bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A042: Characterization of the hormone receptor-positive breast tumor immune microenvironment using single cell transcriptomics and multiplex immunofluorescence
Authors: Michaud Daniel , Shimada Kenichi , Zheng Kelly , Gu Cheryl , Cui Yvonne , Goldberg Jonathan , Ogayo Esther , Sorger Peter , Santagata Sandro , Mittendorf Elizabeth , Guerriero Jennifer 
Published: February 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 & 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 A061: Grb7 is dispensible for normal development and ERBB2-driven mammary tumorigenesis, but maternal Grb7 deletion causes lactational insufficiency
Authors: Lofgren Kristopher A. , Feiszt Peter , Kenny Paraic A. 
Published: February 2024

Abstract
Growth factor receptor-bound 7 (Grb7) is an adaptor protein implicated in signal transduction downstream of multiple receptor tyrosine kinases, including ERBB, FGFR and PDGFR pathways. Experimental studies have implicated Grb7 in regulating cell proliferation, survival, migration, and invasion through its large repertoire of protein-protein interactions. Here, we describe the generation and characterization of a Grb7 knockout (KO) mouse. These mice are viable and fertile. A lacZ knock-in reporter was used to visualize Grb7 promoter activity patterns in adult tissues, indicating widespread Grb7 expression in glandular epithelium, the central nervous system and other tissues. The sole defect observed in these animals was a failure of Grb7 KO females to successfully raise pups to weaning age, a phenotype that was independent of both paternal and pup genotypes. These data suggest a regulatory role for Grb7 in mammary lactational physiology. Grb7 is genomically adjacent to ERBB2 and commonly co-amplified with ERBB2 in human breast cancer. This adaptor protein physically interacts with ERBB2 and has been implicated in oncogenic signal propagation to intracellular pathways. We intercrossed Grb7 KO and MMTV-Neu mice to determine whether Grb7 is required for ERBB2-driven tumorigenesis. Surprisingly, there was no difference in time to tumor detection between cohorts, indicating that Grb7 is not obligately required for ERBB2-driven tumorigenesis. In conclusion, despite a considerable body of literature suggesting key roles for Grb7 in signal transduction pathways involved in both normal and malignant processes, our analysis of Grb7 KO mice demonstrates that Grb7 is largely dispensable for both development and ERBB2-driven tumorigenesis. These data raise the possibility that other Grb family members, Grb10 and Grb14, might compensate for Grb7 loss. Accordingly, a comprehensive assessment of all Grb family members may be needed to fully clarify their physiological roles.
Citation Format: Kristopher A. Lofgren, Peter Feiszt, Paraic A. Kenny. Grb7 is dispensible for normal development and ERBB2-driven mammary tumorigenesis, but maternal Grb7 deletion causes lactational insufficiency [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 A061.
Abstract A087: Morphometric analysis of the terminal ductal lobular unit architecture in human breast
Authors: Peurla Markus , Paavolainen Oona , Tammelin Ella , Sulander Suvi-Riitta , Mourao Larissa , Boström Pia , Brück Nina , Scheele Colinda LGJ , Hartiala Pauliina , Peuhu Emilia 
Published: February 2024

Abstract
The major lactiferous ducts of the human breast branch out and ultimately end at terminal ductal lobular units (TDLUs). These glandular structures are the source of milk upon lactation, and also the most common origin of breast cancer. Despite their functional and clinical importance, the three dimensional (3D) architecture of TDLUs has remained undetermined, largely due to their absence in rodent animal models. By utilizing recent technological advances in optical tissue clearing and microscopy, we imaged the 3D structure of healthy human breast tissue to determine whether general branching patterns or cell type specific niches exist in the TDLU. Our data demonstrate that TDLUs have a consistent shape and their branch parameters are largely comparable between different TDLUs and individuals irrespective of age or parity. Simulation of TDLU branching morphogenesis in 3D by mathematical modelling suggests that evolutionarily conserved mechanisms regulate mammary gland branching in humans and mice, despite their anatomical differences. The data also demonstrate a new level of organization within the TDLU structure identifying a main branch that dominates in bifurcation events and exhibits a more duct-like keratin expression pattern. In all, our data provide the first structural insights into 3D human breast anatomy and branching, and exemplify the power of volumetric imaging in deeper understanding of human breast biology.
Citation Format: Markus Peurla, Oona Paavolainen, Ella Tammelin, Suvi-Riitta Sulander, Larissa Mourao, Pia Boström, Nina Brück, Colinda LGJ Scheele, Pauliina Hartiala, Emilia Peuhu. Morphometric analysis of the terminal ductal lobular unit architecture in human breast [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 A087.
Abstract B008: KDM4C histone demethylase connects redox balance to chromatin remodeling via histone H3 tail clipping
Authors: Li Zheqi , Peluffo Guillermo , Stevens Laura , Qiu Xintao , Seehawer Marco , Huang Xiao-Yun , Egri Shawn , Papanastasiou Malvina , Kingston Natalie , D'Santos Clive , Papachristou Eva , Nishida Jun , Evans Kyle , Seo Ji-Heui , Clement Kendell , Temko Daniel , Ekram Muhammad , Rees Matthew , Ronan Melissa , Roth Jennifer , Simeonov Anton , Kales Stephen , Rai Ganesha , Lal-Nag Madhu , Maloney David , Jadhav Ajit , Michor Franziska , Meissner Alex , Balko Justin , Carroll Jason , Freedman Matthew , Long Henry , Jaffe Jacob , Polyak Kornelia 
Published: February 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 B011: BRCA2 haploinsufficiency induces P53 degradation in primary mammary epithelial cells – a crucial early event in breast tumor promotion
Authors: Duan Haohui , Gillis Margaret , Dillon Deboral , Garber Judy , Pathania Shailja 
Published: February 2024

Abstract
The presence of heterozygous germline BRCA2 mutations is associated with an increased risk of breast and ovarian cancer. In order to design effective preventative strategies, it is critical to understand early tumor promoting events that the mammary epithelial cells undergo on their way to tumorigenesis. To investigate the impact of BRCA2 heterozygosity on tumor formation, we utilized primary BRCA2mut/+ mammary epithelial cells obtained from prophylactic breast tissue of women with BRCA2 mutations. Our findings indicate that BRCA2mut/+ cells display haploinsufficiency for repairing stalled replication forks and resolving RPA32 from these sites, indicative of impaired stalled fork repair. Moreover, they exhibit defects in RAD51 recruitment to double strand break sites indicating a defective homologous recombination dependent double strand break repair efficiency. BRCA2mut/+ cells also show increased sensitivity to both replication stress and double strand break-inducing agents. Interestingly, we find that BRCA2 heterozygous cells downregulate P53 protein levels when compared to BRCA2 wild type cells, and that this downregulation is MDM2-dependent. The decreased P53 levels appear to promote the survival of BRCA2 heterozygous cells under endogenous replication stress conditions. Notably, treatment with nutlin, a P53 protein stabilizer, leads to cell death in BRCA2 heterozygous cells but not in BRCA2 wildtype cells, highlighting the sensitivity of BRCA2 heterozygous cells to endogenous P53 protein levels. Moreover, complete loss of P53 in BRCA2 heterozygous cells results in rescue of sensitivity of these cells to both replication stress and double strand break inducing agents. Furthermore, whole genome sequencing analysis of BRCA2 heterozygous cells deleted for P53 reveal DNA mutational signatures similar to those observed in BRCA2 mutant tumors, implying that loss or downregulation of P53 is an early event driving tumorigenesis in the context of BRCA2 heterozygosity. In summary, our study uncovers the significance of BRCA2 haploinsufficiency in replication stress suppression and highlights the role of P53 loss in promoting BRCA2 heterozygosity-driven cancer. These findings contribute to a better understanding of the molecular mechanisms underlying BRCA2-associated tumorigenesis and may have implications for targeted preventative therapies in the future.
Citation Format: Haohui Duan, Margaret Gillis, Deboral Dillon, Judy Garber, Shailja Pathania. BRCA2 haploinsufficiency induces P53 degradation in primary mammary epithelial cells – a crucial early event in breast tumor promotion [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 B011.
Abstract B020: Pan-RAS inhibitors to treat luminal B beast cancer
Authors: Clark Geoff , Jigo Raphael , Donninger Howard , Burlison Joe , Sabo Mike , Arshad tariq , Trent John 
Published: February 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.
Abstract B055: Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance
Authors: Iqbal Mohammad A , Siddiqui Shumaila , Smith Kirk , Singh Prithvi , Kumar Bhupender , Chouaib Salem , Chandrasekaran Sriram 
Published: February 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&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 B071: A genetic approach to selectively inhibit macropinocytosis while sparing autophagy
Authors: Lim Rebecca M , Chu Brandon , Edinger Aimee Lara 
Published: February 2024

Abstract
Macropinocytosis is a bulk endocytic process that can fuel tumor growth and drug resistance by providing access to extracellular protein and necrotic cell debris. This process is primarily studied by utilizing the chemical inhibitor, 5-(N-ethyl-N-isopropyl)-Amiloride (EIPA), but this inhibitor is nonselective can hinder proliferation even in non-macropinocytic breast cancer cells. Hence, a more selective, genetic approach is needed. Formation of macropinosomes is dependent on the actin cytoskeleton, which in turn is regulated by CARMIL1, a large multimeric protein that regulates the actin capping protein. CARMIL1 is essential for macropinocytosis, and mutation of two residues in the Capping-Protein Interaction (CPI) region of CARMIL1 to alanine (CARMIL1-AA) limits the CARMIL1-capping protein interaction and more importantly, inhibits macropinocytosis upon introduction of exogenous CARMIL1-AA in tumor cells. Therefore, CARMIL1-AA is a genetic tool to study the effects of macropinocytosis on other cellular processes. However, autophagy, a lysosome-dependent recycling system that enables cell survival, additionally utilizes actin to form autophagosomes. The overall goal of this project is to determine whether CARMIL1-AA specifically inhibits macropinocytosis while still supporting autophagy. CARMIL1-WT and -AA mutant cells were generated using the MMTV-PyMT tumor model and HeLa cell lines and validated for CARMIL1 expression by western blot and quantitative PCR and for macropinocytosis by dextran analysis. These cells were evaluated for autophagic flux by western blot for LC3 I/II and by utilizing a GFP-LC3-RFP-LC3ΔG reporter. Our observation that CARMIL1-AA does not impact autophagy enables further investigation of the importance of macropinocytosis in therapeutic resistance and in shaping the tumor microenvironment.
Citation Format: Rebecca M Lim, Brandon Chu, Aimee Lara Edinger. A genetic approach to selectively inhibit macropinocytosis while sparing autophagy [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 B071.