bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germline pathogenic DROSHA variants are linked to pineoblastoma and Wilms tumor predisposition
Authors: Fiorica Peter N. , Golmard Lisa , Kim Jung , Bao Riyue , Lin Frank Y. , Roy Angshumoy , Pribnow Allison , Perrino Melissa R. , Masliah-Planchon Julien , Michalak-Provost Sophie , Wong Jennifer , Filser Mathilde , Stoppa-Lyonnet Dominique , Bourdeaut Franck , Brahimi Afane , Ingster Olivier , Saulnier Sholler Giselle , Jackson Sarah A. , Sasaki Mark M. , Fowler Trent , Ng Anita , Corbett Ryan J. , Kaufman Rebecca S. , Haley Jeremy S. , Carey David J. , Huang Kuan-lin , Diskin Sharon J. , Rokita Jo Lynne , Al-Kateb Hussam , McGee Rose B. , Schiffman Joshua D. , Chen Kenneth S. , Stewart Douglas R. , Williams Parsons D. , Plon Sharon E. , Schultz Kris Ann P. , Onel Kenan 
Published: February 2025

Abstract
Purpose: DROSHA, DGCR8, and DICER1 regulate microRNA biogenesis and are commonly mutated in cancer. Whereas DGCR8 and DICER1 germline pathogenic variants (GPVs) cause autosomal dominant tumor predisposition, no association between DROSHA GPVs and clinical phenotypes has been reported. Experimental Design: After obtaining informed consent, sequencing was performed on germline and tumor samples from all patients. The occurrence of germline DROSHA GPVs was investigated in large pediatric and adult cancer datasets. The population prevalence of DROSHA GPVs was investigated in the UK Biobank and Geisinger DiscovEHR cohorts. Results: We describe nine children from eight families with heterozygous DROSHA GPVs and a diagnosis of pineoblastoma (n=8) or Wilms tumor (WT, n=1). A somatic second hit in DROSHA was detected in all eight tumors analyzed. All pineoblastoma tumors analyzed were classified as miRNA processing altered-1 (PB-miRNA1) subtype. We estimate the population prevalence of germline DROSHA loss-of-function variants to be 1:3,875-1:4,843, but find no evidence for increased adult cancer risk. Conclusions: This is the first report of DROSHA-related tumor predisposition. As pineoblastoma and WT are also associated with DICER1 GPVs, our results suggest the tissues-of-origin for these tumors are uniquely tolerant of general microRNA loss. The PB-miRNA1 pineoblastoma subtype is associated with older age of diagnosis and better outcome than other subtypes, suggesting DROSHA GPV status may have important clinical and prognostic significance. We suggest genetic testing for DROSHA GPVs be considered for patients with pineoblastoma, WT, or other DICER1/DGCR8-related conditions and propose surveillance recommendations through research studies for individuals with DROSHA GPVs.
Abstract A002: cloneTCR: A high-throughput TCR assembly platform for highly multiplexed screening
Authors: Hamberger Moritz , Neuhoff Marie-Therese , Platten Michael , Green Edward Wilhelm 
Published: February 2025

Abstract
Manufacturing T cell receptors (TCRs) de novo has previously been considered costly and time-consuming, limiting the widespread application of TCR transgenic T cell immunotherapies. Here, we introduce a fully automated, cost-effective, and high-throughput TCR cloning platform capable of assembling and quality controlling thousands of TCRs per week. Our pipeline leverages the widely adopted AIRR (VDJ sequence) format as input, generating scripts automatically for streamlined operation of our lab automation. The platform is highly modular and adaptable, accommodating both human and murine V(D)J sequences alongside a broad spectrum of modular constant regions. These constant regions are available in germline-encoded or engineered versions, all designed for orthogonal compatibility. Additionally, the system supports multiple vector formats, enabling diverse delivery solutions such as lentiviral vectors, transposons, direct in vitro transcription, and recombination-based vectors targeting loci like AAVS1 and TRAC. A key innovation of our platform is the integration of Oxford Nanopore-based bulk long-read sequencing for quality control, enabling precise assessment of library uniformity and cloning fidelity. Compared to existing approaches, our method achieves superior library uniformity (frequency 2.5x around the median) and high sequence accuracy of 95%. With its unparalleled capacity to clone and quality-check 2,000 TCRs a week, our platform sets a new benchmark for high-throughput TCR production and screening. It enables large-scale, multiplexed exploration of entire tumor-infiltrating lymphocyte (TIL) repertoires, paving the way for transformative advances in T cell immunotherapy.
Citation Format: Moritz Hamberger, Marie-Therese Neuhoff, Michael Platten, Edward Wilhelm Green. cloneTCR: A high-throughput TCR assembly platform for highly multiplexed screening [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 A002.
Abstract A003: Investigating the effect of lipid metabolism on cDC1 dendritic cell cross-presentation in tumor microenvironment
Authors: Kar Uddipan , Balan Sreekumar , Bhardwaj Nina 
Published: February 2025

Abstract
Dendritic cells, or primary antigen-presenting cells, are critical immune sentinels essential in bridging the body’s adaptive and innate immune responses. Among DC subsets, conventional dendritic cell subset 1 (cDC1) stands out for its unique ability to cross-present antigens, which is crucial for initiating effective cytotoxic T-cell responses against tumors. Unlike normal cells, abnormal lipid accumulation (leading to lipid droplet formation) is observed in several cancers, which is considered one of the major reasons for DC dysfunction. However, very few reports are available on the impact of lipid metabolism on dendritic cells' antigen cross-presentation ability. To achieve this, in-vitro generated cDC1s were cocultured with heat-killed dying tumor cells and subsequently subjected to bulk RNA sequencing. Transcriptomic profiling was performed on cDC1s in the presence or absence of dead cells. Our analysis revealed distinct transcriptome profiles highlighting differential gene expression patterns linked to lipid metabolism, cholesterol regulation, and lipid droplet formation. Furthermore, we carried out various in-vitro metabolic functional assays, such as lipid staining assay, and observed increased lipid drop formation on antigen uptake. We validated this observation using confocal microscopy. In the future, we will reprogram lipid metabolism (using pathway inhibitors and gene knockdowns) and test dendritic cell-based antigen cross-presentation. Our findings suggest a crucial role for lipid metabolism in modulating the cross-presentation machinery of cDC1s within the tumor microenvironment. Understanding the mechanisms underlying this interplay between lipid metabolism and. DC cross-presentation may offer novel insights into the design of immunotherapeutic strategies aimed at harnessing DC-mediated immune responses against cancer.
Citation Format: Uddipan Kar, Sreekumar Balan, Nina Bhardwaj. Investigating the effect of lipid metabolism on cDC1 dendritic cell cross-presentation in 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 A003.
Abstract A007: A meta-analysis of cancer neoantigens curated from the literature
Authors: Kosaloglu-Yalcin Zeynep , Carter Hannah , Nielsen Morten , Sette Alessandro , Peters Bjoern 
Published: February 2025

Abstract
The Cancer Epitope Database and Analysis Resource (CEDAR) aggregates cancer epitope data from peer-reviewed studies, providing a structured repository of epitope-specific T cell, antibody, and MHC ligand assays. Neoantigens, arising from somatic mutations in cancer cells, represent a class of tumor-specific epitopes with potential for precision immunotherapy and as biomarkers for patient prognosis and therapeutic response. Our study harnesses CEDAR’s curated dataset to conduct a meta-analysis on neoantigens across various cancers, identifying factors contributing to neoantigen immunogenicity and their prevalence among patient populations.
Citation Format: Zeynep Kosaloglu-Yalcin, Hannah Carter, Morten Nielsen, Alessandro Sette, Bjoern Peters. A meta-analysis of cancer neoantigens curated from the literature [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 A007.
Abstract A012: Targeting macrophage galactose binding lectin -tumor associated MUC1 immune axis in cancer
Authors: Cudic Mare , Ayyalasomayajula Ramya , Boneva Ivet , Beckwith Donella M. , André Sabine , Kaltner Herbert 
Published: February 2025

Abstract
Carbohydrate-binding proteins, lectins, are the main binding partners of tumor-associated carbohydrate antigens (TACAs) on the cell surface. Interactions between the tumor-associated carbohydrate antigens of Mucin 1 (TA MUC1) and the carbohydrate-binding proteins, lectins, often lead to the creation of a pro-tumor microenvironment favoring tumor initiation, progression, metastasis, and immune evasion. Macrophage galactose binding lectin (MGL) is a C-type lectin receptor found on antigen-presenting cells that facilitates the uptake of carbohydrate antigens for antigen presentation, modulating the immune response homeostasis, autoimmunity, and cancer. MGL has been identified as a receptor of Thomsen-nouvelle (Tn, CD175) and sialylated Tn (sialyl-Tn, CD175s) antigens. The interaction between Tn and sialyl-Tn antigens of tumor-associated MUC1 and hMGL likely plays a critical role in establishing the immunological tolerance to tumor cells. Yet, MGL targeting is an attractive approach to enhance cancer vaccine efficacy. The ability of hMGL to regulate immune response by engaging tumor-associated MUC1 to either augment the anti-tumorigenic effects or minimize the pro-tumorigenic effects is poorly understood. Thus, a thorough understanding of their binding interaction is essential for it to be exploited for cancer vaccine strategies. The synthesis of MUC1 glycopeptide models carrying a single or multiple Tn and/or sialyl-Tn antigen(s) is described. A novel approach for the sialyl-Tn threonine building block suitable for the solid phase peptide synthesis was developed. The thermodynamic profile of the binding interaction between the human MGL and MUC1 glycopeptide models was analyzed using isothermal titration calorimetry. All studied interactions, regardless of the glycan’s site of attachment or density, exhibited enthalpy-driven thermodynamics. The thermodynamic analysis pointed out the critical role of entropy in driving the affinity enhancement of multivalent interactions. Further studies into the nature of the hMGL ligands and their role in shaping the immune responses are warranted.
Citation Format: Mare Cudic, Ramya Ayyalasomayajula, Ivet Boneva, Donella M. Beckwith, Sabine André, Herbert Kaltner. Targeting macrophage galactose binding lectin-tumor associated MUC1 immune axis in 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 A012.
Abstract A016: Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR T cells
Authors: Singh Sheila K , Chokshi Chirayu R , Shaikh Vaseem , Brakel Benjamin , Rossotti Martin , Lazo John , Venugopal Chitra , Kislinger Thomas , Henry Kevin , Moffat Jason 
Published: February 2025

Abstract
Resistance to genotoxic therapies and tumor recurrence are hallmarks of glioblastoma (GBM), an aggressive brain tumor. In this study, we investigated functional drivers of post-treatment recurrent GBM through integrative genomic analyses, genome-wide genetic perturbation screens in patient-derived GBM models and independent lines of validation. Specific genetic dependencies were found consistent across recurrent tumor models, accompanied by increased mutational burden and differential transcript and protein expression compared to its primary GBM predecessor. Our observations suggest a multi-layered genetic response to drive tumor recurrence and implicate PTP4A2 (protein tyrosine phosphatase 4A2) as a modulator of self-renewal, proliferation and tumorigenicity in recurrent GBM. Genetic perturbation or small-molecule inhibition of PTP4A2 acts through a dephosphorylation axis with roundabout guidance receptor 1 (ROBO1) and its downstream molecular players, exploiting a functional dependency on ROBO signaling. Because a pan-PTP4A inhibitor was limited by poor penetrance across the blood–brain barrier in vivo, we engineered a second-generation chimeric antigen receptor (CAR) T cell therapy against ROBO1, a cell surface receptor enriched across recurrent GBM specimens. A single dose of ROBO1-targeted CAR T cells doubled median survival in cell-line-derived xenograft (CDX) models of recurrent GBM. Moreover, in CDX models of adult lung-to-brain metastases and pediatric relapsed medulloblastoma, ROBO1 CAR T cells eradicated tumors in 50–100% of mice. Our study identifies a promising multi-targetable PTP4A–ROBO1 signaling axis that drives tumorigenicity in recurrent GBM, with potential in other malignant brain tumors.
Citation Format: Sheila K Singh, Chirayu R Chokshi, Vaseem Shaikh, Benjamin Brakel, Martin Rossotti, John Lazo, Chitra Venugopal, Thomas Kislinger, Kevin Henry, Jason Moffat. Targeting axonal guidance dependencies in glioblastoma with ROBO1 CAR T cells [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 A016.
Abstract A021: Spatiotemporal Regulation of Chimeric Antigen Receptor T-cells Using Focused Ultrasound Therapy to Enable Use of High-Affinity Binders
Authors: Trope Edward , Su Yun-Yun , Nakata Rie , Golyska Magda , Richman Sarah 
Published: February 2025

Abstract
Pediatric High Grade Glioma (HGG) is an aggressive cancer with a 5-year survival rate of just 10-20% (Fangusaro, 2012). While previous studies using chimeric antigen receptor (CAR) T-cells for brain malignancies demonstrated tolerability (Majzner et al., 2022; Vitanza et al., 2021; Vitanza et al., 2023), the low survival rates demand more efficacious therapies (Majzner et al., 2022). In this study, we perform in vitro modeling of spatiotemporally regulated high-affinity CARs targeting the GD2 antigen to enable use of highly potent CAR variants while mitigating on-target, off-tumor toxicity. By placing CAR affinity variants under control of a heat shock promoter, thermal energy delivered to the tumor tissue by focused ultrasound (FUS) induces CAR expression (Wu et al., 2021) at an optimal temperature of 43oC. We first determine FUS-controlled CAR induction and decay kinetics in vitro for selected signaling domain architectures as well as affinity variants. Following codon optimization, differences in basal expression at 37oC from the heat shock promoter were noted for the three signaling domain architectures, with 28z and BBz displaying the highest and lowest levels of aberrant expression, respectively. Next, we compare expression of CAR constructs with and without 3 cycles of heat shock at 43oC in CAR-T cells. Then, using live cell imaging, we analyze the kinetics of expression and decay of the CAR following heat shock. Finally, we perform effector function assays of the CAR-T cells to compare the cytotoxicity and persistence for each construct. We identify the CAR architecture harboring the CD28 transmembrane domain and the 4-1BB cytoplasmic domain as the optimal balance between basal and induced expression. We plan to move this architecture forward to in vivo studies to assess the ability to maintain robust tumor lysis and minimal on-target, off-tumor toxicity.
Citation Format: Edward Trope, Yun-Yun Su, Rie Nakata, Magda Golyska, Sarah Richman. Spatiotemporal Regulation of Chimeric Antigen Receptor T-cells Using Focused Ultrasound Therapy to Enable Use of High-Affinity Binders [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 A021.
Abstract A024: CD3ζ ITAM diversity determines chimeric antigen receptor force and function
Authors: Echelibe Hilda , Majumdar Shubhabrata , Kolawole Elizabeth , Liu Baoyu , Bettini Maria , Evavold Brian , Bettini Matt 
Published: February 2025

Abstract
The Chimeric antigen receptor (CAR) T cell therapy is a powerful treatment for hematologic malignancies; however, clinical responses vary depending on CAR T cell function and persistence. The optimization of CAR design has gained considerable interest with a new focus on calibrating CAR intracellular signals via the immunoreceptor tyrosine-based activation motifs (ITAMs) to increase the fitness of CAR T cells. Evidence suggests that unique ITAM motifs at positions 1, 2, or 3 (ITAMs-A, B, and C respectively) of the CD3ζ signaling domain may have non-redundant roles in signal strength, T cell functionality, persistence, and memory formation. However, the individual contributions of each CD3ζ ITAM in transmitting force and activating mechanosensitive signals are yet unexplored. We have found that human CARs expressing specific ITAM sequences (ITAM-A, ITAM-B, or ITAM-C only) generate differing amounts of force and bond lifetimes after interacting with their target antigen, CD19. Therefore, a CAR may act as a mechanosensor similar to a TCR, discriminating the quality of the interaction with antigen as cellular-derived forces are applied to the bond. The higher transmission of force directly correlates with better anti-tumor efficacy in vitro and in vivo. Hence, understanding the mechanotransduction in CARs has important implications in “tuning” the activation of a CAR T cell without changing specificity.
Citation Format: Hilda Echelibe, Shubhabrata Majumdar, Elizabeth Kolawole, Baoyu Liu, Maria Bettini, Brian Evavold, Matt Bettini. CD3ζ ITAM diversity determines chimeric antigen receptor force and function [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 A024.
Abstract A030: A deeper understanding of tumor microenvironment modulation induced by IL13Ra2 CAR T cells in a patient with grade 3 ependymoma
Authors: Aftabizadeh Maryam , Aguilar Brenda , D'Apuzzo Massimo , Badie Behnam , Brown Christine E 
Published: February 2025

Abstract
Grade 3 ependymoma is classified as a fast-growing solid tumor that often occurs in the base of the brain with a median survival of less than two years. Despite aggressive standard treatments (surgery, radiation therapy and chemotherapy), grade 3 ependymoma remains uniformly fatal, especially if the tumor cannot be completely removed or if it spreads to other areas of the central nervous system (CNS). Achieving a responsive therapy with chimeric antigen receptor (CAR) T cell therapy has been a significant challenge due to evasive tumor microenvironment, specifically utilized by slid tumors, to resist therapy. Recent studies have highlighted the substantial role of glioma-associated stromal cells in solid tumors by depositing various collagen subunits, including COL1A1, within the extracellular matrix (ECM). This collagen deposition leads to increased ECM stiffness, modulating the tumor microenvironment, inducing immune suppression (e.g. SPP1 overexpression), and hindering T cell trafficking, ultimately worsening clinical outcomes and patient survival. To gain a better understanding of the role of the tumor microenvironment in CAR T persistence and efficacy, we designed and performed ultra-high plex immunofluorescent staining on tissue biopsies obtained from a patient with grade 3 ependymoma before and after treatment with IL13Ra2 CAR T cells. The patient has been received three CAR T infusions at weekly intervals. The tissues were stained for CD3, CD19 (CAR T cells), CD68, CD163, HLA-DR (macrophages), CD3, CD8 (endogenous T cells), SOX2 (stem cells), SPP1 (suppression) and COL1A1 (extracellular matrix). The presence of CAR T cells in tissue biopsies indicated persistence of IL13Ra2 CAR T cells for more than a year. Our preliminary analysis revealed an increase in the number of HLA-DR+ CD163+ macrophages within cellular neighborhoods associated with CAR T cells (around 50% of CD163+ express HLA-DR after treatment) as compared to baseline tumors, which suggests a dynamic interaction between myeloid subsets and CAR T cells within the tumor microenvironment. Ongoing experiments are currently investigating the presence of antigen presenting natural killer cells (CD56, HLA-DR), proliferative T cells (CD3, Ki67) and inflammatory macrophages and/or T cells (IFNg) to gain a better understanding of IL13Ra2 persistence in brain tumor patients.
Citation Format: Maryam Aftabizadeh, Brenda Aguilar, Massimo D'Apuzzo, Behnam Badie, Christine E Brown. A deeper understanding of tumor microenvironment modulation induced by IL13Ra2 CAR T cells in a patient with grade 3 ependymoma [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 A030.