tbuckley/cabot-search huggingface dataset:
Abstract 3590: Tumor intrinsic production of glucocorticoids in ovarian carcinoma
Authors: Pahul Hanjra, Elaine Stur, Steven Cole, Susan Lutgendorf, Anil Sood
Journal: Cancer Research (2024)

Abstract Background: Cortisol is a glucocorticoid (GC) known to be produced by the hypothalamic-pituitary-adrenal (HPA) axis. Dysregulation of the HPA axis is prevalent in patients with ovarian cancer. These patients have elevated nighttime levels of cortisol and increased tumoral expression of the glucocorticoid receptor (GR); both of which correlate with shortened overall survival (OS). We hypothesize that outside the HPA axis, ovarian cancer may have tumor-intrinsic production of GC. In this study, we examined whether 11 beta-hydroxysteroid dehydrogenase 1 (11β-HSD1; enzyme which activates cortisone to cortisol) has steroidogenic activity in the ovarian cancer tumor microenvironment (TME). Methods: We used the Genotype-Tissue Expression (GTex) Portal and the Cancer Cell Line Encyclopedia (CCLE) to determine expression of steroidogenic enzymes in the ovary and ovarian cancer cell lines. We further performed UMAP analysis of a single-cell RNA-seq dataset of tumor samples from patients with ovarian carcinoma to cluster for cell type. ELISAs were performed to quantify cortisol production and secretion by cells stimulated with metabolite, cortisone. Subcellular fractionation and Western blotting were performed to measure protein expression of 11β-HSD1, GR, and phospho-Ser 211 GR. Results: HSD11B1 mRNA (which encodes 11β-HSD1) is detectable in bulk ovarian tissue at a median expression of 78.19 transcripts per million (TPM) as measured in the GTex data. In vitro, primary human ovarian fibroblasts express functional 11β-HSD1 and produce and secrete cortisol upon cortisone stimulation in a time-dependent manner, with a mean total secretion of 17.91 ± 0.21 ng/ml at 12 hours. Analysis of scRNA-seq data identifies that cancer-associated fibroblasts (CAFs) may be a source of HSD11B1 in the ovarian TME, with roughly 9% of CAFs expressing HSD11B1. In HeyA8 ovarian cancer cells (positive for 11β-HSD1), cortisone stimulation in vitro results in cortisol production with a mean total secretion of 22.04 ± 5.46 ng/ml at 12 hours. Moreover, this cortisol results in GR activation in an 11β-HSD1-dependent manner. Discussion: We identify 11β-HSD1 as a potential mechanism of GC production within ovarian cancer, with CAFs being a putative source. We further show that 11β-HSD1 activity can lead to activation of the GR within cancer cells. Citation Format: Pahul Hanjra, Elaine Stur, Steven Cole, Susan Lutgendorf, Anil Sood. Tumor intrinsic production of glucocorticoids in ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3590.
Abstract 6981: p38-mediated EZH2 phosphorylation at T367 regulates HER2 pathway in triple negative breast cancer
Authors: Maria E. Gonzalez, Ahmad Eido, Celina G. Kleer
Journal: Cancer Research (2024)

Abstract Background: Triple negative breast carcinomas (TNBC) are highly aggressive tumors with limited effective treatments. Clinical studies showed that targeting low HER2 levels in TNBC with anti-HER2 agents has survival benefit. Enhancer of Zeste Homolog 2 (EZH2) is a lysine methyltransferase component of the Polycomb Repressive Complex2 that regulates differentiation genes in normal and neoplastic cells. EZH2 phosphorylation at T416 was shown to maintain the TNBC phenotype. We have reported that p38-induced EZH2-T367 phosphorylation enhances metastasis and that high pEZH2-T367 expression is significantly associated with human TNBC tumors compared to other breast cancer subtypes. In this study we tested the hypothesis that pEZH2-T367 may regulate the HER2 pathway in TNBC and that inhibition of pEZH2-T367 may upregulate HER2 signaling, with clinical implications. Methods: MDA-MB-231 (mesenchymal-like TNBC) and CCN6KO cells derived from MMTV-Cre;Ccn6fl/fl (CCN6KO) TNBC mouse model generated in our lab were transduced with vector or EZH2 shRNA knockdown (KD). MDA-MB-231 EZH2 KD cells were rescued with lentivirus containing EZH2-wild-type (WT) or T367A phosphorylation-deficient mutant. Gene and protein expression was analyzed by RNA sequencing, q-RT-PCR, immunoblot and immunohistochemistry. Vector and EZH2-KD rescue MDA-MB-231 cells were treated with anti-HER2 (trastuzumab or pertuzumab 100 ug/ml) followed by Hoestch proliferation assays. TNBC cells were treated with vehicle, EZH2 inhibitor (EPZ-6438, 20uM), p38 inhibitor (p38i, SB202190, 20uM), EPZ+p38i, anti-HER2 (100 ug/ml), and EPZ+p38i+anti-HER2, followed by Hoestch cell proliferation assays. Results: EZH2-T367A deregulates the expression of a 94-gene network of HER2 pathway genes including EREG, SERPINB5, MERTK, IL6R, SOCS3, and FASCN1 compared to EZH2-WT. EZH2-T367A increased protein levels of HER2, EREG, and PP2AB, a major HER2 regulator and was sufficient to sensitize TNBC cells to the anti-proliferative effects of anti-HER2. Supporting the role of pEZH2-T367, we found that the combination of p38i and EPZ significantly sensitizes TNBC cells to anti-HER2 therapies. Conclusions: We demonstrate that T367 phosphorylation mediates the effect of EZH2 on HER2 signaling in TNBC. Our data support a role for pEZH2-T367 in maintaining the HER2-negative phenotype in and suggest that blocking this phosphorylation event may render TNBC tumors amenable to anti-HER2 treatment strategies. Citation Format: Maria E. Gonzalez, Ahmad Eido, Celina G. Kleer. p38-mediated EZH2 phosphorylation at T367 regulates HER2 pathway in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6981.
Abstract 5398: Single-cell transcriptomic analysis of partial endothelial-to-mesenchymal transition in sprouting angiogenesis
Authors: Kapil Thapa, Christopher J. Hatch, Christopher Hughes, Jennifer S. Fang
Journal: Cancer Research (2024)

Abstract Endothelial-to-mesenchymal transition (EndoMT) is a process of morphological, functional, and molecular shift of endothelial cells (EC) towards a mesenchymal identity. This process is critical for embryonic development, and knockout animals lacking copies of the individual master EndoMT transcription factors – including Slug, Snail, and Twist – exhibit significant cardiovascular defects. We previously showed that while Slug knockout animals have a modest developmental vascular phenotype, there is a striking loss of tumor angiogenesis in these animals. Based on these and other data, we hypothesize that sprouting angiogenesis involves transient acquisition of an intermediate state of the EndoMT program –i.e., partial EndoMT (pEndoMT). To test this hypothesis, we used single cell RNA sequencing at day 2 and day 6 following TGF-β activation to map the transcriptomic changes associated with complete endothelial-to-mesenchymal transition. In parallel, we sequenced EC activated to undergo sprouting angiogenesis in vitro at the same timepoints. We show that angiogenic EC transiently acquire a transcriptomic profile of the pEndoMT state, but then later reacquire the transcriptomic profile of committed EC rather than transition completely into mesenchymal cells. We further use this dataset to identify several candidate genes that appear to be regulated by Slug and associated with the pEndoMT state. Future work will use in vitro and in vivo angiogenesis models to identify how pEndoMT is regulated in angiogenesis, and how this regulation may differ in the presence of tumor stroma. Citation Format: Kapil Thapa, Christopher J. Hatch, Christopher Hughes, Jennifer S. Fang. Single-cell transcriptomic analysis of partial endothelial-to-mesenchymal transition in sprouting angiogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5398.
Abstract 2692: ELK3 is a key regulator as the response of natural killer cell therapy in triple-negative breast cancer
Authors: Hae-Yun Jung, Yebin Lee
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer (TNBC) is the most challenging subtype of breast cancer because of its aggressive behavior and the limited therapeutic strategies available. In the last decade, immunotherapy has become a promising treatment to prolong survival in advanced solid cancers including TNBC. However, the efficacy of immunotherapy in solid cancers remains limited because solid tumors contain few tumor-infiltrating lymphocytes. Here, we show that targeting an ETS transcription factor ELK3 (ELK3) enhances the response of nature killer (NK) cells through intracellular and extracellular signaling. In extracellular signaling, ELK3 depletion increases CXCL16 expression level and promotes NK cell cytotoxicity through CXCL16-mediated NK cell recruitment in TNBC. In intracellular signaling, ELK3 depletion controls mitochondrial fission-fusion status to induce NK cell-mediated cell death. In silico analysis showed that ELK3 is negatively correlated with CXCL16 or MID51 expression in breast cancer patient samples. Low expression of ELK3 and high expression of CXCL16 or MID51 were associated with a better prognosis. Low expression of ELK3 and high expression of CXCL16 or MID51 were associated with increased expression of NK cell-related genes. Our findings demonstrate that ELK3-CXCL16 axis controls NK cell recruitment to target cancer cells and ELK2-MID51 axis triggers mitochondrial dysfunction-mediated apoptosis during NK cell therapy, suggesting that targeting the ELK3 gene could be an adjuvant strategy for increasing the efficacy of immunotherapy in TNBC Citation Format: Hae-Yun Jung, Yebin Lee. ELK3 is a key regulator as the response of natural killer cell therapy in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2692.
Abstract 3528: Constructing knowledge graph of N6-methyladnosion regulations in cancer from literature using ChatGPT-4
Authors: Sumin Jo, Xidong Wu, Yiming Zeng, Arun Das, Ting-He Zhang, David Alexander Spellman, Adam Ferris, Shou-Jiang Gao, Jianqiu (Michelle) Zhang, Yu-Chiao Chiu, Yufei Huang
Journal: Cancer Research (2024)

Abstract N6-methyladenosine (m6A) is the most abundant mRNA modification with a crucial role in cellular processes. Its involvement in cancers is well-established. Dysregulation of m6A is linked to cancer initiation, progression, and therapy resistance, impacting the tumor microenvironment (TME) and promoting metastasis. Understanding m6A's regulatory role in cancer is essential for identifying new therapeutic targets. We considered the construction of a knowledge graph (KG) representing molecular regulatory mechanisms (MRMs) of m6A in healthy conditions and different cancers from PubMed papers. Such a KG consists of interconnected triplets of (head node, regulatory relationship, tail node), each denoting regulation between genes or a gene and a phenotype/process. Advances in natural language processing (NLP) have provided tools such as SemRep and GNBR to automate the extraction of these triplets from the literature. However, these methods don’t extract contextual information, such as the type of cancers or cells in which these MRMs occur, leading to contradictory regulations in the constructed KG. In addition, existing approaches were designed to extract generic regulatory relations and therefore struggled in properly capturing unique concepts associated with m6A regulatory mechanisms. To tackle this challenge, we designed a novel ChatGPT-4 prompt to extract relational graphs from papers tailored for m6A regulatory mechanisms. An annotated dataset of 400 titles on m6A-related MRMs were created to evaluate the performance. We then applied the prompt to 1023 papers to create a m6A Molecular Regulatory Mechanism Knowledge Graph (m6A-MRM-KG). This graph illuminates m6A's roles in gene expression regulation, especially in cancer and immunity. Anticipated to enhance our understanding of cancer development, it provides insights into potential therapeutic strategies. The m6A-MRM-KG not only organizes information but also empowers researchers to uncover novel insights in the dynamic relationships of m6A modifications in diverse biological contexts. Citation Format: Sumin Jo, Xidong Wu, Yiming Zeng, Arun Das, Ting-He Zhang, David Alexander Spellman, Adam Ferris, Shou-Jiang Gao, Jianqiu (Michelle) Zhang, Yu-Chiao Chiu, Yufei Huang. Constructing knowledge graph of N6-methyladnosion regulations in cancer from literature using ChatGPT-4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3528.
Abstract 6131: Increasing self efficacy, self confidence, and genetic knowledge via the Community Genetic Navigation Engagement Specialist Train-the-Trainer program
Authors: Janet Rodriguez, Joel Sanchez Mendez, Yaneth L. Rodriguez, Lourdes Baezconde-Garbanati, Charité Ricker, Rosa Barahona, Bianca Rosales, Daisy Hernandez, Natalia Gutierrez, Julie Culver, Mariana Stern
Journal: Cancer Research (2024)

Abstract Background: Colorectal cancer (CRC) is the second and third leading cause of cancer deaths in US Hispanic/Latino (H/L) men and women, respectively. The Community Genetic Navigation Specialists (CoGENES) train-the-trainer program created a workforce of community health workers (CHWs) to educate H/L individuals about genetic testing, counseling, and research. Methods: The CoGENES three-week program, consisted of six in-person sessions, with a curriculum in both Spanish/English developed and delivered by experts, in Spanish, using presentations and hands-on activities. Acculturation, Latino values, self-efficacy, genetics and tumor testing knowledge, and self-confidence were assessed via pre- and post-training. Differences in scores were analyzed via Wilcoxon matched-pairs signed-rank tests with exact p-values. Results: Median age of the 12 participants was 50 (IQR = 12), 9 were female, 92% were Mexican-born, half completed 1-2 years of college, and 67% were very hispanic oriented. Self-efficacy increased after training, with pre- training median-score = 38.5 (IQR = 3) and post-training score = 39.5 (IQR =2.5) (p = 0.0547). Certainty about understanding tumor testing increased after training (p = 0.0039). The median number of correct answers on the 16-item genetic knowledge scale increased from 6.5 to 9.5 and the median number of “don’t know” responses decreased from 5 to 0 after training. Finally, self-confidence to train future CoGENES was significantly higher (p = 0.0098) at post-test. Conclusion: The CoGENES culturally tailored program led to improved self-efficacy, increased genetic knowledge, and self-confidence in a cohort of Hispanic community health educators. Findings will be shared within COPECC, and other NCI funded programs. Citation Format: Janet Rodriguez, Joel Sanchez Mendez, Yaneth L. Rodriguez, Lourdes Baezconde-Garbanati, Charité Ricker, Rosa Barahona, Bianca Rosales, Daisy Hernandez, Natalia Gutierrez, Julie Culver, Mariana Stern. Increasing self efficacy, self confidence, and genetic knowledge via the Community Genetic Navigation Engagement Specialist Train-the-Trainer program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6131.
Abstract 5535: Intracellular negative regulators of RTK-Ras-ERK signaling alter breast cancer perception of metastatic niche-derived growth factors
Authors: Vaibhav Murthy, Cemal Erdem, Jeremy Copperman, Marc Birtwistle, Alexander Davies
Journal: Cancer Research (2024)

Abstract Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype that commonly metastasizes to distant organs, such as the lung, resulting in the poor clinical outcomes. TNBC cells commonly overexpress epidermal growth factor receptor (EGFR), a receptor tyrosine kinase (RTK) which when bound by microenvironmental growth factors, results in the activation of downstream effector kinases ERK-AKT and initiates transcriptional programs that control cell fate. Tumor cells, however, simultaneously receive many growth factor inputs from their respective microenvironments, many of which stimulate RTKs other than EGFR, that converge at ERK and AKT resulting in different transcriptional and cell fate outputs. This raises questions as to how tumor cells perceive, decode, and respond to a complex set of microenvironmental signals and what the relevance of this process may be for disease pathogenesis and treatment. To this end, our study aimed to determine how disseminated breast cancer cells perceive and respond to a complex growth factor milieu upon seeding and engraftment in the lung. Using live-cell microscopy techniques and TNBC cells carrying biosensors for ERK and Akt signaling pathways, we monitored the dynamic signaling behaviors of single tumor cells, in real-time, as they adapted to the environment in living human lung tissue. Strikingly, we found that individual disseminated tumor cells are less responsive to growth factors once seeded in the lung, as compared to outside this tissue, despite the presence of RTK stimulating ligands. We showed that partial activation of EGFR is necessary for complete activation of ERK signaling by other growth factor-RTK pairs, and expression of downstream ERK target genes, whereas AKT signaling was unaffected. Using quantitative modeling and experimentation, we showed that reshaping of ERK signaling response dynamics occurred via dysregulation of negative regulators that are dominantly controlled by EGFR signaling. Together, these results provide novel insight into how tumor cells perceive and respond to complex microenvironmental signals, which has important implications for drug targeting strategies. Citation Format: Vaibhav Murthy, Cemal Erdem, Jeremy Copperman, Marc Birtwistle, Alexander Davies. Intracellular negative regulators of RTK-Ras-ERK signaling alter breast cancer perception of metastatic niche-derived growth factors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5535.
Abstract 5647: Investigating the role of AP-2α in melanomagenesis
Authors: Nicholas Bartschat, Jeremy Chang, Mohammed Suraju, Ryan Nagel, Zhijie Li, Jeffrey White, Colin Kenny, Ronald Weigel
Journal: Cancer Research (2024)

Abstract Introduction: Transcription factor AP-2α (encoded by the TFAP2A gene) is a protein involved in the early development of multiple tissues, particularly the neural crest. Melanocytes are derived from the neural crest and their development appears to rely on AP-2α and its paralogues, along with master regulator MITF. Prior studies have indicated that AP-2α is a crucial regulator of melanoma metastasis. However, it is unclear if AP-2α plays a role in melanomagenesis. We sought to understand the role of AP-2α in melanomagenesis, hypothesizing that knock out (KO) of TFAP2A would suppress malignant potential in vitro and downregulate genetic pathways linked to malignant transformation. Methods: TFAP2A KO was generated with a single-guide RNA CRISPR/Cas9 system targeting exon 3 of the gene in the human melanoma cell line A375. Tumorigenesis phenotype was assessed by evaluating contact-independent colony formation with the in vitro soft agar assay. To identify downstream regulatory programs controlled by TFAP2A, we then utilized RNA-seq and Gene Set Enrichment Analysis (GSEA, San Diego). RNA-seq was performed on four clones each for wildtype and TFAP2A KO samples and the resulting data was processed using GSEA to identify gene sets modified after TFAP2A KO. Results: Targeting of TFAP2A with CRISPR/Cas9 effectively knocked out AP-2α protein expression in the A375 melanoma cell line. Colony formation on soft agar assay was significantly decreased after TFAP2A KO (P &amp;lt; 0.01). RNA-seq revealed significant differential expression of 11,195 genes after TFAP2A KO. Gene sets with negative enrichment after TFAP2A KO included those overall higher in tumors versus normal tissue (FWER P = 0.003) and multiple signaling pathways related to malignant transformation such as TGF-β (FWER P = 0.003), MYC (FWER P = 0.009), KRAS (FWER P = 0.03), and Notch (FWER P = 0.043). Conclusions: Our data suggests that TFAP2A plays a role in cutaneous melanomagenesis. TFAP2A may represent a therapeutic target for melanoma, though further pre-clinical studies are needed. We plan to further test this hypothesis in a melanoma mouse model with conditional TFAP2A KO under the control of inducible Cre recombinase driven by the mouse tyrosinase gene promoter. Citation Format: Nicholas Bartschat, Jeremy Chang, Mohammed Suraju, Ryan Nagel, Zhijie Li, Jeffrey White, Colin Kenny, Ronald Weigel. Investigating the role of AP-2α in melanomagenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5647.