Serrated neoplasia from people with SPS who carry germline RNF43 gene mutations differs in RNF43 protein expression and genome-wide DNA methylation patterns compared with idiopathic SPS cases

Jihoon Joo1,2, Christophe Rosty1,2,3, Ryan Hutchinson1,2, Mark Clendenning1,2, Marie Lorans1,2, Thomas Green1,2, Sharelle Joseland1,2, Julia Como1,2, Julia Arnold4, Varnika Vijay4, Mark Jenkins5,2, Finlay Macrae6,7,8, Ingrid Winship7,8, Susan Parry4, Daniel Buchanan1,2,7

1Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Australia. 2University of Melbourne Centre for Cancer Research, Parkville, Australia. 3Envoi Pathology, Brisbane, Australia. 4New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand. 5Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Australia. 6Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Australia. 7Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia. 8Department of Medicine, The University of Melbourne, Parkville, Australia

Abstract

The serrated polyps and CRCs that develop in people with Serrated Polyposis Syndrome (SPS) are characterised by DNA methylation aberrations at CpG islands (CIMP).  Here, we assess genome-wide DNA methylation changes between normal, polyp and CRC tissues from people with SPS to identify key loci associated with initiation and progression of tumourigenesis.

Genome-wide DNA methylation was measured using the Infinium HumanMethylationEPIC array in colonic tissue from 13 people with SPS (12 normal mucosa, 12 microvesicular hyperplastic polyps (MVHP), 5 traditional serrated adenomas (TSA), 37 sessile serrated adenomas/polyps (SSA) and 13 CRCs), comprising 9 idiopathic cases and 4 who carried RNF43 germline mutations. RNF43 expression was confirmed by immunohistochemistry. Differential methylation changes were identified by regression analysis.

 In 9 idiopathic SPS cases, differentially methylated probes (DMPs) were observed in TSAs and SSAs when compared with normal mucosa, totalling 39,146 (~6%) and 43,141 (~7%) DMPs, respectively.  MVHPs showed only 14,750 (~2%) DMPs when compared with normal mucosa where ~94% of these DMPs were also differentially methylated in TSAs and SSAs.  Only ~20% of SSA-associated DMPs in idiopathic cases were aberrantly methylated in SSAs from germline RNF43 mutation carriers, suggesting significantly less genome-wide DNA methylation changes. The polyps and CRCs from all RNF43 carriers showed complete loss of the RNF43  protein whereas a heterogeneous loss of expression was observed for the idiopathic cases.

 DNA methylation changes occur predominantly during the normal-to-polyp transition in SPS.  Serrated neoplasia arising in RNF43 germline mutation carriers shows loss of RNF43 expression and less aberrations in DNA methylation.

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