tbuckley/cabot-search huggingface dataset:
Abstract A042: Characterization of the hormone receptor-positive breast tumor immune microenvironment using single cell transcriptomics and multiplex immunofluorescence
Authors: Daniel Michaud, Kenichi Shimada, Kelly Zheng, Cheryl Gu, Yvonne Cui, Jonathan Goldberg, Esther Ogayo, Peter Sorger, Sandro Santagata, Elizabeth Mittendorf, Jennifer Guerriero
Journal: Cancer Research (2024)

Abstract Hormone receptor-positive (HR+) breast tumors are the most frequently diagnosed type of breast cancer (~70%) and are characterized by the expression of the estrogen receptor and/or the progesterone receptor. HR+ breast tumors derive limited benefit from immune checkpoint therapy (ICT), which can be at least partially attributed in part, to low levels of T cell infiltration and low expression of T cell immune checkpoint molecules. In other solid tumors, targeting components of the tumor microenvironment outside of T cells have shown the ability to enhance ICT responses, however, such targets have been relatively unexplored in HR+ breast cancer. We hypothesize that there are unidentified targetable non-lymphocyte immune populations within the HR+ breast tumor microenvironment, which can be targeted to increase response to ICT. We performed paired bulk RNA sequencing and cyclic immunofluorescence (CyCIF) from untreated human HR+ tumors (n=30) as well as single-cell RNA sequencing (scRNA-seq) on a subset (N=17) of the tumors, to characterize the spatial composition of the immune infiltrate and identify gene expression profiles that correlate with T cell infiltration. We have identified tumor-associated macrophages (TAMs) as being the immune cell population most abundant in HR+ tumors by both scRNA-seq &amp; CyCIF. We identified SPP1+ CD36+ expressing macrophages to be significantly enriched in T cell-low compared to T cell-high HR+ tumors. These SPP1+ CD36+ macrophages have been previously linked to lipid metabolism in the tumor microenvironment and we confirmed such with gene set enrichment analysis. Inversely, T cell high HR+ tumors displayed a significant enrichment of MUCL1+APOD+ macrophages expressing high levels of MHC class II molecules and enriched for gene sets relating to antigen presentation and interferon responses. Collectively, these findings put forth two populations of macrophages within HR+ tumors as novel immunotherapeutic targets for further investigation to enhance T cell responses and ICT. Citation Format: Daniel Michaud, Kenichi Shimada, Kelly Zheng, Cheryl Gu, Yvonne Cui, Jonathan Goldberg, Esther Ogayo, Peter Sorger, Sandro Santagata, Elizabeth Mittendorf, Jennifer Guerriero. Characterization of the hormone receptor-positive breast tumor immune microenvironment using single cell transcriptomics and multiplex immunofluorescence [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 A042.
Abstract B014: Bioinformatic and in-vitro analyses identify cAMP/PKA/CREB signaling as a major molecular alteration in invasive lobular breast cancer
Authors: Abdalla Wedn, Susrutha Puthanmadhom-Narayanan, Adrian Lee, Steffi Oesterreich
Journal: Cancer Research (2024)

Abstract Invasive lobular cancer (ILC) is the second most common subtype of breast cancers after invasive carcinoma of no special type (NST) but associated with worse outcomes. Despite the known molecular differences between ILC and NST, ILC treatment is the same as stage matched NST making the development of ILC targeted therapies an urgent need. Therefore, this study was conducted to identify novel molecular alterations in ILC that could be exploited for therapeutic purposes. Differential gene expression and Geneset Enrichment and Variation analyses were performed on RNA-seq data from three large public breast cancer databases – the Sweden Cancerome Analysis Network-Breast (SCAN-B), The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC). Pathways enriched in overlapping differentially expressed genes from these datasets were clustered using Jaccard index to identify novel pathways related to ILC. The cAMP/PKA/CREB signaling was studied in ILC, ILC-like and NST cell lines and patient-derived organoids (POD) using Forskolin, an activator of the pathway. Clinicopathological features of patients with ILC and NST in SCAN-B were similar to prior population-based studies. There was a consistent pattern of up-regulation of cAMP/PKA/CREB related signaling in ILC compared to NST tumors in SCAN-B, TCGA and METABRIC. Treatment with forskolin resulted in a greater increase in phospho-CREB in ILC cell lines and organoids compared to NST. CRISPR deletion of CDH1 in NST cell lines did not alter response of cells to forskolin as measured by phospho-CREB. Co-immunofluorescence supported the enhanced nuclear localization and subsequent phosphorylation of CREB at Serine 133 in ILC cell lines. Forskolin treatment caused growth inhibition in ILC and NST cells, with ILC cell lines being more sensitive to forskolin-mediated growth inhibition. Collectively the data indicate that the cAMP/PKA/CREB signaling is higher in ILC than NST tumors. This was consistent across three separate cancer datasets and was validated in cell lines and organoids. Loss of CDH1 is not sufficient to mediate this phenotype in lobular tumors. Future studies should investigate the mechanisms for differential cAMP/PKA/CREB signaling in ILC and NST and investigate the potential for therapeutic targeting especially in patients with ILC. Citation Format: Abdalla Wedn, Susrutha Puthanmadhom-Narayanan, Adrian Lee, Steffi Oesterreich. Bioinformatic and in-vitro analyses identify cAMP/PKA/CREB signaling as a major molecular alteration in invasive lobular 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 B014.
Abstract A027: Targeting MYC-induced reprogramming of mitochondrial metabolism in breast cancer
Authors: Johanna M. Anttila, Mariel Savelius, Daniel Nicorici, Ryan Awadhpersad, Pauliina M. Munne, Linda Id, Topi A. Tervonen, Christopher Jackson, Anni I. Nieminen, Juha Klefström
Journal: Cancer Research (2024)

Abstract Oncogenic MYC is frequently overexpressed in breast cancer, and its overexpression is associated with aggressiveness and unfavorable prognosis of breast cancer. MYC overexpression promotes tumor growth by stimulating cell cycle progression and rewiring metabolism – creating cancer vulnerabilities that can be therapeutically targeted via synthetic lethal strategies. A large part of our current understanding of the MYC overexpression biology and related synthetic lethal pathways is based on findings in various inducible MYC overexpression systems, which demonstrate the acute effects of MYC activation but may poorly represent long-term MYC overexpression status in real cancers. Here we classified 15 triple-negative breast cancer (TNBC) cell lines according to both MYC target gene set expression and MYC protein expression into MYC-high and MYC-low categories and explored the MYC-high status-coupled therapeutic responses and cancer-relevant metabolic changes. We show that mitochondrial respiration inhibiting biguanide drug metformin inhibits cell proliferation and generates senescence-like features in MYC-high TNBC cells. Furthermore, high-resolution respirometry experiments show that MYC-high TNBC cells have higher mitochondrial respiration rates than MYC-low TNBC cells, a phenotype not explained by a higher number of mitochondria. Also, targeting mitochondrial respiration with small molecule inhibitors specifically reduces proliferation in MYC-high TNBC cells and sensitizes them to apoptosis – indicating that MYC-high TNBC cells have higher dependency on mitochondrial respiration than the MYC-low cells. Targeted metabolomic flux experiments demonstrate that small molecule inhibitors of mitochondrial respiration rewire TCA cycle, resulting in suppression of MYC-driven glutamine anaplerosis, which offers a possible explanation for the apoptotic sensitization. In conclusion, our findings provide new insight into the long-term MYC overexpression-associated metabolic changes – highlighting mitochondrial respiration as a potential target for the development of MYC-dependent synthetic lethal strategies against breast cancer. Citation Format: Johanna M. Anttila, Mariel Savelius, Daniel Nicorici, Ryan Awadhpersad, Pauliina M. Munne, Linda Id, Topi A. Tervonen, Christopher Jackson, Anni I. Nieminen, Juha Klefström. Targeting MYC-induced reprogramming of mitochondrial metabolism in 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 A027.
Abstract B055: Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance
Authors: Mohammad A Iqbal, Shumaila Siddiqui, Kirk Smith, Prithvi Singh, Bhupender Kumar, Salem Chouaib, Sriram Chandrasekaran
Journal: Cancer Research (2024)

Abstract Metabolic heterogeneity in breast cancer has limited the deployment of metabolic therapies. To enable patient stratification, we studied global metabolic landscape of breast cancer (N&amp;gt;3000 combined) and identified three metabolic subtypes with increasing degrees of metabolic deregulation. M1 exhibited deregulated bile acid biosynthesis whereas M2 showed reliance on methionine pathway and M3 was found to be the most metabolically aggressive engaging fatty, nucleotide, and glucose metabolism. Extent of metabolic deregulation correlated strongly with tumor aggressiveness and patient outcome Moreover bile acid biosynthesis predicted less aggressive tumors with better prognosis while pyrimidine metabolism predicted the opposite trend. Notably this pattern was reproducible in independent datasets and in vivo tumor metabolite data. Genomic characterization of metabolic subtypes revealed TP53 mutation and MYC amplification as the strongest predictor of metabolic deregulation. Using machine learning, we identified robust and generalizable signatures that recaptured metabolic subtypes in tumors and cell lines. Surprisingly, the least deregulated M1 subtype was not found to be represented by any of the 50 cell line models analyzed. Experimental inhibition of metabolic pathways demonstrated subtype specific sensitivity and improved combinatorial efficacy of chemotherapeutic drugs. In addition, breast cancer cell lines representing metabolic subtypes revealed therapeutically relevant drugs. Taken together, this work presents metabolic stratification of breast cancer patients that may have implications in predicting patient outcome and designing precision therapies. Citation Format: Mohammad A Iqbal, Shumaila Siddiqui, Kirk Smith, Prithvi Singh, Bhupender Kumar, Salem Chouaib, Sriram Chandrasekaran. Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance [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 B055.
Abstract A017: Perturbation and stability of PAM50 subtyping in population-based primary invasive breast cancer
Authors: Srinivas Veerla, Lennart Hohmann, Deborah F. Nacer, Johan Vallon-Christersson, Johan Staaf
Journal: Cancer Research (2024)

Abstract PAM50 gene expression subtypes represent a cornerstone in molecular classification of breast cancer and are included in risk prediction models to guide therapy. We aimed to illustrate the impact of included genes and biological processes on subtyping while considering a tumor’s underlying clinical subgroup defined by ER, PR and HER2 status. To do this we used a population-representative and clinically annotated primary breast tumor cohort of 6233 samples profiled by RNA sequencing and applied a perturbation strategy of excluding co-expressed genes (gene sets). We demonstrate how PAM50 nearest centroid classification depends on biological processes present across, but also within, ER/PR/HER2 subgroups and PAM50 subtypes themselves. Our analysis highlights several key aspects of PAM50 classification. Firstly, we observed a tight connection between a tumor’s nearest and second nearest PAM50 centroid. Additionally, we show that second-best subtype is associated with overall survival in ER-positive, HER2-negative, and node negative disease. We also note that ERBB2 has little impact on PAM50 classification in HER2-positive disease regardless of ER-status, and that the Basal subtype is highly stable in contrast to the Normal subtype. Improved consciousness of the commonly used PAM50 subtyping scheme will aid in our understanding and interpretation of breast tumors that have seemingly conflicting PAM50 classification when compared to clinical biomarkers. Finally, our study adds further support in challenging the common misconception that PAM50 subtypes are distinct classes by illustrating that PAM50 subtypes in tumors represent a continuum that may have clinical implications. Citation Format: Srinivas Veerla, Lennart Hohmann, Deborah F. Nacer, Johan Vallon-Christersson, Johan Staaf. Perturbation and stability of PAM50 subtyping in population-based primary invasive 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 A017.
Abstract A047: Gamma Aminobutyric Acid Subunit Pi (GABRP) Promotes Breast Cancer Metastasis to the Brain
Authors: Rebecca Packard
Journal: Cancer Research (2024)

Abstract Triple negative breast cancer (TNBC) is an aggressive subset of breast cancer associated with poor prognosis. Although TNBC is only responsible for about 10-15% of breast cancer cases, it accounts for nearly 37% of mortalities. A main factor resulting in this poor prognosis is a higher risk of rapid relapse, which is distant metastasis or death within two years of diagnosis, compared to other breast cancer subsets. To begin to tease out mechanisms of this TNBC-specific rapid relapse, we analyzed differential expression between those tumors resulting in rapid relapse versus those tumors with delayed relapse. This analysis was completed in two independent microarray datasets and revealed a significant upregulation of gamma aminobutyric acid subunit pi (GABRP) mRNA in the TNBC tumors that rapidly relapsed. Previous work by us and others has revealed GABRP as a driver of aggressive behaviors in TNBC cell lines; however, its role in metastatic recurrence is still unclear. We have also observed a correlation between high GABRP mRNA and preferential metastatic progression to the brain. Thus, we hypothesized GABRP is a key mediator of metastasis in aggressive TNBCs, specifically in the establishment of brain metastases. To date, we have completed preliminary in vivo experimental metastasis studies of human breast cancer cells with and without GABRP expression where loss of GABRP reduces brain metastasis. Ongoing studies aim to test metastatic progression in a spontaneous metastasis in vivo model. We are also optimizing an antibody for biomarker screening in patients. Combined, our studies provide strong evidence that GABRP is a major driver of brain-specific metastases and subsequent poorer outcomes associated with TNBC, suggesting targeting GABRP has high therapeutic potential to reduce metastasis and mortality in TNBC patients. Citation Format: Rebecca Packard. Gamma Aminobutyric Acid Subunit Pi (GABRP) Promotes Breast Cancer Metastasis to the Brain [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 A047.
Abstract IA05: Leveraging preclinical models of triple negative breast cancer for translational research
Authors: Jeffrey M Rosen, Diego Pedroza, Na Zhao, Xiang H-F Zhang, Charles M Perou
Journal: Cancer Research (2024)

Abstract We have developed multiple novel preclinical syngeneic triple negative breast cancer(TNBC) genetically engineered mouse (GEM) models, which have been characterized genomically and with respect to their immune microenvironments. By integrating the immunological characterization of murine syngeneic mammary tumor models with analyses of human breast cancer datasets, we have demonstrated a relationship between EMT and myeloid cells, specifically tumor-associated macrophages (TAMs). We also have leveraged our syngeneic GEM models to define the response to immune checkpoint blockade therapy (ICBT) with emphasis on the myeloid cell environment. We have used our GEM models to test single agent drugs along with standard-of-care therapies for appropriate durations. Finally, we have tested these treatment regimens on established metastases with sufficient tumor burdens. Specifically, we will present results illustrating how CSF-1R targeting therapy combined with metronomic chemotherapy enhances a B and T cell response for the treatment of metastatic TNBC. In additional we well discuss how targeting the RNA helicase eIF4A that unwinds the secondary structures in the 5’UTR of mRNAs to facilitate translation initiation triggers an interferon response to suppress TNBC. Citation Format: Jeffrey M Rosen, Diego Pedroza, Na Zhao, Xiang H-F Zhang, Charles M Perou. Leveraging preclinical models of triple negative breast cancer for translational research [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 IA05.
Abstract A034: 3D <i>in-vitro</i> model picturing cancer-stromal cell crosstalk &amp; bone metastasis
Authors: Shrinwanti Ghosh
Journal: Cancer Research (2024)

Abstract Breast cancer is presently the most prevalent malignancy and the second leading cause of tumor-related deaths among women. Approximately 75% of patients with advanced breast cancer will develop bone metastasis. Despite the significant improvement in treating primary breast cancer, the 5-year survival rate for metastatic breast cancer remains at 25%. While we recognize the critical importance of cancer cells and Tumor Microenvironment (TME) communication, the field still suffers from a lack of a proper model system to reconstitute 3D multi-cellular TME in-vitro, especially for bone metastasis. Most of the current 3D in-vitro breast cancer models are composed of cancer cells only and are unable to mimic the complex cellular homeostasis within the TME. To address this deficiency along with the tumor heterogeneity, we aimed to develop a unique 3D multi-cellular culture system using patient-derived (PD) cancer cells. In this study, we implemented the “hanging drop” method to create 3D Tumor Spheroids (TSs). This method was not only sufficient to build the 3D structure, but also significantly enhanced patient-derived cancer cell line establishment rate up to 75%. 3D TSs maintained their histopathological characteristics and original hormone receptor status. Over time, TSs exhibited intratumoral hypoxia leading to significant induction of VEGF expression and EMT showcasing the quality of the system. To investigate the complex interrelation between the tumor and TME, we cultured TSs with Endothelial Cells (ECs) and pericytes to introduce the vascular component. To probe these tumor-stromal interactions, we incorporated Cancer-Associated Fibroblasts (CAFs) into TSs and observed the successful growth of Multi-Cellular Tumor Spheroids (MCTSs) alongside the tubular structure. Analysis of our data revealed that the presence of stromal cells in TME enhanced tumor survival. In this study, we define how CAFs aid in the formation of vascular structures of ECs. Recent studies also have found that the effects of CAFs are significantly high in aggressive TNBC and HER2+ cell lines compared to HR+. The long-term goal of this current study is to explore bone-mimicking nano-clay-based 3D scaffold culture systems to investigate the development of metastatic tumors and to understand the influence of bone TME on cellular responses in-vitro. Citation Format: Shrinwanti Ghosh. 3D in-vitro model picturing cancer-stromal cell crosstalk &amp; bone 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 A034.
Abstract B020: Pan-RAS inhibitors to treat luminal B beast cancer
Authors: Geoff Clark, Raphael Jigo, Howard Donninger, Joe Burlison, Mike Sabo, tariq Arshad, John Trent
Journal: Cancer Research (2024)

Abstract The RAS oncoprotein has not traditionally been considered as an important driver of breast cancer due to the paucity of RAS mutations in this disease. However, RAS signaling pathways are frequently hyper-activated in breast cancers and genetic/epigenetic inactivation of RAS negative regulators (GAPs) is common. This is particularly true for Luminal B breast cancer. Luminal breast cancer makes up the majority of Breast Cancers, ~ 65% of cases. About 2/3 of these are classed as Luminal A and about 1/3 being the Luminal B class. Although current therapeutic options for luminal A (surgery, endocrine therapy) can be reasonably effective, Luminal B tumors are much more dangerous. These tumors are less sensitive to therapy in the first place and have a high frequency of relapse. Moreover, Luminal B tumors tend to occur more frequently in younger women and have a higher incidence of metastasis. One recent analysis has shown that Luminal B cancers have little better overall survival rates than the notorious triple negative breast cancers. Therefore, better therapies for Luminal B breast cancer are urgently required. One approach may be to target the hyper-active wild-type RAS oncoprotein that drives many of these Luminal B tumors. We have used in silico library screening followed by Medicinal Chemistry optimization to develop a series of novel small molecules that bind to all three main wild type RAS proteins and inhibit RAS function. We have validated the agents by using Microscale Thermophoresis binding procedures to quantify recombinant protein interaction. We used 3D growth inhibition and protein-based RAS signaling assays to quantify the biological action of the agents. Finally, we validated one of the more effective agents in vivo against a Luminal B cell line xenograft. This may be the first example of an effective anti-RAS therapy in breast cancer. It serves as proof of principal for the use of ant-RAS drugs in Luminal B disease. As basal breast cancers often exhibit loss of function of the RAS GAP called NF1, this strategy may have applications beyond Luminal B disease. Citation Format: Geoff Clark, Raphael Jigo, Howard Donninger, Joe Burlison, Mike Sabo, tariq Arshad, John Trent. Pan-RAS inhibitors to treat luminal B beast 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 B020.