MIT scientists reveal the functional pattern of basic genes

Using a novel, ensemble, image-based screening method, a team of scientists at the Whitehead Institute for Biomedical Research, the Massachusetts Institute of Technology, and Harvard University's Broad Institute systematically assessed the function of
more than 5,000 basic human genes.
Their analysis, which utilizes CRISPR-Cas9 knockout gene activity, forms an unprecedented resource for understanding and visualizing gene function across a wide range of cellular processes, with spatial and temporal resolution
.
The team's findings cover more than 31 million individual cells and include quantitative data on hundreds of different parameters, making it possible to
predict how genes work and work together.
The new study was published Nov.
7 online in the journal Cell
.

"Throughout my career, I've wondered what happens to 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 this, not just for one gene, but for every gene involved in the division of human cells in a dish, which is very powerful
.
" The resources we create will benefit not only our own labs, but labs around the world
.
”

Systematically disrupting the function of essential genes is not a new concept, but traditional approaches are limited by a variety of factors, including cost, feasibility, and the ability to completely eliminate the
activity of essential genes.
Cheeseman, the Herman and Margaret Sokol Professor of Biology at MIT, and his colleagues, along with MIT associate professor Paul Blainey and his team at the Broad Institute, identified and achieved this ambitious joint goal
.
Researchers at the Broad Institute have pioneered a new genetic screening technique that combines two approaches — large-scale, ensemble genetic screening using CRISPR-Cas9 and cell imaging — to reveal quantitative and qualitative differences
.
In addition, this method is inexpensive compared to other methods and is practiced using commercial equipment
.

Blainey, senior author of the study, associate professor in MIT's Department of Bioengineering, member of MIT's Koch Institute for Integrative Cancer Research and core member of the Broad Institute, said: "We are proud to demonstrate the incredible cellular process resolution
achievable with low-cost imaging assays in collaboration with the Whitehead Institute's Iain Laboratory.
Obviously, this is just the tip
of the iceberg of our approach.
The ability to link genetic perturbations based on more detailed phenotypic readings is urgently needed and can now be advanced
in many areas of research.
”

Cheeseman added: "The ability to combine cell bioscreening is a fundamental game-changer
.
You have two adjacent cells, so your ability to make statistically significant calculations on whether they are the same is much higher, and you can discern very small differences
.
”

Cheeseman, Blainey, lead authors Luke Funk and Kuan-Chung Su and their colleagues evaluated the function of
5,072 basic genes in human cell lines.
They analyzed four markers of the cells screened: DNA; DNA damage response, a key cellular pathway that detects and responds to damaged DNA; There are also two important structural proteins, actin and tubulin
.
In addition to the initial screening, the scientists conducted a small-scale follow-up screening
of about 200 genes involved in cell division, also known as "mitosis.
" These genes were identified in the initial screening to play a definite role in mitosis, but they had not previously been found to be associated with
the mitotic process.
The data is available through a companion website that provides resources for other scientists to study the function of genes they are interested in
.

"We collected a lot of information
from these cells.
For example, for the nucleus, it is necessary not only to see how bright its staining is, but also to see how big it is, how round it is, and whether the edges are smooth or bumpy? Computers can really extract a lot of spatial information
.
”

From this rich multidimensional data, the scientists' work provides a cell-biological "fingerprint"
for each gene analyzed.
Using sophisticated computational clustering strategies, researchers can compare these fingerprints to each other and construct potential regulatory relationships
between genes.
Because the team's data confirm multiple known relationships, it can be used to make confident predictions
about genes whose function and/or interaction with other genes are unknown.

The researchers' screening data yielded a number of notable findings, including a startling discovery
related to ion channels.
The two genes, AQP7 and ATP1A1, play a role in mitosis, especially in
the proper separation of chromosomes.
These genes encode membrane-binding proteins that transport ions in and out of cells
.
"In all the years I've been studying mitosis, I never thought ion channels would be involved," Cheeseman said
.
"We're really just scratching the surface
of what can be mined out of our data.
We hope that many others will not only benefit from this resource, but build on it
.
”