bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 808: In vivo targeting of replication protein A for cancer therapy
Authors: VanderVere-Carozza Pamela , Gavande Navnath , Jalal Shadia , Pollok Karen , Ekinci Elmira , Heyza Joshua , Patrick Steve , Masters Andi , Turchi John , Pawelczak Katherine 
Published: June 2022

Abstract
Replication protein A (RPA) plays essential roles in DNA replication, repair, recombination and the DNA-damage response (DDR). Retrospective analysis of lung cancer patient data demonstrates high RPA expression as a negative prognostic biomarker for overall survival in smoking-related lung cancers. Similarly, relative expression of RPA is a predictive marker for response to chemotherapy. These observations are consistent with the increase in RPA expression serving as an adaptive mechanism that allows tolerance of the genotoxic stress resulting from carcinogen exposure. We have developed second generation RPA inhibitors (RPAi’s) that block the RPA-DNA interaction and optimized formulation for in vivo analyses. Data demonstrate that unlike first generation RPAi’s, second generation molecules with increased cellular permeability, induce cell death via apoptosis. Second gen RPAi’s elicit single agent in vitro anticancer activity across a broad spectrum of cancers and the cellular response supports a threshold exists before chemical RPA exhaustion induces cell death. Chemical RPA inhibition potentiates the anticancer activity of a series of DDR inhibitors as well as traditional DNA damaging cancer therapeutics. Consistent with the chemical RPA exhaustion model, we demonstrate that the effects of RPAi on replication fork dynamics. An optimized formulation was developed that resulted in single agent anticancer activity in two non-small cell lung cancer models. These data demonstrate a unique mechanism of action of RPAi’s eliciting a state of chemical RPA exhaustion can provide an effective therapeutic option for difficult to treat lung cancers.
Citation Format: Pamela VanderVere-Carozza, Navnath Gavande, Shadia Jalal, Karen Pollok, Elmira Ekinci, Joshua Heyza, Steve Patrick, Andi Masters, John Turchi, Katherine Pawelczak. In vivo targeting of replication protein A for cancer therapy [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 808.
Abstract 824: Loss of Parkin's inactivation by autoubiquitination induces prostate cancer tumorigenesis
Authors: Lee SeungBaek 
Published: June 2022

Abstract
Mutations in the E3 ubiquitin ligase Parkin have been linked to familial Parkinson’s disease as well as various human cancers. Although the activation of Parkin's E3 ligase is well characterized, the mechanism that tunes down tumorigenesis by phosphorylation-mediated auto-ubiquitination is largely unknown. Here we found that Parkin S378 is phosphorylated in mitosis while Parkin S131 is phosphorylated in late G1-S. Parkin protein levels were significantly lower in interphase compared to mitosis. Also, we checked that parkin itself degraded the protein by autoubiquitination in the cells overexpressing Parkin S131. Parkin S131D mutant significantly increased the rate of tumorigenesis compared to the control in in vitro and mouse models. Furthermore, Parkin S131 mutation was found in several patients with prostate cancer. These results suggest that the inactivation of Parkin by auto-ubiquitination impairs its ubiquitination activity and abolishes its tumor-suppressive effect in prostate cancer.
Citation Format: SeungBaek Lee. Loss of Parkin's inactivation by autoubiquitination induces prostate cancer tumorigenesis [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 824.
Abstract 825: Evasion of apoptosis in MYC dependent T-ALL through epigenetic control
Authors: Dewson Gabrielle , Anchang Benedict , Sears Rosalie , Liefwalker Daniel F. 
Published: June 2022

Abstract
Cancer is a complex landscape of aberrant cell signaling programs, often initiated by oncogenes. The causal oncogene drives the preponderance of accumulated mutations that enable tumorigenesis. Cancers arising this way can be reliant on the initiating oncogene, a term known as oncogene addiction. The proto-oncogene c-MYC is a transcription factor that regulates much of the genome and is deregulated in many cancers. The transgenic Eµ-tTA/Tet-O-MYC mouse model of T-cell acute lymphoblastic leukemia (T-ALL), allows for modulation of c-MYC expression (ON vs OFF). When c-MYC is expressed, T-ALL progression is observed; and when c-MYC expression is revoked, tumor regression occurs. Using cells and microarray data from this model we employed a nested effects model (NEM) that infers hierarchical relationships anchored to master transcription factors that govern critical aspects of cell biology. We identified a critical node governed by a class of histone demethylases influencing transcriptional availability across the genome. KDM5B/JARID1b is known as a transcriptional repressor, and is downregulated in the T-ALL model when c-MYC is overexpressed. Using CRISPR/Cas9 mediated mutagenesis to disrupt KDM5B expression, we observed a potent reduction in cell death when c-MYC expression is abrogated; suggesting KDM5B mediates cell death responses in T-ALL. KDM5B is downregulated in the primary murine model when c-MYC is overexpressed, and upregulated concordantly with the loss of MYC expression. Human lymphoma cell lines that are sensitive to the bromodomain inhibitor JQ1 show downregulation of c-MYC and KDM5B upregulation. Xenografts of KDM5B knockout cells in NOD-SCIDIL-2Rg-/- (NSG) mice show increased tumor progression and burden, and more aggressive time to relapse after c-MYC expression is revoked. Future studies examining the KDM5B/c-MYC axis and its influence on chromatin architecture are ongoing. These studies aim to demonstrate a novel paradigm in understanding how c-MYC promotes tumor development through repression of a tumor suppressive epigenetic landscape regulated by KDM5B and identify therapeutic options for treating c-MYC-induced T-ALL.
Citation Format: Gabrielle Dewson, Benedict Anchang, Rosalie Sears, Daniel F. Liefwalker. Evasion of apoptosis in MYC dependent T-ALL through epigenetic control [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 825.
Abstract 828: Screen for actionable ERBB3 mutations
Authors: Koivu Marika K. , Chakroborty Deepankar , Kurppa Kari J. , Elenius Klaus 
Published: June 2022

Abstract
Activating mutations and copy number variations in ERBB genes have been shown to serve as oncogenic driver mutations and predictive biomarkers for ERBB inhibitor drugs. To address whether mutations in ERBB3 can affect the potential of ERBB3 to promote growth or affect sensitivity to ERBB inhibitors, we set up an unbiased functional screen for ERBB3 missense or nonsense mutations in the context of ERBB2/ERBB3 heterodimers. To this end, the iSCREAM (in vitro screen of activating mutations) pipeline, recently developed in our laboratory, was chosen. This platform exploits randomly mutated cDNA libraries of the gene of interest created with error-prone PCR and allows an unbiased assessment of growth-advantage conferred by thousands of mutations in parallel. To set up the model for screening actionable ERBB3 mutations, interleukin-3 (IL-3)-dependent Ba/F3 cells were engineered to express a homodimerization-incompetent ERBB2 V956R mutant together with ERBB3 constructs. The model was validated to serve as a readout for ERBB3's ability in activating ERBB2 kinase by demonstrating that cells expressing known transforming ERBB3 mutations, together with ERBB2 V956R, survived and expanded in the absence of IL-3. In contrast, control cells expressing ERBB2 V956R together with wild-type ERBB3 rapidly died in the absence of IL-3. The cell background with ERBB2 V956R expression was subsequently used as a target for retroviral expression of a cDNA library of randomly mutated ERBB3 constructs. The cells harboring activating ERBB3 mutations were allowed to evolve for 15-48 days. The identity of the mutations was determined from the surviving cell population by ERBB3-targeted next generation sequencing. The discovered activating mutations were validated by cloning them into expression vectors and addressing their activity by Western analyses and growth assays in Ba/F3, NIH-3T3, and MCF10A cell backgrounds. As a demonstration of the validity of the protocol, the well-characterized activating ERBB3 mutation ERBB3 E928G was identified as one of the major hits. These analyses are expected to identify activating ERBB3 mutations that are directly actionable or that provide predictive value for the use of drugs targeting ERBB signaling.
Citation Format: Marika K. Koivu, Deepankar Chakroborty, Kari J. Kurppa, Klaus Elenius. Screen for actionable ERBB3 mutations [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 828.
Abstract 868: Splicing factor mutant lung cancers: A comprehensive molecular and clinicopathologic characterization
Authors: Harada Guilherme , Falcon Christina J. , Santini Fernando C. , Chang Jason C. , Yang Soo R. , Arcila Maria E. , Rekhtman Natasha , Drilon Alexander 
Published: June 2022

Abstract
Background: Splicing factor mutations can drive oncogenesis in different cancer types. More importantly, strategies to target splicing-dependent cancers have been developed, including PRMT5 inhibition which regulates alternative splicing and targets posttranslational modification; PRMT5 inhibitors are in ongoing phase I clinical trials. The characterization of splicing alterations in non-small cell lung cancer (NSCLC) has not been extensively studied and represents an unmet need.
Methods: Based on previously known genes associated with splicing alterations, genomic and clinicopathologic data from NSCLC patients with hotspot or loss of function mutations identified by next-generation sequencing in the splicing factors SF3B1, SRSF2, U2AF1, ZRSR2, RBM10, and FUBP1 were explored.
Results: Among 626 NSCLC patients with at least one splicing mutation, 85% (529/626) also harbored a co-occurring oncogenic driver, such as alterations involving KRAS (60%; 319/529), EGFR (25%;132/529), MET (5%; 27/529), BRAF(4%; 24/529), and ERBB2 (3%; 17/529). After excluding patients with concurrent drivers, 97 splicing-factor-mutant NSCLCs were identified, with 80 (82%) adenocarcinomas and 6 (6%) squamous cell carcinomas. The median age was 71 years (43-89). Forty-nine patients (51%) were female. Sixty patients (62%) were diagnosed with stage I-III disease. Eleven (11%) were never smokers, while 86 (89%) were former/current smokers, with a median of pack years of 30. The median tumor mutational burden was 7.9 mut/Mb (0.9-90.4). Regarding splicing factor mutations, sixty-two patients (64%) had nonsense or splice-site RBM10 mutations, 17 (17%) had missense hotspot SF3B1 mutations, 16 (16%) had hotspot missense U2AF1 mutations, and 7 (7%) had nonsense, splice-site, or hotspot missense FUBP1 mutation. No patients with ZRSR2 or SRSF2 were identified. Only three patients presented concurrent splicing mutations: one with two SF3B1 mutations; one with RBM10 and SF3B1 mutations; and one with U2AF1 and SF3B1 mutations.
Conclusion: Most patients with splicing factor mutant NSCLCs are smokers whose cancers commonly harbor RBM10 mutations and higher TMB compared to other driver-positive cancers. The characterization of this profile is key to identifying appropriate patients for ongoing targeted therapy trials for this population.
Citation Format: Guilherme Harada, Christina J. Falcon, Fernando C. Santini, Jason C. Chang, Soo R. Yang, Maria E. Arcila, Natasha Rekhtman, Alexander Drilon. Splicing factor mutant lung cancers: A comprehensive molecular and clinicopathologic characterization [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 868.
Abstract 876: Proximity labeling reveals a role for ADAR and DDX54 in suppressing dsRNA sensing in breast cancer
Authors: Cottrell Kyle A. , Ryu Sua , Torres Luisangely Soto , Schab Angela , Weber Jason D. 
Published: June 2022

Abstract
The RNA editing enzyme ADAR has been identified as a therapeutic target for multiple cancers. Through its A-to-I editing activity the p150 isoform of ADAR suppresses activation of dsRNA sensors involved in the innate immune response and translational repression. Recently, our laboratory has shown that p150-ADAR is required for the viability of a subset of triple-negative breast cancer cell lines, thus making p150-ADAR a strong therapeutic target for a disease that lacks targeted therapies. Unlike the p150 isoform, which is interferon inducible, the p110 isoform of ADAR is ubiquitously expressed and has not been shown to suppress dsRNA sensing. To date there is much less known about the role of p110-ADAR in cancer, though it is known to be highly expressed in breast cancer. To begin to explore the role of p110-ADAR in breast cancer, we turned to proximity labeling by APEX2 to identify proteins that may interact with p110-ADAR. Mass-spectrometry of proximity labeled proteins revealed numerous nuclear and nucleolar proteins with roles in multiple aspects of RNA biology, including processing of rRNA and ribosome biogenesis. Among the list of enriched proteins were eight members of the DEAD-box RNA helicase family, including the nucleolar localized DDX54. Co-immunoprecipitation confirmed that p110-ADAR and DDX54 interact, furthermore both localize to nucleoli. Knockdown of DDX54 in non-TNBC cell lines (SK-BR-3 and MCF-7) caused apoptosis and reduced proliferation. Additionally, knockdown of DDX54 caused accumulation of dsRNA within the nucleolus and activation of the dsRNA sensor PKR. Knockdown of ADAR, which alone did not affect proliferation or phosphorylation of PKR in the above cell lines, synergized with DDX54 knockdown to cause increased cell death and further activation of PKR. ADAR knockdown did not synergize with knockdown of another ADAR-interacting DEAD-box helicase, DDX17, suggesting that the observed phenotype is not common to combined knockdown of ADAR and any RNA helicase. These findings suggest that combined inhibition/depletion of ADAR and DDX54 may serve as therapeutic strategy for breast tumors, including those that are refractory to ADAR inhibition/depletion alone.
Citation Format: Kyle A. Cottrell, Sua Ryu, Luisangely Soto Torres, Angela Schab, Jason D. Weber. Proximity labeling reveals a role for ADAR and DDX54 in suppressing dsRNA sensing in breast 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 876.
Abstract 879: SLFN12-mediated depletion of tRNA-Leu-TAA by velcrin treatment induces ribosome pausing at Leu-TTA codons and represses global translation initiation
Authors: Hoyt Stephanie , Lee Sooncheol , McGaunn Joseph , Cherniack Andrew , Meyerson Matthew , Greulich Heidi 
Published: June 2022

Abstract
Velcrin compounds kill cancer cells expressing high levels of PDE3A and SLFN12 by inducing complex formation between these two proteins, but the mechanism of cancer cell killing by the PDE3A-SLFN12 complex is not fully understood. We previously determined that SLFN12 is an RNase, that PDE3A binding upregulates SLFN12 RNase activity, and that SLFN12 RNase activity is required for velcrin response.
Here, we report that the depletion of tRNA-Leu-TAA by velcrin treatment induces ribosome pausing at Leu-TTA codons and global inhibition of protein synthesis. We performed ribosome profiling in HeLa cells treated with DMSO or DNMDP and found that ribosome footprints containing Leu-TTA codons at the A-site of the ribosome were significantly more abundant in DNMDP-treated cells than in cells treated with DMSO, indicating a pausing or stalling of ribosomes at Leu-TTA upon velcrin treatment. Although the overall number of ribosome pausing sites across the transcriptome was doubled by DNMDP treatment, ribosome pausing at Leu-TTA was increased &gt 1000-fold, also resulting in an increased number of genes with TTA pause sites.
Even though Leu-TTA is a rare codon, over 70% of all transcripts contain at least one TTA codon, implying that ribosome pausing at TTA codons could directly impact many genes. Genes with TTA pause sites most enriched upon velcrin treatment prominently include those involved in control of mRNA translation and protein homeostasis. These results imply that, in addition to direct effects on mRNA translation due to ribosome pausing, indirect effects could occur due to decreased availability of particular components of the translation machinery, resulting in a widespread impact on protein synthesis. To test our hypothesis, we measured the effects of velcrin treatment on nascent protein abundance. Treatment of HeLa cells with DNMDP resulted in downregulation of newly synthesized proteins, whereas no significant changes in total protein content were observed. Downregulation of protein translation was observed only in velcrin-sensitive cell lines, indicating that inhibition of protein translation could be the mechanism of action of cancer cell killing by PDE3A-SLFN12 complex formation.
Citation Format: Stephanie Hoyt, Sooncheol Lee, Joseph McGaunn, Andrew Cherniack, Matthew Meyerson, Heidi Greulich. SLFN12-mediated depletion of tRNA-Leu-TAA by velcrin treatment induces ribosome pausing at Leu-TTA codons and represses global translation initiation [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 879.
Abstract 894: CXCR1: A novel therapeutic avenue for CSC-like phenotypes in pancreatic ductal adenocarcinoma
Authors: Molczyk Caitlin , Thomas Elizabeth , Zaman Lubaba , Goel Paran , Singh Rakesh K. 
Published: June 2022

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related deaths in the United States. Often diagnosed late in disease progression, PDAC is notorious for chemotherapy resistance as well as having metastases. A cell population of interest aiding in this progression is the cancer stem cell (CSC). These cells are known for having high resistance to chemotherapy, along with propagating and re-building the tumor after most non-CSCs have been therapeutically targeted. Previous studies have determined CXCR4, ALDH1, CD24, CD44, and CD133 are markers of PDAC CSCs. In the present study, we investigated CXCR1 as a marker and therapeutic target for PDAC CSCs. CXCR1 is a G-coupled transmembrane protein receptor with downstream effects known to aid in anti-apoptosis, proliferation, and angiogenesis via binding CXCL8 and CXCL6. Already known to be a CSC marker and target in triple-negative breast cancer, initial studies by Chen et al. of CXCR1 in PDAC demonstrate CXCL8 induces increased tumorsphere formation in vitro, leading us to investigate CXCR1 in PDAC CSCs. Considering these findings, we hypothesized that PDAC cells with high CXCR1 activity exhibit increased CSC-like characteristics, and targeting CXCR1 will reduce those characteristics. To investigate the role of CXCR1 in PDAC CSC-like phenotype, we used two PDAC cell lines, CD18/HPAF and T3M4, and developed gemcitabine resistant (GemR) counterparts. These GemR cell lines were shown to have over 10-fold higher resistance than their respective parent cell lines. We treated with the CXCR1/2 antagonist navarixin at concentrations known to inhibit CXCR1. Using the parent cell lines’ relative IC50 concentrations for each drug, we treated cells for 72 hours. We used qRT-PCR and ELISAs for analysis of several known CSC markers and CXCR1 axis expression. From our results, we see the beginning trends of GemR cells having increased expression of CSC markers as well as gemcitabine-treated parent and resistant cells having increased expression. Using flow cytometry, we evaluated the CXCR1+ cell populations post-control and gemcitabine treatment. The population of CXCR1+ cells was higher in the gemcitabine-treated groups. Together, our observations suggest an association between CXCR1 and the CSC-like phenotype in PDAC.
Citation Format: Caitlin Molczyk, Elizabeth Thomas, Lubaba Zaman, Paran Goel, Rakesh K. Singh. CXCR1: A novel therapeutic avenue for CSC-like phenotypes in pancreatic ductal adenocarcinoma [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 894.
Abstract 907: CD133 stimulates cell proliferationviaupregulation of amphiregulin in melanoma
Authors: Simbulan-Rosenthal Cynthia M. , Islam Nusrat , Haribabu Yoga , Alobaidi Ryyan , Kuo Li-Wei , Shalamzari Azadeh , Leibowitz Adam , Moulton Joanna , Rosenthal Dean S. 
Published: June 2022

Abstract
Melanoma, a malignant transformation of melanocytes, accounts for 90% of skin cancer deaths due to its ability to efficiently metastasize to other organs. CD133, also known as Prominin1, is a pentaspan glycosylated transmembrane protein that is overexpressed in cancer stem cells from various tumors, including melanoma, and has been associated with tumor recurrence, chemoresistance, and metastasis. To characterize and target CD133-positive cancer stem cells, patient-derived melanoma cell lines BAKP and POT, harboring BRAFWT/NRASQ61K and BRAFWT/NRASQ61R driver mutations, respectively, were co-transduced with a Tet activator (rtTA3) and a Tet-on vector expressing CD133 (TRE3G-CD133) to produce stable doxycycline (Dox)-inducible cell lines. These cell lines were exposed to Dox (1µg/mL) to induce CD133 expression for 24 h; mRNA was extracted and subjected to RNA-seq analysis, followed by bioinformatic analyses, which revealed genes that are significantly up- or down-regulated by Dox-induced CD133 expression. Among the most significantly altered genes was amphiregulin (AREG), which increased 7-fold with Dox induction. These results were validated in both BAKP and POT cell lines by qPCR and immunoblot analysis. AREG binds EGFR and activates RAS/RAF/MEK/ERK and PI3K/AKT signaling pathways, leading to cell proliferation, survival, and migration. Consistently, cell cycle and cell growth analyses revealed that Dox-induced CD133 expression increases the percent of cells in S-phase of the cell cycle, leading to increased cell growth in BAKP cells. The role of CD133 in cell proliferation via AREG upregulation was further studied with immunofluorescent and flow cytometry analysis of proliferation markers PCNA, Ki67, as well as BrdU incorporation into newly synthesized DNA in Dox-induced BAKP cells, with or without siRNA knockdown of AREG. AREG may play an integral role in melanoma progression due to its vital function in cell proliferation, serving as an attractive target for novel therapeutics in melanoma and cancers exhibiting overexpression of both CD133 and AREG. Further studies using specific AREG inhibitors or RNAi knockdown in melanoma cell lines is currently ongoing, and can further elucidate molecular mechanisms highlighting the role(s) of CD133 and AREG in melanoma cancer stem cells.
Citation Format: Cynthia M. Simbulan-Rosenthal, Nusrat Islam, Yoga Haribabu, Ryyan Alobaidi, Li-Wei Kuo, Azadeh Shalamzari, Adam Leibowitz, Joanna Moulton, Dean S. Rosenthal. CD133 stimulates cell proliferationviaupregulation of amphiregulin in melanoma [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 907.