About a quarter century ago, a trio of scientists developed a game-changing technology that enabled researchers to genetically engineer mouse strains with a particular gene missing. Finally, researchers had a tool to observe—in a backhanded way—how mice behaved when a critical piece of their DNA was missing.

And the era of the knockout mouse was born.

Laboratories began generating thousands of these so-called knockout strains—and many of them are now used to study major killers like cancer, central nervous system diseases, metabolic disorders and heart disease. But as is often the case in science, the animals were made on different strains and evaluated under different conditions. Moreover, there weren’t central places to validate KO strains in a standardized manner.

So in 2002, when researchers reached another milestone and successfully sequenced the entire mouse genome—which is quite similar to ours—it represented a golden opportunity to generate targeted knockout mutations for all 20,000 mouse genes and define their function. This led to the creation in 2006 of the International Knockout Mouse Consortium (IKMC), which has since given way to the International Mouse Phenotyping Consortium. The IKMC and IMPC now oversee a dizzying array of grantees from the commercial, public and academic sectors. The subgroups include the Knockout Mouse Project (KOMP), the European Conditional Mouse Mutagenesis Program (EUCOMM), the North American Conditional Mouse Mutagenesis Project (NorComm), and the Texas A&M Institute for Genomic Medicine (TIGM), which have been generating the embryonic stem (ES) cells and then converting a few to mice to demonstrate proof-of-concept. The IMPC is currently making all the rest of the mice from ES cells, and dong the phenotyping.

Yes, the work has been long and tedious and unwieldy at times, but the good news is that the labs now knee-deep into phenotyping KO strains are beginning to whet our appetites by reporting some of their preliminary results. Some of these findings were a hot topic at the recent IMPC meeting in Rome and the Sanger Institute Mouse Genetics Project—which has worked with both KOMP and EUCOMM—discussed some of their work in a recent article in Cell.  

Mice Behaving Strangely
Consider the work of KOMP—which was launched in 2006 with a US$56 million award from the US National Institutes of Health—to jointly produce 17,000 mutant ES cell lines with EUCOMM and make them available from public repositories. KOMP is now in its second phase—or KOMP2—to offer a much broader phenotypic analysis of 2,500 mouse genes by the end of 2016. Among other things, the work is expected to make the process of comparing data easier, and to hopefully identify novel genes with uniquely valuable functions. The work is being done by three consortia groups headed by the University of California-Davis, The Jackson Laboratories in Maine and Baylor College of Medicine in Houston, Texas respectively.

Phenotypic analysis from the University of California-Davis—also home to the KOMP Repository of more than 8,500 unique mutant alleles targeted in ES cells—offers a snapshot of what scientists are starting to learn about the genetic behaviors in adult and embryonic lethal KO mice. In one of the earliest and most interesting findings, scientists at Davis identified a phenotype in which the KO mouse strain has almost no exocrine pancreas! In this case, the gene’s function was previously not known, and it’s unclear at this point how the mouse strain survived. Researchers were learned that the phenotype of another gene was connected with hearing—the KO mouse was slightly deaf—while another was associated with blindness. These genes also had little known function, so the findings were a complete surprise.

The animals were evaluated from 6 weeks to 16 weeks of age. The phenotyping assays include such things as behavioral tests, weekly body weights, EKGs, metabolic tests, nutrition and infectious disease challenges and histopathology and necropsies. The tests span multiple systems that include: immune, musculoskeletal, metabolic, sensory, cardiovascular and pulmonary.

The UC-Davis-led consortia—which also includes Toronto Centre for Phenogenomics (TCP). and Children’s Hospital Oakland Research Institute (CHORI) and Charles River Laboratories, is also conducting phenotypic analysis on 837 strains—they have completed about 200—and the entire KOMP2 is expected to do 2500 strains by 2016. It is unclear if there will be additional funds for the work to continue after the KOMP2’s cooperative agreement is up, but the NIH would like the group to complete the remaining library of around 6000 strains. As part of the DTCC, Charles River receives the lines for in vitro fertilization (IVF) to expand the line, standardize the health status of all lines and assess each line for viability.

In the meantime, the IMPC and its players press onward to try and make better sense of the mouse genome, and create, biologically speaking, the mother of all motherboards with a dashboard that everyone can access.

Whether this effort brings the field to the doorstep of new cures remains to be seen, however. That is certainly the hope.