tbuckley/cabot-search huggingface dataset:
Abstract 4293: Chromosomal instability causes epigenetic aberrations in cancer
Authors: Albert S. Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, Ramya Raviram, Bailey S. Jones, Stephanie Stransky, Lorenzo Scipioni, Jens Luebeck, Melody Di Bona, Danguole Norkunaite, Robert M. Myers, Mercedes Duran, Seongmin Choi, Britta Weigelt, Shira Yomtoubian, Andrew McPherson, Eleonore Toufektchan, Kristina Keuper, Paul S. Mischel, Vivek Mittal, Sohrab P. Shah, John Maciejowski, Zuzana Storchova, Enrico Gratton, Peter Ly, Dan Landau, Mathieu F. Bakhoum, Richard P. Koche, Simone Sidoli, Vineet Bafna, Yael David, Samuel F. Bakhoum
Journal: Cancer Research (2024)

Abstract Chromosomal instability and changes in the epigenome are defining features in most metastatic cancers. Our research links chromosomal missegregation, their containment in micronuclei, and subsequent rupture of the micronuclear envelope to histone post-translational modification aberrations. This relationship was across all tested human and murine cancer cell lines, as well as non-transformed cells. Furthermore, we discovered that the observed changes in histone PTMs were caused by either micronuclear rupture or the persistence of histone PTM status during cell division. Moreover, we revealed substantial chromatin accessibility differences in micronuclei. Notably, there is a distinct bias in chromatin accessibility between promoter regions compared to distal and intergenic regions of the genome, which aligned well with observed changes in histone modifications. The induction of chromosomal instability leads to widespread, heterogeneous, and heritable abnormalities in the epigenetic landscape of cancer cells. Therefore, on top of genomic copy number changes, chromosomal instability causes epigenetic reprogramming, which adds another layer to cancer heterogeneity. Citation Format: Albert S. Agustinus, Duaa Al-Rawi, Bhargavi Dameracharla, Ramya Raviram, Bailey S. Jones, Stephanie Stransky, Lorenzo Scipioni, Jens Luebeck, Melody Di Bona, Danguole Norkunaite, Robert M. Myers, Mercedes Duran, Seongmin Choi, Britta Weigelt, Shira Yomtoubian, Andrew McPherson, Eleonore Toufektchan, Kristina Keuper, Paul S. Mischel, Vivek Mittal, Sohrab P. Shah, John Maciejowski, Zuzana Storchova, Enrico Gratton, Peter Ly, Dan Landau, Mathieu F. Bakhoum, Richard P. Koche, Simone Sidoli, Vineet Bafna, Yael David, Samuel F. Bakhoum. Chromosomal instability causes epigenetic aberrations 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 4293.
Abstract 4292: Unraveling the interplay of aging, smoking, and mutation-driven clonal expansions in lung cancer evolution: A multifaceted approach
Authors: Amy N. Briggs, James DeGregori
Journal: Cancer Research (2024)

Abstract Despite the well-established link between tobacco use and lung cancer, military personnel face additional risks due to heightened smoking rates and exposure to various environmental contaminants. Aging further amplifies susceptibility to lung cancer, contributing to elevated incidence rates among Veterans compared to non-Veterans. Our studies aim to elucidate the intricate relationship between aging, smoking, and mutation-driven clonal expansions in lung tissue, examining their impact on lung function and cancer evolution. Using cell culture and mouse models, we introduce mutations identified in human lung tissue into airway epithelial cells. Using CRISPR, base editing, and genetically engineered mouse models, we assess the effects on barrier function, cell differentiation, and gene expression. Ultimately, we are investigating the interaction between induced mutations, aging, and smoking, exploring how mutation-driven clonal expansions contribute to lung dysfunction and pre-malignant phenotypes, potentially forming a feedforward loop. This research addresses critical gaps in understanding the complex interplay of aging, smoking, and mutation-driven clonal expansions in lung cancer evolution. Findings have the potential to unveil novel insights into the development of lung dysfunction and malignancy, paving the way for safe and accessible interventions to reduce cancer risk and enhance lung health. Citation Format: Amy N. Briggs, James DeGregori. Unraveling the interplay of aging, smoking, and mutation-driven clonal expansions in lung cancer evolution: A multifaceted approach [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 4292.
Abstract 3634: Copy number alterations in chromosome 19 genes associate with reduced immune infiltrate and adverse outcomes in lung cancer
Authors: Brian S. Henick, Yohanna Georgis, Benjamin O. Herzberg, Carla P. Concepcion-Crisol, Alison M. Taylor
Journal: Cancer Research (2024)

Abstract Deleterious mutations in STK11/LKB1, KEAP1, and SMARCA4 have been shown to be associated with adverse response to immunotherapy in several lung cancer cohorts. However, the biological and clinical implications of deletions of these genes, which all reside on chromosome 19p (chr19p), has not been extensively described. We sought to first characterize the association between immune infiltration and these copy number changes in chr19p. To do this, we analyzed mutation, copy number, and gene expression data from non-small cell lung cancer cohorts in the Cancer Genome Atlas (TCGA). Chr19p is frequently deleted across cancers in the TCGA dataset, with higher rates in lung adenocarcinoma. In both lung adenocarcinoma and squamous cell carcinoma, nearly half of TCGA tumors have deletion of chr19p including STK11, KEAP1, and SMARCA4, and these tumors are enriched for STK11 mutation. Immune infiltrate (estimated by methylation patterns) was not significantly associated with STK11 mutation but was significantly reduced in tumors with chr19 deletion when controlling for tumor type and overall copy number load. In addition, low-level deletion of any of these genes correlated with decreased expression of immune signaling pathways. Based on these findings, we next wanted to characterize the association between chr19p copy number and immunotherapy response. We previously reported that low-level deletion of STK11 correlated with an immunosuppressive, treatment-refractory phenotype in samples collected from non-small cell lung cancer (NSCLC) patients with resectable disease in a phase II study of neoadjuvant atezolizumab + chemotherapy. To confirm these findings in a larger cohort, we examined the AACR GENIE NSCLC biopharma collective (BPC) dataset. A subset of this cohort included patients treated with immunotherapy (atezolizumab, nivolumab, and/or pembrolizumab) and with copy number data available or GISTIC analysis of individual genes (n = 204). Here, deletion of any of these three genes correlated with worse overall survival, and this was statistically significant for STK11 deletion. Overall, our data suggests that a broader set of patients, defined by copy number changes in these genes, may experience this adverse immunobiology. Further study to elucidate the mechanistic implications of this association is warranted. Citation Format: Brian S. Henick, Yohanna Georgis, Benjamin O. Herzberg, Carla P. Concepcion-Crisol, Alison M. Taylor. Copy number alterations in chromosome 19 genes associate with reduced immune infiltrate and adverse outcomes in lung 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 3634.
Abstract 4303: Enrichment of nonadherent prostate cancer stem cell populations using simulated microgravity bioreactor
Authors: Kezhan Khazaw, Sebnem Unlu, Abdulrahman M. Dwead, Bekir Cinar
Journal: Cancer Research (2024)

Abstract Prostate cancer is the most prevalent and the leading cause of cancer-related death among men, particularly African Americans. The cellular and molecular mechanisms contributing to this deadly disease remain largely unknown. As such, there are no effective strategies to treat metastatic cancer and improve patient outcomes. Anchorage-independent growth of circulating prostate tumor cell clusters is essential for developing cancer metastasis. However, there is no model system to study the molecular and functional characteristics of prostate tumor cell clusters reminiscent of the bloodstream in a laboratory setting. In addressing this need, we have established nonadherent LNCaP cell clusters, LN-G2 and LN-G3, under androgen-depleted growth conditions in a simulated microgravity bioreactor called Slow Turning Lateral Vessel (STLV). Our quantitative PCR analysis repeatedly demonstrated that LN-G2 and LN-G3 cell populations expressed high levels of the well-characterized CD44 and CXCR4 cancer stem cell maker, respectively, compared to the LNCaP parental. In addition, our functional analysis indicates that, unlike the LNCaP cell, LN-G2 and LN-G3 cells showed superior clonogenic and growth behaviors in response to androgen depletion and enzalutamide-treatment under adherent monolayer and nonadherent conditions. These observations suggest that cancer stem cell-like cell clusters that survived under microgravitational stress confer distinctive molecular and functional properties associated with superior survival and contribute to castration-resistant prostate cancer. Furthermore, the STLV bioreactor could help enrich cancer stem cell populations and enhance our understanding of the underlying mechanisms of lethal cancer, which may lead to novel therapeutics to improve patient outcomes. Citation Format: Kezhan Khazaw, Sebnem Unlu, Abdulrahman M. Dwead, Bekir Cinar. Enrichment of nonadherent prostate cancer stem cell populations using simulated microgravity bioreactor [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 4303.
Abstract 3630: Measuring EGFr on extracellular vesicles in human plasma samples
Authors: Dorte Aa. Olsen, Torben F. Hansen, Ivan Brandslund, Jonna S. Madsen
Journal: Cancer Research (2024)

Abstract Introduction: Extracellular vesicles (EVs), secreted extracellularly by almost all types of cells, play a pivotal role in intercellular communication and have emerged as valuable indicators in disease progression. Their potential for cancer diagnostics and monitoring is particularly noteworthy. Epidermal growth factor receptor (EGFr) is a major driver of several cancers and serve as an important target or co-target in cancer treatment. The purpose of this study was to develop an assay for measuring EGFr on EVs directly in plasma samples. Additionally three assays were developed to measure the total concentration of plasma EVs. Methods: Recognizing the expected low concentrations of EGFr on EVs, the immunoassays were developed using Single molecule array (Simoa) technology, which has shown up to a 1000-fold improvement in sensitivity as compared to conventional immunoassay approaches. Commercial available calibrator material and antibodies against surface markers (EGFr, CD9, CD63 and CD81) were used to develop four assays: CD81-EGFr, CD81-CD9, CD81-CD63, and CD9-CD63. Plasma samples from healthy individuals (n=13) and small cohorts of various cancer patients (n=30, lung, colorectal, ovarian) were used for development, validation and testing. Results: Each assay was tested for dilution linearity, limit of detection, analytical variation and pre-analytical stability of EVs. EGFr on EVs was lower in cancer patients (median: 489 × 106 EVegfr/mL) compared with healthy individuals (median: 663 × 106 EVegfr/mL). Conversely, total EV concentrations were markedly higher in plasma from cancer patients compared with healthy individuals (CD81-CD9: 9157 vs 4088, CD81-CD63: 3634 vs 1582, CD9-CD63: 9538 vs 1210, median values x106 EV/mL). Positive correlations were observed among the total EV assays (r=0.6, p&amp;lt;0.0001). Conclusion: The developed assays allow measurement of EGFr on EVs and total EVs in human plasma samples. Notable, total EV concentrations were highly increased in cancer as compared with healthy individuals. The assays are now ready for a comprehensive validation using large cohorts of cancer samples. Citation Format: Dorte Aa. Olsen, Torben F. Hansen, Ivan Brandslund, Jonna S. Madsen. Measuring EGFr on extracellular vesicles in human plasma samples [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 3630.
Abstract 3645: Unraveling spatial complexity of the tumor microenvironment: A whole transcriptomic perspective with Visium HD
Authors: Yifeng Yin, Jerald Sapida, David Sukovich, David Patterson, Augusto Tentori
Journal: Cancer Research (2024)

Abstract In recent years, advances in spatial transcriptomics have revolutionized our understanding of the tumor microenvironment, providing crucial insights into the complex interplay of different cell types within cancer tissues. In this study, we employed the new, high definition Visium spatial transcriptomics assay (Visium HD) to investigate the intricate molecular landscape of prostate cancer at single-cell scale resolution and across the whole transcriptome. Our research focused on deciphering the spatial heterogeneity of gene expression patterns within the tumor microenvironment, shedding light on the interactions between cancer cells, stromal cells, and vasculature. The Visium HD assay enables an unbiased exploration of the transcriptome on FFPE tissue sections mounted on standard glass slides. Combining gene expression data with H&amp;E images from the same section, it allows precise characterization of local molecular features and disease states at single-cell scale. We analyzed a set of human prostate adenocarcinoma samples with the Visium HD assay, and identified spatially regulated gene signatures associated with specific cell types and functional pathways. Our findings have recapitulated previously identified molecular markers, including VEGFA and MYC which have been implicated in tumor progression and angiogenesis. The spatial gene expression patterns had good correlation with histological annotations of cancerous and normal tissue within the H&amp;E image. However, Visium HD allowed us to further observe molecular processes and pathways specific to this adenocarcinoma sample. This integrative approach offers valuable implications for personalized cancer therapy and the development of targeted interventions tailored to the spatial context of individual tumors. Our study underscores the significance of understanding the spatial organization of the whole transcriptome in cancer tissues, and highlights the potential of the Visium HD platform as a powerful tool for unraveling the complexities of the tumor microenvironment. These insights pave the way for the development of innovative therapeutic strategies and precision medicine approaches, ultimately contributing to improved outcomes for cancer patients. Citation Format: Yifeng Yin, Jerald Sapida, David Sukovich, David Patterson, Augusto Tentori. Unraveling spatial complexity of the tumor microenvironment: A whole transcriptomic perspective with Visium HD [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 3645.
Abstract 2994: MIR99AHG promotes ERα expression and ER-positive breast cancer cells proliferation via activating Hippo signaling
Authors: Wende Wang, Danping Lin, Ziyang Lin, Yangyang Yan, Yusen Qin, Yuanke Liang, Haoyu Lin, De Zeng
Journal: Cancer Research (2024)

Abstract Background: Estrogen receptor (ER) positive breast cancer is the most common subtype of breast cancer. Elucidation of the regulatory network in estrogen receptor pathway is critical to develop and deliver potent targeted therapy for ER-positive breast cancer. The Mir-99a-let-7c cluster host gene MIR99AHG is a long non-coding RNA involving in a variety of tumor formation and disease progression processes. However, the biological functions of MIR99AHG in ER-positive breast cancer have not been reported. Methods: The Western-blot, qRT-PCR, Immunofluorescence and fluorescence in-situ hybridization were used to identify potential target genes and regulatory pathway of estrogen receptor α (ERa), which is a key proliferative driver of ER-positive breast cancer cells. The cell proliferation assay, clone formation assay, xenograft tumor model and rescue assay were used to investigate the effect of differential expression of MIR99AHG on the proliferative capacity of ER-positive breast cancer cells MCF7 and T47D. In addition, correlation analysis was performed to verify the relation of the expression of MIR99AHG, LATS1, LATS2, CYR61, CTGF and ESR1 from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts. And survival analysis was used to predict the prognostic impact of MIR99AHG in breast cancer patients. Results: MIR99AHG expression was significantly higher in ER-positive breast cancer cells MCF7 and T47D than in ER-negative breast cancer cells SKBR3, MDA-MB-231 and BT549. The high expression of MIR99AHG predicted poor prognosis in ER-positive breast cancer patients. In vitro and in vivo assays demonstrated that MIR99AHG positively regulated the proliferation of MCF7 and T47D cells. Importantly, the Hippo signaling was identified to be down-stream mediators of MIR99AHG in modulating ERα transcription. Furthermore, XMU-MP-1, which targets the Hippo signaling upstream kinase MST1/2, was able to reverse the effect of MIR99AHG on MCF7 cell proliferation. Conclusions: MIR99AHG up-regulates ERα expression and promotes proliferation in ER-positive breast cancer cells through activating Hippo signaling pathway. Targeting MIR99AHG/Hippo pathway is a potential strategy for the treatment of ER-positive breast cancer. Citation Format: Wende Wang, Danping Lin, Ziyang Lin, Yangyang Yan, Yusen Qin, Yuanke Liang, Haoyu Lin, De Zeng. MIR99AHG promotes ERα expression and ER-positive breast cancer cells proliferation via activating Hippo signaling [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 2994.
Abstract 2280: HPV integration identifies emerging oncogenes and carcinogenic mechanisms, potentially indicating tumor recurrences
Authors: Shiting Li, Shaomiao Xia, Maria Lawas, Tingting Qin, Bailey Grab, Nisha D'Silva, Laura Rozek, Maureen Sartor
Journal: Cancer Research (2024)

Abstract HPV integration events in Head and neck squamous cell carcinomas (HNSCC) are strongly associated with carcinogenesis and tumor progression. Previous studies have elucidated the mechanisms and structures of HPV-human fusion events, pinpointing potential integration “hotspots” (i.e. genes with nearby HPV integration in recurrent patients). However, none has comprehensively investigated the effects of HPV integration on both HPV and human gene expression, nor assessed the clinical implications of these bidirectional expression changes. In this study, we conducted bulk RNA sequencing on 67 Formalin-Fixed Paraffin-Embedded Oropharyngeal Squamous Cell Carcinoma (OPSCC) tumor samples from the University of Michigan hospital, and analyzed them in conjunction with bulk and single cell RNA-seq from another &amp;gt;200 HPV(+) HNSCC patients from four previous studies. Among the 117 samples confidently identified as HPV integration positive, we recaptured all previously known integration “hotspot” genes as well as several novel ones that have altered expression in the integrated samples. Exploring the impact of HPV integration on the expression of human and HPV genes, we found that HPV integration in HNSCC is strongly associated with keratinization, immune response, and the development of HPV(+) HNSCC subtypes. Upon HPV integration, expression of non-oncogenic HPV genes is often lost. We hypothesized that the expression ratio of these potentially HPV immunogenic genes (E1-E5, L1,L2) to the HPV oncogenic genes E6 and E7 (termed the ImmunOnco Score) would predict clinical outcomes. Survival analysis of 70 University of Michigan patients showed low ImmunOnco Score is associated with tumor recurrence. Citation Format: Shiting Li, Shaomiao Xia, Maria Lawas, Tingting Qin, Bailey Grab, Nisha D'Silva, Laura Rozek, Maureen Sartor. HPV integration identifies emerging oncogenes and carcinogenic mechanisms, potentially indicating tumor recurrences [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 2280.
Abstract 3646: A spatially resolved single cell proteomic atlas of small bowel adenocarcinoma
Authors: Zeynep Dereli, Behnaz Bozorgui, Huamin Wang, John Weinstein, Michael Overman, Anil Korkut
Journal: Cancer Research (2024)

Abstract Small bowel adenocarcinoma (SBA) is a rare malignancy associated with poor prognosis. The cellular and proteomic heterogeneity within the tumor immune microenvironment (TIME) of SBA is a likely driver of prognosis, disease progression and response to therapy. There is, however, a major gap in our knowledge of tumor and immune interactions in SBA. Cyclic Immunofluorescence (CycIF), an antibody-based, highly multiplexed imaging technology for spatially resolved single cell level proteomic profiling, is well suited to map the proteomic heterogeneity and organization of TIME in SBA. Here, using CycIF, we have generated a spatially resolved single-cell proteomic atlas of TIME for 136 tumor and normal samples from clinically and genomically annotated SBA patients (N=37). The SBA TIME Atlas covers information on expression levels, spatial position, and cell morphology for &amp;gt; 40 proteomic markers of tumor-intrinsic processes and states, diverse immune cell types, immune checkpoints, and tumor vascularization. In total, we collected proteomics data from &amp;gt; 600,000 cells. Using a hierarchical decision tree of cell type markers, we have generated the cell identity annotations for &amp;gt; 350,000 cells, with positional information. A comprehensive computational analysis of the SBA atlas revealed various spatial and heterogeneity features that may impact the TIME organization in fine detail. Using those features, we have compared the proteomic heterogeneity in tumor vs. normal cell populations, identifying spatial and single-cell correlates of key clinical variables (e.g., patient survival, age, sex, disease stage, metastatic status). We have also performed differential analyses of spatial features involving protein markers and cell types with respect to genomic alteration states and have mapped the spatial enrichment of likely actionable immune check proteins to immune and tumor cells. Such mapping may guide future therapeutic decisions. Overall, we expect that the SBA TIME Atlas will provide a useful resource and inform future translational studies, as well as basic research for better mechanistic understanding and treatment of this disease. Citation Format: Zeynep Dereli, Behnaz Bozorgui, Huamin Wang, John Weinstein, Michael Overman, Anil Korkut. A spatially resolved single cell proteomic atlas of small bowel adenocarcinoma [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 3646.