bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3691: Dynamic BH3 profiling identifies novel combinations in malignant pleural mesothelioma with in vivo efficacy
Authors: Potter Danielle S. , Du Ruochen , Chow Kin-Hoe , Ligon Keith L. , Bueno Raphael , Letai Anthony 
Published: June 2022

Abstract
Currently, malignant pleural mesothelioma (MPM) is mainly treated with conventional therapies such as surgery, chemotherapy and radiation, and patients often suffer from the lack of second line therapy options. In this study, we aimed to identify efficacious drug combinations in primary MPM patient samples and novel MPM patient-derived xenograft (PDX) models to provide better therapeutic options for MPM patients. BH3 profiling is a functional assay that measures mitochondrial priming of the cell. It uses BH3 peptides derived from the BH3 domain of pro-apoptotic BH3-only Bcl-2 family members to provoke a response from viable mitochondria. When tumor cells are treated with drugs prior to BH3 profiling, early changes in their apoptosis signaling can be captured before frank apoptosis occurs. This method is termed dynamic BH3 profiling (DBP), which has been applied in multiple cancer types to identify efficacious drugs. Here, we used high throughput dynamic BH3 profiling (HTDBP) to assess hundreds of drug treatments simultaneously to identify drug combinations that increased apoptotic priming in primary MPM cells ex vivo. Next, we created novel MPM PDX models and tested these drug combinations to determine the ones that primed MPM PDX cells. The HTDBP result from MPM PDX cells recapitulated the chemical vulnerabilities of the primary MPM cells. Moreover, one of the top combination candidates that comprised of navitoclax (BCL-xL, BCL-2 and BCL-w antagonist) and AZD8055 (mTORC1/2 inhibitor) was shown to be safe and efficacious in vivo in our CPDM_011x MPM PDX model. Finally, on the molecular level, we revealed that treatment with navitoclax drove the anti-apoptotic dependence of MPM cell lines towards MCL-1, whose level was downregulated by AZD8055 treatment. In this study, we identified a novel drug combination for MPM with HTDBP that consists of navitoclax and AZD8055. In addition, our results further corroborated that DBP, as a functional assay, can be used to rationally construct novel drug combinations to improve treatment outcomes for cancer patients.
Citation Format: Danielle S. Potter, Ruochen Du, Kin-Hoe Chow, Keith L. Ligon, Raphael Bueno, Anthony Letai. Dynamic BH3 profiling identifies novel combinations in malignant pleural mesothelioma with in vivo efficacy [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 3691.
Abstract 3695: Overexpression of HSD17B13 induced G1 arrest in hepatic cell lines detected by anti-HSD17B13 recombinant rabbit monoclonal antibody
Authors: Qu Tianli , Wu Lipeng , Yom Jina , Guo Zhaoying , Hu Xiaomin , Ren Qi , Niu Qian , Lin Ruei-Shiuan , Yin Dezhong , Liu Xuan , Wei Fu 
Published: June 2022

Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent tumors worldwide. Hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13), which was newly identified as a liver lipid droplet associated protein, was recently found to be down-regulated in HCC. However, the effects of HSD17B13 on the underlying mechanisms of HCC have not yet been fully explored. For this purpose, HSD17B13 gene was knockdown with CRISPER/Cas9 technique in several HCC cell lines. HSD17B13 expression was detected by Flow cytometry and Western blotting with recombinant rabbit monoclonal antibodies (clone OTIR3G2 and OTIR5C10) against HSD17B13 which were screened for use in immunohistochemistry, western blot, and ELISA application. Overexpressed HSD17B13 induces hepatic cell line G1 capture and increases several G1 arrest-related protein expression, including p21, p27, MMP2 and MMP3. Then the proliferation and cell cycle were suppressed. HSD17B13 gene knockdown will reverse the suppression. These data indicated that HSD17B13 play important roles in the progression of HCC lesions. HSD17B13 might be a potential immune-oncology marker for HCC.
Citation Format: Tianli Qu, Lipeng Wu, Jina Yom, Zhaoying Guo, Xiaomin Hu, Qi Ren, Qian Niu, Ruei-Shiuan Lin, Dezhong Yin, Xuan Liu, Fu Wei. Overexpression of HSD17B13 induced G1 arrest in hepatic cell lines detected by anti-HSD17B13 recombinant rabbit monoclonal antibody [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 3695.
Abstract 3702: UBE4B interacts with the ITCH E3 ubiquitin ligase to induce Ku70 and c-FLIPL K63/K48 branched polyubiquitination and enhanced neuroblastoma HDACi-mediated apoptosis
Authors: Clorennec Christophe Le , Subramonian Divya , Huo Yuchen , Zage Peter E. 
Published: June 2022

Abstract
Expression of the UBE4B ubiquitin ligase is associated with neuroblastoma patient outcomes, but the functional roles of UBE4B in neuroblastoma pathogenesis are not known. We evaluated interactions of UBE4B with the E3 ubiquitin ligase ITCH/AIP4 and the effects of UBE4B expression on Ku70, c-FLIPL, and p53 ubiquitination and proteasomal degradation by co-immunoprecipitation and Western blots. We also evaluated the role of UBE4B in apoptosis induced by HDAC inhibition in our neuroblastoma cell lines model using Western blots. UBE4B was found in a complex with ITCH, with binding mediated by WW domains in the ITCH protein. ITCH activation led to ITCH-UBE4B E3-E4 ubiquitin ligase complex formation and recruitment of Ku70 and c-FLIPL via ITCH WW domains, followed by Ku70 and c-FLIPL Lys48/Lys63 branched polyubiquitination and proteasomal degradation. Histone deacetylase (HDAC) inhibition induced Ku70 and c-FLIPL acetylation, leading to release of c-FLIPL and Bax from Ku70, increased Ku70 and c-FLIPL Lys48/Lys63 branched polyubiquitination via the ITCH-UBE4B complex, and induction of apoptosis. UBE4B depletion in our neuroblastoma cell lines model led to reduced polyubiquitination and increased levels of Ku70 and c-FLIPL proteins leading to the massive reduction of apoptosis induced by HDAC inhibition via stabilization of Ku70 and c-FLIPL proteins allowing the inhibition of the full caspase 8 activation. Our results have identified novel interactions and novel targets for UBE4B ubiquitin ligase activity and a direct role of the ITCH-UBE4B complex in responses of neuroblastoma cells to HDAC inhibition, suggesting that the ITCH-UBE4B complex plays a critical role in responses of neuroblastoma to therapy and suggesting a potential mechanism underlying the association of UBE4B expression with neuroblastoma patient outcomes.
Citation Format: Christophe Le Clorennec, Divya Subramonian, Yuchen Huo, Peter E. Zage. UBE4B interacts with the ITCH E3 ubiquitin ligase to induce Ku70 and c-FLIPL K63/K48 branched polyubiquitination and enhanced neuroblastoma HDACi-mediated apoptosis [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 3702.
Abstract 3710: Synergistic cell death induction in ovarian cancer by cisplatin and ABT-199 is mediated by expression of NOXA
Authors: Schaefer Benjamin , Weller Sandra , Beigl Tobias B. , Schulze-Osthoff Klaus , Kopp Hans-Georg , Aulitzky Walter E. , Essmann Frank 
Published: June 2022

Abstract
Ovarian cancer is among the top ten leading causes of cancer death in women worldwide with a mortality rate of roughly 5% among all cancer deaths. So far, there are no recommended screening tests for the early detection of ovarian cancer. Therefore, patients are frequently diagnosed at late stages of ovarian cancer, which is associated with unfavorable 5-year survival. Patients suffering from ovarian cancer often show a good response to initial therapy with platinum-based compounds and/or taxanes subsequent to resection of the affected tissue. Unfortunately, ovarian cancer shows a high frequency of relapse and after chemotherapy persistent tumor cells re-expand and successively evolve into therapy-resistant tumors.
We recently reported that cisplatin (cisPt) treatment of ovarian cancer cells enhances mitochondrial content and mitochondrial reactive oxygen species (Kleih et al. 2019). We therefore speculated that the enhanced mitochondrial content primes cisPt-treated cells for apoptosis induced by BH3 mimetic drugs, such as Venetoclax (ABT-199), that act on anti-apoptotic Bcl-2 proteins at the outer mitochondrial membrane. To explore this hypothesis, we investigated whether the combined administration of cisPt and ABT-199 leads to a synergistic cell death induction in ovarian cancer cells with different cisPt resistance and mitochondrial content.
Detection of cell death by flow cytometric measurements of the mitochondrial membrane potential and exposure of phosphatidylserine demonstrated a synergistic cell death induction by cisPt and ABT-199 in OVCAR4 and OVCAR8 cells, irrespective of the cisPt resistance. Interestingly, Western blot analysis revealed that ABT-199 induced the accumulation of the BH3-only protein NOXA in both cancer cell lines. Accumulation of NOXA was dependent on ABT-199-mediated activation of the stress-responsive transcription factor ATF4. Knock-down experiments showed that apoptosis of cisPt-resistant OVCAR8 cells by the combined treatment with ABT-199 and cisPt was entirely dependent on NOXA. Moreover, also cisPt-sensitive OVCAR4 cells revealed an initially reduced apoptosis induction by the NOXA knock-down.
Our data therefore elucidate the molecular mechanism of the synergistic efficacy of cisPt/ABT-199 combination therapies, which should be promising especially for the treatment of recurrent tumors developing reduced sensitivity to cisPt-based treatments.
Citation Format: Benjamin Schaefer, Sandra Weller, Tobias B. Beigl, Klaus Schulze-Osthoff, Hans-Georg Kopp, Walter E. Aulitzky, Frank Essmann. Synergistic cell death induction in ovarian cancer by cisplatin and ABT-199 is mediated by expression of NOXA [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 3710.
Abstract 3711: Modulation and inhibition of prostate cancer cells by microbial metabolites and resveratrol
Authors: Stokes James , Singh Rajesh , Mishra Manoj K. 
Published: June 2022

Abstract
The chemotherapeutic compounds resveratrol (RES) and short-chain fatty acids (SCFAs) are potent inhibitors of cancer cell proliferation during in vitro testing. These compounds are naturally occurring and present relatively low toxicity to normal cells and tissues, making them an attractive cancer treatment alternative. SCFAs are the chemical by-products of microbial activity known as fermentation. RES is a polyphenolic compound found in select fruits and vegetables and has been known for its versatility in preventing and reversing many diseases, including several cancers. Butyric and propionic acid are considered the most potent of the SCFAs found within the intestinal lumen. The prime goal of this research is to understand if the RES and SCFA compounds use a shared biological pathway(s) to fight and inhibit cancer. We used TRAMP C1 and C3 prostate cancer cells (transgenic adenocarcinoma mouse prostate) as an experimental model. These cells were treated with the RES and SCFAs both singularly and synergistically for 24hrs. The cells were analyzed to understand the potential cell toxicity and proliferation, the modulation of apoptotic and proapoptotic proteins/genes, and any change in mitochondrial membrane potential pathways. The result demonstrated that the expression of apoptogenic proteins induces programmed cell death in a mitochondria-independent manner. Therefore, the result suggests that RES and SCFAs can facilitate many critical biological functions within the host's body, including cellular respiration, nutrient assimilation, and various immunological responses to inhibit cancer cell proliferation.
Citation Format: James Stokes, Rajesh Singh, Manoj K. Mishra. Modulation and inhibition of prostate cancer cells by microbial metabolites and resveratrol [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 3711.
Abstract 3724: PBRM1 loss in RCC: Implications for immunotherapy
Authors: Metz Alexander , Sikder Rahmat , Ellithi Moataz , Slifker Micheal , Abbosh Philip 
Published: June 2022

Abstract
Introduction The association between mutational status of the polybromo-1 (PBRM1) gene in clear cell renal cell carcinomas (ccRCCs) and papillary RCCs (pRCCs) in the response to immune checkpoint blockade is debatable. Here, we aim to characterize the biological changes that PBRM1 loss causes and how these changes might modulate the immune response to cancer.
Methods and Results Gene set enrichment analysis (GSEA) of PBRM1-mutant RCC tumors from TCGA data sets reveals NF-kB signaling via TNFα, hypoxia, and p53 signaling pathways are enriched compared to PBRM1 WT. PBRM1-mutant tumors also have increased number of insertion/deletion mutations and non-synonymous mutations that are directly proportional to neoantigen burden. CIBERSORT analysis of PBRM1-mutant ccRCC tumors reveals decreased transcriptional signature associated with CD8+ T-cell infiltration and lower levels of two cytolytic signatures. PBRM1-mutant ccRCC cell lines have constitutively activated NF-kB signaling, as well as a greater induction of NF-kB in response to TNFα via western blot when compared with PBRM1 reconstituted cells. Additionally, PD-L1 is more strongly expressed on the cell surface of PBRM1-mutant cells, which may modulate their interactions with the immune system. However, MHC-I expression was not found to be significantly different between PBRM1 mutant and reconstituted cells.
Conclusions These results shed light on changes in biology and immunogenicity associated with or caused by PBRM1 loss. They also implicate NF-kB as a potential moderator of immune response, which should be studied further to characterize its effects on immune checkpoint blockade therapy (ICB).
Citation Format: Alexander Metz, Rahmat Sikder, Moataz Ellithi, Micheal Slifker, Philip Abbosh. PBRM1 loss in RCC: Implications 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 3724.
Abstract 3726: Functional genomic dissection of PIK3CA hotspot mutations using a multi-lineage isogenic breast cell model
Authors: Miranda Adam X. , Hodges Emily , Park Ben Ho 
Published: June 2022

Abstract
PIK3CA is the most commonly mutated gene in breast cancer, and in breast cancer there are two hotspot mutations that represent an outsized proportion of PIK3CA mutations. Previous research suggests that there are distinct prognostic and cell signaling differences induced by these mutational isoforms, however there is currently only one targeted treatment approved for PIK3CA mutant breast cancer. The goal of our research is to leverage a comprehensive multi-lineage isogenic breast cell line model to further interrogate the unique effects of these PIK3CA mutations on breast cells using assays to assess gene expression and chromatin state. Insights gained from these assays shed light on disrupted pathways that may prove to be new targets for PIK3CA mutation-specific treatment of breast cancer.
Citation Format: Adam X. Miranda, Emily Hodges, Ben Ho Park. Functional genomic dissection of PIK3CA hotspot mutations using a multi-lineage isogenic breast cell 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 3726.
Abstract 3735: Regulation of HPV gene expression by 5-azacytidine treatment in head and neck cancer
Authors: Rehmani Hina , Isaeva Natalia , Yarbrough Wendell G. 
Published: June 2022

Abstract
Human papillomavirus (HPV) causes approximately 80% of head and neck squamous cell carcinoma (HNSCC) in the oropharynx, and its incidence is now higher than uterine cervical cancer in the US. The CDC estimates that this common sexually transmitted disease accounts for nearly 13,000 HPV+ HNSCC patients per year in the United States. Despite having a higher cure rate than HPV- HNSCC, the recurrence rate is approximately 30%. These patients have few therapeutic options since resistance to treatment arises from all known therapeutic modalities. Initial therapy for HPV+ HNSCC is aggressive and often results in negative lifelong side effects. The substantial recurrence rate and high morbidity of primary therapy suggest the need for new treatments. Global genome hypermethylation in HPV+ HNSCC, compared to HPV-, prompted our lab to explore demethylation as a therapeutic option. 5-azacytidine (5-aza) and 5-aza-2′-deoxycytidine (decitabine) are synthetic cytidine analogs that cause DNA demethylation by trapping methyltransferases to chromatin. These demethylating agents are FDA approved for the treatment of myelodysplasia and acute myeloid leukemia. Recently, we found that HPV+ HNSCC cells are more sensitive than HPV- cells to 5-aza, that low doses of 5-aza delayed HPV+ xenograft tumor growth, and that HPV+ tumor samples from patients treated with 5-aza in a window trial had increased apoptosis. We also observed a marked downregulation of HPV gene expression after 5-aza. Decreased HPV E6 expression, followed by reactivation of tumor suppressor p53, induced p53-dependent apoptosis in HPV+ HNSCC. Thus, decreased expression of HPV genes is an important component of 5-aza-associated toxicity toward HPV+ HNSCC; therefore, we further explored mechanisms through which demethylation negatively regulates the expression of HPV genes. First, we determined that 5-aza regulates transcription of HPV genes, but not the stability of HPV transcripts. Second, we found that transcriptional regulation of HPV genes after 5-aza depends on the proto-oncogene JunB, a component of the transcription factor Activator Protein 1 (AP-1). Moreover, our experiments revealed that clonogenic survival of HPV+ head and neck cancer cells is dependent on JunB expression. In summary, our study provides an improved mechanistic understanding of the regulation of HPV gene transcription in HNSCC and identifies a novel HPV+ HNSCC dependency on JunB, potentially providing a basis for a new rational targeted therapy.
Citation Format: Hina Rehmani, Natalia Isaeva, Wendell G. Yarbrough. Regulation of HPV gene expression by 5-azacytidine treatment in head and neck 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 3735.
Abstract 3743: Genome-wide profiling of DNA N6-methylation from a breast cancer and a matched normal cell lines
Authors: Xiao Chunlin , Schneider Valerie 
Published: June 2022

Abstract
DNA N6-methyladenine (m6A) modification has been found widely presented in the human genome, and genome-wide DNA methylation profiling in cancer may reveal epigenetic signatures with significant clinical outcomes. Whole genome sequencing data from PacBio single-molecule real-time (SMRT) system provides signals for identifying the presence of m6A in human genomic DNA. We identified 343,199 m6A modification sites with an average density of 122 per Mb in the HCC1395 breast cancer cell line, whereas 722,303 m6A modification sites with average density of 257 per Mb were observed in a matched normal HCC1395BL cell line, meaning that the total number and the average density of m6A methylation sites in the cancer cell line were reduced more than 50% than that in normal cell line. Only small fraction of the methylation sites was found to be shared between the two cell lines, indicating that significant de-methylation (loss) and new methylation (gain) events occurred in HCC1395 cancer cells. A broad distribution of m6A methylation sites across autosomal chromosomes was observed, but the density of m6A methylation sites on chromosome X was extremely low for both HCC1395 and HCC1395BL cell lines. In contrast, the m6A densities on chromosome 7 and chromosome 22, particularly on their q-arms, from HCC1395 were substantially higher (hypermethylation) than other autosomal chromosomes, suggesting that copy number variations may be associated with these chromosomal regions. Most of the m6A methylation sites were located in intergenic and intronic regions, whereas only about 2~3% of the m6A methylation sites were situated in exonic regions, and 12% on ncRNAs. Understanding the genome-wide distinction of DNA methylation between cancer and matched normal cell lines makes it possible to ask more targeted questions and further investigate the role of methylation in cancer.
Citation Format: Chunlin Xiao, Valerie Schneider. Genome-wide profiling of DNA N6-methylation from a breast cancer and a matched normal cell lines [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 3743.