Enhancer RNA transcriptome-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

Many cancer risk variants are located within enhancer regions and lack sufficient molecular interpretation. Here, we constructed the first comprehensive atlas of enhancer RNA (eRNA)-mediated genetic effects from 28,033 RNA sequencing samples across 11,606 individuals, identifying 11,757 eRNA quantitative trait loci (eRNA-QTLs) significantly associated with eRNA expression. Mechanistically, eRNA-QTLs frequently altered binding motifs of transcription factors. In addition, 28.48% of cancer risk variants were strongly colocalized with eRNA-QTLs. We further performed an eRNA-based transcriptome-wide association study and identified 626 cancer susceptibility eRNAs across 23 cancer types. 54.9% of the eRNA target genes were overlooked by traditional gene expression studies, and most are essential for cancer cell proliferation. To substantiate our findings, we confirmed the enhancer functionality of two newly identified susceptibility eRNAs, CCND1e and SNAPC1e, through CRISPR-based inhibition, resulting in a marked decrease in the expression of their respective target genes, consequently suppressing the proliferation of prostate cancer cells. Our study underscores the essential role of eRNA in unveiling new cancer susceptibility genes and establishes a strong framework for enhancing our understanding of human cancer etiology. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was supported by the National Natural Science Foundation of China [no. 32100533 to LL] and Open grant funds from Shenzhen Bay Laboratory [no. SZBL2021080601001 to L.L.]. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The data presented in this study can be freely accessed, queried, visualized, and downloaded through the dedicated eRNA-QTL website portal at http://bioinfo.szbl.ac.cn/eRNA-QTL-atlas/. Sequencing data are deposited in the Gene Expression Omnibus (GEO) database (accession number: GSE242322).