bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1301: T cell intrinsic androgen receptor activity regulates response to immunotherapy
Authors: Moran Amy E. , Polesso Fanny , Xia Zheng , Thomas George , Graff Julie 
Published: June 2022

Abstract
Immune checkpoint blockade has revolutionized the field of oncology inducing durable anti-tumor immunity in many solid tumors. In advanced prostate cancer patients, immunotherapy treatments have largely failed. Androgens have pleiotropic functions in prostate cancer; they are potent drivers of cancer cell growth and can suppress T cell function. In metastatic prostate cancer, intratumor androgen levels can remain high. Androgen deprivation therapy, the backbone of clinical care in prostate cancer, is classically administered to inhibit tumor cell growth. We postulated that this therapy also impacts tumor associated T cells. To test this hypothesis, we performed transcriptome profiling of individual leukocytes isolated from metastatic prostate cancer lesions resistant to androgen deprivation therapy (ADT) and androgen receptor (AR) antagonism and prior to treatment with a PD-1 inhibitor. We reveal that inhibition of AR activity in CD8 T cells prevented T cell exhaustion and improved responsiveness to PD-1 targeted therapy via increased IFNγ expression. Notably, AR directly bound to Ifng and eviction of this transcription factor with a small molecule significantly increased cytokine production in CD8 T cells. Furthermore, genomic deletion of Ar prevented chronically stimulated CD8 T cells from losing their ability to make IFNγ upon restimulation. Finally, we demonstrate that AR blockade sensitizes multiple tumor mouse models to effective checkpoint blockade by directly enhancing CD8 T cell function. Together, our findings establish T cell specific AR activity as one mechanism of immunotherapy resistance and show that targeting AR can improve immunotherapy outcomes.
Citation Format: Amy E. Moran, Fanny Polesso, Zheng Xia, George Thomas, Julie Graff. T cell intrinsic androgen receptor activity regulates response to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1301.
Abstract 1337: Pan-cancer analysis of immune-associated genes and pathways dysregulated by tobacco reveals osteopontin as a key mediator of smoking-associated carcinogenesis
Authors: Chakladar Jaideep , Shende Neil , Li Wei Tse , Ongkeko Weg M. 
Published: June 2022

Abstract
Background: Smoking remains a primary etiological agent of 12 different cancers. However, current understanding of the pathogenesis and progression of these smoking-induced cancers remains unclear. Though vaping has been proposed as a safer alternative to cigarette smoking, more research is needed to fully understand its potential to cause cancer. In particular, the chemicals in e-cigarette (e-cig) vapor have previously been demonstrated to cause immune dysregulation, similar to conventional cigarette smoke. In this study, we aimed to investigate the immune-associated (IA) genomic and transcriptomic landscapes of a panel of smoking-induced cancers in order to identify common and unique elements among these cancers and to determine whether certain immune dysregulations may be shared between smoking and vaping.
Methods: Whole genome sequencing data from tumors and adjacent normal samples was obtained from The Cancer Genome Atlas (TCGA) to compare the IA landscapes of 5 different smoking-induced cancers: head and neck squamous cell carcinoma (HNSCC), esophageal carcinoma (ESCA), bladder urothelial carcinoma (BLCA), lung adenocarcinoma (LUAD), and lung squamous cell carcinoma (LUSC). Differentially expressed genes were identified and correlated to tumor stage and patient survival. Gene Set Enrichment Analysis and ReactomeFi were used to correlate IA gene expression to cancer pathway enrichment. The REVEALER algorithm was used to correlate gene expression to copy number variations and mutations.
Results: We found that the genomic landscapes of smoking-induced cancers were largely unique. However, Osteopontin (OPN), an IA gene capable of regulating the EGFR and CD44 signaling cascades, was found to be upregulated along with its downstream targets in HNSCC, LUAD, LUSC, and ESCA smoking patients. Such upregulation was correlated to poorer prognosis for all 4 cancers. In vitro study indicated an upregulation of OPN and its downstream targets in cell lines exposed to both e-cig vapor and cigarette smoke.
Conclusions: Despite few similarities among the IA landscapes of these smoking-induced cancers, we suggest the importance of OPN upregulation in HNSCC, LUSC, LUAD, and ESCA pathogenesis caused by smoking and, potentially, vaping.
Citation Format: Jaideep Chakladar, Neil Shende, Wei Tse Li, Weg M. Ongkeko. Pan-cancer analysis of immune-associated genes and pathways dysregulated by tobacco reveals osteopontin as a key mediator of smoking-associated carcinogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1337.
Abstract 1343: CD8+ resident memory T (TRM) cells in tumors
Authors: Mami-Chouaib Fathia 
Published: June 2022

Abstract
Tumor-resident memory T (TRM) cells play an important role in cancer diseases. Accumulating evidence indicates that subpopulations of CD3+CD8+ tumor-infiltrating lymphocytes (TIL) are TRM cells, and are emerging as activated tumor-specific T cells. These TRM cells are characterized by expression of CD103 integrin and identify tumor-reactive cytotoxic T lymphocytes (CTL). Human lung tumor CD103+CD8+ TRM cells co-express CD49a and CD69, and are associated with a favorable prognosis. They also express a panel of T-cell inhibitory receptors, including PD-1, and are able to kill autologous tumor cells upon blockade of PD-1 with neutralizing antibodies. This CD103+CD8+ TRM subset also emerges as a predictive biomarker of response to PD-1 blockade and expands during anti-PD-1 treatment in responder, but not in non-responder lung cancer patients. It is now widely admitted that expression of CD103 on activated CD8+ T lymphocytes and persistence of TRM cells in epithelial tissues requires transforming growth factor (TGF)-β. This cytokine is secreted in the tumor microenvironment in its inactive form bound to latency-associated protein (LAP), and is activated by αV integrins on tumor cells and immune cells. Using multiplex immunofluorescence staining on cohorts of anti-PD-(L)1-treated lung cancer patients, we recently showed that decreased expression of tumor αV is associated with improved immunotherapy-related-progression-free survival (PFS) and correlates with an increased density of CD8+CD103+ TIL. Cancer cell αV activates autocrine TGF-β and participates in inducing CD103 on activated CD8+ T cells. Our more recent studies in mouse tumor models and human cancers demonstrate that different CD8+ TRM subsets participate to response different immune checkpoint inhibitors and therapeutic cancer vaccines.
Citation Format: Fathia Mami-Chouaib. CD8+ resident memory T (TRM) cells in tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1343.
Abstract 1391: PBMC humanized mouse model for ImmunoOncology drug evaluation
Authors: Xie Bin , Chen Hongkui , Hou Xin , Wen Danyi 
Published: June 2022

Abstract
Since the first immune checkpoint blocker Ipilimumab was approved by US FDA in 2011, more and more immune therapeutic drugs popped up. Humanized PBMC reconstitution in immune deficient mice is becoming a good model for evaluating therapeutic antibodies, especially the BsAb with one arm of anti-CD3 that mediates immune cells and another arm targeting a tumor antigen. However, limited window of dosing regimen triggered by graft-versus-host-disease (GvHD) after 30-40 days of reconstitution, and insufficient tumor-infiltrated immune cells naturally from reconstituted circulatory system hindered the widely application of the model in immunotherapy in development of multiple immune checkpoint inhibitors or immune agonists. To overcome this, LIDE has developed a unique human PBMC-cancer cells co-inoculated model instead. In our platform, cancer-priming PBMCs were mixed with the fresh cancer cells in MatriGel, co-inoculated into NCG mice to form a huPBMC well-infiltrated tumor tissue for immunotherapy. Our platform has been successfully helped evaluate biological function of PD1, Tigit, PVRIG, CD73, CD47, CD38, CD40, GITR Antibodies, Tgfb1/PDL1 BsAb, DLL3/CD3 BsAb in multiple cancers, such as melanoma, breast cancer and lung cancer.
Citation Format: Bin Xie, Hongkui Chen, Xin Hou, Danyi Wen. PBMC humanized mouse model for ImmunoOncology drug evaluation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1391.
Abstract 1399: Discovery and development of PARP inhibitor senaparib
Authors: Cai Sui Xiong , Ma Ning , Wang Xiaozhu , Jiang Yangzhen , Guo Mingchuan , Hsieh Chih-Yi , Tian Ye Edward 
Published: June 2022

Abstract
Poly (ADP-ribose) polymerase (PARP) is a key enzyme for DNA repair. PARP inhibitors have been shown to be effective against cancers with DNA repair defects, such as with BRCA1 or BRCA2 mutations. Several PARP inhibitors, including olaparib, rucaparib, niraparib, talazoparib, fluzoparib and pamiparib have been approved for the treatment of several types of cancer. In this presentation, we will report our discovery and development of senaparib (IMP4297) as a potent PARP inhibitor. We will present studies led to the identification of senaparib as a clinical candidate, as well as IND enabling in vitro and in vivo characterization of senaparib. Preclinical data indicated that senaparib had a wide therapeutic window (single agent effective dose of 2.5-21 mg/kg QD, in a BRCA1 mutated MDA-MB-436 human breast cancer xenograft model), which was confirmed in clinical studies (effective dose of 20-120 mg QD, and no DLT was found up to 150 mg QD). Senaparib is currently in several phase I/II, phase II and phase III clinical studies for the treatment of multiple tumor types either as single agent or in combination with temozolomide (TMZ). The most advanced study of senaparib is a phase III study as maintenance therapy in platinum-sensitive advanced ovarian cancer patients following first-line chemotherapy (ClinicalTrials.gov Identifier: NCT04169997).
Citation Format: Sui Xiong Cai, Ning Ma, Xiaozhu Wang, Yangzhen Jiang, Mingchuan Guo, Chih-Yi Hsieh, Ye Edward Tian. Discovery and development of PARP inhibitor senaparib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1399.
Abstract 1454: Interaction of obesity loci with energy intake and physical activity on the risk of colorectal cancer: Evidence from UK Biobank
Authors: Cho Sooyoung , Shin Aesun 
Published: June 2022

Abstract
Colorectal cancer is one of the common cancers worldwide. Obesity and physical activity are well-established risk factors for colorectal cancer. Studies have shown that as a consequence of energy metabolism, imbalance between energy intake and physical activity can lead to obesity. In order to precisely examine the close interrelationship between obesity, energy intake, and physical activity, we conducted a genome-wide interaction study of obesity with energy intake and physical activity. We also evaluated the interaction between obesity susceptibility loci with energy intake and physical activity for colorectal cancer using the nested case-control design. We analyzed data on participants in the UK Biobank. Genome-wide interaction analyses of obesity with energy intake and physical activity was performed on 65,514 and 250,369 participants who have information on genotype, body mass index, and energy intake/physical activity, respectively. We assessed the effect of obesity loci in the participants comprised 3523 colorectal cancer cases and 10,522 matched controls. The logistic regression model was used for finding obesity loci under a p-value threshold of 10-4. Odds ratios (ORs) and 95% confidence intervals (CIs) for colorectal cancer were estimated using a conditional logistic regression model. We found 21 loci and 44 loci of obesity with energy intake and physical activity, respectively. We also observed significant interaction of obesity loci with energy intake and physical activity for colorectal cancer. The obesity loci interacting with energy intake, including rs10828896 and rs7099260, were significantly interacted with physical activity for colorectal cancer. Rs426345 and rs12551684, which were the obesity loci interacting with physical activity, were significantly interacted with energy intake for colorectal cancer. The results of this study may provide evidence for bioenergetics in colorectal cancer carcinogenesis.
Citation Format: Sooyoung Cho, Aesun Shin. Interaction of obesity loci with energy intake and physical activity on the risk of colorectal cancer: Evidence from UK Biobank [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1454.
Abstract 1459: Identification of transcription factor enrichments in HPV+ head and neck cancer using ChIP-seq and cistrome analysis
Authors: Zamuner Fernando , Chan Spencer S. , Kessler Michael , Vorontsov Ilya , Danilova Ludmila , Erbe Rossin , Kelley Dylan , Guo Theresa , Imada Eddie , Fertig Elana J. , Kulakovskiy Ivan , Favorov Alexander , Gaykalova Daria A. 
Published: June 2022

Abstract
The subset of head and neck squamous cell carcinomas (HNSCC) that are driven by infection with the Human Papilloma Virus (HPV+ HNSCC) are increasing in prevalence and are defined by distinct biological signatures and mechanisms, such as abnormal transcriptional regulation. Here, we use optimized protocols to perform ChIP-seq and RNA-seq on patient surgical samples, which we use to define promoter, typical-enhancer, and super-enhancer (SE) regulatory regions with differential chromatin states (i.e. H3K27ac signal) between tumor and normal samples. We then leverage publicly available transcription factor (TF) cistrome data to test 372 TFs for tumor or normal specific enrichment across these differential regulatory regions. We identify 31 tumor-specific TF enrichments, such as TP53/63/73, NKX2-1, JUNB/D, FOSL1/2, E2F1/3, KLF3/4/5, SMAD3/4, TEAD1/4, TFAP2A/C, HIF1A, PPARG, GRHL2, EPAS1, and SNAI2. A number of these enriched TFs, including TP63, TP73, FOSL1, and E2F1, show both significantly increased expression in tumors and significant transcriptional reductions after JQ1 treatment. These results provide novel insight into the regulatory biology of HPV+ HNSCC, and suggest that the transcriptional networks and feedback loops governing TF expression and dysregulation in HPV+ HNSCC can be targeted using JQ1 treatment.
Citation Format: Fernando Zamuner, Spencer S. Chan, Michael Kessler, Ilya Vorontsov, Ludmila Danilova, Rossin Erbe, Dylan Kelley, Theresa Guo, Eddie Imada, Elana J. Fertig, Ivan Kulakovskiy, Alexander Favorov, Daria A. Gaykalova. Identification of transcription factor enrichments in HPV+ head and neck cancer using ChIP-seq and cistrome analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1459.
Abstract 1520: Replication stress and the inability to repair damaged DNA, the potential “Achilles' heel” of ecDNA+ tumor cells
Authors: Chowdhry Sudhir , Garcia Salvador , Nguyen Nam-Phuong , Celeste Anthony , Tse Edison , Milutinovic Snezana , Wilkinson Deepti , Hassig Christian , Kasibhatla Shailaja 
Published: June 2022

Abstract
Replication stress (RS) is a primary source of genomic instability, tumorigenesis, and cancer progression. RS is defined as an uncoupling of the replicative helicase and DNA polymerase, resulting in long stretches of fragile single stranded DNA (ssDNA) that is prone to damage. Excessive RS can result in replication catastrophe and cell death, which could be leveraged as a therapeutic strategy to treat high-RS cancers. While overexpression of certain oncogenes has been implicated as a driver of RS in cancer, the precise cellular conditions that result in RS have been difficult to predict. Here we demonstrate that high copy number amplification of genes on non-native extrachromosomal DNA (ecDNA) is associated with elevated RS in comparison to the same amplification on linear chromosomes. The ecDNA bearing cells display heightened basal levels of phosphorylated RPA, a hallmark of ssDNA, and decreased replication fork velocities. Consistent with this finding, the ecDNA amplified cells display greater sensitivity to inhibitors of deoxyribonucleotide production relative to cells harboring chromosomal gene amplification and to normal cells. Moreover, ecDNA bearing cells demonstrate a dramatic vulnerability to reduction in the conditionally essential amino acid glutamine, the primary nitrogen source for de novo nucleotide biosynthesis. The enhanced sensitivity to glutamine starvation is directly correlated with a reduction in ecDNA in tumor cells, and a corresponding selection for chromosomally integrated gene amplification in the surviving population. These phenotypes are rescued with nucleoside supplementation but not anaplerotic TCA cycle intermediates, further reinforcing a link between ecDNA and RS biology. Collectively, observations made here support a novel mechanism for oncogene-induced RS shaped by ecDNA driven oncogene amplification, revealing a novel molecular strategy to identify high-RS tumors and a therapeutic approach to target this “Achilles heel” of tumor biology.
Citation Format: Sudhir Chowdhry, Salvador Garcia, Nam-Phuong Nguyen, Anthony Celeste, Edison Tse, Snezana Milutinovic, Deepti Wilkinson, Christian Hassig, Shailaja Kasibhatla. Replication stress and the inability to repair damaged DNA, the potential “Achilles' heel” of ecDNA+ tumor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1520.
Abstract 1540: Accumulation of the long noncoding RNA Malat1 is a central driver and therapeutic target in metastatic lung cancer
Authors: Martínez-Terroba Elena , de Miguel Fernando J. , Robles-Oteiza Camila , Politi Katerina , Dimitrova Nadya 
Published: June 2022

Abstract
The identification and functional characterization of long noncoding RNAs (lncRNAs) have suggested a potential source of unexplored cancer therapy targets. The metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was initially identified as a transcript significantly overexpressed in metastatic lung adenocarcinoma (LUAD) and strongly correlated with poor patient outcomes. Despite decades of effort to elucidate Malat1 functions and mechanisms of action in cancer, two key questions have remained unresolved: 1) Is Malat1 overexpression a driver of LUAD progression? and 2) What is the mechanism by which Malat1 overexpression promotes LUAD progression? We utilized CRISPR activation to model Malat1 overexpression in patient-derived LUAD cell lines and in the autochthonous KrasG12D/p53-deficient murine model of LUAD. We observed that Malat1 overexpression cooperates with p53 loss to promote LUAD progression and metastatic dissemination in vivo. Compared to controls, Malat1-overexpressing KrasG12D/p53-deficient tumors appeared poorly differentiated and were characterized by excessive stromal infiltration. Single-cell RNA sequencing of dissociated tumors revealed that Malat1 overexpression triggers pleiotropic immune and stromal responses that favor a metastasis-permissive tumor microenvironment through the secretion of cytokines and metalloproteinases and the recruitment of CAFs and tumor-associated macrophages. Consistent with the in vivo findings, we observed that Malat1 overexpression in vitro does not affect the proliferation but promotes the migration of tumor cells and cancer-associated fibroblasts (CAFs) through secreted factors, including inflammatory cytokines. Importantly, targeting the stabilizing ENE domain of overexpressed Malat1 by two independent approaches in vitro - direct mutagenesis and non-degrading antisense oligonucleotide (ASO) - led to Malat1 destabilization and rescued the increased cellular migration. Similarly, cytokine-targeted blocking antibodies reversed the effects of Malat1 overexpression. In sum, our results represent the first successful efforts to model the increased Malat1 levels observed in human LUAD and to dissect the pro-metastatic molecular consequences of overexpressed Malat1. Our findings indicate that Malat1 is both necessary and sufficient to rewire metastatic pathways and our preliminary data support further efforts to therapeutically target Malat1 and its downstream mediators in metastatic LUAD.
Citation Format: Elena Martínez-Terroba, Fernando J. de Miguel, Camila Robles-Oteiza, Katerina Politi, Nadya Dimitrova. Accumulation of the long noncoding RNA Malat1 is a central driver and therapeutic target in metastatic lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1540.