Document Type
Article
Publication Date
Spring 4-25-2016
Keywords
DNA methylation, Colorectal Cancer, MicroRNAs, RNA sequencing, Gene expression, Carcinogenesis, Colon, Inflammatory bow
Abstract
Background Incidence and mortality rates of colorectal carcinoma (CRC) are higher in African Americans (AAs) than in Caucasian Americans (CAs). Deficient micronutrient intake due to dietary restrictions in racial/ethnic populations can alter genetic and molecular profiles leading to dysregulated methylation patterns and the inheritance of somatic to germline mutations. Materials and Methods Total DNA and RNA samples of paired tumor and adjacent normal colon tissues were prepared from AA and CA CRC specimens. Reduced Representation Bisulfite Sequencing (RRBS) and RNA sequencing were employed to evaluate total genome methylation of 5’-regulatory regions and dysregulation of gene expression, respectively. Robust analysis was conducted using a trimming-and-retrieving scheme for RRBS library mapping in conjunction with the BStool toolkit. Results DNA from the tumor of AA CRC patients, compared to adjacent normal tissues, contained 1,588 hypermethylated and 100 hypomethylated differentially methylated regions (DMRs). Whereas, 109 hypermethylated and 4 hypomethylated DMRs were observed in DNA from the tumor of CA CRC patients; representing a 14.6-fold and 25-fold change, respectively. Specifically; CHL1, 4 anti-inflammatory genes (i.e., NELL1, GDF1, ARHGEF4, and ITGA4), and 7 miRNAs (of which miR-9-3p and miR-124-3p have been implicated in CRC) were hypermethylated in DNA samples from AA patients with CRC. From the same sample set, RNAseq analysis revealed 108 downregulated genes (including 14 ribosomal proteins) and 34 upregulated genes (including POLR2B and CYP1B1 [targets of miR-124-3p]) in AA patients with CRC versus CA patients. Conclusion DNA methylation profile and/or products of its downstream targets could serve as biomarker(s) addressing racial health disparity.
Recommended Citation
Wang, Xuefeng; Ji, Ping; Zhang, Yuanhao; LaComb, Joseph F.; Tian, Xinyu; Li, Ellen; and Williams, Jennie L., "Aberrant DNA Methylation: Implications in Racial Health Disparity" (2016). Department of Biomedical Engineering Faculty Publications. 5.
https://commons.library.stonybrook.edu/dbme-articles/5
Included in
Applied Mathematics Commons, Preventive Medicine Commons, Public Health Commons, Statistics and Probability Commons
Comments
Published PLoS ONE 11(4): e0153125. doi: http://dx.doi.org/10.1371/journal.pone.0153125
Funding: This study was supported by the National Institutes of Health - National Cancer Institute; http://www.cancer.gov/; grant number R01CA140487 to JLW and award number P20CA192994 to EL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.