Abstract
Epidermal growth factor receptor (EGFR) has been shown to be overexpressed in human cancers due to mutation, amplification, and epigenetic hyperactivity, which leads to deregulated transcriptional mechanism. Among the eight different EGFR isoforms, the mechanism of regulation of full-length variant 1 is well-known, no studies have examined the function & factors regulating the expression of variant 8. This study aimed to understand the function of EGFR super-enhancer loci and its associated transcription factors regulating the expression of EGFR variant 8. Our study shows that overexpression of variant 8 and its transcription was more prevalent than variant 1 in many cancers and positively correlated with the EGFR-AS1 expression in oral cancer and HNSCC. Notably, individuals overexpressing variant 8 showed shorter overall survival and had a greater connection with other clinical traits than patients with overexpression of variant 1. In this study, TCGA enhancer RNA profiling on the constituent enhancer (CE1 and CE2) region revealed that the multiple enhancer RNAs formed from CE2 by employing CE1 as a promoter. Our bioinformatic analysis further supports the enrichment of enhancer RNA specific chromatin marks H3K27ac, H3K4me1, POL2 and H2AZ on CE2. GeneHancer and 3D chromatin capture analysis showed clustered interactions between CE1, CE2 loci and this interaction may regulates expression of both EGFR-eRNA and variant 8. Moreover, increased expression of SNAI2 and its close relationship to EGFR-AS1 and variant 8 suggest that SNAI2 could regulates variant 8 overexpression by building a MegaTrans complex with both EGFR-eRNA and EGFR-AS1. Our findings show that EGFR variant 8 and its transcriptional regulation & chromatin modification by eRNAs may provide a rationale for targeting RNA splicing in combination with targeted EGFR therapies in cancer.
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Acknowledgements
We are grateful to the patients for agreeing to provide clinical samples for this study. SRC & AKM acknowledge the support of the DHR-MRU grant and infrastructural facility. SD and MMR acknowledge the research fellowship from the University Grant Commission (UGC), Govt. of India. We also gratefully acknowledge the UGC-SAP and DST-FIST of the Genetics department infrastructural facility.
Funding
This study was supported by grants Department of Health Research- starter grant (No. V.25011/536-HRD/2016-HR), DHR, Government of India and by National Institute of Genetics, NIG-JOINT (1A2022), Japan to A.K. Munirajan.
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Designed study—SRC, AKM. Performed research—SRC, KVU, SD, MMR. Analyzed data—SRC, KVU. Contributed new methods (qPCR)—AKM, SRC. supervision—AKM. Writing—original draft—SRC. Writing—review and editing—AKM, II, AKM. Funding acquisition— AKM.
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Ethical approval was obtained from the institutional ethics committee (IEC) of Madras Medical College, Chennai (No.04092010 and 0202201) and performed within the ethical framework of Dr. ALM PG Institute of Basic Medical Sciences, Chennai.
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Chakkarappan, S.R., Umadharshini, K.V., Dhamodharan, S. et al. Super enhancer loci of EGFR regulate EGFR variant 8 through enhancer RNA and strongly associate with survival in HNSCCs. Mol Genet Genomics 299, 3 (2024). https://doi.org/10.1007/s00438-023-02089-z
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DOI: https://doi.org/10.1007/s00438-023-02089-z