Positional Integration of Lung Adenocarcinoma Susceptibility Loci with Primary Human Alveolar Epithelial Cell Epigenomes

Abstract

Aim: To identify functional lung adenocarcinoma (LUAD) risk SNPs. Materials & methods: Eighteen validated LUAD risk SNPs (p ≤ 5 × 10^-8) and 930 SNPs in high linkage disequilibrium (r² > 0.5) were integrated with epigenomic information from primary human alveolar epithelial cells. Enhancer-associated SNPs likely affecting transcription factor-binding sites were predicted. Three SNPs were functionally investigated using luciferase assays, expression quantitative trait loci and cancer-specific expression. Results: Forty-seven SNPs mapped to putative enhancers; 11 located to open chromatin. Of these, seven altered predicted transcription factor-binding motifs. Rs6942067 showed allele-specific luciferase expression and expression quantitative trait loci analysis indicates that it influences expression of DCBLD1, a gene that encodes an unknown membrane protein and is overexpressed in LUAD. Conclusion: Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression.

Data deposition: Data are provided in GEO record GSE84273.

Graphical abstract

Keywords::

• alveolar epithelial cells
• DCBLD1
• enhancer
• epigenomics
• eQTL
• FAIRE
• lung adenocarcinoma
• rs6942067
• SNP

Acknowledgements

The H1648 and H522 cells were kind gifts from E Haura.

Financial & competing interests disclosure

This work was supported by National Institute of Health (https://www.nih.gov/) grants R01 HL114094 (to IA Offringa and Z Borok), R01 HL126877 and R01 HL112638 (to Z Borok), the Norris Comprehensive Cancer Center core grant (National Cancer Institute P30CA01408, supporting IA Offringa), Department of Defense (http://cdmrp.army.mil/funding/lcrp) Concept Award W81XWH-14-1-0174-1 (to IA Offringa), the Tobacco-Related Disease Research Program (award ID 500806, to IA Offringa) and the California Community Foundation (http://www.calfund.org/) (to IA Offringa, supporting C Yang and J Luo) and support from the Thomas G. Labrecque Foundation (https://tglfoundation.com/) (to IA Offringa), the Whittier Foundation (to IA Offringa), the Hastings Foundation (to Z Borok) and generous donations from Conya and Wallace Pembroke (to IA Offringa). Z Borok is the Ralph Edgington Chair in Medicine and Hastings Professor of Medicine. TR Stueve was supported by the National Institute of Health National Institute of Environmental Health Sciences (NIEHS, NIH T32ES013678) and by the USC Provost’s Postdoctoral Scholar Research Grant. DJ Mullen was supported by a University of Southern California Provost Fellowship and a Roy E. Thomas Foundation graduate scholarship. CN Marconett was supported by American Cancer Society (https://www.cancer.org/research.html)/Canary Foundation (http://www.canaryfoundation.org/) postdoctoral fellowship # PFTED-10-207-01-SIED and later the Department of Surgery, Keck School of Medicine. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Author contributions

Conceptualization was done by C Yang, TR Stueve, CN Marconett and IA Offringa. Data curation was done by C Yang and CN Marconett. Formal analysis was done by C Yang, TR Stueve and DJ Mullen. Funding acquisition was done by CN Marconett, TR Stueve, B Zhou, Z Borok and IA Offringa. Investigation was done by C Yang, TRS and CL Yan. C Yang, TR Stueve, CN Marconett, SK Rhie and DJ Mullen contributed in methodology. Project administration was done by IA Offringa. Resources were provided by Z Borok, J Luo, BZ and IA Offringa. Software was provided by C Yang and SK Rhie. CN Marconett and IA Offringa were involved in supervision. Validation was done by C Yang, TR Stueve and CL Yan. Visualization was done by C Yang, TR Stueve, DJ Mullen and IA Offringa. C Yang, TR Stueve and IA Offringa wrote the original draft. All the authors were involved in writing and editing this review.

Additional information

Funding

This work was supported by National Institute of Health (https://www.nih.gov/) grants R01 HL114094 (to IA Offringa and Z Borok), R01 HL126877 and R01 HL112638 (to Z Borok), the Norris Comprehensive Cancer Center core grant (National Cancer Institute P30CA01408, supporting IA Offringa), Department of Defense (http://cdmrp.army.mil/funding/lcrp) Concept Award W81XWH-14-1-0174-1 (to IA Offringa), the Tobacco-Related Disease Research Program (award ID 500806, to IA Offringa) and the California Community Foundation (http://www.calfund.org/) (to IA Offringa, supporting C Yang and J Luo) and support from the Thomas G. Labrecque Foundation (https://tglfoundation.com/) (to IA Offringa), the Whittier Foundation (to IA Offringa), the Hastings Foundation (to Z Borok) and generous donations from Conya and Wallace Pembroke (to IA Offringa). Z Borok is the Ralph Edgington Chair in Medicine and Hastings Professor of Medicine. TR Stueve was supported by the National Institute of Health National Institute of Environmental Health Sciences (NIEHS, NIH T32ES013678) and by the USC Provost’s Postdoctoral Scholar Research Grant. DJ Mullen was supported by a University of Southern California Provost Fellowship and a Roy E. Thomas Foundation graduate scholarship. CN Marconett was supported by American Cancer Society (https://www.cancer.org/research.html)/Canary Foundation (http://www.canaryfoundation.org/) postdoctoral fellowship # PFTED-10-207-01-SIED and later the Department of Surgery, Keck School of Medicine. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.