MSI Testing Research Articles

Improved survival with immunotherapy for microsatellite unstable colorectal cancer with peritoneal metastases.

KEYNOTE-177 demonstrated that immunotherapy was superior to chemotherapy for microsatellite-instability-high(MSI-high) metastatic colorectal cancer. Colorectal cancer with peritoneal metastases (CRPM) has a poorer prognosis than other metastatic sites, with an unclear role of immunotherapy. We evaluated trends in immunotherapy use and overall survival (OS). Patients with CRPM and MSI testing were identified in the National Cancer Database (2016-2020). We evaluated immunotherapy use by year and associated patient/hospital factors. OS was compared for immunotherapy versus chemotherapy, cytoreductive surgery (CRS), and immunotherapy plus CRS. Among 15 322 CRPM patients, 7072 (46.2%) patients had documented MSI testing, with 819 (11.6%) MSI-high. Ninety-eightMSI-high patients received immunotherapy alone (12.3%), increasing from 0% in 2016to 19.1% in 2020 (p < 0.01). On multivariable analysis, only higher comorbidity was associated with immunotherapy (OR: 2.83 [1.22-6.52]). Two-year OS with immunotherapy versus chemotherapy was 64.2% versus 54.1% (p < 0.05). In patients receiving CRS plus systemic therapy (N = 96), 2-year OS was 68.4%. Among patients who underwent immunotherapy and CRS versus immunotherapy alone, 2-year OS was 80.0% versus 60.0% (p = 0.14). Immunotherapy was associated with significantly better survival compared to chemotherapy in MSI-high CRPM. Two-year OS with systemic + CRS was 68.4%. Despite its role in guiding treatment, MSI testing remains low for these patients.

Performance of the Idylla microsatellite instability test in endometrial cancer

ContextDNA mismatch repair (MMR) deficiency (dMMR) testing is now recommended in endometrial cancer. Defect identification in the molecules participating in this pathway, or the presence of microsatellite instability, are commonly employed for this purpose. Novel methods are continuously evolving to report dMMR/microsatellite instability and to easily perform routine diagnoses. ObjectiveThe main aim of this study was to compare the concordance of the Idylla microsatellite instability test for the identification of dMMR endometrial cancer samples defined by immunohistochemistry and MMR genomic status. DesignWe applied the Idylla MSI test to 126 early-stage endometrial cancer cases with MMR testing by immunohistochemistry and genomic characterization (methylation in MLH1 and sequence alterations in MLH1, PMS2, MSH2 and MSH6). Individual markers and overall specific performance indicators were explored. ResultsThe Idylla platform achieved a higher global concordance rate with MMR genomic status than with immunohistochemistry (75 % and 66 %, respectively). Sensitivity and specificity are also higher (75 % vs 66 % and 96 % vs 90 %, respectively). Clustering analysis split the patients into 2 well-differentiated clusters, the pMMR and the dMMR group, represented by MLH1/PMS2 loss and the MLH1 methylated promoter. Overall, immunohistochemistry and MMR genomic status identified more dMMR cases than did the Idylla test, although correlations were improved with a modified Idylla test cut-off. ConclusionsPerformance of the Idylla test was better correlated with MMR genomic status than MMR immunohistochemistry status, which improved with a modified test cut-off. Further studies are needed to confirm the cut-off accuracy.

Clinical performance of the TrueMark™ MSI assay for microsatellite instability detection in a Chinese colorectal cancer cohort

BackgroundMicrosatellite instability (MSI) and mismatch repair (MMR) detection is valuable in assessing prognosis and treatment options. However, the conventional detection methods such as immunohistochemistry (IHC) are limited by not fully consistent results as well as a long turnaround time. TrueMark™ MSI Assay is a novel solution for MSI analysis, but lack of research support in the Chinese colorectal cancer (CRC) patients. Materials and methods60 dMMR and 60 pMMR CRC samples identified by IHC were collected and their MSI status were detected using TrueMark™ MSI assay with an expanded panel of 13 markers. The overall performance and diagnostic concordance between TrueMark™ MSI test and MMR IHC analysis were assessed and analyzed. ResultsAccording to the TrueMark™ test, 55 out of the 120 (45.8 %) CRCs were identified as MSI-high (MSI-H) with an instability at ≥ 4/13 markers. Compared with the MMR IHC analysis, an overall percent agreement of 94.2 % and a Kappa of 0.883 were achieved. For the seven inconsistent samples, tumor mutation burden analysis was performed and the results supported the diagnosis by TrueMark™ test. To confirm the robustness of the above findings, a validation was performed in an independent cohort comprising 51 consecutive CRCs. Furthermore, an optimized panel composed of NR-21, NR-24, NR-27, ABI-16, ABI-17 and ABI-20B was developed by multivariate logistic regression model, and showed 100 % agreement with the 13-marker panel for MSI detection in both the derivation and validation sets. ConclusionTrueMark™ MSI provides a fast, reliable and highly automated solution to MSI detection in Chinese CRC patients, and the new 6-marker panel we established shows promise deserving further evaluation.

Timeliness and Completeness of Endometrial Cancer Pathology Reports Before and After the FIGO 2023 Endometrial Cancer Staging Guidelines Update

Introduction: Uterine cancer is the most common gynecologic malignancy among women in the United States with an estimated 66,200 new cases and 13,030 deaths in 2023.1 These cancers are divided into endometrial adenocarcinomas (EAC) and uterine sarcomas. In 2013, the Cancer Genome Atlas (TCGA) proposed four new molecular classifications based on genome and exome sequencing of EACs including POLE-mutant, mismatch repair deficiency (MMRd), p53 abnormal, and no specific molecular profile (NSMP).4 In June of 2023, the International Federation of Gynecology and Obstetrics (FIGO) published an updated staging system for uterine cancer to incorporate these molecular indices along with the traditional anatomical distribution of disease and histology used in older FIGO staging guidelines.5 The primary objective of this project was to analyze the timeliness and completeness of pathology reports and IHC staining of patients who underwent hysterectomies for uterine cancer at Detroit Medical Center from October 2022 – December 2023. Methods: Patients were identified from the list of patients presented at the Karmanos Cancer Insitute’s (KCI) Gynecologic Oncology Tumor Board. Given the June publication timing of the FIGO 2023 staging guidelines, this served as the intervention for the study. The pre-intervention group consists of surgical cases from October 2022 through June 2023, and the post-intervention group consists of cases from July 2023-December 2023. Differences in time from surgery to pathology report, surgery to IHC result, pathology report to IHC result as well as completeness of IHC results were compared pre- and post-intervention. Because neither group was normally distributed, a MannWhitney-U test was used to calculate P-value. IHC result completeness pre- and post-intervention was calculated using a Fisher exact test. Results: A total of 106 cases were included, of which 67 were preintervention (63%) and 39 were postintervention. The median number of days from surgery to final pathology report was statistically significant (p=0.003) between the groups. The median number of days from pathology report to IHC result was not a statistically significant difference (p=0.19). The median number of days from surgery to completed IHC also not statistically significant. In terms of IHC staining, there was a statistically significant difference in the number of specimens pre- and post-intervention for p53 (p=0.004) and HER2 (p=0.04). There was no change in the MMR and MSI testing between the two groups. Conclusions: Following the implementation of the FIGO 2023 staging guidelines in June of 2023, there was a significant decrease in the time from surgery to finalized pathology report and a significant change in the completeness of staining for p53 and HER2 on hysterectomy specimens. By finalizing the results of both pathology and IHC for endometrial cancer specimens in a timelier manner, patients can be informed of their diagnosis sooner. Additionally, with a complete pathologic and molecular diagnosis, our gynecologic oncologists can also more efficiently and effectively communicate within a multidisciplinary team of providers including radiation oncology and genetic counseling colleagues to formulate a treatment plan.

Molecular insights from comprehensive genomic profiling data in advanced metastatic colorectal cancer in South Asian population: A retrospective observational study

ABSTRACT Background: An increase in colorectal cancer incidence has been reported in India, often presenting in advanced stages and resulting in poor survival. However, the genomic and therapeutic landscape is not well understood. Objective: The primary objective of the study was to understand the mutational profile of metastatic colorectal cancer in the Southeast Asian cohort, and the secondary objective was to define the proportion of patients with therapeutically significant variants. Materials and Methods: This retrospective study was conducted between January 2021 and September 2023, at 4baseCare Onco Solutions Pvt. Ltd., Bengaluru, Karnataka, India. Comprehensive genomic profiling (CGP) and biomarker testing for MSI, TMB, and PD-L1 was carried out in 477 metastatic advanced (Stage III/IV) colorectal cancer patients, for the current retrospective-observational study. Results: With CGP, we identified drivers/clinically actionable variants in 78.6% of the cohort (375 patients). Although 30.8% of our cohort (147 patients) was eligible to available targeted therapy, 29.5% (141 patients) were found to harbor variants imparting therapeutic resistance. The combined mutation frequency of APC, TP53, and KRAS was &gt;50%, while KRAS constituted &gt;90% of all RAS mutations. The mismatch repair (MMR) genes including MLH1, MLH3, MSH3, and POLE were exclusively found in colon cancers. Genomic alterations in several genes of prognostic/therapeutic significance were seen (mutations in PIK3CA, SMAD4, BRAF, and amplifications in KRAS, EGFR, and ERBB2). Of those tested, 15.8% (41 patients) of the cohort had high tumor mutation burden (TMB-H), 14% had high microsatellite instability (MSI-H) (46 patients), and 26.8% were programmed death-ligand 1 (PD-L1) positive (30 patients). Conclusion: Our study shows that CGP is an advantageous option for identifying subsets of patients eligible for various targeted therapies, thus, improving patient outcomes.

Abstract 2498: Assessing the clinical value of ctDNA sequencing for initial tumor profiling in metastatic colorectal cancer patients with sufficient tumor tissue

Abstract Introduction Tumor profiling including RAS, BRAF, HER2, and MSI/MMR status, is required to determine the treatment for patients with metastatic colorectal cancer (mCRC) at the time of diagnosis. While comprehensive tumor profiling using tissue-based next-generation sequencing (NGS) is increasingly adopted for initial profiling in mCRC, the role of circulating tumor DNA (ctDNA) NGS as initial testing in patients with sufficient tumor tissue is not clearly understood. We assessed the clinical value of ctDNA sequencing compared to tumor NGS in patients with newly diagnosed mCRC who have sufficient tumor specimens. Methods We prospectively enrolled consecutive patients with newly diagnosed mCRC at the National Cancer Center Korea. As per the institutional protocol for mCRC, initial tumor profiling was performed on primary tumor tissue using an in-house NGS panel (NCC PCP ver.3), which included 525 genes. For ctDNA sequencing, patients were evaluated using the AlphaLiquid®100 comprehensive cancer panel (IMBdx, Inc.), which included 118 genes, before the initiation of chemotherapy. Additionally, immunohistochemical (IHC) testing for HER2 and polymerase chain reaction (PCR)/IHC testing for MSI and/or MMR were performed to assess the accuracy of HER2 and MSI/MMR status. Results A total of 188 patients were enrolled. In 139 eligible patients, 275 potentially actionable mutations were found in 12 selected CRC-related genes (APC, TP53, KRAS, NRAS, BRAF, FBXW7, PIK3CA, ERBB2, SMAD4, NF1, EGFR, MET). Of these, 32% were found both in ctDNA and tissue; 54% were found in ctDNA only; 12% in tissue only, and 2% were discordant. For RAS/BRAF mutations, which are required for anti-EGFR treatment decisions, the concordance rate between ctDNA and tissue NGS was 83.1%, and the concordance was higher in patients with higher ctDNA concentrations. For 9 patients with potentially actionable copy number variations (CNV) in EGFR, HER2, MET, and FGFR1, 3 cases were found by both assays; 4 were found by ctDNA only, and 2 were found by tissue only. ctDNA NGS correctly predicted MSI/MMR status in 2 out of 4 patients with MSI-H/dMMR; in the 2 other patients, the MSI and MMR statuses were different, suggesting potential false positivity. In addition, the fold changes in ctDNA dynamics during treatment significantly correlated with changes in tumor size and CEA levels, as well as with droplet digital PCR copy number fold changes. In a patient with MET amplification, ctDNA NGS identified MET Y1230H as a potential acquired resistance mutation after crizotinib treatment, which responded to cabozantinib but not to capmatinib. Conclusions Initial tumor profiling using ctDNA NGS yielded outcomes comparable to those of tumor tissue NGS in guiding treatment for patients with newly diagnosed mCRC, thereby suggesting its utility as an initial profiling method in mCRC. Citation Format: Yongjun Cha, Bun Kim, Dong Woon Lee, Hyun Yang Yeo, Chang Won Hong, Kyung Su Han, Byung Chang Kim, Hee Jin Chang. Assessing the clinical value of ctDNA sequencing for initial tumor profiling in metastatic colorectal cancer patients with sufficient tumor tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2498.

Abstract 7385: Explainable AI model incorporating uncertainty estimation for enhanced MSI-H prediction and immunotherapy response in gastrointestinal cancer

Abstract Background: Microsatellite instability-high (MSI-H) tumors respond well to immune checkpoint blockade and oftentimes not to chemotherapeutics. Despite value of determining MSI status to guide therapy, many patients’ samples are not untested. Deep learning models may be able to predict MSI status by analyzing hematoxylin and eosin (H&amp;E) stained whole-slide images (WSIs). Validation of this tool will provide another tool to increase MSI testing. However, to be deployed into clinical routine care, prediction models need be externally validated in large and diverse patient cohorts. In addition, these models should provide uncertainty of prediction to help clinicians make informed decisions. Results: In this study, we introduce a novel Bayesian prediction model using whole-slide images (WSIs) and deep Gaussian processes (DGPs) in a weakly supervised learning context. Extensively tested on large datasets (n=3,146) from multiple centers, our model not only demonstrated superior performance but also showed that incorporating uncertainty into predictions significantly improves MSI prediction accuracy, achieving AUROC of &amp;gt;0.91 in colon cancer and &amp;gt;0.94 in gastric cancer. Additionally, an in-depth analysis within the gastric cancer cohort indicated a significant correlation between predicted MSI-H regions and immunotherapy response. Patients who responded to immune checkpoint inhibitors had a higher proportion of MSI-H regions (P-value &amp;lt; 0.05). This correlation was also observed in patients categorized as MSS but responsive to ICIs, highlighting the potential of our model to identify MSI-H patterns not detected through standard laboratory tests. This advancement could lead to more precise patient selection for ICI therapy, enhancing personalized treatment strategies in gastrointestinal cancer. Citation Format: Sunho Park, Minj Kim, Ji-Youn Sung, Jeong Hwan Park, Sung Hak Lee, Sam C. Wang, Jaeho Cheong, Tae Hyun Hwang. Explainable AI model incorporating uncertainty estimation for enhanced MSI-H prediction and immunotherapy response in gastrointestinal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7385.

Trends in utilization of MSI testing and reporting among patients with gastrointestinal cancers: A review of NCDB Database.

221 Background: MSI-H tumors have a different disease biology and clinical outcomes compared to MSS/MSI-low tumors. The frequency and pattern for MSI testing and reporting is unknown. The aim of this study was to characterize the trends of MSI testing and reporting among GI cancers. Methods: From the National Cancer Database, we identified all GI cancer patients from 2010 to 2016 to determine the number of patients where MSS/MSI low or MSI-H data were available. We describe the basic tumor and disease characteristics and treatment utilization for the two groups. Results: Between 2010-2016, MSI testing was done in 140,602 patients in colon, small intestine and rectal cancers among all GI cancers. MSI testing increased significantly during this study period (11,400 in 2010; 15,021 in 2011; 17,968 in 2012; 20,810 in 2013; 21,973 in 2014; 25,012 in 2015; 28,418 in 2016). We identified a total of 120,349 patients with MSI status reported, among these three tumor types, most commonly among colon followed by rectal and then small intestinal cancers. Overall 111,694 (92.8%) were MSS/MSI-low and 8,655 were MSI-H (7.2%). Among patients with reported MSI status, 52.1% were males and 47.9% were females. The mean age was 64.4 years. Most patients were whites (87.6%) and had insurance (96.8%), no existing comorbidities (70.4%), and grade 2 (70.8%) and AJCC Clinical Stage 4 (26.1%) GI cancer. A higher proportion of GI cancer patients with MSS/MSI-low utilized chemotherapy as first course compared to those with MSI high (48.2% vs 34.0%) whereas a lower proportion of GI cancer patients with MSS/MSI-low underwent a surgical procedure compared to those with MSI high (94.7% vs 97.1%). MSI status was reported most frequently in comprehensive community cancer program (40.3%) and academic center (34.8%), followed by integrated network cancer program (16.8%) and Community Cancer program (8.1%). Conclusions: The utilization of MSI testing has increased significantly between 2010 and 2016. Among all GI cancer patients, MSI status was most frequently reported in colon, rectum and small intestinal cancers. Comprehensive community cancer centers and academic centers reported MSI status more frequently than Integrated Network Cancer program and Community Cancer program.

Retrospective review of compliance with guideline-directed germline testing in microsatellite instability-high colorectal cancer treated at the Veterans Health Administration.

86 Background: Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome that confers an increased risk of colorectal cancer (CRC). As clinical and history features under-recognize LS cases (3-5% of CRC), universal screening of CRCs for LS is recommended. Patients whose CRCs are mismatch repair protein deficient (dMMR) and/or microsatellite instability high (MSI-H) are recommended to have subsequent genetics evaluation to screen for germline mutations. Confirmed LS changes cancer surveillance recommendations for affected patients and their relatives. Within Veterans Health Administration (VHA), GT is ordered by genetic counselors at genomic medicine telehealth centers (GMTC), after initial consultation. We aim to quantify rates at which CRC patients treated at the VHA complete germline testing (GT) when indicated. Methods: The electronic health records (EHRs) of VHA patients with known dMMR/MSI-H CRC were reviewed. Cases were extracted from both Veterans Affairs (VA) Puget Sound and referral VA MSI testing laboratories. Surgical pathology reports and clinical documentation were reviewed in Joint Longitudinal Viewer (JLV) to determine if GT was indicated and reason for non-testing, if not performed. Patients with known LS prior to development of CRC were excluded, and patients with dMMR in MLH1 or MSI-H with concurrent BRAFV600 mutation and/or MLH1 hypermethylation were considered to have sporadic CRC. Results: Of 110 patients with abnormal tumor LS screening; 39 (36%) patients’ tumor tissue underwent IHC for dMMR, 16 (14%) underwent PCR for MSI, and 55 (50%) had both. 45 (41%) patients were classified as somatic MSI-H. 65 (59%) patients met criteria for referral for GMTC and GT. Of these 65, 49 ultimately did not undergo GT and 16 did, which confirmed 4 cases of LS and revealed 1 variant of uncertain significance in the MLH1 gene. Reasons for non-testing were: 7 (14%) declined all cancer testing and treatment after CRC diagnosis or were lost to follow-up/declined establishment of cancer care, 3 (6%) declined referral to GMTC, 14 (29%) accepted referral to GMTC but never had consultation, 7 (14%) accepted referral to GMTC but declined GT when offered, and 18 (37%) were never offered GMTC referral or GT. Conclusions: A majority of dMMR/MSI-H cases with an indication for GT were referred for genetic counseling, but only a small subset completed testing. This analysis identified multiple areas for improvement, including a lack of recognition by providers for the need for GT, and lack of completion of testing by patients at multiple levels. Further evaluation of VHA-specific barriers is needed to improve the quality of delivered care.

A Panel-Based Mutational Signature of Mismatch Repair Deficiency is Associated With Durable Response to Pembrolizumab in Metastatic Castration-Resistant Prostate Cancer

Introduction/BackgroundImmune checkpoint inhibitors (ICIs) have limited efficacy in prostate cancer (PCa). Better biomarkers are needed to predict responses to ICIs. We sought to demonstrate that a panel-based mutational signature identifies mismatch repair (MMR) deficient (MMRd) PCa and is a biomarker of response to pembrolizumab. Patients and MethodsClinico-genomic data was obtained for 2664 patients with PCa sequenced at Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering (MSK). Clinical outcomes were collected for patients with metastatic castration-resistant PCa (mCRPC) treated with pembrolizumab at DFCI. SigMA was used to characterize tumors as MMRd or MMR proficient (MMRp). The concordance between MMRd with microsatellite instability (MSI-H) was assessed. Radiographic progression-free survival (rPFS) and overall survival (OS) were collected for patients treated with pembrolizumab. Event-time distributions were estimated using Kaplan-Meier methodology. ResultsAcross both cohorts, 100% (DFCI: 12/12; MSK: 43/43) of MSI-H tumors were MMRd. However, 14% (2/14) and 9.1% (6/66) of MMRd tumors in the DFCI and MSK cohorts respectively were microsatellite stable (MSS), and 26% (17/66) were MSI-indeterminate in the MSK cohort. Among patients treated with pembrolizumab, those with MMRd (n = 5) versus MMRp (n = 14) mCRPC experienced markedly improved rPFS (HR = 0.088, 95% CI: 0.011-0.70; P = .0064) and OS (HR = 0.11, 95% CI: 0.014-0.80; P = .010) from start of treatment. Four patients with MMRd experienced remissions of >= 2.5 years. ConclusionSigMA detects additional cases of MMRd as compared to MSI testing in PCa and identifies patients likely to experience durable response to pembrolizumab.

Detecting Microsatellite Instability in Endometrial, Colon, and Stomach Cancers Using Targeted NGS.

To develop a method for testing the MSI based on targeted NGS. Based on the results of previous studies, 81 microsatellite loci with high variability in MSI-H tumors were selected, and a method for calculating the MSI score was developed. Using the MSI score, we defined the MSI status in endometral (162), colon (153), and stomach (190) cancers. Accuracy of the MSI scores was evaluated by comparison with MMR immunohistochemistry for 137 endometrium (63 dMMR and 74 pMMR), 76 colon (29 dMMR and 47 pMMR), and 81 stomach (8 dMMR and 73 pMMR) cancers. Classification of MSS and MSI-H tumors was performed with AUC (0.99), sensitivity (92%), and specificity (98%) for all tumors without division into types. The accuracy of MSI testing in endometrial cancer was lower than for stomach and colon cancer (0.98, 87%, and 100%, respectively). The use of 27 loci only, the most informative for endometrial cancer, increased the overall accuracy (1.00, 99%, and 99%). Comparison of MSI score values in 505 tumors showed that MSI score is significantly higher in colon (p < 10-5) and stomach (p = 0.008) cancer compared with endometrial cancer. The MSI score accurately determines MSI status for endometrial, colon, and stomach cancers and can be used to quantify the degree of MSI.

A simplified two-marker immunohistochemistry strategy for Lynch syndrome screening in endometrial cancer patients.

To examine the efficacy of MSH6 and PMS2 immunohistochemistry (IHC) as a screening method for Lynch syndrome in endometrial cancer patients. Through multidisciplinary discussions, an institutional MSH6 and PMS2 IHC-initiated cascade test (MSH6, PMS2 IHC→microsatellite instability [MSI] assay→germline mismatch repair [MMR] gene sequencing) was developed to screen for Lynch syndrome in endometrial cancer patients. Testing was performed on a consecutive cohort of 218 newly diagnosed endometrial cancer patients who underwent surgery at a tertiary hospital in the Republic of Korea between August 2018 and December 2020. The number of MMR deficiencies (MSH6 or PMS2 loss in IHC) and. of subsequent tests (MSI assay and germline MMR gene sequencing) were examined. MMR deficiency was detected in 52 of the 218 patients (24.0%). Among these 52 patients, 34 (65.0%) underwent MSI testing, of which 31 (91.0%) exhibited high MSI. Of the 31 patients with MSI-high status, 15 (48.0%) underwent germline MMR gene sequencing. Subsequently, Lynch syndrome was diagnosed in five patients (33.0%). Lynch syndrome screening using MSH6 and PMS2 IHC-initiated cascade testing is a viable strategy in the management of endometrial cancer. A simplified strategy (MSH6 and PMS2 IHC→germline MMR gene sequencing) was proposed because most women with MMR deficiencies exhibited high MSI.

Pan-Cancer Prevalence of Microsatellite Instability-High (MSI-H) Identified by Circulating Tumor DNA and Associated Real-World Clinical Outcomes.

Immune checkpoint inhibitors are approved for advanced solid tumors with microsatellite instability-high (MSI-H). Although several technologies can assess MSI-H status, detection and outcomes with circulating tumor DNA (ctDNA)-detected MSI-H are lacking. As such, we examined pan-cancer MSI-H prevalence across 21 cancers and outcomes after ctDNA-detected MSI-H. Patients with advanced cancer who had ctDNA testing (Guardant360) from October 1, 2018, to June 30, 2022, were retrospectively assessed for prevalence. GuardantINFORM, which includes anonymized genomic and structured payer claims data, was queried to assess outcomes. Patients who initiated new treatment within 90 days of MSI-H detection were sorted into immunotherapy included in treatment (IO) or no immunotherapy included (non-IO) groups. Real-world time to treatment discontinuation (rwTTD) and real-world time to next treatment (rwTTNT) were assessed in months as proxies of progression-free survival (PFS); real-world overall survival (rwOS) was assessed in months. Cox regression tests analyzed differences. Colorectal cancer, non-small-cell lung cancer (NSCLC), prostate cancer, gastroesophageal cancer, and uterine cancer (UC) were assessed independently; all other cancers were grouped. In total, 1.4% of 171,881 patients had MSI-H detected. Of 770 patients with outcomes available, rwTTD and rwTTNT were significantly longer for patients who received IO compared with non-IO for all cancers (P ≤ .05; hazard ratio [HR] range, 0.31-0.52 and 0.25-0.54, respectively) except NSCLC. rwOS had limited follow-up for all cohorts except UC (IO 39 v non-IO 23 months; HR, 0.18; P = .004); however, there was a consistent trend toward prolonged OS in IO-treated patients. These data support use of a well-validated ctDNA assay to detect MSI-H across solid tumors and suggest prolonged PFS in patients treated with IO-containing regimens after detection. Tumor-agnostic, ctDNA-based MSI testing may be reliable for rapid decision making.

Efficacy of Immune Checkpoint Inhibition and Cytotoxic Chemotherapy in Mismatch Repair-Deficient and Microsatellite Instability-High Pancreatic Cancer: Mayo Clinic Experience.

Pancreatic cancer (PC) carries a poor prognosis with high rates of unresectable/metastatic disease at diagnosis, recurrence after resection, and few systemic therapy options. Deficient mismatch repair (dMMR)/high microsatellite instability (MSI-H) PCs demonstrated uncharacteristically poor outcomes in KEYNOTE-158, evaluating pembrolizumab in MSI-H solid tumors. Our study aggregates the Mayo Clinic experience with dMMR/MSI-H PCs, characterizing the clinical, molecular, and treatment response patterns with a focus on response to immune checkpoint inhibitors (ICIs). Retrospective data were collected from the electronic medical record from December 2009 to February 2023. Patients were included if they had a pathologically confirmed pancreatic malignancy and had (1) deficient expression of mismatch repair (MMR) proteins by tumor immunohistochemistry, (2) pathogenic mutation of MMR genes on genomic sequencing, and/or (3) MSI-H by polymerase chain reaction. Thirty-two patients were identified for inclusion, with all stages of disease represented. Sixteen of these patients underwent surgery or chemoradiotherapy. Of these patients, uncharacteristically favorable responses were seen, with a recurrence rate of only 19% (n = 3) despite a median follow-up of 25 months. In the palliative setting, excellent responses to ICI were seen, with overall response rate (ORR) of 75% (20% complete response). Median time to disease progression was not reached. Response rates to cytotoxic chemotherapy in the palliative setting were poor, with 30% ORR and median time to progression of 4 months. We observed a high rate of discrepancy between MMR and MSI testing methods, representing 19% of the entire cohort and 26% of evaluable cases. Our data argue for the preferential use of ICI over cytotoxic chemotherapy in any patient with dMMR/MSI-H PC requiring systemic therapy, including in the metastatic and adjuvant/neoadjuvant settings.

A comparison of performance of 6-mononucleotide site panel and NCI panel for microsatellite instability detection in patients with colorectal adenocarcinoma

BackgroundMicrosatellite instability (MSI) represents as a molecular hallmark of deficient MMR system at the genomic level. Increasing clinical significance of MSI status highlights the necessity of simple, accurate markers for detection. Although 2B3D NCI panel is the most widely applied, it has been questioned whether the performance of NCI panel is second to none in MSI detection. MethodsWe evaluated the efficacy of the NCI panel versus a 6-mononucleotide site panel (BAT25, BAT26, NR21, NR24, NR27, and MONO-27) in assessing MSI status of 468 Chinese patients with CRC, and compared MSI test results with the results by immunohistochemistry of four MMR proteins (MLH1, PMS2, MSH2, MSH6) in the present study. Clinicopathological variables were also collected, and their associations with MSI or MMR proteins status were analyzed using either the chi-square test or the Fisher’s exact test. ResultsMSI-H/dMMR was significantly associated with right colon involvement, poor differentiation, early stage, mucinous adenocarcinoma, negative lymph node, less neural invasion, and KRAS/NRAS/BRAF wild-type. As to the efficiency of detecting deficient MMR system, both panels had good concordance with MMR proteins expression by IHC, and 6-mononucleotide site panel outperformed NCI panel in sensitivity, specificity, positive predictive value, and negative predictive value numerically despite the lack of statistical significance. The advantage was more obvious in the sensitivity and specificity analyses of each single microsatellite markers from 6-mononucleotide site panel in comparison with NCI panel. Additionally, the rate of MSI-L detected by 6-mononucleotide site panel was much lower than that detected by the NCI panel (0.64% vs. 2.86%, P = 0.0326). Conclusion6-mononucleotide site panel had a greater ability to help resolve cases of MSI-L into either MSI-H or MSS. We propose that 6-mononucleotide site panel may be potentially more suitable than NCI panel for Chinese CRC population. Large-scale studies are warranted to validate our findings.

A novel somatic mutation in POLE exonuclease domain associated with ultra-mutational signature and MMR deficiency in endometrial cancer: a case report

BackgroundDefect in proofreading exonuclease activity of polymerases epsilon and delta (Pols ε and δ) leads to mutagenesis and genomic instability and has been described in several cancer types. Somatic POLE exonuclease domain mutations (EDMs) have been reported in 7–12% endometrial cancers (ECs) and defined a subgroup of endometrial cancers with ultrahigh somatic mutation frequencies, high tumor infiltrated lymphocytes and favorable outcomes.Case presentationHerein, we presented a novel somatic mutation in POLE exonuclease domain associated with ultra-mutational signature and MMR deficiency in endometrial cancer. A novel POLE EDM (p.T278K) was found by a 11-gene NGS panel. The MSS status detected by the MSI test was inconsistent with the dMMR status by IHC. The loss of MSH6 expression in the tumor could be interpreted by the two nonsense mutations (p.E1234* and p.E1322*) of the MSH6 gene which may lead to truncated proteins. The T278K mutation was pathogenic identified by a 602-gene NGS panel with 27.3% of C > A substitution, 0.6% of indels, 0.6% of C > G substitution and a high TMB of 203.8 mut/Mb.ConclusionsWe report an endometrial cancer patient harbored a novel somatic POLE T278K mutation. This mutation was a novel pathogenic POLE EDM should be considered as “POLE (ultramutated)” in clinical practice for the molecular classification of EC.

Clinical and mutational profiles of microsatellite instability (MSI-H) in intrahepatic cholangiocarcinoma (iCCA).

607 Background: Microsatellite instability (MSI-H) and increased tumor mutation burden (TMB) have been associated with clinical benefit from immunotherapy. A small subset of patients with intrahepatic cholangiocarcinoma (iCCA) have microsatellite instability (MSI-H). Understanding their clinical outcomes and genomic landscape has been limited. These patients may derive clinical benefit from immunotherapy compared to chemotherapy. Methods: 7565 cases of iCCA underwent comprehensive genomic profiling of 324 genes (FoundationOne CDx). Prevalence of genomic alterations in cases with MSI-H were compared with MSI-low and MSS iCCA using Fischer’s exact test with Bonferonni correction. Clinical and pathological data were collected by retrospective chart review for patients with MSI-H/dMMR iCCA. Results: Among 7565 iCCA cases identified, 137 (1.8%) were MSI-H. Compared to MSS/MSI-low cases, MSS-H patients were more likely to be male and have Lynch syndrome. Median TMB was 21.7 (muts/Mb). MSI-H cases were enriched for genomic alterations (GA) in APC (13.9%), TP53 (59.9%), ARID1A (13.9%), and PRBM1 (37.2%). MSI-H cases had lower frequencies of previously identified, actionable iCCA drivers such as FGFR2 fusions (0% v 9%, p=NS), IDH1 (3.7% v 14.5%, p&lt;0.0001) and IDH2 (0% v 4.1%, p=0.007). Compared to MSS/MSI-low, MSI-H cases had higher GA in PIK3CA (16.8% v 6.6%, p=&lt;0.0001), PTEN (10.9% v 2.8%, p=&lt;0.0001), and BRCA2 (10.2% v 2%, p=&lt;0.0001). MSI-H cases had lower GA in CDKN2A (24.1% v 30.9%, p=0.09) and MTAP loss (3.4% v. 15.5%, p&lt;0.0001). Five patients were identified with dMMR/MSI-H iCCA out of 974 patients at a single institution (0.5%). Median age at diagnosis was 53 years (range 46-70) and 83% were male (n=4). Two patients had resectable disease at time of diagnosis. TMB range was 20-29 (muts/Mb). Patients had 4-6 co-mutations on average with the most common GA being TP53, ARID1A and CDKN2A. One patient had Lynch syndrome with germline alteration of MLH1 gene and one patient had a germline BRCA mutation. One patient was noted to have FGFR2 rearrangement. Gemcitabine/Cisplatin was given to 3 of 6 patients as first-line (1L) therapy, with median progression free survival of 4 months. One hundred percent of patients received immunotherapy (IO) as first or second-line (2L) therapies. Patients receiving IO in the 1L had responses ranging from 4 to 9 months. Three patients have ongoing responses. Median overall survival ranged from 12 months to &gt;18 months. Two patients presented with CNS involvement and did not respond to immunotherapy-based regimens. Conclusions: MSI-H represents a small subset of patients with iCCA. High-TMB noted amongst MSI-H iCCA. Currently, MSI testing is not universally performed and may be necessary to identify and best treat these patients. These findings support the development of personalized immunotherapy treatment strategies for this distinct patient population.

Fast and label-free automated detection of microsatellite status in early colon cancer using artificial intelligence integrated infrared imaging

PurposeMicrosatellite instability (MSI) due to mismatch repair (MMR) defects accounts for 15–20% of colon cancers (CC). MSI testing is currently standard of care in CC with immunohistochemistry of the four MMR proteins representing the gold standard. Instead, label-free quantum cascade laser (QCL) based infrared (IR) imaging combined with artificial intelligence (AI) may classify MSI/microsatellite stability (MSS) in unstained tissue sections user-independently and tissue preserving. MethodsParaffin-embedded unstained tissue sections of early CC from patients participating in the multicentre AIO ColoPredict Plus (CPP) 2.0 registry were analysed after dividing into three groups (training, test, and validation). IR images of tissue sections using QCL-IR microscopes were classified by AI (convolutional neural networks [CNN]) using a two-step approach. The first CNN (modified U-Net) detected areas of cancer while the second CNN (VGG-Net) classified MSI/MSS. End-points were area under receiver operating characteristic (AUROC) and area under precision recall curve (AUPRC). ResultsThe cancer detection in the first step was based on 629 patients (train n = 273, test n = 138, and validation n = 218). Resulting classification AUROC was 1.0 for the validation dataset. The second step classifying MSI/MSS was performed on 547 patients (train n = 331, test n = 69, and validation n = 147) reaching AUROC and AUPRC of 0.9 and 0.74, respectively, for the validation cohort. ConclusionOur novel label-free digital pathology approach accurately and rapidly classifies MSI vs. MSS. The tissue sections analysed were not processed leaving the sample unmodified for subsequent analyses. Our approach demonstrates an AI-based decision support tool potentially driving improved patient stratification and precision oncology in the future.

Microsatellite Status Detection of Colorectal Cancer: Evaluation of Inconsistency between PCR and IHC.

Objective: An essential component of precision medical treatment for colorectal cancer (CRC) is the use of microsatellite state in combination with polymerase chain reaction (PCR) and immunohistochemistry (IHC) as the primary clinical detection methods. Microsatellite instability-high (MSI-H) or mismatch-repair deficiency (dMMR) accounts for about 15% of all CRC patients. Characterized by a high mutation burden, MSI-H is a predictive biomarker of immune checkpoint inhibitors (ICIs). Misdiagnosis of microsatellite status has been shown to be an important cause of resistance to immune checkpoint inhibitors. Therefore, a rapid and accurate assessment of microsatellite status can be beneficial for precision medicine in CRC. Methods: We evaluated the rate of discordance between PCR and IHC detection of microsatellite status from a cohort of patients that had 855 colorectal cancers. PCR-based microsatellite assay was performed using a set of five monomorphic mononucleotide makers (NR-24, BAT-25, CAT-25, BAT-26, MONO-27) and two polymorphic pentanucleotide (Penta D and Penta E). IHC was used to detect the absence of mismatch repair proteins (MLH1, MSH2, MSH6, and PMS2). The inconsistency rates of the two assays were evaluated. Results: Among 855 patients,15.6% (134 to 855) cases were identified as MSI-H by PCR, whereas 16.9% (145 to 855) cases were identified as dMMR by IHC. There were 45 patients with discordant results between IHC and PCR. Of these, 17 patients were classified as MSI-H/pMMR and 28 patients as MSS/dMMR. When the clinicopathological characteristics of these 45 patients were compared to those of the 855 patients, it was found that more patients were younger than 65 years old (80% to 63%), more were male (73% to 62%), more were located in the right colon (49% to 32%), and more were poorly differentiated (20% to 15%). Conclusion: Our study demonstrated a high concordance between the PCR and IHC results. In order to reduce the ineffective treatment of ICIs due to MSI misdiagnosis, the patient's age, gender, tumor location and degree of differentiation should be included in the clinician's selection of MSI testing in colorectal cancer.

Clinicopathological characteristics of high microsatellite instability/mismatch repair-deficient colorectal cancer: A narrative review.

Colorectal cancers (CRCs) with high microsatellite instability (MSI-H) and deficient mismatch repair (dMMR) show molecular and clinicopathological characteristics that differ from those of proficient mismatch repair/microsatellite stable CRCs. Despite the importance of MSI-H/dMMR status in clinical decision making, the testing rates for MSI and MMR in clinical practice remain low, even in high-risk populations. Additionally, the real-world prevalence of MSI-H/dMMR CRC may be lower than that reported in the literature. Insufficient MSI and MMR testing fails to identify patients with MSI-H/dMMR CRC, who could benefit from immunotherapy. In this article, we describe the current knowledge of the clinicopathological features, molecular landscape, and radiomic characteristics of MSI-H/dMMR CRCs. A better understanding of the importance of MMR/MSI status in the clinical characteristics and prognosis of CRC may help increase the rates of MMR/MSI testing and guide the development of more effective therapies based on the unique features of these tumors.