bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5483: Macrospatial ecotype heterogeneity in early-stage breast cancer identified by spatial nucleus barcoding
Authors: Wang Kaile , Xiao Zhenna , Lin Yiyun , Wei Runmin , Bai Shanshan , Ye Jie , Ye Rui , Hu Min , Thennavan Aatish , Sei Emi , Thompson Alastair , Krishnamurthy Savitri , Navin Nicholas 
Published: March 2024

Abstract
Ductal carcinoma in situ (DCIS), the predominant form of early-stage breast cancer and a precursor to invasive breast cancer, remains inadequately understood in terms of spatial microenvironment reprogramming. In this study, we developed a Spatial Nucleus Barcoding (SNuBar) approach for single-nucleus RNA sequencing (SNuBar-RNA) that utilizes a single oligonucleotide adaptor to preserve spatial information. The accuracy and scalability of SNuBar was validated using cell line mixture experiments. We then applied SNuBar-RNA to investigate the macrospatial ecotype heterogeneity in early-stage breast cancer. By analyzing single cells from different macrodissected spatial regions in normal breast tissues, matched normal and DCIS tissues, we identified 13 major cell types and 43 distinct cell states, co-localizing in diverse combinations across four primary topographic areas (adipose-enriched, normal epithelial, activated stroma and tumor). Spatial analysis revealed the reprogramming of vascular and myoepithelial cells in localized zones near premalignant cells, while fibroblasts, T-cells, and myeloid cells exhibited reprogramming across broader fields. Validation using the MERSCOPE assay confirmed stromal heterogeneity between tumor and normal areas. Collectively, our data shows that many diverse cell types are reprogrammed in spatially-defined areas in the early-stage breast cancer microenvironment, relative to the normal breast tissue regions.
Citation Format: Kaile Wang, Zhenna Xiao, Yiyun Lin, Runmin Wei, Shanshan Bai, Jie Ye, Rui Ye, Min Hu, Aatish Thennavan, Emi Sei, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. Macrospatial ecotype heterogeneity in early-stage breast cancer identified by spatial nucleus barcoding [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 5483.
Abstract 5487: Improved spatial biology analysis of the tumor microenvironment with the next generation of the MultiOmyxTMplatform
Authors: Lazare Michael , Nunns Harry , Moghaddam Fatemeh Jelvhei , Jin Xiaowei , Todorov Courtney , Leones Eric , Thio Marianne , Sahafi Flora , Parnell Erinn , Au Qingyan 
Published: March 2024

Abstract
Multiplexed Immunofluorescence is a powerful tool for spatially characterizing and phenotyping cells within the tumor microenvironment. MultiOmyx has been one of the leading platforms for generating multiplexed immunofluorescence data to support translational and clinical research for more than 10 years. However, MultiOmyx and other similar platforms are often hampered by a limited imaging area due to either restricted staining areas or being cost prohibitive due to excessive imaging times. Here, we demonstrate the capabilities of an improved MultiOmyx platform which can be used to generate whole-tissue data from the iterative MultiOmyx multiplexing process using the CyteFinder® II microscope and a customized software package developed by RareCyte, Inc. The new NeoLYTX image analysis pipeline in conjunction with the whole-tissue image output allows for improved interaction with pathologists, better histological context, and unbiased spatial analysis. In this study we utilized a 16-marker panel consisting of CD3, CD4, CD8, FoxP3, CD20, CD68, CD163, HLA-DR, PD-1, PD-L1, CTLA-4, CD34, Vimentin, SOX10, Ki67, and PanCK to generate immune profiles for colorectal carcinoma, prostate carcinoma, non-Small cell lung cancer, and triple negative breast cancer samples. We showed concordance with the current MultiOmyx imager - the IN Cell 2200 - for each of the markers in the panel. Additionally, we demonstrated that the updates made to the proprietary NeoLYTX image analysis pipeline are able to facilitate the significantly larger data sets that will be generated with the new MultiOmyx platform. This study successfully demonstrates the capability of the improved MultiOmyx system to characterize the distribution of T-cell and myeloid phenotypes in the tumor microenvironment using the proven MultiOmyx workflow, now enhanced by whole slide images and analysis.
Citation Format: Michael Lazare, Harry Nunns, Fatemeh Jelvhei Moghaddam, Xiaowei Jin, Courtney Todorov, Eric Leones, Marianne Thio, Flora Sahafi, Erinn Parnell, Qingyan Au. Improved spatial biology analysis of the tumor microenvironment with the next generation of the MultiOmyxTMplatform [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 5487.
Abstract 5491: Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level
Authors: Aguirre Karmen , Yiwen-Yeh Christine , Laveroni Olivia 
Published: March 2024

Abstract
Immune exclusion and evasion are central barriers to the success of immunotherapies and cell therapies in solid tumors. Here we applied single cell spatial and perturbational transcriptomics alongside clinical,histological, and genomic profiling to elucidate immune exclusion and evasion in high-grade serous tubo-ovarian cancer (HGSC). Using high-plex spatial transcriptomics we profiled more than 1.3 million cells from 95 tumors and 60 patients, revealing generalizable principles in HGSC tumor tissue organization.Our data demonstrates that effector T cells resist stroma-mediated trapping and sequestration. However, upon infiltration into the tumor, T cells, as well as Natural Killer (NK) cells, preferentially co-localize only with a subset of malignant cells that manifest a distinct transcriptional cell state. The latter consists of dozens of co-regulated genes and is repressed under various copy number alterations. Performing CRISPR Perturb-seq screens in ovarian cancer cells, we identified functionally diverse genetic perturbations - including knockout of the insulin sensing repressor PTPN1 and the epigenetic regulator ACTR8 - that de-repress the proposed immunogenic malignant cell state identified in patients and indeed sensitize ovarian cancer cells to T cell and NK cell cytotoxicity. Taken together, our study uncovered a profound connection between somatic genetic aberrations, malignant cell transcriptional dysregulation, and immune evasion at the cellular and tissue level, allowing us to identify targets that reprogram malignant cell states as an avenue to unleash anti-tumor immune responses.
Citation Format: Karmen Aguirre, Christine Yiwen-Yeh, Olivia Laveroni. Mapping ovarian cancer spatial organization uncovers immune evasion drivers at the genetic, cellular, and tissue level [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 5491.
Abstract 5513: Sexual differences in the aged melanoma tumor microenvironment dictates metastasis and therapeutic responses
Authors: Chhabra Yash , Fane Mitchell , Pramod Sneha , Hueser Laura , Zabransky Daniel , Wang Vania , Kumah Edwin , Carey Alexis , Harper Elizabeth , Rocha Murilo Ramos , Weeraratna Ashani 
Published: March 2024

Abstract
There is documented sex disparity in cutaneous melanoma incidence and mortality, increasing disproportionately with age and in the male sex. However, the underlying mechanisms remain unclear; while biological sex differences and inherent immune response variability have been assessed in tumor cells, the role of the microenvironment surrounding the tumor, contextually in aging, has been overlooked. We find that skin fibroblasts undergo age-mediated changes in their proliferation, senescence, ROS levels and stress response that vary with sex. We find that aged male fibroblasts selectively drive an invasive and slow-cycling phenotype in melanoma cells in vitro by increasing AXL expression. This is also evident in syngeneic mouse models where metastasis is increased in aged male mice. Mechanistically, intrinsic aging in male fibroblasts coupled with elevated ROS promotes EZH2 decline thereby increasing BMP2 secretion, which in turn drives the slower-cycling, highly invasive, and therapy-resistant melanoma cell phenotype, characteristic of the aged male TME. Inhibition of BMP2 activity blocks the emergence of the invasive phenotype and sensitizes melanoma cells to BRAF/MEK inhibition. Our data provides an integrated view of how age and sex of the host contributes to melanoma progression and therapy responses. Bridging this knowledge gap will improve patient stratification and assist in tailoring the therapy to the individual.
Citation Format: Yash Chhabra, Mitchell Fane, Sneha Pramod, Laura Hueser, Daniel Zabransky, Vania Wang, Edwin Kumah, Alexis Carey, Elizabeth Harper, Murilo Ramos Rocha, Ashani Weeraratna. Sexual differences in the aged melanoma tumor microenvironment dictates metastasis and therapeutic responses [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 5513.
Abstract 5517: Chronic stress causes metastasis via neutrophil-mediated changes to the microenvironment
Authors: He Xue-Yan , Gao Yuan , Ng David , Michalopoulou Evdokia , George Shanu , Adrover Jose M. , Sun Lijuan , Albrengues Jean , Daßler-Plenker Juliane , Han Xiao , Wan Ledong , Wu Xiaoli S. , Shui Longling S. , Huang Yu-Han , Liu Bodu , Su Chang , Spector David L. , Vakoc Christopher R. , VanAelst Linda , Egeblad Mikala 
Published: March 2024

Abstract
Chronic stress is associated with increased risk of metastasis and poor survival in cancer patients, yet the reasons are unclear. We show that chronic stress increased lung metastasis from disseminated cancer cells 2- to 4-fold in mice. Chronic stress significantly altered the lung microenvironment, with fibronectin accumulation, reduced T cell infiltration, and increased neutrophil infiltration. Depleting neutrophils abolished stress-induced metastasis, indicating their critical role. Chronic stress shifted neutrophils’ normal circadian rhythm, and, via glucocorticoid release, caused increased neutrophil extracellular trap (NET) formation. Importantly, in mice with neutrophil-specific glucocorticoid receptor deletion, chronic stress failed to increase NETs and metastasis. Furthermore, digesting NETs with deoxyribonuclease (DNase) I prevented chronic stress-induced metastasis. Together, our data show that glucocorticoids released during chronic stress cause NET formation and establish a metastasis-promoting microenvironment. Therefore, NETs could be targets for preventing metastatic recurrence in cancer patients, many of whom will experience chronic stress due to their disease.
Citation Format: Xue-Yan He, Yuan Gao, David Ng, Evdokia Michalopoulou, Shanu George, Jose M. Adrover, Lijuan Sun, Jean Albrengues, Juliane Daßler-Plenker, Xiao Han, Ledong Wan, Xiaoli S. Wu, Longling S. Shui, Yu-Han Huang, Bodu Liu, Chang Su, David L. Spector, Christopher R. Vakoc, Linda VanAelst, Mikala Egeblad. Chronic stress causes metastasis via neutrophil-mediated changes to the microenvironment [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 5517.
Abstract 5568: Understanding the role of immune exclusion in mammary tumor growth
Authors: Mitra Payal , Azpurua Jorge , Chiang Huai-Chin , Li Rong 
Published: March 2024

Abstract
Multiple solid tumor types, including triple-negative breast cancer (TNBC), respond poorly to immunotherapy due to low infiltration of CD8+ T cells into the tumor core. The extracellular matrix (ECM) and its components such as collagen have been found to contribute to immune cell exclusion. Discoidin domain receptor 1 (DDR1) is a collagen receptor known to be aberrantly expressed in TNBC among multiple solid tumor types. We have uncovered a previously unappreciated function of DDR1 in immune exclusion through shaping a collagen fiber-based tumor defense against anti-tumor immunity (Sun et al, Nature 599, 673-678 (2021)). Our study showed that deletion of DDR1 in mouse mammary carcinoma cell lines such as E0771 and M-Wnt (syngeneic with C57BL/6 strain background) promotes infiltration of CD8+ T cells and reduces tumor growth in an immunocompetent mouse model. Extending the published study to other immunocompetent mouse strain backgrounds, we observed that deletion of DDR1 in EMT6 cells, another immune excluded TNBC mouse model in the BALB/c strain, increased the infiltration of CD8+ T cells to the tumor core and reduced tumor growth. Data concerning the DDR1-dependent spatial architecture of the mammary tumor microenvironment will be presented. Identifying specific immune and stromal cell populations and proteins spatially modified in the presence or absence of DDR1 may aid in development of new stand-alone or combination anti-cancer treatments with anti DDR1 antibody.
Citation Format: Payal Mitra, Jorge Azpurua, Huai-Chin Chiang, Rong Li. Understanding the role of immune exclusion in mammary tumor growth [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 5568.
Abstract 5612: MRE11 function in DNA damage response is regulated by SIRT2 deacetylation
Authors: Essien Mark , Sesay Fatmata , Zhang Hui , Jung Andrew , Yu David 
Published: March 2024

Abstract
MRE11 is known to play a role in DNA damage repair through the MRE11-RAD50-NBS1 (MRN) complex and homologous recombination. However, the upstream signaling mechanisms regulating MRE11 in DNA repair are unclear. Here, we aimed to determine the extent to which MRE11 is regulated by deacetylation by the SIRT2 sirtuin deacetylase and tumor suppressor protein. We overexpressed MRE11 in HEK293T cells, induced DNA damage through radiation treatment, and performed a series of co-immunoprecipitation (co-IP) studies with and without ionizing radiation (IR). Additionally, we evaluated the acetylation of MRE11 with and without the presence of SIRT2. In a series of functional experiments, immunofluorescence staining assays were performed in U2OS-265 Fok1 cells with SIRT2 knockdown to determine the effect of on MRE11 recruitment to DNA damage sites. Co-IP studies and in vitro DNA pulldown assays were performed to determine the role of SIRT2 in impacting MRE11 interaction with RAD50 and NBS1 and binding to DNA damage. We also examined for IR-induced RPA70 foci formation and downstream ATM-dependent signaling. We found that SIRT2 interacts with and deacetylates MRE11. Furthermore, SIRT2 deacetylation facilitated MRE11 binding to DNA but not interaction with RAD50 and NBS1. Finally, SIRT2 deacetylation facilitated DNA end resection and ATM-dependent phosphorylation of KAP1. In conclusion, our results define a role for SIRT2 in directing MRE11 localization and binding to DNA to promote DNA end resection and ATM-dependent signaling through deacetylation.
Citation Format: Mark Essien, Fatmata Sesay, Hui Zhang, Andrew Jung, David Yu. MRE11 function in DNA damage response is regulated by SIRT2 deacetylation [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 5612.
Abstract 5613: Study of long non-coding RNA TUG1 kinetics under replication stress conditions in cancer cell
Authors: Fujita Tomoya , Suzuki Miho , Masui Osamu , Shinjo Keiko , Kondo Yutaka 
Published: March 2024

Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides that are not translated into proteins. In contrast to protein-coding mRNAs, certain lncRNAs carry out their functions within the nucleus. A detailed elucidation of the kinetics of lncRNAs contributes to a comprehensive understanding of their bona fide biological characteristics. Consequently, advancements in the in vivo visualization of lncRNAs have continued. Currently, various techniques, including RNA imaging technologies, have been employed to facilitate real-time tracking and visualization of RNA molecules within living cells. Taurine upregulated gene 1 (TUG1) is an oncogenic lncRNA, playing a pivotal role in cancer cells by resolving R-loops formed at stalled replication forks, particularly under replication stress conditions such as Hydroxyurea (HU) treatment. Despite its significance, the dynamic regulation of TUG1 under replication stress conditions remains largely unknown. In this study, we developed a stem loop-based live imaging system enabling real-time visualization of TUG1, providing insights into its subcellular localization and dynamic roles in physiological contexts. Upon treatment with HU, a chemical that interferes with replication, TUG1 expression was rapidly upregulated in the nucleus within 20 minutes. Additionally, we observed TUG1 molecules relocating close to the nuclear membrane. Considering the reported relocation of collapsed forks to the nuclear pore complex, this suggests that TUG1 may be involved in this relocation structure. These data indicate that TUG1 is associated with the fork restore mechanism occurring at the relocated collapsed forks, and the current live-cell imaging system holds potential for further uncovering the critical roles of TUG1 in cancer cells. Our stem loop-based imaging may contribute to a more precise understanding of RNA dynamics in live cells.
Citation Format: Tomoya Fujita, Miho Suzuki, Osamu Masui, Keiko Shinjo, Yutaka Kondo. Study of long non-coding RNA TUG1 kinetics under replication stress conditions in cancer cell [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 5613.
Abstract 5645: HuR regulates aerobic glycolysis in triple negative breast cancer (TNBC)
Authors: Dev J R Arundhathi , Gogia Ajay , Mathur Sandeep R. , Deo S.V.S. , Prasad Chandra Prakash 
Published: March 2024

Abstract
Introduction: The RNA-binding protein Human Antigen R (HuR/ELAVL1) is ubiquitously expressed and exerts post-transcriptional regulation on mRNAs characterized by U/AU-rich sequences in their 3' UTR. Elevated cytoplasmic expression of HuR has been associated with various malignancies, influencing key cellular processes such as proliferation, apoptosis, angiogenesis, and metastasis. The involvement of HuR influences prognostic outcomes and hence is a potential biomarker and therapeutic target in cancer research. The present study investigates the oncogenic role of HuR in TNBCs, an aggressive subtype of breast cancer.
Methods: Immunohistochemistry was performed on TNBC patient tumor tissue (n=40) to asses the expressions of HuR and MMP9. Human TNBC cell lines MDA-MB-231 and MDA-MB-468 were used for in vitro studies after confirming cytoplasmic HuR accumulation in these cells via Immunofluorescence. The RNA binding activity of HuR was disrupted using CMLD2, a specific inhibitor of HuR, and subsequent physiological changes were assessed through functional assays. An exploratory investigation of HuR-moderated metabolic changes was performed employing NANOSTRING nCounter XT gene expression assay using metabolic pathways panel. Investigation and/or validation of molecular changes were done via immunoblotting.
Results: Meta-analysis using Liu-2014 TNBC dataset correlated high HuR protein expression with reduced patient survival (p=0.028). HuR (77%) and MMP9(55%) were found to be overexpressed in TNBC tissues. Inhibiting HuR with CMLD2 resulted in the downregulation of the protein and its downstream targets CDK2, MMP9, and β catenin. HuR inhibition compromised proliferation, migration, Matrigel invasion and EMT (downregulated E-Cadherin, N-Cadherin, and Vimentin) in TNBC cell lines. Further, HuR inhibition resulted in decreased clonogenicity in 2D and 3D TNBC cultures. Transcriptomics studies showed that HuR inhibition in MDA-MB-231 altered the profile of glycolytic genes in addition to other pathways such as cell cycle and DNA damage repair. In accordance, the expression of glycolytic proteins was reduced upon CMLD2 treatment. Similar results were obtained on HuR knockdown by siRNA suggesting that HuR-mediated effects on TNBC progression might be in part through its modulation of aerobic glycolysis.
Conclusion: Overall, our results demonstrate HuR as a positive regulator of aerobic glycolysis in TNBCs and the ability of CMLD2 to inhibit HuR provides a rationale to consider it as a potential anticancer agent for TNBCs.
Citation Format: Arundhathi Dev J R, Ajay Gogia, Sandeep R. Mathur, S.V.S. Deo, Chandra Prakash Prasad. HuR regulates aerobic glycolysis in triple negative breast cancer (TNBC) [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 5645.
Abstract 5672: Transcriptomic profiling of lung adenocarcinoma from never-smokers reveals molecular subtypes with clinical implications
Authors: Zhao Wei , Zhang Tongwu , Hoang Phuc H. , Sang Jian , Landi Maria Teresa 
Published: March 2024

Abstract
Lung cancer is the leading cause of cancer mortality worldwide and about 10-25% of lung cancers are from never-smokers (LCINS). Previous genomic studies of LCINS identified multiple genomic subtypes with different genetic drivers and evolutionary processes. To dissect the profile of LCINS cell states and tumor microenvironment, and their relationship with genomic lesions, we sequenced and assembled a large RNA-seq data set of 685 samples of lung adenocarcinoma from never-smokers and integrated them with whole genome sequencing data, pathological features and clinical outcomes from the same subjects. We identified three transcriptomic subtypes defined by distinct gene expression patterns. The three subtypes were associated with different pathway activities and showed remarkable heterogeneity in cell composition, lineage fidelity and pathological features. The genomic driver events and mutational signatures were significantly enriched in specific subtypes. Clinical outcomes also differed across the subtypes. For example, one subtype had prolonged overall survival and was associated with predicted response to immune checkpoint blockade. This study emphasizes the importance of transcriptome-based classification of LCINS, which has profound clinical implications beyond those provided by genomic and pathological assessment.
Citation Format: Wei Zhao, Tongwu Zhang, Phuc H. Hoang, Jian Sang, Maria Teresa Landi. Transcriptomic profiling of lung adenocarcinoma from never-smokers reveals molecular subtypes with clinical 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 5672.