Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer

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Rajamäki , K , Taira , A , Katainen , R , Välimäki , N , Kuosmanen , A , Plaketti , R-M , Seppälä , T T , Ahtiainen , M , Wirta , E-V , Vartiainen , E , Sulo , P , Ravantti , J , Lehtipuro , S , Granberg , K J , Nykter , M , Tanskanen , T , Ristimäki , A , Koskensalo , S , Renkonen-Sinisalo , L , Lepistö , A , Böhm , J , Taipale , J , Mecklin , J-P , Aavikko , M , Palin , K & Aaltonen , L A 2021 , ' Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer ' , Gastroenterology , vol. 161 , no. 2 , pp. 592–607 . https://doi.org/10.1053/j.gastro.2021.04.042

Title: Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease–Associated Colorectal Cancer
Author: Rajamäki, Kristiina; Taira, Aurora; Katainen, Riku; Välimäki, Niko; Kuosmanen, Anna; Plaketti, Roosa-Maria; Seppälä, Toni T.; Ahtiainen, Maarit; Wirta, Erkki-Ville; Vartiainen, Emilia; Sulo, Päivi; Ravantti, Janne; Lehtipuro, Suvi; Granberg, Kirsi J.; Nykter, Matti; Tanskanen, Tomas; Ristimäki, Ari; Koskensalo, Selja; Renkonen-Sinisalo, Laura; Lepistö, Anna; Böhm, Jan; Taipale, Jussi; Mecklin, Jukka-Pekka; Aavikko, Mervi; Palin, Kimmo; Aaltonen, Lauri A.
Other contributor: University of Helsinki, Department of Medical and Clinical Genetics
University of Helsinki, Department of Medical and Clinical Genetics
University of Helsinki, Lauri Antti Aaltonen / Principal Investigator
University of Helsinki, Department of Computer Science
University of Helsinki, Helsinki Institute of Life Science HiLIFE
University of Helsinki, Department of Medical and Clinical Genetics
University of Helsinki, HUS Abdominal Center
University of Helsinki, Department of Pathology
University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, ATG - Applied Tumor Genomics
University of Helsinki, Molecular and Integrative Biosciences Research Programme
University of Helsinki, Finnish Cancer Registry
University of Helsinki, Department of Pathology
University of Helsinki, HUS Abdominal Center
University of Helsinki, HUS Abdominal Center
University of Helsinki, HUS Abdominal Center
University of Helsinki, Department of Pathology
University of Helsinki, Medicum
University of Helsinki, Lauri Antti Aaltonen / Principal Investigator
University of Helsinki, Lauri Antti Aaltonen / Principal Investigator















Date: 2021-08-21
Language: eng
Number of pages: 16
Belongs to series: Gastroenterology
ISSN: 0016-5085
DOI: https://doi.org/10.1053/j.gastro.2021.04.042
URI: http://hdl.handle.net/10138/333170
Abstract: Background & Aims Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. Methods Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. Results Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNT-induced epithelial–mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4α binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 5′untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. Conclusions Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.
Subject: 3122 Cancers
Colorectal Cancer
Inflammatory Bowel Disease
Epithelial-Mesenchymal Transition
DNA Methylation
Consensus Molecular Subtype
CONSENSUS MOLECULAR SUBTYPES
INTESTINAL INFLAMMATION
MUTATIONAL PROCESSES
METHYLATION
PATHWAY
COLON
SIGNATURES
PHENOTYPE
EVOLUTION
DRIVERS
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