MHC Class Research Articles

Abstract 7521: Tumor NLRP3 inflammasome activity mediates resistance to Anti-PD-1 immunotherapy in advanced gastroesophageal cancer

Abstract The addition of anti-PD-1 immunotherapy to the therapeutic armamentarium of advanced gastroesophageal (GE) cancer patients has resulted in modest improvements in clinical outcomes for a subset of patients. More robust predictive biomarkers to guide patient management and to select optimal combination immunotherapy strategies for the individual patient are needed. Our previous studies indicate that the tumor-intrinsic NLRP3 inflammasome-HSP70 signaling axis promotes the recruitment of granulocytic myeloid-derived suppressor cells (PMN-MDSCs) and drives resistance to anti-PD-1 immunotherapy. The KEYLargo phase II clinical trial evaluated the efficacy of pembrolizumab (pembro) in combination with capecitabine/oxaliplatin (CAPOX) in HER2-negative advanced GE cancer patients. An 8-day lead-in period of pembro monotherapy in 36 advanced GE cancer patients allowed for the acquisition of blood and tumor tissue specimens to determine which immune-mediated alterations within the tumor microenvironment correlated with resistance to anti-PD-1 immunotherapy. Baseline and on-treatment specimens were collected for HSP70 ELISA, immunofluorescence microscopy, spatial transcriptomics, NLRP3 FISH, IHC, and NLRP3-ASC proximity ligation assays (PLA) to measure NLRP3 pathway activity levels. All data was correlated with best objective response, progression-free survival (PFS), and overall survival (OS). Tumor-infiltrating CD8+ T cells and PMN-MDSCs were increased in responders and non-responders, respectively. While PD-L1 CPS failed to associate with response, elevated baseline NLRP3 PLA activity correlated with increased tumor-infiltrating PMN-MDSCs (P = 0.001) and resistance to pembro/CAPOX therapy (P = 0.01). Only non-responding tumors exhibited an increase in NLRP3 PLA activity and NLRP3 amplification. Transcriptional studies revealed tumors with enhanced NLRP3 activity to exhibit decreased expression of the NLRC5 transactivator, MHC class I antigen presentation genes, and an increase in the NK cell negative regulator, HLA-G. Baseline plasma HSP70 levels correlated with tumor NLRP3 activity (P = 0.043) and with resistance to pembro/CAPOX therapy (P = 0.001). Elevated baseline NLRP3 PLA activity and amplification were associated with diminished PFS (P = 0.008) and OS (P = 0.009). In additional studies, pharmacologic inhibition of the NLRP3 inflammasome suppressed PMN-MDSC recruitment, upregulated MHC class I, and reversed anti-PD-1 resistance in an orthotopic model of GE cancer. Together, these findings implicate tumor-intrinsic NLRP3-HSP70 signaling as an important mediator of anti-PD-1 resistance in advanced GE cancer. The NLRP3-HSP70 pathway is a promising source of therapeutic targets and biomarkers capable of improving treatment outcomes for this patient population. Additional clinical studies are warranted. Citation Format: Nagendra Yarla, Kaylee Howell, Y-Van Nguyen, Donna Niedwiecki, Hope Uronis, John Strickler, Nicholas C. DeVito, Bala Theivanthiran, Brent A. Hanks. Tumor NLRP3 inflammasome activity mediates resistance to Anti-PD-1 immunotherapy in advanced gastroesophageal 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 7521.

Abstract 10: Non-viral engineered T cell therapy specific for the hotspot mutation p53 R175H that integrates signal 1 (TCR), signal 2 (co-stimulation) and signal 3 (cytokine) and co-opts FasL-dependent apoptosis to achieve a coordinated antitumor CD4/8 T cell response

Abstract Adoptive T cell therapy (ACT) has demonstrated antitumor efficacy in patients with solid cancers but requires further optimization to become a reproducibly effective treatment. T cell receptor (TCR)-engineered T cells recognize peptides derived from intracellular and surface proteins presented in the context of MHC class I. Targeting mutated oncogenic drivers addresses many of the major obstacles of this modality, in that the antigenic epitope is: 1) tumor-specific, 2) essential for tumor survival, and 3) derived from a stably expressed protein. However, the immune-suppressive tumor microenvironment makes further optimization of engineered T cells necessary to bring long-term clinical benefit to patients. For an optimal anti-tumor response, T cells require three signals: TCR, co-stimulation, and cytokine signaling. The tumor suppressor TP53 is the most frequently mutated gene across human cancers, with a highly recurrent arginine to histidine hotspot alteration in codon 175 leading to novel tumor-dependent functions. Here we report the use of a novel CRISPR-Cas nuclease system to knock-in a six-parameter multi-cistronic cassette into the TRAC locus with high efficiency. We employed several strategies to maximize the potency and durability of a TCR-T cell product targeting the p53 R175H oncogenic driver, including: 1) A high-affinity TCR (α and β chains) specific for the p53 R175H mutation presented by HLA-A*02:01 permits the recognition of tumor cells expressing even low levels of the epitope (Signal 1), 2) Inclusion of the CD8αβ co-receptor drives stimulation of CD4+ T cells with the MHC class I restricted TCR, allowing for a physiologic coordinated immune response required for maximal efficacy, 3) A FAS-41BB switch receptor acts as a dominant negative to the FASL-inducing apoptotic signal in the tumor microenvironment and drives stimulation and persistence of the T cell product via 41BB co-stimulatory signaling (Signal 2), 4) A chimeric cytokine receptor (constitutive Interleukin Receptor) promotes expansion and survival while avoiding immunologic exhaustion (Signal 3). Together, these strategies deliver the three signals required for maximal T cell function: antigen-driven activation, co-stimulation, and growth/survival-promoting cytokine signaling. The non-viral TRAC-knocked-in T cells demonstrate robust and specific cytotoxicity against endogenously expressing HLA-A*02:01 and p53 R175H cell lines in vitro and effective anti-tumor activity in vivo while maintaining a favorable preclinical safety profile. These data support the planned clinical development of a novel non-viral TRAC-knocked-in T cell therapy for the treatment of p53 R175H-mutant solid tumors. Citation Format: Santosh Narayan, Ken Gareau, Ankit Gupta, Josh Ferrell, Nicholas Rouillard, Tyler Warner, Jinsheng Liang, Luhua Shen, Tanya Tetrault, Joshua Francis, Xingyue He, Patrick J. Browne, Rebecca Lamothe, Meghan D. Storlie, Gregory J. Cost, Thomas M. Schmitt, Philip D. Greenberg, Smita S. Chandran, Damien Hallet, Michael Gormally, Chistopher A. Klebanoff, Gary Shapiro, Kim Nguyen, Loïc Vincent. Non-viral engineered T cell therapy specific for the hotspot mutation p53 R175H that integrates signal 1 (TCR), signal 2 (co-stimulation) and signal 3 (cytokine) and co-opts FasL-dependent apoptosis to achieve a coordinated antitumor CD4/8 T cell response [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 10.

Abstract 1158: Spatially resolved cell profiling unveils tumor metabolic states associated with immunotherapy response in NSCLC

Abstract Background. Only a subset of non-small cell lung cancer (NSCLC) patients benefit from immune checkpoint inhibitors (ICIs). Thus, there is a clinical need to develop predictive biomarkers for ICIs. Deeper insights from the tumor microenvironment (TME) can lead to identification of spatial features associated with clinical responses to immune checkpoint inhibitors (ICI). In this study, we investigated functional profiles within cell subtypes as a surrogate for ICI clinical endpoints. Methods. We profiled a retrospective cohort of 39 NSCLC tissue cores from 27 patients treated with ICI, using highly multiplexed immunofluorescence (mIF) stained by the Phenocycler Fusion platform (Akoya Biosciences) capturing 45 proteins. Utilizing a deep learning based multiplex imaging analysis pipeline, cells were classified to 15 cell types by known marker expression and were further subclassified by unsupervised clustering. Cells were assigned to the tumor area or TME and more than 1000 spatial features were calculated based on cell type, marker positivity, and area assignments, and were compared between responders and non-responders to ICI therapy using Fisher’s exact and logrank tests. Results. Unsupervised cell subtyping of the 15 cell types identified 43 cell subsets, which were mostly segregated by their metabolism and activation status. Interestingly, all lymphocytes showed a similar pattern of clustering resulting in two clusters of metabolically active and inactive cells. The most significantly differentially expressed proteins between these cell types were oxidative phosphorylation proteins such as CS, SDHA and ATPA5, and other metabolic enzymes such as HK1, GLUT1 and LDHA. We found a direct connection between metabolic state, effector functions and tissue localization as the metabolically active lymphocytes exhibited higher levels of PD-1, MHC class I and II and CD44 positivity, and were more abundant within tumor infiltrating lymphocytes (TILs) and tertiary lymphoid structures (TLS). Unsupervised clustering of tumor cells demonstrated segregation to three main metabolic states - OXPHOS+, OXPHOS- and a third cluster (PPP+) which was characterized by upregulation of ASCT2, a glutamine transporter, as well as pNRF2 and G6PD, regulators of the pentose phosphate pathway. These cells also exhibited higher proliferation rate and CD44, a tumor stemness marker, positivity. All tumors with high content of PPP+ tumor cells (>40%) were resistant to PD-1 blockade (0/8 vs. 10/18 response rate in other tumors, p=0.009) and showed reduced overall survival (OS) rates (median OS of 27.6 vs 90.3 months, p=0.02). Conclusions. Taken together, this study reveals connections between metabolic states, effector functions, and immunotherapy outcome and contributes to the evolving landscape of predictive biomarkers for ICI therapies. Citation Format: James Monkman, Rotem Czertok, Shai Bookstein, Becky Arbiv, Yuval Shachaf, Ron Elran, Kenneth Bloom, Oscar Puig, Ken O'Byrne, Ettai Markovits, Arutha Kulasinghe. Spatially resolved cell profiling unveils tumor metabolic states associated with immunotherapy response in NSCLC [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 1158.

Abstract 2373: Functional and specific T-cell engagers against a peptide-MHC tumor target

Abstract Accessing peptides from intracellular tumor antigens displayed on MHC class I (pMHC) can expand the T-cell engager (TCE) target pool for solid tumor applications. A challenge limiting TCE development for pMHC targets is the identification of rare, high-affinity, and high-specificity pMHC-binders. In this work, we describe TCEs in a 1 × 1 format with potent tumor-cell killing activity and high specificity for MAGE-A4, a pMHC tumor antigen expressed in multiple cancer types. We identified functional MAGE-A4 x CD3 TCEs with high specificity and affinity to a human MAGE-A4 peptide sequence of 10 amino acids presented on MHC-I (HLA-A:02*01). We strategically selected MAGE-A4-binders with high binding specificity for pMAGE-A4230-239, but not MHC-I or many closely related MHC-restricted peptides. We then paired them with diverse and developable CD3-binders with a range of binding affinities, subunit specificities, and binding kinetic profiles. High-throughput in vitro functional characterization of hundreds of these TCEs enabled identification of molecules with optimal T-cell dependent cellular cytotoxicity in MAGE-A4-expressing tumor cell lines, with comparable tumor-killing activity and cytokine release to a clinical-stage TCE in a 2 × 1 format. Previous studies have highlighted unique challenges associated with pMHC targets, including their potential for cross-reactive binding to pMHCs on healthy tissues, and the absence of pharmacologically relevant species for preclinical toxicity testing. To address these challenges, we have designed and implemented an in vitro and in silico workflow to identify antibody binding to potential off-target peptides. Using this approach, we selected TCEs with several pMHC binding orientations and high specificity and affinity. These TCEs killed tumor cell lines endogenously expressing MAGE-A4 pMHCs and not isogenic cells with MAGE-A4 knocked out. Results demonstrate that our high-resolution, multiparametric antibody discovery capabilities can identify pMHC-binding antibodies with desired functional and specificity attributes. This approach unlocks the discovery and development of optimal TCEs against complex pMHC antigens. Citation Format: Davide Tortora, Peter Bergqvist, Allison Goodman, Ryan Blackler, Nathalie Blamey, Stefania Carrara, Lauren Chong, Gabrielle Conaghan, Cindy-Lee Crichlow, Valentine de Puyraimond, Harveer Dhupar, Patrick Farber, Jessica Fernandes Scortecci, Kate Gibson, Rodrigo Goya, Ahn Lee, Franco Li, Tova Pinsky, Craig Robb, Patrick Rowe, Antonios Samiotakis, Eduardo Solano Salgado, Ping Xiang, Irene Yu, Kelly Bullock, Tara Fernandez, Stephanie K. Masterman, Kush Dalal, Tim Jacobs, Bryan C. Barnhart. Functional and specific T-cell engagers against a peptide-MHC tumor target [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 2373.

Abstract 5889: An immunoproteasome activator that expands the MHC-class I immunopeptidome, unmasks neoantigens and enhances antimyeloma T-cell activity

Abstract A hallmark of cancer is the ability to evade immunosurveillance mechanisms and thwart the efficacy of immunotherapeutic agents. The proteasome functions as an essential component of immunosurveillance by generating peptides from intracellular proteins that are then presented to T-cells. Antigens generated by the proteasome promote the infiltration of immune cells into tumors and improve tumor regression in response to immunotherapy. Cancer cells can evade elimination by the immune system by deregulating the antigen presentation machinery to downregulate the expression of proteins recognized by immune cells as antigens, creating an immunosuppressive microenvironment. In contrast to constitutive proteasomes, immunoproteasomes are a highly specialized proteasome variant that are highly expressed in antigen-presenting cells. Immunoproteasomes contain distinct catalytic subunits with active site substrate specificities distinct from constitutive proteasomes. Immunoproteasome degrade intracellular proteins to generate antigenic peptides that are the presented by MHC-class I (MHC-I) molecules on tumor cells for recognition by cytotoxic T-cells. We hypothesized that immunoproteasome activation could concomitantly increase the relative abundance and diversity of MHC-I antigens presented on multiple myeloma (MM) cells. High-throughput screening identified a novel small molecule (Compound A) that selectively increased immunoproteasome catalytic activity. Global proteomic integral stability assays determined that Compound A binds the proteasome structural subunit PSMA1 and that treatment with Compound A increased association of the proteasome activator PA28α/β (PSME1/2) activator with immunoproteasomes. The effect of Compound A on immunoproteasomes was abolished after the ablation of PSMA1, PSME1, or PSME2 or by the treatment of cells with suicide inhibitors that target immunoproteasome-specific catalytic sites. Treatment of MM cells with Compound A doubled the total number of MHC-I-bound peptides and increased the level of specific MHC-bound peptides up to 200-fold. Interestingly, a number of tumor-associated antigens and neoantigens were dramatically unmasked following treatment of MM cells with the immunoproteasome activator. Importantly, the treatment of patient CD138+ cells with Compound A promoted the antimyeloma activity of allogenic and autologous patient-derived CD8+ T-cells. Taken together, our results demonstrate the paradigm-shifting translational impact of immunoproteasome activators to expand the myeloma immunopeptidome and have revealed novel, actionable antigenic targets to personalize T-cell-directed immunotherapy. Citation Format: Priyanka S. Rana, James J. Ignatz-Hoover, James J. Driscoll. An immunoproteasome activator that expands the MHC-class I immunopeptidome, unmasks neoantigens and enhances antimyeloma T-cell activity [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 5889.

Abstract 1204: Neoantigen MHC presentability ratios influence the tumor microenvironment and response to immunotherapy

Abstract Introduction: Recent literature suggests that neoantigens presented via MHC-II induce a CD4+ T Cell mediated immune response, and MHC-I presented neoantigens expand CD8+ cytotoxic T Cells populations. We developed an algorithm to stratify patients into MHC-I Reliant and MHC-II Reliant immune checkpoint blockade (ICB) responders. Experimental Procedures: Our algorithm generates patient mean harmonic best rank scores (PHBR) of each neoantigen in a tumor to estimate the proportion of neoantigens that are likely well presented by each MHC complex, given a patient’s specific HLA alleles. From there, the ratio of neoantigens presented by each MHC (class-I and class-II) can be used to stratify patients into MHC-I or MHC-II Reliant groupings. The primary goals of our study were to investigate tumor immune microenvironment and survival differences between these groups. First, we used CIBERSORTx infiltration estimates of the ratio of these CD4/CD8 T cell populations across our MHC Reliance categories and by response vs nonresponse in two separate cohorts: Discovery (110) and Validation (77). Results: We first observed that the CD4/CD8 ratio is higher in MHC-II responders than in MHC-I responders (Fig 6. A, P=~0.0057 Discovery; P=0.025 Validation), but no such a difference was found in nonresponders. Using an alternate digital cytometry tool (xCell) we obtained similar results (MHC-II vs MHC-I responders discovery P=0.44; validation P=0.0015) (Fig. S7). We applied an identical methodology to immune-hot ICB-naive cancer samples from TCGA and found that there was a powerful protective effect of the CD4/CD8 ratio in TCGA MHC-II Reliant patients (Fig S6. HR=-0.76, P=0.0092), there was a significantly harmful effect of that same ratio in TCGA MHC-I Reliant patients (Fig S6 HR=0.59, P=0.0352). These data demonstrate a benefit to having some level of concordance between CD4/CD8+ T cell infiltration and MHC-II/MHC-I neoantigen presentability ratios. Since CD4 memory based immune responses have a longer duration of action over more transient CD8 cytotoxic immune responses (cite), we compared the survival of responders in MHC-II vs MHC-I Reliance groups. MHC-II Reliant responders had a significantly longer overall survival in both discovery and validation cohorts (Fig 6. B-C, discovery P=0.0073; validation P=0.0398). Conclusions: While neoantigens are already used in ICB stratification in the context of tumor mutational burden, we demonstrate that the balance of which MHC is presenting a set of neoantigens is relevant to immune infiltration and treatment outcome. Citation Format: Timothy J. Sears, Ko-Han Lee, Meghana Pagadala, Andrea Castro, Maurizio Zanetti, Hannah Carter. Neoantigen MHC presentability ratios influence the tumor microenvironment and response to immunotherapy [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 1204.

Abstract 6533: Pivotal role of specific LYVE1+ tissue resident macrophages in PDAC progression & immunotherapy resistance

Abstract Pancreatic ductal adenocarcinoma (PDAC) is characterized by dense fibrotic stroma and abundant myeloid cell infiltration, which render it resistant to any therapeutic interventions, including immunocheckpoint blockade (ICB) therapy. Understanding the composition and function of myeloid cells within the PDAC microenvironment may help identify promising targets for PDAC immunotherapy. Tissue resident macrophages (TRMs) contribute to organogenesis and tissue regeneration and metabolism. In this study, we discovered a distinct population of pancreas TRMs that highly express lymphatic vessel hyaluronan receptor 1 (LYVE-1). Single cell RNAseq data reveal that LYVE-1+ TRM cluster in the pancreas expresses high levels of complement activation genes and transcription factors such as c-Maf and Stab1. RNAseq data also confirm that LYVE-1+ TRMs express enriched genes related to mannose binding, endocytosis, and glutathione metabolic process, while LYVE-1 negative macrophages express enriched genes related to antigen processing and presentation, T cell activation, and phagocytosis. Multiparameter flow cytometric analysis demonstrates that LYVE-1+ TRMs express M2-like markers, including increased CD163, CD206 and decreased MHC Class II molecule. During PDAC development and progression, LYVE-1+ TRMs expand and localize around the tumor border, promoting fibrotic stroma formation. Imaging mass cytometry (IMC) also reveals abundant infiltration of LYVE-1+CD14+CD68+ macrophages in human PDAC tumors and colocalized with collagen deposition. This subset of macrophages also highly express c-Maf. Through the use of Lys-Cre-c-Maf f/f mice, we demonstrate that depletion of c-Maf from myeloid cells significantly reduces LYVE-1+ TRMs and polarizes them to resemble an M1-like phenotype. In conclusion, our findings suggest that LYVE-1+ macrophages are a unique subset of myeloid cells within the pancreas and likely play a critical role in PDAC progression and immunotherapeutic resistance. Future work will focus on targeting LYVE1+ TRMs using various approaches, such as conditional knockout mice and small molecule inhibitors, to determine their therapeutic potential for PDAC treatment. Presented by Dr. Hong Li Citation Format: Hong Li, Jun Yan. Pivotal role of specific LYVE1+ tissue resident macrophages in PDAC progression & immunotherapy resistance [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 6533.

Abstract 6737: Pharmacologic modulation of nonsense-mediated decay induces anti-tumor immunogenicity in ex vivo patient tumors

Abstract Introduction: Immunogenic neoantigens derived from somatic tumor mutations are essential to initiate and sustain robust anti-tumor immune responses. Frameshift insertion/deletions (fs-indels) are a key source of immunogenic neoantigens. However, fs-indels often result in the introduction of premature termination codons (PTCs), leading to mRNA degradation by the nonsense-mediated mRNA decay (NMD) pathway. In human malignancies, NMD activity is increased in response to the heightened burden of somatic fs-indel mutations and effectively prevents the generation of highly immunogenic tumor-specific neoantigens, thereby promoting immune evasion. Approach: Here, we pharmacologically targeted SMG1, a core component of the NMD pathway, for the first time in patient tumor and normal samples as well as in a panel of human cancer cell lines and patient-derived organoids, to prevent the degradation of highly immunogenic frame-shifted transcripts. We analyzed the changes in transcriptome, proteome and immunopeptidome following SMG1 inhibition (SMG1i). We then made use of tumor-T cell co-cultures and Patient-Derived Tumor Fragments (PDTFs) to assess the effects of SMG1i on anti-tumor immunogenicity. Ex vivo immunological responses were measured by high-dimensional flow cytometry, cytometric bead array and single cell RNA and TCR sequencing. Results: Our data demonstrates a significant increase in T cell activation, expansion of tumor-reactive intratumoural CD8+ lymphocytes and cytokine secretion following SMG1 inhibition in ex vivo PTDFs (n=15) but not in matched normal-adjacent tissue (n=10). Mechanistically, SMG1 inhibition increased the abundance of frame-shifted mRNA transcripts, and aberrant HLA-presented peptides. Co-culture of tumor cells and patient-derived organoids with CD8+ T cells upon SMG1 inhibition induced potent MHC class I antigen-dependent T cell activation and tumor cell killing. Conclusion: Our findings, in a clinically relevant platform, highlight SMG1 inhibition as a novel cancer immunotherapy approach to promote neoantigen production and to induce anti-tumor immunogenicity irrespective of the tumor type or TMB status. Citation Format: Roberto Vendramin, Hongchang Fu, Yue Zhao, Shanila Fernandez-Patel, Danwen Qian, Lorena Ligammari, Gordon Beattie, Ronen Levy, Polina Greenberg, Osnat Bartok, Krupa Thakkar, Jun Murai, Despoina Karagianni, Chris Sng, Mansi Shah, Felipe Galvez-Cancino, Krijn Djikstra, Sergio Quezada, Yardena Samuels, TRACERx consortium, James Reading, Charles Swanton, Kevin Litchfield. Pharmacologic modulation of nonsense-mediated decay induces anti-tumor immunogenicity in ex vivo patient 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 6737.

Abstract 6115: Genetic ancestry specific meQTLs control immune function regulation in a breast cancer cohort of African and European patients

Abstract Black women with significant African ancestry experience a disproportionately higher incidence of the most aggressive and invasive breast cancer subtypes, along with worse clinical outcomes across all demographic groups within the United States. These health disparities arise from complex interactions between genetic, sociocultural, and environmental factors. Epigenetic mechanisms, such as DNA methylation (DNAm), which regulate gene expression have been proposed as a means to capture the molecular impact of adverse environments on tumor biology. While DNAm levels can be influenced by environmental stimuli, they are also regulated by individual genotypes at methylation quantitative trait loci (meQTLs), posing a challenge to modeling the impact of the environment on cancer molecular characteristics. We hypothesized that ancestry differential DNAm in breast cancer is a result of differential genotype frequencies of SNPs due to ancestry at meQTL loci that can result in phenotypic differences between breast cancer patients of African and European ancestry through differential gene expression regulation. To investigate this hypothesis, we leveraged multi-omic data from The Cancer Genome Atlas (TCGA) breast cancer cohort to perform integrative analysis in patients of European and African ancestry (n=578). 804 CpGs were significantly differentially methylated between European and African ancestry breast cancer patients. meQTL analysis at these sites identified 37 cis-meQTLs and 748 trans-meQTLs, regulating methylation at CpG sites enriched in CpG Islands, enhancers, and other open chromatin regions. 54% of the cis- and 69% of the trans-meQTLs show evidence of differential genotype frequencies by ancestry. Association analysis between methylation and local gene expression revealed that 683 of the 804 ancestry differentially methylated sites regulate the expression of 5,774 genes. We found a statistically significant enrichment for genes involved in immune-related functions such as MHC class II protein complex assembly and the regulation of leukocyte cell-cell adhesion. Intriguingly, 10.5% of these genes encode transcription factors (TFs), and out of these ~23% are linked to African-ancestry specific open chromatin regions in breast cancer cell lines derived from African-ancestry donors. Our findings show that ancestry specific DNAm differences display strong genetic associations via ancestry associated meQTLs, affecting fundamental immunological processes in breast cancer. Our findings suggest that the effects of ancestry-specific genetic regulation may be more profound than previously appreciated, while pointing to the potential for confounding due to genetic ancestry when using DNA methylation as a molecular readout of environmental exposures. Citation Format: Kyriaki Founta, Nyasha Chambwe. Genetic ancestry specific meQTLs control immune function regulation in a breast cancer cohort of African and European 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 6115.

Abstract 5377: Investigating human leukocyte antigen (HLA) class 1 leukemogenic pathways in acute myelogenous leukemia

Abstract Background: Aging, smoking and germline predisposition are known to accelerate leukemogenesis. However, the the ability for myeloid clonal pathogenic variants (MCPV) to elicit an antigen-driven host antileukemia immune response is not well characterized. A better understanding on how cellular immunity selectively discriminates leukemia-related “neopeptides” could uncover mechanisms supporting tumor genome evolution. Methods: 122 patients with acute myelogenous leukemia (AML) were included and 111 had available protein coding sequences. A neopeptide library was created using protein FASTA coding extracted for individual myeloid clonal mutations via National Center for Biotechnology Information (NCBI). Patient class 1 HLA typing was obtained through Tempus, and Genomic Testing Cooperative laboratories. Prediction of number and strength of AML neopeptide bindings to MHC class I molecules were obtained via NetMHCPan-1. Analysis was performed with K-means algorithm assigning age at diagnosis, detected MCPV, number of neopeptides binding (as continuous variable), overall survival (OS) and event-free survival (EFS) as variables. Unsupervised data input allowed 3 cluster partitions for differential survivals allowing HLA class 1 peptide binding aggregation with potential roles in leukemogenesis and patient outcome. Descriptive statistics were performed with SAS. Results: Sixty-six different MCPV were detected. Of 111 patients, 70 (63%) with available MCPV produced at least 1 MHC I neopeptide binding. Frequently observed variants were P53 (13%), FLT3 (9.2%), WT1 (7%), DNMT3A (6.5%), RAS (5%), ASXL1 (4.3%), RUNX1 (4.2%), NPM1 (4.2%) and IDH1/2 (2.6%). Cluster 2 demonstrated a lack of favorable and higher proportion of adverse ELN 2022 subgroups. Cluster 3 exhibited a higher of P53 [p=0.03] and MDS-related mutations. OS was 79, 239, and 1551 days for cluster 2,1 and 3, respectively [p=0.0001]. EFS was 134, 363 and 451 days for cluster 2,1 and 3, respectively [p=0.0001]. Interestingly, Cluster 2 and 3 assembled the highest probability for peptide binding [1 v 2 v 3 = 1.76% v 36.6% v 62%, p=0.01]. Lastly, albeit in low frequencies, higher diversity of DNA repairing enzymes was seen in cluster 2. Conclusions: Different MCPV arising in AML genome are variably immunogenic and leukemia-related neopeptide binding’s ability is differentially expressed in our 3 clusters. Frequent neopeptide bindings in clusters 2 and 3 may reflect higher AML immunogenicity resulting in genomic instability. It is possible that less “edited” genomes in cluster 1 preserve higher chemosensitivity resulting in better OS, while highly edited genomes in cluster 2 and 3 are less chemo-sensitive and circumvent host immunosurveillance. Further expansion of cluster 2 is necessary to better understand the role of DNA repairing enzymes in younger patients’ outcomes, especially when genomic instability is observed. Citation Format: Paul Sackstein, Sarah Mudra, Lacey Williams, Garrett Diltz, Rachel Zemel, Sravanti Teegavarapu, Martha Mims, Catherine Lai, Kimberley Doucette, Anne Renteria, Olga Timofeeva, Gustavo A. Rivero. Investigating human leukocyte antigen (HLA) class 1 leukemogenic pathways in acute myelogenous leukemia [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 5377.

Abstract 6550: Biopsy analysis of trial S1616: Ipilimumab plus nivolumab versus ipilimumab alone in patients with anti-PD-1 refractory melanoma

Abstract Background: The phase II randomized trial S1616 (NCT03033576) showed that patients with melanoma refractory to anti-PD-1-based therapy had improved progression free survival (HR=0.63, p=0.037) and objective response (28% vs 9%) to the combination of ipilimumab with nivolumab compared to ipilimumab. Here, we report molecular and spatial proteomic features of biopsies collected from patients on S1616, both prior to and during therapy. Methods: Biopsies collected from patients from both arms at baseline (N=68 patients total) and early on-therapy (N=51; 43 with paired timepoints) were analyzed by whole exome sequencing (n=185 samples), RNA sequencing (n=105), histopathologic staining (n=149), and multiplexed ion beam imaging (n=45). Multiple biopsies were available for some patients. Mutations, gene expression, and tumor microenvironment were compared across timepoints and response to combination (N=18 responders [CR/PR], N=44 nonresponders [SD/PD]). Results: Baseline biopsies from patients responsive to combination had increased expression of genes (n=482, FDR<0.05) associated with coagulation and complement, fatty acid metabolism, oxidative phosphorylation, hypoxia, and interferon gamma response gene sets (FDR<0.05), compared to nonresponsive biopsies. Baseline biopsies from responders also had low levels of effector CD8 T cells (PD1+, TIM-3+, GZMB+, Ki67+) colocalized with tumor cells and myeloid populations expressing higher levels of MHC Class II. On-therapy biopsies from responders showed decreased detection of driver mutations by genomics, reduced gene expression of pathways enriched at baseline (oxidative phosphorylation, complement) by transcriptomics, and increased CD8 T cell to tumor cell ratios by histopathology, supporting observations of tumor regression. On-therapy biopsies from responders also had increased gene expression of genes related to inflammatory cytokine signaling. This correlated with increased proportions of effector CD8 T cells, compared to paired baseline or nonresponding biopsies, and increased organization of nonactivated CD8 T cells near mature endothelial structures (SMA+, CD31+ regions) adjacent to tumor. Biopsies from nonresponders did not demonstrate these dynamics and instead contained exhausted CD8 T cells (PD1+, TIM-3+, granzyme B-, Ki67-) colocalized with FOXP3+, CD4+ Tregs and CD163+, PD-L1+ M2 macrophages, both at baseline and on-therapy. Conclusion: In patients with melanoma refractory to anti-PD-1, addition of anti-CTLA-4 facilitates tumor-reactive CD8 T-cell infiltration and decreased suppressor cell dynamics, resulting in regression of some tumors with distinct transcriptome features. Conversely, biopsies from patients whose tumors progress on combination therapy lack expression of metabolic pathways and show CD8 T-cells restricted in proximity to M2 macrophages and Tregs. Citation Format: Katie M. Campbell, Zaid Bustami, Daniel G. Chen, Egmidio Medina, Cynthia R. Gonzalez, Nataly Naser Aldeen, Ignacio Baselga-Carretero, Agustin Vega-Crespo, Jessica Maxey, Jia M. Chen, Lawrence F. Kuklinski, Kari L. Kendra, Bartosz Chmielowski, Thach-Giao Truong, Nikhil I. Khushalani, Frances Collichio, Alexandra Ikeguchi, Adrienne I. Victor, Kim Margolin, Jeffrey A. Sosman, Sapna P. Patel, Siwen Hu-Lieskovan, James Moon, Shay Bellasea, Daniel K. Wells, Christine N. Spencer, Marshall A. Thompson, Michael Wu, Philip O. Scumpia, Ari VanderWalde, Antoni Ribas. Biopsy analysis of trial S1616: Ipilimumab plus nivolumab versus ipilimumab alone in patients with anti-PD-1 refractory 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 6550.

Signals that control MAIT cell function in healthy and inflamed human tissues.

Mucosal-associated invariant T (MAIT) cells have a semi-invariant T-cell receptor that allows recognition of antigen in the context of the MHC class I-related (MR1) protein. Metabolic intermediates of the riboflavin synthesis pathway have been identified as MR1-restricted antigens with agonist properties. As riboflavin synthesis occurs in many bacterial species, but not human cells, it has been proposed that the main purpose of MAIT cells is antibacterial surveillance and protection. The majority of human MAIT cells secrete interferon-gamma (IFNg) upon activation, while some MAIT cells in tissues can also express IL-17. Given that MAIT cells are present in human barrier tissues colonized by a microbiome, MAIT cells must somehow be able to distinguish colonization from infection to ensure effector functions are only elicited when necessary. Importantly, MAIT cells have additional functional properties, including the potential to contribute to restoring tissue homeostasis by expression of CTLA-4 and secretion of the cytokine IL-22. A recent study provided compelling data indicating that the range of human MAIT cell functional properties is explained by plasticity rather than distinct lineages. This further underscores the necessity to better understand how different signals regulate MAIT cell function. In this review, we highlight what is known in regards to activating and inhibitory signals for MAIT cells with a specific focus on signals relevant to healthy and inflamed tissues. We consider the quantity, quality, and the temporal order of these signals on MAIT cell function and discuss the current limitations of computational tools to extrapolate which signals are received by MAIT cells in human tissues. Using lessons learned from conventional CD8 T cells, we also discuss how TCR signals may integrate with cytokine signals in MAIT cells to elicit distinct functional states.

Abstract 7479: Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer immunotherapy

Abstract The widespread success of cancer immunotherapies suggests a promising future - but has been subverted by unresponsiveness and resistance. Current research has furthered the understanding of immunotherapy resistance through the findings of “hot” (responsive) and “cold” (unresponsive) tumors. Here, we focus on the genetic and pharmacological inhibition of PIKfyve, a lipid kinase regulator of autophagic flux and lysosomal biogenesis. We find that inhibition of PIKfyve results in the upregulation of major histocompatibility complex class I (MHC-I) surface expression in cancer cells (through inhibition of autophagic flux), resulting in increased CD8+ T cell-mediated cancer cell death. These findings were corroborated in multiple syngeneic mouse models, which also displayed increased intratumoral functional CD8+ T cells. In addition, the Pikfyve-depletion antitumor responses are CD8+ T cell and MHC-I dependent - as CD8+ T cell and B2m knockout rescued tumor growth - resulting in improved response to immune checkpoint blockable (ICB), adoptive cell therapy, and a therapeutic vaccine. Further, high PIKfyve expression predicts poor ICB response and is prognostic of poor survival in ICB-treated cohorts. Ultimately, these findings collectively suggest PIKfyve as an effective target to enhance immunotherapies through elevation of MHC-I surface expression in cancer cells, and accordingly, PIKfyve inhibitors have novel potential to increase immunotherapy response in cancer patients. Citation Format: Parth Borker, Yi Bao, Yuanyuan Qiao, Arul Chinnaiyan, Jae Eun Choi, Yuping Zhang, Rahul Mannan, Caleb Cheng, Tongchen He, Yang Zheng, Jiali Yu, Mahnoor Gondal, Gabriel Cruz, Sara Sara Grove, Xuhong Cao, Fengyun Su, Rui Wang, Yu Chang, Ilona Kryczek, Marcin Cieslik, Michael D. Green, Weiping Zou. Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer immunotherapy [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 7479.

Abstract 2564: Circulating monocytes decrease significantly following disease-directed therapy and may reflect disease expansion in Langerhans cell histiocytosis

Abstract Introduction: Langerhans Cell Histiocytosis (LCH) is a rare disorder characterized by clonal hematopoietic cell expansion forming eosinophilic granulomas. Treatment approaches vary based on disease severity. Despite established therapies, assessing treatment response, particularly regarding peripheral blood monocytes, lacks comprehensive markers. Methods: We studied 76 LCH patients, collecting data on demographics, diagnostic methods, and treatment responses. Peripheral blood absolute monocyte counts were analyzed at key time points, including disease onset, progression, and post-therapy reinstatement, using statistical tests for comparison. Results: Analyzing data from 76 patients (average age: 38), we found diverse disease presentations, with common imaging modalities being CT (37), PET (29), and MRI (22). Complete responses were observed in 17 of 49 patients, with 11 undergoing local therapy. Conversely, 5 patients with pulmonary LCH and chronic tobacco use showed persistent progression. Notably, peripheral blood monocyte counts did not differ between initial and latest assessments, but on disease progression, the mean count (0.94 K/µL) significantly exceeded that following therapy reinstatement (0.31, p=0.000794). Results: Analyzing data from 76 patients (average age: 38), we found diverse disease presentations, with common imaging modalities being CT (37), PET (29), and MRI (22). Complete responses were observed in 17 of 49 patients, with 11 undergoing local therapy. Conversely, 5 patients with pulmonary LCH and chronic tobacco use showed persistent progression. Notably, peripheral blood monocyte counts did not differ between initial and latest assessments, but on disease progression, the mean count (0.94 K/µL) significantly exceeded that following therapy reinstatement (0.31, p=0.000794). Discussion: LCH is proposed to result from dysregulated hematopoiesis, leading to sequential somatic mutations during monocyte differentiation leading to clonal expansion of CD1A and CD207+ histiocytes. Our finding of increased monocyte count during disease progression may suggest elevated circulating LCH or heightened monocyte production for subsequent differentiation, potentially contributing to MHC Class 1 upregulation. This phenomena mirrors published findings from our own group in patients with Rosai Dorfman and Erdheim Chester Disease. To further elucidate the molecular underpinnings of LCH and explore the etiology of this monocyte trend, genetic sequencing analysis is in progress. Ultimately, monitoring peripheral blood monocyte dynamics could offer valuable insights into LCH progression and treatment response. Citation Format: Haadi Ali, Sam Reynolds, Sabrina Wilcox, Naina Chipalkatti, Asra Ahmed. Circulating monocytes decrease significantly following disease-directed therapy and may reflect disease expansion in Langerhans cell histiocytosis [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 2564.

Abstract 1425: Epigenetic modulation synergizes with a novel TCR β chain directed antibody-fusion molecule to suppress checkpoint-refractory tumors irrespective of MHC I status

Abstract Background: Epigenetic silencing of MHC-I, and poor T cell infiltration and function in the tumor microenvironment (TME) are prevalent in solid malignancies and associate with lack of response to immune checkpoint blockade (ICB). Novel combination therapies may overcome these barriers, thereby providing clinical benefit across solid tumors. STAR0602 is a first-in-class bifunctional therapeutic molecule, that simultaneously engages a nonclonal mode of T cell receptor (TCR) activation with costimulation to promote activation and expansion of αβ T cell subsets expressing distinct variable β (Vβ) TCR chains. Here, we examined the tumor-suppressive ability and mode of action of a murine surrogate of STAR0602 (mSTAR1302) in combination with the class I HDAC inhibitor Entinostat, an epigenetic modulator that enhances tumor immune cell recognition, in multiple tumor models, including ICB-refractory. Methods: mSTAR1302 and/or Entinostat were administered to mice bearing ICB-responsive breast EMT6 wild-type (wt) and ICB-refractory EMT6 β2-microglobulin (B2m)-deleted and CT26 (Kras G12Dmut colon) tumors. Anti-tumor efficacy, survival, and protective memory were monitored. Immune cell depletion studies were conducted. Comprehensive proteomic and immune profiling of tumor, tumor-draining lymph node (tdLN), and spleen cell populations was conducted. Antigen-specific IFNg T cell responses were evaluated by ELISpot. Results: Combination therapy demonstrated significant enhancement in tumor suppression and prolonged survival in CT26 (MHC-I+), EMT6 wt (MHC-I+) and EMT6 β2m-deleted (MHC-Inull) tumors relative to single agent therapy, as well as enhanced tumor-specific protective memory responses. Tumor suppression was independent of CD4+ T cell immunity and associated with sustained activation and expansion of Vβ13 CD8+ T cells. Conclusions: Ongoing mechanistic studies indicate combination therapy to elicit complimentary mechanisms of tumor suppression beyond CD8+ T cells. Ongoing proteomic and single-cell transcriptomic investigation of MHC-I competent and null tumors will provide a deeper insight into the mode of action of this combination therapy. Collectively, these data support the use of STAR0602 in combination with Entinostat for the treatment of solid malignancies, including for patients harboring ICB-refractory tumors devoid of MHC class I. Citation Format: Katherine E. Lothstein, Asma S. Khelifa, Masaya Miyamoto, Christine M. Minnar, Lisa Poppe, Nicholas Roller, Andrew Bayliffe, Ke Liu, Jacques Moisan, Madan Katragadda, Zhen Su, Jeffrey Schlom, Sofia R. Gameiro. Epigenetic modulation synergizes with a novel TCR β chain directed antibody-fusion molecule to suppress checkpoint-refractory tumors irrespective of MHC I status [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 1425.

Abstract 1320: Engineered expression of HLA-E and HLA-G protects iPSC-derived cells from killing by primary NK cells

Abstract Background: A major challenge to off-the-shelf allogeneic cell therapies is the HLA-targeted elimination of genetically dissimilar cells. To combat this, HLA Class I can be deleted through transgene insertion at the beta-2 microglobulin (B2M) locus, while HLA Class II can be deleted by disruption of the gene encoding MHC Class II Transactivator (CIITA). Lack of HLA Class I expression, however, marks cells for elimination by natural killer (NK) cells, which normally receive inhibitory signals from this protein family. HLA-E and HLA-G are non-classical HLA Class I molecules that are far less polymorphic than HLA-A/B/C. They can inhibit natural killer cell-mediated activation by engaging NKG2A, KIR2DL4, ILT2, and ILT4. The objective of this study was to assess allo-evasion from NK cells by iPSC-derived cells engineered to overexpress HLA-E and -G. Methods: Allo-evasion by HLA-E, -G or both was first assessed in the chronic myelogenous leukemia K562 cell line, which expresses very low HLA Class I and is highly susceptible to NK-mediated killing. K562 cells were engineered using CRISPR/CAS9 to express chimeric molecules encoding either HLA-E or HLA-G heavy chains tethered to a defined nominal self-peptide and B2M, or HLA-E/peptide/B2M-P2A-HLA-G/peptide/B2M. Along with parental K562, these were used as targets in co-cultures with allogeneic PBMCs (n=22 donors) at different E:T ratios. Target killing was observed using flow cytometry and normalized to parental K562. Phenotyping of effector PBMCs for NK frequency and expression of HLA-E and -G receptors (NKG2A, KIR2DL4, ILT2, and ILT4) was performed to study correlations with killing efficiency and allo-evasion. IPSCs with endogenous B2M knocked out were also engineered to overexpress HLA-E and -G with the constructs described above. These were then differentiated into NK cells and gamma delta T cells using proprietary processes. Allo-evasion of these cells from killing by the same PBMC cohort was evaluated by flow cytometry. Results: While NK cells across donors expressed heterogeneous combinations of HLA-E and -G receptors, the strongest correlation with PBMC allo-responsiveness was NK frequency. K562 and iPSC-derived cells lacking HLA were susceptible to killing by PBMCs. Overexpression of HLA-E and -G offered protection to K562 and iPSC-derived cells against all tested donors. HLA-E offered more protection than HLA-G, and the combination of both HLA-E and -G was most potent. Conclusion: When genetically dissimilar HLA Class I protein family must be deleted to prevent graft rejection, expression of the more-conserved HLA-E and -G can effectively protect allogeneic drug products from elimination. These Allo-evasionTM edits may increase the in vivo persistence and enable multi-dosing of our iPSC-derived allogeneic cell therapies. Citation Format: Andriana Lebid, Dae Hwan Kim, Gabrielle Greco, Heidi Jessup, Alyssa Suarez, Shelby Brown, Nicholas Alexander, Mitan Desai, Buddha Gurung, Barry Morse, Daniel J. Perry, Michael F. Naso, Hyam Levitsky. Engineered expression of HLA-E and HLA-G protects iPSC-derived cells from killing by primary 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 1320.

Abstract 4112: Identification of Th1-specific epitopes from non-mutated KRAS lesions for off-the-shelf cancer vaccines

Abstract Background KRAS is crucial for cell growth, differentiation, and signaling. Mutations in the KRAS gene (i.e., codon 12 or 13) are frequently associated with the development and progression of cancer, particularly lung, colorectal, and pancreatic cancers. Recently, it has been captured that KRAS targeting cancer vaccine research and clinical trials have been conducted in certain tumor types and vaccine approaches are encouraged to move forward. It has been well known that the tumor-eradicating efficacy of cancer vaccines arises from Th1 epitope selection. While tumor growth may persist after immunization with non-selected epitopes (including full-length), immunization with a highly selected Th1-specific epitope vaccine can lead to tumor regression by suppressing the activation of immune inhibitory cells. The Th-Vac® discovery platform uses a combination of in-silico, in-vitro, and in-vivo studies to precisely identify Th1-specific epitopes. It consists of two modules: module 1 (in-silico) and module 2 (in-vitro and efficacy evaluation). The aim is to identify MHC class II epitopes that are specific to antigens for CD4+ T cells, displaying the most favorable binding affinity across diverse alleles. Th1-specific epitope vaccines aim to boost and sustain T cell immunity against tumor antigens, overcoming the lack of a precise T cell response or pre-existing tolerance in the immunosuppressive TME. This study aimed to explore Th1-specific epitopes for KRAS vaccine to be potentially effective in numerous KRAS mutation-driven cancers. Methods Peptide sequence candidates that have highly potential of MHC class II binding affinity were comprehensively predicted via a module 1 (ASEP program). All of peptides selected in ASEP were synthesized as 15 mers. Each peptide was evaluated for immunogenicity using ELISpot and/or FACS analysis in module 2 (2a for in vitro and 2b for in vivo immunologic evaluation) of the Th-Vac® discovery platform. Specifically, in Module 2b, immunogenicity was evaluated using a 38-mer peptide formed by combining five overlapping peptides selected in 2a. These kinds of immunogenicity evaluations were conducted using type 1 and/or type 2 cytokine(s) produced by CD4+ T cells. Results In ASEP prediction, twelve peptides were selected as potential candidates demonstrating a high affinity to MHC class II, which were in different lesions of common mutation of KRAS. In module 2 using ELISpot and FACS analysis, two epitopes (non-mutated sequences) were finally selected as Th1-specific epitopes based on the type 1 T cell response. Conclusion Unlike previous vaccines using mutant lesions, in this study, two non-mutated Th1-specific epitopes are under the in-vivo efficacy studies as mono and combining regimen(s) in certain tumor types. Additionally, the Th-Vac® platform was fully validated in terms of the performance and its application would be expanded beyond a cancer vaccine. Citation Format: Youngki Choi, Jinback Lim, Hyo-Hyun Park, Jinho Kang, Hun Jung. Identification of Th1-specific epitopes from non-mutated KRAS lesions for off-the-shelf cancer vaccines [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 4112.

Abstract 2632: A new paradigm for brain tumors treatment: Guadecitabine as a fundamental player to improve tumor immune response

Abstract Background:Glioblastoma multiforme (GBM) is a highly aggressive primary brain tumor refractory to standard treatments and to immunotherapy with immune-checkpoint inhibitors (ICI) (PMID: 35626018). Interestingly, melanoma brain metastases (MM-BM), sharing the same niche as GBM, often respond to current ICI immunotherapies (PMID: 36521332). The role of epigenetic modifications in regulating GBM cellular proliferation, invasion, and prognosis, as well as their impact on the cross-talk between GBM and immune cells in the tumor milieu, has become evident (PMID: 34361090). Consequently, manipulating the epigenome has emerged as a therapeutic opportunity in GBM. Methods:Microarray transcriptional and methylation profiles, followed by gene set enrichment and IPA analyses, were conducted to study the differences in constitutive expression profiles between GBM and MM-BM cells compared to extracranial MM cells. Additionally, the modulatory effects of the DNA hypomethylating agent (DHA) guadecitabine on different tumor cells were investigated. The prognostic relevance of DHA-modulated genes was assessed through Cox analysis in a TCGA GBM patients' cohort. Results:The most notable differences between constitutive GBM and MM-BM cells lie in the enrichment of biological processes associated with tumor growth, invasion, and extravasation, as well as the inhibition of MHC class II antigen processing/presentation in GBM cells. Guadecitabine treatment appeared to shrink these differences, shifting the phenotype of GBM cells towards the more immunogenic MM-BM profile. This was achieved through promoter hypomethylation and subsequent up-regulation of genes mainly associated with the activation, proliferation, and migration of T and B cells, along with MHC class II antigen processing/presentation. Among DHA-modulated genes in GBM, 7.6% exhibited significant prognostic relevance. Moreover, a substantial set of immune-related upstream regulators (URs) were commonly modulated by DHA in GBM, MM-BM, and/or MM cells: DHA-activated URs enriched biological processes mainly involved in the regulation of cytokines and chemokines production, inflammatory response, and Type I/II/III IFN-mediated signaling. DHA-inhibited URs were associated with metabolic and proliferative pathways. Conclusions:Epigenetic remodeling of GBM by DHA represents a promising strategy to enhance the efficacy of cancer immunotherapy, supporting the rationale for developing new combinatorial approaches for the treatment of brain malignancies. Citation Format: Maria Fortunata Lofiego, Francesca Piazzini, Francesca Pia Caruso, Francesco Marzani, Laura Solmonese, Emma Bello, Fabrizio Celesti, Maria Claudia Costa, Teresa Maria Noviello, Roberta Mortarini, Andrea Anichini, Michele Ceccarelli, Sandra Coral, Anna Maria Di Giacomo, Michele Maio, Alessia Covre. A new paradigm for brain tumors treatment: Guadecitabine as a fundamental player to improve tumor immune response [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 2632.

Abstract 6345: In vitro characterization of a dual antagonistic anti-LILRB2/LILRB4 monoclonal antibody

Abstract Introduction: Myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment are a potential therapeutic target in immune checkpoint cancer therapy, but MDSC-targeted therapies have yet been shown to improve survival. The leukocyte immunoglobulin (Ig)-like receptor B2 is a member of the leukocyte Ig-like receptor (LILR) family and is predominantly expressed on the surface of cells of the myelomonocytic lineage (monocytes, macrophages and dendritic cells). LILRB2 is a negative regulator of myeloid cells and is an immune checkpoint receptor. We chose to generate mAbs against LILRB2 as a potential immunotherapeutic for cancer. Methods: PentaMice® strains (5 WT mouse strains comprising 9 MHC class II haplotypes to maximize Ab diversity) were immunized with human LILRB2. Lymphocytes were fused with a myeloma partner to generate lead monoclonal hybridomas. 24 purified anti-LILRB2 mAbs were generated and evaluated by arrayed surface plasma resonance (SPR, Carterra® LSA® instrument) to assign epitope bins. mAb humanization was performed in silico to maximize T20 “humanness” scores (algorithm developed by Curia). Humanized mAbs were transiently expressed using Curia’s TunaCHO™ platform and tested in in vitro MDSC assays. Autologous co-cultures of magnetic bead enriched-human blood-derived MDSC (HLA-DR-CD14+) model cells and T cells (CD3+) were stimulated with plate-bound anti-CD3/CD28 to induce T cell activation. Cytokine secretion was assessed 4 days later. Results: A total of 384 hybridoma supernatants were selected from the primary screen. 245 were confirmed by ELISA and 178 stained HEK293 cells expressing LILRB2 cells by flow cytometry (FACS). 24 hybridomas were further selected, cloned and sequenced. Five epitope bins were identified via Carterra® LSA® instrument. Two clones were chosen for humanization, designated 6-I11A and 4-O19A and were recombinantly expressed with the human IgG4 isotype. FACS analysis on HEK293 cells expressing either huLILRB2 or huLILRB4 revealed that clone hu4-O19A-IgG4 was specific for huLILRB2. Surprisingly, clone hu6-I11A-IgG4 stained both huLILRB2 and huLILRB4. FACS analysis with hu4-O19A-IgG4 on human MDSCs exhibited an EC50 of 11.9 nM and a KD of 1.5 nM in binding to recombinant huLILRB2 antigen, while hu6-I11A-IgG4 had an EC50 of 3.2 nM and a KD of 0.6 nM. In co-cultures with human MDSCs and T cells, both hu6-I11A-IgG4 and hu4-O19A-IgG4 reversed cytokine suppression by the MDSCs by increasing GM-CSF, IL-10, TNFα, and IL-6, while suppressing IL-13, and had little effect on IL-17A, MIP-3α, IL-4, IL-2 and IFNγ compared to treatment with the isotype control, with hu6-I11A-IgG4 having a greater effect as an antagonist than hu4-O19A-IgG4. Conclusions: We have identified a dual anti-LILRB2/LILRB4 antagonist. Targeting MDSCs with this antibody offers great promise for immunotherapy for cancer as well as its immense potential for synergy with PD-1 blockade. Citation Format: Bruce L. Daugherty, Xiaomei Ge, Christine L. Hsieh, Brian A. Zabel, Seth Lederman. In vitro characterization of a dual antagonistic anti-LILRB2/LILRB4 monoclonal antibody [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 6345.

Abstract 3766: Utilizing whole-transcriptome digital spatial profiling for glioblastoma clinical biomarker discovery

Abstract Objective: IDH-wildtype glioblastoma (GBM) is the most aggressive brain tumor in adults. Notable for substantial inter- and intra-tumoral heterogeneity, GBM is highly resistant to standard-of-care treatment. Emerging spatial omics technologies, such as GeoMx Digital Spatial Profiling (DSP), offer novel approaches to interrogate the molecular features of regionally defined cellular ecosystems in cancer. Here, we leverage DSP to study whole-transcriptome gene expression signatures in a spatially defined manner across five IDH-wildtype GBMs. Methods: Formalin-fixed paraffin-embedded tumors were assessed histologically and three spatially distinct areas from each tumor were used to construct a custom “spatial” tissue microarray. From each set of three areas, we identified nine spatially distinct regions of interest (ROIs) for bulk transcriptomic analysis according to two histopathological features: distribution (cellular tumor core or tumor periphery) and vascular proximity (near or far). We evaluated normalized target expression data statistically using linear mixed modeling (LMM) with Benjamini-Hochberg correction. Results: 44 profiled ROIs and 8531 transcriptomic targets were analyzed following quality control trimming. 3D principal component analysis and unsupervised hierarchical clustering analysis showed clustering according to tumor specimen as well as distribution (core versus periphery), thereby substantiating the presence of inter- and intra-tumoral transcriptional heterogeneity. LMM-based differential gene expression analysis identified distinct molecular signatures when comparing core and periphery. Specifically, we observed elevated log2-transformed expression of migration and proliferation markers including LAMC1 (p=0.00297) and FABP7 (p=0.00434) in core ROIs and neurodevelopmental markers including NTRK2 (p=0.00734) and DAAM2 (p=0.00263) in periphery ROIs. Additionally, reactome analysis demonstrated considerable enrichment for the aberrant programmed cell death pathway (R-HSA-9645723, coverage=71.84%) in core ROIs and the MHC class II antigen presentation pathway (R-HSA-2132295, coverage=69.11%) in periphery ROIs. Interestingly, differential gene expression analysis did not reveal any biologically significant targets when subsetting for vascular proximity within cellular tumor core ROIs. However, reactome analysis of this regional subset demonstrated upregulation of various cellular proliferation pathways (G2/M transition, APC/C activity, DNA synthesis, etc.) within vessel-near ROIs when compared with vessel-far ROIs. Conclusions: We preliminarily characterize the molecular heterogeneity of GBM using a spatially guided approach. Ongoing analyses are focused on dataset validation, mixed cell deconvolution, further regional genotyping, and potential biomarkers. Citation Format: Adam Luo, Kelly Casella, Shivang Sharma, Ezra Baraban, Calixto-Hope Lucas, Eugene Shenderov. Utilizing whole-transcriptome digital spatial profiling for glioblastoma clinical biomarker discovery [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 3766.