bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2864: Transcriptional repressor REST controls autophagy in Sonic Hedgehog medulloblastoma through the VHL-HIF1α axis
Authors: Singh Ashutosh , Cheng Donghang , Swaminathan Jyothishmathi , Zheng Yan , Gordon Nancy , Gopalakrishnan Vidya 
Published: March 2024

Abstract
Introduction: Medulloblastoma (MB) is the most common malignant brain tumor in children. It is categorized into four molecular subgroups, each with unique genetic and epigenetic alterations, molecular signatures, and differences in clinical features and treatment responses. Targeted therapy for MB has failed in the clinic, prompting new studies of mechanisms involved in MB tumorigenesis and progression.
Experimental Procedure: The transcriptomic information of the MB patients was obtained from the publicly available RNAseq datasets and was analyzed for differential expression and clustering analysis. Patient-derived orthotopic xenografts of medulloblastoma tumors with high- and low-REST expression were histologically and biochemically studied for autophagy markers. Furthermore, the SHH-MB cell lines were studied to get a mechanistic understanding of the REST-driven autophagy in this MB subgroup.
Summary: Our data showed that autophagy, a process responsible for cellular recycling, and genes associated with this pathway exhibit distinctive expression patterns in human MB subgroups. Specifically, we demonstrate that autophagy is induced in one of the MB subgroups (Sonic Hedgehog-SHH) in response to elevated expression of the RE1-silencing transcription factor (REST), a transcriptional repressor and a canonical regulator of neuronal differentiation genes. REST is also a driver of SHH-MB metastasis. Pharmacological inhibition of autophagy decreases MB cell growth, suggesting it is a pro-survival pathway in REST-driven SHH MBs. In mechanistic studies, we found REST-dependent autophagy induction to involve upregulation of the hypoxia-inducible factor 1-alpha (HIF1α) due to REST-mediated silencing of the von Hippel-Lindau (VHL) gene. The VHL gene product promotes HIF1α ubiquitination and proteasomal degradation, and its loss in SHH-MBs with elevated REST expression drives HIF1α stabilization and nuclear localization to activate target autophagy-related genes.
Conclusion: Our work is the first to link VHL to MB pathology. VHL loss of function in cancers has been mainly attributed to mutational events. Here, we report a novel mechanism of VHL loss, namely its epigenetic silencing by REST. Our findings provide the foundation for future pre-clinical investigations to examine the feasibility of autophagy blockade as a therapeutic strategy for REST-driven SHH MBs.
Citation Format: Ashutosh Singh, Donghang Cheng, Jyothishmathi Swaminathan, Yan Zheng, Nancy Gordon, Vidya Gopalakrishnan. Transcriptional repressor REST controls autophagy in Sonic Hedgehog medulloblastoma through the VHL-HIF1α axis [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 2864.
Abstract 2880: Radiation induces myofibroblast differentiation of pericytes
Authors: Yamazaki Tomoko , Jordan Kelley R. , Crittenden Marka R. , Gough Michael J. , Young Kristina H. 
Published: March 2024

Abstract
Radiation not only kills cancer cells directly through DNA damage, but also indirectly by inducing vascular changes. Endothelial cells (ECs) in small blood vessels and capillaries connect with pericytes, a type of mural cells which are important for vascular stability and structure. Effects of radiation on tumor vasculature are critical for the therapeutic efficacy, however, its impacts on pericytes remain largely unknown. In this study, we focused on the effect of radiation on pericytes and sought to elucidate the mechanism by which radiation affects pericytes. We show 20Gy for C3H10T1/2 (10T1/2) mouse embryonic mesenchymal pericyte precursor cells and 10Gy for human pericytes from placenta (hPC-PL) cells induces pericyte differentiation and activation of adhesion molecules. Radiation enhanced lymphocyte adhesion and decreased permeability in co-culture of ECs and pericytes primarily through endothelial cells, not via pericytes. Furthermore, radiation promoted transdifferentiation of pericytes into myofibroblasts. Supernatant from irradiated cells in combination with a TGFβ inhibitor showed that TGFβ signaling is involved in pericyte differentiation by radiation but not all pericyte marker genes are regulated by TGFβ. Therefore, we performed phospho-kinase array analysis and revealed Akt signaling pathway activation 10 minutes following radiation, which was verified by the phosphorylation of GSK3β and PRAS40. Along with this, generation of intracellular reactive oxygen species (ROS) occurs as early as 5 min following radiation. Inhibitors of Akt and ROS suppress the expression of myofibroblast markers increased by radiation.
To investigate whether radiation induces pericyte differentiation into myofibroblast in tumors, we employed NG2DsRedBAC (NG2DsRed) transgenic mice where DsRed is expressed under the control of NG2 promoter to trace pericytes. The endogenous expression of DsRed was detected in pericytes in the tumors implanted to NG2DsRed mice. Flow cytometry analysis of tumors harvested 7 days after radiation shows radiation increased vimentin+ cells and decreased DsRed+ cells, which indicates radiation induced pericyte differentiation into myofibroblast. In conclusion, radiation promotes pericyte maturation and transdifferentiation into myofibroblast via Akt signaling. Further study using Akt inhibitor with radiation to tumor-bearing N2DsRed mice will be warranted.
Citation Format: Tomoko Yamazaki, Kelley R. Jordan, Marka R. Crittenden, Michael J. Gough, Kristina H. Young. Radiation induces myofibroblast differentiation of pericytes [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 2880.
Abstract 2896: Elucidating the role of transglutaminase 2 (TGM2) in pancreatic ductal adenocarcinoma pathogenesis and its therapeutic implications
Authors: Wright Polina , Atfi Azeddine 
Published: March 2024

Abstract
Pancreatic cancer remains one of the deadliest malignancies, with limited therapeutic options and a poor prognosis due to delayed symptom presentation and disease detection. Pancreatic ductal adenocarcinoma (PDAC) has a 5-year survival rate of less than 8%, predominantly attributed to oncogenic KRAS mutations and loss-of-function mutations in TP53, SMAD4, and P16. Our lab is interested in studying Transglutaminase 2 (TGM2), a multifunctional enzyme involved in protein cross-linking and cellular signaling, because it is highly correlated with cancer cell survival, malignancy, metastasis, and treatment resistance. Clinically, overexpression of TGM2 is associated with poorer survival in patients with Pancreatic Ductal Adenocarcinoma so it is imperative to understand the mechanism of its action in disease progression. To elucidate the role of TGM2 in PDAC, we studied the targeted deletion of TGM2 in the context of a mouse model of PDAC and saw a significant reduction in PDAC incidence and precursor lesion formation, suggesting that TGM2 has a role in the tumor microenvironment. Using single cell sequencing, we found TGM2 levels to be elevated in certain cell populations, specifically endothelial cells and cancer cells. We discovered high TGM2 levels in TIE2-GFP mouse vessels and subsequently found high TGM2 levels in patient tumor vasculature. Further studies aim to conditionally ablate TGM2 in endothelial cells to assess its mechanistic involvement in PDAC initiation and progression. Additionally, we are studying concurrent conditional TGM2 and SMAD4 deletions in mice to investigate pancreatic cancer precursor lesion formation and are further evaluating the protective mechanisms of a TGM2 deletion in a more aggressive mouse model of PDAC. Our preliminary findings substantiate TGM2 as a critical player in PDAC pathogenesis, opening avenues for targeted therapeutics to ultimately improve patient prognosis.
Citation Format: Polina Wright, Azeddine Atfi. Elucidating the role of transglutaminase 2 (TGM2) in pancreatic ductal adenocarcinoma pathogenesis and its therapeutic implications [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 2896.
Abstract 293: Distinctive roles of mammary adipomes in breast cancer progression: Insights from functional analysis and differential gene expression
Authors: Thangavel Hariprasad , Lizardo Kezia , Glazer Robert I. , Nagajyothi Jyothi F. 
Published: March 2024

Abstract
Breast Cancer (BC) is a heterogeneous disease that impacts treatment response. This is due in part to the tumor microenvironment (TME), which contributes significantly to BC pathogenesis, including metastasis. Women with higher breast density and reduced breast fat face an increased BC risk across multiple tumor subtypes. This is exemplified by the correlation between increased tumor progression, the appearance of fibrosis and the loss of mature adipocytes. While the role of adipokines in this process has been studied extensively, the contribution of adipocyte-derived extracellular vesicles (EV) or "adipomes" in tumorigenesis and metastasis remains poorly understood. To address this question, we developed a novel technique for isolating intact adipomes from normal mammary fat (MF) obtained from wild-type C57BL/6 mice as well as from tumor-associated MF (TAMF) obtained from mice inoculated orthotopically with EO771 mammary tumor cells. Adipome isolation involved high-speed centrifugation to separate macro- and micro-vesicles, purification using the ExoQuick EV isolation system, and immunomagnetic capture of adipomes. Characterization of adipomes by transmission electron microscopy revealed two adipome populations, large L-adipomes of ~350 nm, and small S-adipomes of ~40 nm. Notably, the quantity of L-adipomes in tumor-associated mammary fat (TAMF) was 10-fold greater than the amount of L-adipomes in the MF of non-tumor-bearing mice. To identify possible functional roles of L-adipomes in the pathogenesis of BC, lipidomic profiling was undertaken. L-Adipomes from TAMF showed significantly altered lipid species in comparison to MF-derived L-adipomes. Adipomes were further characterized by treating EO771 cells for 72 hr with TAMF- or MF-derived adipomes at a cell to adipome ratio of 1:10, followed by RNAseq analysis. Differentially upregulated genes in TAMF-derived L-adipomes included Esr1, Erbb2, Tgfb1, Bcl2, MMP2, and Notch associated with fibrosis, EMT, angiogenesis and invasion and downregulation of genes linked to tumor suppression, apoptosis, and mitochondrial metabolism. Overall, our study illustrates the importance of tumor-associated adipomes in regulating gene expression in tumor cells, which emphasizes the specificity of adipome content relating to the cell-of-origin and the host's pathologic and metabolic state and in modulating signaling pathways involved in BC progression.
Citation Format: Hariprasad Thangavel, Kezia Lizardo, Robert I. Glazer, Jyothi F. Nagajyothi. Distinctive roles of mammary adipomes in breast cancer progression: Insights from functional analysis and differential gene expression [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 293.
Abstract 2935: NGS panel customization for comprehensive genomic profiling
Authors: Ruvolo Michael , Khare Akanksha , Matcha-Balaguruvappa Nishita , Wilkins Katherine , Forsmark Linus , Gupta Swati 
Published: March 2024

Abstract
Introduction: We have developed a custom SureSelect Cancer design pipeline for the creation of target enrichment gene panels for comprehensive profiling of single nucleotide variations (SNP/INDEL), gene-level copy number variations (CNV), and DNA translocations (TL) as well as content for measuring of microsatellite instability (MSI) and tumor mutational burden (TMB).
Methods: The performance of individual probes was measured for the 679-gene SureSelect Cancer CGP panel and the information used to generate a reference database. When creating a new design, the gene list is cross-referenced with the database and when applicable, the probe information is applied to the new design. If genes are included in the custom design that are not present in the database, a second design algorithm selects the optimal probe based on its sequence characteristics (% GC, homology, etc.). Content is selected based on the biomarker to be measured and can be defined based on gene name (SNV/indel and CNV) or genomic coordinates (SNV/indel, TL). Pre-defined content for MSI measurement can be added to any design to cover 288 microsatellite sites. The performance of these sites in determining MSI status was demonstrated by comparing to the MSI-PCR reference method. To assess the performance of the design methodology, designs of various sizes (50 to 650+ genes) and content type were generated and assayed on reference samples and FFPE with known biomarkers. Sequencing metrics were evaluated for capture specificity and coverage of the target regions.
Results: The design methodology allowed for sub-selection of content present in the 679-gene SureSelect Cancer CGP assay as well as addition of de-novo content. The design algorithm uses empirical data on probe performance to provide robust and reproducible results for the range of supported design sizes. Biomarkers were reliably detected with SNV detection down to 1% allele frequency, detection of gene amplifications and translocations concordant with FISH, and MSI and TMB determination concordant with PCR and Exome sequencing respectively. The design workspace was implemented in the SureDesign platform, providing a web-based interface for creating the designs.
Conclusions: We demonstrated full customization capability of the SureSelect Cancer target enrichment platform that pairs user-defined content with an optimized probe design methodology to enable the sensitive detection of the common types of DNA alterations found in FFPE samples.
Citation Format: Michael Ruvolo, Akanksha Khare, Nishita Matcha-Balaguruvappa, Katherine Wilkins, Linus Forsmark, Swati Gupta. NGS panel customization for comprehensive genomic profiling [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 2935.
Abstract 294: The HOXB7 protein promotes breast cancer cell growth through activation of the CCL5/CCR5 pathway in the crosstalk of adipocyte
Authors: Akume Ahone Gina , Jin Kideok 
Published: March 2024

Abstract
Homeobox genes are regulatory genes that encode nuclear proteins acting as transcription factors during normal development and differentiation. One such gene, HOXB7, plays a role in various developmental processes, including hematopoietic differentiation, lymphoid development, and mammary gland development. However, the role of HOX genes in breast cancer development remains largely unexplored. Our previous studies revealed that HOXB7 expression was significantly elevated in primary cancer and distant metastasis. HOXB7 overexpression promoted cell proliferation in SKBR3 breast cancer cells, leading to robustly vascularized xenografts in immunodeficient mice. Furthermore, HOXB7 enhanced tumor growth through TGF beta signaling and recruitment of macrophages, indicating the role of HOXB7 in the crosstalk of stromal components. We found evidence that HOXB7 overexpression in ER+ breast cancer cells promotes tumor cell growth through increased expression and signaling of CCL5/CCR5 in crosstalk with adipocytes. By screening secreted factors in adipocytes induced by TCM of MCF-7-HOXB7 cells, it was also found that CCL5 is highly expressed in HOXB7-overexpressing MCF-7 cells. The CCR5 inhibitor, maraviroc, sensitized MCF-7-HOXB7 cells compared to control cells. These findings suggest that blocking the interaction between CCL5 and CCR5 signaling significantly inhibits ER+ breast cancer with HOXB7 overexpression. We aim to further investigate if HOXB7 overexpression in ER+ breast cancer cells promotes tumor cell growth through increased expression and signaling of CCL5/CCR5 in crosstalk with adipocytes and the role of CCL5 in breast cancer cell growth and migration.
Citation Format: Ahone Gina Akume, Kideok Jin. The HOXB7 protein promotes breast cancer cell growth through activation of the CCL5/CCR5 pathway in the crosstalk of adipocyte [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 294.
Abstract 2945: Using pooled minimal genome-wide sgRNA libraries to drive oncology drug discovery
Authors: Lukasiak Sebastian , Kalinka Alex , Gupta Nikhil , Saeed Khalid , Papadopoulos Angelos , McDermott Ultan , Hannon Gregory J. , Ross-Thriepland Douglas , Walter David 
Published: March 2024

Abstract
The emergence of CRISPR technologies has enabled rapid and precise gene editing opportunities. The Functional Genomics Centre (FGC) - a joint venture between Cancer Research UK’s (CRUK) drug discovery engine, Cancer Research Horizons, and AstraZeneca has been launched to better utilize and improve the CRISPR technology within cancer research. The FGC leverages the strengths of both CRUK’s and AstraZeneca’s world-class oncology research and drug discovery experience, with the potential to drive scientific innovation in how new drug targets are identified and validated, and uniquely democratize access to the latest cutting-edge research tools and expertise for many thousands of scientists and clinicians funded by CRUK.
Here, we will showcase how the FGC is leading the development and refinement of functional genomics technologies. Through independent evaluation of publicly available CRISPR tools and leveraging this data we have designed optimized, minimal genome-wide CRISPR libraries. These libraries permit a reduction of the experimental scale of CRISPR screens by 50% and enable our Target Discovery platform to impact more projects, faster, at a lower cost and importantly - more sustainably.
Citation Format: Sebastian Lukasiak, Alex Kalinka, Nikhil Gupta, Khalid Saeed, Angelos Papadopoulos, Ultan McDermott, Gregory J. Hannon, Douglas Ross-Thriepland, David Walter. Using pooled minimal genome-wide sgRNA libraries to drive oncology drug discovery [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 2945.
Abstract 2970: Anti-diabetic drug, semaglutide, prevents doxorubicin-induced endothelial cell toxicity
Authors: Bakhit Sandra , Amaefuna Chelsea , Ramana Kota 
Published: March 2024

Abstract
Doxorubicin (Dox) is part of the anthracycline drug family and is known for its broad and effective use as a chemotherapeutic agent. It is commonly used to treat solid tumors and malignancies such as leukemia, breast, lung, and ovarian cancers. Unfortunately, its use in treating advanced cancers is limited due to its cardiotoxic side effects. Therefore, various adjuvant approaches are required to increase Dox's efficacy and to reduce unwanted toxicities including cardiotoxicity. Semaglutideis a glucagon-like peptide-1 (GLP-1) receptor agonist commonly used to treat type-2 diabetes. In his study, the effect of Semaglutide in preventing Dox-induced endothelial cell toxicity was investigated. Our data indicate that Semaglutide prevents Dox-induced cell death in human umbilical vein endothelial cells (HUVEC) in a dose- and time-dependent manner. Similarly, live and dead cell staining assay also confirms Semaglutide prevents Dox-induced endothelial cell death. Semaglutide also prevented the Dox-induced apoptosis of HUVECs. It also prevented the Dox-induced reactive oxygen species and activation of caspase-3. Further, Semaglutide regulated the expression of various anti- and pro-apoptotic and inflammatory factors induced by Dox. Inconclusion, our current results suggests that the anti-diabetic drug, Semaglutide, could prevent Dox-induced endothelial cell death by regulating the expression of various pro-apoptotic, anti-apoptotic and inflammatory markers. Thus, our data indicate that Semaglutide could be used as a potential adjuvant drug to reduce the adverse effects of anthracycline chemotherapeutic drugs.
Citation Format: Sandra Bakhit, Chelsea Amaefuna, Kota Ramana. Anti-diabetic drug, semaglutide, prevents doxorubicin-induced endothelial cell toxicity [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 2970.