Epigenetic screen identifies genotype-specific promoter dna methylation and oncogenic potential of chrnb4

ABSTRACT Genome-wide association studies have highlighted three major lung cancer susceptibility regions at 15q25.1, 5p15.33 and 6p21.33. To gain insight into the possible mechanistic

relevance of the genes in these regions, we investigated the regulation of candidate susceptibility gene expression by epigenetic alterations in healthy and lung tumor tissues. For genes up

or downregulated in lung tumors, the influence of genetic variants on DNA methylation was investigated and _in vitro_ studies were performed. We analyzed 394 CpG units within 19 CpG islands

in the susceptibility regions in a screening set of 34 patients. Significant findings were validated in an independent patient set (_n_=50) with available DNA and RNA. The most consistent

overall DNA methylation difference between tumor and adjacent normal tissue on 15q25 was tumor hypomethylation in the promoter region of _CHRNB4_ with a median difference of 8%

(_P_<0.001), which resulted in overexpression of the transcript in tumors (_P_<0.001). Confirming previous studies, we also found hypermethylation in _CHRNA3_ and _telomerase reverse

transcriptase_ (_TERT_) with significant expression changes. Decitabine treatment of H1299 cells resulted in reduced methylation levels in gene promoters, elevated transcript levels of

_CHRNB4_ and _CHRNA3_, and a slight downregulation of _TERT_ demonstrating epigenetic regulation of lung cancer cells. Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948,

rs660652, rs8040868 and rs2036527 on 15q25.1, previously identified as lung cancer risk or nicotine-addiction modifiers, were associated with tumor DNA methylation levels in the promoters of

_TERT_ and _CHRNB4_ (_P_<0.001), respectively, in two independent sample sets (_n_=82; _n_=150). In addition, _CHRNB4_ knockdown in two different cell lines (A549 and H1299) resulted in

reduced proliferation (_P_A549<0.05;_P_H1299<0.001) and propensity to form colonies in H1299 cells. These results suggest epigenetic deregulation of nicotinic acetylcholine receptor

subunit (_nAChR_) genes which in the case of _CHRNB4_ is strongly associated with genetic lung cancer susceptibility variants and a functional impact on tumorigenic potential. Access through

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BEING VIEWED BY OTHERS IDENTIFYING POLYMORPHIC CIS-REGULATORY VARIANTS AS RISK MARKERS FOR LUNG CARCINOGENESIS AND CHEMOTHERAPY RESPONSES IN TOBACCO SMOKERS FROM EASTERN INDIA Article Open

access 10 March 2023 INTEGRATIVE GENOMICS IDENTIFIES SHPRH AS A TUMOR SUPPRESSOR GENE IN LUNG ADENOCARCINOMA THAT REGULATES DNA DAMAGE RESPONSE Article Open access 18 June 2024 UNRAVELING

THE INTRICATE MOLECULAR LANDSCAPE AND POTENTIAL BIOMARKERS IN LUNG ADENOCARCINOMA THROUGH INTEGRATIVE EPIGENOMIC AND TRANSCRIPTOMIC PROFILING Article Open access 17 March 2025 REFERENCES *

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Google Scholar  Download references ACKNOWLEDGEMENTS We thank Frau Heinzmann-Groth, Birgit Jäger and all other members of the clinical and laboratory teams for help with sample and/or data

collection and archiving for the Heidelberg lung study. We are grateful to all patients at the Thoraxklinik Heidelberg, who participated in the study. We thank Ruprecht Kuner for the cell

lines, Oliver Mücke for competent technical assistance, Chris Amos for helpful comments on the manuscript and the members of the Plass Laboratory for thoughtful discussions. The scientific

development and funding of this project were in part supported by the Genetic Associations and Mechanisms in Oncology (GAME-ON): a NCI Cancer Post-GWAS Initiative. This work was in part

supported by the National Institute of Health (USA; grant number CA148127) and earlier sample collection by the Deutsche Krebshilfe (grant number 70–2387). JLB was in part supported by a

grant of the Deutsche Forschungsgemeinschaft (DFG, SFB/TRR77, project Z2). AUTHOR INFORMATION Author notes * T Muley, M Meister, H Dienemann and A Risch: Translational Lung Research Centre

Heidelberg (TLRC-H), Member of the German Center for Lung Research. AUTHORS AND AFFILIATIONS * Division of Epigenomics and Cancer Risk Factors (C010), German Cancer Research Center (DKFZ),

Heidelberg, Germany D B Scherf, N Sarkisyan, H Jacobsson, R Claus, L Gu, C Plass & A Risch * Division of Molecular Genetic Epidemiology, Institute of Medical Biometry and Informatics,

University Hospital Heidelberg, German Cancer Research Center, Heidelberg, Germany J L Bermejo & B Peil * Translational Research Unit, Thoraxklinik-Heidelberg gGmbH, University of

Heidelberg, Germany T Muley & M Meister * Department of Thoracic Surgery, Thoraxklinik-Heidelberg gGmbH, University of Heidelberg, Germany H Dienemann Authors * D B Scherf View author

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ARTICLE Scherf, D., Sarkisyan, N., Jacobsson, H. _et al._ Epigenetic screen identifies genotype-specific promoter DNA methylation and oncogenic potential of _CHRNB4_. _Oncogene_ 32,

3329–3338 (2013). https://doi.org/10.1038/onc.2012.344 Download citation * Received: 26 January 2012 * Revised: 21 May 2012 * Accepted: 20 June 2012 * Published: 03 September 2012 * Issue

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shareable link is not currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative KEYWORDS * DNA methylation * risk factors *

non-small cell lung cancer (NSCLC) * _CHRNB4_ * _TERT_