The first part of this thesis evaluates the proportion of germline APC and MUTYH pathogenic variants in colorectal polyposis patients and subsequently identifies the substantial proportion... Show moreThe first part of this thesis evaluates the proportion of germline APC and MUTYH pathogenic variants in colorectal polyposis patients and subsequently identifies the substantial proportion polyposis patients remaining unexplained. Part II of this thesis elucidates the significance of APC mosaicism in these unexplained polyposis patients. Analysis of more than 400 patients resulted in a suggestion for both testing and surveillance guidelines. Moreover, chapter 4 describes the interesting finding of multiple APC mosaicism cases in one family with the family members having distinct mosaic patterns and phenotypes. The last part of this thesis assesses another explanation for the development of colorectal adenomatous polyps, namely the presence of pks+ E. coli and colibactin-associated mutational signatures. In this part we describe the common c.835-8A>G APC splice variant as fitting the mutational signature caused by colibactin, which is produced by pks+ E. coli. Moreover, we examine this mutational signature and fecal pks genes in a random selection of our cohort. Show less
Bajwa-ten Broeke, S.W.; Ballhausen, A.; Ahadova, A.; Suerink, M.; Bohaumilitzky, L.; Seidler, F.; ... ; Kloor, M. 2021
Lynch syndrome (LS) is caused by a pathogenic heterozygous germline variant in one of the DNA mismatch repair (MMR) genes: MLH1, MSH2, MSH6 or PMS2. LS-associated colorectal carcinomas (CRCs) are... Show moreLynch syndrome (LS) is caused by a pathogenic heterozygous germline variant in one of the DNA mismatch repair (MMR) genes: MLH1, MSH2, MSH6 or PMS2. LS-associated colorectal carcinomas (CRCs) are characterized by MMR deficiency and by accumulation of multiple insertions/deletions at coding microsatellites (cMS). MMR deficiency-induced variants at defined cMS loci have a driver function and promote tumorigenesis. Notably, PMS2 variant carriers face only a slightly increased risk of developing CRC. Here, we investigate whether this lower penetrance is also reflected by differences in molecular features and cMS variant patterns. Tumor DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue cores or sections (n = 90). Tumors originated from genetically proven germline pathogenic MMR variant carriers (including 14 PMS2-deficient tumors). The mutational spectrum was analyzed using fluorescently labeled primers specific for 18 cMS previously described as mutational targets in MMR-deficient tumors. Immune cell infiltration was analyzed by immunohistochemical detection of T-cells on FFPE tissue sections. The cMS spectrum of PMS2-deficient CRCs did not show any sig-nificant differences from MLH1/MSH2-deficient CRCs. PMS2-deficient tumors, however, displayed lower CD3-positive T-cell infiltration compared to other MMR-deficient cancers (28.00 vs. 55.00 per 0.1 mm(2), p = 0.0025). Our study demonstrates that the spectrum of potentially immunogenic cMS variants in CRCs from PMS2 gene variant carriers is similar to that observed in CRCs from other MMR gene variant carriers. Lower immune cell infiltration observed in PMS2-deficient CRCs could be the result of alternative mechanisms of immune evasion or immune cell exclusion, similar to those seen in MMR-proficient tumors. Show less
Heterozygous carriers of a pathogenic variant in the mismatch repair genes have an increased risk to develop colorectal cancer and various other types of cancer during adulthood. This cancer... Show moreHeterozygous carriers of a pathogenic variant in the mismatch repair genes have an increased risk to develop colorectal cancer and various other types of cancer during adulthood. This cancer predisposition syndrome is called Lynch syndrome. Children who carry a mutation on both copies of a mismatch repair gene develop malignancies during childhood or adolescence. This syndrome is called constitutional mismatch repair deficiency (CMMRD). The aim of this thesis is 1) to provide insights that may help in the identification of patients with Lynch syndrome and CMMRD, and 2) to further elucidate the phenotype and potential modifying factors that result from carrying a germline pathogenic variant in one of the mismatch repair genes. Both aims are important to further facilitate adequate detection and surveillance. Show less
Lynch syndrome is the most frequent hereditary colorectal cancer (CRC) syndrome, affecting approximately 1 in 300 in the Western population. It is caused by pathogenic variants in the mismatch... Show moreLynch syndrome is the most frequent hereditary colorectal cancer (CRC) syndrome, affecting approximately 1 in 300 in the Western population. It is caused by pathogenic variants in the mismatch repair (MMR) genes including MLH1, MSH2 (EPCAM), MSH6 and PMS2, and is associated with high risks of CRC, endometrial cancer and other cancers. In view of these risks, carriers of such variants are encouraged to participate in colonoscopic surveillance programs that are known to substantially improve their prognosis. In the last decade several important studies have been published that provide detailed cancer risk estimates and prognoses based on large numbers of patients. These studies also provided new insights regarding the pathways of carcinogenesis in CRC, which appear to differ depending on the specific MMR gene defect. In this report, we will discuss the implications of these new findings for the development of new surveillance protocols. Show less
Notwithstanding the hereditary colorectal cancer (CRC) syndromes where the underlying genetic defects have been characterized, for the vast majority of familial cases (15-20%) the disease-causing... Show moreNotwithstanding the hereditary colorectal cancer (CRC) syndromes where the underlying genetic defects have been characterized, for the vast majority of familial cases (15-20%) the disease-causing genes remain unknown, posing serious problems for genetic counselling and patient management of individuals at risk. Aiming to improve the molecular classification of familial CRC, an omics-based approach employing BAC (aCGH), cDNA microarrays and distinct in silico analytical strategies were used to study both the genomic and expression profiles generated from a large collection of colorectal adenomatous polyps. Though the overall results showed a high degree of similarity shared by genomic and expression profiles of familial colonic adenomas, which casts several serious doubts on the classification of hereditary CRC syndromes by omics technologies, the presented findings also argue in favour of a common molecular basis for CRC formation and contribute to the elucidation of the early events associated with colorectal tumorigenesis, namely the early occurrence of CIN and of the complex cross-talk between signalling pathways, in hereditary and in sporadic CRC and even across-species, and additionally in highlighting the power of integrated approaches in the discovery and prioritization of putative targets involved in colorectal tumorigenesis. Show less
