Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma

Ballester, M.; Kurilla, A.; Dai, Y.; Maurer, C.; Espinet, E.; Hoj, K.; Marisch Delgado, A.; Seymour, P. A.; Omar, S.; Rift, C. V.; Hasselby, J.; Klaussen, P.; Vilmann, P.; Sandelin, A.; Arnes Perez, L.

doi:10.1101/2025.06.06.658264

bioRxiv · 10.1101/2025.06.06.658264

Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma

Ballester, M.·Kurilla, A.·Dai, Y.·Maurer, C.·Espinet, E.·Hoj, K.·Marisch Delgado, A.·Seymour, P. A.·Omar, S.·Rift, C. V.·Hasselby, J.·Klaussen, P.·Vilmann, P.·Sandelin, A.·Arnes Perez, L.

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Abstract

Cellular plasticity and transitional cellular states are crucial for tissue regeneration across multiple organs. In the pancreas, oncogenic Kras hijacks this program, acting on tissue-specific enhancers to prevent the resolution of acinar-to-ductal metaplasia (ADM) and lock regeneration into a pro-inflammatory state that progresses to cancer. Enhancer transcription, an early event during cellular state transitions, can generate stable enhancer-associated long noncoding RNAs (lncRNAs) positioned near key transcription factors and chromatin contact boundaries, often enriched for disease-associated variants. While enhancer-associated lncRNAs have been implicated in transcriptional regulation and genome organization, their role in pancreas regeneration and cancer initiation has remained unexplored. In this study, we investigated the expression of epithelial long noncoding RNAs (lncRNAs) and their target genes in PDAC precursor lesion formation. We focus on lncRNAs transcribed from enhancer elements near cell identity transcription factors. We demonstrate that LINC00673, expressed from a Sox9-associated super-enhancer during pancreatic development, is reactivated in PDAC. Conditional deletion of LINC00673 in the murine pancreatic epithelium accelerates resolution of ADM and significantly impairs PDAC initiation. Notably, LINC00673 harbors a variant associated with risk of developing PDAC. Our study identifies a critical function of LINC00673 in regulating both cell-autonomous and non-cell-autonomous processes during pancreas regeneration and Kras-driven cancer initiation. Furthermore, we highlight a previously unrecognized role of transcribed super-enhancers in facilitating long-range gene regulation during pancreatic cancer initiation. These findings reveal a novel regulatory layer linking developmental enhancer activity, cellular plasticity and pancreatic disease progression. TeaserLong noncoding RNAs from developmental enhancers play a role in long-range gene regulation with crucial biological impacts in development and cancer. Grant supportThis project has been supported by the Danish Cancer Society (R302-A17481). LA is supported by core funding of the Biotech Research and Innovation Center, the Danish Cancer Society (R302-A17481, R322-A17.350), The Novo Nordisk Foundation (NNF21OC0070884) and The Innovation Fund (Eurostars 2807). The Novo Nordisk Foundation Center for Stem Cell Biology was supported by Novo Nordisk Foundation grants NNF17CC0027852.

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Ballester, M., Kurilla, A., Dai, Y., Maurer, C., Espinet, E., Hoj, K., Marisch Delgado, A., Seymour, P. A., Omar, S., Rift, C. V., Hasselby, J., Klaussen, P., Vilmann, P., Sandelin, A., Arnes Perez, L.. 2025-06-08. Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma. https://doi.org/10.1101/2025.06.06.658264

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