bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A108: Sub-clonal copy number variations between on-treatment lesions in immunotherapy resistant melanoma patients
Authors: Yang Muyi , Kolbeinsdottir Solrun , Hammarlund Katarina , Grozman Vitali , Enge Martin , Egyhazi-Brage Suzanne , Helgadottir Hildur
Published: February 2025

Metastatic melanoma is a lethal form of cancer. Immunotherapy is recommended for metastatic melanoma and known to elicit beneficial response even after disease progression per RECIST. On-treatment samples hold irreplaceable predictive value. We collected needle biopsies from the metastases of different body sites from the same patient that progressed upon PD-1 treatment. Leveraging Direct Nuclear Tagmentation and RNA sequencing (DNTR- seq), we conducted single-cell genomic analyses on melanoma metastases and jointly sequenced the transcriptomes of each single melanoma cell. After 3 months of PD-1 inhibitor treatment, single-cell DNA-seq analyses on melanoma metastases from different anatomic locations displayed distinct cancer subclones evidenced by their copy number aberrations. Joint transcriptomic analyses of the dominant genomic subclones from each body site showed converging phenotypes, under the selective pressure of immunotherapy. Our preliminary analyses of on-treatment needle biopsies shed light on the challenges of treating heterogeneous tumors and underscore the pressing need to identify an ideal denominator to reach disease control.

Citation Format: Muyi Yang, Solrun Kolbeinsdottir, Katarina Hammarlund, Vitali Grozman, Martin Enge, Suzanne Egyhazi-Brage, Hildur Helgadottir. Sub-clonal copy number variations between on-treatment lesions in immunotherapy resistant melanoma patients [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr A108.
Abstract A124: Deciphering RIOK2 as a Potential Target for Hepatocellular Carcinoma via Enhancing Tumor Immune Infiltration and experimental in vitro validation
Authors: He Jian
Published: February 2025

Background: RIOK2 is a principal transcription factor (TF) that is a key component of the pro-40S ribosomal complex in its final maturation step. But few studies have proved the rule of RIOK2 in carcinoma, especially in liver cancer. Furthermore, the relationship between RIOK2 and the prognostic potential and tumor-infiltrating immune cells of various cancers remains unclear. Methods: The clinical characteristics and mRNA expression level of RIOK2 were appraised among different databases. The relationship between RIOK2 and immunological infiltration of various types of cancer was determined via TIMER 2.0. Furthermore, RIOK2 inhibitors virtual screening was conducted from the 13633 natural compounds (L6020) and implemented secondary library construction according to the types of top results, then secondary virtual screening was conducted for 367 alkaloids. Finally, in vitro assays of RIOK2 ATPase activity assay, cell viability assays, and colony formation assay were performed to demonstrate the pharmacological potency of the screening RIOK2 inhibitors. Results: RIOK2 expression is higher in most types of tumors than in paracancerous tissues, including liver hepatocellular carcinoma (LIHC). Higher RIOK2 expression correlated with poorer OS, as well as a significant positive association between RIOK2 expression levels and infiltration levels of macrophages, neutrophils, and dendritic cells in LIHC patients. Moreover, we also found that K-252c and 2,3-Bis(3-indolylmethyl)indole are potent inhibitors of RIOK2. We have demonstrated in vitro that K-252c and 2,3-Bis(3-indolylmethyl)indole can inhibit the proliferation and clone formation of HepG2 cell lines by suppressing the expression of RIOK2. Conclusions: The findings showed that RIOK2 appears to be a promising prognostic biomarker for LIHC patients. Besides, K-252c and 2,3-Bis(3-indolylmethyl)indole may be effective therapeutic RIOK2 inhibitors for LIHC patients, providing a theoretical basis for the clinical treatment of LIHC.

Citation Format: Jian He. Deciphering RIOK2 as a Potential Target for Hepatocellular Carcinoma via Enhancing Tumor Immune Infiltration and experimental in vitro validation [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr A124.
Abstract B005: Identification of tumor-reactive TILs from lung cancer organoids co-culture through ruthenium-based proximity labeling
Authors: Hu Weilei , Bian Yifei , Zhao Zihan , Ouyang Shian , Li Jie P. , Ji Hongbin
Published: February 2025

Tumor-reactive T cells are crucial for the success of tumor-infiltrating lymphocyte (TIL) therapies. Currently, identifying tumor-reactive T cells and their corresponding TCRs typically relies on pre-characterized tumor antigens. Many solid tumors, including lung cancer, exhibit considerable heterogeneity and consequently possess diverse tumor antigenic profiles. Markers such as PD-1 and CD39 are commonly used to identify tumor-reactive TILs, yet these empirically derived markers can produce false positives or fail to capture rare tumor-reactive populations. We here used an unbiased ruthenium-based photocatalytic proximity labeling approach to do co-culture of TILs derived from lung cancer and autologous tumor organoids to identify and validate tumor-specific T cells and their TCRs in six NSCLC samples. We found that labeled TILs were significantly enriched for tumor antigen-reactive T cells, which could be readily separated from bystander T cells via flow cytometry. Single-cell TCR and RNA sequencing revealed that labeled TILs, in contrast to bystander TILs, exhibited a distinct TCR repertoire and transcriptional profile, characterized by effector cytotoxic and activation signatures with partial expression of exhausted T cell markers. We selected the top 10 CD8+ TCR clones with the highest labeling intensity and assessed the reactivity of their corresponding TCR-transduced, CD8-overexpressing Jurkat cells against autologous organoids. We identified 5 novel tumor antigen-reactive TCRs that demonstrated tumor responsiveness and these T cells displayed a mixed transcriptional profile, including hallmark markers of exhaustion. Additionally, we identified clonally expanded, cytotoxic CD4+ T cell states within the labeled TILs that could kill autologous tumors in an MHC class II-dependent and/or Fas-FasL-dependent manner. The ruthenium-based photocatalytic proximity labeling approach, which requires no gene editing, enables identification of tumor-reactive TILs and TCRs independent of specific antigen/HLA contexts. This platform, especially when combined with organoid technology, has the potential to streamline the development of personalized TIL and TCR-T cell therapies.

Citation Format: Weilei Hu, Yifei Bian, Zihan Zhao, Shian Ouyang, Jie P. Li, Hongbin Ji. Identification of tumor-reactive TILs from lung cancer organoids co-culture through ruthenium-based proximity labeling [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B005.
Abstract B007: Targeting the evolving immunopeptidome of metastatic colorectal cancer
Authors: Lee Jaeyop , Scheinberg David A , Ganesh Karuna
Published: February 2025

Chimeric antigen receptor (CAR) T cell therapies have achieved limited success in solid tumors, in part due to challenges in identifying cancer-specific targets. Investigating the immunopeptidome, peptides presented by human leukocyte antigen (HLA) class I molecules, offers an opportunity to expand the repertoire of targetable antigens. Recent findings reveal that metastatic colorectal cancer (mCRC) cells adopt a highly stereotyped fetal-like phenotype, characterized by the activation of a developmental WNT-signaling signature as a mechanism of cell-fate reprogramming. This transcriptional signature, accentuated in metastasis-initiating cells and conserved across diverse patients, is hypothesized to translate into a cancer-specific immunopeptidome. Utilizing an integrated platform, we collected and analyzed resected normal colon, primary tumor, and metastatic lesions from CRC patients, establishing patient-derived organoids (PDOs) that recapitulate CRC cell states ex vivo. Mass spectrometry profiling of PDOs from HLA-A*02:01+ patients identified peptide targets derived from fetal WNT-pathway gene states, referred to as oncofetal protein 1 (OFP1). These peptides were specific to CRC, absent in healthy tissues, and demonstrated immunogenicity through healthy donor T cell reactivity and expansion assays. To further harness these findings, we aim to systematically profile the immunopeptidome evolution from normal colon to metastatic CRC to identify conserved CRC-specific peptides for therapeutic targeting. Furthermore, we employed large-scale yeast display technology to isolate peptide-centric T cell receptor mimics (TCRms) that specifically recognize OFP1 peptides presented by HLA-A*02:01. Preliminary results demonstrate the successful isolation of OFP1-specific, HLA-A02:01-restricted TCRms, paving the way for the development of TCRm-based CAR T cells tailored for CRC therapy. This work provides the first comprehensive atlas of immunopeptidome evolution in CRC, elucidates CRC-specific intracellular molecular signatures as potential therapeutic targets, and advances the preclinical development of TCRm-engineered CAR T cells, paving the way for precision immunotherapies in metastatic CRC.

Citation Format: Jaeyop Lee, David A Scheinberg, Karuna Ganesh. Targeting the evolving immunopeptidome of metastatic colorectal cancer [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B007.
Abstract B015: Local delivery of mRNA lipid nano particles encoding an autoactivated cGAS mutant and membrane-tethered IL-12 enhances local and distal tumor control
Authors: Zhang Anli , Chen Zhijian (James)
Published: February 2025

Local cancer treatments are often effective in controlling primary tumor growth. However, the abscopal effect induced by local treatment—critical for treating metastatic tumors—is rarely achieved and particularly challenging in less immunogenic tumors. Here, we report that local administration of lipid nanoparticles (LNPs) containing mRNAs encoding an autoactivated cyclic GMP-AMP (cGAMP) synthase (cGAS) R241E mutant and membrane-tethered IL-12 (IL-12TM) induces potent local and systemic tumor control in multiple non-immunogenic murine models, including B16 and TC-1 tumors. The cGAS R241E mutant but not wild-type cGAS mRNA LNPs spontaneously produce cGAMP in vivo and predominately activate conventional DC1, enhancing innate immune sensing and inhibiting tumor growth in a host STING-dependent manner. IL-12TM mRNA LNPs synergize with cGAS R241E mRNA LNPs to promote local IFN-γ production while minimizing systemic exposure compared to soluble IL-12 mRNA LNPs. Mechanistically, combining cGAS R241E and IL-12TM mRNA LNPs (Combo) enhances dendritic cell activation and stimulates antigen-specific CD8+ T cells within the tumor, facilitating their migration to draining lymph nodes. While the multiple immune cell populations contribute to anti-tumor efficacy against local tumors, CD8+ T cells and intact IFN-γ signaling are responsible for distal tumor control. Additionally, Combo treatment synergizes with PD-L1 checkpoint blockade to further reduce distal tumor burden. Taken together, these findings demonstrate that mRNA LNP-mediated delivery of the autoactivated cGAS mutant and IL-12TM provides a safe and effective strategy for treating both primary and metastatic tumors.

Citation Format: Anli Zhang, Zhijian (James) Chen. Local delivery of mRNA lipid nano particles encoding an autoactivated cGAS mutant and membrane-tethered IL-12 enhances local and distal tumor control [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B015.
Abstract B018: Ex vivo modeling of precision immuno-oncology responses in lung cancer
Authors: Alsaed Bassel , Smolander Johannes , Linh Lin , Bobik Nina , Laitinen Hanna , Lahtinen Lilja , Räsänen Mikko , Jansouz Shadi , Peltonen Karita , Jokinen Emmi , Klievink Jay , Ainola Mari , Sutinen Eva , Saharinen Pipsa , Mustjoki Satu , Ilonen Ilkka , Haikala Heidi
Published: February 2025

Immunotherapy has transformed cancer treatment, offering promising outcomes even in previously incurable cancers. However, responses to immuno-oncology (IO) treatments remain limited, with only a fraction of patients benefiting from these therapies. This limited efficacy arises from a lack of predictive biomarkers, unknown mechanisms of immune resistance, and the complex tumor-immune interactions, making it challenging to predict which patients will benefit from these costly treatments. To address these issues, we developed a precision ex vivo platform that integrates patient-specific tumor and immune cells to study the mechanisms of antitumor immune response, predict immunotherapy outcomes, and identify effective treatments. In order to establish this, we first stimulate patient-derived immune cells with autologous tumor organoids, followed by a tumor-killing assay using the stimulated immune cells in the presence or absence of different IO combinations. Lastly, single-cell sequencing is performed across different treatment conditions to reveal changes in immune and tumor cells following their interactions. Our ex vivo model demonstrated the ability to mimic primary resistance to anti-PD-1 therapy in lung cancer, enabling the identification of individual responders to anti-PD-1 combination with chemotherapy agents. Additionally, we identified a synergistic IO-drug combination: anti-PD-1 with a Cbl-b inhibitor, which successfully overcame anti-PD-1 resistance in some patients. Moreover, interferon gamma-stimulated cytokines were predictive of combination efficacy, whereas the presence of immunosuppressive cytokines correlated with poor response. Finally, single-cell sequencing revealed immune response mechanisms and sensitivities to standard of care immunotherapies. Our findings underscore the platform's potential in tailoring immunotherapies and advancing drug development, offering new avenues for personalized cancer treatment.

Citation Format: Bassel Alsaed, Johannes Smolander, Lin Linh, Nina Bobik, Hanna Laitinen, Lilja Lahtinen, Mikko Räsänen, Shadi Jansouz, Karita Peltonen, Emmi Jokinen, Jay Klievink, Mari Ainola, Eva Sutinen, Pipsa Saharinen, Satu Mustjoki, Ilkka Ilonen, Heidi Haikala. Ex vivo modeling of precision immuno-oncology responses in lung cancer [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B018.
Abstract B022: Targeting the innate immune checkpoint TREX1 elicits antitumor immunity through tumor-intrinsic cGAS-STING signaling
Authors: Xing Cong , Yan Nan
Published: February 2025

Three-prime repair exonuclease 1 (TREX1) is the major DNase in mammalian cells that degrades cytosolic DNA to prevent activation of the cGAS-STING pathway. Genotoxic stress, DNA damage, and radiotherapy induce TREX1 expression in cancer cells, allowing them to evade innate immune activation of type I interferon (IFN-I)-mediated antitumor response. How TREX1 can be targeted for cancer immunotherapy remains elusive. Here, we show that genetic deletion of TREX1 in tumors elicits robust antitumor immunity through tumor-intrinsic cGAS-STING activation, IFN-I signaling, and recruitment of CD8+ T cells. To therapeutically target TREX1, we perform a high-throughput small-molecule inhibitor screen of TREX1 using a cell-free DNase assay. We identify two lead compounds that inhibit TREX1 DNase activity at low micromolar concentrations, induce IFN-I signaling in cancer cells, and inhibit tumor growth in mice in a type I IFN receptor-dependent manner. Additionally, TREX1 inhibitor treatment sensitizes B16-F10 melanoma to anti-PD-1 immunotherapy. We further show that Trex1 knockout cancer cells elicit systemic antitumor immunity and can be used as autologous cancer vaccines to protect against future tumor challenge and metastasis. We also establish an inducible whole-body Trex1 knockout mouse model to simulate “on-demand” systemic TREX1 inactivation in adult mice. Sustained TREX1 loss in adult mice suppresses a broad range of solid tumors and metastatic tumors. Although TREX1 deficiency is associated with severe autoimmune diseases, inducible Trex1 knockout in adult mice does not cause immune toxicity, demonstrating feasibility of an immune-safe therapeutic window. Together, our data present multiple therapeutic modalities for targeting TREX1 using small-molecule inhibitors and as an autologous cancer vaccine, as well as antitumor efficacy and immune safety, which should pave the way for developing TREX1-targeted cancer immunotherapy.

Citation Format: Cong Xing, Nan Yan. Targeting the innate immune checkpoint TREX1 elicits antitumor immunity through tumor-intrinsic cGAS-STING signaling [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B022.
Abstract B023: Enhancing the efficacy of oncolytic virus immunotherapy using eicosapentaenoic acid in preclinical cancer models
Authors: Khumo Nametso Koobotse , Volpato Milene , Errington-Mais Fiona
Published: February 2025

Introduction Despite significant advances in cancer immunotherapy, response rates remain limited and variable across patients and cancer types. Oncolytic viruses (OVs) are cancer immunotherapeutic agents, which kill cancer cells and promote an anti-tumor immune response. However, upregulation of immune evasion pathways, such as COX-2 mediated prostaglandin E2 (PGE2) signaling by cells in the tumor microenvironment (TME), including tumor associated macrophages (TAMs), can hinder their immunotherapeutic potential. This study investigated whether combining OVs with eicosapentaenoic acid (EPA), an omega-3 polyunsaturated fatty acid with anti-inflammatory properties, including inhibition of PGE2 production, could enhance OV anti-cancer activity. Methods Balb/c mice were injected with colorectal CT26 cells and treated with OV (reovirus), EPA, or a combination of both reovirus/EPA, and tumor growth was monitored. Upon sacrifice, immune cell infiltration within harvested tumors was assessed by immunohistochemistry (IHC). PGE2 and cytokine production was determined by ELISA while MTT assays were employed to measure cell growth inhibition, in vitro. Co-culture of cancer cells with human peripheral blood mononuclear cells (PBMCs) was used to generate tumor-associated macrophages (TAMs), which were then isolated by magnetic bead CD14+ cell separation Results Assessment of EPA and reovirus in vivo suggested that the combination treatment reduced tumor volume more than the single agent treatments and confirmed that EPA significantly reduced PGE2 production. The combination treatment strategy also significantly inhibited the production CXCL9 and reduced the percentage of arginase-1 positive cells, a marker of TAMs. In vitro, EPA supplementation did not alter abrogate reovirus direct oncolysis and furthermore potentially enhanced reovirus oncolysis of CT26 cells. Additionally, EPA supplementation hindered PGE2 production and significantly inhibited the in vitro generation of TAMs by 50-90%. Conclusion These results suggest that EPA could render the TME less immunosuppressive without compromising on the direct oncolytic effect of the virus, ultimately enhancing OV-based immunotherapy.

Citation Format: Nametso Koobotse Khumo, Milene Volpato, Fiona Errington-Mais. Enhancing the efficacy of oncolytic virus immunotherapy using eicosapentaenoic acid in preclinical cancer models [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B023.
Abstract B068: A novel murine model for interrogating immune response to tumor heterogeneity in non-small cell lung cancer
Authors: Oh Michael , Abascal Jensen W , Tran Linh M , Salehi-Rad Ramin , Lim Raymond J , Dumitras Camelia , Yean Cara , Xiao Sunny , Kahangi Bitta P , Crosson William P , Reyes Edgar Perez , Coleman Nalani , Rennels Austin K , Krysan Kostyantyn , Liu Bin , Dubinett Steven M
Published: February 2025

Resistance to immune checkpoint inhibitors (ICIs) represents a major barrier to effectively treating patients with NSCLC. Increased tumor heterogeneity has been linked with diminished response to ICIs, but the mechanisms underlying such an effect remain underexplored, in part due to the lack of models for studying the impact of heterogeneity. To address this issue, we have developed a novel murine model of NSCLC that utilizes clonal cell lines to modulate tumor heterogeneity. Specifically, we isolated single cells from a murine NSCLC cell line harboring 3 common driver mutations (Kras G12D Tp53 +/- Lkb1 -/- , or “KPL”). We mutagenized KPL cells with N-methyl-N-nitrosourea in order to increase the tumor mutational burden, and then isolated single cells to derive clonal cell lines. Whole exome sequencing and subsequent phylogenetic analysis of tumor mutations yielded categorization of these clones into 5 clusters. Clones within the same cluster demonstrated comparable in vivo growth kinetics and similar response to anti-PD-1 immunotherapy. These clones exhibited unique tumor immune microenvironments that did not fully correlate with genomic factors such as tumor mutation burden. Notably, heterogeneous polyclonal tumors grew more aggressively than monoclonal tumors, and they exhibited response to anti-PD-1 therapy that differed from the response seen in the component single clones. Tracking of individual clones with fluorescent proteins and mutation tracing illustrated clonal shifts induced by ICI treatment. Our results validate this system as a model of NSCLC that can modify tumor heterogeneity and provide insights into the effects of heterogeneity on ICIs and other immunotherapies.

Citation Format: Michael Oh, Jensen W Abascal, Linh M Tran, Ramin Salehi-Rad, Raymond J Lim, Camelia Dumitras, Cara Yean, Sunny Xiao, Bitta P Kahangi, William P Crosson, Edgar Perez Reyes, Nalani Coleman, Austin K Rennels, Kostyantyn Krysan, Bin Liu, Steven M Dubinett. A novel murine model for interrogating immune response to tumor heterogeneity in non-small cell lung cancer [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B068.
Abstract B083: Centrosome De-clustering as an Immune-Modulating Radiosensitizer: Implications for Enhancing RT-Induced Innate Immunity
Authors: KIM JAE SUNG
Published: February 2025

Radiotherapy (RT) increases the number of centrosomes in cancer cells, leading to centrosome clustering that supports bipolar mitosis and tumor cell proliferation. Targeting centrosome clustering has emerged as a potential strategy to enhance RT effects in breast cancer cells. However, the role of centrosome de-clustering in activating innate immunity in response to RT is still unclear. Our study demonstrates that centrosome de-clustering in irradiated cancer cells influences the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING)-mediated immune response in monocytes and macrophages after co-culture. While centrosome de-clustering heightened mitotic errors and increased cytosolic dsDNA in breast cancer cells post-irradiation, it did not directly activate the cGAS-STING pathway in the cancer cells themselves. Notably, it triggered this pathway in human monocytes and mouse macrophages following co-culture with the irradiated cancer cells. These findings provide the first evidence that centrosome de-clustering in irradiated breast cancer cells promotes innate immune activation in tumor-associated immune cells, offering insights for potential immunotherapy strategies.

Citation Format: JAE SUNG KIM. Centrosome De-clustering as an Immune-Modulating Radiosensitizer: Implications for Enhancing RT-Induced Innate Immunity [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B083.
Abstract B086: Disease-critical macrophage populations interact with stroma to modulate the tumor microenvironment
Authors: Zhong Weiwei , Ansariola Mitra , Tatman Micaela , Wester Rachel , Van Naarden Braun Kim , Biswas Shameek
Published: February 2025

Myeloid cells in the tumor microenvironment (TME) exhibit diverse functions, from pro-tumor to anti-tumor. To elucidate myeloid heterogeneity, we developed a deep-learning model to annotate 20 myeloid subtypes in single-cell data. We identified two macrophage populations, macro_SPP1 and macro_C1QC, which were pan-cancer, enriched in tumors compared to normal tissues, and linked to clinical outcomes. Higher macro_SPP1 abundance correlated with IO non-responders, pre-IO treatment, and lower inflammation, while macro_C1QC showed the opposite trends. We developed and validated gene signatures to quantify these macrophages in bulk RNAseq. Applying these signatures to TCGA and real-world data, we confirmed that macro_SPP1 was associated with worse survival and poor IO response, whereas macro_C1QC was linked to better outcomes. Tumors with chromosome 9p21 deletions had higher macro_SPP1 and fibroblast signatures, suggesting a TME influence on macrophage heterogeneity. Cell-cell communication analysis in single-cell data revealed that fibroblasts sent the strongest signals to macrophages in lung and pancreatic cancers. Fibroblast-derived ligands such as FN1 and collagens exhibited stronger signaling to macro_SPP1 than macro_C1QC, and colocalized with macro_SPP1 spatially. Conversely, macro_SPP1 sent higher total signals to other cells in the TME than macro_C1QC, with SPP1 to fibroblasts and endothelial cells being the most differentiating signal. In summary, we identified two disease-critical macrophage populations: pro-tumor macro_SPP1 and anti-tumor macro_C1QC. We found interactions between macrophages and fibroblasts as key modulators of the TME.

Citation Format: Weiwei Zhong, Mitra Ansariola, Micaela Tatman, Rachel Wester, Kim Van Naarden Braun, Shameek Biswas. Disease-critical macrophage populations interact with stroma to modulate the tumor microenvironment [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B086.
Abstract B088: Axl regulation of NK cell activity creates an immunosuppressive tumor immune microenvironment in head and neck cancer
Authors: Harmon Regan L , Kostecki Kourtney L , Iida Mari , Harris Madelyn A , Crossman Bridget E , Bruce Justine , Salgia Ravi , Wheeler Deric L
Published: February 2025

Head and neck cancer (HNC), the sixth most common cancer worldwide, utilizes many strategies to evade the immune system, including manipulation of immune cell composition in the tumor immune microenvironment (TIME). Previous studies in our laboratory have demonstrated that the receptor tyrosine kinase Axl is a crucial driver of proliferation, survival, metastasis, and therapeutic resistance in HNC. This study explores the role of tumor-bound Axl in immune evasion in HNC. Using a series of Axl CRISPR knockout (AxlKO) cell lines (MOC2-398, MOC2-399, MOC2-400) from the immunologically "cold" MOC2 mouse model of HNC, we found that Axl loss significantly delayed tumor growth in immunocompetent C57BL/6 mice. Further, Axl loss led to a marked reduction of immunosuppressive cells- including MDSCs, Tregs, B cells, and neutrophils- accompanied by an enhanced infiltration of cytotoxic immune cells such as CD8+ T cells and NK cells within the TIME. To identify the immune cell population(s) responsible for the observed tumor growth delay, AxlKO tumors were implanted in immune-deficient mouse models, including NCG and athymic nude mice. While AxlKO tumor growth in athymic nude mice, which lack T-cells, was unchanged, tumor growth in NCG mice-which notably lack NK cells- was “rescued,” suggesting that NK cells may critically mediate the slowed growth of AxlKO tumors. These observations led us to hypothesize that Axl modulates NK cell recruitment and activation within the TIME. To test this, we first assessed in vitro NK cell cytotoxicity and found that Axl loss in tumor cells appeared to significantly enhance NK cell cytotoxicity. Further, NK cell depletion studies in C57BL/6 mice bearing AxlKO tumors demonstrated that the lack of NK cell "rescued" tumor growth in AxlKO models. To investigate if Axl regulates cytokines and chemokines relevant to NK cell recruitment and activation, we conducted analyses using NanoString nCounter, Luminex, and quantitative PCR. These revealed downregulation of NK modulators CD73 and CCL2, along with increased expression of CCL5 and CXCL10 in AxlKO tumor cells. These findings suggest that Axl regulates key immunomodulators to inhibit NK cell recruitment and activation, creating an immunosuppressive TIME that promotes HNC tumor growth.

Citation Format: Regan L Harmon, Kourtney L Kostecki, Mari Iida, Madelyn A Harris, Bridget E Crossman, Justine Bruce, Ravi Salgia, Deric L Wheeler. Axl regulation of NK cell activity creates an immunosuppressive tumor immune microenvironment in head and neck cancer [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B088.
Abstract B100: Dietary Intervention in Melanoma Patients Treated with Immune Checkpoint Inhibitors
Authors: Shaverdashvili Khvaramze
Published: February 2025

The goal of the proposal is to determine how dietary intervention modulates gut microbiome and immune, proteomic, and metabolomic changes in immune checkpoint inhibitor (ICI)-treated melanoma patients. There is ample evidence that diet represents a major regulator of the gut microbiome. To uncover the mechanism used by specific diet interventions to modulate gut microbiome composition, immune, proteomic, and metabolomic changes we have designed the first prospective dietary intervention clinical trial with high-fermented food diet followed by high-fiber supplementation in melanoma patients treated with ICI. We hypothesize that dietary interventions with high-fermented food and high-fiber supplementation will promote intestinal microbial signatures that may enhance antitumor immunity through immune, proteomic, and metabolomic changes to potential clinical response and occurrence of immune-related adverse events (irAEs). The study aims are: 1) Longitudinally assess gut microbial signatures upon sequential high-fermented food and high-fiber supplementation in ICI-treated cancer patients. We hypothesize that diet modification will distinctly modulate gut microbial diversity and function. 2) To assess whether high-fermented food and high-fiber supplementation will exert distinct immunological, proteomic, and metabolomic effects in ICI-treated cancer patients. We will also assess the association between gut microbiome diversity and occurrence and frequency of irAEs. In summary, the proposed study will improve our understanding of how specific adjuvant dietary interventions can shape the human gut microbiome and modulate anti-tumor immunity in ICI-treated melanoma patients.

Citation Format: Khvaramze Shaverdashvili. Dietary Intervention in Melanoma Patients Treated with Immune Checkpoint Inhibitors [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B100.
Abstract B102: Clinical response to checkpoint inhibitors is associated with distinct gut bacteria that promote anti-tumor immunity through different mechanisms
Authors: Bakdash Ghaith , Popple Amy , Klisko Dominika , Hudson Robyne , Castan Laure , Villemin Clelia , Schreiber Fernanda , Berlato Chiara , Corrie Pippa , Sharpington Tim , Lawley Trevor D , Robinson Matthew J
Published: February 2025

The gut microbiome of cancer patients impacts response to immune checkpoint inhibitor (CPI) therapy. We have recently identified nine species of gut commensal bacteria that are all strongly associated with CPI response in four independent cohorts of advanced melanoma patients. A consortium of nine strains, each representing one of these species, synergistically inhibited tumor growth in combination with anti-PD1 in a syngeneic tumor model thereby demonstrating these bacteria as active drivers of the anti-tumor immune response. The mechanisms by which each of the nine bacteria exert their systemic anti-tumor effects was investigated using in vitro assays with primary human immune cells. Eight of the strains triggered dendritic cells maturation, which led to the induction of CD8+ Cytotoxic T Lymphocytes (CTLs) with very potent tumoricidal activity. In addition, metabolites derived from four of the bacterial species, from two different phyla, triggered CTLs to upregulate the expression of granzyme B (GzB) and Interferon (IFN)γ and kill tumor cells in vitro. Furthermore, the bacterial metabolites derived from a different species were able to counteract the CD8+ T cell inhibitory effects of in vitro generated tumor-associated macrophages (TAMs), restoring CTL cell proliferation and the expression of GzB and IFNγ. In summary, nine species of gut commensal bacteria were identified as being associated with CPI response in melanoma. All species directly activated dendritic cells to trigger potently tumoricidal CTLs. Certain bacteria promoted anti-tumor effects through metabolites that can either promote CTL activation or hinder the inhibitory effects of TAM within the tumor microenvironment. This demonstrates that different bacteria associated with CPI response can interact with the immune system in distinct ways to enhance the efficacy of CPIs. All nine strains have now been combined to create a Live Biotherapeutic Product, MB097. MELODY-1 (NCT06540391) is an ongoing phase 1b study to evaluate MB097 in combination with pembrolizumab in advanced melanoma patients.

Citation Format: Ghaith Bakdash, Amy Popple, Dominika Klisko, Robyne Hudson, Laure Castan, Clelia Villemin, Fernanda Schreiber, Chiara Berlato, Pippa Corrie, Tim Sharpington, Trevor D Lawley, Matthew J Robinson. Clinical response to checkpoint inhibitors is associated with distinct gut bacteria that promote anti-tumor immunity through different mechanisms [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B102.
Abstract B103: Attenuated Salmonella secreting interleukin-21 activates T-cells and induces anti-tumor effects
Authors: Han Minju , Kim Eunji , Jeong Minchan , Kim Solbi , Jeon Heung Jin , Lee Hyo Jin
Published: February 2025

The tumor microenvironment is often characterized by an immunosuppressive state, limiting the efficacy of immunotherapies. Although blocking programmed death-1 (PD-1) and its ligand (PD-L1) can activate the immune system, its clinical success is often limited, prompting the exploration of combination therapies. Recent research has renewed interest in using attenuated Salmonella strains as cancer therapeutics due to their ability to target tumors, stimulate immune responses, and promote tumor cell death, though complete tumor eradication remains a challenge. In this study, we aimed to enhance anti-tumor immunity by leveraging Salmonella-mediated delivery of interleukin-21 (IL-21) to activate the suppressed immune system within the tumor microenvironment. Using Salmonella’s flagellar type III secretion system, we engineered the strain to secrete IL-21 directly into the tumor. In a mouse model, we assessed the local immune response and tested the combination of Salmonella-mediated IL-21 delivery with anti-PD-L1 therapy. Our results confirmed IL-21 secretion and showed enhanced recruitment and activation of CD4+ and CD8+ T cells in the tumor. Mice receiving the combination treatment exhibited improved survival and reduced tumor growth compared to monotherapy. Safety studies confirmed the viability of the IL-21-secreting Salmonella strain for therapeutic use. This study highlights Salmonella as a promising platform for cancer immunotherapy.

Citation Format: Minju Han, Eunji Kim, Minchan Jeong, Solbi Kim, Heung Jin Jeon, Hyo Jin Lee. Attenuated Salmonella secreting interleukin-21 activates T-cells and induces anti-tumor effects [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B103.
Abstract B109: Drug repurposing for T315I mutation in CML through virtual screening and md simulation
Authors: Zulfiqar Nimra
Published: February 2025

Currently, many health incidentals are allocated to diagnosing and treating cancer. Even with the significant advancements in cancer research, there are still many challenges in treating the drug resistance issue. Drug resistance is typically the result of target molecular changes that cause non-response to recommended therapy. Drug resistance to TKIs can be increased by mutations in the kinase domain, impairing the effectiveness of treatment. In the same way, Chronic myeloid Leukemia (CML) is a tumor that obeys this rule. All relevant medicines target BCR-ABL since it has been demonstrated to play a key role in the pathogenesis of CML. Some alterations in the BCR-ABL, such as Y253H, and T315I, reduce the efficiency of treatments in patients. Therefore, more accurate and effective alternative therapies are urgently needed. To address this issue, we screened FDA-approved drugs by virtual screening, MD simulation, binding free energy calculations, ADMET assessment, and Toxicity prediction to identify new inhibitors for this mutant ABL1 protein. Research studies conclude that Tepotinib could inhibit the T315I mutant ABL1. Using this newly identified drug is not just a simple hypothesis in drug discovery. After a simple kinase selectivity assay, this drugs can be evaluated in phase 2 clinical trials. Notably, safety concerns underscore the potential of Tepotinib as a safer and potentially more effective alternative, pending successful phase 2 trial validation.

Citation Format: Nimra Zulfiqar1. Drug repurposing for T315I mutation in CML through virtual screening and md simulation [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B109.
Abstract B113: Does targeted long read sequencing allow classification of tumor reactive T cells using predicTCR?
Authors: Neuhoff Marie-Therese , Green Edward , Tan Chin Leng , Platten Michael
Published: February 2025

Tumor-reactive T cells can be identified based on their transcriptomic profile using ML tools such as predicTCR. Sequencing cost remains high as single cell sequencing of not only the receptor information but also the whole transcriptome meaning > 20k genes/cell is needed. Here we propose that targeted sequencing of only a minor fraction of the transcriptome may be sufficient to be able to classify a T cell as tumor reactive or not thus massively reducing sequencing cost. This is tested using targeted long read sequencing.

Citation Format: Marie-Therese Neuhoff, Edward Green, Chin Leng Tan, Michael Platten. Does targeted long read sequencing allow classification of tumor reactive T cells using predicTCR? [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B113.
Abstract B120: Therapeutic cancer vaccine targeting the endogenous retroviral envelope protein ERVMER34-1 facilitates expansion of neoepitope specific T cells and improves responsiveness to PD-L1 blockade
Authors: Hamilton Duane H , Maldonado Maria , Gracia-Hernandez Maria , Donahue Renee N , Palena Claudia M , Schlom Jeffrey
Published: February 2025

Purpose: Endogenous retroviruses (ERVs) are remnants of retrovirus germline infections that occurred over the course of evolution and constitute between 5-8% of the human genome. While ERVs tend to be epigenetically silenced in normal adult human tissues, they are often overexpressed in carcinomas and may represent novel immunotherapeutic targets. However, therapeutic cancer vaccines targeting ERVs have not been assessed clinically. For the first time, this study characterizes the ERV envelope protein ERVMER34-1 as target for a therapeutic cancer vaccine. Experimental Design: The expression of ERVMER34-1 in multiple healthy adult and cancer tissues was assessed, as was its immunogenicity to ascertain whether specific T-cells could lyse human carcinoma cell lines expressing ERVMER34-1. Furthermore, the ability of a rationally designed ERVMER34-1 targeted therapeutic vaccine to induce tumor clearance in two murine carcinoma models expressing ERVMER34-1 was examined either as a monotherapy or in combination with immune-oncology agents. Results: The ERVMER34-1 protein is overexpressed in several types of human carcinomas while being absent in most healthy adult tissues. ERVMER34-1 specific T-cells were detected in PBMCs of cancer patients but not healthy donors following an overnight stimulation. However, reactive T-cells are readily expanded from both healthy donor and cancer patient PBMCs following a 7-day in-vitro stimulation. Furthermore, specific T-cells selectively kill human carcinoma cell lines expressing ERVMER34-1. A novel, rationally designed, therapeutic cancer vaccine targeting ERVMER34-1 mediated tumor control in established syngeneic murine tumors expressing ERVMER34-1 and promoted expansion of neoepitope-reactive T cells, which was enhanced when combined with rationally selected immune-oncology agents. Conclusions: This study supports the potential clinical development of a therapeutic cancer vaccine targeting the retroviral envelope protein ERVMER34-1, which would represent a new class of therapeutic cancer vaccine targeting ERVs.

Citation Format: Duane H Hamilton, Maria Maldonado, Maria Gracia-Hernandez, Renee N Donahue, Claudia M Palena, Jeffrey Schlom. Therapeutic cancer vaccine targeting the endogenous retroviral envelope protein ERVMER34-1 facilitates expansion of neoepitope specific T cells and improves responsiveness to PD-L1 blockade [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr B120.
Abstract IA02: Developing and manufacturing next generation cell therapies in the academic setting
Authors: Shy Brian R
Published: February 2025

The UCSF Investigational Cell Therapy Program streamlines preclinical development, regulatory interactions, and GMP manufacturing to accelerate the translation of cutting-edge cell and gene therapy technologies within the academic setting. This presentation will highlight our experience developing and manufacturing a range of experimental cellular therapies, leveraging next-generation genome and epigenome engineering strategies. I will showcase current and upcoming products incorporating targeted CRISPR-based approaches, multiplexed engineering, pooled T cell therapies, multi-receptor logic circuits, and platform technologies for rare diseases. Additionally, I will discuss the unique strengths and challenges of advancing these therapies in an academic environment and explore opportunities to expand access and bring these transformative treatments to more patients.

Citation Format: Brian R Shy. Developing and manufacturing next generation cell therapies in the academic setting [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr IA02.
Abstract IA03: Towards personalized minimally-invasive T-cell therapies
Authors: Gros Alena
Published: February 2025

Ex vivo expansion of tumor-infiltrating lymphocytes can lead to durable tumor regression in patients with metastatic melanoma. Accumulating evidence suggests that TIL frequently recognize neoantigens and that neoantigen reactive TIL play an important role in the antitumor responses of patients treated with immune checkpoint blockade and TIL therapy. These are optimal targets for cancer immunotherapy as their expression is exquisitely confined to the tumor site, and T cells targeting these antigens have not undergone negative selection in the thymus. Despite the promising efficacy of TIL therapy against melanoma tumors, current research in the field focuses on trying to extend this efficacy to other tumor types. We will discuss the existing possibilities to develop personalized T-cell therapies targeting neoantigens for solid cancers, with particular emphasis on minimally invasive T-cell therapies.

Citation Format: Alena Gros. Towards personalized minimally-invasive T-cell therapies [abstract]. In: Proceedings of the AACR IO Conference: Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2025 Feb 23-26; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2025;13(2 Suppl):Abstract nr IA03.