Abstract 1569: TGFβ signaling suppresses alternative end joining associated with genomic mutations and PARP Inhibition sensitivity

Abstract

Abstract Differential use of DNA repair pathways in cancer leads to distinct clinical outcomes following genotoxic therapies. We found that deficient TGFβ signaling due to human papilloma virus (HPV) in head and neck squamous cell carcinoma (HNSCC) results in impaired DNA repair proficiency, increased use of alternative end joining (alt-EJ) and that a 50-gene TGFβ signature is negatively correlated with prognosis (Clin Ca Res 2018, 24(23): 6001). To assess the molecular consequence of TGFβ signaling in the DNA damage response (DDR), we performed a Nanostring assay on SAS HNSCC and U251 glioblastoma cell lines using the 180 gene DNA damage and repair panel. The results showed that treatment with TGFβ type 1 receptor kinase inhibitor LY2157299 or TGFβ profoundly altered DDR gene expression profiles. TGFβ inhibition for 24 hr significantly (p<0.05) increased critical alt-EJ genes, POLQ (DNA polymerase theta) and PARP1 (poly(ADP-ribose) polymerase 1), which was confirmed by qRT-PCR. To interrogate the relationship between TGFβ and alt-EJ in The Cancer Genome Atlas (TCGA), we used the literature to curate a 36 gene alt-EJ signature. Single specimen gene set enrichment analyses (ssGSEA) showed that the alt-EJ signature was significantly anti-correlated with the TGFβ signature in 15 of 17 cancer types (PCC = -0.35; p =10-16). This anti-correlation was also observed in 875 cancer cell lines in Catalogue of Somatic Mutations in Cancer (COSMIC) database, suggesting a conserved, cancer cell intrinsic mechanism by which TGFβ regulates alt-EJ. Alt-EJ is an error prone DNA repair mechanism that generates gross genomic alterations. Consistent with this, low ssGSEA score for TGFβ and high ssGSEA score for alt-EJ are correlated with increased deletions or insertions in genome sequence of patient tumors in TCGA as well as cancer cell lines in COSMIC (p<0.05). PARP1 requirement prompted analyses of drug sensitivity data in the Sanger database, which showed that cell lines with high alt-EJ and low TGFβ ssGSEA score are significantly more sensitive to PARP1 inhibitors, olaparib and ABT-888, (p < 0.0001). These data lead to the novel hypothesis that TGFβ signaling actively suppresses alt-EJ. If true, the TGFβ/alt-EJ signature may be useful as a biomarker for precision cancer medicine with genotoxic agents, TGFβ or PARP inhibitors. Citation Format: Qi Liu, Luis Palomero, Jade Moore, Ines Guix, Miquel Angel Pujana, Mary Helen Barcellos-Hoff. TGFβ signaling suppresses alternative end joining associated with genomic mutations and PARP Inhibition sensitivity [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1569.