High Microsatellite Instability Research Articles

Intrahepatic Cholangiocarcinoma with High Microsatellite Instability and Tumor Mutation Burden That Responded Significantly to Pembrolizumab but Perforated within a Short Period.

Cholangiocarcinoma has a poor prognosis, and resection is the only curative treatment. Pembrolizumab, a programmed death receptor 1 inhibitor, has proven effective against unresectable or metastatic solid tumors with high microsatellite instability (MSI-H) or a high tumor mutation burden (TMB-H). In the present case, pembrolizumab treatment was initiated after standard chemotherapy for MSI-H and TMB-H unresectable intrahepatic cholangiocarcinoma. Intrahepatic tumor necrosis perforated the abdominal cavity. Emergency surgery was performed, but the patient died 36 days after admission. A pathological autopsy revealed that the intrahepatic tumor had almost completely disappeared.

Neoadjuvant immunotherapy in a locally advanced colon cancer patient with MSI-H and suspected Lynch syndrome: A case report.

Carrilizumab, a PD-1 inhibitor, has shown therapeutic effectiveness in patients with late-stage or metastatic solid tumors exhibiting DNA mismatch repair deficiency (dMMR) or microsatellite instability-high (MSI-H). dMMR/MSI-H cancer patients are known to be responsive to PD-1 inhibitors. However, the use of carrilizumab for preoperative immunotherapy in early, unresectable MSI-H/dMMR primary colon cancer lesions is relatively underexplored. We present the case of a 46-year-old male who sought medical attention at our institution due to a history of hematochezia for two weeks, right-sided abdominal pain for one week, and loose stools. Imaging indicated duodenal involvement, and a biopsy confirmed ascending colon adenocarcinoma with MSI-H status. Given that the patient's family exhibited a history of more than three confirmed cases of colorectal cancer spanning two generations, Lynch syndrome was considered. After four cycles of PD-1 antagonist immunotherapy with carrilizumab, the patient's symptoms resolved, and physical examination revealed no abdominal tenderness or palpable masses. Following radical colectomy, the primary tumor exhibited a pathological complete response. This case highlights the potential of preoperative neoadjuvant immunotherapy to improve staging accuracy and increase surgical resection rates in T4b MSI-H colon cancer patients without distant metastasis, suggesting a need for reconsideration of the treatment approach.

Development and validation of a deep learning-based microsatellite instability predictor from prostate cancer whole-slide images

Microsatellite instability-high (MSI-H) is a tumor-agnostic biomarker for immune checkpoint inhibitor therapy. However, MSI status is not routinely tested in prostate cancer, in part due to low prevalence and assay cost. As such, prediction of MSI status from hematoxylin and eosin (H&E) stained whole-slide images (WSIs) could identify prostate cancer patients most likely to benefit from confirmatory testing to evaluate their eligibility for immunotherapy and need for Lynch syndrome testing. Prostate biopsies and surgical resections from prostate cancer patients referred to our institution were analyzed. MSI status was determined by next-generation sequencing. Patients sequenced before a cutoff date formed an algorithm development set (n = 4015, MSI-H 1.8%) and a paired validation set (n = 173, MSI-H 19.7%) that consisted of two serial sections from each sample, one stained and scanned internally and the other at an external site. Patients sequenced after the cutoff date formed a temporally independent validation set (n = 1350, MSI-H 2.3%). Attention-based multiple instance learning models were trained to predict MSI-H from H&E WSIs. The predictor achieved area under the receiver operating characteristic curve values of 0.78 (95% CI [0.69–0.86]), 0.72 (95% CI [0.63–0.81]), and 0.72 (95% CI [0.62–0.82]) on the internally prepared, externally prepared, and temporal validation sets, respectively, showing effective predictability and generalization to both external staining/scanning processes and temporally independent samples. While MSI-H status is significantly correlated with Gleason score, the model remained predictive within each Gleason score subgroup.

Microsatellite Instability Detection in Cancer: A Multiplex qPCR Approach that Obviates the Need for Matching Normal Samples.

Microsatellite instability (MSI) indicates DNA mismatch repair deficiency in certain types of cancer, such as colorectal cancer. The current gold standard technique, PCR-capillary electrophoresis (CE), requires matching normal samples and specialized instrumentation. We developed VarTrace, a rapid and low-cost quantitative PCR (qPCR) assay, to evaluate MSI using solely the tumor sample DNA, obviating the requirement for matching normal samples. One hundred and one formalin-fixed paraffin-embedded (FFPE) tumor samples were tested using VarTrace and compared with the Promega OncoMate assay utilizing PCR-CE. Tumor percentage limit of detection was evaluated on contrived samples derived from clinical high MSI (MSI-H) samples. Analytical sensitivity, specificity, limit of detection, and input requirements were assessed using synthetic commercial reference standards. VarTrace successfully analyzed all 101 clinical FFPE samples, demonstrating 100% sensitivity and 98% specificity compared to OncoMate. It detected MSI-H with 97% accuracy down to 10% tumor. Analytical studies using synthetic samples showed a limit of detection of 5% variant allele frequency and a limit of input of 0.5 ng. This study validates VarTrace as a swift, accurate, and economical assay for MSI detection in samples with low tumor percentages without the need for matching normal DNA. VarTrace's capacity for highly sensitive MSI analysis holds potential for enhancing the efficiency of clinical work flows and broadening the availability of this test.

Abstract LB395: NetraAI-driven discovery of novel biomarkers in MSI-high colon cancer for precision immunotherapy

Abstract By leveraging NetraAI, a novel machine learning (ML) approach, we identify potential biomarkers in microsatellite instability-high (MSI-H) colon cancer. MSI, marked by DNA mismatch repair (MMR) defects characterizes 5-20% of colorectal cancers (CRCs). MSI-H tumors harbor higher mutational burdens, produce neoantigens, and enhance immune recognition and responsiveness to immunotherapy. The innovative Sub-Insight Learning approach of NetraAI, allows us to overcome challenges associated with smaller data sets not reflecting the totality of the disease they represent. This approach utilizes a set of validated mathematical methods to identify sub-insights about patients even from small data sets. This allows the system to decompose the data sets into high and low confidence patient subpopulations, enhancing predictive model accuracy and reducing overfitting. Further, the system explains what variables are driving the etiology defining the subpopulations of patients. Utilizing a small data set consisting of 141 RNA expression profiles of CRC samples (E-GEOD-41258) with MSI-H and MSI-low colon cancer, we were able to derive several unique insights into patients’ molecular profiles. NetraAI analysis identified several unique variables, including CATSPERB, FUT8, PLLP, DUSP4, and MLPH that may play significant roles in MSI-H colon cancer pathology. These markers hold potential for personalizing clinical trials as well as potential therapeutic targets. Furthermore, protein-protein interaction (PPI) networks revealed co-expression and co-localizations that exist amongst these genes, suggesting a complex interplay among these genes, particularly in the context of spermatogenesis. The application of NetraAI and its Sub-Insight Learning paradigm has revealed novel insights into the molecular profile of MSI-H colon cancer. These findings pave the way for more targeted and effective precision immunotherapy strategies, demonstrating the power of AI in advancing the understanding and treatment of complex cancers. Citation Format: Bessi Qorri, Mike J. Tsay, Paul Leonchyk, Larry Alphs, Luca Pani, Joseph Geraci. NetraAI-driven discovery of novel biomarkers in MSI-high colon cancer for precision immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB395.

Abstract NG07: Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors

Abstract Background: Colorectal cancer (CRC) is a critical public health concern as the third most commonly diagnosed cancer and second leading cause of cancer death globally. CRC is a heterogeneous disease with many different mechanisms and molecular subtypes. Around 15% of sporadic CRCs are classified as exhibiting high microsatellite instability (MSI-high) due to deficient DNA mismatch repair (dMMR). In the presence of MSI-high, colorectal tumors accumulate somatic mutations, resulting in high neoantigen burden, which, in turn, elicits a strong T cell response. Several previous studies have shown that MSI-high status is associated with overall levels of T cell infiltration in CRC and, specifically, with CD45RO+ T cell density. However, many studies have measured T cell densities using single-plex immunohistochemistry assays of individual T cell markers, which fail to capture the complexity of the T cell response in tumors, and the contributions of different T cell subsets. Using a multiplex immunofluorescence panel, we aimed to characterize the composition of the T cell response in CRC tumors in relation to MSI-high and hypermutation status in CRC. Methods: This study was conducted within a subset of participants from three well-characterized epidemiologic studies included in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO): the Ontario Family Colon Cancer Registry (OFCCR), the Nurses’ Health Study (NHS), the Health Professionals Follow-up Study (HPFS). In a total of N=637 participants with CRC, we profiled the in-situ T cell landscape of CRC using digital imaging, machine learning, and a multiplexed immunofluorescence panel. Our customized 9-plex panel included antibodies directed against CD3, CD4, CD8, CD45RA, CD45RO, FOXP3, and MKI67, as well as a pan-cytokeratin antibody to identify tumor/epithelial cells and nuclear DAPI (4’, 6-diamidino-2-phenylindole) stain. Assays were conducted using tissue microarrays (TMAs) where all slides were sent to Dana Farber Cancer Institute for analysis. In brief, core selection from donor FFPE blocks was guided by pathologist review of H&E-stained slides. For each CRC case, TMA blocks have 2-4 cores (0.6 mm) from tumor areas. T cell immune microenvironment is assessed for each tumor histologically using a multispectral imaging platform (PerkinElmer Vectra 3.0) for multiplexed immunofluorescence (mIF), where TMAs are stained with all markers concurrently and imaged. With pathologist supervision, a machine learning algorithm segmented tissue into epithelial and stromal area regions as well as phenotyped individual cells. The mIF panel has been validated against traditional chromogenic IHC. Based on these markers, we quantified counts and densities of naive, memory, and regulatory subsets of helper (CD3+CD4+) and cytotoxic (CD3+CD8+) T cells, and looked separately at these subsets within epithelial and stromal tissue, resulting in 12 unique subsets. Microsatellite instability and hypermutation status were determined from one of two targeted sequencing panels that included either 205 or 298 genes. MSI status was called using mSINGS. Hypermutation status was defined by plotting point mutations for all samples and observing different peaks, separately by panel. The minimum value between the two peaks was 23 and 26 point mutations per sample, respectively, which were used as cut-points. We used multivariable ordinal logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between MSI/hypermutation status with quantiles of specific T cell densities in CRC. As an alternative approach where counts were modeled directly, we used negative binomial count models with an offset term for area. Ordinal logistic regression either used quartiles or tertiles of T cell densities as the outcome, where different subsets were assessed for zero-inflation considering both epithelial and stromal tissue, so the same subset used the same categorization in each tissue. Subsets with less than 25% zero counts were divided into quartiles, subsets with greater than 25% zero counts into tertiles. Study-specific quantile cut points were used to limit potential batch effects across TMAs. Models were adjusted for age, sex, and study, and p-values were adjusted for multiple testing using the false discovery rate method for 12 independent tests. Results: Among 637 CRC tumors with targeted tumor sequencing and T cell immune profile available, 107 were classified as MSI-high, and 106 were classified as hypermutated. 98 tumors were both MSI-high and hypermutated. Compared to tumors with low microsatellite instability (MSI-low) or microsatellite stable (MSS) tumors, MSI-high tumors were strongly associated (ORs around 2 or higher) with higher T cell densities for all epithelial area CD3+CD4+, epithelial area CD3+CD8+, and stromal area CD3+CD8+ T cells (adjusted p-values <0.001). Compared to MSI-low/MSS tumors, MSI-high tumors had 3 times the odds of greater quantile of epithelial area CD3+CD8+ subsets defined as naive, memory, and regulatory [OR= 3.2 95% CI (2.14, 4.79), OR=3.19 (2.15, 4.72), OR=3.31 (2.20, 4.97), respectively]. MSI-high tumors were not associated with higher densities of stromal area CD3+CD4+ naive, memory, or regulatory cells. Effect estimates for hypermutation status showed consistent results and the same conclusions as MSI. Effect estimates from negative binomial models showed consistent findings with the ordinal logistic results presented. Conclusions: While it is well known that T cells overall are strongly associated with MSI status in CRC, the present study improves our understanding of what specific T cell subsets in what location in the tumor are associated with MSI and hypermutation status. Additionally, given the high level of T cell infiltration in MSI-high/dMMR tumors, these tumors are more likely to respond favorably to immune checkpoint inhibitors (ICIs). A more granular understanding of specific T cell subsets that are associated with these tumor phenotypes may improve our understanding of underlying biology and help inform targeted immunotherapy treatment decision-making for the MSI-high/dMMR CRC subtype. In future work we aim to examine increasing mutation frequency as a continuous variable and with more specific categorization of mutation frequency than binary cut-points in association with T cell profile. Citation Format: Claire Elizabeth Thomas, Yasutoshi Takashima, Tomotaka Ugai, Daniel D. Buchanan, Conghui Qu, Li Hsu, Andressa Dias Costa, Stephen Gallinger, Robert C. Grant, Jeroen R. Huyghe, Sushma S. Thomas, Robert S. Steinfelder, Shuji Ogino, Amanda I. Phipps, Jonathan A. Nowak, Ulrike Peters. Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr NG07.

The Expression Patterns of Immune Checkpoint Molecules in Colorectal Cancer: An Analysis Based on Microsatellite Status

Recently, immunotherapy has arisen as a novel treatment approach for patients with colorectal cancer (CRC), but the effectiveness of immunotherapy varies in these patients. We hypothesized that immune checkpoint molecules (ICMs), which are the targets of immunotherapy, are often exhibited concomitantly. Our objective was to investigate the patterns of ICM expression in patients with CRC and the differences in ICM expression based on microsatellite instability status. The immunohistochemical expression of programmed cell death protein 1 (PD-1), programmed cell death ligand 1 (PD-L1), T cell immunoglobulin and mucin-domain containing-3 (TIM-3), and lymphocyte-activation gene 3 (LAG-3) in the tumor center and periphery was assessed in patients with non-metastatic colorectal cancer. We enrolled 83 patients with CRC: a total of 40 microsatellite-stable (MSS) and 43 microsatellite-instability-high (MSI-H) cancer patients. PD-L1 was more frequently expressed in the tumor center in the MSI-H patients with than that in the MSS patients (18 [41.9%] vs. 3 [7.5%], respectively; p < 0.001), and the same trend was observed for TIM-3 expression (30 [69.8%] vs. 19 [47.5%], respectively; p = 0.047). The concomitant expression of two or more ICMs was more frequently observed than no expression or the expression of a single molecule in both the MSS and MSI-H groups; a total of 34 (79.7%) patients with MSI-H cancer and 23 (57.5%) with MSS cancer showed ICM expression at the tumor center, whereas 34 (79.7%) patients with MSI-H cancer and 22 (55%) with MSS cancer showed expression at the tumor periphery. Patients with the genetic characteristics of MSI-H cancer showed higher expression levels of ICMs than those in patients with MSS cancer, and predominantly, two or more ICMs were concurrently expressed. Our findings highlight the potential efficacy of the dual-blockade approach in immunotherapy, particularly in patients with MSI-H 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.

Significance of Microsatellite Instability in Colorectal Carcinoma- A Complete Review

The microsatellite instability (MSI-H) or mismatch repair deficient (dMMR) colorectal tumors recently have been reported that can benefit from immunotherapy, and MSI can be used as a genetic instability of a tumor detection index. Many studies have shown that there are many heterogeneous phenomena in patients with MSI tumors in terms of immunotherapy, prognosis and chemotherapy sensitivity. Here we mainly review the research results of MSI detection methods, its mechanisms, occurrence and its relationship with related tumors, aiming in such a way for brief analysis of the micro satellite instability. Microsatellites (MS) are the repeated sequences of DNA that play an important role in maintaining the tissue morphology. Any mutation of the DNA or chromosomes, lead to the instability of the microsatellites, thereby causing the microsatellite instability. There are three types of microsatellite instability (MSI). High microsatellite instability (MSI-H), low microsatellite instability (MSI-L) and microsatellite stability (MSS). Recent clinical research tends to classify MSS-L and MSS as similar. Microstaellite instability plays an important role in colorectal carcinoma. Based on different molecular mechanisms, MSI in colorectal cancer can be divided into colorectal cancer (CRC) with no obvious family genetic history and Lynch syndrome with non-polyposis with family genetic history. Lynch syndrome is an autosomal dominant disorder and syndrome caused by mutations in MMR strains, and it can also cause tumors in other parts of the colon and rectum. With the recent development of MSI detection technology and immunosuppressant in tumor therapy, researchers found that MSI-H tumors respond well to immunotherapy. There are several methods to detect the microsatellite instability. 1. Next Generation sequencing (NGS), 2. Fluoresence multiplex PCR and capillary electrophoresis. 3. Immunohistochemistry. 4. Single molecule- molecular inversion probes (SmMIP). The main mechanism of MSI includes, Slipped strand mispairing, MMR deficient.

Abstract 1040: Development of a novel RNA-based microsatellite stable predictive response signature (MSS-PRS) to identify MSS colorectal cancer (CRC) patients with a microsatellite instability-high (MSI-H) molecular phenotype

Abstract Introduction: MSI-H and mismatch repair deficient (dMMR) tumors are associated with favorable immune checkpoint inhibitor (ICI) responses (PMID: 3326454). However, up to 95% of CRC tumors are MSS/proficient MMR (pMMR) leading to poorer prognosis and treatment outcomes than MSI-H/dMMR patients (PMID: 12867608, 26028255). In MSS/pMMR metastatic CRC, multiple combination therapies are being investigated despite a lack of biomarkers to guide therapy. Therefore, we developed an RNA-based MSS-PRS with a primary objective to identify MSS tumors that have MSI-H/dMMR molecular features indicative of ICI response. Experimental Procedures: The MSS-PRS was developed using the TCGA CRC cohort (COAD; n=268). Training labels were assigned using the MSI Mantis score and mutation status from 8 genes with reported MSI association. Samples called “activated” had both a gene mutation and an MSI Mantis score > 0.4 (i.e., MSI-H), and samples called “non-activated” were wild type for all genes and had MSI Mantis score < 0.4. All other samples were designated “ambiguous” and excluded from training. Two thirds of the non-ambiguous samples were assigned to the classifier training set and all remaining samples were assigned to the test set. Using ClaNC software (PMID: 16269418) and cross-validation in the training set, a nearest centroid classifier was developed from a set of high mean, high variance candidate genes to select an optimal gene set to separate activated and non-activated groups. The classifier performance was evaluated in the test set. Results: The MSS-PRS contained 112-genes enriched for mismatched DNA binding, DNA damage repair, PD-L1, innate and adaptive immune response, cellular immunity, and cytokines. In the test set, the classifier called 44 of 46 MSI-H samples activated; of the remaining 77 samples that were MSS tumors, 38 were called activated and 39 were called not activated. Visual inspection of heat maps of tumor by MSI/MSS-PRS status and their association with TMB and CRC-related mutations suggest greater differences between MSS tumors called activated and MSI-H tumors than between MSS tumors called activated and MSS tumors called not activated. In contrast, immune marker expression profiles in MSS tumors called activated were markedly more similar to MSI-H tumors compared to MSS tumors called non-activated. Summary and Conclusions: Herein we described the development of a novel MSS-PRS that captures an MSI-H/dMMR-like molecular phenotype in a subset of patients with MSS tumors despite their lack of high TMB or overt MSI defects. Based upon these initial findings, further development of the MSS-PRS and its clinical validation as a tool to select patients with MSS tumors who may benefit from ICI-containing treatment regimens is warranted. Citation Format: Kirk Pappan, Gregory Mayhew, Jonathan Shepherd, Yuelong Guo, Kirk Beebe, Joel Eisner, Michael Milburn. Development of a novel RNA-based microsatellite stable predictive response signature (MSS-PRS) to identify MSS colorectal cancer (CRC) patients with a microsatellite instability-high (MSI-H) molecular phenotype [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 1040.

Abstract 5533: The difference of immune microenvironment betweende novometastatic and non-metastatic microsatellite instability-high colorectal cancer

Abstract Introduction: Microsatellite instability-high (MSI-H) colorectal cancer (CRC) consists of 15% of all CRC but only 2-4% of metastatic CRC. The favorable prognosis of non-metastatic (early-stage) MSI-H CRC may be related to vigorous immune reaction in tumor microenvironment. However, the mechanisms of immune evasion in metastatic (late stage) MSI-H CRC are largely unknown. Materials and Methods: We retrospectively collected patients with MSI-H CRC from National Taiwan University Hospital and Kaohsiung Chang Gung Memorial Hospital. The archival tumor specimens were used for immune cells analysis by Nanostring PanCancer Immune Panel, and spatial immune characterization by multiplex immunofluorescence stains. Only surgical resected primary tumors and metastatic tumors were included. Gene expression and immune cells composition were compared between non-metastatic and de novo metastatic tumors. Results: We enrolled 59 and 27 patients with early-stage and late-stage MSI-H CRC, respectively. Twelve metastatic site tumors were also collected. The clinicopathologic characteristics between patients who have early- and late-stage MSI-H CRC were not significantly different. There are heterogeneous immune cell compositions in these 98 MSI-H tumors. Compared to early-stage MSI-H tumors, there are significantly fewer cytotoxic (difference -0.497, p = 0.001) and dendritic cells (difference -0.528, p = 0.021) in late-stage MSI-H tumors. Gene set enrichment analysis disclosed significantly decrease in the expression of JAK-STAT-IFN-γ- and antigen processing-related pathways in late-stage MSI-H tumors. The top 5 genes with significantly differential expression between late-stage and early-stage tumors are C7, TNFRSF12A, MFGE8(up-regulated) and CXCL5, IFNL1, GZMH, HMGB1 and CXCR1 (down-regulated). Conclusions: There are significantly fewer cytotoxic and dendritic cells in late-stage MSI-H CRC, compared to early-stage MSI-H CRC, which is associated with decrease expression in JAK-STAT-IFN-γ- and antigen processing-related pathways. Citation Format: Kuo-Hsing Chen, Chia-Lang u Hs, Yu-Li Su, Chang-Tsu Yuan, Jia-Huei Tsai, Yi-Hsin Liang, Ann-Lii Cheng, Kun-Huei Yeh. The difference of immune microenvironment betweende novometastatic and non-metastatic microsatellite instability-high colorectal 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 5533.

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&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 >0.91 in colon cancer and >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 < 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.

Abstract 3889: Genomic landscape of gynecologic cancers with poor prognosis in Japan, an analysis of the national database of comprehensive genomic profiling tests

Abstract Objective: Comprehensive genomic profiling (CGP) tests were approved in Japan in June 2019 under universal health insurance coverage for cancer patients who have finished (or almost finished) standardized treatment. All the data are collected to the “Center for Cancer Genomics and Advanced Therapeutics (C-CAT)” under written informed consent. Up to date, over 60,000 CGP data have been deposited with a 99.7% consent rate. This study aims to analyze mutational landscape of gynecologic cancers, especially with poor prognosis, by using this database. Methods: We analyzed CGP datasets from 3,006 gynecologic cancer patients using FoundationOne® CDx (F1CDx), the most commonly tested in Japan. This study was ethically approved by our institutional ethics committee (#2021341G) and the Information Utilization Review Board of C-CAT (#CDU2022-026N). Results: Endometrial cancers (n=561) showed high rates of tumor mutational burden-high (TMB-H) (13.9%) and MSI-high (MSI-H) (10.8%), especially in endometrioid carcinomas. POLE exonuclease mutations were less frequent (1.4%) compared to TCGA data (7%), while TP53 mutations were more common (54.4% vs. 29% in TCGA), suggesting the impact of prognosis of the molecular subtypes. Other frequently mutated genes included PIK3CA (41%), PTEN (35%), ARID1A (31%) and KRAS (26%). In 839 cervical cancers, TMB-H prevalence was 14.2%, with low MSI-H at 1.5%. TMB-H was significantly higher in squamous cell carcinomas (20.6%) than adenocarcinomas (8.3%). Frequent mutations included PIK3CA (32%), STK11 (20%), TP53 (20%), KRAS (14%), and CDKN2A (11%). TP53 mutations were significantly higher than TCGA data (<5%), particularly in mucinous carcinomas (60%), indicating a prevalence of HPV-independent tumors with poorer prognosis. Actionable mutations were generally more frequent in adenocarcinomas than in squamous cell carcinomas, including KRAS (32.2%), TP53 (29.4%), CDKN2A (18.3%), and ERBB2 (16.7%). In 1,606 ovarian cancers, the ratio of TMB-H was 5.0%, and MSI-H was 1.2%. TMB-H rates varied between 3.3-6.5% across histological types, while the ratio of MSI-H was significantly lower in serous carcinomas (0.3%) than non-serous carcinomas. Pathogenic mutations in the POLE exonuclease domain were rare in cervical (0.0%) and ovarian (0.2%) cancers. Conclusion: The C-CAT database offers insights into the mutational landscape of various cancers and histological subtypes, especially those with poor prognosis, highlighting the unmet needs for drug development in these gynecologic cancers. Citation Format: Qian Xi, Hidenori Kage, Miho Ogawa, Asami Matsunaga, Akira Nishijima, Kenbun Sone, Kei Kawana, Katsutoshi Oda. Genomic landscape of gynecologic cancers with poor prognosis in Japan, an analysis of the national database of comprehensive genomic profiling tests [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 3889.

Abstract 1282: Gavage with Candida albicans leads to fungal colonization of colorectal tumors and decreased response to radiotherapy

Abstract The host microbiome in the gut and tumors have been shown to affect tumor growth and therapeutic response in cancer. Furthermore, the presence of specific fungal taxa are associated with tumor hypoxia, tumor progression, therapeutic response, and clinical outcomes in colorectal cancer (CRC). Preliminary data from our group found that the presence of Candida species increased tumor hypoxia and decreased overall survival in CRC. However, whether intratumoral Candida drive, support, or simply inhabit tumors with poor prognoses remains unclear. Here, we investigate a casual role for Candida albicans in tumor progression and therapy response using a syngeneic mouse model of microsatellite-instability high (MSI-H) colorectal cancer. We subcutaneously implanted MC38 colorectal cancer cells into C57BL/6 mice and then orally gavaged these mice with C. albicans, Saccharomyces cerevisiae, or PBS. The site of tumor formation was locally irradiated once (7.5 Gy), and growth of the tumor was measured over time. Differences in tumor volume were assessed by longitudinal mixed-effect models. Tumor sections were stained for fungi using calcofluor white (CFW) and underwent bulk RNA sequencing to detect differential gene expression, which were interpreted using gene set enrichment analysis (GSEA). Mice gavaged with C. albicans showed decreased response to radiation compared to mice gavaged with either S. cerevisiae (p<0.05) or PBS (p<0.001). Additionally, hyphae were observed in murine tumors gavaged with C. albicans, suggesting translocation of gavaged C. albicans from the gut to tumors. Further, tumors from mice gavaged with C. albicans displayed unique gene expression profiles, including decreased interferon alpha and IL-6 and STAT3 signaling, decreased oxidative phosphorylation, and decreased apoptosis-related gene expression. Here, we show that C. albicans may confer resistance to radiation therapy and affects immune and cancer cell activity in the MC38 (MSI-H) syngeneic in vivo model of colorectal cancer. Further, we show that hyphal fungi can be visualized in heterotopic murine tumors from our C. albicans gavage condition. These data establish that fungi can translocate from the gut to distal tumor sites, and that upon translocation, changes in gene expression and therapy response are observed. Future directions will explore the mechanism by which these effects occur and whether these findings can be leveraged to improve radiotherapy outcomes. Citation Format: Dennis J. Grencewicz, Alexander Loncar, Rebecca Hoyd, Aaditya Pallerla, Nyelia Williams, Martin Benej, McKenzie Kreamer, Yogita Mehra, Shiva Jahanbakhshi, Matthew Anderson, Nicholas Denko, Daniel Spakowicz. Gavage with Candida albicans leads to fungal colonization of colorectal tumors and decreased response to radiotherapy [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 1282.

Abstract 5921: PH027-1, a potent and selective small-molecule WRN inhibitor that targets MSI-H tumors

Abstract Background: High microsatellite instability (MSI-H) is highly prevalent across many cancer types including endometrium, gastric, ovary and colorectal cancer. It is well known that there is a clear synthetic lethality (SL) interaction between MSI-H and Werner syndrome protein (WRN) inhibition. WRN is a member of RecQ helicase family and involved in the maintenance of genome integrity. Different from other RecQ family members, WRN has two activity centers responsible for helicase and exonuclease activity, respectively. Further studies confirmed that an inhibition on helicase activity, but not exonuclease activity, is responsible for SL interaction with MSI-H. Also, Recent clinical observations supported that though loss-of-function of WRN could cause an early-aged disease Werner syndrome, selective loss of helicase but not exonuclease leads to only mild to moderate symptoms, suggesting a selective inhibitor of helicase activity has the potential to induce the SL interaction with MSI-H and keep patients safe. Methods: Biochemical assays and cell-based assays were performed to evaluate in vitro activity and selectivity of PH027-1. The in vivo anti-tumor efficacy was tested in two cell-derived xenograft (CDX) mouse models with tumors harboring MSI-H. The in vivo pharmacokinetics (PK) properties were evaluated in mice, rats and dogs, and other in vitro and in vivo PK and safety properties were assessed with corresponding assay methods. Results: Biochemical assays showed that PH027-1 potently inhibited helicase activity of WRN (IC50, 0.8 nM), but had no effect on other RecQ family members even at the highest tested concentration of 10 μM (IC50, all≥10 μM for BLM, RecQ4 and RecQ5). At the same time, PH027-1 did not affect the exonuclease activity of WRN at all tested concentrations. In cell-based assays, PH027-1 potently inhibited cell viability of MSI-H cancer cells SW48 and HCT116 at tens of nM, but had no effect on MSS cells (HT29 cancer cells and CD34+ hematopoietic stem cells) even at 10 μM. The tests were further expanded to 18 cancer cell lines covering uterus, gastric, ovary and colorectal cancer. Nine of twelve MSI-H cell lines were very sensitive to WRN inhibition, and all six MSS cell lines were totally resistant to the treatment. PH027-1 possessed excellent PK profiles as shown by in vivo PK studies, with absolute bioavailability of 58%~102% in mice, rats and dogs. In two CDX models (SW48 and HCT116), oral administration of PH027-1 dose-dependently inhibited tumor growth, and a nearly complete inhibition was observed at a dose of 20 mg/kg QD. Tumor regression was clearly shown at higher doses. All other in vitro and in vivo PK and safety tests showed favorable results and supported for preclinical development of PH027-1. Conclusion: As a highly selective and potent inhibitor on helicase activity of WRN, PH027-1 has the potential to become a novel and safe approach for treatment of MSI-H tumors. Citation Format: Feng Gao, Bin Liu, Liandong Jing, Jing Wang, Yongyong Wu, Jun Wan, Pengzhi Zhang, Yu Gao, Zhizhong Li, Yongqi Guo. PH027-1, a potent and selective small-molecule WRN inhibitor that targets MSI-H tumors [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 5921.

Abstract 6845: MAGEA3 expression and secretion in MMR-MSH6 and MMR-PMS2 microsatellite-stable colorectal cancer

Abstract Despite the breakthrough of PD-1/PD-L1 blockade therapy in the recent years, mixed responses have been shown across multiple tumor types, including in colorectal cancer (CRC), the second leading cause of death worldwide. This immunotherapy has proven to be successful for a subtype of CRC that carries mismatch repair deficiency (dMMR) and high microsatellite instability (MSI-H), despite a lack of response by microsatellite-stable CRC. For these types of non-responsive cancers, new immunotherapy targets are currently being investigated for alternative therapy such as the MAGE-A cancer testis antigen family whose expression is restricted to germline cells in normal tissue but is overexpressed in many cancer cells. In this study, we examine the relationship between MAGEA3 and MMR proteins MSH6 and PMS2. Immunohistochemical staining of CRC tissues demonstrated co-expression between MAGEA3 with both MSH6 and PMS2. Immune cells were observed to express MAGEA3 in CRC as well. To investigate the possibility of secreted MAGEA3 from tumor cells, we performed western blot analysis of CRC cell lines, ELISA, and binding assay on cell lines and the positive results suggest that MAGEA3 protein is secreted. The results suggest that MAGE-A3 may be a promising target for microsatellite-stable colorectal cancer immunotherapy. Citation Format: Jina Yom, Rachel Gonzalez, Bailey Gilmore, Zhaoying Guo, Andy Han, Eden Zewdu, Dehe Kong, Tianli Qu, Hailey Guo, Alex Strom, Zoe Zhao, Xiaomin Hu, Qi Ren, Yan Ma, Ranran Zhang, Zhaohui Wu, Xuan Liu, Wei Fu. MAGEA3 expression and secretion in MMR-MSH6 and MMR-PMS2 microsatellite-stable colorectal 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 6845.

Abstract 3557: A pancancer gamma delta T cell repertoire atlas

Abstract While representing only a small portion of T cell population, Gamma delta (γδ) T cells have unique contributions to both innate and adaptive immunity. Compared to αβ T, γδ T cells have a more diverse TCR repertoire, allowing them to recognize a broader range of tumor antigens. Recent breakthrough discoveries indicate that the antitumor efficacy of γδ T cells can be potentiated or rescued through targeted therapeutic approaches. Despite their functional and translational significance, a comprehensive understanding of the γδ T cell repertoire within tumor tissues has yet to be fully achieved.In this work, we generated a pan-cancer γδ T cell repertoire Atlas through reanalyzing RNA-seq data from more than 11,000 tumors in TCGA utilizing TRUST4, an advanced computational method for reconstruction of TCR repertoires. This allowed us to offer the most accurate and comprehensive examination of the γδ TCR landscape spanning 33 cancer types, marking it the largest collection of γδ clones on human cancer to date. We processed 660 billion RNAseq reads, identified ~3 million CDR3 reads, applied a series of stringent filtering criteria to remove biologically implausible, ambiguous sequences, and out-of-frame TCRs, which resulted in 22,205 unique γδ TCR clones from 6,751 tumors. TCR gene enrichment scores were calculated to represent overall expression of γδ in each tumor. The γδ enrichment is highly variable between and within cancer types. As expected, tumors traditionally classified as immune-cold (UVM and GBM) show the lowest scores. Cancers intrinsically related to lymphatic system (LAML, THYM and DLBC), exhibit the highest scores. Beyond THYM, the top five solid-tumor cancers carrying the highest enrichment are PRAD, KIRC, TGCT, LUAD and KICH. We further profiled the clone counts, spectrum of clone sizes, CDR3 length, V-J pair usage, and clonality in 33 cancers. Overall, a dominant presence of large clone segment is not observed in most cancers. The most prevalent V-J pairs are TRGV10/9/2-TRGJ1 for γ, and TRDV1-TRDJ1 for δ chain. Cancers including LAML, KIRC, LUAD, SKCM, CESC, LUSC, STAD, display a relatively higher proportion of intermediate to larger clones. THYM exists the highest γδ diversity, with the lowest clonality and most diverse V-J pairs. In addition, we evaluated the prognostics value of γδ genes by multivariate Cox regression, adjusting for age, sex, stage, and tumor purity, and identified 38 γδ genes associated with patient survival with p<0.05 in 25 cancer types. Finally, within HNSC, we observed higher γδ gene enrichment (p=1.6e-9) and clone diversity (p=0.014) in HPV+ vs. HPV- tumors. The γδ gene enrichment is also found associated with patients’ survival (p=0.002) in HPV+, but not in HPV- HNSC. Similarly, COAD tumors with high Microsatellite Instability (MSI) shows higher γδ gene enrichment and clone diversity compared to MSI low COAD. Collectively, our findings serve as a foundational resource for γδ T cell research in oncology. . Citation Format: Xiaoqing Yu, Song Li, Ling Cen, Xuefeng Wang. A pancancer gamma delta T cell repertoire atlas [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 3557.

Abstract 3095: A high-throughput phenotypic screen to identify small molecule inhibitors of Werner helicase

Abstract Werner helicase (WRN) is a RecQ DNA helicase involved in genome maintenance and DNA damage repair. It has recently been shown to be essential to cancer cells with high microsatellite instability (MSI-H). In MSI-H cancer cells, WRN depletion was shown to induce DNA damage and disrupt mitoses, resulting in a distinct phenotype of enlarged and fragmented nuclei. Here, we present a high-throughput phenotypic screen to identify compounds that selectively induce enlarged nuclei in MSI-H cancer cells. In HCT116, an MSI-H colorectal cancer cell line, approximately 40% of cells exhibited enlarged nuclei when WRN was depleted using siRNA. In contrast, fewer than 10% of control cells displayed this phenotype. In HT29, a microsatellite stable (MSS) cancer cell line, no such difference in nuclear morphology was observed, suggesting that the phenotype is specific to MSI-H cells. We used high content imaging to screen our in-house diversity library of approximately 175,000 compounds in 384-well format. 4,260 compounds induced enlarged nuclei in HCT116 cells, a 2.4% hit rate. After re-screening hits in HCT116 along with two additional MSI-H cancer cell lines, SW48 and SNU-407, and counter-screening in HT29 cells, 144 hits were confirmed to specifically enlarge nuclei in MSI-H but not MSS cells. Using the ADP-Glo Kinase Assay, two of these compounds were confirmed to inhibit WRN ATPase activity, suggesting WRN inhibition as a potential mechanism for their specific effects in MSI-H cells. This screen will also identify compounds which selectively kill MSI-H cells through mechanisms beyond direct inhibition of WRN, including interaction with WRN complex members or other members of DNA damage repair pathways. Validation studies including the assessment of cell viability and DNA damage in a panel of MSI-H and MSS cell lines will be performed. Our study proposes a phenotypic screening strategy for identifying small molecules with the potential to target WRN and uncover additional novel mechanisms for treating MSI-H cancers. Citation Format: Christine A. Moomau, Yipin Lu, Xiaobin Zhang, Xiang Zhai, Lina Gu, Qing Sheng, Fang Li, Yaoyu Chen. A high-throughput phenotypic screen to identify small molecule inhibitors of Werner helicase [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 3095.

Abstract 5275: Celecoxib and chloroquine enhance the antitumor effect of immune checkpoint blockade therapy, in a syngeneic mouse model for pancreatic cancer

Abstract Immune checkpoint inhibitors (ICIs) have shown impressive clinical activities in some cancer types, but they have yet to demonstrate any meaningful clinical benefit in patients with pancreatic ductal adenocarcinoma (PDAC) except those with microsatellite instability high (MSI-H) tumors. Several recent studies showed that concomitant use of NSAIDs such as celecoxib by patients with certain cancers could improve the survival benefit of ICI treatment (e.g., Sebastian et al, Clin Lung Cancer, 2023;). Furthermore, autophagy inhibitors such as chloroquine were also reported to sensitize pancreatic tumors to the treatment of ICIs in mouse models for PDAC (Yamamoto, et al, Nature, 2020). We recently reported that the combination of chemotherapy (triple combination of nab-paclitaxel + gemcitabine + cisplatin) and a mouse surrogate of the IFc-enhanced anti-CTLA-4 antibody botensilimab, showed significantly improved antitumor activity in immune competent KPC syngeneic mouse model for PDAC [Tanne, et al, Cancer Res (13_Supplement), 2020]. In this study, we sought to determine whether or not the addition of celecoxib and/or chloroquine further improve the antitumor activity of triple chemotherapy and ICI in the syngeneic KPC model. We first found that celecoxib (30mg/kg P.O. QDx21) significantly enhanced the tumor growth inhibition when added to triple chemotherapy (Gemcitabine 70mg/kg I.P., Cisplatin 4mg/kg I.P., Nab-paclitaxel 25mg/kg I.V. days 1,4 and 7) plus the murine equivalents of botensilimab (100ug I.P. BIW for three weeks) and balstilimab (200ug I.P. BIW for three weeks) (p=0.004, N=10). We then performed a pilot study to assess if adding chloroquine could further improve the activity. While adding chloroquine (60mg/kg I.P. QDx21) alone did not significantly affect tumor growth the addition of both chloroquine and celecoxib greatly improve the tumor growth inhibition compared to just the triple chemotherapy and ICIs (p=0.009, N=5). Overall, our data showed that celecoxib or the combination of celecoxib and chloroquine could substantially sensitize the mouse pancreatic tumors to the treatment of chemotherapy and ICIs. (This work was supported in part by the Seena Magowitz Foundation and the Purple Pansies) Citation Format: Jaeger Moore, Dhan Chand, Daniel Levey, Daniel Von Hoff, Haiyong Han. Celecoxib and chloroquine enhance the antitumor effect of immune checkpoint blockade therapy, in a syngeneic mouse model for pancreatic 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 5275.

Abstract 6393: The predictive role of TNF-related genes in patients receiving immune checkpoint inhibitors

Abstract Introduction: Not all patients respond to immune checkpoint inhibitors (ICI) even when they have favorable FDA-approved biomarkers. The tumor necrosis factor superfamily (TNFSF) and tumor necrosis factor receptor superfamily (TNFRSR) play critical roles in various biological processes, including inflammation, immune regulation, and cell death. In this study, we sought to investigate the predictive role of TNF-related genes in patients receiving ICI. Methods: The RNA expression levels of 18 TNF-related genes were assessed in a pan-cancer cohort of 217 patients treated with immune checkpoint inhibitors (ICI) at the University of California San Diego (UCSD) Moores Cancer Center. Using a reference population of 735 tumors and 35 histologies, transcript abundance was adjusted to internal housekeeping gene profiles and rated (0-100th percentile). The patients were clustered into two groups based on the 18 TNF-related genes expression using Ward’s hierarchical clustering. Associations between overall survival and previously demonstrated independent ICI predictive variables were assessed. Bonferroni correction for multiple comparisons was used and considered statistically significant when p-value ≤ 0.05. Results: Four TNF-related genes (CD137, CD70, GITR, and TNFSF9) were associated with positive programmed death-ligand 1 (PD-L1) expression (PD-L1≥1% immunohistochemistry TPS), while TNFSF18 was associated with negative PD-L1 expression (corrected p-value<0.05). No gene was associated with microsatellite instability-high (MSI-H) or high tumor mutational burden (TMB-H) (TMB≥10 mutations/Mb) (corrected p-value>0.05). We clustered the patients based on their 18 TNF-related genes expression into two signature clusters, high (n=94) and low (n=123). Patients in the high expression signature cluster were more likely to have high PD-L1 compared to the low expression cluster (corrected p-value<0.05). The high expression signature cluster was associated with better survival compared with the low expression cluster (HR=1.49, 95%CI: 1.05-2.13 (p=0.026)). When adjusting for TMB, MSI, PD-L1, TP53 and KRAS status, the TNF high expression signature cluster was still associated with better overall survival (HR=1.71, 95%CI:1.11-2.66 (p=0.016)). Other than the TNF high expression signature cluster group, only the presence of KRAS mutation was a predictor of a longer survival (HR=2.09, 95%CI:1.28-3.42 (p=0.003)). Conclusion: A high TNF-related gene expression profile may serve as an independent predictor for longer overall survival for patients treated with ICI. Citation Format: Obada Ehab Ababneh, Shumei Kato, Daisuke Nishizaki, Hirotaka Miyashita, Suzanna Lee, Mary Nesline, Sarabjot Pabla, Jeffrey Conroy, Paul DePietro, Heidi Ko, Razelle Kurzrock. The predictive role of TNF-related genes in patients receiving immune checkpoint inhibitors [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 6393.