bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5422: Identification of ZEB1-regulated circular RNAs in lung cancer cells
Authors: Cho Seongran , Choi Jin-A , Ahn Young-Ho
Published: March 2024

ZEB1 is a master transcription factor playing a crucial role in promoting epithelial-mesenchymal transition (EMT), as well as the progression and metastasis of lung cancer. The progression of lung cancer is regulated by non-coding RNAs, including microRNAs, long non-coding RNAs, and circular RNAs (circRNAs). In this study, we aimed to identify circRNAs under the regulation of ZEB1 and elucidate their functions within lung cancer cells. Through RNA sequencing and subsequent CIRI-full analysis in ZEB1-overexpressing lung cancer cells, we identified 25 circRNAs displaying differential expression compared to control cells. Among these circRNAs, we targeted circDennd1b, which showed down-regulation in ZEB1-overexpressing cells. We used siRNAs to target the back-splicing junction of circDennd1b, resulting in its knockdown and consequently promoting the invasion of lung cancer cells. Now, we are studying how circDennd1b affects the progression and metastasis of lung cancer. In summary, the circRNAs modulated by ZEB1 are anticipated to play a key role in the invasion, progression, and metastasis of lung cancer.

Citation Format: Seongran Cho, Jin-A Choi, Young-Ho Ahn. Identification of ZEB1-regulated circular RNAs in lung 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 5422.
Abstract 5440: TM4SF1 maintains cancer stemness in cholangiocarcinoma
Authors: Zhu Xiao Bin , Golino Jihye , Wang Xin , Xie Changqing
Published: March 2024

Cholangiocarcinoma (CCA) is an aggressive liver malignancy with increased incidence globally but poor prognosis. Cancer stemness plays critical roles on tumor initiation, recurrence, and resistance to therapy. However, the mechanism of stemness maintenance in CCA has been less explored. Previously, we have reported TM4SF1 is associated with poor survival in CCA and high expression of TM4SF1 tends to promote tumorigenesis. In this study, we found that the expression of TM4SF1 gene is upregulated in tumor tissues compared to adjacent normal tissues in CCA based on bulk RNA sequencing dataset from The Cancer Genome Atlas (TGCA) CCA cohort. There is a positive correlation between the expression of TM4SF1 and stemness genes, ITGB3, SOX9, ALDH1A3, and ITGB1. Interestingly, knockdown of TM4SF1 with siRNA in CCA cell line HuCCT-1 cells demonstrated a decrease in expression of cancer stem cell surface markers, CD24 and Prom1. Furthermore, with a CRISPR-based lentivirus construct to knockdown TM4SF1 gene in HuCCT-1 cells in vitro, we found that spheroid formation in TM4SF1 knockdown was attenuated in comparison to TM4SF1 wild type. In addition, the results from flow cytometry and RT-PCR showed a corresponding decrease in CD24 and CD133 expression with TM4SF1 knockdown when comparing to TM4SF1 wild type. In conclusion, TM4SF1 is associated with the stemness of CCA and could be a therapeutic target for CCA therapy to overcome therapy resistance in future.

Citation Format: Xiao Bin Zhu, Jihye Golino, Xin Wang, Changqing Xie. TM4SF1 maintains cancer stemness in cholangiocarcinoma [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 5440.
Abstract 5497: Towards a drag and drop spatial biology workflow: Introducing sample reinterrogation as a conduit for the progressive development and on-line analysis of high parameter spatial biology data
Authors: Ingalls Matthew H. , Meshik Xenia , Jackson Charles E. , Cashion Kayla E. , Christians Arne , Brix Anke , Boettcher Marcus , Schwarz J Spencer , Braubach Oliver
Published: March 2024

The potential for spatial biology in cancer research is understood and edified. With it we can understand the tumor microenvironment, unravel responsiveness to drug treatments and cell therapies, and ultimately stratify patients for targeted treatment and clinical trial enrollment. Yet, researchers exploring spatial biology may be discouraged by what can be a resource intensive exercise, and most importantly, a commitment of high value patient samples. Furthermore, the design of reagent panels used to study samples is not trivial, and a specimen’s unique biomarker expression profile may require adjustments. Here we present a novel solution that permits sample re-interrogation and in-flight adjustments of reagent panels in our spatial biology workflow.

The CellScape™ platform for Precise Spatial Multiplexing paired with VistaPlex™ Assay Kits provide a ready-to-use cyclic multiplex immunofluorescence (IF) solution to interrogate fresh frozen and FFPE tissue samples. Tissues are mounted in enclosed fluidic chambers, while staining and imaging are conducted on the CellScape instrument. The experiment requires no additional autostainer equipment and is divided into separate staining and imaging rounds. The end user may therefore pause between rounds and conduct inter-round analyses, which can then guide decisions of whether and how to continue the experiment. To illustrate the benefit of this approach, we present a use case in which we applied VistaPlex antibody panels to reveal the spatial distribution of major immune cell populations. Inter-round analysis and conclusions were then drawn from this preliminary phenotype map before successive rounds of rationally planned staining were conducted to further deepen the depth and breadth of spatial phenotyping.

The CellScape sample reinterrogation feature is a pragmatic spatial biology solution that optimizes the use of precious resources, whilst allowing researchers to generate informed decisions about antibody panel designs almost in real time. This enhanced utility may reduce the resistance to spatial biology among researchers working with samples that are limited or irreplaceable.

Citation Format: Matthew H. Ingalls, Xenia Meshik, Charles E. Jackson, Kayla E. Cashion, Arne Christians, Anke Brix, Marcus Boettcher, J Spencer Schwarz, Oliver Braubach. Towards a drag and drop spatial biology workflow: Introducing sample reinterrogation as a conduit for the progressive development and on-line analysis of high parameter spatial biology data [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 5497.
Abstract 5498: Multi-modal examination of spatial heterogeneity in the astrocytoma microenvironment
Authors: Moffet Joel , Kriel Jurgen , Lu Tianyao , Freytag Lutz , Whittle James , Best Sarah , Freytag Saskia
Published: March 2024

Astrocytoma is a diffuse tumor that infiltrates the brain. Despite post-operative therapy including radiation and chemotherapy, 52% of patients’ tumors recur within five-years of surgery. These tumors are characterized by mutations in the IDH1 or IDH2 gene that confer metabolic alterations, most notably the production of the onco-metabolite 2-hydroxyglutarate. To reveal the metabolic alterations and their upstream regulation across the tumor microenvironment, we applied spatial metabolomics and spatial transcriptomics to sequential sections from resected tumor samples of patients with low grade astrocytoma. This necessitated extensive optimization of atmospheric-pressure MALDI-TOF, including the establishment of a custom automated computational pipeline with abilities to identify metabolic niches. Additionally, using sequential sections of the same tumor, we also compared all commercially available imaging-based spatial transcriptomic technologies (10x Genomics Xenium, Nanostring CosMx, Vizgen MERSCOPE) to evaluate their suitability with regards to building a multi-modal model of metabolic activity and regulation across the tumor microenvironment. We found that 10x Genomics Xenium was most suited for this task as image registration across sequential sections was comparatively straight-forward. Combining spatial transcriptomics generated with 10x Genomics Xenium and spatial metabolomics across 8 matched sequential slices of the same tumor, we identified metabolic niches associated with distinct cell type composition and transcriptional regulation.

Citation Format: Joel Moffet, Jurgen Kriel, Tianyao Lu, Lutz Freytag, James Whittle, Sarah Best, Saskia Freytag. Multi-modal examination of spatial heterogeneity in the astrocytoma microenvironment [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 5498.
Abstract 5577: TRPM8 mediated Ca2+ signaling as a therapeutic target in prostate cancer
Authors: Asuthkar Swapna , Velpula Kiran , Griend Vander Don
Published: March 2024

Prostate cancer (PC) is a prevalent and deadly malignancy, necessitating the development of innovative therapeutic strategies. Transient receptor potential melastatin 8 (TRPM8), an ion channel highly expressed in prostate epithelium, has emerged as a potential target. Our preliminary studies demonstrate that TRPM8 plays a crucial role in PC progression. We observed an initial increase in TRPM8 mRNA expression during early-stage PC, followed by a decline in advanced and androgen-independent prostate cancer (AIPC) stages. Additionally, TRPM8 knockout mice exhibited elevated serum testosterone levels, heightened androgen receptor (AR) activity, and increased cell cycle, invasion, and adhesion-related effects. In xenograft models, TRPM8 demonstrated potent antitumor properties in both AR+ and AR- contexts. Our research suggests that TRPM8 activation on the plasma membrane promotes calcium influx and induces apoptosis in PC cells. Conversely, TRPM8 internalization correlates with PC pathogenesis. By exploring the effects of TRPM8 on PTEN-mediated cellular signaling, we aim to uncover novel insights into the molecular mechanisms underlying TRPM8's role in PC. This abstract underscores the potential of targeting TRPM8-mediated Ca2+ signaling as a promising therapeutic approach to combat PC progression, offering hope for improved patient outcomes.

Citation Format: Swapna Asuthkar, Kiran Velpula, Vander Don Griend. TRPM8 mediated Ca2+ signaling as a therapeutic target in prostate 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 5577.
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

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

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

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

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

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

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

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

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 <0.001 for both), while processes related to epithelial-mesenchymal transition (p-adj < 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 < 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

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.
Abstract 574: Adipocyte-derived FABP4 promotes non-alcoholic fatty liver disease (NAFLD)-induced hepatocellular carcinoma by driving ITGB1-mediated β-catenin activation
Authors: Leung Carmen Oi Ning , Gurung Shilpa , Chung Katherine Po Sin , Chan Sze Man , Lee Terence Kin Wah
Published: March 2024

Nonalcoholic fatty liver disease (NAFLD)-induced hepatocellular carcinoma (HCC) is an emerging malignancy in the developed countries. However, the mechanisms contributing to its formation remain largely unknown. Given the role of cancer stem cells (CSCs) in tumor initiation and therapeutic resistance, we hypothesize that adipocytes, one of the key cellular factors within the tumor microenvironment of NAFLD-induced HCC, may play a critical role in HCC development and drug resistance by regulating liver CSCs. Using a co-culture system in which differentiated adipocytes were grown with HCC cells, we found that adipocytes enhanced the self-renewal ability of HCC cells through indirect paracrine secretion. HCC cells pre-incubated with conditioned medium from adipocytes showed enhanced liver CSC properties including self-renewal, tumorgenicity, invasiveness and chemo-resistance to doxorubicin and sorafenib. Secretome profiles showed that FABP4 was preferentially secreted by adipocytes and its level was further augmented when co-cultured with HCC cells. Concurrently, recombinant FABP4 enhanced CSC properties of HCC cells. Drastic delay in the onset of tumor development in FABP4−/- mice upon DEN-injected and high fat diet-induced mouse models of NAFLD-HCC. Mass spectrometry analysis revealed ITGB1 as a direct binding partner of FABP4 for the first time. This data, together with the observation of significant downregulation of the Wnt/β-catenin pathway in tumors of FABP4−/− mice, revealed the role of adipocyte-derived FABP4 promotes liver CSC function by activating the PI3K/Akt/β-catenin signaling pathway via ITGB1. Overexpression of ITGB1 led to poorer survival of HCC patients with NAFLD as a risk factor. The development of a monoclonal neutralizing antibody against FABP4 successfully blocked FABP4-driven CSC functions, implicating the targetability of FABP4 for the treatment of NAFLD-induced HCC.

Citation Format: Carmen Oi Ning Leung, Shilpa Gurung, Katherine Po Sin Chung, Sze Man Chan, Terence Kin Wah Lee. Adipocyte-derived FABP4 promotes non-alcoholic fatty liver disease (NAFLD)-induced hepatocellular carcinoma by driving ITGB1-mediated β-catenin activation [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 574.
Abstract 5747: Microwave responsive thermosensitive lipid nanoparticles for spatiotemporal delivery of chemotherapeutics
Authors: Aparicio-Lopez Cesar B.
Published: March 2024

Pancreatic cancer is a highly lethal malignancy with an urge for the exploration of novel treatments. One promising approach is microwaved-induced hyperthermia, which has shown great antitumor and synergistic effects when combined with other therapies. The application of microwaves produces heat by dielectric hysteresis which depends on the dielectric properties of molecules. Ionic liquids (ILs) are compounds composed of ions with <100 °C melting point and have strong dielectric properties. In short, we propose the creation of microwave-sensitive nanoparticles using IL, enabling precise hyperthermia induction with low-powered microwaves in localized areas. To achieve this, we stabilize a core composed of 1-butyl-methylimidazolium bromide or 1-butyl-3-methylimidazolium hexafluorophosphate using Span 80, Tween 20, and Triton-X as surfactants, along with phosphatidylcholine lipids as “cosurfactants”. Employing a double emulsion procedure for fabrication, nanoparticles are characterized using dynamic light scattering, Fourier-transform infrared spectroscopy, and transmission electron microscopy. Furthermore, we assess microwave sensitivity by comparing thermal changes between liposomes loaded with 120 mM and 250 mM NaCl solutions. Subsequently, we evaluate biocompatibility and heat effects by incubating IL nanoparticles with BXPC3 and KPC cells, monitoring cell viability through MTT assays. We aim to confine the ILs within the nanoparticle core rather than incorporating them into the membrane. We anticipate increased microwave sensitivity, translating to reduced off-target effects and enhanced precision in hyperthermia treatment. This research holds promise for improving the therapeutic outcomes of pancreatic cancer treatment.

Citation Format: Cesar B. Aparicio-Lopez. Microwave responsive thermosensitive lipid nanoparticles for spatiotemporal delivery of chemotherapeutics [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 5747.
Abstract 5756: Silver graphene quantum dots as drug delivery platforms for anti-cancer application
Authors: Villanueva Rafael A. , Cole Tori , Medina Nataniel , Morell Dr. Gerardo , Weiner Brad
Published: March 2024

Prostate cancer (PCa) stands as the most frequently diagnosed cancer and the third leading cause of cancer-related deaths among men in the United States (2019). Various cancer treatments, including Rehabilitation therapy, Immunotherapy, Hormone therapy, Stem Cell Therapy, and Chemotherapy, are available. However, chemotherapy has notable limitations due to its tendency to harm healthy cells, resulting in side effects such as nausea, vomiting, alopecia, diarrhea, anemia, bleeding, and sterility. In response to these challenges, we developed nanoparticle (NP) drug delivery platforms for cancer treatment. These platforms utilize silver graphene quantum dots nanocomposites (AgGQD), known for their ability to enhance drug therapies. Silver nanoparticles (AgNPs) exhibit toxicity towards both normal and cancer cells by impacting mitochondrial function, reactive oxygen species (ROS) production, lactate dehydrogenase (LDH) release, cell cycle dysregulation, induction of apoptotic genes like Bax, micronucleus formation, chromosome aberration, and DNA damage. Additionally, AgNPs demonstrate antiangiogenic and antiproliferative properties by inhibiting PI3K phosphorylation of Akt, disrupting the signaling pathway, ultimately halting angiogenesis, depriving cells of oxygen, and causing tumor cell death. To mitigate the toxicity of AgNPs in healthy cells and enhance their performance as drug delivery platforms, graphene quantum dots (GQDs) were introduced in this study. Moreover, GQDs may contribute to improving the solubility of drugs with low water solubility. The NPs were synthesized using graphene quantum dots as reducing agents. The study involved identifying the IC50 value, conducting validation tests on AgGQD and AgGQD doped, and comparing their toxicity on cells. Confocal microscopy was employed to identify the intracellular location of the drug.

Citation Format: Rafael A. Villanueva, Tori Cole, Nataniel Medina, Dr. Gerardo Morell, Brad Weiner. Silver graphene quantum dots as drug delivery platforms for anti-cancer application [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 5756.
Abstract 5772: Structural insights and rational design, optimization of highly potent and selective novel GRK5/6 inhibitors for cancer therapy
Authors: Chen Yueyi , Sonawane Amol D. , Manda Rajesh , Gadi Ranjith K. , Ghosh Arun K. , Tesmer John J.
Published: March 2024

G protein-coupled receptor kinases (GRKs) regulate cell signaling by triggering receptor desensitization via phosphorylation on G protein-coupled receptors (GPCRs). There are seven human GRKs (GRK1−GRK7) where GRK5 and GRK6 are structurally similar. GRK5 is ubiquitous and required for cancer progression in various cancer types. Knock-down of GRK5 has been shown to suppress prostate cancer and non-small-cell lung cancer growth. GRK6 is highly abundant in immune cells and is overexpressed in multiple myeloma (MM). Knocking down GRK6 has been shown to cause apoptosis of MM cells. Therefore, targeting GRK5 or 6 is a potential chemotherapeutic strategy. Currently, we are developing a series of inhibitors for GRK5/6 based on a lead compound derived from sunitinib and utilizing Cys474 residue unique in GRK5/6 to enhance selectivity by covalent capture. We tested a series of novel inhibitor warheads to improve potency and selectivity without potentially toxic functional groups. So far, we have identified several inhibitors with low nanomolar IC50 for GRK5 and more than 100,000-fold selectivity over GRK2, another closely related member expressed in the heart. I have developed a pipeline of X-ray crystallography of GRK5 available for soaking various ligands and have solved several structures of novel inhibitor-bound GRK5. The structure elucidated the binding mode of this new class of GRK5 inhibitors, where the core interacts with the adenine site, a fluorophenyl group stabilizes the P loop and density suggests in some cases covalent bond forming between the reversible covalent warhead and Cys474. Our ongoing studies focus on further compound optimizations based on SAR. Overall, the discovery of the inhibitors can significantly facilitate understanding and treatment and cancers.

Citation Format: Yueyi Chen, Amol D. Sonawane, Rajesh Manda, Ranjith K. Gadi, Arun K. Ghosh, John J. Tesmer. Structural insights and rational design, optimization of highly potent and selective novel GRK5/6 inhibitors for cancer therapy [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 5772.
Abstract 5773: Multi-omics profiling of chemotactic characteristics of brain microglia and astrocytoma
Authors: Chen Chih-Yi , Huang Yu-Ching , Su Wen-Hsiu , Liu Yi-Ting , Chen Chi-Sheng , Li Chia-Yang , Chang Kun-Che , Dai Chia-Yen , Wang Shu-Chi
Published: March 2024

Brain cancer is a deadly disease with low survival rates for over 70 % of patients. Therefore, there is a critical need to develop better treatment methods and strategies to improve patient outcomes. In this study, we explored the tumor microenvironment and discovered unique characteristics of microglia to interact with astrocytoma cells and promote proliferation and migration of collisions. The conditioned medium from the collisions expressed cell chemoattraction and anti-inflammatory responses. To further understand the interactions between microglia and astrocytoma cells, we used flow sorting and protein analysis found that the protein alterations were related to biogenesis in the astrocytoma cells and metabolic processes in the microglia. Both types of cells were involved in binding and activity in cell-cell interactions. Using STRING to demonstrate the protein cross-interaction between the cells. Furthermore, PHB and RDX interact with oncogenic proteins, which were significantly expressed in patients with Glioblastoma Multiforme (GBM) and low-grade glioma (LGG) according to GEPIA. To study the role of RDX in chemoattraction, the inhibitor-NSC668394 suppressed collision formation and migration in BV2 cells in vitro by down-regulating F-actin. Additionally, it suppressed macrophage infiltration in infiltrating islands in vivo of intracranial tumor-bearing mice. These findings provide evidence for the role of resident cells in mediating tumor development and invasiveness and suggest that potential interacting molecules may be a strategy for controlling tumor growth by regulating the infiltration of tumor-associated microglia in the brain tumor microenvironment.

Citation Format: Chih-Yi Chen, Yu-Ching Huang, Wen-Hsiu Su, Yi-Ting Liu, Chi-Sheng Chen, Chia-Yang Li, Kun-Che Chang, Chia-Yen Dai, Shu-Chi Wang. Multi-omics profiling of chemotactic characteristics of brain microglia and astrocytoma [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 5773.