Immune Checkpoint Blockade Response Research Articles

LORIS robustly predicts patient outcomes with immune checkpoint blockade therapy using common clinical, pathologic and genomic features.

Despite the revolutionary impact of immune checkpoint blockade (ICB) in cancer treatment, accurately predicting patient responses remains challenging. Here, we analyzed a large dataset of 2,881 ICB-treated and 841 non-ICB-treated patients across 18 solid tumor types, encompassing a wide range of clinical, pathologic and genomic features. We developed a clinical score called LORIS (logistic regression-based immunotherapy-response score) using a six-feature logistic regression model. LORIS outperforms previous signatures in predicting ICB response and identifying responsive patients even with low tumor mutational burden or programmed cell death 1 ligand 1 expression. LORIS consistently predicts patient objective response and short-term and long-term survival across most cancer types. Moreover, LORIS showcases a near-monotonic relationship with ICB response probability and patient survival, enabling precise patient stratification. As an accurate, interpretable method using a few readily measurable features, LORIS may help improve clinical decision-making in precision medicine to maximize patient benefit. LORIS is available as an online tool at https://loris.ccr.cancer.gov/ .

Lack of TGFβ signaling competency predicts immune poor cancer conversion to immune rich and response to checkpoint blockade.

Transforming growth factor beta (TGFβ) is well-recognized as an immunosuppressive player in the tumor microenvironment but also has a significant impact on cancer cell phenotypes. Loss of TGFβ signaling impairs DNA repair competency, which is described by a transcriptomic score, βAlt. Cancers with high βAlt have more genomic damage and are more responsive to genotoxic therapy. The growing appreciation that cancer DNA repair deficits are important determinants of immune response prompted us to investigate the association of βAlt with response to immune checkpoint blockade (ICB). We predicted that high βAlt tumors would be infiltrated with lymphocytes because of DNA damage burden and hence responsive to ICB. We analyzed public transcriptomic data from clinical trials and preclinical models using transcriptomic signatures of TGFβ targets, DNA repair genes, tumor educated immune cells and interferon. A high βAlt, immune poor mammary tumor derived transplant model resistant to programmed death ligand 1 (PD-L1) antibodies was studied using multispectral flow cytometry to interrogate the immune system. Metastatic bladder patients in IMvigor 210 who responded to ICB had significantly increased βAlt scores and experienced significantly longer overall survival compared to those with low βAlt scores (hazard ratio 0.62, P=0.011) . Unexpectedly, 75% of high βAlt cancers were immune poor as defined by low expression of tumor educated immune cell and interferon signatures. The association of high βAlt with immune poor cancer was also evident in TCGA and preclinical cancer models. We used a high βAlt, immune poor cancer to test therapeutic strategies to overcome its inherent anti-PD-L1 resistance. Combination treatment with radiation and TGFβ inhibition were necessary for lymphocytic infiltration and activated NK cells were required for ICB response. Bioinformatic analysis identified high βAlt, immune poor B16 and CT26 preclinical models and paired biopsies of cancer patients that also demonstrated NK cell activation upon response to ICB. Our studies support βAlt as a biomarker that predicts response to ICB albeit in immune poor cancers, which has implications for the development of therapeutic strategies to increase the number of cancer patients who will benefit from immunotherapy.

A spatial architecture-embedding HLA signature to predict clinical response to immunotherapy in renal cell carcinoma.

An important challenge in the real-world management of patients with advanced clear-cell renal cell carcinoma (aRCC) is determining who might benefit from immune checkpoint blockade (ICB). Here we performed a comprehensive multiomics mapping of aRCC in the context of ICB treatment, involving discovery analyses in a real-world data cohort followed by validation in independent cohorts. We cross-connected bulk-tumor transcriptomes across >1,000 patients with validations at single-cell and spatial resolutions, revealing a patient-specific crosstalk between proinflammatory tumor-associated macrophages and (pre-)exhausted CD8+ T cells that was distinguished by a human leukocyte antigen repertoire with higher preference for tumoral neoantigens. A cross-omics machine learning pipeline helped derive a new tumor transcriptomic footprint of neoantigen-favoring human leukocyte antigen alleles. This machine learning signature correlated with positive outcome following ICB treatment in both real-world data and independent clinical cohorts. In experiments using the RENCA-tumor mouse model, CD40 agonism combined with PD1 blockade potentiated both proinflammatory tumor-associated macrophages and CD8+ T cells, thereby achieving maximal antitumor efficacy relative to other tested regimens. Thus, we present a new multiomics and spatial map of the immune-community architecture that drives ICB response in patients with aRCC.

Abstract IA008: Dissecting innate immune mechanisms of resistance to immune checkpoint blockade therapy in bladder cancer

Abstract We have explored the TME of bladder cancer (BC) leveraging single-cell RNA sequencing (scRNAseq) and clinical trial data to ascertain the complexity of tumor-infiltrated immune ecllls in BC. As a first step we identify distinct tumor-associated macrophage (TAM) populations associated with immune checkpoint blockade (ICB) response and resistance. Through plasma cytokine profiling, in vitro assays, and spatial analyses, we uncover novel cytokine-driven axes influencing these TAM populations and their impact on T cells, offering insights into enhancing anti-tumor T cell immunity in BC. Second, we investigate the potential of urine-derived cells (UDCs) as surrogates for monitoring the BC TME. Our scRNAseq atlas of BC patient UDCs reveals a diverse composition of immune cell populations, strikingly transcriptionally similar to tumor immune cells and containing immune subsets absent or rare in peripheral blood, suggesting their utility as biomarkers for response to therapeutic intervention. Collectively, these findings provide new insights into the immune landscape of BC and provide putative targets to enhance existing immunotherapy strategies in BC. Citation Format: Nina Bhardwaj. Dissecting innate immune mechanisms of resistance to immune checkpoint blockade therapy in bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr IA008.

BET inhibition sensitizes innate checkpoint inhibitor resistant melanoma to anti-CTLA-4 treatment.

Approximately 50% of melanoma patients fail to respond to immune checkpoint blockade (ICB), and acquired resistance hampers long-term survival in about half of initially responding patients. Whether targeting BET reader proteins, implicated in epigenetic dysregulation, can enhance ICB response rates and durability, remains to be determined. Here we show elevated BET proteins correlate with poor survival and ICB responses in melanoma patients. The BET inhibitor IBET151, combined with anti-CTLA-4, overcame innate ICB resistance however, sequential BET inhibition failed against acquired resistance in mouse models. Combination treatment response in the innate resistance model induced changes in tumor-infiltrating immune cells, reducing myeloid-derived suppressor cells (MDSCs). CD4+ and CD8+ T cells showed decreased expression of inhibitory receptors, with reduced TIM3, LAG3, and BTLA checkpoint expression. In human PBMCs invitro, BET inhibition reduced expression of immune checkpoints in CD4+ and CD8+ T cells, restoring effector cytokines and downregulating the transcriptional driver TOX. BET proteins in melanoma may play an oncogenic role by inducing immune suppression and driving T cell dysfunction. The study demonstrates an effective combination for innately unresponsive melanoma patients to checkpoint inhibitor immunotherapy, yet highlights BET inhibitors' limitations in an acquired resistance context.

Time-course RNAseq data of murine AB1 mesothelioma and Renca renal cancer following immune checkpoint therapy

Time-critical transcriptional events in the immune microenvironment are important for response to immune checkpoint blockade (ICB), yet these events are difficult to characterise and remain incompletely understood. Here, we present whole tumor RNA sequencing data in the context of treatment with ICB in murine models of AB1 mesothelioma and Renca renal cell cancer. We sequenced 144 bulk RNAseq samples from these two cancer types across 4 time points prior and after treatment with ICB. We also performed single-cell sequencing on 12 samples of AB1 and Renca tumors an hour before ICB administration. Our samples were equally distributed between responders and non-responders to treatment. Additionally, we sequenced AB1-HA mesothelioma tumors treated with two sample dissociation protocols to assess the impact of these protocols on the quality transcriptional information in our samples. These datasets provide time-course information to transcriptionally characterize the ICB response and provide detailed information at the single-cell level of the early tumor microenvironment prior to ICB therapy.

Abstract PO2-13-04: Single cell characterization of senescent CD8+ T cell promotes immunotherapy resistance in early-stage triple-negative breast cancer

Abstract Background: Immune checkpoint blockade (ICB) has been explored in triple-negative breast cancer (TNBC) and has been proven to improve patient survival in advanced TNBCs (IMpassion130) or increase the pathological complete response rate in early TNBCs (KEYNOTE522). However, ICB could only benefit a subset of patients, highlighting the urgent need to optimize patient selection. Unlike in advanced TNBCs, a predictive biomarker for ICB in early TNBCs is still lacking. The main reason might be that previous studies neglected the heterogeneity of tumor ecosystems between early and advanced TNBCs. There is an urgent need to understand the unique ecosystem of early-stage TNBC and develop biomarkers for precision immunotherapy. Objective: This study aims to characterize the micro-loop associated with the immune efficacy of early TNBC, so as to explain the mechanisms behind the differences in early and late efficacy markers, identify efficacy markers in early TNBC immunotherapy, and search for clinical targeting strategies to sensitize TNBC for neoadjuvant therapy. Methods: We conducted an in-depth analysis of 32 single-cell transcriptomes, comprising 26 early-stage TNBC enrolled in prospective clinical trials (NCT04418154 and NCT04613674), receiving neoadjuvant chemotherapy alone (n=8) or combined with anti-PD1 (n=18), and 6 advanced TNBC. We analyzed the microenvironmental differences between early and advanced tumors, and between different treatment response groups in early stages, and identified a subpopulation of cells specific to early stages and associated with immunotherapeutic efficacy. We used mIHC, flow-through, and validated the presence of this cell in clinical samples. We also explored its predictive performance on four independent cohorts of TNBCs with ICB treatment (GSE194040, NCT04129996, GSE169246, GSE124821). Furthermore, to understand the impact of ISG+ T cells on immunotherapy efficacy and explore targeting strategies, we employed a multi-faceted approach to assess their tumor-killing ability, response to Anti-PD1 treatment, and sensitization effect of drugs targeting ISG+ T cells. ISG+ T cells were sorted using flow cytometry for further experiment. In vitro, we established a co-culture model of primary TNBC patients-derived organoid (PDO) and tumor infiltrated CD8+T cells and evaluated the tumor cell viability as well as T cell cytotoxicity. In vivo, we established TS/A tumor cell bearing BalB/c mouse and E0771 tumor cell-bearing C57BL mouse and measured tumor size and tumor microenvironment by flow cytometry. Results: We obtained 236,017 high-quality cells and identified cell subsets across 32 samples with different stages, treatments and responses. We then uncovered an enriched subset of interferon-induced (ISG+) CD8+ T cells specific to early TNBC, serving as a predictive factor for ICB resistance. Mechanistically, the upregulation of the IFN pathway in early-stage TNBC triggers a transition in ISG+ CD8+ T cells, resulting in cellular senescence, diminished cytotoxicity, and impaired response to ICB. Encouragingly, we made a noteworthy discovery that Nicotinamide mononucleotide, an anti-aging drug, effectively restores the functionality of ISG+ CD8+ T cells, amplifying immunotherapy sensitivity. Conclusions: This study provided a comprehensive single-cell transcriptome atlas of early-stage TNBC and depicted stage-related ISG+CD8+ T cell for predicting ICB response in early TNBC. We emphasize the critical role of T cell dysfunction prompted by cellular senescence in driving ICB resistance during the early stages of TNBC and propose an approach for sensitizing immunotherapy with aging drugs. Citation Format: Tong Fu, Yi-Yu Chen, Xi Jin, Yi-Zhou Jiang, Zhi-Ming Shao. Single cell characterization of senescent CD8+ T cell promotes immunotherapy resistance in early-stage triple-negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-13-04.

Diffuse Pleural Mesotheliomas with Genomic Near-Haploidization: A Newly Recognized Subset with Distinct Clinical, Histologic, and Molecular Features.

Diffuse pleural mesotheliomas (DPM) with genomic near-haploidization (GNH) represent a novel subtype first recognized by The Cancer Genome Atlas project; however, its clinicopathologic and molecular features remain poorly defined. We analyzed clinical genomic profiling data from 290 patients with DPM using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay. Allele-specific copy number analysis was performed using the Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing (FACETS) algorithm. A total of 210 patients were evaluable for loss of heterozygosity (LOH) analysis using FACETS from MSK-IMPACT tumor:normal sequencing data. In this cohort, GNH, defined as LOH across >80% of the genome, was detected in 10 cases (4.8%). Compared with non-GNH tumors, GNH DPMs were associated with younger age and less frequent self-reported history of occupational asbestos exposure. Histologically, GNH DPMs were enriched in biphasic subtype (80% vs. 14.5%) and showed abundant tumor-infiltrating lymphocytes (TILs). Genomic analysis revealed a higher frequency of TP53 alterations, whereas SETDB1 mutations were present in nearly all and only in this subset. The clinicopathologic and molecular findings were further validated in a separate cohort. Despite the younger age, patients with GNH DPMs had a shorter overall survival (10.9 vs. 25.4 months, P = 0.004); the poor prognostic impact of GNH remained significant after controlling for biphasic histology. Of three patients with GNH DPMs who received immune checkpoint blockade, two achieved a clinician-assessed partial response. GNH defines an aggressive subtype of mainly biphasic DPMs in younger patients with recurrent alterations in SETDB1 and TP53. The enrichment in biphasic histology and TILs, together with our preliminary immune checkpoint blockade response data and anecdotal clinical trial data, suggests that further evaluation of immunotherapy may be warranted in this subset.

Chitin-mediated blockade of chitinase-like proteins reduces tumor immunosuppression, inhibits lymphatic metastasis and enhances anti-PD-1 efficacy in complementary TNBC models

BackgroundChitinase-like proteins (CLPs) play a key role in immunosuppression under inflammatory conditions such as cancer. CLPs are enzymatically inactive and become neutralized upon binding of their natural ligand chitin, potentially reducing CLP-driven immunosuppression. We investigated the efficacy of chitin treatment in the context of triple-negative breast cancer (TNBC) using complementary mouse models. We also evaluated the immunomodulatory influence of chitin on immune checkpoint blockade (ICB) and compared its efficacy as general CLP blocker with blockade of a single CLP, i.e. chitinase 3-like 1 (CHI3L1).MethodsFemale BALB/c mice were intraductally injected with luciferase-expressing 4T1 or 66cl4 cells and systemically treated with chitin in combination with or without anti-programmed death (PD)-1 ICB. For single CLP blockade, tumor-bearing mice were treated with anti-CHI3L1 antibodies. Metastatic progression was monitored through bioluminescence imaging. Immune cell changes in primary tumors and lymphoid organs (i.e. axillary lymph nodes and spleen) were investigated through flow cytometry, immunohistochemistry, cytokine profiling and RNA-sequencing. CHI3L1-stimulated RAW264.7 macrophages were subjected to 2D lymphatic endothelial cell adhesion and 3D lymphatic integration in vitro assays for studying macrophage-mediated lymphatic remodeling.ResultsChitin significantly reduced primary tumor progression in the 4T1-based model by decreasing the high production of CLPs that originate from tumor-associated neutrophils (TANs) and Stat3 signaling, prominently affecting the CHI3L1 and CHI3L3 primary tumor levels. It reduced immunosuppressive cell types and increased anti-tumorigenic T-cells in primary tumors as well as axillary lymph nodes. Chitin also significantly reduced CHI3L3 primary tumor levels and immunosuppression in the 66cl4-based model. Compared to anti-CHI3L1, chitin enhanced primary tumor growth reduction and anti-tumorigenicity. Both treatments equally inhibited lymphatic adhesion and integration of macrophages, thereby hampering lymphatic tumor cell spreading. Upon ICB combination therapy, chitin alleviated anti-PD-1 resistance in both TNBC models, providing a significant add-on reduction in primary tumor and lung metastatic growth compared to chitin monotherapy. These add-on effects occurred through additional increase in CD8α+ T-cell infiltration and activation in primary tumor and lymphoid organs.ConclusionsChitin, as a general CLP blocker, reduces CLP production, enhances anti-tumor immunity as well as ICB responses, supporting its potential clinical relevance in immunosuppressed TNBC patients.

Strategies for improving the performance of prediction models for response to immune checkpoint blockade therapy in cancer

Immune checkpoint blockade (ICB) therapy holds promise for bringing long-lasting clinical gains for the treatment of cancer. However, studies show that only a fraction of patients respond to the treatment. In this regard, it is valuable to develop gene expression signatures based on RNA sequencing (RNAseq) data and machine learning methods to predict a patient’s response to the ICB therapy, which contributes to more personalized treatment strategy and better management of cancer patients. However, due to the limited sample size of ICB trials with RNAseq data available and the vast number of candidate gene expression features, it is challenging to develop well-performed gene expression signatures. In this study, we used several published melanoma datasets and investigated approaches that can improve the construction of gene expression-based prediction models. We found that merging datasets from multiple studies and incorporating prior biological knowledge yielded prediction models with higher predictive accuracies. Our finding suggests that these two strategies are of high value to identify ICB response biomarkers in future studies.

Abstract CT030: Randomized placebo-controlled, biomarker-stratified phase 1b microbiome modulation trial for metastatic melanoma demonstrates impact of antibiotic pre-conditioning regimen on the microbiome and immunity

Abstract Background: Gut microbiota modulation shows promise in improving immune checkpoint blockade (ICB) response; however, precision biomarker-driven trials using rationally-designed consortia are lacking. To address this, we performed a multi-center, randomized placebo-controlled, biomarker-stratified phase 1 trial in patients with ICB-naïve unresectable or metastatic melanoma using SER-401, a bacterial consortia enriched for Firmicutes spores and Ruminococcaceae. Methods: MCGRAW was a multi-center, randomized, blinded, and placebo-controlled phase 1b study in patients with advanced melanoma. Patients were randomized 2:1 to the SER-401 active or placebo arm, respectively, and stratified by baseline stool Ruminococcaceae abundance. Patients received an oral vancomycin (vanco) preparative regimen+SER-401 (vanco+SER-401 arm), versus placebo antibiotic+placebo (Placebo arm), followed by nivolumab. Stool, blood and tumor samples were collected at baseline and on treatment. The primary endpoint was safety, with additional secondary endpoints (SER-401 microbiome engraftment, overall response rate (ORR), disease control rate (DCR), and other translational endpoints). The study was not powered for comparison between arms. Results: 14 patients were randomized (n=8 vanco+SER-401, n=6 placebo). In the vanco+SER-401 arm, ORR was 25.0% and DCR was 37.5%, with no Grade 3-4 treatment-related adverse events (TRAE); in the placebo arm, ORR was 66.7% and DCR was 83.3%, with 1 (17%) TRAE. Notably, pre-conditioning with vanco was associated with significant shift in the microbiome taxonomic composition, with depletion of target families such as Ruminococcaceae (p=0.008, Wilcoxon signed-rank test), and other spore-formers, followed by their recovery post dosing with SER-401. There was a significant increase in multiple ICB-resistance associated pathways (e.g. butyrate synthesis, p<0.0001), and a decrease in response-associated pathways after vanco preconditioning; these changes did normalize by nivolumab initiation. There was corresponding increase in systemic proteomic markers of inflammation after vanco, which also normalized by first dose of immunotherapy. Conclusions: This first-of-its-kind, placebo-controlled, randomized biomarker-driven microbiome modulation trial demonstrated that SER-401 and anti-PD1 are a safe combination in melanoma patients. The study was limited by poor accrual during the COVID-19 pandemic. Nonetheless, important insights were gained via translational analyses, suggesting that antibiotic preconditioning and interventional drug dosing regimens should be carefully considered when designing such trials. Additional placebo-controlled biomarker-driven microbiome trials are needed in this age of precision medicine. Trial registration: ClinicalTrials.gov (NCT03817125) Citation Format: Isabella C. Glitza Oliva, Yongwoo David Seo, Christine N. Spencer, Jennifer R. Wortman, Elizabeth M. Burton, Farah A. Alayli, Christopher Loo, Shikha Gautam, Ashish V. Damania, Julie Densmore, Justin Fairchild, Christopher Cabanski, Matthew C. Wong, Christine B. Peterson, Brian Weiner, Nathan Hicks, John Aunins, Christopher McChalicher, Michael T. Tetzlaff, Omid Hamid, Patrick A. Ott, Genevieve M. Boland, Ryan J. Sullivan, Kenneth F. Grossmann, Nadim J. Ajami, Theresa M. LaVallee, Matthew R. Henn, Hussein A. Tawbi, Jennifer A. Wargo. Randomized placebo-controlled, biomarker-stratified phase 1b microbiome modulation trial for metastatic melanoma demonstrates impact of antibiotic pre-conditioning regimen on the microbiome and immunity [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 CT030.

Pan-cancer and single-cell analyses identify CD44 as an immunotherapy response predictor and regulating macrophage polarization and tumor progression in colorectal cancer.

Cluster of differentiation (CD) 44 is a non-kinase cell surface transmembrane glycoprotein critical for tumor maintenance and progression. We conducted a systematic analysis of the expression profile and genomic alteration profile of CD44 in 33 types of cancer. The immune characteristics of CD44 were comprehensively explored by TIMER2.0 and CIBERSORT. In addition, the CD44 transcriptional landscape was examined at the single-cell level. Then, Pseudotime trajectory analysis of CD44 gene expression was performed using Monocle 2, and CellChat was utilized to compare the crosstalk differences between CD44+monocytes and CD44- monocytes. Tumor immune dysfunction and exclusion (TIDE) was used to evaluate the predictive ability of CD44 for immune checkpoint blockade (ICB) responses. The effects of CD44 on colorectal cancer (CRC) and macrophage polarization were investigated by knocking down the expression of CD44 in HCT-116 cell and macrophages in vitro. The expression of CD44 elevated in most cancers, predicting unfavorable prognosis. In addditon, CD44 was correlation with immune cell infiltration and key immune regulators. CD44+ monocytes had a higher information flow intensity than CD44- monocytes. CD44 had good predictive ability for immune checkpoint blockade responses. Knockdown of CD44 inhibited the proliferation, migration, and invasion of HCT-116 cell in vitro. Knockdown of CD44 inhibited M2 macrophage polarization. These findings suggest that CD44 is involved in regulating tumor development, macrophage polarization, and has certain predictive value for patient clinical prognosis and response to immunotherapy.

Abstract 5140: ITGB6 as a predictive biomarker for overall prognosis and PD-(L)1 immune checkpoint blockade response in various cancer types

Abstract Our previous work studying the effects of integrin αvβ6 knockdown in cancer cells demonstrated αvβ6 as a method of T cell suppression in a co-culture model. ITGB6, the gene encoding the β6 subunit of αvβ6, is a potent prognostic marker across multiple cancer types. As a major activator of latent TGFβ, αvβ6, and consequently, ITGB6, has considerable therapeutic implications due to the immunosuppressive effect that activated TGFβ has on the tumor microenvironment. A Human Protein Atlas search of ITGB6 expression surveyed the upregulation of ITGB6 across cancer types. Cancer ITGB6 expression was then compared to expression in paired adjacent normal tissue using the TNMplot tool (Bartha, 2021) on a concatenated set of GEO, GTex, TCGA, and TARGET RNA-seq databases. Kaplan-Meier curves were generated using TCGA mRNA data through the cBio portal, splitting the cohorts according to an ITGB6 mRNA expression threshold of one standard deviation above the mean (z-score ± 1.0). ITGB6 expression and immune checkpoint blockade (ICB) response were evaluated with the Kaplan-Meier Plotter tool (Kovacs, 2023). ITGB6 expression levels between ICB responders and non-responders were quantified using the ROC Plotter tool (Fekete, 2023), and the figures were generated using Matplotlib in Python. Lung, bladder, head and neck, pancreatic, and cervical cancer all demonstrated high expression of ITGB6. Head and neck squamous cell carcinoma (median fold change 2.70, p<0.0001), bladder urothelial carcinoma (FC 2.41, p<0.001), cholangiocarcinoma (FC 5.33, p<0.01), and esophageal carcinoma (FC 2.72, p<0.03) showed strong upregulation of ITGB6 compared to normal tissue. Interestingly, lung adenocarcinoma (FC 0.77, p<0.04) and lung squamous cell carcinoma (FC 0.55, p<0.0001) showed downregulation of ITGB6 compared to normal tissue. Survival data revealed that ITGB6 was a potent marker of a poor prognosis in pancreatic adenocarcinoma (high ITGB6 median survival 16.79 mos, vs. low ITGB6 21.88 mos, p<0.004) and head and neck squamous cell carcinoma (high ITGB6 30.06 mos vs. low ITGB6 57.42 mos, p<0.03). However, no significant prognostic difference was observed in non-small cell lung cancers. Finally, high pan-cancer expression of ITGB6 led to poorer response to αPD-1 (high ITGB6 Hazard Ratio 1.37, p<0.05) and αPD-L1 (high ITGB6 HR 1.50, p<0.001). In vitro and in vivo experiments to validate the benefit of ITGB6 as a biomarker and as a therapeutic target are underway. Citation Format: William J. MacDonald, Praveen R. Srinivasan, Maximilian Pinho-Schwermann, Vida Tajiknia, Connor Purcell, Lindsey Carlsen, Wafik S. El-Deiry. ITGB6 as a predictive biomarker for overall prognosis and PD-(L)1 immune checkpoint blockade response in various cancer types [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 5140.

Abstract 3861: Associations of intragenic rearrangement burden with immune cell infiltration and response to immune checkpoint blockade in cancer

Abstract While immune checkpoint blockade (ICB) induces durable cancer remission, only a small subset of patients can receive benefits, whereas a substantial portion of patients encounter severe immune-related adverse events. Further, about 4-29% of patients experience dramatic acceleration of disease progression after ICB treatment. Predictive biomarkers of ICB responses are in high demand to ensure patient benefits and avoid tragic clinical outcomes. In addition to PD-L1 tests, several genetic biomarkers are associated with ICB effectiveness, such as tumor mutation burden (TMB), somatic copy number aberrations, indels, and microsatellite instability. However, none of these neoantigen markers are sufficient to discriminate ICB responders in diverse cancer entities of distinct genetic profiles. In particular, TMB fails to predict in the cancer types with low simple mutation rates, such as triple-negative breast cancer (TNBC), ovarian cancer, and esophageal cancers. In TNBC, high TMB only accounts for 5-10% of patients, whereas a much larger proportion of tumors are inflamed (26-50%), which suggests a possible uncharacterized major source of neoantigens. Similarly, TMB is not predictive of ICB response in ovarian cancers according to the IMagyn050 trial. In esophageal cancer, TMB is not associated with T cell infiltration and does not predict ICB response. Our analyses of Pan-cancer whole genomes revealed that intragenic rearrangement (IGR) burden is a pivotal contributor to immune infiltration in breast, ovarian, esophageal, and endometrial cancers, which correlates with increased Macrophage M1 and CD8+ T cell signatures. IGRs result in exon duplications or deletions through rearrangements of a genomic distance of tens of kilobases. Multivariate regression against spatially counted tumor infiltrated lymphocytes in breast, endometrial, and ovarian cancers suggest that IGR burden is a more influential covariate than other genetic aberrations in these cancers. In the MEDI4736 trial evaluating durvalumab in esophageal adenocarcinoma, IGR burden correlates with patient benefits. In the IMVigor210 trial evaluating atezolizumab in urothelial carcinoma, IGR burden increases with platinum exposure and predicts patient benefits for TMB-low, platinum-exposed tumors. Altogether, we demonstrate that IGR burden contributes to T-cell inflammation and predicts ICB benefits in TMB-low, IGR-dominant tumors, or in platinum-exposed tumors. IGRs as a cryptic class of structural variants have been heretofore overlooked in cancer genomics studies. The association of IGRs with ICB response has not been previously reported in cancer in general. The development of IGR burden-based predictive marker could increase effectiveness of ICB therapy, reduce severe side-effects and unnecessary costs. Citation Format: Han Zhang, Sanghoon Lee, Renee R. Muthakana, Binfeng Lu, David N Boone, Daniel Lee, Xiaosong Wang. Associations of intragenic rearrangement burden with immune cell infiltration and response to immune checkpoint blockade in 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 3861.

Abstract 6551: Comprehensive genomic and transcriptomic analyses capture the effects of epigenetic therapy priming on immune checkpoint blockade response in non-small cell lung cancer

Abstract Introduction: Emergence of resistance to immune checkpoint blockade (ICB) mandates the development of strategies for ICB sensitization. Here we employed a multi-omic approach to understand the effects of epigenetic priming in re-shaping the tumor microenvironment, together with genomic drivers of therapeutic response of epigenetic therapy followed by ICB in non-small cell lung cancer (NSCLC). Methods: We performed whole exome sequencing (WES) on 39 baseline tumors and bulk RNA sequencing (RNAseq) on 18 serial tumors across 42 patients with metastatic immunotherapy-naïve NSCLC, who received azacitidine and entinostat followed by nivolumab (NCT01928576). WES was utilized to assess co-mutations, mutation signatures and genome-wide structural changes. RNAseq was utilized for gene and gene set enrichment analysis (GSEA) and repeat element analysis. Response after nivolumab initiation was assessed using RECIST 1.1 criteria. Patients who were progression-free at 6 months or alive at 2 years after initial treatment were defined as exceptional responders. Results: We found an enrichment in inactivating mutations in homologous recombination genes in radiographic responders (Fisher’s exact, p=0.0007). Higher germline and somatic HLA class II diversity (Mann-Whitney U-test, p=0.05 and p=0.03 respectively), and an enrichment of smoking and DNA damage mutational signatures were noted in radiographic responders (Mann-Whitney U-test, p=0.03 and p=0.15 respectively). Radiographically responding tumors harbored a higher number of mutations in genomic regions that were haploid or present in multiple copies (persistent tumor mutation burden; Mann-Whitney U-test, p=0.018). GSEA revealed an upregulation of inflammatory response gene sets post-epigenetic therapy in patients attaining an exceptional response. Antigen presentation, interferon-alpha, and interferon-gamma related gene sets were upregulated in exceptional responders post epigenetic priming (FDR-adjusted p=0.005, p=0.009, and p=0.011 respectively). Additionally, we observed an enrichment in interferon-alpha, cancer testis antigens, and interferon-gamma related gene sets in patients with a longer progression-free survival (FDR-adjusted p=0.007, p=0.011, and p=0.013 respectively). Repeat element analysis showed an increase in long terminal repeats on-therapy in exceptional responders, suggesting induction of repeat element expression with epigenetic therapy. A higher expression of MAGE family tumor associated antigens (MAGEA10, MAGEB1, MAGEB2) was noted post-epigenetic therapy in exceptional responders. Conclusions: Genomic and transcriptomic analyses reveal the potential of epigenetic-priming to re-shape the tumor microenvironment and highlight patients that could benefit from combination epigenetic therapy with immunotherapy. Citation Format: Blair V. Landon, Kristen A. Marrone, Michael J. Topper, Akshaya Annapragada, Hua-Ling Tsai, Archana Balan, Noushin Niknafs, Christopher Cherry, James R. White, Gavin Pereira, Vilmos Adleff, Chen Hu, Joanne Riemer, Margaret Fitzpatrick, Patrick Forde, Christine L. Hann, Ronan J. Kelly, David S. Ettinger, Benjamin Levy, Jorge Nieva, James Herman, Victor E. Velculescu, Stephen Baylin, Julie Brahmer, Valsamo Anagnostou. Comprehensive genomic and transcriptomic analyses capture the effects of epigenetic therapy priming on immune checkpoint blockade response in non-small cell lung 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 6551.

Abstract 1424: Epigenetic activation of tumoral IFNγresponse and pyroptosis overcomes immunotherapy resistance in hepatocellular carcinoma

Abstract Background: Immune checkpoint blockade (ICB) therapies by antibodies have revolutionized the treatment paradigm for a variety of cancers. Although subsets of people exhibit durable responses, resistance and relapse are common in hepatocellular carcinoma (HCC). We therefore aim to delineate the mechanism underlying the failure of ICB therapy in HCC, and more importantly to identify ICB-sensitizing therapeutic approaches. Methods: ICB-resistant orthotopic-grafted murine models were established via a serial selection of HCC cells in ICB-treated mice. Integrated multi-omics analysis (single-cell RNA-seq, single-cell ATAC-seq and ChIP-seq) were applied to decode the mechanisms underlying the ICB resistance and an epigenetic-mediated ICB response. Results: We successfully established the ICB-resistant murine models of HCC, in which tumor intrinsic interferon-gamma (IFNγ) response was most significantly suppressed and characterized by a “cold” tumor microenvironment with decreased lymphocyte activation and intratumoral infiltration. On the other hand, single cell RNA-seq analysis of human HCC biopsies revealed that patients with HDAC1/2/3-high HCC exhibit poor survival upon ICB therapy. Notably, we found that a novel specific HDAC1/2/3 inhibitor CXD101 synergized with PD-(L)1 antibody to induce immunogenic cell death, eradicate tumor and prolong survival in our ICB-resistant mouse models, which was accompanied by enhanced intratumoral infiltration, activation and anti-tumor memory formation of cytotoxic lymphocytes. Mechanistically, CXD101 combined with PD-(L)1 inhibition synergistically reactivated tumor IFNγ pathway via enhancing chromatin accessibility of downstream genes associated with antigen presentation and lymphocytes recruitment. Moreover, the activated immune system induced tumor cell pyroptosis, further igniting antitumor immunity and ICB response. Conclusions: Our findings suggest that corruption of tumor intrinsic IFNγ signaling may confer ICB resistance upon ICB therapy, which can be rectified by class I HDAC inhibitor mediated IFNγ response and tumor cell pyroptosis. Based on these findings, we have commenced a Phase II clinical study of a new epigenetic immunotherapy (CXD101 plus anti-PD-1) for HCC patients resisting anti-PD-(L)1 alone. This project is supported by the CRF (C4045-18W), GRF (14115820), TRS (T11-706/18-N), Li Ka Shing Foundation, CUHK Strategic Seed Funding for Collaborative Research Scheme. We also acknowledge support (funding and study medications) by Celleron Therapeutics. Citation Format: Yalin Tu, Haoran Wu, Chengpeng Zhong, Zhewen Xiong, Jing Wang, Patrick Pak-Chun Wong, Weiqin Yang, Jiahuan Lu, Zhixian Liang, Shufen Chen, Lingyun Zhang, Siyun Chen, Jingying Zhou, Ka-Fai To, Joseph Jao-Yiu Sung, Stephen Lam Chan, David Kerr, Nick La Thangue, Alfred Sze-Lok Cheng. Epigenetic activation of tumoral IFNγresponse and pyroptosis overcomes immunotherapy resistance in hepatocellular carcinoma [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 1424.

Abstract 584: Synergistic action of ATF6 and EZH2 in sensing metabolic stress to boost anti-tumor immunity

Abstract Although immune checkpoint blockade (ICB) marked a breakthrough in melanoma treatment, half of patients fail to respond, underscoring the crucial need for complementary adjuvant and neo-adjuvant therapies. Due to the low overall response rate and the stark contrast in outcomes between patients that respond and those that fail to respond, identifying the defining characteristics of immune checkpoint blockade (ICB) response is essential for enhancing the efficacy of melanoma treatments. To recapitulate and investigate the ICB-responsive phenotype in vitro, melanoma cells were metabolically adapted to an environment lacking glucose which successfully drove the dependence on oxidative metabolism and restored MHC-I expression, two established characteristics of ICB responsive tumors. Further, metabolic adaptations significantly enhance the tumor sensitivity to T-cell killing. Surprisingly even in JAK1 and IFNAR1 deficient cells, metabolic adaptation restored MHC I antigen presentation, indicating an interferon-independent mechanism of MHC-I regulation. Proteomic analysis of three metabolically conditioned melanoma cells lines (human and mouse) identified downregulation of the histone methyltransferase EZH2 and the activating transcription factor ATF6 as key corollaries of MHC-I expression. Interestingly, EZH2 and ATF6 activity were found to be inversely related in metabolically adapted cells and patient tumor samples. These studies mechanistically explore the epigenomic control of antigen presentation machinery and the transcriptional targets of ATF6 controlling sensitivity T cell killing. Here, through in vitro and in vivo studies, we demonstrate that constitutive activation of ATF6, and thereby activation of the adaptive unfolded protein response (UPR), sensitizes melanoma to immune control. These data suggest that EZH2 and ATF6 act synergistically to balance immune mediated killing during metabolic stress whereby loss of EZH2 increases MHC-I antigen presentation and activation of ATF6 sensitizes tumor cells to T cell-mediated control. Ongoing therapeutic studies combining EZH2 inhibition, ATF6 activation, and ICB in pre-clinical models further suggest targeting the synergy between EZH2 and ATF6 is a putative adjuvant or neo-adjuvant target to improve the clinical response of ICB. Citation Format: Jacob L. Edmondson, Megan R. Reed, Daniel Fil, Billie Heflin, Brian Koss, Alan J. Tackett. Synergistic action of ATF6 and EZH2 in sensing metabolic stress to boost anti-tumor immunity [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 584.

Abstract 3258: A potential oncogenic role and immunoregulatory mechanisms of MZB1 in melanoma

Abstract While immune checkpoint blockade (ICB) therapies have drastically improved melanoma treatment, a majority of patients fail to achieve a durable response. Thus, there is a critical need to advance our understanding of melanoma immune evasion mechanisms and identify novel targets capable of enhancing ICB responses. MZB1 (Marginal Zone B and B1 Cell Specific Protein), an immune regulator gene, is differentially expressed in metastatic melanoma compared to primary melanoma or normal skin. In a limited number of cancers, MZB1 has been shown to function as either an oncogene or a tumor suppressor. However, its role and significance in melanoma is not known. In this study, we determined the functional significance and immunoregulatory mechanisms of MZB1 in human melanoma cell lines using MZB1 overexpression (OE) (in SK-MEL-2, and SK-MEL-28) and CRISPR knockout (KO) (in A375 and Hs294T) lines. MZB1 OE significantly increased melanoma cell proliferation and expression of the proliferation markers Ki67 and PCNA, while MZB1 KO yielded the opposite effect. To identify immunoregulatory mechanisms associated with MZB1, we performed differential gene expression analysis of 770 immune-related genes using NanoString nCounter technology. nSolver analysis identified 153 differentially expressed genes (DEGs) as a result of MZB1 knockout in Hs294T cells (adjusted p <0.05, 1.5-fold change cutoff). MZB1 KO strongly reduced the expression of the HLA class-II family genes and altered the expression of various cytokines, suggesting an immunoregulatory role of MZB1. Further, MZB1 KO significantly downregulated genes related to cancer progression and metastasis promotion. Additionally, MZB1 KO reduced expression of common “cancer stem cell” genes, such as RXRG, ALDH1A1, AQP1, NFATC2, LPAR1, indicating MZB1 expression in melanoma may promote a dedifferentiated or neural crest-like state. In addition, an Ingenuity Pathway Analysis (IPA) of the DEGs revealed many cancer-related functions altered upon MZB1 KO (p adjusted < 0.05) and displayed a negative enrichment for cancer-promoting pathways including tumor growth, metastasis, and proliferation. IPA regulatory analysis predicted MZB1 KO to decrease the activation of oncogenic signaling components including PI3K, MEK, and ERK1/2. Further, IPA predicted that MZB1 inhibition could positively sensitize melanoma cells towards higher immune responses by activating mechanisms associated with T cell proliferation and activation, leukocyte migration, and macrophage activation. Overall, our study suggests MZB1 promotes oncogenic signaling in melanoma to drive proliferation and dedifferentiation, as well as regulates a wide range of immune-related genes that may be responsible for immune evasion in melanoma cells. Thus, MZB1 merits further investigation to determine if the immune consequences yielded by targeting MZB1 can complement ICB approaches in the management of melanoma. Citation Format: Gagan Chhabra, Carl A. Shirley, Julia M. Krien, Mary A. Ndiaye, Nihal Ahmad. A potential oncogenic role and immunoregulatory mechanisms of MZB1 in melanoma [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 3258.

Abstract 6651: Compromised TGFβ signaling and DNA repair primes immune poor tumors response to immune checkpoint blockade by activating NK cells

Abstract We investigated the interplay between transforming growth factor beta (TGFβ) regulation of immunosuppressive signaling and immunogenic DNA repair. Loss of TGFβ signaling by cancer cells is accompanied by increased use of error-prone repair. We described a transcriptomic score, βAlt, that reports the TGFβ/DNA repair functional relationship. Pan-cancer analysis showed that high βAlt cancers (i.e., low TGFβ and high error-prone DNA repair) are sensitive to chemoradiation and have a greater fraction of genome altered compared to low βAlt cancers. Defective mismatch repair is associated with T cell infiltration and response to immune checkpoint blockade (ICB), hence we investigated the immune context of bAlt. Unsupervised clustering of RNAseq profiles 12 independent immunocompetent mouse tumor derived transplant (mTDT) tumors based on βAlt score indicated that high βAlt was associated with immune poor phenotype and lack of type I interferon signatures. A similar relationship was evident in the bladder, breast, and lung TCGA data. A high βAlt, immune poor mTDT in which T cells were only 20% of 10% CD45 were treated with monotherapy consisting of single fraction 10 Gy radiation, anti-PD-L1 or TGFβ inhibition, dual or triple treatment. Only monotherapy or combinations with radiation significantly increased survival. However, these ICB resistant tumors responded to triple treatment. Response was accompanied by increased tumor infiltrating CD45+ cells (P=0.02), circulating CD8 T cells (P<0.001) and natural killer (NK) cells (P<0.001). As NK cells tripled and TGFβ broadly impairs NK cell effector function, we depleted NK cells to test whether they were required for the response to triple treatment. NK depletion completely abrogated response (P<0.00001) indicating NK cells can provoke an ICB response in high βAlt immune poor tumors. Both mouse tumors and human cancers show that loss of TGFβ signaling resulting in error-prone DNA damage response is strongly associated with immune poor tumors and suggests that TGFβ inhibition can override NK cell dysfunction to create vulnerability to ICB. Citation Format: Jade T. Moore, Jim Gkantalis, Ines Guix, Mary Helen Barcellos-Hoff. Compromised TGFβ signaling and DNA repair primes immune poor tumors response to immune checkpoint blockade by activating NK cells [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 6651.

Abstract 2282: Predictive association of tumor cells hijacked NFATC2 activities with resistance to immune checkpoint inhibition in melanoma patients

Abstract Background: Immune checkpoint blockade (ICB) has emerged as an effective cancer therapy. However, only a small fraction of patients receives benefits whereas a significant subset of patients experienced severe or even lethal autoimmune diseases. Stratifying patients that would benefit from immunotherapy remain a highly unmet clinical need. Dysregulations of transcriptional programs have been implicated in cancer initiation and progression. To date, there is a paucity of studies on the predictive values of transcriptional factors on ICB response based on the most recently emerged ICB clinical trial datasets. We reasoned that cancer cells may hijack key transcriptional programs in hematological cells to evade the attack from immune cells and acquired tolerance to immunotherapy. Method: Herein, we used an R package singscore/1.14.0 to compute the TFs activity scores based on their validated gene targets (TGs). Leveraging melanoma clinical trial datasets, we analyzed the predictive association of the TF scores with resistance to anti-PD1 ICB. The R package, iGenSig was used to evaluate the potential confounding variables. Results: Our landscape correlation analysis revealed NFATC2 (Nuclear Factor Of Activated T Cells 2)-TGs as the most significant predictor of anti-PD-1 ICB resistance in melanoma. NFATCT-TGS as a predictor of anti-PD1 resistance is confounded by liver metastasis and achieved AUC range between 0.71 to 0.74 in three datasets (PRJEB23709, GSE160638, and Phs000452). In addition, prior anti-CTLA4 exposure (AUC=0.87 and 0.89) is associated with higher predictive efficacy of NFATC2-TGS than anti-CTLA4 naïve tumor (AUC=0.61 and 0.69) in phs000452 and GSE91061 datasets. Survival analysis revealed that NFATC2 is a better predictor of progressive-free survival (PFS; HR=5.95), and overall survival (OS; HR= 3.28-3.38) in anti-CTLA4 exposed tumor than anti-CTLA4 naïve tumor (PFS: HR=1.92, and OS; HR=1.64-2.17). Finally, NFATC2-TGS show strong inhibitory correlation with B cells and T cells infiltration, but strongly correlated with tumor purity. Conclusion: We demonstrate that NFATC2 TGS predicts ICB benefits in melanoma patients, and thus may guide the recruitment of melanoma patients for anti-PD1 ICB. Our data provide support to the hypothesis that melanoma acquired NFATC2 transcriptional program to avoid immune cells evasion and acquired tolerance to ICB immunotherapy Citation Format: Bashir Lawal, Yue Wang, Parisa Lotfinejad, Xiaosong Wang. Predictive association of tumor cells hijacked NFATC2 activities with resistance to immune checkpoint inhibition in melanoma patients [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 2282.