Implications of mismatch repair genes hMLH1 and hMSH2 in patients with sporadic renal cell carcinoma

The Association Between hMLH1 and hMSH2 Polymorphisms and Renal Tumors in Northeastern China

Aim: Although hMLH1 and hMSH2 are closely associated with the development and drug resistance of multiple types of tumors, their role in renal tumors remains unclear. This study was designed to examine the relationship between renal tumor development and polymorphisms in the hMLH1 and hMSH2 genes. Methods: The study included 180 patients with renal tumors that were confirmed by pathological examination and 199 healthy controls. The clinical and pathological stages of the tumor samples were determined, and DNA was extracted from the peripheral blood of the subjects. Polymorphisms in the hMLH1 and hMSH2 loci were identified using the 1000 genomes database and the multiplex ligase detection method. Correlation analyses was performed using single nucleotide polymorphism tests. Results: 88.9% (160/180) of the tumor specimens were identified as clear cell renal cell carcinoma (CCRC) and 89.4% (161/180) were stage I carcinomas. Three hMLH1 and nine hMSH2 polymorphic sites were identified, and the frequency of the AA genotype of the hMSH2 rs2303424 variant was found to be significantly higher in the renal tumor group (odds ratio [OR] = 1.37, 95% confidence interval [CI]: 1.02-1.86) in the additive model (p = 0.029), the recessive model (p = 0.005), and codominant model (p = 0.02). Multiple testing corrections were performed and the differences between the clear cell carcinoma and control samples remained significant. Compared with the controls, the distribution of the GG genotype of the hMSH2 rs11886591 locus was significantly higher in the clear cell carcinoma group (OR = 0.80, 95% CI: 0.59-1.10, p = 0.04) after multiple testing corrections in the dominant model. Conclusion: The AA genotype at the rs2303424 locus and GG genotype at rs11886591 locus of the DNA repair gene hMSH2 were closely associated with the development of renal tumors. Further studies are needed on larger cohorts to confirm this correlation.

The Identification of Immunological Biomarkers in Kidney Cancers

The recent approval of several agents have revolutionized the scenario of therapeutic management of metastatic renal cell carcinoma (RCC) allowing us to reach important clinical end points with extended patients' survival. Actually, every new drug approved has represented an important step forward to the improvement of patient's survival. On the other hand, we now understand that RCC includes a large group of tumor entities, each of them with different genetic and mutational alterations, but also showing different clinical behavior; a reason behind the needs of subtype specific personalized approach to therapy of RCC. Immunotherapy is gradually becoming a key factor in the therapeutic algorithm for patients with locally advanced or metastatic RCC. Due to the combination of potent treatment success and potentially deadly adverse effects from immune checkpoint inhibitors (ICI), gathering prognostic and predictive information about FDA-indicated tumors seems to be prudent. Robust and reliable biomarkers are crucial for patient's selection of treatments with immunomodulatory drugs. PD-L1 expression is a poor prognostic factor and predictive of better responses from both PD-1 and PD-L1 inhibitors in a variety of tumor types including RCC. Each FDA approved PD-1/PD-L1 drug is paired with a PD-L1 Immunohistochemistry (IHC) assay. Thus, there is need for improved knowledge and application of PD-1/PD-L1 IHC biomarkers in daily practice. IHC staining appears in membranous fashion. The atezolizumab approved IHC assay is unique in that only immune cell staining is quantified for the use of this assay in RCC. A single biomarker for patient selection may not be feasible, given that immune responses are dynamic and evolve over time. Biomarker development for ICI drugs will likely require integration of multiple biologic components like PD-L1 expression, TILs and mutational load. New methodological approaches based on digital pathology may be relevant since they will allow recognition of the biomarker and to objectively quantitate its expression, and therefore might produce objective and reproducible cut-off assessment. Multidisciplinary approach is very much needed to fully develop the current and future value of ICI in clinical practice.

Loss of MLH1 confers resistance to PI3Kβ inhibitors in renal clear cell carcinoma with SETD2 mutation

Renal clear cell carcinoma (ccRCC) is characterized by frequent mutation in SETD2, which has recently been shown to regulate mismatch repair (MMR). We aim to investigate the association between MMR machinery genes and SETD2 mutation in ccRCC. We exploited the Genomics of Drug Sensitivity in Cancer (GDSC) database to identify selective inhibitors for SETD2 mutant ccRCC cells. We also exploited the Cancer Genome Atlas (TCGA) database to study the association between SETD2 status and MMR-related genes. In vitro studies were performed to validate the in silico findings. Reproduction of the GDSC database revealed four compounds with significant selectivity for SETD2 mutant ccRCC cells, amongst which two compounds targeted PI3Kβ. Phosphorylation of AKT at both S473 and T308 was decreased following PI3Kβ inhibitor treatment in SETD2 mutant ccRCC cells, whereas the basal pAKT level was not changed between mutant and wild-type SETD2. Both decreased MLH1 and increased AKT levels induced lower PMS2, indicating that MMR was mediated by SETD2 via both AKT and MLH1 in ccRCC. Analysis of the TCGA database further revealed high tendency of homozygous co-deletion of SETD2 and MLH1. In the absence of MLH1, suppression of pAKT by PI3Kβ inhibitor was mitigated and inhibition in cell proliferation, invasiveness, migratory ability and tumourigenesis was partially restored. Besides the reported H3K36-trimethylation pathway, we found that SETD2 mutation also mediated MMR via AKT-induced PMS2 decrease and co-loss of MLH1 loss in ccRCC.

Novel DNA variants and mutation frequencies of hMLH1 and hMSH2 genes in colorectal cancer in the Northeast China population

Research on hMLH1 and hMSH2 mutations tend to focus on Lynch syndrome (LS) and LS-like colorectal cancer (CRC). No studies to date have assessed the role of hMLH1 and hMSH2 genes in mass sporadic CRC (without preselection by MSI or early age of onset). We aimed to identify novel hMLH1 and hMSH2 DNA variants, to determine the mutation frequencies and sites in both sporadic and LS CRC and their relationships with clinicopathological characteristics of CRC in Northeast of China. 452 sporadic and 21 LS CRC patients were screened for germline and somatic mutations in hMLH1 and hMSH2 genes with PCR–SSCP sequencing. We identified 11 hMLH1 and seven hMSH2 DNA variants in our study cohort. Six of them were novel: four in hMLH1 gene (IVS8-16 A>T, c.644 GAT>GTT, c.1529 CAG>CGG and c.1831 ATT>TTT) and two in hMSH2 gene (−39 C>T, insertion AACAACA at c.1127 and deletion AAG at c.1129). In sporadic CRC, germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 15.59% and 17.54%, respectively (p = 0.52). Germline mutations present in hMLH1 and hMSH2 genes were 5.28% and 10.78%, respectively (p<0.01). Somatic mutations in hMLH1 and hMSH2 genes were 6.73% and 11.70%, respectively (p = 0.02). In LS CRC, both germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 28.57%. The most prevalent germline mutation site in hMSH2 gene was c.1168 CTT>TTT (3.90%), a polymorphism. Somatic mutation frequency of hMLH1/hMSH2 gene was significantly different in proximal, distal colon and rectal cancer (p = 0.03). Our findings elucidate the mutation spectrum and frequency of hMLH1 and hMSH2 genes in sporadic and LS CRC, and their relationships with clinicopathological characteristics of CRC.

Mismatch repair proteins hMLH1 and hMSH2 are differently expressed in the three main subtypes of sporadic renal cell carcinoma

OBJECTIVES

We studied the role of minor mismatch repair proteins (MMR) human MutL homologue 1 (hMLH1) and human MutS homologue 2 (hMSH2) in the main subtypes of renal cell carcinoma (RCC).

METHODS

Expression of MMR proteins hMLH1 and hMSH2 were investigated in 166 RCC tumors, containing the main subtypes by immunohistochemistry. Furthermore, each tumor was screened for microsatellite instability (MSI) using the National Cancer Institute consensus panel for hereditary non-polyposis colon carcinoma as well as for elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) by 10 additional markers.

RESULTS

MSI was found only in 2.0% of analyzable cases and EMAST was detected only in 1 patient. hMLH1 and hMSH2 expression was reduced in 83.7 (118/141) and 51.2% (65/127) of cases, respectively, in a subtype-specific manner. None of the clear cell RCC tumors retained a high hMLH1 expression and 92.0% lost hMLH1 completely, while papillary and chromophobe RCC preserved the expression in 25.0 and 33.3% of cases (p < 0.001). Subtype specificity was also present in hMSH2 staining, where chromophobe RCC retained a high expression in 41.7% of cases, while clear cell and papillary tumors did not (29.9 and 23.1%; p = 0.01).

CONCLUSION

MSI and EMAST are rare events in sporadic RCC, whereas diminished MMR protein expression is linked to tumor entity and might contribute to the different biological behavior of the RCC subtypes.

Association of genomic instability, and the methylation status of imprinted genes and mismatch-repair genes, with neural tube defects

We studied the genomic instability and methylation status of the mismatch-repair (MMR) genes hMLH1 and hMSH2, and the imprinted genes H19/IGF2, in fetuses with neural tube defects (NTDs) to explore the pathogenesis of the disease. Microsatellite instability (MSI) was observed in 23 of 50 NTD patients. Five NTD patients showed high-degree MSI (MSI-H) and 18 showed low-degree MSI (MSI-L). The frequencies of mutated microsatellite loci were 3/50 (6%) for BatT-25, 10/50 (20%) for Bat-26, 3/50 (6%) for Bat34C4, 6/50 (12%) for D2S123, 4/50 (8%) for D2S119, and 3/50 (6%) for D3S1611. The promoter regions of the hMLH1 and hMSH2 genes were unmethylated in NTD patients, as determined by methylation-specific PCR. The hMLH1 and hMSH2 promoter methylation patterns, the methylation levels of H19 DMR1, and IGF2 DMR0 were detected by bisulfite sequencing PCR, sub-cloning, and sequencing. The hMSH2 promoter sequence was unmethylated, and the hMLH1 promoter showed a specific methylation pattern at two CpG sites. The methylation levels of H19 DMR1 in the NTD and control groups are 73.3% ± 15.9 and 58.3% ± 11.2, respectively. The methylation level of the NTD group was higher than that of the control group (Student's t-test, P<0.05). There is no significant difference in IGF2 DMR0 methylation level between the two groups. All of the results presented here suggest that genomic instability, the MMR system, and hyper-methylation of the H19 DMR1 may be correlated with the occurrence of NTDs.

Difficulties in finding DNA mutations and associated phenotypic data in web resources using simple, uncomplicated search terms, and a suggested solution

DNA mutation data currently reside in many online databases, which differ markedly in the terminology used to describe or define the mutation and also in completeness of content, potentially making it difficult both to locate a mutation of interest and to find sought-after data (eg phenotypic effect). To highlight the current deficiencies in the accessibility of web-based genetic variation information, we examined the ease with which various resources could be interrogated for five model mutations, using a set of simple search terms relating to the change in amino acid or nucleotide. Fifteen databases were investigated for the time and/or number of mouse clicks; clicks required to find the mutations; availability of phenotype data; the procedure for finding information; and site layout. Google and PubMed were also examined. The three locus-specific databases (LSDBs) generally yielded positive outcomes, but the 12 genome-wide databases gave poorer results, with most proving not to be search-able and only three yielding successful outcomes. Google and PubMed searches found some mutations and provided patchy information on phenotype. The results show that many web-based resources are not currently configured for fast and easy access to comprehensive mutation data, with only the isolated LSDBs providing optimal outcomes. Centralising this information within a common repository, coupled with a simple, all-inclusive interrogation process, would improve searching for all gene variation data.

Analysis of the hMSH2 gene variants in head and neck cancer

The hMSH2 (human MutS homolog 2) gene plays a central role in DNA mismatch repair. Structural variations in the gene may lead to protein instability and deficient mismatch repair. However, the role of polymorphic variants of the hMSH2 gene have not been defined in head and neck cancer. In this study, the roles of three polymorphic variants in the functional domains of the gene were investigated in 166 patients with head and neck cancer by allele-specific PCR, electronical array addressing, and PCR/RFLP (restriction fragment length polymorphism). This is the first study to investigate the gIVS12-6T --> C polymorphism in head and neck cancer. A significant association between the CC genotype and reduced risk of disease suggests that the gIVS12-6T --> C substitution at the splice-acceptor site may affect the risk of head and neck cancer. We did not observe an association between the Asn127Ser and Gly322Asp polymorphisms and cancer risk. A possible role of the gIVS12-6T --> C substitution warrants further validation in larger cohorts because of low allele frequency.

Contemporary epidemiology of renal cell cancer

We analyzed renal cell cancer incidence patterns in the United States and reviewed recent epidemiologic evidence with regard to environmental and host genetic determinants of renal cell cancer risk. Renal cell cancer incidence rates continued to rise among all racial/ethnic groups in the United States, across all age groups, and for all tumor sizes, with the most rapid increases for localized stage disease and small tumors. Recent cohort studies confirmed the association of smoking, excess body weight, and hypertension with an elevated risk of renal cell cancer, and suggested that these factors can be modified to reduce the risk. There is increasing evidence for an inverse association between renal cell cancer risk and physical activity and moderate intake of alcohol. Occupational exposure to trichloroethylene has been positively associated with renal cell cancer risk in several recent studies, but its link with somatic mutations of the von Hippel-Lindau gene has not been confirmed. Studies of genetic polymorphisms in relation to renal cell cancer risk have produced mixed results, but genome-wide association studies with larger sample size and a more comprehensive approach are underway. Few epidemiologic studies have evaluated risk factors by subtypes of renal cell cancer defined by somatic mutations and other tumor markers.