Prevalence Of Microsatellite Instability Research Articles

Molecular pathogenesis of microsatellite instability-high early state colorectal adenocarcinoma in India.

The prevalence of microsatellite instability (MSI) subtype among all colon cancers in India is about 30 %, approximately two times more than that of western population suggesting different molecular pathogeneses. A NanoString analysis-based Pan cancer differential expression (DE) profile was determined in a primary cohort of early-stage CRC (tumor=10, normal=7), and correlated against MSI status. Using RT-PCR, tumor-specific DE genes were validated in another cohort of MSI-high CRC (n=15). Among the most differentially expressed genes, AXIN2, ETV4, and RNF43 were tumor cell-specific signals, while a set of genes including COL11A1, COMP, INHBA, SPP1, MMP3, TLR2, and others were immune cell-specific signals, that had a differential expression between MSI and MSS groups. When overlapped with The Cancer Genome Atlas (TCGA) studies using the Tumor immune estimation resource tool (TIMER), and protein-protein interaction analysis by STRING.db, these genes were segregated to representative tumor cells and immune cells. On validation, the tumor-specific gene signals were inversely associated with TLR4 expression. The differential expression distribution of AXIN2, ETV4, and RNF43 among tumor and immune cells, suggests more than one pathological subset in the MSI-H subgroup of early-stage CRC in the Indian population.

Multiparametric MRI subregion radiomics for preoperative assessment of high-risk subregions in microsatellite instability of rectal cancer patients: A multicenter study.

Microsatellite instability (MSI) is associated with treatment response and prognosis in patients with rectal cancer (RC). However, intratumoral heterogeneity limits MSI testing in patients with RC. We developed a subregion radiomics model based on multiparametric magnetic resonance imaging (MRI) to preoperatively assess high-risk subregions with MSI and predict the MSI status of patients with RC. This retrospective study included 475 patients (training cohort, 382; external test cohort, 93) with RC from two participating hospitals between April 2017 and June 2023. In the training cohort, subregion radiomic features were extracted from multiparametric MRI, which included T2-weighted, T1-weighted, diffusion-weighted, and contrast-enhanced T1-weighted imaging. MSI-related subregion radiomic features, classical radiomic features, and clinicoradiological variables were gathered to build five predictive models using logistic regression. Kaplan-Meier survival analysis was conducted to explore the prognostic information. Among the 475 patients (median age, 64 years [interquartile range, IQR: 55-70 years];304 men and 171 women), the prevalence of MSI was 11.16% (53/475). The subregion radiomics model outperformed the classical radiomics and clinicoradiological models in both training (area under the curve [AUC]=0.86, 0.72, and 0.59, respectively) and external test cohorts (AUC=0.83, 0.73, and 0.62, respectively). The subregion-clinicoradiological model combining clinicoradiological variables and subregion radiomic features performed the optimal, with AUCs of 0.87 and 0.85 in the training and external test cohorts, respectively. The 3-year disease-free survival rate of MSI groups predicted based on the model was higher than that of the predicted microsatellite stability (MSS) groups in both patient cohorts (training, P=0.032; external test, P=0.046). We developed and validated a model based on subregion radiomic features of multiparametric MRI to evaluate high-risk subregions with MSI and predict the MSI status of RC preoperatively, which may assist in individualized treatment decisions and positioning for biopsy.

Abstract 6422: Comprehensive proteogenomic profiling and biomarker analyses in resected extrahepatic cholangiocarcinoma: A prespecified exploratory analysis of the phase 2 STAMP trial

Abstract Background: Biliary tract cancer constitutes a heterogeneous group of diseases with a limited understanding of its molecular characteristics and prognostic/predictive biomarkers. We performed prespecified exploratory analyses of the STAMP trial, a multicenter randomized phase 2 trial of adjuvant capecitabine (CAP) or gemcitabine plus cisplatin (GemCis) for patients with resected extrahepatic cholangiocarcinoma (EH-CCA) with regional lymph node metastasis. Methods: Among 101 patients included in the intention-to-treat population of the STAMP trial, a total of 89 patients (45 in the GemCis group and 44 in the CAP group) were included in the current biomarker analysis after excluding 12 patients without available tissue and blood samples. Whole exome sequencing and proteomics were performed using surgical specimens. Results: TP53 (63%), SMAD4 (20%), and KRAS (18%) mutations were the most frequent in the pooled population. Somatic mutations in homologous recombination deficient (HRD) genes were present in 20% of patients, while one patient (1%) had a germline ATM mutation. The prevalence of microsatellite instability was 1%. Somatic mutations in known targetable genes were observed in 54 patients (60.7%) and proteogenomic integrative analysis revealed significant HER2 pathway alteration with HER2 amplification in 4 patients (7%). The characteristics of prognostic biomarkers varied by the adjuvant regimen used. In the adjuvant GemCis group, somatic mutations were associated with poor disease-free survival (DFS) and overall survival (OS), including KRAS (log-rank p=0.004 for DFS and p=0.003 for OS), FBXW7 (p=0.021 for DFS and p=0.011 for OS), and PIK3CA (p<0.001 for DFS and p=0.042 for OS) mutations. In the adjuvant CAP group, copy number alterations (CNAs) such as 8q24.21 amplification (p=0.006 for DFS and p=0.707 for OS) and 3q26.1 amplification (p=0.020 for DFS and p=0.026 for OS) were associated with poor survival, while 11q13.3 amplification (p=0.017 for DFS and p=0.099 for OS) was associated with improved survival. Additionally, a higher HRD score showed a tendency toward better DFS and OS in the GemCis group, but not in the CAP group, although it did not reach statistical significance in both groups (p>0.05). Non-negative matrix clustering of proteomics data classified patients into 4 clusters. Among those, cluster 2, which showed alterations in the metabolism pathway, was associated with higher CNA level, higher tendency of HRD scores, and favorable survival with GemCis (p=0.039 for DFS and p=0.100 for OS) but not with CAP. Conclusions: Comprehensive proteogenomic analyses enable the identification of prognostic biomarkers and may guide the selection of adjuvant chemotherapy in resected EH-CCA. Citation Format: Hyehyun Jeong, Ji-Hye Oh, Hee-Sung Ahn, Baek-Yeol Ryoo, Kyu-pyo Kim, Jae Ho Jeong, Inkeun Park, Seung-Mo Hong, Jinho Shin, Chae Won Park, Yoo Sook Cho, Kyunggon Kim, Chang Ohk Sung, Changhoon Yoo. Comprehensive proteogenomic profiling and biomarker analyses in resected extrahepatic cholangiocarcinoma: A prespecified exploratory analysis of the phase 2 STAMP trial [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 6422.

Clinical characterization and therapeutic outcomes of patients (pts) with colorectal cancer (CRC) harboring somatic BRCA1/2 mutations.

134 Background: Somatic BRCA1/2 mutations in BRCA-associated cancers increase therapeutic sensitivity to platinum-based chemotherapies and PARP inhibitors, but the implications of BRCA mutations in non- BRCA-associated cancers such as CRC is unknown and hypothesized to be shaped by tumor lineage. We thus conducted a retrospective analysis of outcomes with platinum-based chemotherapy and PARP inhibition in pts with CRC, where the estimated prevalence of BRCA1/2 alterations is 3-4%. Methods: Pts with blood or tissue next generation sequencing (NGS) positive for a somatic BRCA1/2 variant and a diagnosis of CRC were identified from a single institution database. The pathogenicity of each mutation was annotated using public genomic databases (e.g. ClinVar). Pt characteristics were compared using Fisher’s exact test. Log-rank test was used for comparison of survival distribution among groups. Results: 8,258 NGS reports with a BRCA1/2 alteration from 1760 cancer pts were identified of which 189 (11%) had a diagnosis of CRC. 54/189 CRC pts (29%) had ≥1 pathogenic BRCA1/2 variant, 19 pts (10%) had ≥1 benign variant, and 134 pts (69%) had 1 ≥ variant of unknown significance (VUS); 26 pts (14%) had more than one BRCA1/2 variant. Pts with ≥1 pathogenic mutation (n=54) were more likely to have an inactivating DNA polymerase epsilon (POLE) mutation versus pts with only benign/VUS BRCA1/2 variants (n=135) (20% vs 6%, p=0.004) while prevalence of microsatellite instability (MSI-H) (19% vs 13%, p=0.37) and Ras/Raf (53% vs 53%, p=1.00) were similar between groups. Median progression free survival (PFS) among 115 CRC pts (unselected for BRCA1/2 pathogenicity) who received an oxaliplatin-based regimen for advanced disease in the 1st line (n=52) was similar to the median PFS among pts who received an irinotecan-based regimen (n=63) (7.0 mths vs 7.0 mths, p=0.48). Median PFS with an oxaliplatin-based regimen in the 1st line among 52 pts with pathogenic BRCA1/2 variants (n=13) was 5.1 mths vs 7.4 mths among pts with benign/VUS BRCA1/2 variants (n=39) (p=0.398). There were no significant differences in median PFS among pts with a pathogenic vs benign/VUS BRCA1/2 variants when the analysis was restricted to pts with BRCA1/2 variants identified in tissue (p=0.76) and to pts without co-occurring driver mutations (Ras/Raf, MSI-H, and/or POLE) (p=0.1). Overall survival in patients with advanced disease was similar between pts with a pathogenic (n=52) vs benign/VUS (n=122) BRCA variants (37.1 mths vs 45.1 mths, p=0.14). 6 pts (4 with pathogenic BRCA1/2 and 3 with VUS) received a PARP inhibitor after a median of 3 lines of treatment and the best response was disease progression in 6 pts (100%). Conclusions: In the context of CRC, somatic BRCA1/2 mutations frequently co-occur with pathogenic POLE mutations, but do not appear to confer therapeutic benefit to platinum-based chemotherapy and PARP inhibitors.

Abstract B042: Clinical and molecular characterization of Lynch syndrome-associated pancreas adenocarcinoma (PDAC)

Abstract Background: Lynch syndrome (LS) is a pan-cancer predisposition syndrome caused by pathogenic germline alterations (gPVs) in DNA mismatch repair genes (PMS2, MSH6, MLH1, MSH2, EPCAM). It is characterized by microsatellite instability (MSI)/deficient DNA mismatch repair (dMMR) of associated tumors, which predicts immune checkpoint blockade (ICB) response. Clinical and molecular features of LS-PDAC are not well defined. Herein we sought to describe clinical characteristics, MSI prevalence, and ICB response. Methods: Patients (pts) with LS-associated gPV and PDAC who had consented to IRB-approved protocol of matched tumor-normal sequencing (MSK-IMPACT from which MSIsensor status derivable) were included. MiMSI utilized to assess microsatellite stable (MSS) PDACs to account for low tumor content. MMR status defined with immunohistochemistry (IHC). Composite MSI adjudicated as either loss of MMR protein expression by IHC or MSI by MSISensor or MiMSI. FACETS algorithm assessed biallelic MMR gene alteration status. Mutational signature analysis performed on MSI tumors with deconstructSigs. Results: N=29 pts identified with LS-associated gPVs and PDAC: 10 MSH2 (34%), 9 MSH6 (31%), 7 PMS2 (24%), 2 MLH1 (7%), 1 EPCAM (3%). Majority white (24, 83%) and female (15, 52%). At diagnosis 62% pts early-stage disease (8 stage II, 10 stage III), 11 stage IV. Median age at diagnosis: 68 yrs (range 45-88). Eighteen (62%) had first-degree family history of LS spectrum cancers. Four pts had metachronous cancers (2 CRC, 1 uterine, 1 CRC and uterine). Orthogonal tumor testing feasible in 22 pts (76%). MiMSI (conducted for 16) reclassified 4 as MSI that were indeterminate by MSISensor; IHC (conducted for 15) classified 1/8 tumors as dMMR previously MSS on MSISensor. Whole cohort MSI status: 16 composite MSI (59%), 11 MSS (41%), and 2 MS unknown. gPVs in N= 16 with MSI tumors: 9 MSH2, 4 MSH6, 2 MLH1, and 1 PMS2; amongst N= 11 MSS tumors: 6 gMSH6, 4 gPMS2, and 1 EPCAM. Amongst 24 evaluable pts biallelic loss identified in 6 pts with MSI disease. The dominant mutational signature in 4/6 was Clock/aging and not MSI; 2 of these 4 harbored gMSH2, and 2/4 gMSH6. KRAS and TP53 mutations more common in sporadic MSS PDAC than LS-PDAC (p=0.001, p=0.005 respectively); KRAS G12R was enriched in LS PDAC vs sporadic PDAC (31.6% vs 15.3%, p=0.06). N= 13 (47%) received ICB, inclusive of 4 reclassified by MiMSI and 8 with metastatic disease. In evaluable pts with MSI disease, overall response rate 60% (2 CR, 4 PR, 4 SD). N= 1 MSS PDAC had POD as best response. Median ICB duration: 27.7 months (95% CI 9.0, NR). Conclusion: In this LS PDAC cohort we observed a higher proportion of MSH6, MSH2, PMS2 gPVs relative to other cohorts. LS-PDAC MSI arises frequently in association with gMSH2, gMLH1. MSI status determination with orthogonal testing is critical to appropriately select pts for ICB. Outcome to ICB in LS PDAC MSI comparable to other tumor types highlighting the importance of MSI as a predictive biomarker in PDAC. Citation Format: Emily Harrold, Catherine A. O'Connor, David Lin, Andrea Gazzo, Henry Walch, Megha Ranganathan, Amanda Catchings, Sarah Kane, Fergus Keane, Deborah M. Thurtle-Schmidt, Fiyinfolu Balogun, Anna Varghese, Kenneth Yu, David Kelsen, Alicia Latham, Britta Weigelt, Wungki Park, Zsofia Stadler, Eileen M. O'Reilly. Clinical and molecular characterization of Lynch syndrome-associated pancreas adenocarcinoma (PDAC) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B042.

The identification of a PTEN-associated gene signature for the prediction of prognosis and planning of therapeutic strategy in endometrial cancer.

Endometrial cancer (EC) is one of the most common malignancies among women. To improve the prognosis and treatment of EC, finding out a phosphatase and tensin homolog deleted on chromosome 10 (PTEN)-associated prognostic signature would be beneficial. EC clinical data, genetic mutation data, and transcriptome data were downloaded from The Cancer Genome Atlas (TCGA) database. To clarify the specific PTEN-associated signature, cox regression analyses were performed. The clinical value of the selected signature on the overall survival (OS) and the secretoglobin family 2A member 1 (SCGB2A1)-independent analysis, immune and functional analysis were investigated respectively. Five hundred and fourteen EC samples were screened and PTEN mutation occupied 57%. Enrichment analysis indicated that mutant-type PTEN was enriched for pathways related to the upregulated human T-cell leukemia virus-1 (HTLV-1) infection and estrogen signaling pathway. SCGB2A1 was identified by cox regression analysis. Immune analysis exhibited significant immune infiltration with higher expression of T cells, B cells, and macrophage groups. Immune-checkpoint transcripts CD274 molecule (CD274), and cytotoxic T-lymphocyte associated protein 4 (CTLA4), hepatitis A virus cellular receptor 2 (HAVCR2), lymphocyte activation gene 3 (LAG3), programmed cell death 1 (PDCD1), PDCD1 ligand 2 (PDCD1LG2), T cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibition motif domains (TIGIT), and sialic acid binding immunoglobulin like lectin 15 (SIGLEC15) were discovered statistically different. In addition, the low-SCGB2A1 group had worse OS than the high-SCGB2A1 group. SCGB2A1 showed significant area under the curve (AUC) values in a time-dependent receiver operating characteristic (ROC) analysis. Prevalence of microsatellite instability (MSI) was detected and SCGB2A1 showed a negative correlation with EC. Immune checkpoint blockade (ICB) response indicated a worse immune response in the low-SCGB2A1 group. The distribution of one-class linear regression (OCLR) scores reflected the negative correlation between messenger RNA expression-based stemness index (mRNAsi) and prognostic gene expression. Furthermore, several SCGB2A1-related signaling pathways in EC were identified. SCGB2A1 is a prognostic immunometabolic signature for patients with EC, which may help improve the prognosis and therapeutic effect.

Variation in KRAS/NRAS/BRAF-Mutation Status by Age, Sex, and Race/Ethnicity Among a Large Cohort of Patients with Metastatic Colorectal Cancer (mCRC).

Racial/ethnic disparities in metastatic colorectal cancer (mCRC) survival are well documented as is the impact that tumor mutation of KRAS and BRAF has on prognosis. It has been suggested that frequency differences of KRAS- and BRAF-mutated tumors may partially explain this disparity. Demographic differences in mutation frequency are not well established nor whether mutation and microsatellite instability (MSI) differentially impact survival among groups. Using data for 11,117 patients diagnosed with de-novo mCRC from an electronic health record-derived database we estimated adjusted odds ratios (aOR) to characterize the association between demographics and MSI and KRAS/NRAS/BRAF-mutation status. Stratified Cox models were used to identify differences in overall survival (OS), adjusting for treatment and demographics. Being female, compared to male, (aORKRAS:1.33 (1.23-1.44); aORBRAF:1.84 (1.56-2.16)), and non-Hispanic Black race (NHB), compared to non-Hispanic White (NHW) (aORKRAS:1.62 (1.42-1.85); aORBRAF: 0.55 (0.38-0.77)) were associated with KRAS- or BRAF-mutant tumors. MSI prevalence was similar across race/ethnicity but higher in women. BRAF-mutant tumors were associated with poorer prognosis overall, especially among non-white patients. Among patients who had KRAS/NRAS/BRAF-WT tumors we observed no difference in OS by race or MSI. Among patients with KRAS-mutant tumors, Hispanic patients had more favorable prognosis adjusted hazards ratio (aHR) = 0.76 (0.65-0.89)) than their NHW counterparts. Among those with BRAF-mutant tumors, NHB patients had poorer prognosis than NHW patients (aHR:1.78 (1.08-2.93)). MSI and frequency of KRAS and BRAF mutations differed by demographics. Racial/ethnic disparities in OS differed by mutation. Future studies should explore biological and/or social determinants underlying these differences.

The Role of Immunotherapy in Advanced and Recurrent MMR Deficient and Proficient Endometrial Carcinoma

ABSTRACT The incidence of endometrial cancer has increased approximately 40% in the last decade along with a 60% increase in the number of associated deaths. Although surgery along with possible adjuvant therapy provides good results in patients with early-stage disease, patients with advanced or recurrent disease have limited options and typically undergo chemotherapy with no standard second-line therapy. Immunotherapy with checkpoint inhibitors (ICIs) is a promising option in this setting. This review aims to improve knowledge on the role of ICIs in advanced/recurrent endometrial cancer in different contexts based on molecular and genomic profiling. The DNA mismatch repair (MMR) system is a highly conserved mechanism that acts to restore DNA integrity after mismatching mistakes during replication, recombination, or iatrogenic damage. Somatic or germline mutations or epigenetic silencing can all result in possible inactivation of MMR genes, resulting in an MMR-deficient (dMMR) genotype. Short tandem repeats, called microsatellites, are repetitive DNA sequences that facilitate slippage or replication errors that are generally repaired by MMR; however, in a dMMR context, these can result in repeat mutations called microsatellite instability (MSI). The presence of MSI characterizes a hypermutable state of cell, and MSI tumors have elevated expression of the checkpoint programmed death 1 ligand (PD-L1). Microsatellite instability/dMMR testing may have potential prognostic value as a predictor of response to immunotherapy. Endometrial cancer is the solid tumor characterized by the highest prevalence of MSI−/dMMR, which is present in 30% and 13% to 30% of primary and recurrent endometrial cancer, respectively. Recently, results from the KEYNOTE-158 trial reporting on the efficacy and safety of pembrolizumab (programmed death 1 [PD-1] ICI) in patients with MSI-H/dMMR endometrial cancer who progressed after a prior line of chemotherapy showed an objective response rate of 48%, median progression-free survival of 13.1 months, and a low rate of high-grade toxicity. Results from the GARNET study reporting on the use of dostarlimab (PD-1 ICI) in dMMR advanced endometrial tumors showed that 80% of patients experienced progression-free survival of 18 months and an objective response rate of 44.7%. Several trials have examined the use of ICIs for patients with advanced endometrial carcinoma in MMR-proficient tumors; however, they seem to show a lesser effect in this setting. Results are more promising in MMR-proficient patients when ICIs are combined with other agents such as tyrosine kinase inhibitors; however, the toxicity profile is significantly worse, and efficacy remains significantly higher in the dMMR group. The KEYNOTE-775 study, a phase III randomized controlled trial, found that in patients with advanced or recurrent endometrial cancer pembrolizumab plus lenvatinib (tyrosine kinase inhibitor) increased progression-free survival (6.6 vs 3.8 months) and overall survival (17.4 vs 12 months) compared with conventional chemotherapy; however, treatment discontinuation and dose reduction occurred in 33% and 70% of patients, respectively. This review describes and evaluates the use of new lines of treatment including immunotherapy agents for advanced and recurrent endometrial cancer. Many trials are still ongoing, with several testing ICIs alone or in combination with other agents to improve safety profiles and efficacy.

Abstract 2120: Exploring the genomic landscape of colorectal cancer for enabling clinical genomics informed and real-world data based clinical development

Abstract Background: Activation of the MAPK-signaling by RAS- (KRAS or NRAS) alterations is an important driver event in colorectal cancer (CRC) tumorigenesis that determines treatment selection (1).Real-world data (RWD) mining is an important tool to inform patient selection and stratification (2,3). Here, RWD genomics data mining was conducted using the Foundation Medicine database to explore RAS and BRAF-alterations in CRC patients and to investigate the general alterations’ landscape - including rare alterations. The prevalence of microsatellite instability (MSI) and tumor mutational burden (TMB) were also explored. Methods: The prevalence of gene alterations and their co-occurrence with RAS/BRAF-alterations in tumor tissue of CRC patients (N=42800) were investigated using the FoundationInsightsTM web platform, which includes harmonized results from the FoundationOneCDx, FoundationOneHeme, and PD-L1 assays from 2012 to March 2022. Data was collected from FMI solid and heme tests from 2012 to March 2022. Alterations that render a particular gene ‘altered’ included single nucleotide variants (SNVs) or insertion-deletion mutations (Indels), collectively referred to as short variants (SVs), rearrangements (RE) and copy number events (CN). TMB (cut-off 10 mut/MB) and MSI status were also characterized. Results: Altogether, 36.9% of CRC samples were RAS/BRAF-WT and 63.1% had a known or likely functional RAS/BRAF-alteration, respectively. Of all KRAS and NRAS alterations (SV, CN and RE regardless of annotation as functional or presence in a hotspot), SVs in exons 2, 3 and 4 constituted 96.1% and 94.2% of all alterations, respectively. Relative to all samples the potentially targetable KRAS p.G12C, p.G12D and p.G12V mutations were present in 3.6%, 15.1% and 10.2% of samples, respectively. The p.G12E variant was present in less than ten samples. The five most frequently altered potentially targetable genes were PIK3CA (19.6%), PTEN (8.7%), ERBB2 (4.7%), EGFR (2.5%) and FGFR1 (2.0%). NTRK-alterations (NTRK1/2/3) were present in 0.9%, ROS1-alterations in 0.4%, RET-alterations in 0.6% and ALK-alterations in 0.5% of samples, respectively. The prevalence of immuno-oncology biomarkers was also explored; overall, 9.6% of samples were TMB-high, 6.1% MSI-high and 0.6% POLE-altered. MSI-high or TMB-high samples were significantly more abundant in the RAS/BRAF-altered subset. In the RAS/BRAF-WT subset 4.6% were MSI-high and 7.9% TMB-high, whereas in the RAS/BRAF-altered subset 7.1% were MSI-high and 10.6% TMB-high. Conclusion: RWD based clinical genomic profiling confirms that the vast majority of RAS-alterations in CRC are SVs in exons 2, 3 and 4. Both TMB-high and MSI-high samples are significantly more abundant in the RAS/BRAF-altered cohort. RWD confirms that PI3K-, ERBB- and FGFR-signaling pathways are frequently altered in CRC. RWD based clinical genomic profiling has the potential to support comprehensive clinical study design as well as patient selection/stratification. Citation Format: Markus Schulze, XiaoZhe (Janet) Wang, Jawad Hamad, Julia F. Hopkins, Julia F. Hopkins, Jürgen Scheuenpflug, Zheng Feng. Exploring the genomic landscape of colorectal cancer for enabling clinical genomics informed and real-world data based clinical development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2120.

Preoperative Prediction of Microsatellite Instability in Rectal Cancer Using Five Machine Learning Algorithms Based on Multiparametric MRI Radiomics.

Objectives: To establish and verify radiomics models based on multiparametric MRI for preoperatively identifying the microsatellite instability (MSI) status of rectal cancer (RC) by comparing different machine learning algorithms. Methods: This retrospective study enrolled 383 (training set, 268; test set, 115) RC patients between January 2017 and June 2022. A total of 4148 radiomics features were extracted from multiparametric MRI, including T2-weighted imaging, T1-weighted imaging, apparent diffusion coefficient, and contrast-enhanced T1-weighted imaging. The analysis of variance, correlation test, univariate logistic analysis, and a gradient-boosting decision tree were used for the dimension reduction. Logistic regression, Bayes, support vector machine (SVM), K-nearest neighbor (KNN), and tree machine learning algorithms were used to build different radiomics models. The relative standard deviation (RSD) and bootstrap method were used to quantify the stability of these five algorithms. Then, predictive performances of different models were assessed using area under curves (AUCs). The performance of the best radiomics model was evaluated using calibration and discrimination. Results: Among these 383 patients, the prevalence of MSI was 14.62% (56/383). The RSD value of logistic regression algorithm was the lowest (4.64%), followed by Bayes (5.44%) and KNN (5.45%), which was significantly better than that of SVM (19.11%) and tree (11.94%) algorithms. The radiomics model based on logistic regression algorithm performed best, with AUCs of 0.827 and 0.739 in the training and test sets, respectively. Conclusions: We developed a radiomics model based on the logistic regression algorithm, which could potentially be used to facilitate the individualized prediction of MSI status in RC patients.

Microsatellite instability detection in breast cancer using drop-off droplet digital PCR.

The use of conventional methods (immunohistochemistry, pentaplex PCR) for detecting microsatellite instability (MSI), a predictive biomarker of immunotherapy efficacy, is debated for cancers with low MSI prevalence, such as breast cancer (BC). We developed two multiplex drop-off droplet digital PCR (ddPCR) assays targeting four microsatellites, initially identified from public BC whole-genome sequencing dataset. Performances of the assays were investigated and 352 tumor DNA and 28 circulating cell-free DNA from BC patients, with unknown MSI status were blindly screened. Cross-validation of ddPCR MSI status with other MSI detection methods was performed. We then monitored circulating tumor DNA (ctDNA) dynamics before and during pembrolizumab immunotherapy in one patient with MSI-high (MSI-H) metastatic BC. The assays showed high analytical specificity and sensitivity (limit of detection = 0.16%). Among N = 380 samples, seven (1.8%) were found as MSI-H by ddPCR with six of them confirmed by next-generation sequencing (NGS). Specificity was 100% in N = 133 microsatellite stable BC submitted to NGS. In the patient with MSI-H metastatic BC, ctDNA monitoring revealed an early decrease of microsatellite mutant allelic frequencies during immunotherapy. These results demonstrated MSI detection by ddPCR, a non-invasive, fast and cost-effective approach, allowing for large pre-screening of BC patients who may benefit from immunotherapy.

Molecular genetic characteristics of colorectal cancer depending on the status of microsatellite instability

Introduction. The emergence of new markers that determine the choice of therapy for metastatic colorectal cancer (CRC) has led to an increase in overall survival. The optimal treatment tactics now take into account both clinical and molecular-genetic characteristics of the tumor.Aim. Investigation of the features of the KRAS, NRAS and BRAF mutations and amplification of the HER2 gene depending on microsatellite instability (MSI) in CRC.Materials and methods. The study included 400 patients with CRC. MSI, BRAF V600E mutation, mutations in the KRAS and NRAS genes was identified to them. MSI was determined by fragment analysis, and mutations in the KRAS, NRAS, BRAF genes by realtime PCR. HER2 amplification was determined in 100 patients with a negative RAS/BRAF. NTRK translocations were determined in all patients with MSI. Data on preoperative levels of CEA and CA19-9 were obtained from 185 patients.Results and discussion. The prevalence of MSI was 6.8%. The prevalence of KRAS, NRAS, BRAF mutations in CRC with MSI was 66.7%, and in CRC with MSS - 52.3%. In patients with MSI, the level of CEA was lower than in MSS (p = 0.0061). The overall prevalence of KRAS and NRAS mutations was 45% and 2.5%. The overall prevalence of the BRAF V600E mutation was 5.8% and was more common in MSI-positive tumors (p < 0.0001). Regardless of MSI, BRAF-positive tumors were characterized by right-sided localization (p < 0.0001), category T3-4 (p = 0.013), lymph node involvement (p = 0.004), carcinomatosis (p = 0.046), high levels of CA19-9 (p = 0.014). HER2 amplification was found in 7% of wild-type RAS/BRAF cases and was associated with rectal cancer (p = 0.044), category T3-4 (p = 0.041), and distant metastases (p = 0.038). HER2 amplifications and NTRK translocations were not detected in cases with MSI.Conclusion. MSI-positive CRC had a higher prevalence of mutations in major genes. CRC with the BRAF V600E mutation and HER2 amplification had aggressive clinical and morphological parameters.

Abstract 5179: Comprehensive characterization of rectal cancer reveals less cancer treatment with worse nutritional status and more comorbidities in the older patients

Abstract Background The population aged over 65 years is growing fast. The incidence of most cancers increases with age, and the cancer burden is projected to increase in the future. Colorectal cancer is the second most common cancer worldwide in patients over 65 years. The proportion of rectal cancer has been increasing. Therefore, we specifically characterized the older rectal cancer patients to provide an insight into cancer care for this population. Method A total of 428 and 26,765 patients diagnosed with non-metastatic rectal cancer after 50 years old from a referral tertiary care center (SYSU cohort) and Surveillance Epidemiology and End Results database (SEER cohort) were included in the current study. Patients were categorized by age into intermediate-aged adults (aged 50-65 years, n=223) and older adults (aged≥65 years, n=205). The demographic and clinicopathological features, molecular profiles, treatment strategies, and clinical outcomes were compared between the two groups. The inverse probability weighting method was used to perform risk factors-adjusted survival analysis. Results In the SYSU cohort, the difference between the two age groups was not significant in the clinicopathological features that were reported to be prognostic factors in previous studies, including tumor-node stage, poor differentiation, lymphovascular and perineural invasion and mucinous tumor. In the subset with molecular profiles, the distribution of CpG island methylator phenotype, mutations of KRAS and BRAF, and CD3+ and CD8+ tumor-Infiltrating lymphocyte counts were similar between two age groups. Of note, the older patients had higher prevalence of microsatellite instability (34.3% vs 22.2%, P=0.344). In the whole cohort, the older age was significantly associated with less cancer treatment, including neoadjuvant (6.8% vs 15.2%, P=0.009) and adjuvant (32.7% vs 57.8%, P<0.001) treatment. In addition, significantly lower BMI (median: 21.92 vs 22.92 kg/m2, P=0.004), lower baseline albumin (median: 39.75 vs 41.20 g/L, P=0.003), and higher incidence of high blood pressure (29.3% vs 12.1%, P<0.001) were found in the older patients. Finally, the older patients had significantly worse overall survival outcome (adjusted hazard ratio 2.17 [95% Cl 1.44-3.27, P<0.001]), and this finding was validated in the SEER cohort (adjusted hazard ratio 1.65 [95%Cl 1.58-1.72, P<0.001]). Conclusions Older patients present with more comorbidities and worse nutritional status, and they are less likely to receive cancer therapies. Although older patients had the similar clinicopathological profiles compared with intermediate-aged patients, they had unfavorable survival outcomes. Further studies are needed to confirm the extent to which our findings reflect the insufficient cancer care for older patients and improve the clinical outcomes of this population. Citation Format: Zhuoyang Zhao, Jianru Wang, Jinxin Lin, Shunlun Chen, Xiaolin Wang, Meijin Huang, Yanxin Luo, Huichuan Yu. Comprehensive characterization of rectal cancer reveals less cancer treatment with worse nutritional status and more comorbidities in the older patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5179.

Blood-based tumor mutational burden from circulating tumor DNA and immune checkpoint inhibitors in advanced prostate cancer.

165 Background: A prior study of patients with advanced cancers treated with immune checkpoint inhibitors (ICI) associated improved overall survival with tissue tumor mutational burden above the 80th percentile in each histology (tTMB-H). TMB can also reliably be calculated via liquid biopsy (bTMB), and trends higher than tTMB in analogous tumors. Here, we generate a plasma-informed benchmark for bTMB-H in advanced prostate cancer and report preliminary data from an ongoing multi-institutional case series of patients treated with ICI. Methods: Circulating tumor DNA (ctDNA) next generation sequencing (NGS) results from 3,504 patients with advanced prostate cancer who received a Guardant360 liquid biopsy within a 12-month period were analyzed. The 80th percentile of TMB was defined as the benchmark for bTMB-H in this cohort, and prevalence of microsatellite instability (MSI-H) was determined. Subsequently, clinical data were collected from patients across five institutions who received pembrolizumab based on bTMB scores or other tumor characteristics (i.e. CDK12 mutation). Results: Overall, mean and median bTMB were calculated as 12.34 mut/Mb and 8.61 mut/Mb, respectively (range: 0 – 1164.75 mut/Mb). The 80th percentile of bTMB was 13.4 mut/Mb and the 90th percentile was 16.6 mut/Mb. 2.6% of patients were both MSI-H and bTMB-H. No patients with bTMB < 13.4 mut/Mb (TMB-L) were found to be MSI-H. Ten patients from five institutions received pembrolizumab (8 monotherapy) after a median of 4.5 lines of prior therapy (Table). Four patients were MSI-H. The 3 patients in the cohort with PSA decreases > 50% had both MSI-H and bTMB ≥ 13.4 mut/Mb. Per RECIST criteria, disease was controlled (CR, PR, SD) in 6 of 7 (86%) patients with bTMB scores ≥ 13.4 mut/Mb. Conclusions: These data continue to affirm that ctDNA NGS is a practical and cost-effective means of assessing potential predictors of ICI activity in patients with advanced prostate cancer. Preliminary data from this growing cohort of patients who have received ICI guided by bTMB scores and other molecular parameters identified via ctDNA NGS, including MSI-H, demonstrate a clinical benefit from therapy. Further studies are warranted for contextualizing individual tumor bTMB scores with established, pathology-specific benchmarks.[Table: see text]

Medullary carcinoma of the colon: A comprehensive analysis of a large cancer database.

180 Background: Medullary carcinoma (MC) of the colon was described first in 1999 and is characterized by undifferentiated sheets of epithelial cells in a solid growth pattern with pushing borders and prominent lymphoplasmacytic infiltrates. It frequently shows microsatellite instability (MSI). However, the clinicopathological and survival outcomes between MC and the more common adenocarcinoma of the colon (AC) are not well defined in a large database. Therefore, we used a large national registry to explore the association of survival characteristics with sociodemographic, geographic, and disease variables in this cohort of patients. Methods: We sampled the National Cancer Database (NCDB) for colon cancer patients diagnosed with MC from 2004-2018. Multivariate cox regression models were used to compare hazard ratios for demographic, geographic, and disease characteristics. In addition, Kaplan-Meier survival plots were utilized to assess survival rate differences between MC and AC tumors located in the ascending, transverse, or descending colon. A p-value<0.05 was considered statistically significant. Results: Only 2,709 (0.29%) of the 922,667 patients with AC had MC. MC was seen in older patients than AC (76 vs. 69 years). MC was also more common in females than AC (72.5 vs. 49%). The most striking finding in our analysis was the predominance of poorly differentiated (63%) and undifferentiated (21.7%) pathologies in MC. This was in sharp contrast to AC, where 15.8% of patients were poorly differentiated, and only 2% were undifferentiated. Furthermore, undifferentiated and poorly differentiated MC tumors had a poor prognosis (HR 1.45, 95% CI 1.26-1.68, p<0.001 and HR 1.44, 95% CI 1.29-1.62, p<0.001 respectively) as compared to the other histological grades. Another notable finding in our analysis was the high prevalence of MSI in MC vs. AC (82.4% vs. 25.9%). Cecal MC (HR 1) had the worst prognosis of any colonic site. Left-sided MC tumors also had an inferior prognosis compared to AC (63.21 vs. 87.72 months), although not statistically significant (p=0.217). Conclusions: Colon cancer presenting as undifferentiated or poorly differentiated with associated MSI should raise the possibility of a medullary carcinoma diagnosis. However, given the rarity and difficulty in its pathological delineation, MC may remain underdiagnosed. In the modern treatment era, with the approval of immunotherapy for metastatic MSI colon cancer patients, survival and outcomes for metastatic MC may be improved.

Microsatellite instability in Chinese gastric cancer and its correlation with clinical characteristics.

Microsatellite instability (MSI) remains a focus of interest in cancer research, but the characteristics of MSI in gastric cancer (GC) are ambiguous. In this retrospective study, we analyzed the prevalence of MSI and the expression of programmed death-ligand 1 (PD-L1) and cluster of differentiation 8 (CD8) cells in Chinese GC patients. A total of 393 GC patients admitted to two centers from January 2010 to December 2017 were enrolled. The prevalence of MSI in this cohort was 3.4% and most frequently occurred in females, patients aged between 59 and 69 years, and patients at a lower clinical stage. All MSI GCs had CD8 expression but lacked PD-L1 expression, indicating that MSI was related to CD8 expression but irrelevant to PD-L1 expression. However, there was no significant difference in the expression of CD8/PD-L1 between MSI GC and microsatellite stable (MSS) GC. Kaplan-Meier survival curves revealed that patients with MSI had a significantly longer overall survival (OS) than patients with MSS. In Chinese GC patients, MSI frequently occurred in females, patients aged between 59 and 69, and patients with lower clinical stages. Patients with MSI-High (MSI-H) and MSI-Low (MSI-L) had a longer OS than patients with MSS. MSI was related to CD8 expression but irrelevant to PD-L1 expression.

Analysis of microsatellite instability in Korean patients with pancreatic cancer.

Pancreatic cancer (PC) is a dangerous malignancy with a high mortality rate. Diagnosing PC at an early stage is difficult, and approximately 5% of the patients survive for 5 years. Microsatellite instability (MSI) plays an important role in colorectal cancer (CRC) for prognosis and immunotherapy. Evaluation of MSI status is important as it is recognized biomarker for the positive response of immune checkpoint blockade therapy in cancer. To our knowledge, there is no report yet on the prevalence of MSI in Korean PC patients. Studies have reported conflicting prevalence of MSI in PC. Therefore, to improve the likelihood of MSI identification in PC, we included 133 patients with PC; paired tumor and normal tissue DNA were isolated and MSI was analyzed using Promega panel and immunohistochemistry (IHC) was also performed. Our results from the Promega panel indicated that one (0.7%) tumor was MSI-high (MSI-H), 13 (9.8%) were MSI-low (MSI-L), and 119 (89.5%) were microsatellite stable (MSS). IHC result also confirmed dMMR in only one sample. The finding of low incidence of MSI-H observed by the Promega panel also matched IHC results, so this study suggested that in Korean PC patients, MSI prevalence is infrequent.

Pilot Nanostring PanCancer pathway analysis of colon adenocarcinoma in a tertiary healthcare centre in Kerala, India.

The prevalence of microsatellite instability and deoxyribonucleic acid mismatch repair deficiency in colorectal adenocarcinoma (CRC) cases is higher in India compared to western populations. No major study on the molecular pathogenesis is currently available in the Indian population. We conducted a pilot study to explore the differences in molecular pathogenesis of microsatellite stable (MSS) and microsatellite unstable CRC from a tertiary care centre in Kerala, South India. Using Nanostring PanCancer panel assay in Stage II colorectal adenocarcinoma, tumour tissues (n = 11) were compared against normal colon tissues (n = 4). Differentially expressed (DE) genes were identified and super-imposed onto colon adenocarcinoma cohort of The Cancer Genome Atlas (TCGA) data (TCGA Colon Adenocarcinoma (TCGA COAD)), from the Genome Expression Profiling Interactive Analysis and Tumor Immune Estimation Resource (TIMER) to compare the gene associations. Significant DE genes were 59 out of 730 (false discovery rate adj. p-value < 0.05), 18 of which had a fold-change |FC(log2)| ≥ 2. On superimposition to TCGA COAD, 33 genes were significant in both TCGA and current study. ETV4 was expressed significantly higher in MSS with no immune cell infiltration. Other significant DE genes with high FC(log2), unique to the study were INHBA, COL1A1, COL11A1, COMP, SFRP4 and SPP1, which were clustered in STRING network analysis and correlated with tumour-infiltrating immune cells in TIMER, suggesting a specific interaction pathway. The preliminary study suggests a distinct pathogenesis of MSS CRC involving ETV4 in the Indian population and warrants further clinically extensive and high-dimensional expression studies.

Frequency of microsatellite instability (MSI) in upper tract urothelial carcinoma: comparison of the Bethesda panel and the Idylla MSI assay in a consecutively collected, multi-institutional cohort

AimsUpper tract urothelial carcinoma (UTUC) is a rare malignancy with a poor prognosis which occurs sporadically or in few cases results from a genetic disorder called Lynch syndrome. Recently, examination...

Clinical and morphological portrait of tumors with microsatellite instability

Background. Microsatellites are short tandem nucleotide repeats, the change in length of which plays a key roles in the pathogenesis of various malignant neoplasms. This change is called microsatellite instability. It is caused by aberrations in the genes of DNA mismatch repair system. Tumors with microsatellite instability are a special subtype regardless of location and are characterized by high sensitivity to immune checkpoint inhibitors.Objective – determination of characteristic clinical and morphological patterns of tumors of various localizations with microsatellite instability.Materials and methods. The study included 512 patients with malignant tumors of different localizations. Of these, 359 patients were diagnosed with colorectal cancer, 57 with uterine body cancer, and 57 with stomach cancer. Determination of the status of microsatellite instability was performed by a PCR-based method using 5 mononucleotide markers: BAT-25, BAT-26, NR-21, NR-24, NR-27.Results. The prevalence of microsatellite instability in colorectal cancer, uterine neoplasm and gastric cancer was 6.4; 22.8 and 1.75 %, respectively. Patients with MSI-positive colorectal cancer are characterized by yonger age (p = 0.023), right-sided localization of the tumor (p &lt;0.0001), presence of multiple primary tumors (p = 0.0299), poorly differentiation (p = 0.0025), mucinous component (p &lt;0.0001), tumor-infiltrating lymphocytes (p &lt;0.0001) and Crohn-like reaction (p = 0.0006). Patients with uterine neoplasms with microsatellite instability are characterized by the presence of endometrial adenocarcinoma (p = 0.047), as well as the presence of tumor-infiltrating lymphocytes (p = 0.0022) and cribriform growth (p = 0.0011).Conclusion. A common pattern for colorectal cancer and uterine neoplasms is the presence of tumor-infiltrating lymphocytes. Certain clinical and morphological features of tumors of these localizations will more accurately identify candidates for microsatellite instability status determination for further immunotherapy.