High resolution analysis of chromosome 18 alterations in ulcerative colitis-related colorectal cancer

DNA Methylation Profiling of MYC, SMAD2/3 and DNMT3A in Colorectal Cancer

Epigenetic modifications, particularly DNA methylation, is commonplace and a remarkable factor in carcinogenesis transformation. Conspicuously, previous findings have presented a cluster of irregular promoter methylation alterations related with silencing of tumor suppressor genes, little is accepted regarding their sequential DNA methylation (hypo and hyper) modifications during the cancer progression. In this way, fluctuations of DNA methylation of many genes, especially MYC, SMAD2/3, and DNMT3A, have an impressive central key role in many different cancers, including colorectal cancer (CRC). CRC is distinguished by DNA methylation, which is related to tumorigenesis and also genomic instability. Importantly, molecular heterogeneity between multiple adenomas in different patients with CRC may show diverse developmental phenotypes for these kinds of tumors. Conclusively, studying factors that are involved in CRC carcinogenesis, especially the alterations in epigenetic elements, such as DNA methylation besides RNA remodeling, and histone modification, acetylation and phosphorylation, can be influential to find new therapeutic and diagnostic biomarkers in this type of malignancy. In this account, we discuss and address the potential significant methylated modifications of these genes and their importance during the development of CRC carcinogenesis.

Mendelian Disease Associations Reveal Novel Insights into Inflammatory Bowel Disease

Background

Monogenic diseases have been shown to contribute to complex disease risk and may hold new insights into the underlying biological mechanism of Inflammatory Bowel Disease (IBD).

Methods

We analyzed Mendelian disease associations with IBD using over 55 million patients from the Optum's deidentified electronic health records dataset database. Using the significant Mendelian diseases, we performed pathway enrichment analysis and constructed a model using gene expression datasets to differentiate Crohn's disease (CD), ulcerative colitis (UC), and healthy patient samples.

Results

We found 50 Mendelian diseases were significantly associated with IBD, with 40 being significantly associated with both CD and UC. Our results for CD replicated those from previous studies. Pathways that were enriched consisted of mainly immune and metabolic processes with a focus on tolerance and oxidative stress. Our 3-way classifier for UC, CD, and healthy samples yielded an accuracy of 72%.

Conclusions

Mendelian diseases that are significantly associated with IBD may reveal novel insights into the genetic architecture of IBD.

SMAD2 and the Relationship of Colorectal Cancer to Inflammatory Bowel Disease

Inflammatory bowel diseases (IBDs) affecting the colon [Crohn's disease (CD) and ulcerative colitis (UC)] are associated with an increased risk of colorectal cancer (CRC). Our previous work using oligonucleotide array data indicated that SMAD2 was significantly underexpressed in UC dysplastic tissue compared to benign UC. The aim of this current study was to determine whether single nucleotide polymorphisms (SNPs) within the SMAD2 gene are associated with IBD dysplasia/cancer. We performed an SNP haplotype-based case-control association study. Leukocyte DNA was obtained from 489 unrelated Caucasians (158 UC, 175 CD, 71 CRC, 85 controls). Eleven SNPs were genotyped. All 11 SNPs were in Hardy-Weinberg equilibrium in the control population. Strong linkage disequilibrium was observed among nearly all SMAD2 SNPs. There were no significant associations between SMAD2 allele or haplotype frequencies. Power calculations indicated good power for single-marker analysis (>0.8) and reasonably good power against effects of 0.1–0.15 for haplotype analysis. SMAD2 SNPs were not associated with the development of IBD dysplasia/cancer. This incongruity between our previous microarray data and the findings from this genotype study may be attributed to mechanisms such as alternative splicing of pre-mRNA SMAD2 and/or cross talk with other cellular pathways.

Analysis of mutations in TP53, APC, K-ras, and DCC genes in the non-dysplastic mucosa of patients with inflammatory bowel disease

BACKGROUND AND AIMS

Patients with ulcerative colitis (UC) and Crohn's disease (CD) have a high risk for colorectal cancer (CRC). To understand the molecular basis of colitis-associated CRC, we analyzed alterations in TP53, APC, K-ras, and DCC genes in the non-dysplastic UC and CD colon.

MATERIALS AND METHODS

Endoscopic biopsies were collected from six predefined colon sites of 35 UC and 12 CD patients for DNA extraction and genetic analysis.

RESULTS

A mutation was found in codon 1141 of the APC gene of two CD patients, being somatic in one and germinative in the other. The mutation seen in both patients was a base exchange of thymine for cytosine, resulting in an exchange of leucine for serine. We did not detect any mutations in the other samples analyzed.

CONCLUSIONS

Mutations in APC gene may occur in the non-dysplastic CD mucosa of patients with disease for more than 10 years. The follow-up of these patients will show the likelihood of mutant APC progressing to CRC in CD. Further analysis will be required for evaluating the impact of these findings in the context of cancer surveillance in inflammatory bowel disease.

Risk for colorectal cancer in ulcerative colitis: changes, causes and management strategies

The risk of colorectal cancer for any patient with ulcerative colitis is known to be elevated, and is estimated to be 2% after 10 years, 8% after 20 years and 18% after 30 years of disease. Risk factors for cancer include extent and duration of ulcerative colitis, primary sclerosing cholangitis, a family history of sporadic colorectal cancer, severity of histologic bowel inflammation, and in some studies, young age at onset of colitis. In this review, the authors discuss recent epidemiological trends and causes for the observed changes. Population-based studies published within the past 5 years suggest that this risk has decreased over time, despite the low frequency of colectomies. The crude annual incidence rate of colorectal cancer in ulcerative colitis ranges from approximately 0.06% to 0.16% with a relative risk of 1.0-2.75. The exact mechanism for this change is unknown; it may partly be explained by the more widespread use of maintenance therapy and surveillance colonoscopy.

Epithelial and stromal genetic instability linked to tumor suppressor genes in ulcerative colitis-associated tumorigenesis

OBJECTIVE

We have previously documented not only epithelial but also stromal genetic instability in ulcerative colitis (UC)-associated lesions, including adenocarcinomas, using microsatellite markers close to the p53 gene on chromosome 17 (Chr.17). However, about half of the UC-associated tumors do not have p53 gene alterations. The purpose of this study was to detect early genetic instability (loss of heterozygosity (LOH) and microsatellite instability (MSI)) of both epithelial and stromal cells in UC-associated tumorigenesis, using different microsatellite markers from the p53 gene.

MATERIAL AND METHODS

The laser-captured microdissection-PCR-GeneScan method was applied to investigate genetic instability in both the epithelial and stromal elements of early UC-associated lesions (regenerative mucosa and dysplasia) and carcinomas using multiple microsatellite markers, chiefly close to tumor suppressor genes (TSGs: p16(INK4A), Rb, Smad4 and fragile histidine triad (FHIT)). Furthermore, expression of their gene products was analyzed by immunohistochemistry.

RESULTS

In epithelium, although LOH for Chr.17 markers increased along with histological progression, the frequencies of LOH or MSI for TSG markers were found to be almost constantly increased in both stromal and epithelial components of all lesion types. In contrast, genetic instability of National Cancer Institute (NCI)-recommended standard markers was not found to be significantly correlated with UC-associated tumorigenesis. Immunohistochemically, epithelial p16(INK4A) expression tended to be decreased in LOH-positive lesions (p = 0.0780) and Smad4 expression was significantly decreased (p < 0.05).

CONCLUSIONS

These results suggest that genetic instability in the stroma, especially regarding TSG markers, may play an important role in early-phase, UC-associated tumorigenesis. In addition, decreased expression of TSG due to genetic alteration might contribute to tumorigenesis.

Genetic alterations of the TGF-beta signaling pathway in colorectal cancer cell lines: a novel mutation in Smad3 associated with the inactivation of TGF-beta-induced transcriptional activation

To investigate genetic alterations involved in the TGF-beta signaling pathway in colorectal cancer, we assayed DNA synthesis rates after treating TGF-beta and checked for genetic alterations in TGF-betaRII, TGF-betaRI, Smad2, Smad3, and Smad4 in 12 colorectal cancer cell lines. Eleven lines, except SNU-61, show no significant change in DNA synthesis rate after TGF-beta treatment. In these 11 lines, several mutations were found in genes involved in the TGF-beta signaling pathway: (i) frameshift deletions in the poly(A)(10) tract of the TGF-betaRII gene in SNU-407, SNU-769A, SNU-769B, and SNU-1047 cell lines, (ii) a missense mutation of Smad2 (R321Q) in SNU-81, (iii) two missense mutations in TGF-betaRI (R487W in SNU-175 and A202V in SNU-1040), and (iv) a monoallelic loss at the Smad4 locus in three cell lines. Interestingly, a missense mutation (R373H) in Smad3 gene was found in SNU-769A. To our knowledge, this is the first report of Smad3 mutation in human malignancy. This mutation was found to result in the inhibition of translocation of Smad3 protein to the nucleus and a reduction in the activity of Smad3 during TGF-beta-induced transcriptional activation. These results indicate that the majority of cell lines, which are insensitive to TGF-beta, have alterations in genes involved in the TGF-beta signaling pathway in colorectal cancer cell lines.

Cancer surveillance in inflammatory bowel disease: new molecular approaches

PURPOSE OF REVIEW

Patients with chronic inflammatory bowel disease, such as ulcerative colitis and Crohn's disease, have an increased risk of colorectal cancer. Life-long colonoscopy surveillance is performed to detect the presence of dysplasia, but this approach is expensive and time-consuming. Thus, there is intensive research to identify molecular factors with prognostic value. This review summarizes recent research, with a special emphasis on the mechanisms underlying these molecular alterations.

RECENT FINDINGS

The role of chromosomal instability in the progression to inflammatory bowel disease-associated colorectal cancer is clear and likely relates to chronic cycles of injury, inflammation, repair and telomere shortening. The role of microsatellite instability has been a subject of discussion, and data suggest that microsatellite instability in inflammatory bowel disease might be different from microsatellite instability in sporadic colorectal cancer. Methylation, as a mechanism of gene silencing, also plays a role in ulcerative colitis tumorigenesis. Chronic inflammation has been linked to p53 activation and oxidative stress, contributing to the extensive genomic DNA damage observed in ulcerative colitis.

SUMMARY

Improved understanding of the molecular biology of cancer progression in inflammatory bowel disease will hopefully lead to the identification of useful prognostic biomarkers. Efforts are needed to prove the clinical utility of the most promising markers now identified.

Molecular phenotype of inflammatory bowel disease-associated neoplasms with microsatellite instability

BACKGROUND & AIMS

Patients with inflammatory bowel disease (IBD) are at increased risk of developing colorectal cancer (CRC). We sought to determine the frequency of high-level microsatellite instability (MSI-H) and the mutational and methylation profile of MSI-H IBD-related neoplasms (IBDNs).

METHODS

A total of 124 IBDNs (81 cancers, 43 dysplasias) from 78 patients were studied for the frequency of MSI-H and hypermethylation of 3 target genes: MLH1 , HPP1 , and RAB-32 . Fifteen MSI-H IBDNs were characterized according to their profile of frameshift mutations in 28 mononucleotide repeats and compared with 46 sporadic MSI-H CRCs.

RESULTS

Nineteen of 124 IBDNs were MSI-H. The frequency of frameshift mutations in coding mononucleotide repeats was significantly lower in MSI-H IBDNs than in sporadic MSI-H CRCs for TGFBR2 (7 of 14 vs 34 of 43 samples; P = .047) and ACVR2 (3 of 14 vs 25 of 43 samples; P = .029). In contrast, ICA1 was mutated in 3 of 9 MSI-H IBDNs vs 2 of 54 sporadic MSI-H CRCs ( P = .028). HPP1 and RAB32 methylation was independent of MSI status and was observed in 4 of 59 and 0 of 64 nondysplastic mucosae, 20 of 38 and 1 of 25 dysplasias, and 28 of 61 and 20 of 60 carcinomas, respectively.

CONCLUSIONS

The profiles of coding microsatellite mutations (instabilotypes) differ significantly between MSI-H IBDNs and MSI-H sporadic CRCs. Specifically, TGFBR2 and ACVR2 mutations are significantly rarer in MSI-H IBDNs than in MSI-H sporadic CRCs. Furthermore, HPP1 methylation occurs early, in 7% of nondysplastic and approximately half of dysplastic mucosae, whereas RAB32 methylation occurs at the transition to invasive growth, being rarer in dysplasias.