Contribution of rare germline copy number variations and common susceptibility loci in Lynch syndrome patients negative for mutations in the mismatch repair genes

Abstract

In colorectal carcinoma (CRC), 35% of cases are known to have a hereditary component, while a lower proportion (~5%) can be explained by known genetic factors. In this study, copy number variations (CNVs) were evaluated in 45 unrelated patients with clinical hypothesis of Lynch syndrome (Amsterdam or Bethesda criteria); negative for MLH1, MSH2, MSH6, PMS2, CHEK2*1100delC and TP53 pathogenic mutations; aiming to reveal new predisposing genes. Analyses with two different microarray platforms (Agilent 180K and Affymetrix CytoScan HD) revealed 35 rare CNVs covering 67 known genes in 22 patients. Gains (GALNT6 and GALNT11) and losses (SEMA3C) involving the same gene families related to CRC susceptibility were found among the rare CNVs. Segregation analysis performed on four relatives from one family suggested the involvement of GALNT11 and KMT2C in those at risk of developing CRC. Notably, in silico molecular analysis revealed that 61% (41/67) of the genes covered by rare CNVs were associated with cancer, mainly colorectal (17 genes). Ten common SNPs, previously associated with CRC, were genotyped in 39 index patients and 100 sporadic CRC cases. Although no significant, an increased number of risk alleles was detected in the index cases compared with the sporadic CRC patients. None of the SNPs were covered by CNVs, suggesting an independent effect of each alteration in cancer susceptibility. In conclusion, rare germline CNVs and common SNPs may contribute to an increased risk for hereditary CRC in patients with mismatch repair proficiency.Colorectal cancer (CRC) is the third most common neoplasm worldwide and the fourth leading cause of cancer death for both genders. 1 Among the most prevalent neoplasms, CRC presents a significant case burden ( 35%), with its development having been associated to a genetic predisposition. 2 However, only a minor proportion ( 5%) can be explained by germline mutations in genes related to well-known hereditary diseases, as Lynch syndrome (LS) (mismatch repair genes-MMR: MLH1, MSH2, MSH6 and PMS2). 3 Approximately 11% of germline alterations found in LS patients are associated with MSH2 deletions. 4 Moreover, EPCAM deletions leading to epigenetic silencing of MSH2 have also been reported in LS. 5 Copy number variations (CNVs) and single-nucleotide polymorphisms (SNPs), which are responsible for the vast majority of variations observed in the human genome, have been reported as being associated with hereditary cancers (family history of cancer, multiple tumors and/or early-onset neoplasms). 6,7 Recent studies have demonstrated the involvement of rare germline CNVs with cancer risk in patients suggestive of Li-Fraumeni and Hereditary Breast and Ovarian Cancer syndromes, but negative for mutations in TP53 and BRCA1/BRCA2 genes, respectively. 8-10 Furthermore, rare germline CNVs that cover genes potentially associated to an increased risk of CRC development, including GREM1, CDH18 and RERGL, have been reported in patients suspected of having LS and no mutations in the MMR genes. 11-13 Famil...

Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression

“…Cells were transfected with KMT2CinsG-rAAV as described [52] and selected for 2 weeks at limiting dilution in the presence of 0.8 mg/ml (RKO) or 0.4 mg/ml (HCT116) Geneticin (Gibco). Single-cell clones with site-specific integration of the targeting vector were identified by PCR (primers [13][14][15][16][17][18], and the insertion of a G in the A9 repeat, as well as the integrity of the sequence surrounding the insertion site, was confirmed by Sanger sequencing. The IRES neo selection cassette was removed by Ad-Cre virus (Vector Biolabs, Malvern, PA, USA) infection as described [52], and single-cell clones identified by PCR (primers [19][20] to lack selection cassette were verified by their inability to grow in the presence of Geneticin.…”

“…Deletion of KMT2C has also been identified in colorectal cancer (CRC) [13], and somatic mutations in KMT2C have been identified as potential drivers of tumorigenesis in several tumor types, including CRC [1,14]. Missense and non-sense germline KMT2C variants have also been associated with cancer development in families with suspected hereditary cancer [15][16][17][18]. Of mutations present in the COS-MIC database, 28.3% of KMT2C and 37.0% of KMT2D mutations, primarily frameshift and nonsense mutations, were previously found to impact the catalytic SET domain of the respective proteins [4].…”

Rare copy number alterations and copy‐neutral loss of heterozygosity revealed in ameloblastomas by high‐density whole‐genome microarray analysis

“…cnLOH arises by uniparental disomy (UPD) or deletion of one copy and compensatory duplication of the other allele . Over the past years, germ line copy number variations (CNVs) and cnLOH have been associated with risk and pathogenesis of several complex diseases and cancer types, including breast and colorectal cancer .…”

Broad and thematic remodeling of the surface glycoproteome on isogenic cells transformed with driving proliferative oncogenes

“…Unsurprisingly, alterations in heparan sulfate formation has been shown to have emerging roles in oncogenesis, of which EXT2 is a primary facilitator (Knelson et al, 2014). GALNT11 is a protein involved in the initiation of mucin-type O-glycosylation a well known marker that over-expressed in cancer (Villacis et al, 2016) ((Libisch et al, 2014 (Hussain et al, 2016). MUC-1 is also a very important drug target for immunotherapy (Bafna et al, 2010;Posey et al, 2016;Rivalland et al, 2015;Vassilaros et al, 2013).…”