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328 results for “TNBC”
Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC (Spatial Transcriptomic 10X Visium portion)
<p>Racial disparities in triple-negative breast cancer (TNBC) outcomes have been reported. However, the biological mechanisms underlying these disparities remain unclear. We integrated imaging mass cytometry and spatial transcriptomics, to characterize the tumor microenvironment (TME) of African American (AA) and European American (EA) patients with TNBC. The TME in AA patients was characterized by interactions between endothelial cells, macrophages, and mesenchymal-like cells, which were associated with poor patient survival. In contrast, the EA TNBC-associated niche is enriched in T-cells and neutrophils suggestive of an exhaustion and suppression of otherwise active T cell responses. Ligand-receptor and pathway analyses of race-associated niches found AA TNBC to be “immune cold” and hence immunotherapy resistant tumors, and EA TNBC as ‘inflamed’ tumors that evolved a distinctive immunosuppressive mechanism. Our study revealed the presence of racially distinct tumor-promoting and immunosuppressive microenvironments in AA and EA patients with TNBC, which may explain the poor clinical outcomes.</p> <p> </p> <p>This dataset contains the 10X Visium Spatial Transcriptomic data of TNBC patients. There are two cohorts.</p> <p> </p> <p><strong>Baylor Scott and White (BSW) cohort</strong>: <strong>10x.visium.tar.gz</strong>, containing 10 patients with TNBC from Baylor Scott and White affiliated Hospital. </p> <p>Each sample is made of Space Ranger processed spot-separated gene expression data (processed to HDF5 AnnData file). There are also H&E images, and spot coordinate files available. </p> <p> </p> <p>For <strong>Georgia validation cohort</strong>, 400 genes used for validation of ESG signatures (associated with BA-Community 1 and WA-Community-1) were obtained and provided by Ritu Aneja's lab. These 400 genes' spot-based expression data across Black and White TNBC patients are provided. See file <strong>georgia.validation.visium.tar.gz</strong>. Expression was normalized by total counts per spot, followed by log-normalization by Giotto.</p> <p> </p> <p>As well in our paper, we integrated a published racial TNBC cohort for deriving some of initial results in the paper. This refers to the Bassiouni et al (Cancer Research) paper in Carpten's group. <strong>GSM_giotto_processed.tar.gz</strong> refers to this dataset, which we deposit here. The data were normalized by Giotto using standard procedure.</p>
Supplementary Figures, Files and Datasets: Reduction of Metastasis via Epigenetic Modulation in a Murine Model of Metastatic Triple Negative Breast Cancer (TNBC)
<p>*denotes authors contributed equally to this work</p> <p>FileS1_Figures_Proofread.pdf: (Updated) Supplementary Figures (Figure S1: RNA-sequencing experimental design; Figure S2: Experiments measuring proliferation between drug-treated and control conditions indicate no significant difference 6 hrs. after scratch; Figure S3: Effect of 4SC-202 treatment on 4T1 tumor volume in mice; Figure S4: Differential expression between 4SC-202- and Vorinostat-treated 4T1 tumors; Figure S5: Top underexpressed differentially expressed genes 4SC-202 vs Control; Figure S6: HDACi target genes are not differentially expressed in RNA-sequencing data from 4SC-202-treated mice relative to control mice; Figure S7: Differential expression and expression of genes implicated gene ontology biological processes of interest; Figure S8: IPA visualization of the Regulation of Epithelial Mesenchymal Transition By Growth Factors Pathway emphasizing influence of 4SC-202-induced consensus DEGs; Figure S9: 4SC-202 modulates gene networks related to Cancer, Endocrine System Disorders, and Organismal Injury and Abnormalities; Figure S10: 4SC-202 modulates gene networks related to Cancer, Cellular Movement, and Organismal Injury and Abnormalities; Figure S11: 4SC-202 modulates gene networks related to Cell-mediated Immune Response, Cellular Movement, and Hematological System Development and Function; Figure S12: 4SC-202 differentially modulates gene networks related to Cellular Movement, Hematological System Development and Function, and Immune Cell Trafficking relative to Vorinostat); File S2: DAVID 4SC vs. Control 70DEG results: DAVID Annotation 4SC-202 vs Control 70 DEGs: Full functional annotation clustering results from DAVID Bioinformatics Resource for the 4SC-202-induced, consensus differentially expressed genes.; File S3: DAVID 4SC vs. Vori 33 DEGs results: DAVID Annotation 4SC-202 vs Control 33 DEGs: Full functional annotation clustering results from DAVID Bioinformatics Resource for the 4SC-202 versus Vorinostat consensus differentially expressed genes.; File S4: IPA 70 All Results: IPA Canonical Pathways Enrichment 70 DEGs: Full Ingenuity Pathway Analysis (IPA) canonical pathways enrichment results for the 4SC-202-induced, consensus differentially expressed genes.; File S5: IPA 33 Summary: Ingenuity Pathway Analysis (IPA) summary of the enrichment results for the 4SC-202-induced, consensus differentially expressed genes against Vorinostat.; File S6: Experiment RIN Numbers: RNA extraction quality control step, one of the various steps of quality control within the RNA-sequencing workflow. These RNA Integrity numbers are from the Agilent 2100 Bioanalyzer that looks for RNA contamination and degradation.; File S7: 4SC vs. Control all DEGs: Workflow results including all DEGs for 4SC-202 vs Control: Full excel file that contains all of the DEGs from the results of all workflows for 4SC-202.</p>
Extention to the TNBC dataset, brain section and cell type
<p>This dataset is partly an extension of the TNBC dataset that can be found in the following link: https://zenodo.org/record/1175282#.Ws2n_vkdhfA</p> <p>In particular, we give the cellular type annotations of each annotated cell.<br> In addition to the TNBC, we added 18 annotated images of brain section downloaded from the TCGA.<br> This is still officially unpublished and has been submitted.<br> Currently, if you use this dataset please our paper "Scale dependant layer for self-supervised nuclei encoding" by Peter Naylor, Yao-Hung Hubert Tsai, Marick Laé and Makoto Yamada.</p>
Imaging Mass Cytometry (IMC) data for TNBC Samples
<p>Imaging mass cytometry (IMC) data was collected on multiple regions of interest (ROIs) from a racially balanced and clinically matched cohort of 57 surgically resected tissues, primarily TNBC, as identified by H&E images. This cohort consisted of 26 self-reported Black American (BA) women and 31 self-reported White American (WA) women. ROIs were selected from both the tumor center and tumor periphery, and were categorized as either immune-rich or immune-poor.</p>
Liposomal Doxorubicin, Bevacizumab, and Everolimus in Patients With Locally Advanced TNBC With Tumors Predicted Insensitive to Standard Chemotherapy; A Moonshot Initiative
ClinicalTrials.gov study NCT02456857. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Study of Olaparib Plus Pembrolizumab Versus Chemotherapy Plus Pembrolizumab After Induction With First-Line Chemotherapy Plus Pembrolizumab in Triple Negative Breast Cancer (TNBC) (MK-7339-009/KEYLYNK
ClinicalTrials.gov study NCT04191135. IPD Sharing: YES. Countries: 15. Publications: 0.
Phase 2 Trial of Selinexor (KPT-330) for Metastatic Triple Negative Breast Cancer (TNBC)
ClinicalTrials.gov study NCT02402764. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Women's MoonShot: Neoadjuvant Treatment With PaCT for Patients With Locally Advanced TNBC
ClinicalTrials.gov study NCT02593175. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Sacituzumab Govitecan +/- Pembrolizumab in Metastatic TNBC
ClinicalTrials.gov study NCT04468061. IPD Sharing: YES. Countries: 1. Publications: 1.
OXEL: Immune Checkpoint or Capecitabine or Combination Therapy as Adjuvant Therapy for TNBC With Residual Disease
ClinicalTrials.gov study NCT03487666. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Trial of Sacituzumab Govitecan in Participants With Refractory/Relapsed Metastatic Triple-Negative Breast Cancer (TNBC)
ClinicalTrials.gov study NCT02574455. IPD Sharing: YES. Countries: 7. Publications: 9.
A Study Of PF-05212384 In Combination With Other Anti-Tumor Agents and in Combination With Cisplatin in Patients With Triple Negative Breast Cancer in an Expansion Arm (TNBC)
ClinicalTrials.gov study NCT01920061. IPD Sharing: NO. Countries: 5. Publications: 1.
A Study of Atezolizumab and Paclitaxel Versus Placebo and Paclitaxel in Participants With Previously Untreated Locally Advanced or Metastatic Triple Negative Breast Cancer (TNBC)
ClinicalTrials.gov study NCT03125902. IPD Sharing: Not stated. Countries: 24. Publications: 1.
Sacituzumab Govitecan In TNBC
ClinicalTrials.gov study NCT04230109. IPD Sharing: YES. Countries: 1. Publications: 1.
Gemcitabine Plus Cisplatin Versus Gemcitabine Plus Paclitaxel in Triple Negative Breast Cancer (TNBC)
ClinicalTrials.gov study NCT01287624. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Study Assessing the Efficacy and Safety of Alpelisib + Nab-paclitaxel in Subjects With Advanced TNBC Who Carry Either a PIK3CA Mutation or Have PTEN Loss
ClinicalTrials.gov study NCT04251533. IPD Sharing: YES. Countries: 30. Publications: 0.
An Umbrella Trial Based on Molecular Pathway for Patients With Metastatic TNBC.
ClinicalTrials.gov study NCT04395989. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Personalized Vaccine for TNBC Immunotherapy
ClinicalTrials.gov study NCT06195618. IPD Sharing: NO. Countries: 1. Publications: 1.
FUSCC Refractory TNBC Umbrella (FUTURE)
ClinicalTrials.gov study NCT03805399. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Tavo and Pembrolizumab With or Without Chemotherapy in Patients With Inoperable Locally Advanced or Metastatic TNBC
ClinicalTrials.gov study NCT03567720. IPD Sharing: NO. Countries: 2. Publications: 1.
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.