First comprehensive map of genes in human cells ties every gene to its function

MIT Professor Jonathan Weissman and his colleagues released the first comprehensive functional map of genes expressed in human cells, which ties each gene to its job in the cell. This release of data was made possible through the Perturb-seq method, a single-cell sequencing approach that allows researchers to follow the impact of turning on or off genes with unprecedented depth. 

According to a recent release from MIT, this project was a massive undertaking that involved the sequencing of more than 2.5 million cells. The Human Genome Project, which sought to sequence every piece of human DNA, was completed in 2003, but this latest project goes beyond simply sequencing the genome to provide a comprehensive functional map. The data from the project, published in Cell on June 9, 2022, is now available for use by other researchers around the world. 

"It’s a big resource in the way the human genome is a big resource, in that you can go in and do discovery-based research,” Weissman said in the release. “Rather than defining ahead of time what biology you're going to be looking at, you have this map of the genotype-phenotype relationships and you can go in and screen the database without having to do any experiments.”

The Perturb-seq approach reportedly makes it possible to follow the impact of turning on or off genes with unprecedented depth. While this method was first published in 2016 by Weissman and fellow MIT Professor Aviv Regev, it could only be used on small sets of genes and at great expense. However, the team was able to scale up the method to the entire genome with the help of MD-PhD student Joseph Replogle and others.

According to the release, the Perturb-seq method uses CRISPR-Cas9 genome editing to introduce genetic changes into cells and then uses single-cell RNA sequencing to capture information about the RNAs that are expressed resulting from a given genetic change. With this, researchers used human blood cancer cell lines as well as noncancerous cells derived from the retina, performing Perturb-seq across more than 2.5 million cells. They used the data to build a comprehensive map tying genotypes to phenotypes.

This method can help decode the many cellular effects of genetic changes and data can be used to explore a wide range of biological questions, including the cellular effects of genes with unknown functions, the response of mitochondria to stress and the screening of genes that cause chromosomes to be lost or gained. The data is expected to enable all sorts of analyses that haven't even been thought up yet, according to the co-senior author of the paper Tom Norman.

This comes as the first application of the data was to investigate genes with unknown functions. The screen also read out phenotypes of many known genes, allowing the researchers to compare unknown genes to known ones and look for similar transcriptional outcomes, which could suggest the gene products worked together as part of a larger complex. One gene, in particular, called C7orf26, stood out. 

At that time, researchers noticed that genes whose removal led to a similar phenotype were part of a protein complex called Integrator that played a role in creating small nuclear RNAs. The researchers were able to confirm that C7orf26 made up a 15th component of the Integrator complex and discovered that the 15 subunits worked together in smaller modules to perform specific functions within the Integrator complex. 

Another advantage of Perturb-seq is that researchers can use the data to look at more complex phenotypes that become muddied when they are studied together with data from other cells. This approach allows the researchers to take all the cells where 'gene X' is knocked down and look at how they changed, without having to average them together with data from other cells.

 The release of this comprehensive functional map of genes expressed in human cells represents a significant breakthrough in our understanding of genetics and will enable researchers to study a wide range of biological questions in unprecedented detail. The researchers responsible for the project hope that their data will be used by other scientists to further our understanding of human biology and disease.