HomeScienceGeneticsScientists reveal the functional landscape of essential genes | MIT news

Scientists reveal the functional landscape of essential genes | MIT news

A team of scientists from the Whitehead Institute for Biomedical Research and the Broad Institute at MIT and Harvard has systematically evaluated the functions of more than 5,000 essential human genes using a new pooled image-based screening method. Their analysis uses CRISPR-Cas9 to knock down gene activity and represents a first-of-its-kind tool for understanding and visualizing gene function in a wide range of cellular processes with both spatial and temporal resolution. The team’s findings span more than 31 million individual cells and include quantitative data on hundreds of different parameters that enable predictions about how genes work and interact. The new study appears in the November 7 online issue of the magazine Cell.

“All my career I’ve wanted to see what happens in cells when the function of an essential gene is eliminated,” said MIT professor Iain Cheeseman, senior author of the study and a member of the Whitehead Institute. “Now we can do that, not just for one gene, but for every single gene that matters to a human cell dividing in a shell, and it’s tremendously powerful. The resource we’ve created will not only support our own laboratory, but laboratories around the world.”

Systematically disrupting the function of essential genes is not a new concept, but conventional methods are limited by several factors, including cost, feasibility, and the ability to completely eliminate essential gene activity. Cheeseman, the Herman and Margaret Sokol Professor of Biology at MIT, and his colleagues worked with MIT Associate Professor Paul Blainey and his team at the Broad Institute to define and realize this ambitious shared goal. The Broad Institute researchers have pioneered a new genetic screening technology that combines two approaches: large-scale, pooled genetic screens using CRISPR-Cas9 and cell imaging to reveal both quantitative and qualitative differences. In addition, the method is inexpensive compared to other methods and is performed with commercially available equipment.

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“We are proud to show the incredible resolution of cellular processes accessible with low-cost imaging assays in collaboration with Iain’s lab at the Whitehead Institute,” said Blainey, a senior author of the study, an associate professor in the Department of Biological Engineering. at MIT, member of the Koch Institute for Integrative Cancer Research at MIT, and core member of the Broad Institute. “And it is clear that this is just the tip of the iceberg for our approach. The ability to correlate genetic perturbations based on even more detailed phenotypic readouts is necessary, and now accessible, for many future research areas.”

Cheeseman adds: “The ability to do pooled cell biological screening fundamentally changes the game. You have two cells sitting next to each other and so your ability to make statistically significant calculations about whether they are the same or not is that much greater , and you can distinguish very small differences.’

Cheeseman, Blainey, lead authors Luke Funk and Kuan-Chung Su and their colleagues evaluated the functions of 5,072 essential genes in a human cell line. They analyzed four markers about the cells in their screen – DNA; the response to DNA damage, a major cellular pathway that detects and responds to damaged DNA; and two major structural proteins, actin and tubulin. In addition to their primary screen, the scientists also performed a smaller follow-up screen, targeting about 200 genes involved in cell division (also called ‘mitosis’). The genes were identified in their initial screening as having a clear role in mitosis, but had not previously been associated with the process. This data, which is made available via an accompanying websiteprovide a resource for other scientists to investigate the functions of genes they are interested in.

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“There is an enormous amount of information that we have gathered about these cells. For example, for the cell nucleus, it’s not just about how brightly colored it is, but how big is it, how round is it, are the edges smooth or bumpy?” says Kaasman. “A computer can really extract a wealth of spatial information.”

Flowing from this rich, multidimensional data, the scientists’ work provides a kind of cell biology “fingerprint” for each gene analyzed in the screen. Using advanced computational clustering strategies, the researchers can compare these fingerprints with each other and construct possible regulatory relationships between genes. Because the team’s data confirm multiple relationships that are already known, they can be used to confidently make predictions about genes whose functions and/or interactions with other genes are unknown.

There are a host of remarkable discoveries emerging from the researchers’ screening data, including a surprising one involving ion channels. two genes, AQP7 and ATP1A1, were identified for their role in mitosis, specifically the proper segregation of chromosomes. These genes code for membrane-bound proteins that transport ions in and out of the cell. “In all the years I’ve worked on mitosis, I never thought there were ion channels involved,” says Cheeseman.

He adds: “We are just at the beginning of what can be excavated from our data. We hope that many others will not only benefit from – but also build on – this resource.”

This work was supported by grants from the US National Institutes of Health and by the Gordon and Betty Moore Foundation, a National Defense Science and Engineering Graduate Fellowship, and a Natural Sciences and Engineering Research Council Fellowship.

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