Purpose: Patients with inflammatory bowel diseases, i.e., ulcerative colitis (UC) and Crohn's disease (CD), face an increased risk of developing colorectal cancer (CRC). Evidence, mainly from UC, suggests that TP53 mutations represent an initial step in the progression from inflamed colonic epithelium to CRC. However, the pathways involved in the evolution of CRC in CD patients are poorly characterized. Experimental Design: Here, we analyzed 73 tissue samples from 28 patients with CD-CRC, including precursor lesions, by targeted next generation sequencing of 563 cancer-related genes and array-based comparative genomic hybridization. The results were compared to 24 sporadic CRCs with similar histomorphology (i.e., mucinous adenocarcinomas), and to The Cancer Genome Atlas data. Results: CD-CRCs showed somatic copy number alterations (SCNAs) similar to sporadic CRCs with one notable exception: the gain of 5p was significantly more prevalent in CD-CRCs. CD-CRCs had a distinct mutation signature: TP53 (76% in CD-CRCs versus 33% in sporadic mucinous CRCs), KRAS (24% versus 50%), APC (17% versus 75%), and SMAD3 (3% versus 29%). TP53 mutations and SCNAs were early and frequent events in CD progression, while APC, KRAS and SMAD2/4 mutations occurred later. In four CD-CRC patients, at least one mutation and/or SCNAs were already present in non-dysplastic colonic mucosa, indicating occult tumor evolution. Conclusions: Molecular profiling of CD-CRCs and precursor lesions revealed an inflammation-associated landscape of genome alterations: 5p gains and TP53 mutations occurred early in tumor development. Detection of these aberrations in precursor lesions may help predicting disease progression and distinguishes CD-associated from sporadic colorectal neoplasia.
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