the tougher it becomes to make bigger gene edits intending to influence complex traits without unintentionally damaging the rest of the genome.

  It certainly should be our assumption that the interconnected ecosystems of the human body are almost always more complex than we tend to think they are. It also makes logical sense that our diseases and traits span a wide range of genetic foundations, from the single-gene mutation diseases like Huntington’s and single-gene-determined traits like having wet ear wax on the one hand to complex diseases and traits like coronary heart disease and personality style on the other.22 The omnigenic model may be a worst-case scenario for aspiring genetic engineers that, even if true in some instances, certainly won’t apply equally to all diseases and traits.

  But we won’t need anything even approaching an omnigenic level of understanding when people are selecting from among their own natural and unedited preimplanted embryos during IVF and PGT. The steady increase in our understanding of complex genetic patterns, even omnigenic ones, will be enough to inform moderately educated guesses by parents about which embryos to implant in the mother. As our imperfect knowledge of these complex traits increases, so will our confidence in selecting and ultimately genetically altering our future children.