bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 122: Hypoxia-reoxygenation couples enzyme and cofactor upregulation to quicken prostate cancer androgen biosynthesis and hormone therapy resistance
Authors: Qin Liang , Chung Yoon-Mi , Berk Michael , Naelitz Bryan , Klein Eric , Chakraborty Abhishek A , Sharifi Nima 
Published: June 2022

Abstract
Androgen deprivation therapy depletes circulating testosterone and is the mainstay treatment for advanced prostate cancer by suppressing tumor androgen receptor signaling. Despite initial treatment response, castration-resistant prostate cancer nearly always develops and remains driven primarily by the androgen axis. We investigated how changes in oxygenation affect androgen synthesis. Our study indicates that when chronic hypoxia is coupled to reoxygenation, prostate cancer cells efficiently metabolize androgen precursors to produce androgens and activate AR. Hypoxia induces 3βHSD1, the rate-limiting androgen synthesis regulator, and reoxygenation replenishes necessary cofactors. Therefore, hypoxia and reoxygenation are both essential for potent androgen synthesis. The EGLN1/VHL/HIF2α pathway promoted transcription of HSD3B1 by directly binding the 5’ regulatory region of HSD3B1. HIF2α overexpression facilitated prostate cancer progression, which largely depends on 3βHSD1. PT2399, a specific HIF2α inhibitor, prevented prostate cancer cell proliferation. Our study indicates HIF2α is a potential therapeutic target in prostate cancer.
Citation Format: Liang Qin, Yoon-Mi Chung, Michael Berk, Bryan Naelitz, Eric Klein, Abhishek A Chakraborty, Nima Sharifi. Hypoxia-reoxygenation couples enzyme and cofactor upregulation to quicken prostate cancer androgen biosynthesis and hormone therapy resistance [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 122.
Abstract 1220: Accurately genotyping HLA and KIR alleles using cfDNA assay and k-mer based algorithm for immunotherapy
Authors: Gnerre Sante , Tsui Brian Yik Tak , Jiang Tingting , Kim Yvonne , Ma Dustin , Wu Indira , Nagy Rebecca , Chuang Han-Yu 
Published: June 2022

Abstract
Background: HLA and KIR genotypes show great promise as emerging biomarkers for immune checkpoint inhibitors (ICIs) and understanding patient prognosis. Multiple studies have shown that HLA-I heterozygosity and high sequence divergence across alleles positively correlates with response to ICIs. However the high degree of polymorphism and allele sequence similarities in HLA and KIR present a challenge to accurate allele calling. To address these difficulties we developed kmerizer, a novel allele caller optimized for short fragments, such as reads from a cfDNA assay.
Methods: We tested kmerizer on MHC class1 and class2 genes, and on KIR genes, on both simulated datasets and real samples (cell lines and plasma samples). To assess the capability of the algorithm to distinguish highly homologous allele pairs, we simulated cfDNA-like fragments with errors on randomly selected allele pairs, and on allele pairs with a high level of homology. Twelve plasma samples and 19 reference cell lines fragmented to cfDNA size were analyzed using a NGS cfDNA assay. For plasma samples, paired buffy coats were sent to an external vendor for HLA typing using multiplex PCR-based amplicon and sequenced by 300bp paired-end reads.
Results: Of the 19 cell lines and 12 plasma samples for HLA typing (A, B, C, and DQB1 loci), kmerizer delivered 100% sensitivity with 98% specificity. On the simulated dataset, kmerizer achieved 99% sensitivity and specificity on all the MHC class1 and class 2 loci, and 90% sensitivity and specificity on all KIR loci, for both homozygous and heterozygous pairs. The novel allele caller kmerizer also demonstrated a lighter footprint on computational resource need: one deep-sequencing plasma sample on average can be processed in less than 2 minutes which is about 15 times faster than the most commonly used HLA typing tool HISAT21, which does not support KIR typing.
Conclusions: As utilization of ICIs increases, the use of genetic and genomic information to accurately identify patients more likely to respond to ICIs will be critical. kmerizer is a fast and highly sensitive and specific allele caller, and it can effectively call alleles on both HLA and KIR.
References: [1] Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8), 907-915.
Citation Format: Sante Gnerre, Brian Yik Tak Tsui, Tingting Jiang, Yvonne Kim, Dustin Ma, Indira Wu, Rebecca Nagy, Han-Yu Chuang. Accurately genotyping HLA and KIR alleles using cfDNA assay and k-mer based algorithm for 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 1220.
Abstract 125: The role of oxidative stress on the polyaneuploid cancer cell state in metastatic cancer
Authors: Li Melvin , Amend Sarah R. , Pienta Kenneth J. 
Published: June 2022

Abstract
Metastatic cancer is responsible for 90% of cancer deaths and is currently incurable due to resistance to all systemic anticancer therapies. Our lab hypothesizes that this resistance is driven by a subpopulation of cells in the tumor that enter the polyaneuploid cancer cell (PACC) state by undergoing a polyaneuploid transition (PAT). Cells in the PACC state are found in cell culture, xenograft, and genetically engineered mouse models, as well as in clinical samples. We have shown that cancer cells are induced to undergo a PAT upon exposure to external stress, such as chemotherapeutic treatments that include platinum-based therapy, etoposide, and taxane drugs. In addition, cells that enter the PACC state are resistant to that stress. One mechanism of therapy-induced cancer cell death is due to the resultant oxidative stress. We hypothesize that this oxidative stress drives a subset of cancer cells to undergo the PAT, thus enabling them to persist following treatment. To test the effects of oxidative stress on the PACC state, we treated cancer cells with cisplatin to induce the PAT and measured mitochondrial function and levels of reactive oxygen species (ROS). Using fluorescence microscopy with live-cell mitochondrial and ROS dyes, we showed that cells in the PACC state have higher mitochondrial mass, exhibit two to three times more mitochondrial activity per total mitochondria, and have over a five-fold increase in intracellular ROS levels per unit area when compared to typical cancer cell populations that they arise from. Moreover, PACCs exhibit a three-fold increase in their oxygen consumption rate and have higher expression of genes related to mitochondrial respiration and antioxidant pathways when compared to cells that did not undergo the PAT. Taken together, this suggests that cells in the PACC state may have a higher tolerance for stress since they can withstand higher amounts of ROS that result from both therapy and mitochondrial activity without exhibiting cell death. Our goal is to investigate how oxidative stress affects PACC formation and identify mechanisms of how PACCs manage stress to ultimately target these cells. If we can prevent PACC formation or find a method to eliminate cells in the PACC state, we can attack and resolve the issue of therapeutic resistance and incurability of metastatic cancer.
Citation Format: Melvin Li, Sarah R. Amend, Kenneth J. Pienta. The role of oxidative stress on the polyaneuploid cancer cell state in metastatic 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 125.
Abstract 1305: Tumor Treating Fields (TTFields) promote a pro-inflammatory phenotype in macrophages
Authors: Barsheshet Yiftah , Brant Boris , Voloshin Tali , Volodin Alexandra , Koren Lilach , Koltun Bella , Klein-Goldberg Anat , Zemer-Tov Efrat , Kan Tal , Paz Rom , Giladi Moshe , Weinberg Uri , Palti Yoram 
Published: June 2022

Abstract
Introduction: Tumor Treating Fields (TTFields) are low intensity (1-3 V/cm), intermediate frequency (100-500 kHz), alternating electric fields that are delivered non-invasively to tumors. TTFields therapy is approved in the US and Europe for the treatment of patients with glioblastoma or mesothelioma. In addition to an established anti-mitotic mechanism of action, previous studies have shown that TTFields-induced cell death stimulates anti-tumor immunity and promotes the maturation of dendritic cells. In the current research, the effect of TTFields on the polarization of unstimulated macrophages and the phenotypic regulation of M1 and M2 macrophages was investigated.
Methods: Bone marrow-derived macrophages (BMDMs) were generated from the femurs and tibias of 5-8-week-old Balb\C mice. TTFields (150 kHz) were applied for 24 h to unstimulated (M0 phenotype) BMDMs and BMDMs stimulated with LPS+IFN-γ (M1 polarization) or IL-4 (M2 polarization). Flow cytometry was used to identify surface expression of the macrophage biomarker F4/80 and activation markers CD80, major histocompatibility complex class II (MHC II), inducible nitric oxide synthase (iNOS), CD206, and ARG-1. Multiplexed secretion assays were conducted to quantify CXCL1 (KC), IL-18, IL-23, IL-12p70, IL6, TNF-α, IL-12p40, free active TGF-β1, CCL22 (MDC), IL-10, IL-6, G-CSF, CCL17 (TARC), and IL-1β as to examine the heterogeneity of the stimulated macrophages.
Results: The percentage of cells expressing the pro-inflammatory M1 markers CD80+ and MHC IIhigh was significantly increased following application of TTFields to polarized (M1 or M2) or unpolarized BMDMs, while expression of the M2 markers CD206 and ARG-1 was significantly decreased. A pro-inflammatory secretion pattern, with increased levels of CXCL1, IL-18, IL-23, IL-12p70, TNF-α, IL-12p40, CCL22, G-CSF, CCL17 and IL-1β was observed in cell supernatants of M1 and M2 stimulated BMDMs, and unstimulated M0 BMDMs, following delivery of TTFields. Taken together, TTFields polarized unstimulated BMDMs to the M1 phenotype, and induced phenotype skewing of M2 polarized BMDMs to the M1 phenotype.
Conclusions: TTFields therapy displays a novel immunoregulatory role in macrophage polarization and promotes a pro-inflammatory phenotype. Future investigations will focus on defining the underlying mechanism of this phenotypic skewing.
Citation Format: Yiftah Barsheshet, Boris Brant, Tali Voloshin, Alexandra Volodin, Lilach Koren, Bella Koltun, Anat Klein-Goldberg, Efrat Zemer-Tov, Tal Kan, Rom Paz, Moshe Giladi, Uri Weinberg, Yoram Palti. Tumor Treating Fields (TTFields) promote a pro-inflammatory phenotype in macrophages [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 1305.
Abstract 1317: The role of PAX8 in copy number-high uterine cancers: Inflammatory cytokine modulation
Authors: Karnolt Lauren , Okuka Maja , Read Susan , Dou Yongchao , Zhang Bing , Rutherford Thomas J. , Anderson Matthew L. 
Published: June 2022

Abstract
Paired Box 8 (PAX8) is a transcription factor clinically utilized as a histologic biomarker for cancers arising in tissues derived from the embryonic Mullerian tract. Although dysregulated PAX8 expression has recently been shown to promote the growth of ovarian and renal cancers, its role in uterine cancer remains poorly understood. Here, we hypothesized that overexpression of PAX8 promotes uterine cancer growth and metastasis. When 108 uterine cancer specimens were evaluated by mass spectroscopy, the highest levels of PAX8 were found in TP53-mutated, copy number (CN)-high specimens. In vitro, we found that targeting PAX8 expression resulted in decreased rates of both proliferation and apoptosis in multiple representative cell lines (ARK2 and ARK4). PAX8 knockdown also negatively impacted rates of in vitro migration and invasion assessed using commercially available Boyden chamber assays. Using whole-exome and transcriptomic profiling performed by Next Generation Sequencing, we found that PAX8 knockdown resulted in increased expression of 268 gene products by &gt;1.5-fold, and decreased expression of 179 gene products (adj p&lt;0.01; FDR&lt;1%). Specific gene products whose expression was altered by targeting PAX8 expression included IL-1β, IL-11, and MUC1. With qPCR, we confirmed that levels of IL-1β were 13.8-fold and 3.4-fold higher in cultures of ARK2 and ARK4 cells transfected with PAX8-specific siRNA, respectively, when compared to cultures transfected with a nontargeting control (p&lt;0.01). Using these transfections, we also confirmed increased expression of IL-11 in ARK2 cells (RQ=3.22, p&lt;0.01) and ARK4 cells (RQ = 2.28, p&lt;0.01), and increased expression of MUC1 in ARK2 cells (RQ=1.13, p&lt;0.01). Collectively, our findings demonstrate that PAX8 regulates the proliferation of CN-high uterine cancers, potentially through the regulation of IL-1β expression. Notably, our data also implicates PAX8 expression as a key mediator of the inflammatory response to these aggressive cancers. Key differences in PAX8’s relationship with proliferation and these select few signaling molecules, compared to what is seen in other PAX8-dependent cancers, suggest unique roles for PAX8 as an oncogene in uterine cancers.
Citation Format: Lauren Karnolt, Maja Okuka, Susan Read, Yongchao Dou, Bing Zhang, Thomas J. Rutherford, Matthew L. Anderson. The role of PAX8 in copy number-high uterine cancers: Inflammatory cytokine modulation [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 1317.
Abstract 1332: Adar1 impacts pancreatic homeostasis and pancreatic tumor biology
Authors: Rupani Dhwani , Cowan Robert , Gates Chris , McAllister Florencia , Rhim Andrew 
Published: June 2022

Abstract
Adenosine-to-Inosine (A-to-I) RNA editing is mediated by Adenosine deaminase acting on RNA (Adar) enzymes. The resulting A-to-I edit in RNA alters its post-transcriptional processing making Adar1 a critical regulator of gene expression. In line with its role in gene regulation, Adar1 has been implicated in development and organogenesis. We investigated the role of Adar1 in pancreatic development and homeostasis, and observed that though Adar1 is not required for pancreatic development, it is essential for pancreatic homeostasis. We observed that loss of Adar1 can stimulate a Mavs-mediated innate immune pathway and results in influx of immune cells in the pancreas. Pancreatic tumors are notorious for their immunosuppressive microenvironment. Since loss of Adar1 can activate a Mavs-mediated innate immune pathway, we next investigated the role of ADAR1 in human pancreatic ductal adenocarcinoma cell lines. We developed a bioinformatics pipeline, Cancer RSNV (RNA Single Nucleotide Variant) Identifier and Annotator (CRIDA) to identify A-to-I RNA edits in pancreatic cancer and observed wide-spread ADAR1-mediated RNA editing in pancreatic cancer cells. We analyzed genes that are differentially regulated between ADAR1 knockdown and control cells, and observed a differential immune signaling. Together, our data suggests that Adar1 is important for pancreatic homeostasis and tumor biology.
Citation Format: Dhwani Rupani, Robert Cowan, Chris Gates, Florencia McAllister, Andrew Rhim. Adar1 impacts pancreatic homeostasis and pancreatic tumor biology [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 1332.
Abstract 1352: In vivo CRISPR screening identifies mediators of immune evasion in KRAS-mutant lung cancer
Authors: Boumelha Jesse , Romero-Clavijo Pablo , de Carné Sophie , Molina-Arcas Miriam , Downward Julian 
Published: June 2022

Abstract
Oncogenic KRAS mutations drive tumourigenesis in 30% of non-small cell lung cancer (NSCLC). Despite much effort, targeted therapies that aim to directly inhibit signalling pathways downstream of KRAS have limited clinical benefits for NSCLC patients, but the recent approval of PD-1/PD-L1 antibodies has led to striking durable responses. However, only a fraction of patients respond and therefore a deeper understanding of the mechanisms that drive immune evasion are required in order to broaden the clinical efficacy of immunotherapy. Increasing evidence suggests that oncogenic signalling pathways greatly influence the tumour immune landscape to impair anti-tumour immune responses. We therefore aim to understand the mechanisms by which KRAS signalling mediates immune evasion in lung cancer.
Current mouse models of KRAS-mutant lung cancer are poorly immunogenic, limiting investigations into tumour-immune interactions. To overcome this, we generated a novel transplantable KRAS-mutant lung cancer model, KPAR1.3, which triggers spontaneous anti-tumour immune responses and is sensitive to immune checkpoint blockade. To identify mechanisms of immune evasion we carried out an in vivo pooled CRISPR-Cas9 screen targeting 240 KRAS-regulated genes using this novel immunogenic model. This identified the prostaglandin synthase COX-2 as a mediator of immune evasion and its expression was driven by KRAS in multiple models of mouse and human lung cancer. Loss of COX-2 promoted a pro-inflammatory tumour microenvironment and sensitised tumours to both innate and adaptive anti-tumour immune responses. Furthermore, therapeutic COX inhibition extended the survival of tumour-bearing mice and synergised with PD-1 blockade. Together these data suggest that targeting KRAS-driven mechanisms of immune evasion could broaden the clinical efficacy of immunotherapy in KRAS-mutant NSCLC.
Since the approval of immunotherapy, a novel class of mutant-specific KRAS-G12C inhibitors have recently been approved for the treatment of KRAS-mutant NSCLC, however acquired drug resistance is common. We are therefore also currently investigating whether the inhibition of the COX-2/PGE2 axis enhances the therapeutic benefit of KRAS-G12C inhibitors.
Citation Format: Jesse Boumelha, Pablo Romero-Clavijo, Sophie de Carné, Miriam Molina-Arcas, Julian Downward. In vivo CRISPR screening identifies mediators of immune evasion in KRAS-mutant 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 1352.
Abstract 1354: Regulation and roles of polyamines in CD8+ T cell fate and function
Authors: Elmarsafawi Aya G. , Hesterberg Rebecca S. , Cleveland John L. 
Published: June 2022

Abstract
CD8+ T cells play central roles in tumor immune surveillance and are major effectors in adoptive cell therapy (ACT). Thus, strategies that enhance their functions are an urgent clinical need. Metabolic reprogramming determines T cell fate and function, where glycolysis principally drives an effector phenotype while oxidative phosphorylation (OxPhos) drives T cell memory [1]. However, the roles of amino acid catabolism in controlling effector and memory CD8+ T cell fate and function are less well understood [1, 2]. Glutamine is essential for nucleotide biosynthesis and as an anaplerotic fuel source for the tricarboxylic acid (TCA) cycle. Isotope tracing experiments with 13C glutamine or 13C arginine revealed that glutamine is the major source of polyamines in activated CD8+ T cells. Further, activation of CD8+ T cells provokes marked increases in the expression and activity of enzymes that direct polyamine biosynthesis, specifically ornithine decarboxylase (Odc), spermidine synthase (Srm) and spermine synthase (Sms), as well as to increases in the polyamines putrescine, spermidine and spermine. Notably, pharmacologic inhibition of Odc using difluoromethylornithine (DFMO), or genetic deletion of Odc using CD8+ T cells from CD4-Cre;Odcfl/fl mice, augments cytokine production in activated CD8+ T cells, including IFN-γ, TNF-α and granzyme B. Further, metabolic flux analysis indicates that DFMO treatment switches the metabolism of activated CD8+ T cells to rely on OxPhos, a phenotype found in CD8+ tissue resident memory (TRM) cells that play key roles in tissue and anti-tumor immunity anti-tumor reactivity. Indeed, inhibition or loss of Odc augments other TRM phenotypes, including increases in CD69high;CD44high;S1PR1low;CD62Llow cells that define the TRM phenotype. In addition, ACT of DFMO treated CD8+ T cells augments their survival in vivo and augments the generation of CD69+CD103+CD69+CXCR6+ and Ly6C+ TRMs in the bone marrow. Finally, DFMO treatment enhances IFN-γ and TNF-α production in human TILs, and co-treatment with TGF-β polarizes TILs into CD69+CD103+ and CD69+CD49a+ TRM-like cells. We conclude that polyamines are a metabolic check point in CD8+ TRM generation and are an actionable target to improve the anti-tumor immunity of T-cell based immunotherapies.
Citation Format: Aya G. Elmarsafawi, Rebecca S. Hesterberg, John L. Cleveland. Regulation and roles of polyamines in CD8+ T cell fate and function [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 1354.