Investigations of possible epigenetic mechanisms of ID3 in DNA repair and genomic stability - Potential implications for cancer therapy

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The inhibitor of DNA-binding 3 (ID3) is a transcriptional repressor protein that limits the binding of basic helix-loop-helix (bHLH) transcription factors to DNA. ID3 expression is frequently deregulated in human cancers. We recently reported (Bakr et al., 2021) that ID3 exhibits a dual role to promote DNA double-strand break (DSB) repair, particularly homologous recombination (HR), and that its loss confers sensitivity to therapeutically available PARP inhibitor. Mechanistically, ID3 interacts with the MRN complex and RECQL helicase to activate DSB repair and it facilitates RAD51 loading and downstream steps of HR. In addition, ID3 promotes the expression of HR genes in response to ionizing radiation by regulating both chromatin accessibility and activity of the transcription factor E2F1. Further unpublished data of our lab demonstrate possible protein interactions between ID3 and important chromatin modifiers as well as downregulation of key epigenetic players in ID3-depleted cells. In addition, preliminary ChIP-qPCR analyses showed a reduced enrichment of H4K16ac, H3K27ac and H3K36me3 upon cellular ID3 knockdown, in particular at HR-prone DSBs. We also observed that the loss of ID3 leads to sensitivity of tumor cells to HDAC inhibition which might offer a new therapeutic opportunity to treat ID3-deficient tumors. Based on these data we hypothesize (i) that ID3 has the potential to epigenetically affect DNA repair and genome stability by changing the chromatin environment of genomic regions flanking DSBs, and (ii) that epigenetic drugs could be effective tools to kill ID3-deficient cancer cells. In this application, it is our aim to elucidate the mechanisms how ID3 deficiency affects both chromatin accessibility and histone post-translational modifications around DSBs. For this, ATAC-seq (assay for transposase-accessible chromatin using sequencing), ACT-seq (antibody‐guided chromatin tagmentation using sequencing) and ChIP-seq (chromatin immunoprecipitation followed by sequencing) technologies will be used to monitor the dynamics of chromatin accessibility and histone modifications both genome-wide and at specific DSB sites in wild-type and ID3-depleted cells. In addition, we will perform a comprehensive drug screening with an epigenetic drug library in ID3-deficent cells to identify potential therapeutic candidates. The efficacy of the most promising candidates will subsequently be validated in vivo using ID3-WT and ID3-KO xenograft models. The resulting knowledge of this research project should allow to elucidate the epigenetic consequences of ID3 deficiency and provide evidence how ID3-deficient cancer cells can be actively treated.