Inflammatory bowel disease-associated colorectal cancers (IBD-CRC) are associated with a higher mortality than sporadic colorectal cancers. The poorly defined molecular pathogenesis of IBD-CRCs limits development of effective prevention, detection, and treatment strategies. We aimed to identify biomarkers using whole-exome sequencing of IBD-CRCs to guide individualized management. Whole-exome sequencing was performed on 34 formalin-fixed paraffin-embedded primary IBD-CRCs and 31 matched normal lymph nodes. Computational methods were used to identify somatic point mutations, small insertions and deletions, mutational signatures, and somatic copy number alterations. Mismatch repair status was examined. Hypermutation was observed in 27% of IBD-CRCs. All hypermutated cancers were from the proximal colon; all but one of the cancers with hypermutation had defective mismatch repair or somatic mutations in the proofreading domain of DNA Hypermutated IBD-CRCs had increased numbers of predicted neo-epitopes, which could be exploited using immunotherapy. We identified six distinct mutation signatures in IBD-CRCs, three of which corresponded to known mechanisms of mutagenesis. Driver genes were also identified. IBD-CRCs should be evaluated for hypermutation and defective mismatch repair to identify patients with a higher neo-epitope load who may benefit from immunotherapies. Prospective trials are required to determine whether IHC to detect loss of MLH1 expression in dysplastic colonic tissue could identify patients at increased risk of developing IBD-CRC. We identified mutations in genes in IBD-CRCs with hypermutation that might be targeted therapeutically. These approaches would complement and individualize surveillance and treatment programs. .

<p>Supplementary Table S1 Phenotypic characteristics of IBD-CRC cases. Supplementary Table S2A Selected somatic mutations in IBD-CRC hypermutators. Supplementary Table S2B Selected somatic mutations in IBD-CRC non-hypermutators. Supplementary Table S3 Cosine similarities of IBD-CRC signatures and Alexandrov signatures. Supplementary Table S4 Genes implicated in susceptibility to colorectal cancer. Supplementary Table S5 Selected germline variants. Supplementary Table S6 Estimated cellularity, ploidy and SCNAs in IBD-CRC samples.</p>

<p>Supplementary Figure S1: Exome sequencing fold coverage of inflammatory bowel disease associated colorectal cancer cases and matched normal lymph nodes. Supplementary Figure S2 Mismatch repair protein expression analysis. Supplementary Figure S3: CpG island methylation of MLH1 promoter region. Supplementary Figure S4: Rainfall plot for case 21M. Supplementary Figure S5: Proportion of IBC-CRC genomes with SCNAs. Supplementary Figure S6: Nanostring nCounter® pan-cancer immune panel analysis. Supplementary Figure S7: Validation of InDel mutations.</p>

<div>Abstract<p><b>Purpose:</b> Inflammatory bowel disease–associated colorectal cancers (IBD-CRC) are associated with a higher mortality than sporadic colorectal cancers. The poorly defined molecular pathogenesis of IBD-CRCs limits development of effective prevention, detection, and treatment strategies. We aimed to identify biomarkers using whole-exome sequencing of IBD-CRCs to guide individualized management.</p><p><b>Experimental Design:</b> Whole-exome sequencing was performed on 34 formalin-fixed paraffin-embedded primary IBD-CRCs and 31 matched normal lymph nodes. Computational methods were used to identify somatic point mutations, small insertions and deletions, mutational signatures, and somatic copy number alterations. Mismatch repair status was examined.</p><p><b>Results:</b> Hypermutation was observed in 27% of IBD-CRCs. All hypermutated cancers were from the proximal colon; all but one of the cancers with hypermutation had defective mismatch repair or somatic mutations in the proofreading domain of DNA <i>POLE</i>. Hypermutated IBD-CRCs had increased numbers of predicted neo-epitopes, which could be exploited using immunotherapy. We identified six distinct mutation signatures in IBD-CRCs, three of which corresponded to known mechanisms of mutagenesis. Driver genes were also identified.</p><p><b>Conclusions:</b> IBD-CRCs should be evaluated for hypermutation and defective mismatch repair to identify patients with a higher neo-epitope load who may benefit from immunotherapies. Prospective trials are required to determine whether IHC to detect loss of MLH1 expression in dysplastic colonic tissue could identify patients at increased risk of developing IBD-CRC. We identified mutations in genes in IBD-CRCs with hypermutation that might be targeted therapeutically. These approaches would complement and individualize surveillance and treatment programs. <i>Clin Cancer Res; 24(20); 5133–42. ©2018 AACR</i>.</p></div>

<p>Supplementary Materials and Methods</p>

<div>Abstract<p><b>Purpose:</b> Inflammatory bowel disease–associated colorectal cancers (IBD-CRC) are associated with a higher mortality than sporadic colorectal cancers. The poorly defined molecular pathogenesis of IBD-CRCs limits development of effective prevention, detection, and treatment strategies. We aimed to identify biomarkers using whole-exome sequencing of IBD-CRCs to guide individualized management.</p><p><b>Experimental Design:</b> Whole-exome sequencing was performed on 34 formalin-fixed paraffin-embedded primary IBD-CRCs and 31 matched normal lymph nodes. Computational methods were used to identify somatic point mutations, small insertions and deletions, mutational signatures, and somatic copy number alterations. Mismatch repair status was examined.</p><p><b>Results:</b> Hypermutation was observed in 27% of IBD-CRCs. All hypermutated cancers were from the proximal colon; all but one of the cancers with hypermutation had defective mismatch repair or somatic mutations in the proofreading domain of DNA <i>POLE</i>. Hypermutated IBD-CRCs had increased numbers of predicted neo-epitopes, which could be exploited using immunotherapy. We identified six distinct mutation signatures in IBD-CRCs, three of which corresponded to known mechanisms of mutagenesis. Driver genes were also identified.</p><p><b>Conclusions:</b> IBD-CRCs should be evaluated for hypermutation and defective mismatch repair to identify patients with a higher neo-epitope load who may benefit from immunotherapies. Prospective trials are required to determine whether IHC to detect loss of MLH1 expression in dysplastic colonic tissue could identify patients at increased risk of developing IBD-CRC. We identified mutations in genes in IBD-CRCs with hypermutation that might be targeted therapeutically. These approaches would complement and individualize surveillance and treatment programs. <i>Clin Cancer Res; 24(20); 5133–42. ©2018 AACR</i>.</p></div>

<p>Supplementary Table S7 Somatic variants in IBD-CRC samples. Shown are variants found in coding regions and splice sites of Ensembl canonical transcripts only. Supplementary Table S8 Somatic variants in IBD-CRC samples. Shown are all variants coding regions and splice sites in all Ensembl transcripts and variant consequences for each transcript.</p>

<p>Supplementary Table S1 Phenotypic characteristics of IBD-CRC cases. Supplementary Table S2A Selected somatic mutations in IBD-CRC hypermutators. Supplementary Table S2B Selected somatic mutations in IBD-CRC non-hypermutators. Supplementary Table S3 Cosine similarities of IBD-CRC signatures and Alexandrov signatures. Supplementary Table S4 Genes implicated in susceptibility to colorectal cancer. Supplementary Table S5 Selected germline variants. Supplementary Table S6 Estimated cellularity, ploidy and SCNAs in IBD-CRC samples.</p>