Abstract 2478: The interplay between Apurinic/apyrimidinic Endonuclease 1 (APE1) and DNA G-quadruplex (G4) in regulating triple-negative breast cancer (TNBC) metastasis
Authors: Chen Yingling , Pramanik Suravi , Tarpley Mason , Kalluchi Achyuth , Mohapatra Bhopal , Hewitt Kyle , Rowley Michael J. , Band Vimla , Bhakat Kishor 
Published: April 2023

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer (BC) among all the BC subtypes due to its exceptionally high metastasis rate. TNBC patients with metastasis have a short overall survival as the endocrine therapy and chemotherapy are inefficient in TNBC treatment. Hence, efforts are still needed to figure out the molecular mechanism driving TNBC metastasis and find promising therapeutic targets for TNBC treatment. A newly published study revealed that a secondary DNA structure G-quadruplex (G4) is highly enriched in TNBC signature genes’ promoters, and our lab was the first one to uncover that DNA repair protein Apurinic/apyrimidinic endonuclease 1 (APE1) binds to G4 and regulates its stability in cells, so we are aimed to investigate the interaction between APE1 and G4 in TNBC and their roles in regulating TNBC metastasis. We found that knocking out or knocking down APE1 in TNBC cell lines, MDA-MB-231 and BT-549, significantly impaired the cell migration ability. RNA-seq analysis and Gene Ontology analysis revealed that APE1 knockout downregulated expression of genes such as CXCL1, VEGFA, PIK3R3, BMI1, etc. which are mostly involved in promoting cell migration. Further, APE1 ChIP-seq analysis showed that APE1 was highly enriched in CXCL1, VEGFA, PIK3R3 and BMI1 gene promoters, and these regions contained potential G4 folding sequences, suggesting a potential interaction between APE1 and G4 in these gene promoters. Consisted with this, our study with the enzyme linked immunosorbent assays (ELISA) showed that recombinant APE1 bound with high affinity to CXCL1 and VEGFA G4 secondary structures as compared to double-strand DNA oligos in vitro, suggesting that APE1’s enrichment to the metastasis-related gene promoters attributes to the G4 structures in those promoter regions. Promoter-directed ChIP assay further revealed that downregulating APE1 inhibited transcription factor (TF) c-JUN’s occupancy to VEGFA promoters. Interestingly, we discovered that the G4-targeted small molecule TMPyP4 blocked APE1-G4 binding in vitro and reduced APE1’s occupancy at gene promoters in cells. Treatment of cells with TMPyP4 significantly downregulated CXCL1, VEGFA, PIK3R3, and BMI1 gene expression as well as inhibiting cell migration. In orthotopic TNBC metastasis mouse model, mice treating with TMPyP4 significantly reduced the frequency and volume of metastatic tumors in lung tissues. Overall, our study revealed that G4 in gene promoters recruited APE1 which further promoted transcription factors’ binding to promoters and enhanced metastasis-related gene expression. Blocking APE1-G4 interaction by TMPyP4 is a potential therapeutic approach to inhibit TNBC metastasis.

Citation Format: Yingling Chen, Suravi Pramanik, Mason Tarpley, Achyuth Kalluchi, Bhopal Mohapatra, Kyle Hewitt, Michael J. Rowley, Vimla Band, Kishor Bhakat. The interplay between Apurinic/apyrimidinic Endonuclease 1 (APE1) and DNA G-quadruplex (G4) in regulating triple-negative breast cancer (TNBC) metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2478.