A milestone on the path to a better understanding of mammalian gene function, health and disease

An abstract picture representing the Knockout Mouse Phenotyping Program (KOMP2)

As key players in KOMP2, JAX researchers have now generated and characterized more than 2,000 knockout mice, gaining important insights into mammalian genetics and potential health impacts.

The Knockout Mouse Phenotyping Program (KOMP2) is a monumental international initiative, involving a consortium of 21 research institutions working to characterize the function of nearly all protein-coding genes in the mouse. The Jackson Laboratory (JAX) has long played a key role in the program, and it has now reached an impressive milestone: 2,000 knockout mouse lines generated and characterized, well over a fifth of the total generated worldwide thus far. The culmination of the effort, scheduled to wind down in 2027, will serve as a foundational resource for the entire research community that sheds light on genes with no current known function and provides additional insight for others.

These mice have already proven to be exceedingly valuable for the study of rare, single-gene diseases in humans. In fact, at this time The International Mouse Phenotyping Consortium (IMPC), the umbrella organization for this global research effort, reports that 889 known rare disease-gene associations have been made with a specific mouse strain that displays at least one disease symptom, providing a key resource for research and discovery for the rare disease community. And the number of such strains continues to grow.

“The program has provided a wealth of resources,” says Professor Robert Braun, Ph.D. who co-leads the KOMP2 Center with Associate Professor Stephen Murray, Ph.D., and Director, Center for Biometric Analysis Jacqueline White, Ph.D. “There are mice that model rare diseases, mice that are infertile, mice with developmental deficits, and many more. The new strains and data are all available to the research community to accelerate research and provide critical insights into mammalian and human genetics.”

The unknowns of gene function

Humans have approximately 20,000 genes that code for proteins in our genomes. While some are widely studied because of their direct impact on health and disease (BRCA1/2 (cancer) and CFTR (cystic fibrosis) for example), the function of nearly a third of our genes remains unclear or, in many cases, completely unknown. KOMP2 is working to change that and identify the precise impact of specific genes on human health—with the help of mice.

Given that engineering human genomes is out of the question, researchers have turned to mice to serve as our proxies. Mice and humans share a vast majority of those 20,000 genes, with about 19,000 sharing homology, meaning they didn’t substantively change even as the two species evolved from a common ancestor in drastically different ways. Therefore, knocking out such genes in mice and closely measuring the results provides a vital window into human genetics and gene function as well.

Precisely disabling each gene one at a time and carefully phenotyping (thoroughly characterizing) the thousands of resulting mouse strains is a massive task and beyond the scope of any one institution. Among the 21 participating research institutions, there are three main sites in the United States supported by the National Institutes of Health: The Jackson Laboratory (JAX), Baylor College of Medicine, and the University of California Davis. It’s no surprise that JAX, a world leader in mouse genetics, has helped lead the effort throughout.

At JAX, scientists use a CRISPR/Cas9 genomic editing protocol to precisely knock out each gene to create the new mouse strains. Once a viable knockout strain is established, each one is screened using a high throughput phenotyping pipeline based on JAX’s own experience in the field as well as IMPC recommendations. More than 200 traits spanning multiple organs systems are accurately measured between two and five months of age, including weekly body weight, body composition, glucose tolerance, grip strength, vision and hearing acuity, blood biochemistry, and many more. Certain strains are subsequently re-screened at between 15-18 months of age to identify any abnormalities that may arise later in life.

Living (or not) without a gene

Each gene codes for a protein that carries out a biological function or functions, but knocking out different genes has very different consequences. Knock out a gene that is crucial for development, and no mice lacking both copies of the gene will survive. On the other hand, knocking out genes with redundant pathways and/or no detectable role can yield mice that appear to be exactly the same as their wild-type (normal) counterparts, even after exhaustive characterization. And there is a vast spectrum in between, where the mice survive but have measurable changes to physiology and function.

In 2016, Murray led a group that studied essential genes: genes where knockouts are partially or completely incompatible with life. The team found that these genes are highly enriched for human disease genes. The results of the study suggest that IMPC data on gene essentiality will likely point to new disease-causing genes, helping human geneticists with patient diagnoses for rare and unsolved disease cases. More recently, a group at JAX used KOMP2-generated strains to discover genes that contribute to drug-intake and related behaviors in mice. 

An end and a beginning in sight

While 2,000 new strains is an impressive milestone, much more remains to be done. When the project reaches its planned completion, the collective effort of KOMP2, IMPC, and the scientific community will have completed a draft of mammalian genome function, targeting more than 90% of the genes. As such, the end of the official KOMP2 project will also represent a beginning—a starting point for genetics inquiries of all kinds as we delve into our complex biology for further discovery and to improve human health.