Genotranscriptomic meta‐analysis of the CHD family chromatin remodelers in human cancers – initial evidence of an oncogenic role for CHD 7

Chromodomain helicase DNA binding proteins ( CHD s) are characterized by N‐terminal tandem chromodomains and a central adenosine triphosphate‐dependent helicase domain. CHD s govern the cellular machinery's access to DNA , thereby playing critical roles in various cellular processes including transcription, proliferation, and DNA damage repair. Accumulating evidence demonstrates that mutation and dysregulation of CHD s are implicated in the pathogenesis of developmental disorders and cancer. However, we know little about genomic and transcriptomic alterations and the clinical significance of most CHD s in human cancer. We used TCGA and METABRIC datasets to perform integrated genomic and transcriptomic analyses of nine CHD genes in more than 10 000 primary cancer specimens from 32 tumor types, focusing on breast cancers. We identified associations among recurrent copy number alteration, gene expression, clinicopathological features, and patient survival. We found that CHD 7 was the most commonly gained/amplified and mutated, whereas CHD 3 was the most deleted across the majority of tumor types, including breast cancer. Overexpression of CHD 7 was more prevalent in aggressive subtypes of breast cancer and was significantly correlated with high tumor grade and poor prognosis. CHD 7 is required to maintain open, accessible chromatin, thus providing fine‐tuning of transcriptional regulation of certain classes of genes. We found that CHD 7 expression was positively correlated with a small subset of classical oncogenes, notably NRAS , in breast cancer. Knockdown of CHD 7 inhibits cell proliferation and decreases gene expression of several CHD 7 targets, including NRAS , in breast cancer cell lines. Thus, our results demonstrate the oncogenic potential of CHD 7 and its association with poor prognostic parameters in human cancer.