Harnessing transcriptional regulation of alternative end-joining to predict cancer treatment

Abstract

Transcriptional regulation; Cancer treatment

Regulación transcripcional; Tratamiento del cáncer

Regulació transcripcional; Tractament del càncer

Alternative end-joining (alt-EJ) is an error-prone DNA repair pathway that cancer cells deficient in homologous recombination rely on, making them vulnerable to synthetic lethality via inhibition of poly(ADP-ribose) polymerase (PARP). Targeting alt-EJ effector DNA polymerase theta (POLθ), which synergizes with PARP inhibitors and can overcome resistance, is of significant preclinical and clinical interest. However, the transcriptional regulation of alt-EJ and its interactions with processes driving cancer progression remain poorly understood. Here, we show that alt-EJ is suppressed by hypoxia while positively associated with MYC (myelocytomatosis oncogene) transcriptional activity. Hypoxia reduces PARP1 and POLQ expression, decreases MYC binding at their promoters, and lowers PARylation and alt-EJ-mediated DNA repair in cancer cells. Tumors with HIF1A mutations overexpress the alt-EJ gene signature. Inhibition of hypoxia-inducible factor 1α or HIF1A expression depletion, combined with PARP or POLθ inhibition, synergistically reduces the colony-forming capacity of cancer cells. Deep learning reveals the anticorrelation between alt-EJ and hypoxia across regions in tumor images, and the predictions for these and MYC activity achieve area under the curve values between 0.70 and 0.86. These findings further highlight the critical role of hypoxia in modulating DNA repair and present a strategy for predicting and improving outcomes centered on targeting alt-EJ.

This study was funded by the “GINKGO Apac del Berguedà” patient association; the Instituto de Salud Carlos III [co-funded by the European Regional Development Fund (ERDF), “A way to build Europe”] grants PI21/0136 and PI24/01327 to M.A.P., and PI19/00342 and PI23/00513 to A.A.; the Asociación Española Contra el Cáncer (AECC) grant LABAE21170 to A.A.; the Department of Defense PC210340 PCRP-IDA grant to A.A.; the Ministerio de Ciencia, Innovación y Universidades, Agencia Estatal de Investigación [co-funded by the European Regional Development Fund (ERDF), “A way to build Europe”] grants PID2020-117815RB-I00 and PID2023-150836OB-100 to F.V., and CNS2023-145615 to A.A.; and the Generalitat de Catalunya, Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR) grants SGR 2017-449 and 2021-00184 to F.V. and M.A.P., and 2021-00895 to A.A. R.E. and M.A.P.-C. were supported by contracts from the Departament de Salut, Generalitat de Catalunya, PERIS-PFI SLT017-20-000076 and PERIS-Suport SLT017/20/000072, respectively, and A.S. was supported by Generalitat de Catalunya AGAUR fellowship 2022-FI-B01068. We also acknowledge the support of the Centres de Recerca de Catalunya (CERCA) Program to IDIBELL and IDIBGI. The open-access publication of this article was funded by the Instituto de Salud Carlos III grants PI24/01327 to M.A.P., PI23/00513 to A.A., and PID2023-150836OB-100 to F.V.