Bats are one of the most fascinating groups of mammals in the animal kingdom. Along with remarkable traits such as echolocation and an extremely long lifespan, bats are also tolerant of myriad viral infections, suggesting a long history of coevolution with viruses.

Previous studies have suggested that, upon viral infection, bats rapidly modulate their innate immune response to develop a state of tolerance. To further investigate the host–virus relationship in bats, researchers led by Thomas Zwaka at the Icahn School of Medicine at Mount Sinai have generated the first bat induced pluripotent stem (iPS) cells.

In a study reported in Cell, the team initially discovered that the protocol established for reprogramming human or mouse cells into iPS cells using the Yamanaka factors failed for bat embryonic fibroblasts, leading instead to the formation of non-proliferating primitive stem cell colonies. Following optimization, the team identified a combination of the Yamanaka factors and additional growth factors that led to successfully reprogrammed bat iPS cells. These cells expressed the pluripotency marker Oct4, as do other mammalian iPS cells, and had a proliferation capacity comparable to that of human iPS cells. Interestingly, the bat iPS cell nucleus has one or two large nucleoli filled with tiny vesicles, a feature not observed in other mammalian cells.

Transcriptomic and epigenetic analyses confirmed the pluripotent state of the bat iPS cells, but the researchers noticed that these cells simultaneously expressed key markers for both naive and primed iPS cells, suggesting a distinct stage of pluripotency. The team then functionally confirmed pluripotency by differentiating the iPS cell into the three germ layers and by demonstrating the formation of embryoid bodies, teratomas and blastoids.

Next, the researchers collected transcriptomic profiles from iPS cells from five divergent mammalian species — mouse, human, marmoset, dog and pig — and compared them to the bat transcriptome. Principal component analysis revealed that the bat iPS cells were the furthest away from all the other species, indicating a transcriptomic state unique to bats. This bat-specific gene signature was highly enriched for pathways associated with viral infection, implying that antiviral transcriptional pathways were probably triggered by the presence of endogenous viral sequences. Of note, the team discovered that the most enriched pathway in the bat transcriptome was related to coronavirus disease.

Indeed, metagenomic analyses confirmed the presence of a vast diversity of integrated and expressed viral elements in bat iPS cells, including those belonging to endogenous retroviruses and coronaviruses as well as sequences with homologies to viruses like monkeypox, squirrelpox and others.

This method to efficiently and reproducibly generate bat iPS cells is a starting point for studies into mechanisms of viral tolerance and reservoir establishment, for insights into bat biology and for efforts towards pandemic preparedness.

Original reference: Cell 186, 957–974.e28 (2023).