bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1133: Novobiocin-mediated polymerase theta inhibition induces cGAS/STING pathway activation and T-cell infiltration in BRCA-associated cancers
Authors: Patterson-Fortin Jeffrey , Jadhav Heta , Phan Tin , D'Andrea Alan , Shapiro Geoffrey I. 
Published: June 2022

Abstract
Recently developed inhibitors of polymerase theta have demonstrated synthetic lethality in pre-clinical tumor models of BRCA-associated cancers. Given that other DNA damage repair inhibitor therapies, including PARP inhibitors, induce changes in the tumor immune microenvironment, we asked whether polymerase theta inhibition would also alter the tumor microenvironment in BRCA-associated cancers. We have demonstrated that novobiocin, a first-in-class inhibitor of the polymerase theta ATPase domain, induces both innate and adaptive immune responses through activation of the cGAS/STING pathway in BRCA-deficient tumor cells. Novobiocin-mediated polymerase theta inhibition generates micronuclei, activating the cGAS/STING pathway in both BRCA1-deficient MDA-MB-436 triple-negative breast cancer and BRCA2-deficient CAPAN1 pancreatic cancer models in vitro. Activation of the STING pathway upregulated the expression of interferon response genes, which was abrogated upon siRNA-mediated STING depletion. As an adaptive response, novobiocin also increased expression of PD-L1 in BRCA-deficient tumor cells. These effects were not observed in isogenic cell lines in which wild-type BRCA expression was corrected by add-back. Using a genetically engineered syngeneic mouse model of BRCA1-deficient breast cancer, we confirmed novobiocin-mediated activation of the cGAS/STING pathway in vivo, resulting in the induction of pro-inflammatory signaling and ultimately robust CD8+ T-cell infiltration and activation. Taken together, our findings demonstrate that novobiocin-mediated polymerase theta inhibition induces local and systemic immune responses in a cGAS/STING-dependent manner and provide a rationale for combining polymerase theta inhibition with immunotherapies for the treatment of BRCA-associated cancers.
Citation Format: Jeffrey Patterson-Fortin, Heta Jadhav, Tin Phan, Alan D'Andrea, Geoffrey I. Shapiro. Novobiocin-mediated polymerase theta inhibition induces cGAS/STING pathway activation and T-cell infiltration in BRCA-associated cancers [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 1133.
Abstract 1168: From clinical mutational data to a novel lung cancer mouse model -NF1inactivation cooperates withRASA1inactivation to drive non-small cell lung cancer (NSCLC)
Authors: Song Lin , Rodriguez Thaidy Y. , Olshen Adam , Collisson Eric 
Published: June 2022

Abstract
11% of non-small cell lung cancer (NSCLC) patients harbor NF1 mutations. The enrichment of NF1 mutations in lung adenocarcinoma (LUAD) cases that otherwise lack activated oncogene mutations indicates that NF1 loss may play a necessary role in the activation of the RAS pathway. However, conditional, biallelic loss of Nf1 in the mouse lung is insufficient for LUAD initiation over 2 years, indicating additional genetic or epigenetic events cooperate with Nf1 loss in lung tumorigenesis. To better understand NF1 mutant lung cancers, we analyzed a lung cancer dataset with 47227 patients’ genomic mutation data from Foundation Medicine (FMI) and found that NF1 mutations (5270 patients) are associated with a higher mutational burden compared to NF1 wild type lung cancer patients in the lung cancer patients’ clinical database. We then analyzed the AACR GENIE non-small cell lung cancer datasets for genes mutated concurrently with NF1 mutation. We found that NF1 mutation statistically significantly cooccurs with RASA1 (p &lt;0.001 for concurrency) and with TP53 mutations in the non-small lung cancer dataset. NF1-mutated samples lack other key driver oncogene mutations such as EGFR (p &lt;0.001 for mutual exclusivity). To functionally validate our findings of genetic cooperativity, we conditionally deleted the two key GAPs: Nf1 and Rasa1 (with Trp53) in vivo. Deletion of both Nf1 and Rasa1 but neither the Nf1 or Rasa1 deletion alone lead to LUAD when combined with Trp53 deletion. Our new mouse model provides a unique tool for our ongoing effort to understand the mechanism of Nf1 & Rasa1 tumor initiation in the lung and will aid preclinical investigations of targeted therapies.
Citation Format: Lin Song, Thaidy Y. Rodriguez, Adam Olshen, Eric Collisson. From clinical mutational data to a novel lung cancer mouse model -NF1inactivation cooperates withRASA1inactivation to drive non-small cell lung cancer (NSCLC) [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 1168.
Abstract 1200: COSMIC cancer mutation census: Classifying somatic coding variants by their potential to drive cancer
Authors: Sondka Zbyslaw , Harsha Bhavana , Pedro Helder , Dhir Nidhi Bindal , Hathaway Charlie , Nair Sumodh , Sondheimer Doron , Forbes Simon A. 
Published: June 2022

Abstract
Somatic mutations accumulate in cells throughout their life. Most of them do not bring any negative effect. However, certain mutations change protein behaviour, structure, or level of expression. More importantly, some mutations are known to initiate and drive oncogenic transformation. These mutations often make good therapeutic targets but recognising this small subset in a cancer sample is a major challenge. The average cancer cell carries a life-long baggage of somatic mutations, and the mutational process is sped up in these cells through genomic instability (one of the hallmarks of cancer). As a result, there are hundreds of thousands of variants of unknown significance identified through sequencing of cancer DNA. COSMIC Cancer Mutation Census (CMC) answers this challenge by identifying coding mutations with a potential to drive cancer. This is achieved by combining manually curated information regarding cancer genes and genetic variants with data on variant frequencies in cancer and non-cancer populations, and algorithmic evaluation of variant significance. It applies a simple and transparent set of rules to the whole set of coding mutations in COSMIC to identify variants with the highest potential of clinical relevance. In current version (v95, November 2021) the CMC describes 4.7 million somatic variants and segregates them into four tiers. Tier 1 is the highest confidence set. This set includes 1558 mutations that are found in Cancer Gene Census genes and are also described as pathogenic in cancer by ClinVar. Tiers 2 and 3 contain variants with less extensive evidence of involvement in carcinogenesis. The dN/dS algorithm is used to include variants that are under positive selection in cancer cells. Finally, mutations without evidence for driving cancer are classified as Tier 4. In addition to this classification, CMC integrates and presents the information used to prioritise variants, including their frequencies in various cancer types (COSMIC), germline frequencies (gnomAD), ClinVar annotations, dN/dS analysis results, and nucleotide and amino acid conservation. Data can be accessed and scrutinised through a dedicated website at https://cancer.sanger.ac.uk/cmc.
Citation Format: Zbyslaw Sondka, Bhavana Harsha, Helder Pedro, Nidhi Bindal Dhir, Charlie Hathaway, Sumodh Nair, Doron Sondheimer, Simon A. Forbes. COSMIC cancer mutation census: Classifying somatic coding variants by their potential to drive 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 1200.
Abstract 1210: Resolving clonal substructure from single cell genomic data in primary and metastatic tumors using CopyKit
Authors: Minussi Darlan Conterno , Wang Junke , Schalck Aislyn , Yan Yun , Wu Hua-Jun , Peng Cheng , Hu Min , Sei Emi , Edgerton Mary , Chen Hui , Contreras Alejandro , Hui David , Damodaran Senthil , Kopetz Scott , Lim Bora , Navin Nicholas 
Published: June 2022

Abstract
Advances in single cell copy number sequencing technologies have enabled the generation of data on hundreds to thousands of cells in parallel. Despite the rapid development in these technologies, there is a significant bottleneck for the analysis of the resulting large-scale datasets. Here we present CopyKit, a comprehensive and user-friendly toolkit for the analysis of single cell copy number data. CopyKit provides a suite of tools for pre-processing, QC, copy number inference, and subclone clustering to delineate the clonal diversity of tumors. We performed single cell copy number sequencing of 2977 cells from two breast tumor liver metastasis. CopyKit identified 4 and 12 subclonal populations, including amplification of PDGFRA, KRAS, and MYC as well as losses of PTEN, FOXO1, RB1, and BRCA1, many of which were spatially segregated in the tumor mass of the two tumors. Additionally, we applied CopyKit to study metastatic dissemination from a primary ER+ breast tumor with two matched metastatic sites and two colorectal carcinomas with matched liver metastatic tissues. This analysis demonstrated that the breast metastatic tumors selected for subclones that were lacking ERBB2 amplification in the primary site. Furthermore, the liver metastasis had deletions of chromosomes 18, 19, and 20p and a focal gain of FGFR1, while the pleural effusion acquired two additional focal gains on chromosome 8, including MYC. The colorectal metastatic tumors diverged from the primary tumor with copy number events affecting important cancer genes such as gain of SOX4, MYC, CDK8 and deletions of FHIT, CHEK1, and CHEK2. Collectively, this study shows that CopyKit provides a comprehensive set of tools for resolving clonal substructure from single cell copy number data for diverse applications in cancer biology.
Citation Format: Darlan Conterno Minussi, Junke Wang, Aislyn Schalck, Yun Yan, Hua-Jun Wu, Cheng Peng, Min Hu, Emi Sei, Mary Edgerton, Hui Chen, Alejandro Contreras, David Hui, Senthil Damodaran, Scott Kopetz, Bora Lim, Nicholas Navin. Resolving clonal substructure from single cell genomic data in primary and metastatic tumors using CopyKit [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 1210.
Abstract 124: PRDX4 links ER-specific redox vulnerability to innate immunity in pancreatic cancer
Authors: Malbeteau Lucie , Jain Pallavi , Harding Shane , Wouters Bradley , Koritzinsky Marianne 
Published: June 2022

Abstract
The prognosis of pancreatic ductal carcinoma (PDAC) remains dismal, with an overall 5-year survival rate of 7%. Immunotherapy (IT) has provided new hope for other hard-to-treat cancers, but PDAC has shown striking resistance to IT by orchestrating mechanisms of immune escape. This spurs an interest to identify novel strategies to improve PDAC sensitivity to IT. We recently unveiled that perturbating redox homeostasis by targeting the antioxidant protein peroxiredoxin 4 (PRDX4) render pancreatic cancer cells highly vulnerable. PRDX4 supports redox homeostasis by metabolizing H2O2 in the endoplasmic reticulum (ER), and its loss leads to oxidative stress and toxicity. Interestingly, cell death induced by PRDX4 depletion is accompanied by DNA damage and accumulation of cytosolic DNA, a potent primer for immune therapy. In line with that, PRDX4 knockdown results in the transcriptional upregulation of inflammatory genes, including type I interferons (IFNs), primary cytokines and interferon-stimulated genes (ISGs). Importantly, our data indicate that this induction is dependent on the critical regulator of the innate immune responses, STING, as treatment with a STING inhibitor, or a STING knockdown, substantially blunts their upregulation. It is known that following DNA damage detection, the ER-localized STING translocates to the Golgi, where it associates with the kinase TBK1 and mediates the induction of inflammatory target genes, depending on IRF3 and NF-κB transcription factors. We observe an activation of downstream STING effectors upon PRDX4 loss, and co-depletion with NFκB significantly rescues the upregulation of those genes. As such, we propose that PRDX4 links ER-specific redox vulnerability to innate immunity signaling in PDAC. Since PRDX4 loss causes increased DNA damage and inflammatory signaling, our preliminary data suggest that PRDX4 could be a novel therapeutic target that may act synergistically with immune checkpoint inhibitors.
Citation Format: Lucie Malbeteau, Pallavi Jain, Shane Harding, Bradley Wouters, Marianne Koritzinsky. PRDX4 links ER-specific redox vulnerability to innate immunity in pancreatic 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 124.
Abstract 126: Defining how oxidative stress drives the evolution of aggressive breast cancers
Authors: Mirabelli Caitlynn N. , La Selva Rachel , Heath John , Hébert Steven , Steinberger Jutta , Jiang Jialin , Kleinman Claudia , Huang Sidong , Ursini-Siegel Josie 
Published: June 2022

Abstract
Breast cancer is the most commonly diagnosed malignancy in women worldwide. It is a molecularly heterogeneous disease, which poses difficulties in the treatment of more advanced cancers. Despite this fact, the mechanisms contributing to the emergence of aggressive breast cancers remains poorly understood. We focus on reactive oxygen species (ROS), which are induced by a variety of stimuli in breast cancer cells. Moderately elevated ROS levels are tumor-promoting and facilitate the emergence of more aggressive tumours. Our laboratory has developed a unique model of HER2+ breast cancer that evolved to acquire more aggressive properties under conditions of chronic oxidative stress. We identified 20 transcription factors/co-regulators that were specifically overexpressed in these aggressive breast cancers, compared to their parental counterparts. We hypothesize that these transcription factors are central to the ability of breast tumors to adapt to chronic oxidative stress and acquire more aggressive properties. To test this, I have performed an in vivo functional shRNA screen to identify those transcriptional regulators that drive an aggressive phenotype. This will be followed by functional validation studies to interrogate whether and how these unique transcription factors overexpressed in aggressive breast cancers impact tumour growth, metastasis, and drug resistance. Mechanistically, we will explore whether and how these transcriptional responses mediate adaptive responses to tumor microenvironmental stressors, including altered metabolism, hypoxia, and tumor immune responses. This research will broaden our understanding of how breast cancers adapt to oxidative stress responses and represents a necessary first step in the development of novel therapeutics against these invulnerable malignancies.
Citation Format: Caitlynn N. Mirabelli, Rachel La Selva, John Heath, Steven Hébert, Jutta Steinberger, Jialin Jiang, Claudia Kleinman, Sidong Huang, Josie Ursini-Siegel. Defining how oxidative stress drives the evolution of aggressive breast cancers [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 126.
Abstract 127: Pre-exposure to stress-inducing agents increase the anticancer efficacy of focused ultrasound against aggressive prostate cancer cells
Authors: Murad Hakm Y. , Chandra Partha K. , Kelly Charles A. , Khurana Namrata , Yu Heng , Bortz Emma P. , Hong Shirley N. , Mondal Debasis , Khismatullin Damir B. 
Published: June 2022

Abstract
Despite the initial success in treatment of localized prostate cancer (PCa) using surgery, radiation or hormonal therapy, recurrence of aggressive tumors dictates morbidity and mortality. Focused ultrasound (FUS) is being tested as a targeted noninvasive approach to eliminate the localized PCa foci, and strategies to enhance the anticancer potential of FUS have a high translational value. Since aggressive cancer cells utilize oxidative stress (Ox-stress) and endoplasmic reticulum stress (ER-stress) pathways for their survival and recurrence, we hypothesized that pre-treatment with drugs that disrupt stress-signaling pathways in tumor cells may increase FUS efficacy. Using four different PCa cell lines, i.e. LNCaP, C4-2B, 22Rv1 and DU145, we tested the in vitro effects of FUS, alone and in combination with two clinically-tested drugs that increase Ox-stress (i.e. CDDO-me) or ER-stress (i.e. Nelfinavir). As compared to standalone FUS, significant (p&lt;0.05) suppressions in both survival and recurrence of PCa cells were observed following pre-sensitization with low dose CDDO-me (100 nM) and/or nelfinavir (2 µM). In drug pre-sensitized cells, significant anticancer effects were evident at a FUS intensity of as low as 0.7 kW/cm2. This combined mechanochemical disruption (MCD) approach decreased cell proliferation, migration and clonogenic ability, and increased apoptosis/necrosis and reactive oxygen species (ROS) production. Furthermore, although activated in cells that survived standalone FUS, pre-sensitization with CDDO-me and/or nelfinavir suppressed both total and activated (phosphorylated) NF-κB and Akt protein levels in surviving cells. Thus, a combined MCD therapy may be an effective noninvasive approach towards targeted elimination of aggressive PCa cells.
Citation Format: Hakm Y. Murad, Partha K. Chandra, Charles A. Kelly, Namrata Khurana, Heng Yu, Emma P. Bortz, Shirley N. Hong, Debasis Mondal, Damir B. Khismatullin. Pre-exposure to stress-inducing agents increase the anticancer efficacy of focused ultrasound against aggressive prostate cancer 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 127.
Abstract 1283: Single intra-tumoral injection of gaseous nitric oxide induces an adaptive immune response in a mouse CT-26 solid tumor model
Authors: Confino Hila , Goldshtein Matan , Levi Yakir , Malka Lidor , Avniel Amir , Lisi Steve , Wolf Ido 
Published: June 2022

Abstract
Background: Metastases are responsible for a significant portion of the morbidity and mortality in cancer patients. In situ destruction of tumor mass has been reported to provide the immune system with an antigen source for the induction of antitumor immunity, which can then attack distant metastases. Nitric oxide (NO) acts as a signaling molecule in multiple disease states, including cancer. NO has been shown to activate innate and adaptive responses of the immune system against tumors. In a previous Beyond Air study, 89% of CT26 tumor bearing mice treated with 50,000 parts per million (ppm) gaseous NO (gNO), rejected a secondary tumor induction. Here, we assessed the effects of a single intra-tumoral injection of gNO at concentrations of 20,000-50,000 ppm on immune cell recruitment in the tumor, spleen, and blood.
Methods: Mouse colon carcinoma (CT26) tumor bearing Balb/c mice underwent a single intra-tumoral treatment with 20,000 (n=3) or 50,000 (n=4) ppm gNO for 5 minutes. Mice treated with N2 (n=3), under the same conditions, served as a control. Tumors were removed 14 days post treatment and were histologically analyzed to test for immune cell penetration, inflammation, and necrosis. Immune cells from the spleen and blood were harvested 21 days post treatment and assessed via flow cytometry.
Results: 1. Treatment with 50,000 ppm gNO resulted in higher levels of inflammation, lymphocytes and T-cell infiltration, and necrosis within the tumor compared to both N2 and 20,000 ppm NO, as viewed histologically. 2. Flow cytometry analysis of immune cells from the spleen revealed a 1.3-fold increase of both B cells and IFN-γ expressing T cells with 50,000 NO treatment, and a 1.3-fold increase of B cells and 1.1-fold increase of IFN-γ expressing T cells with 20,000 NO treatment, compared to N2. 3. A 29% reduction of myeloid-derived suppressor cells (MDSCs) was detected in spleens of mice treated with 50,000 ppm gNO, and 40% for 20,000 ppm, compared to mice treated with N2.
Conclusion: Intra-tumoral injection of ultra-high doses of NO at 20,000 and 50,000 ppm gNO led to an increased recruitment and concentration of T and B cells. Additionally, 50,000 ppm NO led to an increase of lymphocyte infiltration to the tumor. Taken together, the data suggest that the increase in lymphocyte infiltration, B and T cell population, and the reduction of MDSCs, are indicative of an adaptive immune response that results in rejection of secondary tumors in gNO-treated mice.
Citation Format: Hila Confino, Matan Goldshtein, Yakir Levi, Lidor Malka, Amir Avniel, Steve Lisi, Ido Wolf. Single intra-tumoral injection of gaseous nitric oxide induces an adaptive immune response in a mouse CT-26 solid tumor model [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 1283.
Abstract 1285: Chemotherapy induces PD-L1 overexpression in CRC through NF-κBp65
Authors: Fan Fan , Ghosh Susmita , Ellis Lee , Bhattacharya Rajat 
Published: June 2022

Abstract
Background: The programmed cell death ligand (PD-L1) is an immune-inhibitory molecule that suppresses the activation of T cells, leading to the survival and growth of tumors. Overexpression of PD-L1 on cancer cells is associated with poor clinical outcomes in many types of cancers. PD-L1 upregulation contributes to chemoresistance in several types of cancer, but little is known about the mechanisms for alterations in PD-L1 expression associated with chemotherapy, especially in patients with CRC. Therefore, a better understanding of the mechanisms underlying changes in PD-L1 levels in response to standard of care chemotherapeutics in CRC is important. In this study, we examined the effects of thechemotherapeutics that are approved for the treatment of patients with CRC (oxaliplatin, 5FU, and irinotecan whose metabolite is SN38) in inducing PD-L1 expression and determining the molecular pathwaysinvolved in PD-L1 regulation.
Methods: PD-L1 expression in CRC cell lines was determined in vitro using western blotting and FACS analysis. Changes in PD-L1 transcript levels were measured using real time PCR. RPPA analyses were performed to identify proteins/pathways affected by chemotherapeutics. Pharmacological inhibitors and siRNAs were used to target specific proteins in determining their role in PD-L1 expression.
Results: We observed that oxaliplatin, 5FU, and SN38, resulted in induction of PD-L1 to various degrees. Interestingly this induction was observed in KRAS or BRAF mutated CRC cells but not in CRC cells with wild-type KRAS and BRAF. Increased levels of PD-L1 were due to increased transcription of PD-L1 resulting from exposure to chemotherapeutics. Chemotherapeutics lead to the activation of the DNA damage signaling mediator Chk1 and the downstream transcription activator NF-κBp65. Inhibition of Chk1 or NF-κBp65 resulted in abrogated PD-L1 induction in response to chemotherapeutic treatment.
Conclusion: PD-L1 can be induced following treatment with chemotherapy in CRC cells harboring mutations in BRAF or KRAS. Our findings provide a rationale for studies combining inhibitors of NF-κBp65 with standard of care chemotherapeutics in CRC to block PD-L1 expression and enhance the efficacy of chemotherapy damaged-tumor cell clearance by innate immunity that, in turn, should improve patient outcomes.
Citation Format: Fan Fan, Susmita Ghosh, Lee Ellis, Rajat Bhattacharya. Chemotherapy induces PD-L1 overexpression in CRC through NF-κBp65 [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 1285.