Discovery and Validation of Methylation Biomarkers for Ulcerative Colitis Associated Neoplasia

Abstract Background and aims Ulcerative colitis (UC) is associated with a higher background risk of dysplasia and/or neoplasia due to chronic inflammation. There exist few biomarkers for identification of patients with dysplasia, and targeted biopsies in this group of patients are inaccurate in reliably identifying dysplasia. We aimed to examine the epigenome of UC dysplasia and to identify and validate potential biomarkers Methods Colonic samples from patients with UC-associated dysplasia or neoplasia underwent epigenome-wide analysis on the Illumina 450K methylation array. Markers were validated by bisulphite pyrosequencing on a secondary validation cohort and accuracy calculated using logistic regression and receiver-operator curves. Results Twelve samples from 4 patients underwent methylation array analysis and 6 markers (GNG7, VAV3, KIF5C, PIK3R5, TUBB6, and ZNF583) were taken forward for secondary validation on a cohort of 71 colonic biopsy samples consisting of normal uninflamed mucosa from control patients, acute and chronic colitis, “field” mucosa in patients with dysplasia/neoplasia, dysplasia, and neoplasia. Methylation in the beta-tubulin TUBB6 correlated with the presence of dysplasia (P < 0.0001) and accurately discriminated between dysplasia and nondysplastic tissue, even in the apparently normal field mucosa downstream from dysplastic lesions (AUC 0.84, 95% CI 0.81–0.87). Conclusions Methylation in TUBB6 is a potential biomarker for UC- associated dysplasia. Further validation is needed and is ongoing as part of the ENDCAP-C study.

Download Full-text

A data-driven approach to preprocessing Illumina 450K methylation array data

BMC Genomics ◽

10.1186/1471-2164-14-293 ◽

2013 ◽

Vol 14 (1) ◽

pp. 293 ◽

Cited By ~ 490

Author(s):

Ruth Pidsley ◽

Chloe C Y Wong ◽

Manuela Volta ◽

Katie Lunnon ◽

Jonathan Mill ◽

...

Keyword(s):

Data Driven ◽

Methylation Array ◽

Array Data ◽

Illumina 450K ◽

Data Driven Approach ◽

450K Methylation

Download Full-text

Functional normalization of 450k methylation array data improves replication in large cancer studies

10.1101/002956 ◽

2014 ◽

Cited By ~ 5

Author(s):

Jean-Philippe Fortin ◽

Aurélie Labbe ◽

Mathieu Lemire ◽

Brent W. Zanke ◽

Thomas J. Hudson ◽

...

Keyword(s):

Microarray Platform ◽

The Cancer Genome Atlas ◽

Methylation Array ◽

Illumina 450K ◽

Normalization Methods ◽

Cancer Genome Atlas ◽

Cancer Studies ◽

Control Study ◽

Large Case ◽

450K Methylation

AbstractWe propose an extension to quantile normalization which removes unwanted technical variation using control probes. We adapt our algorithm, functional normalization, to the Illumina 450k methylation array and address the open problem of normalizing methylation data with global epigenetic changes, such as human cancers. Using datasets from The Cancer Genome Atlas and a large case-control study, we show that our algorithm outperforms all existing normalization methods with respect to replication of results between experiments, and yields robust results even in the presence of batch effects. Functional normalization can be applied to any microarray platform, provided suitable control probes are available.

Download Full-text

Report on the Infinium 450k Methylation Array Analysis Workshop

Epigenetics ◽

10.4161/epi.20941 ◽

2012 ◽

Vol 7 (8) ◽

pp. 961-962 ◽

Cited By ~ 7

Author(s):

Tiffany Morris ◽

Robert Lowe

Keyword(s):

Array Analysis ◽

Methylation Array ◽

450K Methylation

Download Full-text

Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

Clinical Epigenetics ◽

10.1186/s13148-016-0241-2 ◽

2016 ◽

Vol 8 (1) ◽

Cited By ~ 6

Author(s):

Emma Cazaly ◽

Russell Thomson ◽

James R. Marthick ◽

Adele F. Holloway ◽

Jac Charlesworth ◽

...

Keyword(s):

Methylation Array ◽

Array Data ◽

Illumina 450K ◽

450K Methylation

Download Full-text

Clinical Implications of Histologic Abnormalities in Colonic Biopsy Specimens from Patients with Ulcerative Colitis in Clinical Remission

Inflammatory Bowel Diseases ◽

10.1097/mib.0b013e318281f4ae ◽

2013 ◽

Vol 19 (7) ◽

pp. 1477-1482 ◽

Cited By ~ 20

Author(s):

Linda A. Feagins ◽

Shelby D. Melton ◽

Ramiz Iqbal ◽

Kerry B. Dunbar ◽

Stuart J. Spechler

Keyword(s):

Ulcerative Colitis ◽

Clinical Remission ◽

Clinical Implications ◽

Biopsy Specimens ◽

Colonic Biopsy

Download Full-text

Development of Mucosal PNAd+ and MAdCAM-1+ Venules during Disease Course in Ulcerative Colitis

Cells ◽

10.3390/cells9040891 ◽

2020 ◽

Vol 9 (4) ◽

pp. 891

Author(s):

Britt Roosenboom ◽

Ellen G. van Lochem ◽

Jos Meijer ◽

Carolijn Smids ◽

Stefan Nierkens ◽

...

Keyword(s):

Ulcerative Colitis ◽

Disease Activity ◽

High Endothelial Venules ◽

Cell Homing ◽

Colonic Biopsy ◽

T Cell Homing ◽

N 93 ◽

Active Inflammation ◽

Active Disease

PNAd and MAdCAM-1 addressins on venules are of importance in T-cell homing and potential therapeutic targets in ulcerative colitis (UC). Normally, PNAd+ high endothelial venules (HEVs) are only present in lymphoid organs, whereas small numbers of MAdCAM-1+ venules can be seen in non-lymphoid tissue. We aimed to study their presence in the intestinal mucosa of UC patients at diagnosis and during follow-up, and their correlation with disease activity. Colonic biopsy specimens of 378 UC patients were analyzed by immunohistochemistry for CD3, CD20, ERG, MECA-79 (PNAd) and MECA-376 (MAdCAM-1) and compared to healthy controls (HC). The proportion of PNAd+HEVs in UC at diagnosis was 4.9% (IQR 2.0%–8.3%), while none were detected in HC. During follow-up, PNAd+HEVs completely disappeared in remission (n = 93), whereas the proportion in active disease was similar to baseline (n = 285, p = 0.39). The proportion of MAdCAM-1+venules in UC at baseline was 5.8% (IQR 2.6–10.0). During follow-up, the proportion in remission was comparable to diagnosis, but upregulated (7.5% (IQR 4.4–10.9), p = 0.001) in active disease. In conclusion, PNAd+HEVs appear in UC during active inflammation which could thus serve as a marker for disease activity, whereas MAdCAM-1+venules remain present after inflammation is resolved and increase after subsequent flares, reflecting chronicity and potentially serving as a therapeutic target.

Download Full-text