The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells

Warheit-Niemi, H. I.; Huang, J.; Cook, K. C. S.; Alysandratos, K. A.; Fernandes, S.; Basak, P.; Zhao, B.; Vilker, E.; Villacorta-Martin, C.; Elitz, A.; Bawa, P. S.; Toth, A.; Herriges, M.; Kotton, D. N.; Zacharias, W. J.

doi:10.64898/2026.03.03.708777

bioRxiv · 10.64898/2026.03.03.708777

The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells

Warheit-Niemi, H. I.·Huang, J.·Cook, K. C. S.·Alysandratos, K. A.·Fernandes, S.·Basak, P.·Zhao, B.·Vilker, E.·Villacorta-Martin, C.·Elitz, A.·Bawa, P. S.·Toth, A.·Herriges, M.·Kotton, D. N.·Zacharias, W. J.

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Abstract

Maintenance of the gas exchange surface throughout life and regeneration of the lung after injury requires tight regulation of epithelial cell fate and function. Alveolar epithelial type 2 (AT2) cells serve as the progenitors of the distal epithelium, differentiating into alveolar epithelial type 1 (AT1) cells or proliferating to maintain the quorum of AT2 cells. Here we describe the role of the chromatin regulator polycomb repressive complex 2 (PRC2) in the maintenance of AT2 cell fate in the adult alveolus. Cross-species single-cell transcriptomic analyses identified PRC2 activation in proliferative AT2 populations. PRC2 loss of function in human iPSC-derived AT2 (iAT2) cells and primary murine AT2 cells in vitro resulted in loss of AT2 cell state and emergence of programs reminiscent of alveolar-basal intermediate (ABI) cell states, while overexpression of the PRC2 enzymatic component EZH2 in human iAT2 cells augmented the AT2 cell program. Genetic loss of PRC2 function in the AT2 lineage in adult mice in vivo led to emphysematous remodeling of the lung and induced a time-dependent series of transitions of AT2 cells through an alveolar-basal intermediate (ABI) state into Krt5+ basal-like cells. Comparison of murine ABI cells to human disease-associated ABI cells demonstrates de-repression of canonical PRC2 targets during transition to ABI and basal-like states in human fibrosis, implicating PRC2 is a conserved regulator of AT2 cell fate. Together, these findings define PRC2 complex function during AT2 cell self-renewal as a critical guardrail for maintaining epithelial cell fate in the adult lung.

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Warheit-Niemi, H. I., Huang, J., Cook, K. C. S., Alysandratos, K. A., Fernandes, S., Basak, P., Zhao, B., Vilker, E., Villacorta-Martin, C., Elitz, A., Bawa, P. S., Toth, A., Herriges, M., Kotton, D. N., Zacharias, W. J.. 2026-03-05. The chromatin remodeling complex PRC2 safeguards cell fate in alveolar epithelial type 2 cells. https://doi.org/10.64898/2026.03.03.708777

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