bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5603: Defining the functions of the BRCA2 BRC repeats in modulating RAD51 binding and activity
Authors: Jensen Julia R. , Jensen Ryan B. 
Published: March 2024

Abstract
The BRCA2 (Breast Cancer Susceptibility 2) gene is critical for preserving genome integrity by regulating homology-directed repair (HDR) of DNA double-strand breaks (DSBs). Germline mutations in BRCA2 predispose individuals to a high risk for ovarian, breast, prostate, and pancreatic cancer. BRCA2 contains eight BRC repeats that mediate binding to RAD51. It remains unclear how exactly the different BRC repeats regulate RAD51 functions. In our study, we explore the importance of each BRC repeat, their interconnections, and their impact on RAD51 binding and filament stability. We engineered amino acid substitutions into the BRC FxTAS motif required for specific contacts within a hydrophobic binding pocket of RAD51 to disrupt BRC binding to RAD51. We further created mutations in RAD51 (F86E/A89E) that either prevent self-association but retain binding to the BRC repeats or a mutation (K133R) that results in a hyper-stable RAD51 nucleoprotein filament. Using both cell-based models and biochemical analyses, we have begun studies to parse out the specific functions of each BRC repeat. Our ultimate goal is to incorporate single amino acid changes into each BRC repeat within the context of the full-length BRCA2 protein to comprehensively characterize the contribution of each BRC repeat to HDR and response to chemotherapeutics such as PARP inhibitors.
Citation Format: Julia R. Jensen, Ryan B. Jensen. Defining the functions of the BRCA2 BRC repeats in modulating RAD51 binding and activity [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 5603.
Abstract 5628: Aberrant 3'UTR processing regulates a tumor suppressor network in AML
Authors: Wang Eric , Han Cuijuan , Calderon Alexander , Lawal Abimbo , Rajendran Sakthi Harini , Karma Sadik , Hariramani Nidhi , Aifantis Iannis , Tsirigos Aristotelis 
Published: March 2024

Abstract
Differentiation blockade is a hallmark of acute myeloid leukemia (AML). While inactivating mutations in tumor suppressor genes (TSGs) have been well-studied, non-genetic mechanisms that impair TSGs to promote myeloid differentiation and influence drug response remain poorly understood. In this study, we performed genome-wide loss-of-function CRISPR/Cas9 screens to identify suppressors of myeloid differentiation. These screens converged on the zinc finger transcriptional repressor, ZBTB7A whose ablation restricted myeloid maturation and promoted a dysregulated inflammatory state to protect leukemic cells from undergoing differentiation. Moreover, genetic deletion of ZBTB7A or its paralog, ZBTB7B impeded leukemia differentiation and conferred resistance to differentiation-inducing agents. Mechanistically, we found that leukemia cells hijack 3’UTR processes to reduce mRNA expression of the tumor suppressor gene paralogs ZBTB7A and ZBTB7B. These findings provide a molecular framework of altered 3’UTR regulation that orchestrate a tumor suppressive function and promote resistance to AML differentiation-based therapies.
Citation Format: Eric Wang, Cuijuan Han, Alexander Calderon, Abimbo Lawal, Sakthi Harini Rajendran, Sadik Karma, Nidhi Hariramani, Iannis Aifantis, Aristotelis Tsirigos. Aberrant 3'UTR processing regulates a tumor suppressor network in AML [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 5628.
Abstract 5629: MEF2D regulates T cell function via the CD70-CD27 signaling axis and promotes immune escape in hepatocellular carcinomas
Authors: Kong Fanhua , Wang Liqing , Ye Qifa , Xiong Yan , Hancock Wayne W. 
Published: March 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 563: Targeting PDE4D reinstates toxic PARP trapping via cAMP-ROS-DNA damage axis and restores the efficacy of standard of care in treatment-refractory ER+ breast cancer
Authors: Saatci Ozge , Cetin Metin , Uner Meral , Tokat Unal M. , Chatzistamou Ioulia , Montaudon Elodie , Akyol Aytekin , Aksoy Sercan , Uner Aysegul , Marangoni Elisabetta , Sajish Mathew , Sahin Ozgur 
Published: March 2024

Abstract
Endocrine therapies, modulating ER level and/or activity, and the CDK4/6 inhibitors are among the standard-of-care (SOC) therapies used in estrogen receptor-positive (ER+) breast cancer. However, most ER+ breast cancer patients eventually develop resistance to SOC, representing a major clinical challenge that reduces clinical outcome. Therefore, elucidating the common mechanisms of sensitivity and resistance to SOC therapies, and identifying novel actionable targets are urgently needed. Here, we demonstrated that cell death induced by endocrine therapies and CDK4/6 inhibitors involves toxic PARP1 trapping and generation of a functional BRCAness (i.e., BRCA1/2 deficiency) phenotype, leading to transcriptional blockage. We showed that this is achieved by activation of the cAMP/reactive oxygen species (ROS)/DNA damage axis upon downregulation of phosphodiesterase 4D (PDE4D). Importantly, we identified PDE4D as a novel ER target gene that in turn stimulates ER activity in a feedforward loop in endocrine-responsive models. However, during SOC resistance, an ER-to-EGFR switch induces PDE4D overexpression via c-Jun. Inhibition of PDE4D using BPN14770, the first-in-class PDE4D allosteric inhibitor that has successfully completed Phase II trials in Fragile X syndrome, reinstates PARP1 trapping and BRCAness, leading to drug sensitization in vitro and in vivo. Furthermore, inhibition of EGFR or PARP1 recapitulates the effects of PDE4D targeting and overcomes SOC resistance irrespective of the BRCA1/2 status in cell line models, primary cultures and organoids of endocrine resistant ER+ PDXs. Notably, we demonstrated that high PDE4D mRNA and protein expression is associated with dramatically worse disease-free survival and overall survival in endocrine therapy-treated ER+ breast cancer. Given the availability of potent and non-toxic PDE4D inhibitors, and clinically approved EGFR and PARP1 inhibitors, our findings have great translational potential to improve the clinical outcome of refractory ER+ breast cancers.
Citation Format: Ozge Saatci, Metin Cetin, Meral Uner, Unal M. Tokat, Ioulia Chatzistamou, Elodie Montaudon, Aytekin Akyol, Sercan Aksoy, Aysegul Uner, Elisabetta Marangoni, Mathew Sajish, Ozgur Sahin. Targeting PDE4D reinstates toxic PARP trapping via cAMP-ROS-DNA damage axis and restores the efficacy of standard of care in treatment-refractory ER+ 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 563.
Abstract 5631: YAP1 is a critical factor for FUS::DDIT3/BAF/c-Jun complex assembly in myxoid liposarcoma
Authors: Berthold Ruth , Isfort Ilka , Heinst Lorena , Wardelmann Eva , Åman Pierre , Scholl Claudia , Trautmann Marcel , Fröhling Stefan , Hartmann Wolfgang 
Published: March 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 5638: The BAF complex mediates intertwined activity of YAP1 and β-catenin in synovial sarcoma
Authors: Isfort Ilka , Berthold Ruth , Heinst Lorena , Kuntze Anna , Wardelmann Eva , Trautmann Marcel , Hartmann Wolfgang 
Published: March 2024

Abstract
Introduction: Synovial sarcoma (SySa) is a rare malignant soft tissue tumor characterized by a specific reciprocal translocation t(X;18). The resulting chimeric SS18::SSX fusion protein drives SySa tumorigenesis by integrating into BAF chromatin remodeling complexes, changing their composition and dysregulating gene transcription. The role of BAF complexes in cancer steadily increases with ∼20% of all malignancies having alterations in BAF complex subunits. BAF complexes are multiprotein complexes with several interaction partners determining their localization and functionality. Since previous analyses revealed an induced activation of the transcriptional coregulators YAP1 and β-catenin in SySa, the aim of this study was to analyze if nuclear YAP1 and β-catenin are interacting with BAF complexes and if this has an impact on their transcriptional activity.
Experimental procedures: Co-immunoprecipitation experiments on nuclear protein extracts and proximity ligation assays were performed to investigate interactions between YAP1, β-catenin, and BAF complex subunits in SySa cells. Knockdown of common and specific BAF complex subunits was conducted employing RNA interference. To assess changes in YAP1 and β-catenin transcriptional activities, TEAD and TOPFlash luciferase reporter assays were performed, respectively, and protein expression levels were detected by immunoblotting.
Results: In SySa, protein-protein interaction experiments revealed nuclear interactions between β-catenin, YAP1, the SS18::SSX fusion protein and various BAF subunits. YAP1 and β-catenin’s transcriptional activities were found to be interdependent as they mutually enhanced each other’s activation. Knockdown of SS18::SSX as well as specific BAF complex subunits was associated with diminished transcriptional activities of these coregulators and, interestingly, substantially affected their mutual activation. This indicates that SS18::SSX-containing BAF complex assembly is crucial for interdependent YAP1 and β-catenin activation in SySa cells.
Conclusions: This study reveals a significant role of the SySa-specific fusion protein and BAF chromatin remodeling complexes in mediating intertwined activation of YAP1 and β-catenin.
Citation Format: Ilka Isfort, Ruth Berthold, Lorena Heinst, Anna Kuntze, Eva Wardelmann, Marcel Trautmann, Wolfgang Hartmann. The BAF complex mediates intertwined activity of YAP1 and β-catenin in synovial sarcoma [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 5638.
Abstract 5641: Transcriptional regulation by nuclear deformation
Authors: Cook Andrew , Stephens Rebecca , Fursova Nadezda , Chow Carson C. , Larson Dan , Miroshnikova Yekaterina 
Published: March 2024

Abstract
Establishment and maintenance of cell identities requires transcriptional rewiring and modulation of three-dimensional genome organization. The nucleus is subject to constant mechanical forces, both intrinsic from the cytoskeleton and extrinsic, such as compression, confinement, and stretch. Recently, work from us and others implicate mechanical force, through activating biochemical signaling pathways as well as direct nuclear deformation, in remodeling nuclear architecture, chromatin state and global gene expression patterns. Thus, we hypothesize that mechanical force plays an important role in coordinating and thresholding transcriptional responses. Here, we challenge this hypothesis by quantifying the effect of nuclear deformation on transcription in real time at single cell resolution quasi genome wide. Further, recent work elucidated that the MYC oncogene exerts global effects on transcriptional output by altering the binding dynamics of transcription factors involved in the activation and productive elongation of RNA Polymerase II. This contrasts with mechanical stress which reduces global levels of RNA Polymerase II. Here we interrogate how transcriptional output is tuned for specific genetic programs/loci by mechanical force using MYC as a paradigm.
Citation Format: Andrew Cook, Rebecca Stephens, Nadezda Fursova, Carson C. Chow, Dan Larson, Yekaterina Miroshnikova. Transcriptional regulation by nuclear deformation [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 5641.
Abstract 5660: Gene expression signatures from FFPE to predict recurrent metastatic nasopharyngeal cancer
Authors: Tay Joshua K. , Teo Wei Keat , Foley Joseph W. , Suryani Luvita , Wu Bing Cheng , Siow Chor Hiang , Loh Kwok Seng 
Published: March 2024

Abstract
Nasopharyngeal cancer (NPC) is an EBV-driven epithelial cancer endemic to Southeast Asia, Southern China and the Middle East. Accurate profiling of the gene expression of NPC has been challenging because of its intense inflammatory infiltrate, as well as the 3 - 4mm size of biopsies limiting the amount of available material. Here we present a large cohort of 339 micro-dissected gene expression libraries from formalin-fixed paraffin-embedded (FFPE) biopsies from NPC patients treated at the National University Health System, Singapore, as well as healthy controls. NPC tumors from patients who subsequently developed recurrent or metastatic disease (Group A), and patients who did not develop recurrent or metastatic disease (Group B) were profiled. Tumor epithelial and microenvironment compartments were separately obtained using laser-capture microdissection, followed by library preparation performed for RNA-Seq using an in-house specialised technique. Gene signatures for NPC tumor epithelial and microenvironment content were used to validate the purity of gene expression libraries. Our preliminary analysis revealed that primary, pre-treatment tumors from patients who subsequently developed recurrence (Group A) showed downregulation of processes related to interferon gamma and interferon alpha response (p-adj &lt;0.001 for both), while processes related to epithelial-mesenchymal transition (p-adj &lt; 0.05) were enriched compared to patients who remained healthy (Group B). In contrast to primary tumors, recurrent tumors in Group A were enriched for cellular respiration including oxidative phosphorylation (p-adj &lt; 0.0001). Our approach highlights the utility of whole transcriptome profiling from small quantities of archival FFPE material. The gene signatures identified from the primary tumors of high-risk patients are biologically relevant and have the potential to be used in precision medicine to guide additional targeted intervention.
Citation Format: Joshua K. Tay, Wei Keat Teo, Joseph W. Foley, Luvita Suryani, Bing Cheng Wu, Chor Hiang Siow, Kwok Seng Loh. Gene expression signatures from FFPE to predict recurrent metastatic nasopharyngeal 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 5660.
Abstract 5687: Downregulation of DAX-1 expression by miRNA overexpression as a mechanism to potentiate breast cancer
Authors: DeVito Nicholas C. , Tzagarakis-Foster Christina 
Published: March 2024

Abstract
The orphan nuclear receptor DAX-1 (Dosage Sensitive Sex Reversal, Adrenal Hypoplasia Congenita, critical region on the X chromosome, gene 1) plays a key role in sex determination and the synthesis of steroid hormones. In addition to these canonical examples, DAX-1 has been shown to play a contradictory role in cancer development. While DAX-1 is overexpressed in some types of cancer, it is completely absent or downregulated in several other cancers such as prostate and breast. One of the explanations for the paradoxical role of DAX-1 in cancer development could be microRNAs (miRNAs). Recent research has demonstrated that the dysregulated expression of these short non-coding RNAs increases the proliferative and anti-apoptotic capabilities of cancer cells. After broadly surveying over 180 miRNAs historically upregulated in MCF7 cells, we compared the activity of DAX-1 in MCF7 breast cancer cells and MCF10a normal breast epithelial cells with the presence of specific miRNA inhibitors. Our primary hypothesis remains that multiple miRNAs negatively regulate the expression of DAX-1 in human breast cancer cells and are not overexpressed in normal breast cells, providing another mechanism of lifting the repression of DAX-1 expression. Quantitative PCR and western blot analysis was performed indicating that inhibiting miRNAs 29c, 199a, and 424 significantly upregulate DAX-1 expression in MCF10a cells. We examined the invasive and metastatic properties of MCF7 cells following inhibition of these specific miRNAs. This research will allow clinicians to screen for additional miRNAs that could be elevated in breast cancer patients substantially increasing the number of people diagnosed with breast cancer early on. In addition, elucidating the pathways of how more and more miRNAs influence downstream targets will offer drug designers novel targets to improve treatment for breast cancer and other cancer patients.
Citation Format: Nicholas C. DeVito, Christina Tzagarakis-Foster. Downregulation of DAX-1 expression by miRNA overexpression as a mechanism to potentiate 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 5687.