tbuckley/cabot-search huggingface dataset:
Abstract 3046: The estrogen signaling pathway reprograms prostate cancer cell metabolism and supports proliferation and disease progression
Authors: Camille Lafront, Lucas Germain, Gabriel H. Campolina-Silva, Cindy Weidmann, Line Berthiaume, Hélène Hovington, Hervé Brisson, Cynthia Jobin, Lilianne Frégeau-Proulx, Raul Cotau, Kevin Gonthier, Aurélie Lacouture, Patrick Caron, Claire Ménard, Chantal Atallah, Julie Riopel, Éva Latulippe, Alain Bergeron, Paul Toren, Chantal Guillemette, Martin Pelletier, Yves Fradet, Clémence Belleannée, Frédéric Pouliot, Louis Lacombe, Éric Lévesque, Étienne Audet-Walsh
Journal: Cancer Research (2024)

Abstract Just as the androgen receptor (AR), the estrogen receptor α (ERα) is expressed in the prostate and is thought to influence prostate cancer (PCa) biology. Yet, the incomplete understanding of ERα cellular functions in PCa hinders our ability to fully comprehend its clinical relevance and restricts the repurposing of estrogen-targeted therapies for treatment of this disease. Using two human PCa tissue microarray cohorts, we first demonstrated that nuclear ERα expression was heterogeneous between patients, being only detected in half of tumors. Positive nuclear ERα levels were correlated with disease recurrence, progression to metastatic PCa, and patient survival. Using in vitro and in vivo models of the normal prostate and PCa, bulk and single cell RNA-seq analyses revealed that estrogens partially mimic the androgen transcriptional response and induce specific biological pathways linked to cellular proliferation and metabolism. Bioenergetic flux assays and metabolomics confirmed regulation of cancer metabolism by estrogens, supporting proliferation. Using cancer cell lines and patient-derived organoids, selective estrogen receptor modulators, a pure anti-estrogen, and genetic approaches impaired cancer cell proliferation and growth in an ERα-dependent manner. Overall, our study revealed that, when expressed, ERα functionally reprograms PCa metabolism, is associated with disease progression, and could be targeted for therapeutic purposes. Citation Format: Camille Lafront, Lucas Germain, Gabriel H. Campolina-Silva, Cindy Weidmann, Line Berthiaume, Hélène Hovington, Hervé Brisson, Cynthia Jobin, Lilianne Frégeau-Proulx, Raul Cotau, Kevin Gonthier, Aurélie Lacouture, Patrick Caron, Claire Ménard, Chantal Atallah, Julie Riopel, Éva Latulippe, Alain Bergeron, Paul Toren, Chantal Guillemette, Martin Pelletier, Yves Fradet, Clémence Belleannée, Frédéric Pouliot, Louis Lacombe, Éric Lévesque, Étienne Audet-Walsh. The estrogen signaling pathway reprograms prostate cancer cell metabolism and supports proliferation and disease progression [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 3046.
Abstract 3080: Activation of mTORC2/Akt is amplified during glutamine starvation and is mediated by GCN2
Authors: Tatiana Hernandez, Nikhil Patel*, Jedrick Magsino, Jay Kavia, Aparna Ragupathi, Alysta Paneque, Tracy G. Anthony, Guy Werlen, Estela Jacinto
Journal: Cancer Research (2024)

Abstract Highly proliferative cells like cancer cells depend on glucose and glutamine to augment flux through metabolic and biosynthetic pathways. The mechanistic target of rapamycin (mTOR) integrates signals from nutrients and other growth signals to maintain metabolic homeostasis. Whereas mTOR complex 1 (mTORC1) is activated by the presence of nutrients to promote anabolic metabolism, mTORC2 is activated by nutrient fluctuations, leading to increased Akt phosphorylation at Ser473. How mTORC2 signaling can be augmented by nutrient starvation remains poorly understood. Here, we found that General Control Nonderepressible kinase 2 (GCN2), an amino acid starvation-sensing kinase, conveys glutamine depletion to mTORC2. mTORC2 enhances Akt phosphorylation and Akt feeds back to mTORC2 to augment its activity during glutamine starvation. Amino acid starvation in vivo also enhances mTORC2/Akt signaling via GCN2. Our findings reveal that manipulating the GCN2/mTORC2/Akt signaling cassette could have therapeutic benefit to more effectively starve cancer cells. Citation Format: Tatiana Hernandez, Nikhil Patel*, Jedrick Magsino, Jay Kavia, Aparna Ragupathi, Alysta Paneque, Tracy G. Anthony, Guy Werlen, Estela Jacinto. Activation of mTORC2/Akt is amplified during glutamine starvation and is mediated by GCN2 [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 3080.
Abstract 5629: MEF2D regulates T cell function via the CD70-CD27 signaling axis and promotes immune escape in hepatocellular carcinomas
Authors: Fanhua Kong, Liqing Wang, Qifa Ye, Yan Xiong, Wayne W. Hancock
Journal: Cancer Research (2024)

Abstract Background: Immune escape remains a challenge in the treatment of hepatocellular carcinoma (HCC), one of the most common and deadly cancers in the world. The transcription factor, myocyte enhancer factor 2D (MEF2D), is important in the regulation of differentiation and adaptive responses in many cancers, such that we tested its role in HCC. Methods: We knocked down MEF2D in HCC cell lines and analyzed HCC tissues and cell lines by RNA sequencing, Western blot and immunohistochemistry. MEF2D protein acetylation and proteins that interact with MEF2D were identified by coimmunoprecipitation assay. Chromatin immunoprecipitation was used to analyze the regulation of CD70 transcription by MEF2D. H22 cells, with MEF2D knockout or without (controls), were injected into the livers of syngeneic BALB/c mice. Flow cytometry was used to analyze the function of T cells in tumors, spleens, and lymph nodes. Results: Through database searches, we noted that MEF2D and CD70 were upregulated in HCC and associated with shorter patient survival times. Compared to WT tumors, injection of MEF2D-knockdown HCC cells into immunocompetent mice led to smaller tumors with increased T cell infiltration, activation, and impaired T-regulatory (Treg) cell suppressive function. Mechanistically, we found that MEF2D binds to the promoter region of CD70 gene and activates its transcription. Moreover, acetylation of MEF2D enhances the binding of MEF2D to the CD70 promoter and further promotes its transcription. CD70 blocking antibody inhibited activation of the CD70-CD27 signaling axis in murine HCC tumors, leading to impaired immunosuppressive function of Tregs and enhanced T cell-mediated anti-tumor immune responses. Thus, regulation of the CD70-CD27 signaling axis by MEF2D affects the numbers and functions of Treg cells and thereby controls T cell infiltration. Conclusions: MEF2D in HCC cells increases the expression of CD70 and blocks T cell-mediated anti-tumor immunity via the CD70-CD27 signaling axis. Strategies to manipulate this pathway might increase the efficacy of immune therapies for HCC. Citation Format: Fanhua Kong, Liqing Wang, Qifa Ye, Yan Xiong, Wayne W. Hancock. MEF2D regulates T cell function via the CD70-CD27 signaling axis and promotes immune escape in hepatocellular carcinomas [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 5629.
Abstract 3047: Interrogating TEAD protein interactions in cancer
Authors: Alissa Guarnaccia, Jennie Lill, Anwesha Dey
Journal: Cancer Research (2024)

Abstract The Hippo signaling pathway is a major regulator of cellular growth and is frequently deregulated in cancer. The main effectors of the Hippo pathway are the TEAD transcription factors which function by interacting with other co-effector proteins to modulate transcriptional outputs. Notably YAP and TAZ interact with TEAD to mediate oncogenic transcriptional programs, and blocking interaction of TEAD with YAP and TAZ is a sought-after mechanism for small molecule TEAD inhibitors. However, the interaction network of TEAD extends well beyond YAP and TAZ to a variety of additional cofactors, including chromatin remodelers, epigenetic factors, and other transcriptional regulators. Thus, the impact of inhibiting TEAD could extend to unanticipated protein interactions and cellular functions. The purpose of this study is to investigate, define, and interrogate TEAD interaction networks, providing foundational knowledge for interrogating TEAD biological functions and pharmacological effects. We are employing mass spectrometry-based technologies combined with chemical and genetic tools and biochemistry to interrogate TEAD protein interaction networks. We have performed affinity purification coupled with mass spectrometry for TEAD and have identified dozens of significant interacting proteins. TEAD interactions include expected proteins, such as known Hippo pathway members, as well as unexpected protein interactions, such as DNA damage response proteins. Cellular assays probing these DNA damage protein interactions implicate TEAD as a crucial factor for efficient DNA repair mechanisms and maintaining genomic stability. These results raise questions towards a combinatorial effect for TEAD inhibitors and DNA damaging chemotherapeutic agents. Altogether, these ongoing proteomic studies are providing insights into TEAD interaction networks, leading to a deeper understanding of TEAD biology, and providing foundational knowledge that can inform the development of TEAD inhibitors as effective cancer therapies. Citation Format: Alissa Guarnaccia, Jennie Lill, Anwesha Dey. Interrogating TEAD protein interactions in 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 3047.
Abstract 5632: Advancing transcriptome insights during RNA-Seq library construction of FFPE samples in a novel workflow
Authors: Cissy Jiang, Elizabeth Jordan Dreskin, Angelica Olcott, Linda Lingelbach, Srikanth Perike
Journal: Cancer Research (2024)

Abstract Formalin-fixed, paraffin-embedded (FFPE) tumor tissue has significant clinical benefits in oncology research and is considered vital for studying tumor gene expression through RNA sequencing (RNA-Seq). However, RNA extracted from FFPE samples tends to be severely degraded, making it suboptimal for constructing high-quality RNA-Seq libraries. The RNA-Seq workflow can further impair data quality, as traditional library preparation and pre-library ribodepletion workflows may result in the loss of valuable information due to rare transcripts being not captured or washed away. Moreover, small, degraded fragments are a challenging template for ligases, and the resulting adapter addition may be inadequate. Here we assessed a novel workflow employing a proprietary enzyme to overcome the limitations and biases of cDNA synthesis using reverse transcriptase (RT) and ligases. This innovative RNA-Seq library preparation approach, coupled with a post-library ribodepletion strategy, aims to capture a more complete transcriptome profile from RNA extracted from FFPE breast cancer samples, and can also be used for evaluation of gene regulation through intronic and intergenic bases. The study also compared two commercially available kits, RecoverAll and PureLink, for FFPE RNA extraction, evaluating quality metrics such as RNA integrity number (RIN), DV200, recovery of small RNAs during NGS library construction, and transcriptome coverage. A parallel fresh frozen RNA sample, extracted using a phenol-based reagent, served as a benchmark. Our findings demonstrate that the novel workflow yields a richer dataset, encompassing a wider range of transcriptomic elements, including both small and long RNAs from FFPE samples. Performing ribodepletion after the library preparation procedure led to increased detection of small RNAs compared to pre-library ribodepletion. The robust analytical performance of this streamlined library preparation protocol enables its suitability for RNA-Seq analysis of archived FFPE specimens, offering substantial utility for oncology research. Citation Format: Cissy Jiang, Elizabeth Jordan Dreskin, Angelica Olcott, Linda Lingelbach, Srikanth Perike. Advancing transcriptome insights during RNA-Seq library construction of FFPE samples in a novel workflow [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 5632.
Abstract 5631: YAP1 is a critical factor for FUS::DDIT3/BAF/c-Jun complex assembly in myxoid liposarcoma
Authors: Ruth Berthold, Ilka Isfort, Lorena Heinst, Eva Wardelmann, Pierre Åman, Claudia Scholl, Marcel Trautmann, Stefan Fröhling, Wolfgang Hartmann
Journal: Cancer Research (2024)

Abstract Introduction: FUS::DDIT3 is the dominant fusion protein in myxoid liposarcoma (MLS), resulting from a disease-defining chromosomal translocation. Acting as an aberrant transcription factor, FUS::DDIT3 disturbs gene regulatory networks interfering with adipogenic differentiation, while driving oncogenic gene expression and proliferation. Functionally, FUS::DDIT3 has been shown to cooperate with the transcriptional coregulator YAP1 and to interact with the BAF chromatin remodeling complex. However, mechanistic details on FUS::DDIT3’s function in transcriptional dysregulation leading to proliferative effects and the required interactome are incompletely understood. This study was performed to investigate transcriptional and epigenetic players recruited by FUS::DDIT3 to drive MLS proliferation and tumorigenesis. Experimental Procedures: To study protein-protein interactions between FUS::DDIT3 and its interacting partners, co-immunoprecipitation experiments of nuclear extracts and proximity ligation assays were performed using human MLS cell lines. To further investigate dependencies of nuclear complex assembly, combined RNA interference (RNAi) experiments were conducted. MLS cell viability and proliferation were assessed using MTT assays and xCELLigence real-time analysis, respectively. RT-qPCRs were performed to analyze the expression of FUS::DDIT3 target genes. The expression of FUS::DDIT3’s interacting proteins was evaluated by immunohistochemistry in primary human MLS specimens. Results: Co-immunoprecipitation and proximity ligation assays demonstrated nuclear interactions between FUS::DDIT3, YAP1, and the canonical BAF (cBAF) complex in MLS cell lines. In addition, a novel interaction of FUS::DDIT3 with the AP-1 transcription factor c-Jun was identified. Knockdown of the cBAF-specific subunits ARID1A and ARID1B resulted in reduced MLS cell viability and proliferation. Similarly, RNAi-mediated silencing of c-Jun impaired MLS cell viability and led to decreased expression of FUS::DDIT3 target genes. Strikingly, RNAi-mediated silencing of YAP1 resulted in decreased interaction of FUS::DDIT3 with cBAF components and c-Jun in MLS cells. Conclusions: Our results identify YAP1 as a key factor mediating the nuclear interaction of FUS::DDIT3 with the cBAF complex and the AP-1 transcription factor c-Jun, both shown to be essential for MLS cell proliferation. Citation Format: Ruth Berthold, Ilka Isfort, Lorena Heinst, Eva Wardelmann, Pierre Åman, Claudia Scholl, Marcel Trautmann, Stefan Fröhling, Wolfgang Hartmann. YAP1 is a critical factor for FUS::DDIT3/BAF/c-Jun complex assembly in myxoid liposarcoma [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 5631.
Abstract 3056: Copper chelation modulates YTHDF2 RNA-binding protein localization and global translation, in neuronal cancers
Authors: Jessica L. Bell, Domenico K. Abruzzese, Erin Kasiou, Vu Vu Pham, Jean B. Bertoldo, Filip Michniewicz, Orazio Vittorio
Journal: Cancer Research (2024)

Abstract Cancers are dependent on copper for growth, angiogenesis and metastasis and copper chelators are in clinical trials against breast cancer, however the mechanisms of this emerging cancer treatment are still largely unexplored. We previously demonstrated that copper chelation has efficacy in mouse models of neuroblastoma and glioma. Multiomics analyses in neuronal cancers suggested that RNA-binding proteins were deregulated by copper chelator treatment. We found that the “RNA Binding” gene set was the most significantly ranked molecular function list using differentially expressed RNAs after copper chelation treatment (GO:0003723, p-value 1.02e−32). We subsequently found that the copper chelator drug decreased global protein synthesis, MYC/MYCN expression, as well as the amount a key methylated (m6A) RNA-binding protein called YTHDF2 in glioma cells, by RNA-seq (-log2FC 0.3, p-value 0.005) and western blot. This downregulation was also clear in neuroblastoma and glioblastoma cell lines. Interestingly, copper chelation also shifted YTHDF2 protein location into the nucleus. YTHDF2 knock-out (DepMAP Chronos dependency score, -0.32) and knock-down studies (siRNA pool, 38% decrease in cell confluence) in neuroblastoma cell lines and others, indicated that YTHDF2 depletion is selective against neuronal cancer cell growth. YTHDF2 was found to be a MYCN transcriptional target. Moreover, as YTHDF2 protein also binds MYCN transcripts (the principal oncogene in neuroblastoma), and copper signaling mRNAs, it appears that copper signaling, YTHDF2 and MYCs operates in an oncogenic-axis. Ongoing studies are investigating novel YTHDF2 inhibitors and their neuronal cancer efficacy. Our work represents a significant breakthrough in drugging oncogenic post-transcriptional processes either directly, or indirectly via depleting copper. Citation Format: Jessica L. Bell, Domenico K. Abruzzese, Erin Kasiou, Vu Vu Pham, Jean B. Bertoldo, Filip Michniewicz, Orazio Vittorio. Copper chelation modulates YTHDF2 RNA-binding protein localization and global translation, in neuronal cancers [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 3056.
Abstract 3168: Amphiphilic dendrimer-mediated siRNA delivery for precision regulation of cAMP pathway in cancer cells
Authors: Wanjun Yuan, Zhengyin Gao, Ling Peng, Leo Tsz On Lee
Journal: Cancer Research (2024)

Abstract Exchange proteins directly activated by cAMP (EPACs) are involved in multiple cellular processes. The two EPAC isoforms (EPAC1 and EPAC2) have fundamental differences in structure, expression pattern, and signaling specificity, indicating that they may function independently. Therefore, the highly specific regulation of EPAC1 and EPAC2 could be beneficial in targeting cAMP pathway-related therapies. Small RNA molecules could theoretically target genetic components based on Watson-Crick base pairing, offering a unique and promising approach to achieve precision medicine. In this study, we successfully design small interfere (si)RNAs that specifically target EPAC1 and 2, without cross-reactivity with other isoforms. The use of the amphiphilic dendrimer (AD) efficiently delivers siRNAs, resulting in significant down-regulations of EPAC1 and 2 mRNA and protein expressions in multiple cancer cells, including ovarian, breast, colon, and pancreatic cancers. Functional analysis demonstrate that EPAC1 and EPAC2 regulate cancer progression depending on different mechanisms. siEPAC2-AD is more potent compared to siEPAC1-AD in suppressing cell proliferation by altering energy metabolism. Hence, this siEPACs-AD system not only enhances the drug specificity and reduces potential side effects, but also provides a new strategy for precision pharmaceutical control of the cAMP/PKA/EPAC signaling pathway for cancer treatment. Keywords: EPAC1; EPAC2; siRNA; amphiphilic dendrimer; cAMP signaling; cancer Citation Format: Wanjun Yuan, Zhengyin Gao, Ling Peng, Leo Tsz On Lee. Amphiphilic dendrimer-mediated siRNA delivery for precision regulation of cAMP pathway in cancer cells [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 3168.
Abstract 5614: Mechanical regulation of cisplatin-DNA adduct repair in mesenchymal stem cells
Authors: Anamaria Gabriella Zavala, Nina Nikitina, Crystal Cantu, Dalia DeLaCruz, Gunes Uzer
Journal: Cancer Research (2024)

Abstract This study examined whether loss of mechanotransduction in pluripotent mesenchymal stem cells (MSCs) disrupted repair of bulky DNA adducts, such as those induced by ultraviolet light or cisplatin. MSCs are important for the maintenance and responsiveness of skeletal tissues to environmental mechanical challenges. Beyond regulating proliferative and differentiative capacity of MSCs, emerging evidence suggests that physical activity is associated with improved recovery from DNA damage caused by environmental genotoxic stressors associated with stress and aging. Highlighting the possible crosstalk between DNA repair and bone health, defects in nucleotide excision repair (NER), which removes bulky DNA adducts, are associated with myelosuppression and progeroid aging phenotypes that result in bone defects and lipidodystrophies in mice. Cancer, early aging syndromes, and certain musculoskeletal diseases are associated with disruption of the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex that transduces environmental mechanical signals from the extracellular matrix into the nucleus of a cell. Loss of LINC complex elements is associated with breast cancer progression and poorer prognosis. We hypothesize that LINC-mediated mechanical stimulation into the nucleus is critical for repair of bulky DNA adducts. Our pilot project showed that mechanical stimulation applied in the form of low intensity vibration (LIV) improved NER of cisplatin-induced DNA adducts in cultured MSCs. Our findings show a 20% increase in repair of cisplatin-induced DNA adducts in LIV treated samples compared to non-vibrated samples at 24 hours (P&amp;lt;0.005). We also quantified the effect of LINC complex disruption on cisplatin-induced DNA damage removal. Intact MSCs showed significant adduct removal after 24 hours, while LINC disruption significantly reduced DNA repair (P&amp;lt;0.001). Furthermore, initial experiments suggest that LINC disrupted cells do not arrest at DNA repair checkpoints, therefore, loss of LINC complex may reduce entry into senescence increasing DNA mutagenesis. In conclusion, these findings suggest a novel interaction between mechanical stimulation, the DNA damage response, and LINC complex in DNA repair in multipotent mesenchymal stem cells. Furthermore, we suggest that LINC-mediated mechanical changes associated with LIV treatment may lead to novel therapeutic approaches to combat deleterious musculoskeletal conditions associated with anti-cancer treatments. Citation Format: Anamaria Gabriella Zavala, Nina Nikitina, Crystal Cantu, Dalia DeLaCruz, Gunes Uzer. Mechanical regulation of cisplatin-DNA adduct repair in mesenchymal stem cells [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 5614.