Showed Microsatellite Instability Research Articles

Intraoperative rapid immunohistochemistry of microsatellite instability using non-contact alternating current electric field mixing.

Tumors caused by failure of the DNA-mismatch repair system generally show microsatellite instability (MSI). High-frequency MSI cancers have been shown to be susceptible to immuno-oncology therapies. The aim of this study was to evaluate the clinical reliability of a rapid immunohistochemistry (IHC) technique for intraoperatively assessing molecular status through detection of tumoral deficiencies in the expression of mismatch repair proteins (dMMR; MLH1, MSH2, MSH6, and PMS2). The rapid IHC method uses non-contact alternating current (AC) mixing to achieve more rapid/stable staining within a minimum of 13min during surgery. Sixteen formalin-fixed paraffin-embedded (FFPE) tumor samples from 3 dMMR patients with Lynch syndrome and 6 FFPE samples from 6 dMMR-cancer patients were collected to establish an IHC protocol for MMR proteins. Next, 26 surgical patients treated and whose MSI status was determined using PCR-based tests were retrospectively analyzed. The concordance of dMMR diagnoses for thoracic tumors between the conventional (frozen section (FS)- and FFPE-IHCs) and rapid AC-mixing IHC with FSs were compared. A rapid IHC protocol using primary antibodies against four MMR proteins (mixed 5-10min) was established (entire process within 40min). The concordance rate for MMR-IHC between the conventional and rapid IHC was 100%. dMMR diagnoses including an MSI-high pulmonary sarcoma patient entirely matched between FS- and FFPE-IHC. Rapid MMR-IHC could potentially serve as a clinical tool for intraoperative determination of tumor MSI/dMMR status. AC-mixing technology will contribute to improving pathological diagnostic capability through the development of an original and innovative rapid IHC.

Lynch syndrome

Patients with Lynch syndrome, one of the most common hereditary tumor predisposition syndromes, harbor an increased risk for abroad spectrum of especially gastrointestinal and gynecological tumors. Causative for the syndrome are variants in DNA mismatch repair genes, which are passed on to the offspring at a50% chance (autosomal dominant inheritance). The tumor tissue of these patients usually shows microsatellite instability, which is of increasing relevance regarding prognosis and therapeutic decisions. The detection of acausative genetic variant in apatient enables predictive testing of family members to provide relief to noncarriers and provide carriers with intensified risk-adapted surveillance. In addition, chemoprevention with aspirin (acetylsalicylic acid) has been proven useful for chemoprevention in studies. Therefore, the diagnosis of Lynch syndrome is important for patients and their relatives.

Microsatellite Instability Testing and Prognostic Implications in Colorectal Cancer.

Given the crucial predictive implications of microsatellite instability (MSI) in colorectal cancer (CRC), MSI screening is commonly performed in those with and at risk for CRC. Here, we compared results from immunohistochemistry (IHC) and the droplet digital PCR (ddPCR) MSI assay on formalin-fixed paraffin-embedded tumor samples from 48 patients who underwent surgery for colon and rectal cancer by calculating Cohen's kappa measurement (k), revealing high agreement between the methods (k = 0.915). We performed Kaplan-Meier survival analyses and univariate and multivariate Cox regression to assess the prognostic significance of ddPCR-based MSI and to identify clinicopathological features associated with CRC outcome. Patients with MSI-high had better overall survival (OS; p = 0.038) and disease-free survival (DFS; p = 0.049) than those with microsatellite stability (MSS). When stratified by primary tumor location, right-sided CRC patients with MSI-high showed improved DFS, relative to those with MSS (p < 0.001), but left-sided CRC patients did not. In multivariate analyses, MSI-high was associated with improved OS (hazard ratio (HR) = 0.221, 95% confidence interval (CI): 0.026-0.870, p = 0.042), whereas the loss of DNA mismatch repair protein MutL homolog 1 (MLH1) expression was associated with worse OS (HR = 0.133, 95% CI: 0.001-1.152, p = 0.049). Our results suggest ddPCR is a promising tool for MSI detection. Given the opposing effects of MSI-high and MLH1 loss on OS, both ddPCR and IHC may be complementary for the prognostic assessment of CRC.

Development of the BAT-26 mutation-based electrochemical genosensor for identifying microsatellite instability in relationship to cancer

Screening for microsatellite instability is one of the biggest challenges in the cancer diagnosis due to its association with different types of cancer development. In this sense, the development of fast and highly sensitive analytical devices for early the cancer detection is a high priority. In the present work, a highly sensitive electrochemistry genosensor is developed and described for BAT-26 mutation detection using: differential pulse voltammetry (DPV), and cyclic voltametric (CV) supported by scanning tunnel microscopy (STM). The redox reaction of Fe(CN)63−/4– was monitored to probe the presence DNA target. The results demonstrate that modifying the screen-printed gold electrode surface (SPGE) 250AT with a combination of 11-mercaptoundecanoic acid (MUA) and a single-stranded DNA oligonucleotide successfully altered the electrode's properties, particularly its affinity for detecting the BAT-26 mutation under physiological conditions. The genosensor exhibited a wide linear range (100 aM to 1 μM) and achieved a low detection limit of 71.74 aM under optimal parameters. These characteristics, coupled with its high sensitivity and rapid analysis time, make it a promising candidate for development into a portable microsatellite instability diagnostic kit.

Family history as a major prerequisite for microsatellite instability screening in colorectal cancer is a poor selection tool.

Deficient mismatch repair (MMR) leading to microsatellite instability (MSI) in tumors is thought to be present in over 15% of colorectal cancer (CRC) cases. Testing CRC for MSI has traditionally been recommended following the fulfillment of clinical criteria. However, the performance of clinical criteria, especially the family history, as a selection tool for MSI screening in CRC is questionable. We retrospectively investigated the incidence of high degree MSI (MSI-H) tumors in an unselected population of CRC patients and compared its prevalence between individuals with and without family history of cancers within the spectrum of MSI-H tumors as defined in the revised Bethesda criteria. The study population included 274 patients, 70 with positive and 204 without family history of MSI-H tumors with complete data including findings from MSI analysis. The overall incidence of MSI-H CRC was 18.98%. There was no statistically significant difference in the incidence of MSI-H CRC amongst both groups. The sensitivity and specificity of family history with regard to the presence of an MSI-H tumor in this collective was 36.5% and 77.5%, respectively. A relevant number of cases with high MSI-H CRC may be missed secondary to screening based on clinical criteria like family history alone. Thus, systematic screening independent of clinical characteristics, especially family history of cancer should be recommended in all cases with CRC.

Microsatellite instability is highly prevalent in older patients with colorectal cancer.

Clinical guidelines suggest screening of colorectal cancer (CRC) for microsatellite instability (MSI). However, microsatellite instability-high (MSI-H) CRC is not rare in older patients. This study aimed to investigate the prevalence of MSI-H CRC in an unselected population in an age-based manner. A retrospective analysis of data from patients undergoing radical surgery for CRC was performed. Only cases with results from MSI testing using immunochemistry (IHC) were analyzed. Age-based analyses were performed using two cut-off ages: 50 years. as stated in Amsterdam II guidelines, and 60 years. as outlined in the revised Bethesda criteria. The study population included 343 (146 female and 197 male) patients with a median age of 70 years (range 21-90 years). The prevalence of MSI-H tumors in the entire cohort was 18.7%. The prevalence of MSI-H CRC was 22.5% in the group ≤50 years vs. 18.2% in the group >50 years using the age limit in the Amsterdam II guidelines. MSI-H CRC was present in 12.6% of the group aged ≤60 years compared to 20.6% in the control group >60 years. MSI screening of CRC based on age alone is associated with negative selection of a relevant number of cases. MSI-H CRC is also common in elderly patients, who may be negatively selected secondary to an age-based screening algorithm. Following the results of this study, screening based on clinical criteria should be omitted in favor of systematic screening as is already internationally practiced.

Microsatellite instability screening in colorectal carcinoma: immunohistochemical analysis of MMR proteins in correlation with clinicopathological features and Ki-67 protein expression

BackgroundDefects in mismatch repair (MMR) system or microsatellite instability (MSI) and detected in colorectal carcinoma (CRC), both in sporadic and more frequently in hereditary cases. Immunohistochemistry (IHC) is the most frequent method for MMR protein deficiency screening in CRCs. In this study, we aimed to evaluate immunohistochemical expression of MMR and Ki-67 in colorectal carcinoma with clinicopathological features.MethodsIn this study, we evaluated the immunohistochemical expression of MMR proteins including MSH6, MSH2, PMS2 and MLH1 in 50 resection materials with colorectal carcinoma. Their expression is correlated with clinicopathological features of patients together, with Ki-67 protein expression in attempt to screen the most significant predictor of microsatellite instability.ResultsOf the 50 cases of cancer colon, 28% were classified as MSI-H, 20% were MSI-L, and 52% were MSS. The most frequent pattern in MSI-H tumors was concurrent loss of MSH6 and PMS2 proteins. There was a significant correlation between MMR protein expression pattern with tumor size, grade, T-classification and stage (0.015, 0.0515, 0.0162 and 0.0391), respectively. MSI-H tumors were located more frequently in right colon, early TNM stage and poorly differentiated and infrequent distant metastases. There was a significant correlation between Ki-67 high expression and MSI status patterns in their common biological aspects distinct from MSI-negative tumors.ConclusionsMismatch repair defective colorectal carcinoma has characteristics clinicopathological features different from MSS tumors. The role of immunohistochemistry (IHC) for MSI evaluation is the easiest and effective way for evaluation of MMR deficiency in colorectal carcinoma.

Clinicopathological and molecular characteristics of gastric papillary adenocarcinoma.

Papillary adenocarcinoma is defined as carcinoma with a well-defined papillary or villous structure. Despite sharing clinicopathological and morphological features with tubular adenocarcinomas, papillary adenocarcinomas frequently show microsatellite instability. The present study aimed to clarify the clinicopathological features, molecular classification, and programmed death-ligand 1 (PD-L1) expression characteristics of papillary adenocarcinoma, especially tumors with microsatellite instability. We examined the microsatellite status and expression of mucin core proteins and PD-L1 as well as the clinicopathological features in 40 gastric papillary adenocarcinomas. Surrogate immunohistochemical analysis of p53 and mismatch repair proteins along with Epstein-Barr virus-encoded RNA in situ hybridization were performed for molecular classification. Female predominance and frequent microsatellite instability were observed in papillary adenocarcinoma in comparison with tubular adenocarcinoma. The presence of microsatellite instability in papillary adenocarcinoma was significantly correlated with older age, tumor-infiltrating lymphocytes, and Crohn's-like lymphoid reactions. Surrogate examination demonstrated that the genomically stable type (17 cases, 42.5%) was the most common, followed by the microsatellite-unstable type (14 cases, 35%). Among the seven cases showing PD-L1-positive expression in tumor cells, four involved carcinomas with microsatellite instability. These results reveal the clinicopathological and molecular characteristics of gastric papillary adenocarcinoma.

Immuno-Contexture and Immune Checkpoint Molecule Expression in Mismatch Repair Proficient Colorectal Carcinoma

Colorectal carcinoma (CRC) represents a lethal disease with heterogeneous outcomes. Only patients with mismatch repair (MMR) deficient CRC showing microsatellite instability and hyper-mutated tumors can obtain clinical benefits from current immune checkpoint blockades; on the other hand, immune- or target-based therapeutic strategies are very limited for subjects with mismatch repair proficient CRC (CRCpMMR). Here, we report a comprehensive typing of immune infiltrating cells in CRCpMMR. We also tested the expression and interferon-γ-modulation of PD-L1/CD274. Relevant findings were subsequently validated by immunohistochemistry on fixed materials. CRCpMMR contain a significantly increased fraction of CD163+ macrophages (TAMs) expressing TREM2 and CD66+ neutrophils (TANs) together with decrease in CD4−CD8−CD3+ double negative T lymphocytes (DNTs); no differences were revealed by the analysis of conventional and plasmacytoid dendritic cell populations. A fraction of tumor-infiltrating T-cells displays an exhausted phenotype, co-expressing PD-1 and TIM-3. Remarkably, expression of PD-L1 on fresh tumor cells and TAMs was undetectable even after in vitro stimulation with interferon-γ. These findings confirm the immune suppressive microenvironment of CRCpMMR characterized by dense infiltration of TAMs, occurrence of TANs, lack of DNTs, T-cell exhaustion, and interferon-γ unresponsiveness by host and tumor cells. Appropriate bypass strategies should consider these combinations of immune escape mechanisms in CRCpMMR.

Barriers in the identification and diagnosis of hereditary colon cancer.

e13524 Background: Lynch Syndrome (LS), the most common form of hereditary colorectal cancer (CRC), is due to germline pathogenic variant (PV) in mismatch repair genes (MMR). Since 2009, the National Comprehensive Cancer Network (NCCN) recommends MMR screening for LS for all CRCs regardless of age. The American College of Medical Genetics and Genomics recommends patients with MMR deficiency or microsatellite instability (MSI) be referred for genetic testing. Despite these recommendations, compliance is low. The aim of this study was to evaluate compliance with LS screening and genetic testing in CRC. Methods: A single institution retrospective review of patients diagnosed with CRC from 2018-2021 was performed. A chart review of those diagnosed in 2018 and 2021 was analyzed and combined as a single population from pre and post COVID periods. A student’s T-Test was used to compare continuous variables and chi square for categorical variables within the two populations. The compliance with either MSI or MMR screening was calculated. Meeting criteria for genetic testing was defined as age less than 50, MSI-L/H or MMR deficient. These patients were then analyzed to determine the proportion of genetic referrals, genetic counseling, genetic testing and identification of LS. Results: 276 patients with CRC were reviewed, 153 in 2018, 123 in 2021. 71.2% were Caucasian and 58% male. There was no statistically significant difference in gender, race or ethnicity, however, there was a difference in age, with a younger average age in 2021 (67, 63; p = 0.014). 146 (53%) patients were screened for LS. 44 (16%) with MSI, 19 (7%) MMR and 82 (30%) with both. 78 patients met criteria for genetic testing; 47 due to age alone, 6 age and positive LS screening and 25 screening alone. 35% (27/78) of those meeting criteria were referred to genetics, of which 63% (17/27) completed their appointment, 63% (17/27) were tested, and 37% (10/27) had a PV identified. Conclusions: Despite guidelines for LS screening, compliance is low with only half of CRC patients appropriately screened at our institution. Even patients with positive screening and those less than 50 were not referred for genetic testing. However, of referred patients, 63% completed their appointment and all those were tested. This supports the idea that poor compliance with genetic testing is not due to patient compliance, but shows a systems issue at a higher level. To improve LS identification, reflex screening and genetic referrals are paramount. In our study, 59% of patients with germline testing had a PV, however 65% of those meeting criteria were never referred, which could reflect a proportion of patients with LS going unidentified. This validates the 2022 NCCN guidelines recommending genetic testing for all CRCs despite age or MSI/MMR status. By removing the barrier of MMR testing, more genetic testing will likely be done. [Table: see text]

Immune checkpoint inhibitors and cellular immunotherapy for advanced gastric, gastroesophageal cancer: a long pathway.

Although the incidence rate and mortality of gastric/gastroesophageal cancer (G/GEJC) are declining globally, G/GEJC remains a health issue in East Asia. When diagnosed as advanced stage, treatment after serial lines of chemotherapy is limited, with a median overall survival of less than 1year. Immunotherapy, including immune checkpoint inhibitors (ICIs) and cellular immunotherapy, has changed the prospects of cancer therapy by reversing immune suppression in the tumor microenvironment. As part of this review, we enumerated the clinical uses of ICIs related to the immunosuppressive signaling axis PD-1/PD-L1 and CTLA-4/B7. ICIs were initially approved as a secondary treatment option for patients with severe pretreating advanced gastric and gastroesophageal cancer (AG/GEJC). Till now, it has become the mainstream therapy in combination with chemotherapy and targeted therapy for patients identified by biomarkers. Numerous evidence showed microsatellite instability (MSI), programmed cell death ligand 1 (PD-L1) expression, tumor mutation burden (TMB) and Epstein-Barr virus (EBV) status might be indicative to the use of ICIs. In addition, we discussed the current limitations and prospects of ICIs in AG/GGEJC, as well as the first clinical application of novel CAR-T cell therapies.

Abstract 3931: BRD4, BRD3, NSD3, and ZNF532 fusions in histologies beyond NUT carcinomas: Investigation of a large pan-cancer cohort

Abstract Background: NUT rearrangements drive NUT carcinomas (NCs), which are rare, poorly differentiated tumors with a survival from diagnosis of ~6-7 months. Common NUT fusion partners (NCFPs) include BRD4, BRD3, NSD3, and ZNF532, which are associated with epigenetic changes leading to tumor growth. Recent clinical trials have aimed to address NCs, but little is known about fusions involving NCFPs in other histologies. We characterized NCFPs in a large, pan-cancer cohort. Methods: The MSK-IMPACT (DNA sequencing; n=71,423) and MSK-Fusion (RNA sequencing; n=10,897) clinical cohorts were mined to identify patients (pts) with all forms of structural variants (SVs) involving NCFPs, detected between April, 2015 and June, 2022. The targeted NGS panels included BRD4 and NSD3 only; detection of BRD3 and ZNF532 SVs was possible for fusions with a partner present on either panel. SVs were manually reviewed to identify in-frame fusions with oncogenic potential if critical domains present in NC fusions were conserved. Pts were followed through July 2022 and manual chart review enabled assessment of treatment history and clinical outcomes. Results: SVs involving NCFP genes were detected in 182 (BRD4=110, NSD3=61, BRD3=8 and ZNF532=3) pts (0.002%). Putative NCFP fusions not involving any of the NUT gene family members comprised a total of 20 fusions with likely oncogenic potential including 11 with BRD4 (55%), 5 with NSD3 (25%), 3 with ZNF532 (15%), and 1 with BRD3 (5%). BRD4::NOTCH3 and ZNF532::MALT1 were the most enriched fusions, present in 3 samples each. The most common histologies were breast (3 ductal; 1 lobular), lung (2 squamous cell carcinoma, 1 adenocarcinoma and 1 mixed histology), and colon and esophageal adenocarcinoma (2 samples each). Median age at diagnosis was 62. 11 (55%) pts were female and 9 (45%) were male. 13 (65%) pts ultimately were diagnosed with stage IV disease and had a median overall survival from stage IV diagnosis of 2.5 years (95% CI: 1.41, NR). DNA sequencing in 19/20 tumors revealed a mean tumor mutational burden (TMB) of 5.0 mut/Mb including 15 with low TMB (&amp;lt;10) and 3 with high TMB (&amp;gt;10). No tumor showed microsatellite instability (MSI-high). TP53 mutations were the most common co-alteration, found in 11 (58%) cases. 18/20 pts received systemic therapy; 18 (90%) received cytotoxic chemotherapy and/or mAb therapy, including 13 (65%) who received a platinum. 8 pts (40%) received immunotherapy (IO), and 4 (20%) received small molecule inhibitors. No pts received BET inhibitors. Among pts who received IO, median time to treatment discontinuation was 64 days (95% CI: 20, NR). Conclusion: Tumor sequencing from a large cohort reveals potential oncogenic fusions involving BRD4, BRD3, NSD3, and ZNF532 across multiple histologies. Further biological characterization of their oncogenicity and potential targetability is warranted. Citation Format: Ian R. Nykaza, Christopher A. Febres-Aldana, Sabrina T. Lin, Ryma Benayed, Kerry Mullaney, Emiliano Cocco, Alexia Iasonos, Marc Ladanyi, Alexander E. Drilon, Yonina R. Murciano-Goroff. BRD4, BRD3, NSD3, and ZNF532 fusions in histologies beyond NUT carcinomas: Investigation of a large pan-cancer cohort. [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 3931.

Diagnostic performance of Idylla MSI test in colorectal cancer biopsies

Universal testing for microsatellite instability (MSI) is recommended in colorectal cancer (CRC) to screen for Lynch syndrome and to guide optimal treatment and follow-up of the patients. Especially in neoadjuvant setting, where immuno-oncological treatments have recently shown excellent responses, identification of MSI status at biopsy is a prerequisite. Idylla MSI test offers a rapid and automated test to assess MSI-status from formalin-fixed paraffin-embedded tumor tissue sections. In this study, we compared the performance of the Idylla MSI test to mismatch repair (MMR) protein immunohistochemistry (IHC) using 117 CRC biopsies with previously known deficient MMR status. The concordance between Idylla and IHC was 99.0% (95/96) for biopsies with the recommended ≥ 20% tumor cell content. Further, 85.7% (18/21) of suboptimal CRC biopsy specimens (tumor cell content 5–15%) were diagnosed as MSI. Overall, we identified four discrepant cases of which three had tumor cell content less than 20%, explaining the discordant result. Our study shows that the Idylla MSI test offers a competent tool for MSI screening in CRC biopsy specimens.

Microsatellite instability in the high-grade dysplasia component of duodenal adenoma is associated with progression to adenocarcinoma.

We examined the microsatellite instability of duodenal tumors to evaluate their molecular features associated with the adenoma-carcinoma sequence. Fifty-two non-ampullary duodenal epithelial tumors collected by endoscopic mucosal resection or surgical resection were studied. When a tumor had two or more dysplasia grades, the highest grade was considered. Representative areas were macro-dissected and subjected to a microsatellite instability analysis and immunohistochemical staining. The 52 tumors were classified as either adenoma with low-grade dysplasia (n = 18), adenoma with high-grade dysplasia (n = 20), or adenocarcinomas (n = 14). Among these, 3 adenocarcinoma cases showed microsatellite instability and the remaining 49 tumors showed microsatellite stability. Of the 14 adenocarcinoma cases, 3 contained both high-grade dysplasia and adenocarcinoma components, and 11 contained only the adenocarcinoma component. Interestingly, all three adenocarcinoma + high-grade dysplasia cases were microsatellite instability-high in both the adenocarcinoma and high-grade dysplasia components. Immunohistochemical staining of mismatch repair proteins showed mismatch repair deficiency in three microsatellite instability-high adenocarcinoma + high-grade dysplasia cases. Only adenocarcinoma cases with high-grade dysplasia components were microsatellite instability-high (in both the adenocarcinoma and high-grade dysplasia components). This suggests that microsatellite instability in the high-grade dysplasia component of duodenal adenoma is associated with progression to adenocarcinoma.

Investigation of Molecular Features Involved in Clinical Responses and Survival in Advanced Endometrial Carcinoma Treated by Hormone Therapy.

Hormone therapy (HT) is an effective treatment for metastatic endometrial carcinoma (mEC), with limited toxicity and low cost. We focused on molecular analysis of mECs treated by HT and, for the first time to date, we compared the genomic profiles of paired metastasis and primary ECs. The main objective was to identify predictive factors of the response to HT as well as specific altered signaling pathways driving mEC biology. From 1052 patients with EC treated by HT in two French cancer centers, 32 with endometrioid EC and 6 with high grade serous EC were included. We evaluated hormone receptors (HR) and mismatch repair proteins expression by immunohistochemistry and gene alterations by targeted next-generation sequencing and array-based comparative genomic hybridization. Several variables were tested in univariate and multivariate analyses to identify potential associations with (i) the clinical benefit of HT (CBHT) and (ii) a longer response (>18 months) (LRHT) and overall survival (OS). We compared the biological and genomic profiles of 11 primary/metastatic EC pairs. Thirty tumors (78.9%) were HR-positive and 6 (15.8%) showed microsatellite instability (MSI). The genomic profiles of 34 tumors showed an average altered genome of 3.26%, DNA repair homologous recombination deficiency in five tumors (14.7%), and 17 regions significantly targeted by amplification/deletion. Thirty-three tumors had 273 variants (158 genes, median of 7 mutations/sample), including 112 driver mutations. TP53, PTEN, PPP2R1A, ARID1A, FGFR2, and PIK3CA were the most frequently mutated. Based on the genomic status, nine oncogenic pathways were altered in more than 25% of primary EC. Clinically, 22 (57.9%) and 6 (15.8%) patients presented CBHT and LRHT, respectively. Neither oncogenic pathways alterations nor the variables tested were associated with CBHT and LRHT. Only patient’s age, mitotic index and the presence of at least one HR were associated with OS. Paired analysis of the primary/metastatic samples showed that among the 22 mutations acquired in the metastatic counterparts, the most frequently targeted genes were involved in pathways that might confer a selective advantage to cancer metastasis including hormone resistance. In conclusion, only patient’s age, mitotic index and the presence of at least one HR were associated with OS. The identification of gene mutations newly acquired in metastasis might help to better understand the formation of EC metastasis and select the best actionable candidates for HT-treated patients at the metastatic stage.

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&lt;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&lt;0.001 and HR 1.44, 95% CI 1.29-1.62, p&lt;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.

Ductal and acinar components of mixed prostatic adenocarcinoma frequently have a common clonal origin.

BackgroundDuctal adenocarcinoma (DA) is an aggressive subtype of prostate cancer. It is most commonly seen in mixed tumors together with conventional acinar adenocarcinoma (AA). The genetic profile of DA and its clonal origin is not fully characterized.ObjectiveTo investigate whether DA represents a distinct genetic subtype and to investigate the somatic relationship between the ductal and acinar components of mixed cancers.Design, Setting, and ParticipantsIn 17 radical prostatectomy specimens ductal and acinar tumor components from the same tumor foci were dissected. DNA was extracted and genomic sequencing performed. After exclusion of two cases with low cell yield, 15 paired samples remained for analysis.ResultsIn 12 of 15 cases a common somatic denominator was identified, while three cases had clonally separate components. In DA, TMPRSS2‐ERG gene fusions were detected in 47% (7/15), clonal FOXA1 alterations in 33% (5/15) and SPOP alterations in 27% (4/15) of cases. In one case KIAA1549−BRAF fusion was identified. Genome doubling events, resulting in an increased ploidy, were identified in the DA in 53% (8/15) of cases, but not seen in any AA. PTEN and CTNNB1 alterations were enriched in DA (6/15) but not seen in any AA. No cancers showed microsatellite instability or high tumor mutation burden.ConclusionsDuctal and acinar prostate adenocarcinoma components of mixed tumors most often share the same origin and are clonally related. DA components in mixed tumor often exhibit genome doubling events resulting in aneuploidy, consistent with the aggressive nature of high grade prostate cancer.

Landscape of driver gene events, biomarkers, and druggable targets identified by whole-genome sequencing of glioblastomas.

BackgroundThe survival of glioblastoma patients is poor. Median survival after diagnosis is 15 months, despite treatment involving surgical resection, radiotherapy, and/or temozolomide chemotherapy. Identification of novel targets and stratification strategies of glioblastoma patients to improve patient survival is urgently needed. Whole-genome sequencing (WGS) is the most comprehensive means to identify such DNA-level targets. We report a unique set of WGS samples along with comprehensive analyses of the glioblastoma genome and potential clinical impact of WGS.MethodsOur cohort consisted of 42 glioblastoma tumor tissue and matched whole-blood samples, which were whole-genome sequenced as part of the CPCT-02 study. Somatic single-nucleotide variants, small insertions/deletions, multi-nucleotide variants, copy-number alterations (CNAs), and structural variants were analyzed. These aberrations were harnessed to investigate driver genes, enrichments in CNAs, mutational signatures, fusion genes, and potential targeted therapies.ResultsTumor mutational burden (TMB) was similar to other WGS efforts (1–342 mutations per megabase pair). Mutational analysis in low TMB samples showed that the age-related CpG demethylation signature was dominant, while hyper- and ultramutated tumors had additional defective DNA mismatch repair signatures and showed microsatellite instability in their genomes. We detected chromothripsis in 24% of our cohort, recurrently on chromosomes 1 and 12. Recurrent noncoding regions only resulted in TERT promoter variants. Finally, we found biomarkers and potentially druggable changes in all but one of our tumor samples.ConclusionsWith high-quality WGS data and comprehensive methods, we identified the landscape of driver gene events and druggable targets in glioblastoma patients.

Adoption of universal next generation sequencing for Lynch syndrome screening in endometrial cancer

<h3>Objectives:</h3> To assess implementation of a novel microsatellite instability (MSI) screen using next generation sequencing (NGS) in endometrial cancer (EC) through comparison to prior Lynch syndrome screening strategies, as well as to compare characteristics of patients with microsatellite stable (MSS) and microsatellite unstable endometrial cancer. <h3>Methods:</h3> Retrospective review was performed of patients with newly diagnosed endometrial cancer at a single academic institution during three time periods and using different screening strategies: 1) 01/2010 - 01/2013 with provider-directed mismatch repair immunohistochemistry (MMR IHC) in women ≤60, 2) 01/2013 - 01/2016 with universal MMR IHC in all women ≤60, and 3) 10/2018 - 10/2019 with universal screening for MSI using NGS regardless of age. In cohorts 1 and 2, women with abnormal MMR IHC were referred to a genetic counselor who ordered MLH1 promoter methylation or germline genetic testing as indicated. In cohort 3, reflexive MLH1 promoter methylation was performed for patients with MSI and no MMR germline or somatic mutations, with referral to genetic counseling for suspected germline MMR mutation or unexplained MSI. Statistical analysis was performed using a t-test for continuous variables and Fisher's exact test for categorical variables. ≤60, 2) 01/2013 - 01/2016 with universal MMR IHC in all women ≤60, and 3) 10/2018 - 10/2019 with universal screening for MSI using NGS regardless of age. In cohorts 1 and 2, women with abnormal MMR IHC were referred to a genetic counselor who ordered MLH1 promoter methylation or germline genetic testing as indicated. In cohort 3, reflexive MLH1 promoter methylation was performed for patients with MSI and no MMR germline or somatic mutations, with referral to genetic counseling for suspected germline MMR mutation or unexplained MSI. Statistical analysis was performed using a t-test for continuous variables and Fisher's exact test for categorical variables. <h3>Results:</h3> There were 133 subjects in cohort 1, 135 subjects in cohort 2, and 140 subjects in cohort 3. The proportion of patients screened for Lynch syndrome increased over time (39%, 94%, and 100% of intended screening population). The proportion of positive screens was similar between the 3 cohorts (27%, 21%, and 27%). The proportion with positive screens who underwent confirmatory testing with germline genetic testing or MLH1 promoter methylation was 50% in cohort 1 and 59% in cohort 2. Following implementation of reflexive MLH1 promoter methylation testing when indicated, the proportion increased to 89% (p=0.001). Attendance at genetic counseling appointments following referral was 50%, 59%, and 61% in each cohort. Eleven patients were diagnosed with Lynch syndrome across the 3 cohorts (4%, 3%, and 1% respectively). In cohort 3, subjects with MSI EC had similar clinicopathologic characteristics compared with MSS cancers, and over half of MSI cancers were identified in subjects over the age of 60 (71%). Eight subjects had incidental somatic mutations identified through NGS, including 6 <i>POLE</i> mutations, 1 <i>BRIP1</i> mutation, and a subject with mutations in <i>TP53, AKT1,</i> and <i>FBXW7.</i> At our institution, MSI testing by NGS was billed at $905 versus $1200 for MMR IHC screening. <h3>Conclusions:</h3> Transition to universal screening using NGS with reflexive MLH1 promoter methylation testing increased the number of subjects completing genetic assessment for Lynch syndrome after a positive screen, likely as somatic causes of MSI were ruled out, allowing more focused genetics referrals. Similar characteristics between subjects with MSI and MSS EC supports universal screening regardless of clinical characteristics. In addition to identifying Lynch syndrome, detection of MSI through NGS can identify somatic alterations with therapeutic implications, and can be performed at a lower cost than MMR IHC.

Abstract SY17-01: Analysis of immune contexture to refine prognosis in patients with colon cancer: Implications for immunotherapy

Abstract Current classification of colorectal cancer (CRC) is based on TNM staging which does not account for considerable within stage variability in clinical outcome. Currently, there is no immune-based classification of colon cancer although data suggest that intratumoral T-cell densities can provide prognostic information that is more robust than that has been provided by genomic or transcriptomic profiling. A subset of CRCs show microsatellite instability (MSI) that is a predictive biomarker for immune checkpoint inhibitors whose indication in CRC is limited to metastatic tumors. In a prior study, we compared the density and localization of CD3+ and cytotoxic CD8+ T-cell densities in non-metastatic colon cancers with deficient (dMMR) vs proficient (pMMR) DNA mismatch repair (MMR). CD3+ at the tumor invasive margin (IM) was most strongly associated with patient overall survival, and dichotomization of CD3+ prognostically stratified both dMMR and pMMR tumors. The ability to stratify dMMR tumors was a novel observation and revealed a poorer prognosis dMMR group. By multivariable (MV) analysis, CD3+ density and N (nodal) stage contributed the most to patient survival. In separate studies, expression of FOXP3+ Tregs in CRC has paradoxically been associated with more favorable survival. Interestingly, we found that colon cancers with low FOXP3+ and low CD8+ are a very poor prognostic subset. Immunoscore (IS; HalioDx) is a validated assay that examines CD3+ and CD8+ using digital pathology with conversion of densities into percentile scores using a software algorithm. In patients with stage III colon cancers from a completed adjuvant trial, recurrence rates were inversely related to IS score (0-4), and the dichotomized IS was associated with significantly better survival across all disease subgroups (Forest plot). Stage III colon cancers are categorized into low risk (T1-3N1) and high risk (T4 and/or N2) groups for guiding the duration of adjuvant chemotherapy (3 vs 6 months). IS was shown to prognostically stratify patients within both risk groups and was only a significant variable in low risk tumors by MV analysis. These data suggest the potential of IS to further risk stratify patients and to potentially inform treatment decisions. In patients with metastatic CRC, analysis of IS was shown to predict tumor metastatic burden which had prognostic value. Data also suggest that potential for IS to provide predictive information for chemotherapy (fluoropyrimidine + oxaliplatin) response in CRC, yet further studies are needed. A potential mechanism is immunogenic cell death induced by some anti-cancer drugs, including oxaliplatin. Regarding immune checkpoint inhibitors (ICPs), only 40-50% of patients with metastatic CRC respond to such therapy, and small studies in suggest that TIL densities may be a factor in observed variability in response to ICP inhibitors. To further explore this issue, we are examining tumor immunophenotypes in relationship to response and outcome in CRC patients treated with anti-PD-1 antibodies. We aim to develop a MV model, and to validate it in an independent dataset. Important and relevant issues include the fact that only a fraction of mutations result in neoantigens recognized by T-cells, the potential for poor presentation of neoantigens by MHC1, as well as activating or suppressive cytokines. Citation Format: Frank A. Sinicrope. Analysis of immune contexture to refine prognosis in patients with colon cancer: Implications for immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr SY17-01.