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Identification of Disease-Associated DNA Methylation in B Cells from Crohn’s Disease and Ulcerative Colitis Patients

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Abstract

Background

Changes in the methylation status of inflammatory bowel disease (IBD)-associated genes could significantly alter levels of gene expression, thereby contributing to disease onset and progression. We previously identified seven disease-associated DNA methylation loci from intestinal tissues of IBD patients using the Illumina GoldenGate BeadArray assay.

Aims

In this study, we extended this approach to identify IBD-associated changes in DNA methylation in B cells from 18 IBD patients [9 Crohn’s disease (CD) and 9 ulcerative colitis (UC)]. B cell DNA methylation markers are particularly favorable for diagnosis due to the convenient access to peripheral blood.

Methods

We examined DNA methylation profiles of B cell lines using the Illumina GoldenGate BeadArray assay. Disease-associated CpGs/genes with changes in DNA methylation were identified by comparison of methylation profiles between B cell lines from IBD patients and their siblings without IBD. BeadArray data were validated using a bisulfite polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method. To verify that observed changes in DNA methylation were not due to virus transformation, we compared specific CpG DNA methylation levels of GADD45A and POMC between B cell lines and matching peripheral blood B lymphocytes from five individuals.

Results

Using this approach with strict statistical analysis, we identified 11 IBD-associated CpG sites, 14 CD-specific CpG sites, and 24 UC-specific CpG sites with methylation changes in B cells.

Conclusions

IBD- and subtype-specific changes in DNA methylation were identified in B cells from IBD patients. Many of these genes have important immune and inflammatory response functions including several loci within the interleukin (IL)-12/IL-23 pathway.

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Acknowledgments

This work is supported by a grant from the Philadelphia Health Care Trust (W.A.K.), and a feasibility research grant from Department of Surgery (Z.L.). Thanks to Ashlly A. Kelly for her work on B cell lines.

Conflict of interest

Jian-Bing Fan is an employee and stockholder of Illumina Inc. The authors disclose no other potential conflicts of interests or financial relationship with the organization that sponsored the research.

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Authors and Affiliations

  1. Department of Surgery, College of Medicine, The Pennsylvania State University, 500 University Drive, MC H 137, Hershey, PA, 17033, USA

    Zhenwu Lin, John P. Hegarty, Wei Yu, Jon A. Cappel, Yunhua Wang, Lisa S. Poritz & Walter A. Koltun

  2. Department of Biostatistics, Vanderbilt University, Nashville, TN, USA

    Xi Chen

  3. Institute of Molecular Medicine, Cleveland Clinic, Cleveland, OH, USA

    Pieter W. Faber

  4. Department of Cell and Molecular Physiology, The Pennsylvania State University College of Medicine, Hershey, PA, USA

    Lisa S. Poritz

  5. Illumina Inc., San Diego, CA, USA

    Jian-Bing Fan

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  1. Zhenwu Lin
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  2. John P. Hegarty
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  3. Wei Yu
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  4. Jon A. Cappel
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  9. Jian-Bing Fan
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Correspondence to Zhenwu Lin or Walter A. Koltun.

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Lin, Z., Hegarty, J.P., Yu, W. et al. Identification of Disease-Associated DNA Methylation in B Cells from Crohn’s Disease and Ulcerative Colitis Patients. Dig Dis Sci 57, 3145–3153 (2012). https://doi.org/10.1007/s10620-012-2288-z

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  • DOI: https://doi.org/10.1007/s10620-012-2288-z

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