When one thinks of the most popular and useful animal models in biomedical research, one thinks of mice and rats, followed by rabbits, dogs, monkeys, and so on. The domestic cat is traditionally a long way down the list. But a recently developed cat genome reference assembly promises to push the cat up the charts.

Despite the rapid escalation of our prowess to sequence, the application of genomic insights in medicine is not routine in healthcare, for good reason. Not only do we need accurate and complete sequences, but we must know what changes in sequences mean in the context of biological function before healthcare can adopt genomic medicine—where treatments are directed at underlying genetic causes in an individual patient or a patient population.

Focusing solely on the framework of the human genome is not in the best interests of precision medicine. Comparing conserved sequences in multiple species and exploring what single nucleotide variations (SNVs) and structural variations (SVs) mean for the biology and disease of other species are instrumental in developing precision therapeutics. High-quality reference genomes, particularly of species where genomes are conserved and follow the same order of genes as in humans, are indispensable in understanding the biological impact of genetic variations.

Cats are an asset in identifying disease-causing genetic variations. Leslie Lyons, PhD, professor at the College of Veterinary Medicine, University of Missouri said, “Whole genome sequencing in any species to find causal DNA variants is only successful about 50% of the time. We’re plagued by variants of unknown significance (VUSs). The variant may be staring us in the face, but we don’t understand that it is a significant variant and causes disease. We’re hoping cats will help in that regard because if the cat has the same variant as in human and does not have a health problem, maybe that will lower the priority of many variants that we see in humans by cross-species comparison.”

New cat genomic resource

The domestic cat is not only a household pet and companion, it also serves as a secondary source or “bioproxy” to corroborate human conditions and evolutionary events. Like humans, cats suffer from cancer and a range of common and rare diseases, including neurological disorders.

Last year, a consortium led by scientists at the University of Missouri developed a new cat genome reference assembly from long-read sequences of the entire genomes of 54 domestic cats, annotating the landscape of feline SNVs and SVs in the context of human genes. The domestic cat belongs to the family Felidae, in which there are some 40 different species with conserved genetic makeup. The availability of a variety of hybrid cats may lead to more accurate genome assemblies. This resource holds the potential to identify novel variations responsible for physiological traits and pathological conditions and facilitate the expansion of genomic medicine in both animal and human healthcare.

“We’ve made a huge leap forward,” said Lyons. “By having the new haploid-based phased genome assembly, the cat is now second to none. A lot of researchers might not have focused on the cat because they didn’t have the genome tools needed to study the cat. Well, now you do!” Lyons says the cat now warrants consideration alongside a mouse or a rat. “You want to use the right biomedical model for the right disease. Long-read sequencing technologies are now giving us the opportunity to do that,” she added.

Wesley Warren, PhD, professor of genomics at the University of Missouri and senior author on the 2020 PLOS Genetics paper that reported the cat reference genome assembly, said, “The study of many species offers insight into traits of interest but the domestic cat, in cohabitating with us and sharing a similar fate for some diseases, represents a unique model to advance genomic medicine objectives that benefit the cat and human.” This species-wide collection of felid genome resources that match the human reference in quality “offers up exciting opportunities to study these diseases in the cat.”

Cathryn Mellersh, PhD, senior research associate at the department of veterinary medicine, University of Cambridge, said, “The community-based 99 Lives Cat Genome Sequencing Consortium has directly facilitated significant molecular discoveries, including the identification of novel variants in genes previously associated with disease, novel gene-disease associations, and even novel diseases, all of which have important implications for our understanding of biological processes and disease in all species, including our own.”

Right model for disease research

Scientists are sometimes reluctant in accepting new models, lamented Lyons. Much of the research has consequently focused on a few ubiquitous models, from E.coli to yeast to Drosophila to multiple lines of inbred mice.

In a forum titled, “Cats–telomere to telomere and nose to tail,” and published in Trends in Genetics, Lyons reinforced the use of cats as valuable model organisms for translational research in inherited diseases and the development of precision medicine therapies for both veterinary and human healthcare.

“Using cats in research is really overlooked since people don’t realize the advantages,” said Lyons. “The dog or mouse genome have rearranged chromosomes that are quite different from humans, but the domestic cat has genes that are about the same size as humans.” It is also very well organized and conserved.

Synteny—a term that describes the physical conservation of blocks of genes in order—is higher between humans and cats than say mice or dogs. Synteny, Lyons believes, is a major facet in characterizing the function of a new gene or intergenic region.

No model is perfect, but some models are better than others for specific questions. “We want to promote more effective models for translational medicine. Now that we have better genomic resources, maybe it is better sometimes to use the cat than mice because the translation to humans would be more efficient and more appropriate,” said Lyons.

Using feline models can help researchers refine, reduce and replace animal models in their studies, Lyons emphasized. As cats are larger models than mice, they generate more attention in terms of regulatory guidelines. “We might be able to use fewer cats more efficiently than we would have used mice because it’s the right model for the right disease,” she said. “Working with primates is expensive, but a cat’s affordability and docile nature make them one of the most feasible animals to work with to understand the human genome.”

“Lyons is correct to draw attention to the fact that the cat research community, although small compared to the research communities associated with other domesticated species, is ‘perfectly formed’ and has certainly packed a punch in terms of developing genome tools for the domestic cat,” said Mellersh.

Illuminating dark matter

Cat genomics can be particularly insightful in understanding the functional significance of non-coding sequences, levels of conservation suggesting biological significance. Cats, like humans, also have genetic diseases associated with this genomic dark matter, which contains regulatory elements and three-dimensional structures that regulate genes. Lyons said the relative similarity of the feline genome’s organization to humans makes it a good model to identify regulatory elements.

“If 50% of causal variants are within the genes, where is the other 50%? It must be in the ‘junk’ DNA, we’re realizing is quite important. We’re hoping cats can help us decipher how the upstream regulatory elements of genes and elements that are far away from genes are causing some of our biology and our health concerns.”

Tools of the trade

The first cat clone, Cc, short for CopyCat, was generated in 2001. Her donor was a typical calico cat with black, orange, and white fur, but Cc didn’t have any orange on her coat, defying genetic principles and indicating her coloration did not get reprogrammed during embryogenesis. This clue has led to a better understanding of X-inactivation and methylation.

Genomic and transgenic technologies are also allowing the use of cats to better understand evolution, domestication, and adaptation. “We have many of the required resources to study different aspects of genetics in cats. We can do whole genome sequencing. We have an exome capture array and high-density DNA array through Affymetrix,” said Lyons.

Lyons foresees the development of imputation techniques where low-depth genome sequencing could estimate features of the rest of the cat’s genome. With adequate funding, she hopes more sophisticated techniques such as long-read RNA sequencing, single nuclei technologies, and an atlas of cat gene expression, could be used to further analyze the cat genome.

“Cats have less focus from NIH funding but the community is cohesive, efficient, and collaborative,” Lyons said. “We’ll bend over backward for whatever you need for cat genomics. We hope others will join us.”

Lyons and her team minimized the number of cats while maximizing the potential models they could provide. “We have cats that have inherited blindness and polycystic kidney disease (PKD). Also, we cryopreserve. For our cat models for inherited blindness, we’ve saved embryos and semen, so that we don’t have to have cats living in cages anywhere, but we can resurrect models when needed.”

In a 2020 Cell Report study, Lyons’ group resurrected a cryopreserved cat model for Chediak-Higashi syndrome and defined the causative mutation—a large gene duplication.

Toward tailored healthcare

Cats, if adopted as a research model, can play a major role in precision medicine. Sequencing cats suffering from genetic diseases can help identify genetic causes and develop more effective treatments that would be potentially applicable in humans, given the genomic similarity in structure and sequence.

“We can provide a more tailored healthcare program for our pets, and more funding would put all the different pieces into place. All mammals tend to have very similar genes, so if we find out what causes a disease in cats, then whatever therapies can be used to help cats can potentially be translated to help humans suffering with the same disease. Likewise, human research can potentially be translated to help animals as well,” said Lyons.

Lyons’ group is currently working on feline models of PKD, developing methods to prevent the growth of cysts in cat models of PKD using a ketogenic diet. PKD treatments for cats could apply to humans, said Lyons.

Interestingly, PKD is more common than several well-known genetic disorders, such as sickle-cell disease or cystic fibrosis. It usually affects patients later in life; they experience renal failure in their 50s and 60s, and a shortened lifespan. “A ketogenic diet might be helpful for reducing the size of the cyst in the kidney. Then it won’t destroy the normal kidney tissue and you won’t go into renal failure. The idea is to keep those cysts as small as possible, maybe shrink them,” Lyons explained.

The average lifespan of mice is 2–3 years making them an unsuitable model to test long-term treatments at later stages. Cats with longer lifespans should be more suitable.

“Secondly, the kidney in the mouse is so small, it is hard to evaluate cyst volume and ascertain whether any of your treatments are actually reducing cyst volume whereas the cat kidney is big enough. You can see those changes. We can do MRIs and CTs in a regular vet clinic,” Lyons said.

Mellersh added, “The organization of the cat’s genome is strikingly well-conserved compared to our own, so as long- and longer-read sequencing technologies are employed to fill in gaps in existing genome sequences our feline friends will likely play an important role in deciphering the function of regions of the genome that are currently poorly understood—whether or not Schrodinger’s cat ever helped anyone understand quantum physics is probably debatable but its contribution to genomics may well be more significant.”