Comparison of standard mismatch repair deficiency and microsatellite instability tests in a large cancer series

Tumor molecular signatures: bridging the bench and the operating room

Contemporary diagnostic and therapeutic strategies for many solid tumors rely on understanding the Mismatch Repair (MMR) system, a fundamental DNA repair mechanism responsible for correcting errors introduced during DNA replication. Pathology reports written for tumors excised in surgery, often indicate the expression status of MMR proteins. This is of significant clinical value, as loss of MMR protein expression is associated with the accumulation of DNA replication errors. The MMR system recognizes and replaces mismatched nucleotides, particularly in microsatellite regions. These are short, repetitive non-coding DNA sequences prone to replication errors. When MMR proteins are inactivated by genetic or epigenetic alterations, MMR deficiency (dMMR) occurs, preventing repair and leading to microsatellite instability (MSI). MSI is a hallmark of Lynch syndrome, which is commonly associated with colorectal cancer (CRC) and endometrial cancer. This work highlights the clinical utility of MMR protein and MSI status as molecular signatures and discusses diagnostic, prognostic, and therapeutic implications. Understanding these molecular changes supports clinicians in making informed therapeutic decisions and may improve patient outcomes by providing personalized treatments to fit individual tumor profiles.

A novel algorithm for the detection of microsatellite instability in endometrial cancer using next‑generation sequencing data

The molecular-based detection of microsatellite instability (MSI) in endometrial cancer is complex, due to the low sensitivity of PCR and a lack of standardization in next-generation sequencing (NGS) methods. In the present study, sequenced data were obtained from an NGS panel following the addition of five commonly used microsatellite loci. Subsequently, a novel algorithm, namely MSIPeak, was developed for data analysis. Results of the present study demonstrated that MSI data obtained using MSIPeak were presented in a peak, using a threshold of 1.10 to distinguish stable and unstable loci. MSIPeak was further validated using synthetic DNA samples and endometrial cancer tissue and the results were compared with the immunohistochemical analysis-determined mismatch repair status. The PCR results demonstrated a 3-base-pair (bp) deletion in synthetic DNA samples, compared with 1- and 2-bp deletion controls. Results obtained using MSIPeak demonstrated notable differences in peak profiles and positive scores in synthetic DNA samples with 1-, 2- and 3-bp deletions, compared with controls. Thus, the results of the present study demonstrated that NGS-based MSI detection exhibited a higher sensitivity compared with PCR. In addition, NGS-based MSI detection exhibited higher levels of repeatability and applicability compared with other MSI-NGS-based methods, such as MSISensor2 and MANTIS. Collectively, the results of the present study highlighted that the combination of MSIPeak and NGS exhibits potential in the detection of cancer.

Overview of a comparative analysis of microsatellite instability and standard mismatch repair protein-deficiency tests in a large cancer cohort

BACKGROUND

Mismatch repair deficiency (dMMR) with microsatellite instability (MSI) is frequent in cancer, particularly in gastrointestinal and endometrial malignancies. The increased tumor mutational burden renders dMMR/MSI tumors suitable targets for immune checkpoint inhibitors-provided the regulatory genetic defect can be detected. dMMR and MSI are considered equally effective predictors of the efficacy of ICIs; however, while dMMR testing is based on detection of missing MMR proteins in immunohistochemistry (IHC), MSI polymerase chain reaction (PCR) testing focuses on the consequences of dMMR at the genomic level.

MATERIALS AND METHODS

A retrospective analysis was carried out in a large cancer cohort (n = 1306). dMMR was tested by four IHC reactions (MLH1, PMS2, MSH2, MSH6), and MSI was assessed by pentaplex PCR (BAT-25, BAT-26, MONO-27, NR-21, NR-24) in 703 cases. In 64 cases (5%), technical failures (mostly poor preanalytical fixation) prevented dMMR/MSI testing. Tumors were colorectal (CRC; n: 978), cancer of unknown primary (n: 126), endometrial (n: 39), pancreatic (n: 36), and gastric (n: 33). dMMR was diagnosed as classical, nonclassical, or unusual, depending on IHC.

RESULTS

The MSI-high incidence was 12.1% overall and similar in the CRC subcohort. Interestingly, the dMMR incidence was higher in the total cohort (20.3%) and similar in the CRC subcohort. The incidences of proficient MMR (pMMR) and microsatellite stability (MSS) were similar in the total cohort and in the CRC subcohort. A 19.3% discrepancy was found between MMR IHC and MSI PCR for the entire cohort, independent of tumor types. In the case of pMMR, the discrepancy rate for MSS/MSI-low was low (2.0%; entire cohort and the CRC subcohort). However, the discrepancy between dMMR and MSI-high was high within the entire cohort (60.9%) and in the CRC (58.6%) and non-CRC subcohorts (68%). This high discrepancy was not due to tumors with a low T/N ratio. Regarding dMMR phenotypes, classical dMMR had a ~ 60% correlation with MSI-high status, while non-classical dMMR had a much lower and unusual dMMR a very low (< 10%) correlation with MSI-high in the entire cohort and in the CRC subcohort. Overall, the MSI PCR sensitivity for MMR IHC status was very low.

CONCLUSION

dMMR and MSI-high likely result in an increased rate of structurally altered proteins, i.e., neoantigens, and the efficacy of cancer immunotherapies is thus expected to be higher. We compared MMR IHC to MSI PCR in a large cohort of cancer patients to study how PCR test results correlate to MMR IHC. Our data imply that preanalytical factors strongly influence the results of MMR IHC and MSI PCR and may question the current dogma that dMMR phenotype and genetic MSI status are equivalent predictive markers for immunotherapies.

Microsatellite instability and mismatch repair protein deficiency: equal predictive markers?

Current clinical guidelines recommend mismatch repair (MMR) protein immunohistochemistry (IHC) or molecular microsatellite instability (MSI) tests as predictive markers of immunotherapies. Most of the pathological guidelines consider MMR protein IHC as the gold standard test to identify cancers with MMR deficiency and recommend molecular MSI tests only in special circumstances or to screen for Lynch syndrome. However, there are data in the literature which suggest that the two test types may not be equal. For example, molecular epidemiology studies reported different rates of deficient MMR (dMMR) and MSI in various cancer types. Additionally, direct comparisons of the two tests revealed relatively frequent discrepancies between MMR IHC and MSI tests, especially in non-colorectal and non-endometrial cancers and in cases with unusual dMMR phenotypes. There are also scattered clinical data showing that the efficacy of immune checkpoint inhibitors is different if the patient selection was based on dMMR versus MSI status of the cancers. All these observations question the current dogma that dMMR phenotype and genetic MSI status are equal predictive markers of the immunotherapies.