一本讲基因编辑技术发明人Doudna Jennifer和其竞争者张峰的故事。基因编辑的发现历史不过才十年的时间,下游的应用还尚未打开,但作为一项突破性的技术值得长期跟踪和关注,这样的书读起来对于理解技术和其局限是相当有帮助的。
Researchers were able to devise proteins that could serve as a guide to get the cutting domain to a targeted DNA sequence. One system, zinc-finger nucleases (ZFNs), came from fusing the cutting domain with a protein that has little fingers shaped by the presence of a zinc ion, which allow it to grasp on to a specified DNA sequence. A similar but even more reliable method, known as TALENs (transcription activator–like effector nucleases), came from fusing the cutting domain with a protein that could guide it to longer DNA sequences.”
“With ZFNs and TALENs, you had to construct a new protein guide every time you wanted to target a different genetic sequence to cut; it was difficult and time consuming. But with CRISPR you merely had to fiddle with the genetic sequence of the RNA guide. A good student could do it quickly in a lab.”
“In the Saturday enrichment class, the focus was on DNA and how RNA carried out its instructions, with an emphasis on the role played in this process by enzymes, those protein molecules that act as catalysts to spark actions in a cell. “My teacher loved enzymes,” Zhang says. “He told me that whenever you face a tough question in biology, just say ‘Enzymes.’ It’s the correct answer to most questions in biology.”
“In addition, he used a well-known technique called “codon optimization” to make the CRISPR-Cas9 system work in human cells. Codons are the three-letter snippets of DNA that provide instructions for the specific arrangement of amino acids, which are the building blocks used to make proteins. A variety of codons can code for the same amino acid. In different organisms, one or another of these alternative codons may work more efficiently. When trying to move a gene-expression system from one organism to another, such as from bacteria to a human, codon optimization switches the codon sequence to the one that works best.”
“In September 2013, Gengine, Inc. was founded. Two months later, it changed its name to Editas Medicine. “We have the ability to essentially target any gene,” said Kevin Bitterman, a principal at Polaris Partners who served as the interim president for the first few months. “And we have in our crosshairs any diseases with a genetic component. We can go in and fix the error.”
“On April 15, 2014, she received an email from a reporter asking for her reaction to the news that Zhang and the Broad had just been granted a patent for the use of CRISPR-Cas9 as an editing tool. Doudna and Charpentier still had a patent application pending, but Zhang and the Broad, who had put in their own application later, had paid to have their decision fast-tracked. Suddenly it became clear, to Doudna at least, that Zhang and Lander were trying to relegate her and Charpentier to minor players—both in history and in any commercial use of CRISPR-Cas9.”
“Within a few months, she decided that she would be most comfortable working with her trusted partner and former student Rachel Haurwitz, with whom she had started Caribou Biosciences in 2011. Caribou had created a spinoff called Intellia, with the mission of commercializing CRISPR-Cas9 tools. “I became very interested in Intellia, because the Caribou team was launching it with the academic scientists I most liked and trusted and respected,” Doudna says.
As a result, the pioneers of CRISPR-Cas9 ended up in three competing companies: CRISPR Therapeutics, founded by Charpentier and Novak; Editas Medicine, which included Zhang and Church and Doudna until she resigned; and Intellia Therapeutics, founded by Doudna, Barrangou, Sontheimer, Marraffini, and Haurwitz.”
“As a result, other patent applications were deemed to have an earlier priority date, and the court revoked Zhang’s patent. “Feng’s European patent was nullified because of the way he took me off,” Marraffini says.28 By 2020, Doudna and Charpentier had been awarded the major patents also in Britain, China, Japan, Australia, New Zealand, and Mexico.”
“To an unnecessary extent, the prolonged fight was driven by emotions and resentments. Instead, Doudna and Zhang could have followed the example of Jack Kilby of Texas Instruments and Robert Noyce of Intel who, after five years of wrangling, agreed to share the patent rights for the microchip by cross-licensing their intellectual property to each other and splitting the royalties, which helped the microchip business grow exponentially and define a new age of technology. Unlike the CRISPR contestants, Noyce and Kilby obeyed an all-important business maxim: Don’t fight over divvying up the proceeds until you finish robbing the stagecoach.
“The primary scientific goal of the initiative is to find a method to edit the sickle-cell mutation inside of a patient without needing to extract bone marrow. One possibility is to inject into the patient’s blood a gene-editing molecule with an address label that directs it right to the cells in the bone marrow. The difficult part will be to find the right delivery mechanism, such as a virus-like particle, that won’t trigger the patient’s immune system.”
Cancer: In addition to treating blood disorders, such as sickle-cell anemia, CRISPR has been used to fight cancer. China has been the pioneer in this field, and it is two or three years ahead of the United States in devising treatments and getting them into clinical trials. The first person to be treated was a lung-cancer patient in Chengdu, a city of 14 million in the western Chinese province of Sichuan. In October 2016, a team removed from the patient’s blood some of his T-cells, which are the white blood cells that help fight off diseases and confer immunity. The doctors then used CRISPR-Cas9 to disable a gene that produces a protein, known as PD-1, which stops the cell’s immune response. Cancer cells sometimes trigger the PD-1 response, thus protecting themselves from the immune system. By using CRISPR to edit the gene, the patient’s T-cells become more effective in killing the cancer cells. Within a year, China had seven clinical trials using this technique.”
“Doudna assigned the project to two young postdoctoral students who had just joined her lab, Kyle Watters and Gavin Knott. They focused on a method that some viruses use to disable the CRISPR systems of the bacteria they are attacking. In other words, bacteria developed CRISPR systems to ward off viruses, but then the viruses developed a way to shut down those defenses. It was an arms race the Pentagon could understand: missiles being countered by defense systems being countered by anti–defense systems. The newly discovered systems were dubbed “anti-CRISPRs.”
“One of the primary organizers was a soft-spoken but gently commanding MIT biology professor named David Baltimore, who that year would win the Nobel Prize for his work showing that viruses containing RNA, such as coronaviruses, can insert their genetic material into the DNA of a host cell through a process known as “reverse transcription.” In other words, the RNA can be transcribed into DNA, thus modifying the central dogma of biology, which states that genetic information travels in only one direction, from DNA to RNA. ”
“Stock went on to write a pro-editing manifesto, Redesigning Humans: Our Inevitable Genetic Future. “A key aspect of human nature is our ability to manipulate the world,” he argued. “To turn away from germline selection and modification without even exploring them would be to deny our essential nature and perhaps our destiny.”
“Unlike some other scientists at the time,8 the participants had purposely decided against calling for a ban or moratorium, which can over time become hard to lift. Their goal was to keep open the possibility of germline editing if it was safe and medically necessary. That was why, in the title of the piece, they called for “a prudent path forward,” which had become the watchword of many of the scientific conferences ”
“Over the next six years, Jiankui’s company would receive about $5.7 million in funding from government sources. By 2017, its gene sequencer was on the market and the company, of which Jiankui had a one-third stake, was valued at $313 million. “We confirmed Nana’s CCR5 gene was edited successfully with frameshift mutations on both alleles and Lulu’s was heterozygous,” he admitted. In other words, Lulu had different gene versions on her two chromosomes, which meant that her system would still produce some of the CCR5 protein.”
“Somatic editing can be used on certain types of cells, such as those of the blood, muscles, and eyes. But it is expensive, doesn’t work on all cells, and may not be permanent. Germline edits could make a fix in all of the cells of the body. Thus it holds a lot more promise. And a lot more perceived peril.”
“Memory may be the first mental improvement we will be able to engineer, and fortunately it is a less fraught topic than IQ. It has already been improved in mice, such as by enhancing the genes for NMDA receptors in nerve cells. In humans, enhancing those genes could help prevent memory loss in old age, but it could also enhance memory in younger people as well”
“The role of sports, at least since the first Olympics in 776 BC, is to celebrate two things: natural talent combined with disciplined effort. Enhancements would shift that balance, making human effort less of a component of victory. Therefore the achievement becomes a little less praiseworthy and inspiring. There is a whiff of cheating if an athlete succeeds by obtaining some physical advantages through medical engineering.”
“Likewise, suppose I’m an average height. If I were enhanced by eight inches, I’d be way taller than most people, and that could be a benefit to me. But if everyone else got the same eight-inch enhancement I did, then I would get no real benefit. The enhancement wouldn’t make me or society as a whole better off, especially given the legroom of airline seats these days. The only sure beneficiaries would be carpenters who specialized in raising door frames. So enhanced height is a positional good, while enhanced resistance to viruses is an absolute good”
“At this point in our deliberations, we have to face the potential conflict between what is desired by the individual versus what is good for human civilization. A reduction in mood disorders would be seen as a benefit by most of the afflicted individuals, parents, and families. They would desire it. ”
“In the meantime, we will have to deploy the finite allocation of wisdom that nature has dealt us as we ponder how to use the gene-editing techniques that we’ve discovered. Ingenuity without wisdom is dangerous.”
“Our respect for nature and nature’s God should, indeed, instill some humility about meddling with our genes. But should it absolutely forbid it? After all, we Homo sapiens are part of nature, no less so than bacteria and sharks and butterflies. Through its infinite wisdom or blind stumbling, nature has endowed our species with an ability to edit our own genes. If it’s wrong for us to use CRISPR, the reason cannot merely be that it’s unnatural. It’s just as natural as all of the tricks that bacteria and viruses use.”
It didn’t happen. When the real 1984 actually rolled around, Apple introduced an easy-to-use personal computer, the Macintosh, and in the words that Steve Jobs wrote for its ad, “you’ll see why 1984 won’t be like 1984.” That phrase contained a deep truth. Instead of computers becoming an instrument for centralized repression, the combination of the personal computer and the decentralized nature of the internet became a way to devolve more power down to each individual, thus unleashing a gusher of free expression and radically democratized media. Perhaps too much so. The dark side of our new information technology is not that it allows government repression of free speech but just the opposite: it permits anyone to spread, with little risk of being held accountable, any idea, conspiracy, lie, hatred, scam, or scheme, with the result that societies become less civil and governable.”
“Although this sounds like a scene from Gattaca, a real-world version of this baby-designing service—using preimplantation diagnosis—was launched in 2019 by a New Jersey startup, Genomic Prediction. In vitro fertilization clinics can send the company genetic samples of prospective babies. ”
For all of history, humans (and every other species) have been battling rather than accepting nature’s poisoned offerings. Mother Nature has produced massive suffering and distributed it unequally. Thus we devise ways to combat plagues, cure diseases, fix disabilities, and breed better plants, animals, and children.”
“Evolution’s primary guide is reproductive fitness—what traits might cause an organism to reproduce more—which means it permits, and perhaps even encourages, all sorts of plagues, including coronaviruses and cancers, that afflict an organism once its childbearing use is over. This does not mean that, out of respect for nature, we should quit searching for ways to fight against coronaviruses and cancer.”
“I am not sure how to make a sharp distinction in medicine between what is natural and what is unnatural, and I think it’s dangerous to use that dichotomy to block something that could alleviate suffering and disability.”
“His nerve cells would soon start dying and eventually he would be unable to walk, speak, then swallow or eat. He was doomed to die an early and painful death. The note was a wrenching plea for help. “How could you not want to make progress on coming up with ways to prevent such a thing?” Doudna asks. “My heart broke.” If gene editing could prevent this in the future, it would be immoral not to pursue it, she decided.”
“By limiting gene edits to those that are truly “medically necessary,” she says, we can make it less likely that parents could seek to “enhance” their children, which she feels is morally and socially wrong. The line between medical treatment and enhancement can be blurry, she acknowledges, but it is not totally meaningless.”
“Instead of making a cut in the double-stranded DNA, the newly discovered CRISPR system would insert a new chunk of DNA by harnessing transposons, known as “jumping genes,” which are big segments of DNA that can hop from one place to another on chromosomes.”
“The challenge with human gene editing,” she tells me, “is to get your editing tools past the cell’s outer plasma membrane and past its nuclear membrane to get to where the DNA is, and then you also have to get your tools to find the location in the genome.”
“When the American Masters series on PBS decided to do a documentary on Watson in 2018, it set out to produce a balanced, intimate, complex, and nuanced look at both his scientific triumphs and his controversial views.“What matters now are his perfections, not his past imperfections.”12 Perhaps people may say that of Watson someday, but in 2019 he was an outcast.
“In SARS-CoV-2, the RNA is about 29,900 base letters long, compared to more than three billion in human DNA. The viral sequence provides the code for making a mere twenty-nine proteins.4”
“In addition to the previously known Cas9 and Cas12 enzymes that target DNA, Zhang and Koonin found a class of enzymes that target RNA.3 They became known as Cas13.
Cas13 had the same odd trait as Cas12: when it found its target, it went into a cutting frenzy. The Cas13 not only cut its targeted RNA, it then proceeded to cut up any other nearby RNA.”
“Zhang speculated that it was an evolutionary method to have the cell commit suicide if it got too infected by an invading virus, thus preventing the virus from spreading as fast.”
“Zhang decided to start a diagnostics company to commercialize SHERLOCK, just like Chen and Harrington had launched Mammoth. Zhang’s cofounders included the two graduate students who were the lead authors on many of the papers from his lab describing CRISPR-Cas13”.“You know, nature’s got a ton of amazing secrets in it,” he says.”
“It took a while to get Sherlock Biosciences funded and launched because Zhang and his two graduate students did not want profit to be the main goal of the company. They wanted the technologies to be affordable in the developing world. So the company was structured in a way that allowed it to profit on its innovations while still taking a nonprofit approach in places where there was great need.
“But then, at the beginning of 2020, the world suddenly changed. The ability to quickly detect an attacking virus became critical. And the best way to do it faster and cheaper than the conventional PCR tests, which required a lot of mixing steps and temperature cycles, was to deploy RNA-guided enzymes that had been programmed to detect the genetic material of the virus—in other words, adapt the CRISPR system that bacteria had been deploying for millions of years.”
“The CRISPR-based tests developed by Mammoth and Sherlock are cheaper and faster than conventional PCR tests. They also have an advantage over antigen tests, such as the one developed by Abbott Labs that was approved in August of the plague year. The CRISPR-based tests can detect the presence of the RNA of a virus as soon as a person has been infected. But the antigen tests, which detect the presence of proteins that exist on the surface of the virus, are most accurate only after a patient has become highly infectious to others.”
“The development of home testing kits has a potential impact beyond the fight against COVID: bringing biology into the home, the way that personal computers in the 1970s brought digital products and services—and an awareness of microchips and software code—into people’s daily lives and consciousness.”
“Marson and Wilson devised a way to address the DNA vaccine delivery problem using CRISPR-Cas9. They put together a Cas9 protein, a guide RNA, and a nuclear localization signal that helps the complex get into the nucleus. The result was a “shuttle” that could get the DNA vaccine into cells. The DNA then directs the cells to make coronavirus spike proteins and thus stimulate the immune system to fend off the real coronavirus.4 It’s a brilliant idea that could have uses for many treatments in the future, but it has been difficult to make work. By the beginning of 2021, Wilson and Marson were still trying to prove it could be effective.”
“An RNA vaccine has certain advantages over a DNA vaccine. Most notably, the RNA does not need to get into the nucleus of the cell, where DNA is headquartered. The RNA does its work in the outer region of cells, the cytoplasm, which is where proteins are constructed. So an RNA vaccine simply needs to deliver its payload into this outer region.”
“Afeyan instantly authorized him to start work without waiting for full board approval. Lacking Pfizer’s resources, Moderna had to depend on funding from the U.S. government. Anthony Fauci, the government’s infectious disease expert, was supportive. “Go for it,” he declared. “Whatever it costs, don’t worry about it.” It took Moderna only two days to create the desired RNA sequences that would produce the spike protein, and thirty-eight days later it shipped the first box of vials to the NIH to begin early-stage trials. Afeyan keeps a picture of that box on his cell phone.
“The invention of easily reprogrammable RNA vaccines was a lightning-fast triumph of human ingenuity, but it was based on decades of curiosity-driven research into one of the most fundamental aspects of life on planet earth: how genes encoded by DNA are transcribed into snippets of RNA that tell cells what proteins to assemble. Likewise, CRISPR gene-editing technology came from understanding the way that bacteria use snippets of RNA to guide enzymes to chop up dangerous viruses. Great inventions come from understanding basic science. Nature is beautiful that way.”
“The result was a burst of papers in the spring of 2020 for improving CRISPR-based detection technologies for viruses. These included a system known as CARMEN, designed to detect 169 viruses at one time,11 and a process that combined SHERLOCK’s detection capability with an RNA extraction method called HUDSON to create a single-step detection technique he named SHINE.12 In addition to its CRISPR wizardry, the Broad was a master at devising acronyms.”
“One of the transformations wrought by the coronavirus pandemic is that more meetings in the future will be done virtually. It’s a shame. If COVID doesn’t kill us, Zoom will. As Steve Jobs emphasized when he built a headquarters for Pixar and planned a new Apple campus, new ideas are born out of serendipitous encounters. In-person interactions are especially important in the initial brainstorming of new ideas and the forging of personal bonds. As Aristotle taught, we are a social animal, an instinct that cannot fully be satisfied online.”
“The awarding of the 2020 Nobel Prize in Chemistry to Doudna and Charpentier was not a complete surprise, but the recognition came with historic swiftness. Their CRISPR discovery was merely eight years old. The day before, Sir Roger Penrose had shared the Nobel in physics for a discovery about black holes he had made more than fifty years earlier.”
“All of the scientists I write about in this book say that their main motivation is not money, or even glory, but the chance to unlock the mysteries of nature and use those discoveries to make the world a better place. I believe them. And I think that may be one of the most important legacies of the pandemic: reminding scientists of the nobility of their mission.”
“After millions of centuries during which the evolution of organisms happened “naturally,” we humans now have the ability to hack the code of life and engineer our own genetic future. Or, to flummox those who would label gene editing as “unnatural” and “playing God,” let’s put it another way: Nature and nature’s God, in their infinite wisdom, have evolved a species that is able to modify its own genome, and that species happens to be ours.
Like any evolutionary trait, this new ability may help the species thrive and perhaps even produce successor species. Or it may not. It could be one of those evolutionary traits that, as sometimes happens, leads a species down a path that endangers its survival. Evolution is fickle that way.”