bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A002: Analysis of tumor microenvironments in ovarian cancer patients receiving anti-BTN1A1 immunotherapy combined with standard-of-care therapy
Authors: Yoo Stephen S , Kim Youngseung , Lee Seung Hoon , Lee Soohyeon , Shin Sangjoon , LoRusso Patricia , Jung Hyunjin , Hong David 
Published: December 2023

Abstract
Background Immune checkpoints have emerged as key regulators of the immune responses against various tumor types. Butyrophilin 1A1 (BTN1A1) has been identified as a novel immune checkpoint protein that has the potential to be targeted for new immunotherapeutic treatment options. We have observed that BTN1A1 and PD-L1 expression are mutually exclusive in various human solid tumors. Recently, Nelmastobart (BTN1A1-targeting antibody, hSTC810) has successfully completed phase 1 clinical trials. To ensure the effectiveness of Nelmastobart, it is crucial to possess a profound comprehension of patients’ tumor microenvironment factors involved. Here, we report Opal multiplex immunofluorescence and Hyperion imaging mass cytometry approach that includes a deeper understanding of the spatial relationships in the tumor microenvironment.
Methods In a first-of-its-kind Phase 1 clinical trial, we are to characterize the safety profile and determine the maximum tolerated dose (MTD) and/or recommended Phase 2 dose (RP2D). Nelmastobart is administered as monotherapy at increasing dose levels of 0.3, 1, 3, 6, 10, and 15 mg/kg on a Q2W schedule. To understand the heterogeneity of the interaction mechanisms between immune cells and cancer cells, Patients’ FFPE specimens were stained cancer and immune cells using Opal multiplex immunofluorescence and analyzed Hyperion imaging mass cytometer.
Results We enrolled 45 pts with various cancers in a phase I trial of anti-BTN1A1, a novel immunotherapy. We tested doses from 0.3 to 15 mg/kg and found no DLTs. We report results for ovarian cancer. Opal multiplex immunofluorescence analysis showed that anti-BTN1A1 therapy increased the infiltration and activation of CD8+ T cells and NK cells and decreased the level of regulatory T cells in the tumor microenvironment. We also found the opposite expression of BTN1A1 in PD-L1-expressing cancer cells in KI67-negative tumors from ovarian cancer patients.
Conclusions Nelmastobart treatment activates immune response pathways and enhances anti-tumor activity with anti-PD-L1 combination therapy in vitro, in vivo, and clinical settings. The results of the study suggest that BTN1A1 is a novel immune checkpoint that can be targeted to overcome resistance to conventional therapies in cancer patients.
Citation Format: Stephen S Yoo, Youngseung Kim, Seung Hoon Lee, Soohyeon Lee, Sangjoon Shin, Patricia LoRusso, Hyunjin Jung, David Hong. Analysis of tumor microenvironments in ovarian cancer patients receiving anti-BTN1A1 immunotherapy combined with standard-of-care therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A002.
Abstract A016: Reprogramming of immune-enhancing neutrophils by subclinical low-dose endotoxin for the treatment of cancer
Authors: Zhang Yao , Li Liwu 
Published: December 2023

Abstract
Despite the recent resurgence of the pioneering concept of “Coley’s toxin” in ushering in anti-cancer immune therapies highlight by check-point inhibitors and CAR-T approaches, fundamental mechanisms responsible for the immune-enhancing efficacy of innate low-dose “Coley’s toxin” remain poorly understood. This study aims to reveal the novel reprogramming of immune-enhancing neutrophils by super-low dose endotoxin conducive for innate immunity-based anti-cancer therapies. We perform scRNAseq analyses and reveal that neutrophils trained by super-low dose endotoxin (SL-LPS) adopt a unique immune-enhancing cluster characterized by CD177loCD11BloCD80hiCD40hi. Transfusion of SL-LPS trained neutrophils into recipient mice with AOM/DSS-inducing colorectal tumors exhibit potent efficacy in reducing tumor burden. SL-LPS trained neutrophils show relieved suppression of adaptive T cells as compared to un-trained neutrophils in vivo and in vitro. Mechanistically, SL-LPS enables the generation of immune-enhancing neutrophils through activating STAT5 and reducing innate suppressor IRAK-M. Herein, we present evidence revealing the key principle that underlying the immune-enhancing effects of super-low dose endotoxin, unrevealing the long-held mystery of low-dose “Coley’s toxin” in generically boosting host anti-tumor defense. Our mechanistic and translational observations not only reveal fundamental mechanisms for re-programming immune-enhancing neutrophils, but also provide a proof-of-principle in developing innate neutrophil-based anti-tumor therapeutics.
Citation Format: Yao Zhang, Liwu Li. Reprogramming of immune-enhancing neutrophils by subclinical low-dose endotoxin for the treatment of cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A016.
Abstract A021: Nutrient competition in the tumor microenvironment alters NK cell metabolism in Pancreatic Cancer
Authors: Mehla Kamiya 
Published: December 2023

Abstract
Tumor cells present constant nutritional demand of macronutrients and micronutrients for their rapid growth needs. Often this nutrient limitation hampers the function of anti-tumor immune cells, which need basal energy levels to execute cytotoxic effects against malignant cells. Hence, we investigated nutrient limitation-induced metabolic alterations in NK cells that regulate the anti-tumor activity of NK cells. Using 2D cultures and PDAC organoid models, we demonstrate that pancreatic tumor cells exhaust vitamin B6 (VB6) in the co-culture milieu, causing reduced killing activity of NK cells. Additionally, we demonstrate that PDAC patients have significantly reduced plasma VB6 as compared to the healthy counterparts. This data aligns with the epidemiological studies showing that VB6 intake reduces the risk of pancreatic cancer incidence. Moreover, we noted a significant reduction in circulating VB6 in the pancreatic tumor-bearing mice as compared to healthy counterparts. Utilizing mass spectrometry-based metabolomics we noted that limitation of the VB6 prevents glycogen breakdown in NK cells. This was validated by follow up electron microscopy-based studies that demonstrated glycogen depots in NK cells that were very prominent upon inhibiting glycogenolysis. Metabolic tracing studies demonstrated that NK cells require VB6 for intracellular glycogen breakdown. Correspondingly, knocking down glycogen phosphorylase, a key enzyme involved in glycogen breakdown abrogated anti-tumoral NK cell function. Notably, supplementation of co-cultures in 2D and organoid models and in vivo orthotopic mouse models, with VB6 restored NK cell function against pancreatic tumor cells. In parallel, we observed dependence of tumor cell metabolism on VB6 for sustaining growth. Accordingly, we observed that tumor cells actively deplete VB6 in tumor microenvironments, as observed by comparing VB6 levels in circulation and in tumor interstitial fluids. Finally, we observed that VB6 supplementation in combination with inhibitors targeting VB6-driven metabolic pathway dependencies in tumor cells effectively enhances NK cell frequency and diminishes tumor burden in vivo. These studies demonstrate a novel role of glycogen breakdown as a critical energy source for activated NK cells and demonstrate, for the first time a key role of glycogenolysis in NK cell cytotoxic activities. Our results expand the understanding of the critical role of micronutrients (vitamin B6) in regulating cancer progression and anti-tumor immunity and open new avenues for developing NK cell-based immunotherapies for PDAC patients.
Citation Format: Kamiya Mehla. Nutrient competition in the tumor microenvironment alters NK cell metabolism in Pancreatic Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A021.
Abstract A045: Development of automated deep learning-based off-target distribution prediction system for CRISPR-Cas13 system
Authors: Chuai Guohui , Zhu Yanjing 
Published: December 2023

Abstract
CRISPR-Cas13 RNA editing system is a new member of the CRISPR-Cas gene editing system family, which can perform guided editing on RNA sequence. CRISPR-Cas gene editing system is currently one of the breakthrough technologies in life science, which is easy to operate, has a high editing efficiency and theoretically can perform guided editing on genome of any species. CRISPR-Cas9 system is the most commonly used CRISPR-Cas system, but it is mainly applied to DNA. Hence, fornon-destructive gene therapy and RNA virus detection, CRISPR-Cas13 system has its unique advantage. However, there are severe issues limiting its application, the most important one of which is off-target effect, namely the guide RNA points system to the wrong position causing non-targeted region edited, which leading to wrong expression spectrum of the cell. Therefore, based on automated deep learning and transfer learning techniques, this project aims to establishing an off-target distribution prediction system of CRISPR-Cas13 RNA editing system, in order to make high-specificity RNA editing possible.
Citation Format: Guohui Chuai, Yanjing Zhu. Development of automated deep learning-based off-target distribution prediction system for CRISPR-Cas13 system [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A045.
Abstract A053: Notch completes CD4 T cell help in CD8 T cells and ensures timely departure
Authors: Laurent Adrien Remi Gabriel , Karrich Julien , Babala Nikolina , Amsen Derk 
Published: December 2023

Abstract
Efficient activation, expansion and differentiation of CD8 T cells depend on help from CD4+ T cells. Such help is especially critical for CD8 T cell responses against tumor antigens. Priming of CD8 T cells in lymph nodes (LN) involves two steps that are geographically and temporally separate. Naïve CD8 T cells are first preactivated by a migratory dendritic cell (DC) carrying antigen from tissues. Preactivated CD8 T cells must then find and interact with lymph node-resident XCR1+ DC that have been licensed for optimal CD8 T cell activation via CD4 T cell-mediated activation of CD40. The efferent signals provided by licensed CD8+XCR1+ DC to install the CD4 T cell help program in CD8 T cells are incompletely known. Moreover, it is not clear whether and, if so, how premature lymph node exit by preactivated CD8 T cells before receipt of help is avoided. Here, we show that completion of CD4 help delivery is coupled to the ability to leave lymph nodes through activation of Notch receptors on CD8 T cells. Expression of Notch receptors is induced on naïve CD8 T cells during the first step of priming, while CD40 ligation elicits expression of Notch ligands on XCR1+ lymph node resident DCs. Using a DNA vaccination model that allows induction of CD8 T cell responses in the presence or absence of CD4 T cell help, we show that the Notch1/2 receptors are necessary in CD8+ T cells for CD4+ T cell help-dependent proliferation and acquisition of effector capability. Correspondingly, RNA sequencing revealed that more than half of the genetic CD4 T cell help program in CD8 T cells depends on Notch. Strikingly, activated Notch1/2 deficient and unhelped CD8 T cells remain largely stuck in lymph nodes owing to a lack of expression of the lymph node exit receptor S1PR5. Control of expression of S1PR5 by Notch therefore ensures that preactivated CD8 T cells remain in lymph nodes until completion of their activation process by receiving the CD4 T cell help signal.
Citation Format: Adrien Remi Gabriel Laurent, Julien Karrich, Nikolina Babala, Derk Amsen. Notch completes CD4 T cell help in CD8 T cells and ensures timely departure [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr A053.
Abstract B012: Transcriptional activation of mouse LINE-1 promoter by transcription factor YY1
Authors: Saha Karani , Nielsen Grace , An Wenfeng 
Published: December 2023

Abstract
Long interspersed element type 1 (LINE-1) are highly abundant non-LTR retrotransposons in mammalian genomes. LINE-1 hypomethylation and overexpression has been considered as a hallmark of many human cancers. Moreover, active movement of LINE-1 results in insertional mutagenesis and may contribute to cancer initiation or progression. Transcription is the initial and critical regulatory step for active LINE-1 movement. Therefore, investigating LINE-1 transcriptional regulation is important for our understanding of LINE-1’s role in cancer. In human LINE-1, an intact YY1 transcription factor binding motif is required for accurate transcription initiation. Two subfamilies of mouse LINE-1, Tf_I and Gf_I, have predicted YY1 binding motifs in their promoter region but their role in mouse LINE-1 transcription has not been characterized. In this study, we aim to investigate the role of these putative YY1 motifs in Tf_I and Gf_I subfamilies. Promoter sequences carrying the wild-type or mutant YY1 motifs were cloned into a dual-luciferase reporter system. Reporter assays showed transcription inactivation upon mutation of the YY1 motif for the Tf_I subfamily. The electrophoretic mobility shift assay (EMSA) demonstrated specific interaction of the Tf_I promoter sequence with the YY1 protein. Knockdown of YY1 protein level in cells reduced Tf_I promoter activity by 2-fold compared to the wild-type control. These results indicate that YY1 is a transcriptional activator of mouse LINE-1 Tf_I subfamily. On the other hand, our data suggest that the predicted YY1 binding site in the promoter of Gf_I subfamily is not functional due to one nucleotide deviation from the consensus YY1 motif. Indeed, restoring it to the conserved YY1 motif sequence enhanced the promoter activity by 6-fold. In EMSA, YY1 protein did not interact with the putative YY1 motif of the Gf_I subfamily but did so when the motif was restored to consensus YY1 sequence. Findings from our study increase our understanding of the transcriptional regulation of different mouse LINE-1 subfamilies, highlight the differing roles of YY1 in regulating human and mouse L1 transcription, and have important implications in the role of LINE-1s during cancer development.
Citation Format: Karani Saha, Grace Nielsen, Wenfeng An. Transcriptional activation of mouse LINE-1 promoter by transcription factor YY1 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr B012.
Abstract B027: ATR inhibition upregulates PD-L1 and potentiates the antitumor immune response to chemoimmunotherapy in small-cell lung cancer
Authors: Sen Triparna 
Published: December 2023

Abstract
Introduction: Small cell lung cancer (SCLC) is the most aggressive subtype of lung cancer, with a very poor prognosis and limited therapeutic options. Recent clinical trials of immune checkpoint blockade (ICB) combined with chemotherapy delivered only very modest benefit. Here, we identified that ataxia telangiectasia and rad3 related (ATR), the primary activator of the replication stress response, is highly enriched in SCLC and inhibition of ATR induced DNA damage and apoptosis in multiple SCLC models.
Methods: In this study, we performed genetic and pharmacological inhibition of ATR in a panel of human and murine SCLC models. Furthermore, we investigated the effect of ATR inhibition either alone or in combination with PD-L1 blockade either as a first-line or a second-line treatment in multiple immunocompetent mouse models of SCLC. The downstream effects of ATR inhibition was assessed by single-cell RNA sequencing, multicolor flow cytometry, western blot analysis, IHC, and genomic analysis.
Results: In multiple immunocompetent SCLC mouse models, ATR inhibition (ATRi) remarkably enhanced the anti-tumor effect of PD-L1 blockade. We next tested the ATR inhibition either alone or in combination with PD-L1 in the second-line regimen for SCLC. We observed that ATR inhibition in combination with PD-L1 blockade significantly reduced tumor volume and prolonged survival of aggressive mice models when compared to PD-L1 alone. Targeting ATR enhanced the expression of PD-L1, activated the cGAS/STING pathway, induced the expression of Type I and II interferon pathways, and caused significant infiltration of cytotoxic and memory/effector T-cells into tumors. Interestingly, ATRi also led to significant induction of MHC class I in SCLC in vitro and in vivo models. Analysis of pre- and post-treatment clinical samples from a proof-of-concept study of a first-in-class ATR inhibitor, M6620 (VX970, berzosertib), and TOP1 inhibitor topotecan, in patients with relapsed SCLCs validated the induction of MHC class I and interferon pathway genes, for the first time in this disease.
Conclusion: Our findings highlight ATRi as a potentially transformative vulnerability of SCLC, paving the way for combination clinical trials with anti-PD-L1. Given the increasing importance of immunotherapy for the management of SCLC and that ATR inhibitors are already in clinical trials, combining an ATR inhibitor with PD-L1 blockade may offer a particularly attractive strategy for the treatment of SCLC and contribute to the rapid translation of this combination into the clinic.
Citation Format: Triparna Sen. ATR inhibition upregulates PD-L1 and potentiates the antitumor immune response to chemoimmunotherapy in small-cell lung cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr B027.
Abstract B030: Characterizing MAIT cells in lung cancer: Insights from NSCLC and murine models
Authors: Wong Stephanie WY , Herbozo Carolina de Amat , Vukosich-Pennell Adriana , Wang Ben X , Ohashi Pamela S , Sacher Adrian G 
Published: December 2023

Abstract
Background: Mucosal-associated invariant T cells (MAIT) are unconventional αβT cells with a semi-invariant TCR that recognizes microbially-derived riboflavin metabolites presented by MHC-related protein 1 (MR1). Upon TCR engagement or cytokine stimulation, MAIT cells can rapidly secrete pro-inflammatory cytokines and cytotoxic molecules. The precise role of MAIT cells in the tumor-immune microenvironment remains unclear, as different reports have described them as either beneficial or detrimental to patient prognosis. Considering that MAIT cells constitute a notable proportion (2-4%) of the lung T cell repertoire in both humans and mice, the lung serves as an appropriate setting for ex vivo and in vivo MAIT cell characterization.
Objective: To characterize the phenotype of MAIT cells in lung tumor and uninvolved tissue from non-small cell lung cancer (NSCLC) specimens and orthotopic murine models. Results: Surgical resections of primary tumor and normal adjacent tissue from 29 treatment-naïve NSCLC patients were profiled using a comprehensive 31-marker spectral flow cytometry panel. MAIT cells expressing activating and inhibitory receptors including CD69, PD-1, CTLA-4, and CD39, were enriched in tumor tissue. Conversely, cytotoxic MAIT cells expressing granzyme B, granulysin, and CD57, were enriched in normal adjacent tissue. For in vivo studies, lungs of B6-MAITCAST mice, which harbor higher frequencies of MAIT cells compared to conventional mouse strains, were orthotopically injected with CMT167 tumor cells or vehicle control. MAIT cells from lungs injected with CMT167 tumors also expressed higher levels of activating and inhibitory receptors, and decreased levels of granzyme B. Additionally, there was a slight decrease in IFNγ and IL-17A production upon stimulation in vitro with PMA/ionomycin compared to vehicle controls. Conclusion: In the context of lung cancer, MAIT cells are activated but may lose functionality within the tumor-immune microenvironment.
Rationale: There is growing interest in the immunotherapeutic potential of unconventional T cells due to their rapid effector functions and non-MHC-restricted nature. By investigating the role of MAIT cells in the tumor microenvironment, we can comprehensively identify their biological advantages and limitations.
Citation Format: Stephanie WY Wong, Carolina de Amat Herbozo, Adriana Vukosich-Pennell, Ben X Wang, Pamela S Ohashi, Adrian G Sacher. Characterizing MAIT cells in lung cancer: Insights from NSCLC and murine models [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr B030.
Abstract B038: Targeting a Treg-specific deubiquitinase module for antitumor immune therapy
Authors: Fang Deyu 
Published: December 2023

Abstract
Checkpoint immunotherapies have transformed the treatment landscape for multiple human malignancies, but still with very limited success in treatment of many human cancers. A major hurdle is mediated by regulatory T (Treg) cells, which suppress the function of antitumor effector T cells. However, current approaches in targeting Treg to activate antitumor immune responses have shown only transient efficacy and are highly unspecific. Importantly, our recent studies, through unbiased CRISPR screening, identified the death from cancer cell signature gene USP22 required for optimal FoxP3 expression. USP22 genetic inhibition resulted in an approximately 15-25% reduction of FoxP3 expression in Tregs and partially diminishes Treg suppressive functions, which consequently results in elevated antitumor immunity against a broad spectrum of cancer types in mice. Therefore, a 20% reduction in FoxP3 protein expression, in this case, by USP22 inhibition, creates an ideal therapeutic window to boost antitumor immunity without triggering extensive autoimmune inflammatory responses (Nature, 2020). More recently, we further demonstrated that tumor microenvironment factors, including TGF-β, hypoxia, and tumor metabolites, induce Treg fitness/adaptation through selectively upregulating a deubiquitinase module, including USP21 and USP22 (Science Advances, 2022). Our ongoing study has identified USP22-specific small molecule inhibitors that largely diminish Treg fitness and dramatically inhibit tumor growth at a clinically relevant setting. In addition, our recent unpublished single-cell RNA-seq characterization revealed a novel function of the Treg-specific deubiquitination module in Treg terminal differentiation into a unique immune suppressive subpopulation, specifically in the tumor microenvironment. Collectively, our study defines a novel Treg deubiquitination module in tumor immunosurveillance and provides a rationale for the first Treg-specific targeting in antitumor immune therapy.
Citation Format: Deyu Fang. Targeting a Treg-specific deubiquitinase module for antitumor immune therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr B038.