Virus World

Instead of addressing genetic mutations, the Crispr machinery prompted cells to lose entire chromosomes. A powerful gene-editing tool called Crispr-Cas9, which this month nabbed the Nobel Prize in Chemistry for two female scientists, can cause serious side effects in the cells of human embryos, prompting them to discard large chunks of their genetic material, a new study has found. Administered to cells to repair a mutation that can cause hereditary blindness, the Crispr-Cas9 technology appeared to wreak genetic havoc in about half the specimens that the researchers examined, according to a study published in the journal Cell on Thursday. The consequences of these errors can be quite serious in some cases, said Dieter Egli, a geneticist at Columbia University and an author of the study. Some cells were so flummoxed by the alterations that they simply gave up on trying to fix them, jettisoning entire chromosomes, the units into which human DNA is packaged, Dr. Egli said. “We’re often used to hearing about papers where Crispr is very successful,” said Nicole Kaplan, a geneticist at New York University who was not involved in the study. “But with the amount of power we hold” with this tool, Dr. Kaplan said, it is crucial “to understand consequences we didn’t intend.”

Crispr-Cas9, a scissorslike chemical tool that can precisely cut and customize stretches of genetic material, such as human DNA, stoked international controversy in 2018 when He Jiankui, a Chinese scientist, used the technology to yield the world’s first gene-edited infants. The experiment was widely condemned as irresponsible and dangerous — in large part because many of the ways in which Crispr-Cas9 can affect cells remain poorly understood. Dr. He was found guilty of conducting illegal medical practices in China and sentenced to three years in prison. The new paper’s findings further underscore that “it’s really too soon to be applying Crispr to reproductive genetics,” said Nita Farahany, a bioethicist at Duke University who was not involved in the study.  Crispr-Cas9 treatments have already been given directly to people to treat conditions like blindness — a potential cure that affects that patient, and that patient only. But modifications made to sperm, eggs and embryos can be passed to future generations, raising the stakes for any mistakes made along the way Although scientists have been tinkering with genomes for decades, Crispr-Cas9 can accomplish a precise type of genetic surgery that other tools cannot. Scientists can use Crispr-Cas9 to home in on a specific region of the genome and snip it in two. Sensing trouble, the cell rushes to heal its genetic wound, sometimes using a similar-looking stretch of nearby, intact DNA as a template as it stitches the pieces back together. This gives researchers an opportunity to splice in a tailor-made template of their own, in the hopes that the cell will incorporate the intended change....

Original Study Published in Cell (Oct. 29):

https://doi.org/10.1016/j.cell.2020.10.025

Emmanuelle Charpentier and Jennifer A. Doudna developed the Crispr tool, which can change the DNA of animals, plants and microorganisms with high precision.  The Nobel Prize in Chemistry was jointly awarded on Wednesday to Emmanuelle Charpentier and Jennifer A. Doudna for their 2012 work on Crispr-Cas9, a method to edit DNA. The announcement marks the first time the award has gone to two women. “This year’s prize is about rewriting the code of life,” Goran K. Hansson, the secretary-general of the Royal Swedish Academy of Sciences, said as he announced the names of the laureates. Dr. Charpentier and Dr. Doudna, only the sixth and seventh women in history to win a chemistry prize, did much of the pioneering work to turn molecules made by microbes into a tool for customizing genes — whether in microbes, plants, animals or even humans.“I’m over the moon, I’m in shock,” Dr. Doudna, a professor at the University of California, Berkeley, said at a news conference on Wednesday. It has been only eight years since Dr. Doudna and Dr. Charpentier — now the director of the Max Planck Unit for the Science of Pathogens in Berlin — co-authored their first paper demonstrating the power of Crispr-Cas9. Since then, the technology has exploded. Doctors are testing it as a cure for genetic disorders such as sickle cell disease and hereditary blindness. Plant scientists are using it to create new crops. Some researchers are even trying to use Crispr to bring species back from extinction.

The COVID-19 pandemic has claimed the lives of more than one million people worldwide. The causative agent, SARS-CoV-2, is a member of the Coronaviridae family, which are viruses that cause respiratory infections of varying severity. The cellular host factors and pathways co-opted by SARS-CoV-2 and other coronaviruses in the execution of their life cycles remain ill-defined. To develop an extensive compendium of host factors required for infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E), we performed parallel genome-scale CRISPR knockout screens.

These screens uncovered multiple host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, SREBP signaling, and glycosylphosphatidylinositol biosynthesis, as well as an unexpected requirement for several poorly characterized proteins. We identified an absolute requirement for the VTT-domain containing protein TMEM41B for infection by SARS-CoV-2 and all other coronaviruses. This human Coronaviridae host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus spillover events.

Preprint available in bioRxiv (October 8, 2020):

https://doi.org/10.1101/2020.10.07.326462

How anti-CRISPR proteins and other molecules could bolster biosecurity and improve medical treatments. It started out as “sort of a stupid thing to do”, recalls Joe Bondy-Denomy, a microbiologist at the University of California, San Francisco. As a graduate student in the early 2010s, he tried to infect bacteria with viruses that, on paper, shouldn’t have stood a chance. He knew that these viruses, or phages, were susceptible to CRISPR–Cas, the bacterial defence system that scientists have harnessed as a powerful tool for gene editing. And in most cases, he was right: the CRISPR machinery chopped the incoming phages into bits. But in a few instances, against the odds, the intruders survived. Bondy-Denomy thought he had messed up. “Then a light bulb went off,” he says. Maybe something inside the bacterial genome was disarming its defences. And maybe that self-sabotaging bit of DNA was coming from previous viral invaders.

A quick comparison of DNA sequences proved Bondy-Denomy’s intuition correct. Phage genes nestled inside the bacterial genome were completely shutting down the CRISPR–Cas system, making the bacteria vulnerable1. “Joe got the result that changed everything,” says Alan Davidson, a phage biologist at the University of Toronto in Canada, who was Bondy-Denomy’s PhD adviser at the time. “He found something amazing that we never expected.” Bondy-Denomy — together with Davidson, microbiologist Karen Maxwell and fellow graduate student April Pawluk — had stumbled onto tools now known as anti-CRISPRs. These proteins serve as the rocks to CRISPR’s molecular scissors. And soon, they were popping up everywhere: more than 50 anti-CRISPR proteins have now been characterized, each with its own means of blocking the cut-and-paste action of CRISPR systems.

The expansive roster opens up many questions about the archaic arms race between bacteria and the phages that prey on them. But it also provides scientists with a toolkit for keeping gene editing in check. Some are using these proteins as switches to more finely control the activity of CRISPR systems in gene-editing applications for biotechnology or medicine. Others are testing whether they, or other CRISPR-stopping molecules, could serve as biosecurity counter-measures of last resort, capable of reining in some genome-edited bioweapon or out-of-control gene drive. “For any reason you can think of to turn off CRISPR systems, anti-CRISPRs come into play,” says Kevin Forsberg, a microbial genomicist at the Fred Hutchinson Cancer Research Center in Seattle, Washington....

Published January 15, 2020 in Nature:

 https://doi.org/10.1038/d41586-020-00053-0