STAT3 imparts BRCAness by impairing homologous recombination repair in Epstein-Barr virus-transformed B lymphocytes

Abstract

Epstein-Barr virus (EBV) causes lymphomas and epithelial cell cancers. Though generally silent in B lymphocytes, this widely prevalent virus can cause endemic Burkitt lymphoma and post-transplant lymphoproliferative disorders/lymphomas in immunocompromised hosts. By learning how EBV breaches barriers to cell proliferation, we hope to undermine those strategies to treat EBV lymphomas and potentially other cancers. We had previously found that EBV, through activation of cellular STAT3 prevents phosphorylation of Chk1, and thereby, suppresses activation of the intra-S phase cell-cycle checkpoint, a potent barrier to oncogene-driven proliferation. This observation prompted us to examine the consequences on DNA repair since homologous recombination repair, the most error-free form, requires phosphoChk1. We now report that the defect in Chk1 phosphorylation also curtails RAD51 nucleation, and thereby, homologous recombination repair of DNA double strand breaks. The resulting reliance on error-prone microhomology-mediated end-joining (MMEJ) repair makes EBV-transformed cells susceptible to PARP inhibition and simultaneous accrual of genome-wide deletions and insertions resulting from synthesis-dependent MMEJ. Analysis of transcriptomic and drug susceptibility data from hundreds of cancer lines reveals a STAT3-dependent gene-set predictive of susceptibility of cancers to synthetic lethal PARP inhibition. These findings i) demonstrate how the tumor virus EBV re-shapes cellular DNA repair, ii) provide the first genome-wide evidence for insertions resulting from MMEJ in human cells, and iii) expand the range of cancers (EBV-related and -unrelated) that are likely to respond to synthetic lethal inhibitors given the high prevalence of cancers with constitutively active STAT3. Author summary In a transformation model based on the cancer-causing Epstein-Barr virus (EBV), we previously demonstrated that the cellular oncoprotein STAT3, activated during transformation, impairs ATR's ability to phosphorylate Chk1 in response to replication stress, thereby relaxing the intra-S phase checkpoint. While this relaxation allows EBV-transformed cells to rapidly traverse the S phase checkpoint, we now show that activation of STAT3 has another important consequence. Specifically, impaired Chk1 phosphorylation results in impaired homologous recombination repair, a form of high-fidelity repair in replicating cells. As a result, EBV-transformed proliferating cells become dependent on error-prone microhomology mediated end-joining (MMEJ) repair, accumulate not only deletions but also genome-wide insertions from such repair, and succumb to inhibition of PARP, an enzyme critical for MMEJ repair. These findings also link STAT3 activation, commonly observed in human cancers, to PARP inhibitor susceptibility, and simultaneously provide a predictive STAT3 gene expression signature.