bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A073: Digital assessment of tertiary lymphoid structures in cancer using whole slide scans
Authors: Park Saem Mul , Munoz-Erazo Luis , Lin Shelly , Chun-Jen J Chen , Zhou Lisa Y.Y. , Rhodes Janet L , Jeon Taesung , Fenton Sonya , McCall John L , Kemp Roslyn A , Dunbar P. Rod 
Published: February 2025

Abstract
Tertiary Lymphoid Structures (TLSs) are organized aggregates of immune cells that form in non-lymphoid tissues under chronic inflammation, including cancer. In most cases, TLS presence in tumors correlates with improved clinical outcomes, underscoring their prognostic and predictive value. However, standardizing TLS assessment remains challenging due to their complex cellular composition, multi-lobular structures, and highly variable appearances within tissue sections. Current TLS assessment methods rely largely on manual identification of these structures, which is inefficient for large datasets and introduces significant variability and potential bias. In this pilot study, we therefore applied a novel digital approach to characterize TLSs in whole-slide images of colorectal cancer tissue sections stained with multiplexed immunofluorescence. This approach enabled comprehensive identification of major lymphocyte subsets within TLSs across entire tissue sections and facilitated assessment of their proliferative activity. Compared to traditional methods that require manual counting and phenotyping of individual TLSs, the whole-slide approach proved far simpler and efficiently distinguished patients with strikingly different levels of immune activity within their TLSs. Notably, we observed strong correlations between the proliferation of B-cells within TLSs and that of T-cell subsets. We also present an automated computational pipeline for TLS identification in whole-slide images, providing a fast, unbiased alternative to manual boundary delineation. Overall, our findings demonstrate that whole-section digital quantification of immune cell activity within TLSs offers substantial advantages over traditional methods. This approach has the potential to accelerate immuno-oncology research by enabling robust correlations between TLS states and clinical outcomes. Ultimately, automated TLS analysis could pave the way for standardized clinical tests, maximizing the value of these structures as potential biomarkers and therapeutic targets.
Citation Format: Saem Mul Park, Luis Munoz-Erazo, Shelly Lin, Chun-Jen J Chen, Lisa Y.Y. Zhou, Janet L Rhodes, Taesung Jeon, Sonya Fenton, John L McCall, Roslyn A Kemp, P. Rod Dunbar. Digital assessment of tertiary lymphoid structures in cancer using whole slide scans [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 A073.
Abstract A076: Mono-ADT-ribosylation as a driver of the immunosuppressive tumor microenvironment
Authors: Fuchs Serge Y. 
Published: February 2025

Abstract
The immunosuppressive tumor microenvironment (TME) of solid tumors is central to their ability to escape from immune surveillance and to resist anti-cancer therapies, including immunotherapies utilizing immune checkpoint blockade (ICB) and adoptive cell transfer therapy (ACT). Within the TME, redundant cellular and acellular factors attenuate anti-tumor immune responses. These factors, including adenosine, prostaglandin E2, immunosuppressive myeloid cells, and regulatory T (Treg) cells, suppress the anti-tumor CD8+ cytotoxic T lymphocytes (CTLs) and confer resistance to immune therapies. Inactivation of the type I interferon (IFN1) pathway in the immune cells represents a key mechanism by which CTLs are inactivated, yet tumor-infiltrating Treg cells (TI-Tregs) are enabled to elicit immunosuppressive effects. Two PARP members catalyzing the transfer of mono-(ADP-ribose), PARP7 and PARP11 are involved in this inactivation via suppression of IFN1 production and acceleration of proteolytic degradation of the IFNAR1 receptor for IFN1. Here, we demonstrate that PARP11 is a crucial regulator of the immunosuppressive TME. In the CTLs, PARP11 mediated their inactivation while acting as an essential regulator of TI-Tregs immunosuppressive functions and pro-tumorigenic activities. Expression of PARP11 correlated with TI-Treg infiltration and poor responses to ICB in human cancer patients. PARP11 was induced in the TI-Treg cells by tumor-derived factors, including adenosine and prostaglandin E2. Knockout of PARP11 in the cells of the TME or treatment of tumor-bearing mice with selective PARP11 inhibitor ITK7 inactivated TI-Treg cells and reinvigorated anti-tumor immune responses. Accordingly, ITK7 decelerated tumor growth and significantly increased the efficacy of anti-tumor immunotherapies, including ICB and adoptive transfer of CAR T cells. These results characterize PARP11 as a critical driver of TI-Treg activities and a major regulator of immunosuppressive TME and argue for targeting PARP11 to augment anti-cancer immunotherapies.
Citation Format: Serge Y. Fuchs. Mono-ADT-ribosylation as a driver of the immunosuppressive 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 A076.
Abstract A077: Estrogen-responsive fractions drive the immunosuppressive tumor microenvironment and immunotherapy resistance
Authors: Lee Jin-Ke , Lee Kwanghwan , Kang Hyun Ju 
Published: February 2025

Abstract
Estrogen signaling plays a crucial role in cancer progression, yet its impact on the tumor microenvironment (TME) and immunotherapy outcomes remains poorly understood. This study investigated the influence of estrogen-responsive cell fractions on TME immunosuppression and immune checkpoint inhibitor (ICI) therapy resistance across diverse cancer types. Integrating growth factor-omics, single-cell RNA sequencing, and pan-cancer analysis, we identified two key estrogen-responsive malignant and cancer-associated fibroblast (CAF) cell fractions. These fractions consistently associated with immunosuppressive features across multiple cancer types, including reduced immune cell infiltration and increased regulatory T cell presence. Significantly, the estrogen-responsive CAF fraction strongly correlated with ICI therapy resistance in the majority of analyzed cohorts. These patients also exhibited the highest enrichment scores for immunosuppressive CAF markers, CAF.S1 and TGF-β CAF. Our findings reveal a common mechanism by which estrogen signaling influences tumor immunity and treatment outcomes across cancer types. The identification of FB.TNFSF10, an estrogen-responsive CAF fraction as a potential predictive biomarker for ICI resistance offers new opportunities for patient stratification and treatment optimization. This study provides a foundation for developing novel therapeutic strategies targeting estrogen-responsive cell fractions to enhance immunotherapy efficacy, potentially leading to more personalized and effective cancer treatments.
Citation Format: Jin-Ke Lee, Kwanghwan Lee, Hyun Ju Kang. Estrogen-responsive fractions drive the immunosuppressive tumor microenvironment and immunotherapy resistance [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 A077.
Abstract A084: Regulation of Anti-Tumor Immune Response by EphA2 Receptor Tyrosine Kinase
Authors: Shi Xioajun Roger , Lingerak Ryan , Kim Soyeon , Wang Bingcheng 
Published: February 2025

Abstract
Eph receptors are the largest subfamily of receptor tyrosine kinases (RTK). Overexpression of EphA2 is a common signature for many types of human solid cancer including glioblastoma, melanoma and cancers of breast, lung, colon, pancreas and prostate, which is correlated with poor prognosis, through incompletely understood mechanisms. We report here that EphA2 knock-out potently suppressed tumor development in several multiple syngeneic mouse cancer models. Such effects were missing in immune deficient mice, suggesting the involvement of immune components. Immunophenotyping of the tumors showed elevated T cell infiltration and activity accompanied by reduced MDSC population in the EphA2 KO tumors. Single cell transcriptomic analysis and cytokine measurements supported these results showing increased production of CCL5, CXCL9, CXCL10 and IFNg in the EphA2 KO tumors. Analysis on tumors at very early time points revealed higher levels of CXCL1 and CXCL2 which recruits suppressive MDSCs. In support, larger population of MDSCs was found in PBMCs from the control tumor-bearing mice than those bearing EphA2 KO tumors. These results suggest that EphA2 in cancer cells drives the production of CXCL1 and CXCL2 to recruit suppressive MDSCs to the tumor site, thus subvert the host anti-tumor immune surveillance. Targeting the overexpressed EphA2 in cancer can help reshape the tumor immune microenvironment towards type I anti-tumor immune response.
Citation Format: Xioajun Roger Shi, Ryan Lingerak, Soyeon Kim, Bingcheng Wang. Regulation of Anti-Tumor Immune Response by EphA2 Receptor Tyrosine Kinase [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 A084.
Abstract A099: The IO-Atlas Project: A cross-cohort tumor immunophenotyping platform enhancing precision immuno-oncology
Authors: Ma Liqian , Pfeil Jacob , Lo Hin-Ching , Turan Tolga , Kongpachith Sarah , Zhao Xi , Samayoa Josue , Halliwill Kyle 
Published: February 2025

Abstract
The tumor microenvironment (TME) is complex and significantly influences how patients respond to immunotherapy. Despite decades of research generating numerous gene signatures to describe the TME, there is no consensus on the best way to capture meaningful variation, as the commonly used gene signatures are heavily T cell-biased with high degrees of collinearity. To better understand TME dynamics and represent them consistently and interpretably, we developed a framework for immunophenotyping using disparate immuno-oncology (IO) transcriptional “fingerprints” as part of the AbbVie IO Atlas Project. This framework provides a concise and informative representation of the TME by refining previously published TME gene expression signatures. Using the framework, we integrated bulk RNAseq profiles from two pan-cancer patient cohorts—The Cancer Genome Atlas (TCGA) and a real-world cohort (Aster Insights’ Avatar)—by representing these samples with IO fingerprints, which generated a cross-tumor and cross-dataset representation of the TME across a broad patient spectrum. This integration mitigates the limitation of TCGA data alone by combining treatment-naïve and early-stage cancers with heavily pre-treated, later-stage, and metastatic cancers. Consequently, the IO-centric sample relationships enabled us to identify cross-cohort IO subpopulations within individual tumor indications. Furthermore, by representing tumor profiles from patients treated with immune checkpoint inhibitors, we uncovered novel patient subpopulations with distinct IO fingerprint patterns, which were associated with ICI responses in lung adenocarcinoma and clear cell renal cell carcinoma. By delving into the paired molecular profiles of these patients, we hypothesized the underlying mechanisms driving response or non-response and suggested novel strategies to address the unmet medical needs of patient subpopulations treated with existing IO regimens. Our findings demonstrate that the comprehensive integration of diverse patient data using the IO Atlas framework can lead to more effective immunotherapy strategies. AbbVie Disclosure Statement: All authors are employees of AbbVie. The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication.
Citation Format: Liqian Ma, Jacob Pfeil, Hin-Ching Lo, Tolga Turan, Sarah Kongpachith, Xi Zhao, Josue Samayoa, Kyle Halliwill. The IO-Atlas Project: A cross-cohort tumor immunophenotyping platform enhancing precision immuno-oncology [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 A099.
Abstract A102: Assessment of CIT-drugs MoA with in vivo and 3D in vitro imaging
Authors: Cremasco Floriana , Apostolopoulou Katerina , Menietti Elena , Kunz Leo , Colombetti Sara , Perro Mario 
Published: February 2025

Abstract
Cancer Immunotherapies (CITs) have shown unprecedented results in improving tumor control. However, many patients are still refractory to treatment. A deeper understanding of CIT-drugs mode of action (MoA) may help improve therapeutic approaches to reach better anti-tumor response. To this end, we developed a skinfold chamber model in humanized mice that allows, by multi-photon intra-vital microscopy, the in vivo study of the tumor microenvironment. Analysis at the single cell level upon treatment with a CD20-targeting T-cell bispecific antibody, CD20-TCB (Glofitamab), showed that CD20-TCB localizes in the tumor (diffuse large B cell lymphoma, DLBCL) and acts on tumor-resident T cell motility within 1 hour post-treatment, causing a sharp reduction in their speed and an increase in tumor/T cell interaction time; those changes last up to 72h post-treatment. In addition, we show how the initial tumor/T cell interaction mediated by CD20-TCB leads to peripheral T cell recruitment into the tumor. This mechanism is dependent on the presence of tumor-resident T cells and on IFNg-CXCL10 pathway. Inhibiting any of these two pathways resulted in reduced T cell infiltration from the periphery and reduced anti-tumor efficacy. In order to expand and complement in vivo imaging for CIT-drug discovery e.g. for mid-throughput screening purposes, we further established a fully human mid-throughput 3D in vitro screening platform to image and quantify immune cell dynamics, trafficking and infiltration to tumors in response to CIT. To this aim, we have adopted the microfluidic OrganoPlate 3-lane 40 by MIMETAS. By combining endothelial tubules, peripheral immune cells, solid or liquid tumors, extracellular matrix and stromal components, we can faithfully recapitulate the tumor microenvironment organization and physiological in vivo T cell dynamics. Indeed, the 3D in vitro platform allows faithful reproduction of T cell recruitment and immune synapses formation upon CD20-TCB as observed in vivo. Furthermore, we tested CD20-TCB MoA in the context of three diverse cell lines of DLBCL. We show that treatment of diffuse large B-cell lymphomas leads to the formation of synapses between T cells and tumor cells, the stability of which correlates with tumor cell killing. Such findings offer fundamental observations for a better understanding of CD20-TCB MoA and how immunological synapses formation impacts T cell effector functions and tumor regression.
Citation Format: Floriana Cremasco, Katerina Apostolopoulou, Elena Menietti, Leo Kunz, Sara Colombetti, Mario Perro. Assessment of CIT-drugs MoA with in vivo and 3D in vitro imaging [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 A102.
Abstract A106: Synergistic Effects of CD40 Agonist Antibody and DC-Derived Exosomes Enhance Anti-Tumor Efficacy by Modulating the Tumor Microenvironment and Reducing Metastasis in a Murine Melanoma Model
Authors: Gaur Vidit , Bhattacharyya Jayanta 
Published: February 2025

Abstract
Over the past decade, dendritic cell (DC) vaccines have been extensively studied to reprogram the tumor microenvironment (TME) and delay tumor growth. However, limitations related to long-term storage, patient- specific variability, short half-life, and moderate anti-tumor efficacy highlight the need for further refinement of DC vaccines for effective cancer treatment. As an alternative, DC-derived exosomes (DeX) have demonstrated superior anti-tumor efficacy and stability compared to DCs. However, within tumors, low expression of co- stimulatory molecules such as CD40, CD86, and CD80 limits the effectiveness of these cancer vaccines. The use of a CD40 agonist antibody (αCD40) has shown potential in increasing CD40 expression, enhancing antigen presentation, and contributing to a robust anti-tumor response. In this study, we demonstrate that combining αCD40 with DeX pulsed with cancer cell lysate significantly delayed tumor growth and improved survival in mice bearing B16-F10 melanoma. In tumor, the combination therapy increased the population of CD45+CD8+ T-cells and CD45+CD20+ B-cells, while reducing PD-L1 expression. Additionally, the combination therapy boosted levels of Th1 cytokines (IFN-γ, IL-6, IL-2) compared to Th2 cytokines (IL-4 and IL-10), supporting an enhanced anti-tumor response. Importantly, this approach also augmented anti-tumor immunity in the spleen, significantly lowered the expression of metastatic markers including vimentin, and fibronectin in the primary tumor, and reduced lung metastasis. Overall, these findings suggest that the combined use of αCD40 and DeX is a promising strategy to improve the in vivo anti-tumor efficacy of DC vaccines and supports further exploration of this novel combinatorial therapy in clinical settings.
Citation Format: Vidit Gaur, Jayanta Bhattacharyya. Synergistic Effects of CD40 Agonist Antibody and DC-Derived Exosomes Enhance Anti-Tumor Efficacy by Modulating the Tumor Microenvironment and Reducing Metastasis in a Murine Melanoma Model [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 A106.
Abstract A120: Single-Cell RNA Sequencing Combined with Lineage Tracing Identify Clonal Populations Across Melanoma Organ-Specific Metastasis
Authors: Aedo-Lopez Veronica 
Published: February 2025

Abstract
Melanoma, a highly metastatic skin cancer, exhibits variations in prognosis and response to therapy based on the site of metastasis. Despite the success of immunotherapy and targeted therapies in melanoma, over half of metastatic melanoma patients will experience disease progression due to therapy resistance. The heterogeneity and plasticity of melanoma cells contribute to metastatic dissemination and therapy resistance. We aim to determine whether distinct clones and/or their transcriptional cell states can predict the formation of tumours in various organs. Lineage tracing and clonal heterogeneity were evaluated using the state-of-the-art technology, SPLINTR (Single-cell Profiling and LINeage Tracing), enabling us to match a cells evolution with changes in transcriptional states. To identify melanoma clones across different metastatic sites, specifically subcutaneous, lungs and brain, C57BL/6 mice were injected subcutaneously, intravenously or intracranially with the same pool of cells of barcoded luciferase expressing YUMMER1.7PV1 murine melanoma cells. Transduction conditions ensured that one DNA barcode integrated into cell genomes at one barcode per cell, serving as a lineage tag. Bioluminescence imaging was performed once a week to monitor the tumour growth of mice injected intravenously and intracranially. Subcutaneous tumours were measured by calliper. Mice were euthanized before ethical endpoints. Tumors were harvested and single cell analysis as well as DNA sequencing was performed to identify barcodes expressed by the tumor cells across different tumor-sites. Barcode analysis was conducted both before cell implantation and at tumor harvest. Clonality exhibited significant variability between sites. Single-cell RNA sequencing will unveil states associated with dominant clones present at different metastatic sites. This information will provide a new understanding of melanoma transcriptional phenotype behaviours and biological characteristics at different metastatic sites and in response to therapy.
Citation Format: Veronica Aedo-Lopez. Single-Cell RNA Sequencing Combined with Lineage Tracing Identify Clonal Populations Across Melanoma Organ-Specific Metastasis [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 A120.
Abstract A122: Improving antitumor T cell therapy with membrane-tethered engineered cytokine agonists (MECAs)
Authors: Gumber Diana , Priceman Saul , Brown Christine J , Wang Leo 
Published: February 2025

Abstract
Background: Chimeric antigen receptor (CAR) T cell therapy has demonstrated marked success in the control of hematological malignancies. However, CAR T cell therapy has been less successful when applied to solid tumors. This has been attributed to multiple factors including tumor infiltration, antigen heterogeneity, and the immunosuppressive tumor microenvironment. The hostile milieu and chronic exposure to antigen that CAR T cells face in the tumor microenvironment induces T cell exhaustion which is associated with an overall loss of therapeutic efficacy. Methods: Strategies for overcoming T cell exhaustion are central to improving CAR T cell efficacy in the treatment of solid tumors. The incorporation of survival-promoting proteins, such as cytokines, into CAR T cells have been used to generate a supportive local immune environment. Interleukin-2 (IL-2) is a cytokine that acts as a potent growth factor in T cells; however, therapeutic application of systemic IL-2 has been associated with severe toxicities and T cell exhaustion. To address this, we have developed membrane-tethered engineered cytokine agonists (MECAs) that anchor IL-2 and IL-2 partial agonists to the cell surface membrane of CAR T cells, restricting their signaling to the expressing cells to maximize autocrine signaling and prevent toxicity. Results: Here, we evaluate the influence of MECAs on the proliferation, exhaustion state, and cytotoxic function of CAR T cells. CAR T cells expressing the MECAs demonstrated improved cytotoxic function and proliferation with in vitro models. MECA expressing CAR T cells did not cause toxicity in control mice or in an orthotopic glioma model. Preliminary results from the toxicity study indicate improved in vivo antitumor activity of MECA expressing CAR T cell compared to CAR only. Conclusion: Exhaustion of antigen-specific T cells is a challenge in multiple cancer immunotherapy modalities, and the proposed MECAs have the potential to revolutionize immunotherapy for solid tumors as an effective and widely applicable solution.
Citation Format: Diana Gumber, Saul Priceman, Christine J Brown, Leo Wang. Improving antitumor T cell therapy with membrane-tethered engineered cytokine agonists (MECAs) [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 A122.