DNA Mismatch Repair Deficient Cancer Research Articles

DNA mismatch repair deficient cancer - Emerging biomarkers of resistance to immune checkpoint inhibition.

The DNA mismatch repair pathway is involved in the identification, excision, and repair of base-base mismatches and indel loops in the genome. Mismatch repair deficiency occurs in approximately 20% of all cancers and results in a type of DNA damage called microsatellite instability. In 2017, the immune checkpoint inhibitor, Pembrolizumab, an anti-PD-1 therapy, was approved for use in all unresectable or metastatic tumours that were mismatch repair deficient or had high microsatellite instability regardless of tissue origin. This landmark approval was the first time a drug had been approved in a site agnostic way, but accumulating data has revealed that up to 50% of mismatch repair deficient tumours are refractory to treatment and there is a huge amount of variability in the therapeutic benefit amongst responders. Several mechanisms of resistance to immune checkpoint blockade for mismatch repair deficient cancers have been identified but our understanding of what is driving resistance in a proportion of patients remains lacking. In this review article, we discuss the emerging mechanisms of resistance which may enable optimal stratification of patients for treatment with immune checkpoint inhibitors in the future.

Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer.

Optimum risk stratification in early-stage endometrial cancer combines clinicopathologic factors and the molecular endometrial cancer classification defined by The Cancer Genome Atlas (TCGA). It is unclear whether analysis of intratumoral immune infiltrate improves this. We developed a machine-learning, image-based algorithm to quantify density of CD8+ and CD103+ immune cells in tumor epithelium and stroma in 695 stage I endometrioid endometrial cancers from the PORTEC-1 and -2 trials. The relationship between immune cell density and clinicopathologic/molecular factors was analyzed by hierarchical clustering and multiple regression. The prognostic value of immune infiltrate by cell type and location was analyzed by univariable and multivariable Cox regression, incorporating the molecular endometrial cancer classification. Tumor-infiltrating immune cell density varied substantially between cases, and more modestly by immune cell type and location. Clustering revealed three groups with high, intermediate, and low densities, with highly significant variation in the proportion of molecular endometrial cancer subgroups between them. Univariable analysis revealed intraepithelial CD8+ cell density as the strongest predictor of endometrial cancer recurrence; multivariable analysis confirmed this was independent of pathologic factors and molecular subgroup. Exploratory analysis suggested this association was not uniform across molecular subgroups, but greatest in tumors with mutant p53 and absent in DNA mismatch repair-deficient cancers. Thus, this work identified that quantification of intraepithelial CD8+ cells improved upon the prognostic utility of the molecular endometrial cancer classification in early-stage endometrial cancer.

Abstract A085: Immune evasion and PD-1-positive T cell infiltration in DNA mismatch repair-deficient colorectal cancer

Abstract Background and Aims: DNA mismatch repair-deficient cancers show microsatellite instability (MSI) and accumulate high numbers of somatic insertion/deletion mutations at repetitive sequence stretches. The high mutational load of MSI cancers leads to the generation of multiple frameshift peptide (FSP) neoantigens, which are highly immunogenic and recognized by the immune system as foreign antigens. MSI cancers respond particularly well to treatment with immune checkpoint inhibitors such as anti-PD-1 antibodies. We systematically analyzed immune evasion phenomena in MSI cancers and aimed to identify factors that are related to and potentially determine PD-1 expression on tumor-infiltrating lymphocytes, focusing on alterations of HLA class I and II antigen presentation pathways in cancer cells. Methods: Microsatellites located in Beta2-microglobulin (B2M) and the HLA class II-regulatory genes RFX5 and CIITA were analyzed for mutations in MSI colorectal cancer specimens (n = 53). HLA class I and II antigen expression was examined by immunohistochemistry. In addition, tumor-infiltrating lymphocytes (CD3-positive T cells, PD-1-positive T cells) were quantified using a semi-automated system. Results: We related B2M mutation and HLA class II antigen expression status of MSI colorectal cancer specimens (n = 56) to CD3- and PD-1 positive T cell infiltration in the tumor. PD-1-positive T cell infiltration was significantly higher in B2M-mutant (mt) compared to B2M-wild type (wt) tumors (median: 22.2 cells per 0.25 mm2 in B2M-mt vs. 2.0 cells per 0.25 mm2 in B2M-wt, Wilcoxon's rank sum test p = 0.002). Increasing PD-1-positive T cell infiltration was significantly related to an increased likelihood of B2M mutation and loss of HLA class I antigen expression (OR = 1.81). In contrast, HLA class II antigen expression status was not related to the proportion of PD-1-positive lymphocytes, but significantly associated with enhanced overall T cell infiltration. Conclusions: These results suggest that immune evasion mediated by B2M mutation-induced loss of HLA class I antigen expression predominantly occurs in an environment of activated PD-1-positive T cell infiltration, supporting the validity of the immunoediting concept in MSI colorectal cancers. Moreover, B2M mutation status may predict therapy resistance against anti-PD-1 therapy. Note: This abstract was not presented at the conference. Citation Format: Matthias Kloor, Jonas Janikovits, Julia Krzykalla, Axel Benner, Niels Grabe, Fabian Echterdiek, Meike Mueller, Sandrina Koerner, Aysel Ahadova, Magnus von Knebel Doeberitz. Immune evasion and PD-1-positive T cell infiltration in DNA mismatch repair-deficient colorectal cancer [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A085.

Parallel High-Throughput RNA Interference Screens Identify PINK1 as a Potential Therapeutic Target for the Treatment of DNA Mismatch Repair–Deficient Cancers

Synthetic lethal approaches to cancer treatment have the potential to deliver relatively large therapeutic windows and therefore significant patient benefit. To identify potential therapeutic approaches for cancers deficient in DNA mismatch repair (MMR), we have carried out parallel high-throughput RNA interference screens using tumor cell models of MSH2- and MLH1-related MMR deficiency. We show that silencing of the PTEN-induced putative kinase 1 (PINK1), is synthetically lethal with MMR deficiency in cells with MSH2, MLH1, or MSH6 dysfunction. Inhibition of PINK1 in an MMR-deficient background results in an elevation of reactive oxygen species and the accumulation of both nuclear and mitochondrial oxidative DNA lesions, which likely limit cell viability. Therefore, PINK1 represents a potential therapeutic target for the treatment of cancers characterized by MMR deficiency caused by a range of different gene deficiencies.

Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry-based Detection of Microsatellite Instabilities in Coding DNA Sequences: A Novel Approach to Identify DNA-Mismatch Repair-deficient Cancer Cells

Inherited defects in the DNA mismatch repair system lead to increased loss or gain of repeat units in microsatellites, commonly referred to as microsatellite instability (MSI). MSIs in coding regions of critical genes contribute to the pathogenesis of DNA-mismatch repair-deficient cancers, particularly those associated with the hereditary nonpolyposis colorectal cancer syndrome (HNPCC). MSI typing is therefore increasingly used to guide the molecular diagnosis of HNPCC. We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to identify MSIs in mononucleotide repeats within the coding sequences of genes relevant to the pathogenesis of MSI+ neoplastic lesions. After a primer extension reaction of PCR products encompassing the microsatellites, the molecular masses of the extension products were determined by MALDI-TOF-MS. MSIs were detected by MALDI-TOF-MS in the GART, AC1, TGFBR2, MSH3, and MSH6 genes in neoplastic tissues and MSI+ colorectal cancer cell lines but not in MSI- control tissues. The analysis of peak-integral ratios in a single spectrum of the peaks representing insertions or deletions compared with the full-length microsatellites allowed relative quantification of MSIs. MALDI-TOF-MS-based genotyping results were confirmed by conventional DNA sequencing and electrophoresis. Because of its reliability, short run times, and low costs, this semiquantitative procedure represents an effective alternative, in particular for diagnostic high-throughput typing of MSIs in neoplastic lesions.

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells

Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.

Microsatellite instability (MSI) caused by deficient DNA mismatch-repair functions is a hallmark of cancers associated with the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome but is also found in about 15% of all sporadic tumors. Most affected microsatellites reside in untranslated intergenic or intronic sequences. However, recently few genes with coding microsatellites were also shown to be mutational targets in MSI-positive cancers and might represent important mutation targets in their pathogenesis. The systematic identification of such genes and the analysis of their mutation frequency in MSI-positive cancers might thus reveal major clues to their functional role in MSI-associated carcinogenesis. We therefore initiated a systematic database search in 33,595 distinctly annotated human genes and identified 17,654 potentially coding mononucleotide repeats (cMNRs) and 2,028 coding dinucleotide repeats (cDNRs), which consist of n > or = 6 and n > or = 4 repeat units, respectively. Expression pattern and mutation frequency of 19 of these genes with the longest repeats were compared between DNA mismatch repair-deficient (MSI(+)) and proficient (MSS) cancer cells. Instability frequencies in these coding microsatellite genes ranged from 10% to 100% in MSI-H tumor cells, whereas MSS cancer cells did not show mutations. RT-PCR analysis further showed that most of the affected genes (10/15) were highly expressed in tumor cells. The approach outlined here identified a new set of genes frequently affected by mutations in MSI-positive tumor cells. It will lead to novel and highly specific diagnostic and therapeutic targets for microsatellite unstable cancers.