tbuckley/cabot-search huggingface dataset:
Abstract B015: KDM6A, lysine demethylase, loss affects epithelial-to-mesenchymal related gene expression and breast cancer growth
Authors: Charli Worth, Provas Das, Kelsey Johnson, Joseph Taube
Journal: Cancer Research (2024)

Abstract Epithelial-to-mesenchymal transition (EMT) or its reversal mesenchymal-to-epithelial transition (MET) are of critical importance throughout development and is implicated in wound healing, fibrotic disorders, and cancer metastasis. The ability of a cell to undergo EMT and MET, cellular plasticity, underlies tumor progression through multi-step metastasis and acquisition of chemotherapy resistance as alterations in the cellular and molecular level confer changes in motility, stemness properties, gene expression, and cellular dynamics. These changes facilitate invasion and dissemination of cancer cells. Epigenetic modifications leading to cancer cell plasticity are partially driven by histone modifying proteins including lysine (K)-specific demethylase 6A (KDM6A). KDM6A is a member of the COMPASS-like protein complex, and catalyzes the removal of methyl groups from H3K27me3, facilitating gene expression. KDM6A regulation of H3K27me3 has been associated with bivalent programs in gene expression, associates with oncogenic pathways, and contributes to low survival prognoses in breast cancer. There is critical need to elucidate the mechanisms of KDM6A suppression to understand its control on cellular plasticity. Previously we have shown that KDM6A is suppressed upon EMT. In this study, we sought to identify the regulatory mechanisms of KDM6A expression and how its activity is required to maintain epithelial cellular identity. To investigate the role of KDM6A in the context of EMT, KDM6A expression was compromised using CRISPR-Cas9 to determine the impact on H3K27me3, gene expression and cellular identity. Breast cancer cell lines were transduced with CRISPR-Cas9 and GFP via lentiviral transduction. KDM6A KO and control cell lines were generated via a CRISPR KO. We observed that the KDM6A suppression or inhibition profoundly impacts cellular identity, leading to gain of mesenchymal and stemness properties. Moreover, KDM6A was determined to be regulated through sub-cellular localization leading to partial sequestration of COMPASS-like protein complex outside the nucleus. These findings were validated via Western blot analysis of subcellular protein fractions of breast cancer cell lines and KDM6A KO cell lines and well as immunofluorescence and enzyme activity analysis. We conclude that KDM6A functions as a master regulator of epithelial cellular identity which is controlled by multi-factorial mechanisms including transcriptional suppression and altered protein localization. Citation Format: Charli Worth, Provas Das, Kelsey Johnson, Joseph Taube. KDM6A, lysine demethylase, loss affects epithelial-to-mesenchymal related gene expression and breast cancer growth [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B015.
Abstract IA005: Novel insights into pancreatic cancer evolution from carcinogenesis to metastasis
Authors: Christine Iacobuzio-Donahue
Journal: Cancer Research (2024)

Abstract While the genetic features of pancreatic cancer are well described, the evolutionary features of this tumor type have not been systematically studied to date. We assembled a large cohort of pancreatic cancer research autopies to investigate evolutionary metrics across clinical contexts. The timing of driver mutations, including truncal and subtruncal events, do not differ significantly across stages at diagnosis or types of clinical management. However, high truncal mutation density is significantly associated with worse overall survival after adjusting for stage at diagnosis, age, smoking history and Type II diabetes status, representing a novel prognostic biomarker. Oligometastatic tumors have fewer drivers and allelic losses compared to aggressive metastases, suggesting a more genomically stable subset of tumors. These findings reveal novel insights into pancreatic cancer evolution beyond established paradigms. Citation Format: Christine Iacobuzio-Donahue. Novel insights into pancreatic cancer evolution from carcinogenesis to metastasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA005.
Abstract A077: Investigating the relationship of socioeconomic status on the molecular biology of ER+ breast cancer
Authors: Jerry T DeWitt
Journal: Cancer Research (2024)

Abstract Black women in the US have worse health care options, poorer educational opportunities, and decreased income quality which collectively contribute to an overall lower socioeconomic status (SES) compared to White women. Furthermore, although the incidence of estrogen receptor positive (ER+) breast cancer is similar for Black and White women in the US, Black patients have significantly worse outcomes. The field has traditionally focused on systemic factors such as SES to explain outcome disparities. Consequently, differences in the molecular biology between tumors from Black and White women remains a gap in knowledge in the field. Recent studies have found that Black cancer patients have a unique gene expression profile that may modulate treatment response. For instance, ER+ breast tumors in Black women have distinct signatures of defective DNA damage repair (DDR) that associate with more aggressive tumor growth. However, how SES contributes to these differences in molecular biology and whether these differences alter treatment response remain unknown. One challenge to addressing these questions is that existing datasets significantly underrepresent Black women and are not sufficiently annotated to understand the complex interplay between molecular biology and factors of SES. Here, we present analysis of RNA expression datasets from 60 ER+ patient tumors (38 Black, 22 White), with corresponding SES and patient outcome annotations. Altogether, these data begin to define the complex interplay between factors of SES and changes in gene expression in addition to patient outcomes for women with ER+ breast cancer. Citation Format: Jerry T DeWitt. Investigating the relationship of socioeconomic status on the molecular biology of ER+ breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A077.
Abstract IA11: Using the Cancer Dependency Map
Authors: William C Hahn
Journal: Cancer Research (2024)

Abstract Although molecular profiling of human tumors is now routine, the use of this data to guide therapy remains limited to a subset of patients. To complement genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed both genome scale RNAi and CRISRP-Cas9 screens in hundreds of cancer cell lines to identify differentially essential genes and the context that specifies gene dependency. These studies now allow us to define a Cancer Dependency Map. Using these datasets and approaches, we have defined new categories of potential cancer targets in breast and other cancers. In particular, we have interrogated genes required for MYC-driven breast cancers and identified metabolic dependencies in breast cancers and identified a novel mechanism of estrogen receptor expression. These approaches promise to further operationalize precision cancer medicine. Citation Format: William C Hahn. Using the Cancer Dependency Map [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr IA11.
Abstract B008: KDM4C histone demethylase connects redox balance to chromatin remodeling via histone H3 tail clipping
Authors: Zheqi Li, Guillermo Peluffo, Laura Stevens, Xintao Qiu, Marco Seehawer, Xiao-Yun Huang, Shawn Egri, Malvina Papanastasiou, Natalie Kingston, Clive D'Santos, Eva Papachristou, Jun Nishida, Kyle Evans, Ji-Heui Seo, Kendell Clement, Daniel Temko, Muhammad Ekram, Matthew Rees, Melissa Ronan, Jennifer Roth, Anton Simeonov, Stephen Kales, Ganesha Rai, Madhu Lal-Nag, David Maloney, Ajit Jadhav, Franziska Michor, Alex Meissner, Justin Balko, Jason Carroll, Matthew Freedman, Henry Long, Jacob Jaffe, Kornelia Polyak
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer (TNBC) is a breast cancer subtype with inferior prognosis necessitating the discovery of novel therapeutic targets. In this study, we describe that KDM4C, a histone demethylase amplified and overexpressed in a subset of TNBC is a driver of TNBC tumor growth. Integrative multi-omic analysis using RNA-seq, ChIP-seq and ATAC-seq demonstrated that KDM4C inhibition triggers chromatin and transcriptomic remodeling without substantial changes of its canonical substrates H3K9me3 and H3K36me3 in TNBC breast cancer cells. Rather KDM4C loss surprisingly caused proteolytic cleavage at histone 3 N terminus (A21 site) identified by histone mass spectrometry. Protease inhibitor array pointed out cathepsin L (CTSL) as the endopeptidase mediating this procedure and CTSL proteomic interactome profiling further uncovered that grainyhead like transcription factor 2 (GRHL2) recruited CTSL to the chromatin. Metabolomic profiling showed reduced glutathione levels following KDM4C inhibition partly due to a decrease in glutamate-cysteine ligase (GCLC) triggered by CTSL-mediated histone H3 cleavage and subsequent increase in reactive oxygen species (ROS). Knockout of CTSL rescued KDM4C blockade-associated metabolic dysfunction and tumor suppression in vivo. The expression of KDM4C and GCLC correlated in TNBC and combined targeting of KDM4C and the GSH axis improved response to cisplatin in cell culture and xenograft models. Our study reveals a novel role for KDM4C in TNBC that links cellular redox regulation and epigenetics. Citation Format: Zheqi Li, Guillermo Peluffo, Laura Stevens, Xintao Qiu, Marco Seehawer, Xiao-Yun Huang, Shawn Egri, Malvina Papanastasiou, Natalie Kingston, Clive D'Santos, Eva Papachristou, Jun Nishida, Kyle Evans, Ji-Heui Seo, Kendell Clement, Daniel Temko, Muhammad Ekram, Matthew Rees, Melissa Ronan, Jennifer Roth, Anton Simeonov, Stephen Kales, Ganesha Rai, Madhu Lal-Nag, David Maloney, Ajit Jadhav, Franziska Michor, Alex Meissner, Justin Balko, Jason Carroll, Matthew Freedman, Henry Long, Jacob Jaffe, Kornelia Polyak. KDM4C histone demethylase connects redox balance to chromatin remodeling via histone H3 tail clipping [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B008.
Abstract A084: DEK overexpression in the murine mammary gland promotes epithelial hyperplasia
Authors: Megan Johnstone, Ashley Leck, Taylor Lange, Lisa Privette Vinnedge
Journal: Cancer Research (2024)

Abstract Introduction: Breast cancer (BC) remains a leading cause of cancer-associated mortality for women in the USA, which makes it critically important to identify and study molecular drivers of pathogenesis. We have previously identified the chromatin modifying DEK protein to have oncogenic properties. DEK is a histone H3 chaperone that is over-expressed in over 60% of breast cancers, particularly triple negative breast cancers, and is associated with poor survival. To date, all studies regarding the role of DEK in BC have manipulated DEK expression in cultured immortalized MCF10A human mammary epithelial cells and BC cell lines. However, the oncogenic functions of DEK in vivo and in normal mammary epithelium have remained unexplored. Methods: We utilized a tetracycline-off regulated, DEK overexpressing (DEK-OE) transgenic mouse model that targets mammary epithelium through the mouse mammary tumor virus (MMTV) promoter. We subsequently performed bulk RNA-Seq transcriptomic analyses, western blotting, and both histological and morphological assessments of control vs. DEK-OE mammary gland tissue to identify the oncogenic effects of DEK over-expression in vivo. Results: Bulk RNA sequencing and gene ontology analyses identified cell cycle regulation as a significantly upregulated biological process in DEK-OE versus control glands. Subsequent studies confirmed upregulation of proteins that promote the G1-S cell cycle transition including cyclins A and D and CDKs 2, 4, and 6 as well as increased numbers of Ki67+ cells. We also observed down-regulation of genes that inhibit entry the G1-S transition, such as p21 and p27. This pro-proliferative molecular status correlated with the development of mammary gland hyperplasia. Importantly, in silico analyses demonstrated gene correlations between DEK and cell cycle regulators that were also evident in human breast cancers. One potential mechanism for this transcriptional deregulation is that we identified increased histone H3K27me3 epigenetic modifications in DEK-OE cells, in both mouse and human models, which may occur through EZH2 activity. Conclusions: Combined, our work indicates that DEK is not a tumor initiator, but its oncogenic activities are likely due to its ability to promote proliferation of mammary epithelial cells. Furthermore, we report a novel function for DEK in the epigenetic regulation of histone H3 K27 trimethylation, which is mediated by the well-known EZH2 oncogene in triple negative breast cancers. Citation Format: Megan Johnstone, Ashley Leck, Taylor Lange, Lisa Privette Vinnedge. DEK overexpression in the murine mammary gland promotes epithelial hyperplasia [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A084.
Abstract A033: Nuclear EGFR as a regulator of the tumor microenvironment
Authors: Angelica Escoto
Journal: Cancer Research (2024)

Abstract Overexpression of the Epidermal Growth Factor Receptor (EGFR) is observed in all subtypes of breast cancer and is associated with large tumor size, poor differentiation, and poor clinical outcomes. However, the role of EGFR in driving the disease remains unclear, as EGFR-targeted antibodies and tyrosine kinase inhibitors fail to work effectively in breast cancer patients with EGFR overexpression. A possible explanation for therapeutic resistance is the role of intracellular EGFR, where retrograde trafficking of EGFR to the nucleus results in EGFR functioning directly as a transcriptional cofactor, regulating the expression of genes that promote tumor growth, metastasis, and an immune suppressive microenvironment. Our goal is to understand how targeting nuclear EGFR impacts this microenvironment. Using a novel therapeutic peptide (cSNX1.3) that targets retrograde trafficking of EGFR, we discovered that inhibiting retro-translocation of EGFR elicited an immune response as demonstrated by the secretion of inflammatory cytokines. Using RNA-Seq analysis, we detected an increase in the expression of cytokine receptors and natural killer (NK) cell ligands, such as RAET1 and AICL. We demonstrated that this active immune microenvironment is not observed when we treat with the EGFR kinase inhibitor Erlotinib, indicating a nuclear EGFR-specific outcome. Studies from tumor-bearing WAP-TGFα transgenic mice (an EGFR-dependent model of breast cancer) found the presence of NK cells and the expression of their activating ligands and receptors, IL-33 and SLAM7, respectively, in the tumor microenvironment. We hypothesize that nuclear EGFR is suppressing the expression of inflammatory cytokines, receptors, and ligands important for activation and recruitment of NK cells, thereby allowing immune evasion and ultimately progression of the disease. Future studies will investigate the potential to combine nuclear EGFR inhibitors with immunotherapies to activate the tumor immune microenvironment and promote optimal therapeutic efficacy. Citation Format: Angelica Escoto. Nuclear EGFR as a regulator of the tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A033.
Abstract A070: Examining patient-specific responses to PARP inhibitors in a novel, human induced pluripotent stem cell-based model of breast cancer
Authors: Carly Weddle, Paul Burridge
Journal: Cancer Research (2024)

Abstract Patient-derived human induced pluripotent stem cells (hiPSCs) are a powerful tool for disease modeling because hiPSCs provide a scalable source of cells that retain patient-specific genomic variants. Recently, somatic cell reprogramming has been applied to modeling cancer: cancer cells are reprogrammed into hiPSCs, then re-differentiated into the relevant cancer cell lineage. hiPSCs derived from cancer cells retain tumor- and subclone-specific genomic variants and drug sensitivities, providing a unique tool to deconstruct the contributions of tumor heterogeneity to drug response. While hiPSCs have been shown to model various hematological malignancies, no study to date has examined the potential of hiPSCs to model breast cancer. We demonstrate for the first time that primary human breast cancer cells can be reprogrammed into hiPSCs by transiently overexpressing canonical reprogramming factors. Using an optimized reprogramming methodology, we generated a biobank of &amp;gt;200 hiPSC lines from 10 breast tumor samples, including hormone receptor positive, HER2 positive, and triple negative breast tumors. Breast tumor-derived hiPSCs retain patient-specific oncogenic variants. Additionally, we present a protocol to differentiate hiPSCs into mammary epithelial cells (hiPSC-MECs) and mammary-like organoids for in vitro disease modeling. hiPSC-MECs are proliferative and exhibit a gene expression profile that closely resembles primary MECs. Finally, we demonstrate that this breast tumor model can be used to assess patient-specific responses to PARP inhibitors. We show that hiPSC-MECs derived from BRCA1 and BRCA2 mutant tumors are deficient in homology-directed repair and are more sensitive to PARP inhibitor treatment. This work establishes the foundation of hiPSCs as a novel disease modeling platform for breast cancer and highlights the potential of tumor-derived hiPSCs to predict patient and subclone-specific drug responses. Citation Format: Carly Weddle, Paul Burridge. Examining patient-specific responses to PARP inhibitors in a novel, human induced pluripotent stem cell-based model of breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A070.
Abstract B003: Investigating <i>PHLDA2</i> as a Genetic Driver of Breast Cancer Metastasis
Authors: Paige Halas, Hannah Savage, Dennis Ma, Jacob Insua-Rodriguez, Sharmila Mallya, Connie Chan, Radhika Domadia, Tatyana Lev, Devon Lawson
Journal: Cancer Research (2024)

Abstract Metastasis is cancer’s lethal driver. Metastatic cancer cells leave the primary tumor and travel through the blood stream to distal sites. These cancer cells are aggressive, highly recurring and pose challenges for clinical treatment. There is a critical need to define drivers of metastasis in order to identify novel drug targets and improve patient prognosis. Our previous work identified a potential breast cancer metastasis promoting gene known as PHLDA2. By single cell RNA sequencing, PHLDA2 gene expression was elevated in metastatic lesions compared to primary breast tumor tissue. This gene has not previously been linked to cancer metastasis; therefore, the objective of the current study is to confirm PHLDA2 as a driver of breast cancer metastasis and define the mechanisms by which it exerts its pro-metastatic function. We manipulated multiple breast cancer models to have elevated or reduced PHLDA2 levels to investigate its role in metastasis. We have additionally explored the mechanism of PHLDA2 in metastasis at the RNA level by qPCR, the protein level by western blot analysis, and the organ level using immunofluorescence staining and bulk sequencing. We confirmed using our breast cancer models of elevated or reduced PHLDA2 expression that PHLDA2 has a pro-metastatic function. Bulk RNA sequencing data revealed that PHLDA2 promotes extracellular matrix (ECM) remodeling. This finding is significant as ECM remodeling plays a critical role in cancer progression and metastasis. Investigation of PHLDA2’s pro-metastatic function is necessary to gain deeper insights into the mechanisms of cancer cell spread and reveal novel drug targets to improve patient survival. Citation Format: Paige Halas, Hannah Savage, Dennis Ma, Jacob Insua-Rodriguez, Sharmila Mallya, Connie Chan, Radhika Domadia, Tatyana Lev, Devon Lawson. Investigating PHLDA2 as a Genetic Driver of Breast Cancer Metastasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B003.