Cell Clones Research Articles

Abstract 1516: Large scale, transcriptome-based analysis of TCR clonality reveals functional immunity in non-small cell lung cancer

Abstract Tumor-related T-cell activation and subsequent clonal expansion are essential for an effective anti-cancer immune response. Thus, quantifying the clonal distribution of T-cells in cancer tissue from patients might provide prognostic and predictive information, particularly in high immunogenic tumors like non-small cell lung cancer (NSCLC). We evaluated TCR clonality in the tumor microenvironment of NSCLC, its relation to the in situ immune phenotype, and its clinical impact in a cohort of 182 resected NSCLC patients. The α and β TCR clones were determined based on RNA sequencing data, and the Gini index was used to weight individual clonal distribution. We used matched FFPE cancer tissue for multiplex immunofluorescence cell analysis and in-situ sequencing of T-cell clones. The analysis revealed a broad spectrum of TCR clonality patterns, including tissue with high TCR diversity and high evenness (low Gini coefficient) and tissue with clonal dominance with low evenness (high Gini coefficient). Highly expended clones were detected in 15/182 patients, whereas 43/182 revealed no clonal enrichment. A low TCR clone evenness (high Gini coefficient) was significantly more frequent in normal lung areas than in the corresponding tumor areas (n=20, p=0.02). In the cancer tissue, a high Gini index further correlated with high tumor mutational burden, indicating neoantigen-induced T cell clone expansions. Correspondingly, high TCR clonality was associated with an inflamed tumor phenotype associated with PD-1+ immune cells, CD3+, CD8A+, CD163+, and CD138+ cells, as well as higher expression of genes connected to immune activation (PRF1, GZMB, GZMH) and T cell exhaustion (PD-L1, LAG3, TIGIT). Cancer tissue with dominant T-cell clones also showed higher numbers of mature tertiary lymphoid structures with germinal centers. In situ sequencing suggested a close spatial relation between specific T cell clones and tumor cells. Finally, NSCLC patients with dominant T-cell clones showed strong responses and longer survival when treated with immune checkpoint inhibitors. This suggests that TCR clonality analysis is a strong candidate for precision diagnostics. Plausibly, the dominant clones found in NSCLC are responsible for a specific but malfunctioning anti-tumor response that can be unleashed by immune checkpoint inhibition. Citation Format: Hui Yu, Anastasia Magoulopoulou, Masafumi Hori, Amanda Lindberg, Max Backman, Hans Brunström, Millaray Marincevic Zuniga, Johanna Mattsson, Akira Saito, Karin Leandersson, Mats Nilsson, Rose-Marie Amini, Patrick Micke, Carina Strell. Large scale, transcriptome-based analysis of TCR clonality reveals functional immunity 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 1516.

Abstract 582: Oncogenic PIK3CA fortifies immune determinants in vascular cancers

Abstract Angiosarcomas are a group of vascular cancers that form malignant blood vessels. These malignancies are seemingly inflamed primarily due to their pathognomonic nature, which consists of irregular endothelium and tortuous blood channels. The malignant vascular spaces host a variety of blood and immune components, where a controlled scavenging system is necessary for tumor maintenance. Oncogenes may convey molecular signals to foster the tumor immune niche, and PIK3CA mutations that induce continuous activation of the PI3K pathway occur in a subset of angiosarcomas. Despite the undoubtedly oncogenic properties of PIK3CA mutations, the mechanistic role of these mutations - particularly the potential for controlling the hemato-endothelial system in angiosarcomas - remains undetermined. In this study, we demonstrate the functional consequences of oncogenic PIK3CA and its molecular properties in angiosarcoma cells. We created isogenic cell clones from two angiosarcoma cell lines engineered to harbor hotspot mutations in PIK3CA using CRISPR/Cas9: two homozygous PIK3CA H1047R cell clones (C8 and C35) and one wild-type (WT) clone were generated from DHSA-1426 angiosarcoma cells; and one homozygous mutant clone was created from COSB cells. We found that PIK3CA mutant cells constitutively activated the PI3K/AKT/mTOR pathway at a greater level than that of WT cells. Bulk- and single cell(sc)-RNA-seq data revealed that mutant cells enriched gene sets associated with PI3K signaling and other oncogenic pathways including KRAS, MAPK, and TGF-beta. Also, mutant cells significantly increased cytokines regulating immune cell migration and chemotaxis such as IL-8 and MCP-1. In addition to the common features, we identified functional and molecular divergence between mutant clones. Noticeable changes in cellular morphology, growth kinetics, and tube-forming capacity were observed between two mutant clones. C35 mutant cells were more sensitive to both pan-PI3K and PI3K-alpha specific inhibitor, and DNA damage was greater than in the C8 clone. C35 cells enhanced activation of IL-6/STAT3 signaling compared to C8, despite the increment of the aforementioned immune cytokines in both mutants. Moreover, our comprehensive analysis of bulk- and sc-RNA-seq, ATAC-seq, and metabolomics data identified molecular signatures associated with metabolic vulnerabilities of C35 cells. In summary, we demonstrate that oncogenic PIK3CA perpetuates PI3K signaling activation and reinforces a supply for immune signaling. Furthermore, our data suggest that PIK3CA mutations contribute to establishing cellular heterogeneity that reveals a spectrum of vascular, immunogenic, and metabolic activities. Our ongoing work involves developing an experimental model of angiosarcoma using induced pluripotent stem cells to examine if oncogenic PIK3CA controls immune determinants during malignant endothelial transformation. Citation Format: Donghee Lee, Emma Kozurek, Md Abdullah, Rong Li, Erin B. Dickerson, Jong Hyuk Kim. Oncogenic PIK3CA fortifies immune determinants in vascular cancers [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 582.

Abstract 4090: Gut microbiota mimics as a source of cross-reactive tumor rejection antigens

Abstract The crosstalk between gut microbiome and anti-tumor immunity has recently gained attention in clinical settings. The administration of antibiotics during immune checkpoint blockade (ICB) therapies has been correlated with poorer outcomes in cancer patients, suggesting that microbiome alterations affect overall responses to ICB. The establishment of microbiota-specific T cell clones with tumor cross-reactivity potential was proposed as one of the mechanisms linking the microbiome to anti-tumor responses. Vaccine-based strategies aimed at reactivating these dormant pools of T cells to help eliminate tumors have been proposed as an alternate approach, but the parameters required for successful responses remain poorly understood. Here, we performed in silico selection of bacterial peptides derived from healthy mice based on their mimicry of either tumor-associated antigens (TAAs) or neoantigens expressed by murine melanoma cells and not healthy tissue. We show that in silico predicted peptide binding affinity to MHC I correlates with experimental MHC I binding, a key factor associated with strong immune responses. Moreover, we confirmed that a significant proportion of selected peptide candidates can provoke an immune reaction in a vaccination setting. From this group of peptides, we selected candidates which triggered cross-reactive immune responses against TAAs or neoantigens. Data from preliminary tumor challenge experiments with prophylactic peptide vaccination and ICB allowed us to define key parameters such as target gene expression levels which can predict the cross-reactive potential of bacterial peptides that mimic tumor antigens. These findings provide novel insights into the design of gut microbiome peptide-based tumor vaccines and pave the way for establishing combinatorial therapies with immunomodulatory drugs. Citation Format: Vincent Panneton, Mathieu Gigoux, Abderezak Zebboudj, Norah Sadek, Hyejin Choi, Levi M. Mangarin, Mariam M. George, Guillaume Kulakowski, Joao G. Magalhaes, Jean-Marie Carpier, Thibaud Dugat, Camille Gaal, Francesco Strozzi, Lorenzo Tibaldi, Laurent Chene, Jedd D. Wolchok, Vinod P. Balachandran, Taha Merghoub. Gut microbiota mimics as a source of cross-reactive tumor rejection antigens [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 4090.

Abstract 1191: Personalized neoantigen DNA vaccine GNOS-PV02 and pembrolizumab as second-line treatment for advanced hepatocellular carcinoma

Abstract Background: PD-1 inhibitors have modest efficacy as monotherapy in hepatocellular carcinoma (HCC). A personalized therapeutic cancer vaccine (PTCV) tailored against neoantigens identified in an individual’s tumor may enhance responses to PD-1 inhibitors through the induction of tumor-specific immunity. Here, we present results from a single-arm Phase Ib/2a trial evaluating a DNA plasmid (GNOS-PV02) encoding up to 40 neoantigens co-administered with plasmid-encoded IL-12 (pIL12) in combination with pembrolizumab (PEMBRO) in patients (pts) with advanced HCC.Methods: Pts were eligible for study therapy upon progression or intolerance with a 1L tyrosine kinase inhibitor (TKI). The PTCV [GNOS-PV02 (1mg) and pIL12 (0.34mg)] was administered intradermally via in vivo electroporation Q3w x 4 doses, and Q9w thereafter. PEMBRO was administered at 200mg IV Q3w. The primary endpoints were safety and immunogenicity. To evaluate the secondary endpoint of ORR per RECIST 1.1 by investigator review with a null hypothesis of an ORR of 16.9% (KN-240, Finn et al ASCO 2019), 36 pts were included to provide 80% power to reject the null hypothesis at the one-sided 0.10 level, assuming the true ORR rate of 33.1%. The data cut date was August 18, 2023.Results: Among the 36 enrolled pts who received at least one dose of treatment, there were no DLTs or treatment-related grade ≥3 events. The most common treatment-related adverse events were injection site reactions, observed in 41.6% of pts. ORR (mITT) per RECIST 1.1 was 30.6% (11/36; 9 confirmed and 2 unconfirmed) with 8.3% (3/36) of pts achieving a CR. This achieved statistical significance with a one-sided p-value = 0.031 (1-sided 90% CI 20.4%-100%) The mOS was 19.9 months. ctDNA changes correlated with radiographic responses and preceded them. A complete molecular response (100% ctDNA clearance) was detected in 7 pts including the 3 radiographic CRs, and 4 additional pts who continue to show durable tumor control (3PR, 1 SD). Immunological analyses confirmed the induction of neoantigen-specific T cell responses by IFNγ-ELISpot in 19/22 (86.4%) evaluable pts, and pts with a larger ELISpot response showed a trend towards longer OS. Multi-parametric cellular profiling and single-cell analysis revealed active, proliferative, and cytolytic vaccine-specific CD4+ and CD8+ effector T cells in the blood of immunized pts. In 14/14 (100%) of pts with paired pre- and on-treatment blood and tumor biopsies, we identified by TCRβ bulk sequencing expanded T cell clones in the peripheral blood that also trafficked into the tumor. Conclusions: Our results show that a PTCV plus PEMBRO is well tolerated and has clinical activity in pts with advanced HCC, and support the PTCV mechanism of action based on the induction of anti-tumor T cells in peripheral blood and tumor. A confirmatory phase 3 clinical study assessing OS is planned. Citation Format: Mark Yarchoan, Edward J. Gane, Thomas U. Marron, Renzo Perales-Linares, Jian Yan, Neil Cooch, Daniel Shu, Elana J. Fertig, Luciane T. Kagohara, Gabor Bartha, Josette Northcott, John Lyle, Sarah Rochestie, Joann Peters, Jason Connor, Elizabeth Jaffee, Alfredo Perales-Puchalt, David B. Weiner, Ildiko Csiki, Niranjan Y. Sardesai. Personalized neoantigen DNA vaccine GNOS-PV02 and pembrolizumab as second-line treatment for advanced 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 1191.

Abstract 6: Defining and therapeutically targeting a fusion-derived public neoantigen in desmoplastic small round cell tumor using T cell receptor gene therapy

Abstract Sarcomas are a heterogenous group of mesenchymal cell malignancies that are difficult to treat and often respond poorly to current immunotherapies. Approximately 30% of sarcomas are associated with oncogenic driver fusion proteins. Desmoplastic small round cell tumor (DSRCT) is a prototypical fusion-driven sarcoma defined by a pathognomonic EWSR1-WT1 fusion event. The resultant EWSR1-WT1 fusion protein contains a shared junctional amino acid sequence that is clonally conserved and significantly divergent from normal human proteins. Consequently, the EWSR1-WT1 fusion might yield a highly immunogenic shared, or public, neoantigen (NeoAg) that may serve as a target for novel immunotherapeutic approaches.Using a functional HLA-immunoprecipitation/mass spectrometry (HLA-IP/MS) screen, we identified a 9-amino acid peptide sequence derived from the junction of the most common EWSR1-WT1 fusion protein that is presented in the context of the prevalent HLA-A*03 and -A*11 alleles. We confirmed that HLA-A*03+ DSRCT cells physiologically present the same peptide sequence. Using fluorophore-conjugated HLA-multimers loaded with the HLA-IP/MS-derived fusion NeoAg, we identified a rare population of circulating NeoAg-specific CD8+ T cells in HLA+ DSRCT patients. Through antigen-directed clonal expansion, we discovered n=3 HLA-A*03-restricted and n=1 HLA-A*11-restricted fusion NeoAg-specific T cell clones and retrieved the paired TCRαβ gene sequences of their T cell receptors (TCRs) using 10x single-cell sequencing. Polyclonal CD8+ T cells transduced with candidate TCRαβ gene sequences robustly upregulated TNFα after coculture with HLA+/Fusion+ target cells but not HLA−/Fusion+ or HLA+/Fusion− control cells. Further, T cells expressing candidate TCRs, but not viral-protein-specific TCRs, lysed HLA+ DSRCT cells in vitro and controlled established DSRCT tumors in vivo. Finally, we discovered that one TCR was capable of cross HLA allele fusion NeoAg recognition and could lyse both HLA-A*03+ and -A*11+ DSRCT cells. These findings imply that a single TCR therapeutic could cover >36% of North American DSRCT patients.Collectively, our data establish for the first time that DSRCT cells present a junction-spanning fusion-derived neoantigen in the context of two prevalent HLA alleles that may be therapeutically targeted using TCR gene therapy. These data lay the foundation for first-in-human clinical translation of a T-cell based therapy targeting EWSR1-WT1. More broadly, these findings establish proof-of-principle that recurrent fusion proteins are an actionable source of immunogenic public NeoAgs, providing a framework for developing targeted immunotherapies for other fusion-driven malignancies. Citation Format: Lauren Banks, Hannah Arkin, Smita Chandran, Emily Slotkin, Madelyn Espinosa-Cotton, Neerav Shukla, Luc Morris, Marc Ladanyi, Andrew Kung, Martin Klatt, Christopher Klebanoff. Defining and therapeutically targeting a fusion-derived public neoantigen in desmoplastic small round cell tumor using T cell receptor gene therapy [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 6.

Abstract 3612: Preclinical & clinical activity of autologous mRNA engineered chimeric antigen receptor monocytes for targeted cancer immunotherapy

Abstract Introduction: The tumor microenvironment (TME) is a dynamic and multifaceted system that comprises largely myeloid lineage immune cells including neutrophils, macrophages, dendritic cells and monocytes. When activated, these cells are can effectively infiltrate TME and orchestrate anti-tumor immune response. Reprogramming myeloid cells by arming them with a tumor specific chimeric antigen receptor (CAR) presents an attractive strategy to overcome current limitations in solid tumor treatment. In this study, we present the isolation and mRNA-based engineering of monocytes with chimeric antigen receptors (CARs), followed by their in vivo application for cancer treatment in rodent models and in human T cell lymphoma patients. Results: Engineered monocytes demonstrated the abilities to infiltrate the TME, undergo activation, and differentiate into macrophages and dendritic cells. Upon CAR activation, these reprogrammed myeloid cells utilized both direct and indirect mechanisms to eliminate tumor cells. This included direct tumor cell killing through phagocytosis and TNF-associated mechanisms. Furthermore, engineered monocytes exhibited the capacity to recruit natural killer (NK) cells and T cells to the TME. In the case of T cells, these engineered myeloid cells facilitated the presentation of neoantigens to T cells and stimulate an adaptive immune response. In patients with T cell lymphoma, treatment with engineered monocytes expressing a CAR targeting CD5 exhibited a favorable safety profile and was associated with TME remodeling, expansion of novel T cell clones, and promising survival outcomes. Conclusions: These findings underscore the potential of reprogrammed myeloid cells as a novel avenue for cancer immunotherapy, offering hope for improved treatments and outcomes in the fight against cancer. Citation Format: Yuxiao Wang, Michele Gerber, Michael Gorgievski, Josephine D'Alessandro, Neha Diwanji, Ronald Vale, Siddhartha Mukherjee, Daniel Getts. Preclinical & clinical activity of autologous mRNA engineered chimeric antigen receptor monocytes for targeted 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 3612.

Abstract 3607: Case study: Efficacy and persistence of autologous T cell therapy targeting SLC45A2 in uveal melanoma

Abstract Background: Metastatic uveal melanoma (UM) is an aggressive cancer, with a 1-year overall survival of < 50%. While the bispecific T-cell engager tabentafusp is approved for HLA-A2+ patients with gp100+ UM, there are limited treatment options for patients who do not express HLA-A2. We present a strategy and proof-of-concept for designing and manufacturing a tumor-selective endogenous T-cell therapy (ETC) for a patient with metastatic UM. Methods: PBMC were collected by apheresis in 2013 upon first diagnosis with uveal melanoma; 8 years later, following progression, cryopreserved PBMC were used to generate autologous antigen-specific T cells for adoptive therapy. The validated tumor antigen SLC45A2 was found to be overexpressed in the patient’s metastatic tumor based on RNA expression profiling. Peripheral blood derived SLC45A2-specific HLA-A2402-restricted central memory CD8+ T cells were generated via a process of in vitro priming, IL-21 treatment, tetramer-guided sorting and cell expansion. Clinical response was assessed via longitudinal CT imaging and ctDNA-based MRD monitoring. Persistence of transferred T cells was measured via serial flow cytometry and RNA-sequencing of PBMCs, along with TCR and RNA sequencing of tumor tissue collected post infusion. Results: A 39 year old male received SLC45A2-specific ETC therapy and checkpoint inhibitor treatment for advanced metastatic UM (GNAQ (Q209P), BAP1 (E398*, LOF). Bulk RNAseq data from baseline biopsies were queried for known tumor-associated antigens, and SLC45A2 was expressed at high levels. The patient experienced widespread disease stabilization with minimal toxicity. SLC45A2-specific CD8+ T cells persisted in circulation up to 181 days after the first infusion and 43 days after the second infusion, ranging from 6.7% - 1.5% of total circulating CD3 T cells. T cell clones from the infusion product included the dominating TCR subclone in tumor tissue collected 6 weeks post infusion, comprising 33% of the TCRá and 26% of TCRâ population. SLC45A2-specific T cells were identified in the tumor infiltrating lymphocytes in a separate lesion collected 10 months after the first infusion. A duodenum lesion progressed during treatment, and RNAseq demonstrated reduced expression of genes associated with HLA presentation and SLC45A2 and reduced TIL infiltration, suggesting tissue-specific immune editing of the tumor cell population. Conclusions: 1. Tumor-reactive antigen-specific T cells can be isolated and expanded for adoptive therapy using PBMCs cryopreserved for > 8 years. 2. Following infusion, peripheral blood and tumor profiling support the persistence of transferred T cells in a patient with metastatic uveal melanoma. 3. Disease stabilization in aggressive metastatic UM was achieved with minimal toxicity. Overall, our study provides evidence and rationale for utilizing autologous antigen-specific T cells for treating rare cancers. Citation Format: Shailbala Singh, Esther Ryu, Katie M. Campbell, Amber Smith, Suzanne Phillips, Luisa Soto, Ivy Lai, Gregory Lizee, Benjamin Vincent, Marshall Thompson, William Hoos, Sapna Patel, Cassian Yee. Case study: Efficacy and persistence of autologous T cell therapy targeting SLC45A2 in uveal 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 3607.

Abstract 5373: Decoding the role of intrinsic pancreatic cellular signaling in shaping the immunosuppressive tumor microenvironment

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) has the highest mortality rate among major cancers, with over 50% of patients having liver metastases at diagnosis. Conventional T-cell-based immunotherapies are ineffective against PDAC liver metastases due to the intricate hepatic tumor microenvironment (TME) that hinders effective immune responses. Thus, it is vital to promote the influx of cytotoxic lymphocytes and prime antitumor immunity. PDAC cells exhibit plasticity and intrinsic cellular heterogeneity, leading to varying immune cell infiltrates and immune responses. Concurrently, early metastases to the liver create an immunosuppressive environment. Our study employs multiple PDAC models, originating from a congenic array of distinct PDAC cell clone tumors with varying degrees of T cell infiltration to delineate the signaling pathways that lead to immunosuppression in the pancreas and liver. Methods: The compendium of congenic PDAC murine cell clones mirrors immune heterogeneity observed in tumors, spanning from low to high T cell infiltration. To overcome a scarcity of tumor-specific neoepitopes in PDAC, we engineered PDAC cell clones expressing chicken ovalbumin (OVA) for antigen-specific T and B cell responses. By subcutaneous and intraportal vein injection of PDAC cell clones into mice, we induce primary pancreatic and metastatic liver tumors to explore immune phenotypes and assess anti-tumor adaptive immune responses, including myeloid and lymphoid cell subsets. Results: In vivo engraftment of PDAC clones showed varied CD4+/CD8+ T cells and polymorphonuclear myeloid-derived suppressor cells, accentuated with immunogenic OVA antigen expression. While all OVA+ PDAC lines elicited antigen-specific immune responses, only ‘TIL high’ tumors were eradicated, while ‘TIL low’ clones persisted in vivo. Additionally, ‘TIL low’ clones formed liver metastases upon intraportal injection, despite OVA expression. RNAseq unveiled differential expression in IL-1 family cytokines and receptors, chemokine-like factor gene superfamily, parathyroid hormone relevant function and metabolism. Current investigations include altering these pathways to re-program the tumor microenvironment and induce local immune suppression. Conclusion: Using diverse PDAC models, we created tumors with immune heterogeneity and altered transcriptional profiles. We identified validated differentially expressed immune altering cytokines, such as CXCL1 and CSF3, and potential novel IL-1 family genes and parathyroid signaling genes. The altered TME conferred protection against tumor antigen-specific immunity in certain clones, both in subcutaneous and liver metastasis models. Ongoing studies will assess the impact of these genes in the distinct environments, offering avenues for immunotherapeutic strategies targeting pancreatic cancer liver metastasis. Citation Format: Bushangqing Liu, Ethan Agritelley, Daniel Nussbaum, Junping Wei, Gangjun Lei, Melissa Gajda, Zachary Hartman. Decoding the role of intrinsic pancreatic cellular signaling in shaping the immunosuppressive tumor microenvironment [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 5373.

Abstract 5216: Peripheral T cell receptor repertoire diversity is associated with outcome in bladder cancer

Abstract Bladder cancer is the sixth most common cancer overall, and treatment often involves removal of the bladder, which comes with a significant reduction in quality of life. Within this cancer type, an easily applicable prognostic biomarker may have clinical utility, potentially stratifying patients into bladder-sparing treatments. Expansion of T cell populations targeting cancer-specific neoantigens is an early response to malignancy. To investigate if the T cell receptor (TCR) repertoire could serve as a biomarker for cancer progression, we analyzed the TCR landscape in a cohort of 119 patients with muscle-invasive bladder cancer, treated with neoadjuvant chemotherapy before undergoing radical cystectomy. Peripheral and tumor TCR repertoires were produced using amplicon-based sequencing of the TCR beta chain. Additionally, T cell fraction was determined from whole exome sequencing data using TcellExTRECT, and latent viral DNA was investigated in plasma whole genome sequencing data using Kraken2. Antigen targets were estimated using GLIPH2. To explore the T cell repertoire subtypes, single-cell sequencing was performed on four fresh blood samples. In pre-treatment peripheral blood, low-diversity TCR repertoires were associated with worse survival (HR=2.3, p=0.024). Particularly poor outcome was observed in a subset of patients with both low TCR diversity and low fraction of circulating T cells (HR=4.7, p=5e-4). Low-diversity repertoires were dominated by expanded T cell clones. TCR target annotation revealed that expanded T cell clones disproportionately targeted latent viral infections (p=2e-13), and cytomegalovirus DNA detection was strongly associated with decreased TCR diversity (p=5e-5). Additionally, tumor TCR sequencing revealed that expanded clones were rarely found in the tumor. Single-cell sequencing of peripheral blood found that most expanded clones consisted of cytotoxic T cells, while non-expanded clones mostly consisted of naive T cells. This indicates that low TCR diversity may represent a contraction of the naive T cell compartment, resulting in reduced immune competence. Finally, analysis of patient-matched longitudinal samples revealed that chemotherapy and cystectomy reduced TCR diversity in patients with high pre-treatment diversity (p=0.001), indicating that treatment negatively affected the immune system in the most immune-competent patients. Our results suggest that both low TCR diversity and low T cell fraction represent decreased immune competency. This could be associated with an elevated risk of progression due to a reduced ability to control cancer growth and limit systemic cancer cell dissemination. These findings underline that immune health is an important factor during malignant disease, even when patients are not treated with immunotherapies. Therefore, improving immune health could be a potential future goal for cancer treatment and prevention. Citation Format: Asbjørn Kjær, Nanna Kristjánsdóttir, Iver Nordentoft, Randi Istrup Juul, Karin Birkenkamp-Demtröder, Johanne Ahrenfeldt, Darren Hodgson, Christopher Abbosh, Hugo JWL Aerts, Mads Agerbæk, Jørgen Bjerggaard Jensen, Nicolai J Birkbak, Lars Dyrskjøt. Peripheral T cell receptor repertoire diversity is associated with outcome in bladder 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 5216.

Abstract 288: Middle-aged murine models of triple negative breast cancer (TNBC) show significant differences in tumor immune and stromal environments when compared to classic 6-8 week old models; Challenges and opportunities for preclinical efficacy studies

Abstract The immune system orchestra suffer a deficit of function during aging, and the incidence of the large majority of cancer types is significantly increased in elderly humans. Although BC can occur in young women, it is way more common in middle-age and elderly women. There is evidence that a tonic immune system is pivotal for the success of therapies aimed at awakening a dormant or exhausted immunological response against cancer cells by mean of checkpoint inhibitors (CI). However, rodent models of cancers are currently using very young mice of a few weeks of age, which have a fully functional and tonic immune system and thymus and thus might be poorly representative of adult human cancer patients. We have recently reported that that a triple therapy (TT) involving antigen-presenting cell activation by vinca alkaloids and the generation of new TCF1+ stem cell-like T cell (scT) clones by an alkylating agent can significantly improve the efficacy of the CI anti-PD-1 in models of cancer known to be otherwise CI-resistant such as TNBC and lymphoma (Falvo et al, Cancer Res 2021; Orecchioni et al, JCM 2023). TT effect was due to T cells, as it was abrogated by their in vivo depletion. In the present study we investigated differences in TNBC growth kinetics, TT preclinical activity and tumor microenvironment (TME, including intratumoral immune and stroma cells) in young (6-8w, representative of a 6y old human) versus adult (12m, representative of 40y humans) mice. Models included 4T1 and EMT6 TNBC cells, the former generating a mostly lymphoid TME and the latter generating a mostly myeloid TME. In both models, TT efficacy was similar in young and in adult mice, as the treatment abrogated TNBC local and metastatic growth. CD8+ (but not CD4+) scTs, likely crucial players in TT efficacy, were only slightly reduced in adult mice in spite of age-related thymus involution. This notwithstanding, single cell RNA (10x), IHC and flow cytometry analyses of immune (CD45+EPCAM-) and stroma (CD45-EPCAM-) cell populations indicated major differences in the TME of young vs adult mice. Adults had significantly less CD4+ scTs, B naïve and NK cells and significantly increased memory B cells. TME matrix CAF were skewed in young, while pro-inflammatory stromal populations and myofibroblasts were skewed in adults. Matrix CAFs down regulated a signature involved in different ECM-remodeling abilities, and up regulated metabolic and hypoxic pathways. Expression of genes encoding for glycoproteins, basement membrane components, and collagens were also upregulated. Our data indicate profound differences between young and adult mice immune and stromal TMEs that should be taken into consideration when selecting the age of mice to be used in preclinical efficacy studies in orthotopic immune competent mice. Citation Format: Paolo Falvo, Stephan Gruener, Stefania Orecchioni, Giovanna Talarico, Giulia Bravetti, Giulia Mitola, Federica Pisati, Iros Barozzi, Francesco Bertolini. Middle-aged murine models of triple negative breast cancer (TNBC) show significant differences in tumor immune and stromal environments when compared to classic 6-8 week old models; Challenges and opportunities for preclinical efficacy studies [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 288.

Abstract 1609: Inferring the T cell repertoire dynamics in non-small cell lung cancer metastases

Abstract Non-small cell lung cancer (NSCLC) is a highly complex disease, characterized by extensive genomic heterogeneity and dynamic evolution under therapeutic pressure. This evolution can lead to alterations in the antigens expressed by cancer cells, thereby influencing the T cell repertoire (TCR) as T cells expand in response to foreign antigens. Despite the central role of TCR in cancer progression and treatment response, only few studies have investigated the temporal and spatial changes in the TCR repertoire. In this study, we delve into the role of the TCR repertoire in metastatic progression in NSCLC. We conducted TCR sequencing of multiregion primary tumors, normal-adjacent tissues, and post-mortem metastases sampled from a cohort of 22 patients enrolled in the TRACERx and PEACE studies. Our findings reveal that primary tumor regions and normal-adjacent tissues exhibit similar fractions of expanded clonotypes. However, a higher proportion of expanded intratumoral TCRs were privately expanded in the tumor samples, suggesting a unique TCR landscape within the tumor microenvironment. The TCR repertoire across multiregion primary tumor samples was largely homogenous, with most expanded clonotypes shared across at least two regions. However, only a small fraction of these clonotypes were tracked in metastases, indicating a significant shift in the TCR repertoire during metastatic progression. Notably, the expanded clonotypes that persisted over time from early to late stage disease were significantly enriched for clonotypes ubiquitously expanded in the primary tumor across all regions. This was not shown to be associated with an increased likelihood of generation via VDJ recombination, suggesting a tumor-specific immune response. The expanded TCR repertoire in the postmortem metastases clustered mainly by anatomical site, suggesting an immune response driven by tissue-resident T cells. Moreover, we found a significant positive correlation between repertoire dissimilarity and genomic distance, suggesting that T cell clones track with tumor clones across spatial sites within patients. Our study demonstrates the significant spatiotemporal dynamics of the TCR repertoire during the metastatic progression of NSCLC, orchestrated by both tissue-resident T cells and the genomic evolutionary trajectory of tumors. Such an exploration could provide valuable insights to inform future strategies for immunotherapy treatments and enhance clinical monitoring of patients. Citation Format: Corentin Richard, Sonya Hessey, Cristina Naceur-Lombardelli, Selvaraju Veeriah, Gayathri Nageswaran, Crispin Hiley, Sergio Quezada, Benny Chain, TRACERx and PEACE Consortia, Charles Swanton, Mariam Jamal-Hanjani. Inferring the T cell repertoire dynamics in non-small cell lung cancer metastases [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 1609.

Abstract 2012: Extrachromosomal DNA promotes drug resistance in pancreatic ductal adenocarcinoma cells

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related deaths in Western Countries and has been predicted to become the second leading cause of cancer-related deaths by 2030. Difficulties in early detection as well as strong chemoresistance of the disease prevent the successful treatment of PDAC patients. Although we have previously identified CYP3A5 as a mediator of paclitaxel resistance, further targets remain elusive. Thus, we set out to identify these CYP3A5-independent mechanisms which could lead to the identification of novel biomarkers and drug targets to improve PDAC treatment. For this project, pancreatic cancer cell lines were derived from treatment-naive PDAC samples and exposed to increasing paclitaxel concentrations to induce resistance. The cells were characterized on a genomic and transcriptomic level using short-read sequencing as well as optical mapping to characterize potential candidate genes in vitro. In our results, multi-drug resistance protein 1 (ABCB1) was highly upregulated in our differential gene expression analysis and confirmed as a CYP3A5-independent mediator of acquired paclitaxel resistance. Its overexpression was mediated by extrachromosomal DNA (ecDNA) amplifications upon drug treatment. These circular DNAs were characterized by short-read sequencing as well as long-read optical mapping, which revealed the structures of the most abundant molecules. Furthermore, we investigated the biogenesis of the ecDNA. Current models propose different events such as chromothripsis or breakage-fusion-bridge cycles to initiate ecDNA formation, however, knowledge about the underlying mechanisms remains limited. To study the ecDNA dynamics, we generated ecDNA-negative cell clones from a paclitaxel resistant PDAC cell line. Interestingly, our clonal cell population appears to show the capacity for ecDNA de novo generation and quickly adapts to changing selective pressure such as therapy. This finding might unveil new insights into the triggers of ecDNA formation and its dynamic regulation. In conclusion, our results suggest the clinical relevance of ABCB1 as a mediator of paclitaxel resistance in PDAC and we currently validate our findings in patient samples. However, ABCB1 inhibition is associated with severe side effects. Instead, the regulatory pathways associated with enhanced ABCB1 expression and the formation of ecDNAs might provide therapeutic potential. Additionally, the characterization of ecDNA de novo generation might unveil new insights into how cancer cells adapt to changing selective pressures. Citation Format: Tim Vorberg, Manuel Reitberger, Bernardo Rodriguez-Martin, Maja Starostecka, Ornella Kossi, Vanessa Vogel, Jan Korbel, Andreas Trumpp, Martin Sprick. Extrachromosomal DNA promotes drug resistance in pancreatic ductal adenocarcinoma 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 2012.

Abstract 7508: Distribution prophecy of circulating tumor cell clusters in CTC populace patients of epithelial cancers

Abstract Background: Role of CTCs in metastatic cancers to predict the % prediction of overall survival has been well-established. The effectiveness of three- or six-months adjuvant therapy in colorectal cancer estimation showed association of CTCs with the emergence of resistant cell clones. The presence of CTCs with clusters indicates an aggressiveness of the epithelial cancers. However, the presence of CTC clusters has not been evaluated in large populations. Here, we demonstrate the distribution prophecy of CTCs and CTC clusters in epithelial cancer patients. Methods: Retrospectively, 3458 patients' blood sample was analyzed for the presence and distribution of CTCs and CTC clusters using DCGI approved OncoDiscover platform having immunomagnetic multicomponent system mediated by anti EpCAM antibody. 1.5 mL of peripheral blood was analyzed to capture cells and clusters from Head & Neck, breast, and lung cancer patients. Earlier the sensitivity, specificity and accuracy of OncoDiscover assay was presented. CTCs and clusters were identified with CK 18 +ve, DAPI + ve and CD45 -ve staining using automated motorized fluorescence microscopy. CTCs clusters were defined by the presence of two or more CTCs bound together. Results: Out of 3458 epithelial cancer patients, 65.52 % patients showed the distribution of CTCs ~ 2262 (CTC numbers varied from 1-9/1.5 mL), while 7.54% patients showed CTC clusters (261 clusters). Total number of captured CTCs and clusters were 19345 (mean CTCs and cluster distribution was 5.59), while CTC were predominantly in 19037 numbers (98.41%) and clusters were 308 (1.59 %). Highest number of CTS were observed in HNC (52.98%) and breast cancers (22.75%), followed by lung cancer (5.65%). While, prophecy clusters were observed in breast cancers (26.95%), followed by lung (16.23%). Conclusions: The frequency and distribution of CTCs and CTC clusters was evaluated in epithelial cancers. Patients with CTC alone and patients having CTCs as well CTC clusters represent more aggressive disease and the progression of disease. The effectiveness of adjuvant therapy in epithelial cancers can be estimated with CTC and cluster for association of treatment outmoded with an emergence of resistant cell clones. Citation Format: Jayant Khandare, Gourishankar Aland, Ganesh Khutale, Saloni Andhari, Prathamesh Patil, Meghna Garbhe, Manoj Dongare, Tanvi Deshpande, Vikas Jadhav, Nirmal Raut, Gowhar Shafi, Atul Bharde, Aravindan Vasudevan, Sreeja Jayant. Distribution prophecy of circulating tumor cell clusters in CTC populace patients of epithelial cancers [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 7508.

Abstract 2505: Immune dynamics and response predictors to regorafenib, ipilimumab, and nivolumab (RIN) treatment in chemotherapy resistant microsatellite stable (MSS) metastatic colorectal cancer (mCRC)

Abstract Background: In our previous study, RIN therapy in MSS mCRC patients, excluding those with liver metastases, yielded a notable 36.4% objective response rate. RIN treatment was observed to remodel the local tumor microenvironment by enhancing immune infiltration, especially in responders. Systemic immunity, as assessed through peripheral blood analysis, showed that responders had lower baseline immune activity, which increased markedly post-treatment. Patients with liver metastases demonstrated a reduced CD4/CD8 T cell ratio, indicative of immunosenescence. Methods: Building on our prior research, we analyzed blood samples from 29 chemotherapy-resistant MSS mCRC patients undergoing RIN therapy, collected at baseline and after two consecutive treatment cycles. Two 28-marker spectral flow cytometry panels were used to assess immune senescence and cytokine production in lymphocytes. Additionally, T cell receptor repertoires and transcriptional profiles were analyzed using RNA sequencing from sorted non-naïve T cells. Results: The study unveiled distinct immunological profiles in MSS mCRC patient responders vs non-responders to RIN treatment. Responders demonstrated increased numbers of newly expanding CD8 T cell clones on-treatment, indicative of an active immune responses. In contrast, non-responders displayed evidence of increased DNA damage in circulating lymphocytes (T, B, and NK cells), as marked by elevated γ-H2AX levels. We also identified divergent cytokine production profiles patterns at baseline: T cells in non-responders demonstrated increased capacity for production of IL-2, IL-10, IL-4/-13, and IL-22, while production of IFN-γ in both T cells and NK cells correlated with improved outcomes. Notably, patients with liver metastases exhibited greater frequencies of senescent T cells, characterized by increased expression of senescence markers (SA-βGal, CD57, Granzyme B/K) and a reduction in CD27 and CD28 in CD4 T cells, along with an accumulation of terminally differentiated CD8 T cells both pre- and post-treatment. Additionally, RNA sequencing revealed an upregulation of FOXO1 related genes in non-naive T cells of responder patients, which is consistent with its important role for this pathway in attenuating senescence and maintenance of stem-like properties in T cells. Conclusions: The effectiveness of RIN therapy is associated with baseline functional potential of circulating T cells and an on-treatment expansion of T cell clonotypes. Pre-existing and persistent features of senescence and DNA damage in circulating lymphocytes may be a major barrier to RIN treatment efficacy in MSS colorectal cancer and should be validated further in future studies. Citation Format: Jian Ye, Chongkai Wang, Colt Egelston, Weihua Guo, Peter Lee, Marwan Fakih. Immune dynamics and response predictors to regorafenib, ipilimumab, and nivolumab (RIN) treatment in chemotherapy resistant microsatellite stable (MSS) metastatic colorectal cancer (mCRC) [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 2505.

Abstract 2816: Comparison of MB-49_luc bladder carcinoma cell clones in the orthotopic superficial bladder tumor model in C57BL/6 female mice

Abstract In preclinical research, cell inoculation via bladder wall injection is a standard for studying invasive bladder cancer into the bladder muscle wall. However, a subset of patients presents with non-muscle invasive (superficial) disease. The standard of care for these patients is excision coupled with BCG treatment via catheterization. There is a need to further establish mouse models of cell inoculation via bladder catheterization for early drug development. While the injection places cells into the bladder wall, catheterization coats the inside of the bladder by first instilling Poly-L-Lysine. After instilling Poly-L-Lysine, instillation of luciferase-tagged cell suspension occurs. MB49-luc cell lines were generated to determine the optimal cell lines for use in analyzing treatments for superficial bladder carcinoma. MB49-luc cells display varying degrees of luciferase activity and growth in vitro. A subset of cell lines were selected for further analysis in vivo, via bioluminescent imaging, survival analysis, flow cytometry and necropsy. The data provides a preclinical reference for the selection of a cell line for analysis of new drug candidates in C57BL/6 female mice inoculated via bladder catheterization. Citation Format: Mollie McArthur, Melissa Tran, Aliccia Koznecki, Helen Ketteringham, Corrine Silvio, Shannan Wenzel, Cheryl Davis, Shorena Nadaraia-Hoke, Chris Holding, Logan Salem, Victoria Caruso, Ben Hoerner, Madison Spencer, Marcus Josey, Alexa Tannu. Comparison of MB-49_luc bladder carcinoma cell clones in the orthotopic superficial bladder tumor model in C57BL/6 female mice [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 2816.

Abstract 3875: Glioblastoma mutational profiles drive cancer cell signaling and immune evasion

Abstract Glioblastoma multiforme (GBM) is the most common malignant brain tumor in adults with a median survival below two years. Characterization of GBM through gene expression profiling and DNA sequencing has identified disease subgroups and commonly altered genes and pathways, including alterations in the genes encoding neurofibromin-1 (NF1) and the epidermal growth factor receptor (EGFR). NF1 and EGFR are involved in receptor tyrosine kinase (RTK), RAS/MEK/ERK, and PI3K signaling, and together, are genetically altered in over 60% of adult GBMs. Interestingly, NF1 and EGFR alterations in GBM are almost always mutually exclusive. Here, we designed a multimodal approach integrating spatial proteomics, transcriptomics, and genomics to measure cell composition, immune cell function, cancer cell signaling, cellular spatial organization, gene expression, transcriptional subtypes, and genome alterations in 80 NF1 and EGFR altered human GBMs with extensively curated treatment and survival data. We quantified the spatial expression of 42 proteins in over 31 million single cells measuring RTK/RAS/PI3K and Rb signaling and features of the TME, including 23 cell types covering tumor cells, immune cells, and brain resident cells. In addition to tumor genotype labels, we classified each GBM tumor by its transcriptional subtype (i.e., mesenchymal, classical, or proneural). We identified genotype-phenotype associations in GBM including hyperactive RAS signaling cellular niches, a macrophage-rich TME, and an epithelial-mesenchymal signature in NF1 altered tumors and hyperactive RTK signaling and an immune desert TME in EGFR amplified tumors. Furthermore, we observed spatial heterogeneity in cancer cell signaling patterns suggestive of the presence of different tumor cell clones within different regions of each GBM tumor. Together, we identify several genotype-associated features of GBMs, reinforcing the value of integrating spatial multi-omic data for generation of genotype-driven therapeutic hypotheses, with implications for GBM genotype-based therapeutic stratification. Citation Format: Maryam Pourmaleki, Brian D. Greenstein, Caitlin J. Jones, Subhiksha Nandakumar, Daniel A. Navarrete, Smrutiben Mehta, Carl Campos, Travis J. Hollmann, Nicholas D. Socci, Tejus Bale, Sohrab P. Shah, Ingo K. Mellinghoff. Glioblastoma mutational profiles drive cancer cell signaling and immune evasion [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 3875.

Abstract 1151: Reconstruction of the spatial ecosystem of glioblastoma reveals relationships between tumor cell states and microenvironment

Abstract Glioblastoma multiforme (GBM) is the most aggressive form of primary brain tumor, with no curative treatment options. Multiple studies have characterized at single cell resolution the GBM as being composed of transcriptional cell states interconnected with components in the tumor immune microenvironment (TME). Our group proposed and validated the first single cell guided functional classification of GBM in four tumor-intrinsic cell states which informed clinical outcome and delivered therapeutic options. However, single cell technologies are unable to unravel the spatial relationships among the cell states of GBM and between GBM cell states and TME. Spatially resolved transcriptomic technologies are emerging as powerful tools to reconstruct the spatial architecture of a tissue. We performed spatial transcriptomics of multicellular regions of interest (ROI) in 6 primary IDH wild-type GBM and 2 recurrent GBM with both CosMx Spatial Molecular Imager, which analyzes 1,000 RNA probes and 64 proteins at single cell resolution, and GeoMx Digital Spatial Profiler which profiles the whole transcriptome (~18,000 genes) at ROI resolution. The development of computational tools aimed to integrate spatial proximity and CosMx derived single-cell transcriptomics revealed spatial segregation of the tumor cell clones and cellular states and highlighted recurrent patterns of cell states, distinct TME cell types associated with coherent histopathological features across multiple samples. The development of a spatial informed intercellular communication algorithm and the reconstruction of ligand-receptor-target networks will allow the discovery of tumor cell states-TME cross-talks and the biological signaling regulated by these interactions that are driving the heterogeneity of GBM and therefore potentially therapeutically targetable. Analysis of matched regions of interest profiled by GeoMx and spatial proteomics with CosMx further cross-validated the spatial ecosystem of glioblastoma as reconstructed at single-cell resolution. Our studies established a scalable approach to resolve the transcriptional heterogeneity of GBM and reconstruct the architecture of GBM cell states and tumor microenvironment. Citation Format: Bruno Adabbo, Simona Migliozzi, Luciano Garofano, Fulvio D'Angelo, Pedro Davila, Sakir H. Gultekin, Daniel Bilbao Cortes, Benjamin Currall, Sion L. Williams, Marc Sanson, Franck Bielle, Anna Luisa Di Stefano, Michele Ceccarelli, Anna Lasorella, Antonio Iavarone. Reconstruction of the spatial ecosystem of glioblastoma reveals relationships between tumor cell states and microenvironment [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 1151.

Abstract 6637: The Haemophilus influenzae vaccine mitigates pancreatic tumor progression and lowers immunoregulatory cell levels in the tumor microenvironment

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease projected to become the second leading cause of cancer deaths by 2030. First-line chemotherapies gemcitabine and FOLFIRINOX provide little therapeutic benefit and are accompanied by severe adverse toxicities, precluding long-term treatment. In addition, PDAC is notoriously refractory to checkpoint inhibitor immunotherapies, due to poor immunogenicity and a tumor microenvironment dominated by suppressive cell types. Thus, there is an unmet need for innovative, immune-based strategies to combat PDAC. A previous study utilized engineered bacteria to effectively kill PDAC tumor cells by directly delivering immunogenic tetanus toxoid to the tumor. Given the potential toxicity in using live bacteria, our group utilized a less toxic alternative, an FDA-approved Haemophilus influenzae type b vaccine (HibVx) also containing a tetanus toxoid component. To determine the antitumor potential of HibVx, our group used a physiologically relevant murine model, low T cell clone murine PDAC tumor model 641c95 and clinically relevant KPC mice model for PDAC. After tumors were established, animals received three consecutive daily treatments of HibVx via intraperitoneal injection. HibVx-treated animals experienced a dramatic reduction in tumor growth compared to PBS-treated controls (p<0.001). Given that tetanus toxoid is highly immunogenic in nature, changes in intratumoral immune cell populations following HibVx treatments were of great interest. Using flow cytometry analysis, HibVx-treated tumors had a significant increase in natural killer cells compared to control tumors (p<0.05). In addition, HibVx affected myeloid-derived suppressor cell populations (MDSCs), which are heavily implicated in the suppressive nature of PDAC tumors. HibVx also significantly decreased MDSCs within the tumor (p<0.05). In all, these findings position HibVx as an effective immunostimulatory agent that can be used as an alternative to live bacteria-based therapy for the treatment of PDAC. Citation Format: Eileena F. Giurini, Sam G. Pappas, Kajal H. Gupta. The Haemophilus influenzae vaccine mitigates pancreatic tumor progression and lowers immunoregulatory cell levels in the tumor microenvironment [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 6637.

Abstract 5635: TPM4 overexpression promotes colon epithelial cell tumorigenesis in vitro and correlates with human colon tumor progression in vivo

Abstract Because colon cancer still exerts a heavy burden on human health, we are interested in identifying very early events in colon epithelial cell tumorigenesis in order to develop strategies to treat and possibly prevent colon carcinogenesis. We hypothesize that aberrant expression of genes involved in crypt-luminal colon epithelial cell migration, needed for proliferative, undifferentiated stem cells at the crypt bottom to mature into growth arrested, mature effector cells near the lumen, may disrupt normal differentiation and initiate events that can trigger the transition from a normal to premalignant state in colon epithelial cells. Forced upregulation of tropomyosin 4 (TPM4), an actin-binding protein that exerts many effects on contractility and migration, prevents certain aspects of Caco2 maturation induced by contact inhibition of growth, including increased expression of the digestive enzyme sucrose isomaltase and glutathione S-transferase alpha 1. Furthermore, TPM4.2-overexpressing cells exhibit numerous morphological abnormalities. Compared to untransfected Caco2 cells and empty-vector stable transfectant controls, TPM4.2-overexpressing Caco2 cell clones elaborate aberrant thin membrane protrusions and expanded membrane ruffles. Particularly striking are defective maintenance of dome structures at middle (day 14) and late (day 21) time points of induced differentiation in TPM4.2-overeexpressing clones. We further hypothesize that TPM4 is overexpressed in human colon tumors, particularly at early stages of tumorigenesis. In order to test this hypothesis, we examined TPM4 RNA expression in datasets obtained from human colon tissue at premalignant as well as tumorigenic stages. TPM4 trends toward overexpression in premalignant, relative to normal, human colon tissue (uninvolved mucosa from patients with familial adenomatous polyposis, or FAP) and is significantly overexpressed in adenocarcinoma tissue relative to normal controls. Interestingly, TPM4 overexpression may be more pronounced at earlier, rather than later, stages of adenocarcinoma. Our results suggest that aberrant TPM4 overexpression in colon epithelial cells can promote adoption of a tumorigenic state. Certain aspects of Caco2 cell maturation are disrupted by forced TPM4 overexpression during induced differentiation, and TPM4 overexpression correlates with early stages of colon tumorigenesis. Misregulation of TPM4 gene expression may therefore represent a critical molecular event that can block normal differentiation and induce early events in colon epithelial cell tumorigenesis. TPM4 expression level may therefore prove to be a useful biomarker that can, along with other diagnostics, help to determine tumorigenic progression in human colon tissue and to develop novel strategies to prevent colon cancer and treat it at early stages. Citation Format: Giulio Ferrero, Barbara Pardini, Alessio Naccarati, Michael Papetti. TPM4 overexpression promotes colon epithelial cell tumorigenesis in vitro and correlates with human colon tumor progression in vivo [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 5635.

Identification of apolipoprotein B-reactive CDR3 motifs allows tracking of atherosclerosis-related memory CD4+T cells in multiple donors.

Atherosclerosis is a major pathological condition that underlies many cardiovascular diseases (CVDs). Its etiology involves breach of tolerance to self, leading to clonal expansion of autoreactive apolipoprotein B (APOB)-reactive CD4+T cells that correlates with clinical CVD. The T-cell receptor (TCR) sequences that mediate activation of APOB-specific CD4+T cells are unknown. In a previous study, we had profiled the hypervariable complementarity determining region 3 (CDR3) of CD4+T cells that respond to six immunodominant APOB epitopes in most donors. Here, we comprehensively analyze this dataset of 149,065 APOB-reactive and 199,211 non-reactive control CDR3s from six human leukocyte antigen-typed donors. We identified 672 highly expanded (frequency threshold > 1.39E-03) clones that were significantly enriched in the APOB-reactive group as compared to the controls (log10 odds ratio ≥1, Fisher's test p < 0.01). Analysis of 114,755 naïve, 91,001 central memory (TCM) and 29,839 effector memory (TEM) CDR3 sequences from the same donors revealed that APOB+ clones can be traced to the complex repertoire of unenriched blood T cells. The fraction of APOB+ clones that overlapped with memory CDR3s ranged from 2.2% to 46% (average 16.4%). This was significantly higher than their overlap with the naïve pool, which ranged from 0.7% to 2% (average 1.36%). CDR3 motif analysis with the machine learning-based in-silico tool, GLIPHs (grouping of lymphocyte interactions by paratope hotspots), identified 532 APOB+ motifs. Analysis of naïve and memory CDR3 sequences with GLIPH revealed that ~40% (209 of 532) of these APOB+ motifs were enriched in the memory pool. Network analysis with Cytoscape revealed extensive sharing of the memory-affiliated APOB+ motifs across multiple donors. We identified six motifs that were present in TCM and TEM CDR3 sequences from >80% of the donors and were highly enriched in the APOB-reactive TCR repertoire. The identified APOB-reactive expanded CD4+T cell clones and conserved motifs can be used to annotate and track human atherosclerosis-related autoreactive CD4+T cells and measure their clonal expansion.