bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5836: Autophagy inhibition as a new therapeutic strategy for cancers with transcription elongation defects
Authors: Muhammad Belal , Vinnedge Lisa , Komurov KAkajan 
Published: September 2020

Abstract
Increasing evidence suggests that the tumorigenic process is driven by various forms of transcriptional and epigenetic defects beyond somatic mutations. We recently described a novel non-genomic phenomenon associated with tumorigenesis that we call Transcription Elongation Defects (TEdeff), which is characterized by high levels of truncated transcripts, intron retention, and loss of gene body exon expression. The TEdeff phenotype exists in more than 20% of all human tumors and is linked to immunotherapy resistance (Modur et al, 2018). The aim of this study was to find a new therapeutic strategy for these types of tumors by targeting cellular pathways that are essential for TEdeff tumor survival. Computational analyses of RNA-sequencing data indicate that TEdeff tumors have extensive overexpression of the cytoplasmic protein homeostasis machinery, including several components of autophagy and proteasome degradation pathways. This strongly suggests that these cells may have increased dependency on cellular protein quality control due to elevated proteotoxic stress. Accordingly, we experimentally show that TEdeff cancer cell lines have a profound accumulation of protein aggregates (aggresomes) that appear to be associated with autophagy for clearance. Importantly, TEdeff cells, but not control cells with proficient transcription elongation (TEprof), are highly sensitive to autophagy inhibitors like chloroquine (CQ), but not proteasome inhibitors, which indicates their increased dependency on autophagy for survival. We also show evidence that the proteasomal degradation system may be defective in TEdeff cells, further supporting the hypothesis that these cells are dependent on alternative protein quality control mechanisms. Mechanistically, we propose that blocking the autophagy pathway maximizes proteotoxic stress, due to the accumulation of toxic aggresomes and proteins generated from defective transcripts, leading to a strong synthetic lethality in TEdeff cells. Therefore, autophagy inhibition may be a potent treatment strategy for TEdeff tumors, which are inherently resistant to current immunotherapies.
Citation Format: Belal Muhammad, Lisa Vinnedge, KAkajan Komurov. Autophagy inhibition as a new therapeutic strategy for cancers with transcription elongation defects [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5836.
Abstract 5839: The unfolded protein response gene Ire1α is required for tissue renewal and normal differentiation in the mouse tongue and esophagus
Authors: Chalmers Fiona E. , Stairs Douglas B. , Glick Adam B. 
Published: September 2020

Abstract
IRE1α is a well-characterized stress response signaling protein that adapts the cell to conditions of endoplasmic reticulum (ER) stress. In addition to well-established sources of ER stress such as viral infection, hypoxia and nutrient deprivation, it has recently been proposed that the morphological and epigenetic changes associated with routine cell differentiation are also a source of ER stress for the cell, and that IRE1α has an important role in adapting the cell to its newly differentiated state. Here, we provide evidence that IRE1α is essential for the differentiation of stratified squamous epithelium. We utilized mice expressing K14CreERT2 and floxed IRE1α to enable tamoxifen-inducible deletion of IRE1α targeted to the basal layer and stem cells of stratified squamous epithelium. After tamoxifen injection, IRE1α knockout mice displayed severe weight loss resulting in death within 10 days of treatment. Histological analysis revealed that epithelial homeostasis in the tongue and esophagus was severely disrupted leading to significantly decreased food intake and, as a result, death. The tongue epithelium and esophageal mucosal layer were found to be significantly thinner, and filiform papillae were lost from the tongue. Immunohistochemical staining showed significant downregulation of the proliferative marker Ki67, as well as a marker of differentiation, Sox2, suggesting an almost complete loss of tissue renewal as early as four days after IRE1α deletion. This work highlights the complexity of IRE1α signaling beyond adaptation to external sources of stress and proposes a role of IRE1α in the normal physiology of tissue homeostasis. As inhibition of the IRE1α signaling pathway has been proposed as a therapeutic target in certain cancers, an increased understanding of how broad the scope of IRE1α activity is may provide insight into potential side effects resulting from these treatments.
Citation Format: Fiona E. Chalmers, Douglas B. Stairs, Adam B. Glick. The unfolded protein response gene Ire1α is required for tissue renewal and normal differentiation in the mouse tongue and esophagus [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5839.
Abstract 584: TGN1412 induces dose and time dependent human cytokines in a humanized PBMC mouse model for cytokine release syndrome
Authors: Yang Hongyuan , Jiao Jing , Cai Danying , Cheng Mingshan , Brehm Michael , Grainer Dale , Shultz Leonard , Keck James 
Published: September 2020

Abstract
There have been remarkable progresses in the development of immune therapies for cancer. However, the promise of immune therapy comes with significant challenges of a variety of adverse effects. Due to the lack of predictive preclinical model to evaluate antibody mediated adverse effects, TGN1412, a humanized anti-CD28 monoclonal antibody which acts as a superagonist of CD28 to activate T cells, unfortunately caused life-threatening cytokine release syndrome (CRS) during the first-in-man trial. Therefore there is a critical need for translational protocols that could predict immune toxicity more accurately.
We have developed a sensitive and reproducible PBMC-humanized mouse model that can measure cytokine release induced by bispecifics or checkpoint inhibitors in vivo. In this study the utility of this platform was demonstrated using TGN1412 as a model. NSG™ mice or derivative strains such as SGM3 mice were engrafted with human PBMCs for 6 days before being treated with TGN1412 at different concentrations (0.2, 1.0 and 2 mg/kg). Mouse blood was collected at 1, 2, 4, 6, 24 and 48 hours post dose for flow cytometry and cytokine analysis. We observed dose and time dependent increase of human IFN-γ, TNFα, IL-2, IL-4, IL-6 and IL-10 levels in the serum following TGN1412 treatment with TNFα peaking at 1 h and the others peaking at 2-4 h post dose. A significant decrease in hCD45+ cells was observed in the peripheral blood collected at 6h post treatment. TGN1412 was tested in the humanized NSG™ mice with PBMCs from 7 different donors, and a significant decrease in hCD45+ cell population in the peripheral blood was observed in all donors. We have demonstrated that the novel mouse model using PBMC-humanized NSG™ can successfully detect CRS induced by TGN1412 in a dose and time dependent manner, suggesting that indeed CRS could be a strong adverse effect associated with TGN1412 treatment in human. Our data supports that our newly developed mouse model for CRS assessment may be a valuable tool to assess in vivo safety of experimental human therapeutic antibodies including immune checkpoint inhibitors and bispecifics with better reliability than an in vitro assay.
Citation Format: Hongyuan Yang, Jing Jiao, Danying Cai, Mingshan Cheng, Michael Brehm, Dale Grainer, Leonard Shultz, James Keck. TGN1412 induces dose and time dependent human cytokines in a humanized PBMC mouse model for cytokine release syndrome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 584.
Abstract 5840: IRE1a is required for ROS homeostasis and PERK protein stability in response to UVB irradiation
Authors: Son Jeongin , Worrel Stephen , Glick Adam 
Published: September 2020

Abstract
IRE1α is required for ROS homeostasis and PERK protein stability in response to UVB irradiation
UV induced stress is one of the primary driving factors of human skin cancer. UV irradiation can activate Endoplasmic Reticulum (ER) stress and the Unfolded Protein Response (UPR). Inositol-requiring enzyme 1a (IRE1α) is one of the key players in the UPR. Previous studies have shown that UVB irradiation can activate IRE1α in human and mouse skin cells, but the function of IRE1α in the UV response has not yet been characterized. Here we show that IRE1α expression is transiently downregulated after UVB irradiation and that in the absence of IRE1α the stability and activation of PKR-like endoplasmic reticulum kinase (PERK) is compromised. Basal levels of PERK are reduced in the absecence of IRE1α. Following UV irradiation, loss of IRE1α not only causes rapid degradation of PERK protein but also suppresses phosphorylation of the PERK target, Nuclear factor erythroid-2-related factor 2 (NRF2), and NRF2 dependent antioxidant gene expression. Similarly, PERK protein is rapidly degraded following thapsigargin treatment in the absence of IRE1α, suggesting a general regulation of PERK stability by IRE1α. Additionally, keratinocytes with either knockout or knockdown of IRE1α have increased intracellular ROS and cytosolic calcium. Overexpression of both wildtype and RNase defective human IRE1α can rescue the increased ROS levels. Additionally, the increased ROS is also suppressed by treatment with an inhibitor of the ER localized Inositol triphosphate receptor (InsP3R) which regulates calcium efflux from the ER. Because PERK regulates cytosolic calcium through inhibiting InsP3R, our result suggests that IRE1α is critical for suppressing intracellular ROS through stabilization of PERK. We conclude that crosstalk between IRE1α and PERK is essential for the basal and UVB- induced oxidative stress response, and this may have important implications for UV related damage and skin cancer development.
Citation Format: Jeongin Son, Stephen Worrel, Adam Glick. IRE1a is required for ROS homeostasis and PERK protein stability in response to UVB irradiation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5840.
Abstract 585: Colitis in tumor-bearing mice undergoing checkpoint inhibitor therapy
Authors: Parello Caitlin S. , Cuiffo Benjamin G. , Reardon Kasey , Fusco Alexandria , Van Dam Brett , Lyng Gregory D. , Sonis Stephen T. 
Published: September 2020

Abstract
Checkpoint inhibitor (CPI) therapy represents an exciting new treatment option for patients with advanced malignancies. However, several adverse events (AEs) that affect multiple body systems are associated with CPI treatment, including colitis. The mechanisms mediating these AEs remain to be fully elucidated. That mice treated with CPI fail to develop the spectrum of AEs observed in patients hampers the field's ability to develop supportive care treatment options. Here we sought to examine colitis in tumor bearing mice undergoing CPI therapy. Briefly, naïve TH cells and Treg cells were harvested from C57Bl/6 donor mice and were adoptively transferred into RAG2−/- recipients. Animals were inoculated with B16F10 cells into the left flank seven days later. T cell engraftment was assessed after 13 days, and animals were randomized into treatment groups by rate of T cell engraftment; animals were treated Q3D with either vehicle or anti-CTLA4 for an additional four weeks. Animals were monitored for body weight loss and systemic AEs (gastrointestinal, pulmonary, neurological) daily and tumor volume was measured by digital caliper three times per week. Extent of colitis was evaluated by video endoscopy at several timepoints and colitis severity was scored using a 0-4 scale. Animals developed body weight loss approximately two weeks after T cell transfer and CPI treatment increased the severity of body weight loss observed. Colitis was seen by video endoscopy within a similar timeframe. Mean tumor volume was decreased in animals treated with CPI as compared to those treated with vehicle. Diarrhea, pulmonary symptoms, and neurological symptoms were observed in a subset of animals over the study period; anti-CTLA4 treatment increased the overall incidence of pulmonary symptoms. These data demonstrate the utility of this system for assessment of colitis or other AE supportive care treatment options in the context of CPI-treated, tumor-bearing mice.
Citation Format: Caitlin S. Parello, Benjamin G. Cuiffo, Kasey Reardon, Alexandria Fusco, Brett Van Dam, Gregory D. Lyng, Stephen T. Sonis. Colitis in tumor-bearing mice undergoing checkpoint inhibitor therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 585.
Abstract 5854: New therapeutic targets of ER positive breast cancer are revealed through nascent RNA transcription time series
Authors: Azofeifa Joseph , Basken Joel , Lai Maria , Langendorf Ryan , Norris Laura , Read Tim , Robbins-Pianka Adam 
Published: September 2020

Abstract
Mechanistic understanding of Estrogen Receptor (ER) signaling will lead to new therapeutic targets for ER positive breast cancer. To this end, Arpeggio performed nascent RNA sequencing following estradiol (E2) treatment in MCF7 breast cancer cells every 15 minutes for 6 hours. To date, our study represents the densest time series of estrogen signaling ever reported. Arpeggio noted three transcriptional waves following E2 treatment: peaks at 30 minutes, 2.5 hours and 5 hours, respectively. We noted that the early response was enriched for canonical ER signaling, however, mid and late response were enriched for metabolic processes. Because our study was statistically powered with 24 time points, we could use delay-coordinate embedding to look for causal gene interactions. We implicated NME2 as the causal driver of the 5-hour transcriptional wave. Indeed, NME2 and Estrogen Receptor (ER) have been shown to co-localize where NME2 blocks ER effect. Our study represents a new methodology for target discovery in hormone-driven cancers.
Citation Format: Joseph Azofeifa, Joel Basken, Maria Lai, Ryan Langendorf, Laura Norris, Tim Read, Adam Robbins-Pianka. New therapeutic targets of ER positive breast cancer are revealed through nascent RNA transcription time series [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5854.
Abstract 5861: BOP1 expression contributes to the proliferative/invasive phenotype in melanoma
Authors: Stark Mitchell S. , Hammerlindl Sabrina , Tom Lisa , Jagirdar Kasturee , Tan Jean-Marie , Schaider Helmut , Sturm Richard A. , O'Brien Blake , Walsh Michael , Collins Angus , Soyer H.Peter 
Published: September 2020

Abstract
We recently performed whole exome sequencing of 30 melanocytic nevi which surprisingly revealed numerous regions of copy number loss. It was found that common reticular nevi (mostly with a junctional component) have a high incidence of copy number aberrations (CNA). Importantly, concurrent with the loss of tumor suppressor genes (e.g. CDKN2A, TP53, and NF1) was the loss of potent oncogenes (e.g. NRAS, MITF, and MDM2). We postulated that the balanced nature of these CNAs confers protection from transformation, thus keeping the lesion in the benign state. Along with copy-number loss of these well-known genes, further interrogation of these data revealed a loss on chr8q24.3 which was frequently observed in 7/30 (23%) nevi. In the smallest region of overlap, the block of proliferation 1 (BOP1) gene was identified as a candidate for functional validation. BOP1 is part of the trimeric “PeBoW” complex, essential for ribosome biogenesis and cell cycle progression. In melanoma cell lines (MM96L, HT144, and MM253), we used siRNA mediated gene targeting to achieve differing BOP1 expression levels (high, low, absent), which resulted in altered cell states. For example, high BOP1 expression caused an increase in proliferation and colony formation, whereas low BOP1 expression conferred reduced proliferation, colony formation, and a senescent like phenotype. Interestingly, low BOP1 expression also resulted in increased migration and invasive capacity. BOP1 immunofluorescence assessment of benign nevi revealed limited expression whereas in early invasive melanomas, BOP1 expression was clearly evident in proliferative melanoma nests. These data support the role of BOP1 playing a role in melanoma progression by contributing to phenotype switching.
Citation Format: Mitchell S. Stark, Sabrina Hammerlindl, Lisa Tom, Kasturee Jagirdar, Jean-Marie Tan, Helmut Schaider, Richard A. Sturm, Blake O'Brien, Michael Walsh, Angus Collins, H.Peter Soyer. BOP1 expression contributes to the proliferative/invasive phenotype in melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5861.
Abstract 5863: Improved conversion in extraction, library construction, and capture improve sensitivity for variants in liquid biopsy samples
Authors: Roseman Nicole , Parakh Shilpa , Huang Hsiao-Yun , Lai Kevin , Barnes Timothy , Lewis Lyn , Chakravarty Ushati Das , Potts Anastasia , Jackson Alisa , Yoder Amy , Sheu Jessica , Chen Tzu-Chun 
Published: September 2020

Abstract
Demonstrate performance of a complete automation and reagent workflow for analysis of cfDNA from bodily fluids. The efficient extraction of cfDNA from bodily fluids is a unique challenge due to the very low concentrations of nucleic acid. The extraction process along with library preparation is a laborious workflow, where human variability can lead to increased variability in the downstream analysis. Integrated DNA Technology (IDT) and Beckman Coulter (BC) have teamed up to provide a complete automation and reagent workflow for analysis of low frequency variants in cfDNA. The Apostle MiniMax™ High Efficiency Isolation Kit from BC provides complex, utilized magnetic nanoparticles to effectively capture cfDNA. IDT's library prep kit utilizes novel chemistry to maximize conversion, suppress adapter-dimer formation, reduce chimera rates, and facilitate double strand consensus analysis to call ultra-low frequency variants. Finally, IDT's xGen™ hybrid capture products maintain high library diversity and on-target rates to enable low frequency variant calling regardless of panel size. The Biomek i5 and i7 Hybrid workstations bring out the best performance from these reagents. The Biomek NGS workstations protocol is written with a modular design with safe stop points, making it customizable for each lab. The automated protocol uses Beckman's Demonstrated Method Interface tools which include: Biomek Method Launcher to run the method without going into Biomek software, Method Options Selector to choose the run parameters with a user friendly interface, Guided labware Setup to set the deck with labware based on the run parameters, DeckOptix Final Check software to help reduce deck setup errors. We demonstrate the performance of this complete workflow with a range of plasma inputs (4-8 mL). Using control samples with known variant frequencies, the workflow yields high library complexity, 100% positive predictive value, and reliable detection of &lt;0.5% mutant allele frequency variants. With real cfDNA, the workflow demonstrates both high cfDNA and sequencing library yields along with high library complexity. The combination of these reagents on the Biomek workstations provides a robust and reproducible solution for the analysis of cfDNA.
Citation Format: Nicole Roseman, Shilpa Parakh, Hsiao-Yun Huang, Kevin Lai, Timothy Barnes, Lyn Lewis, Ushati Das Chakravarty, Anastasia Potts, Alisa Jackson, Amy Yoder, Jessica Sheu, Tzu-Chun Chen. Improved conversion in extraction, library construction, and capture improve sensitivity for variants in liquid biopsy samples [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5863.
Abstract 5869: Characterization and therapeutic implications of SMARCA4 mutations in cancer
Authors: Fernando Tharu M. , Piskol Robert , Bainer Russell , Sokol Ethan , Trabucco Sally , Zhang Qing , Trinh Huong , Maund Sophia , Kschonsak Marc , Chaudhuri Subhra , Januario Tom , Modrusan Zora , Yauch Robert L. 
Published: September 2020

Abstract
Genomic studies performed in cancer patients have identified a high frequency of alterations in the core catalytic subunit of the mammalian switch/sucrose non-fermentable (mSWI/SNF) chromatin remodeling complex, SMARCA4. Cells with inactivating SMARCA4 mutations rely on its paralog, SMARCA2, making it an attractive therapeutic target. Here we report the results of genomic profiling of 131,668 cases from patients with solid tumors and identified 8,588 cases with one or more SMARCA4 alterations. We observed a high prevalence of homozygous SMARCA4 truncating and non-truncating mutations in certain tumor types, notably non-small cell lung cancer (NSCLC) and cancers of unknown primary. We found that homozygous SMARCA4 mutations in NSCLC were mutually exclusive with other mutations in mSWI/SNF and oncogenic drivers, including KRAS and EGFR. A retrospective study of NSCLC patients who were treated in the Flatiron Health network (&gt;265 oncology practices in the U.S.) and underwent FoundationOne® or FoundationOne CDx® tumor sequencing as part of routine care revealed that real-world patients with homozygous truncating SMARCA4 mutations had significantly reduced overall survival. The large sample size of our cohort also elucidated novel hotspot missense mutations within the helicase domain of SMARCA4. Functional modeling of these mutations using biochemical and cell-based (ATAC-seq) assays demonstrated that all evaluated mutations have significantly reduced nucleosome remodeling activity upon in vitro reconstitution in SMARCA4-deficient cells. We also addressed whether SMARCA4 missense mutations could rescue the cell growth defects and loss in chromatin accessibility induced upon SMARCA2 loss. Interestingly, we observe that a few missense mutants were able to either partially or fully rescue growth, suggesting hypomorphic activity under the selective pressure of SMARCA2 loss. Overall, these studies highlight NSCLC patients with homozygous truncating SMARCA4 mutations as a novel population with an unmet need who may benefit from SMARCA2-targeted therapy and underscore that careful selection criteria must be employed to identify patients with inactivating, homozygous SMARCA4 missense mutations.
Citation Format: Tharu M. Fernando, Robert Piskol, Russell Bainer, Ethan Sokol, Sally Trabucco, Qing Zhang, Huong Trinh, Sophia Maund, Marc Kschonsak, Subhra Chaudhuri, Tom Januario, Zora Modrusan, Robert L. Yauch. Characterization and therapeutic implications of SMARCA4 mutations in cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5869.