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10,884 results for “metastatic;”
The evolution of genomic, transcriptomic, and single-cell protein markers of metastatic upper tract urothelial carcinoma
<p>The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are unknown. The genomic and transcriptomic differences between primary and metastatic UTUC is not well described either. We combined whole-exome sequencing, RNA-sequencing, and Imaging Mass Cytometry<sup>TM</sup> (IMC<sup>TM</sup>) of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. IMC enables spatially resolved single-cell analyses to examine the evolution of cancer cell, immune cell, and stromal cell markers using mass cytometry with lanthanide metal-conjugated antibodies. We discovered that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature were stable across primary and matched metastatic UTUC. Molecular and immune subtypes were consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single-cells. Molecular subtyping at the single cell level was highly conserved between primary and metastatic UTUC tumors within the same patient.</p>
Dataset of "TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth"
<p>The embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis in immunocompromised mice. Moreover, TWIST1 knock-out tumors displays a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings identified TWIST1 as novel therapeutic target in NB.</p>
Dataset for "TWIST1 expression is associated with high-risk neuroblastoma and promotes primary and metastatic tumor growth"
<p>The embryonic transcription factors TWIST1/2 are frequently overexpressed in cancer, acting as multifunctional oncogenes. Here we investigate their role in neuroblastoma (NB), a heterogeneous childhood malignancy ranging from spontaneous regression to dismal outcomes despite multimodal therapy. We first reveal the association of TWIST1 expression with poor survival and metastasis in primary NB, while TWIST2 correlates with good prognosis. Secondly, suppression of TWIST1 by CRISPR/Cas9 results in a reduction of tumor growth and metastasis in immunocompromised mice. Moreover, TWIST1 knock-out tumors displays a less aggressive cellular morphology and a reduced disruption of the extracellular matrix (ECM) reticulin network. Additionally, we identify a TWIST1-mediated transcriptional program associated with dismal outcome in NB and involved in the control of pathways mainly linked to the signaling, migration, adhesion, the organization of the ECM, and the tumor cells versus tumor stroma crosstalk. Taken together, our findings confirm TWIST1 as promising therapeutic target in NB.</p> <p>This dataset comprise images (.ndpi files) of anti-F4/80 IHC staining used for the quantification of macrophages in subcutaneous and orthotopic neuroblastoma xenografts derived from SK-N-Be2c cells expressing TWIST1 or knocked out for TWIST1 through CRISR/Cas9.</p>
Ergolide Mediates Anti-Cancer Effects on Metastatic Uveal Melanoma Cells and Modulates their Cellular and Extracellular Vesicle proteomes
<p>Underlying dataset and extended dataset of the results described in the article "Ergolide Mediates Anti-Cancer Effects on Metastatic Uveal Melanoma Cells and Modulates their Cellular and Extracellular Vesicle proteomes".</p>
CyTOF data of PBMC samples of patients with metastatic pancreatic ductal adenocarcinoma
<p>These two CyTOF datasets are a part of the manuscript by M. Baretti "E<span>ntinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial" accepted in Nature Communications. The datasets contain FCS files of PBMCs samples of patients with metastatic pancreatic ductal adenocarcinoma treated with entinostat and nivolumab. PBMC samples were run with myeloid- and lymphoid-oriented panels.<br></span></p>
Generated Metastatic CT 3D Femurs with lesions segmentation 1/3
<p>This file regroups the 5675 synthetic femurs used and described in the paper: "Enhanced segmentation of femoral bone metastasis in CT scans of patients using synthetic data generation with 3D diffusion models" Saillard et al. </p> <p><strong>Three repositories are needed </strong>to form the full archive. When all are downloaded, they can be deflated with the following bash command : </p> <pre><code>cat Generated_3DCT_Metastatic_Femurs.tar.gz* | tar faxv -</code></pre> <p> </p> <p>This is the first part (1/3)</p> <p>part 2/3: <a title="Opens in new tab" href="https://doi.org/10.5281/zenodo.13824177" target="_blank" rel="noopener"> 10.5281/zenodo.13824177 </a></p> <p>part 3/3: <a title="Opens in new tab" href="https://doi.org/10.5281/zenodo.13824179" target="_blank" rel="noopener"> 10.5281/zenodo.13824179 </a></p> <p> </p> <p>Generated CT Scans are organized in two directories: one for files generated with DDPM this one) and one without DDPM.</p> <p>├── Generated_3DCT_Metastatic_Femurs_with_DDPM <br>│ ├── img<br>│ ├── lbl<br>│ └── msk</p> <p>└── Generated_3DCT_Metastatic_Femurs_NO_DDPM<br> ├── img<br> ├── lbl<br> └── msk</p> <p>The content of each directory is as follows: </p> <ul> <li>img : the generated 3D CT scan (nii.gz format) from the 26 healthy femurs</li> <li>lbl : the lesions segmentation (nii.gz format) of the generated 3D CT scan</li> <li>msk : the segmentations of the 26 healthy femurs (nii.gz)</li> </ul> <p>A given filename corresponds to in img and lbl directories :</p> <ul> <li>./lbl/MEK03les0MEK14.nii.gz is the lesions segmentation of ./img/MEK03les0MEK14.nii.gz.</li> <li>./lbl/MEK03les197MEK28.nii.gz is the lesions segmentation of ./img/MEK03les197MEK28.nii.gz</li> </ul> <p>But in msk, the corresponding femur mask for these examples is ./msk/MEK03.nii.gz</p> <p> </p>
Tumor-Immune Microenvironment Revealed by Imaging Mass Cytometry in a Metastatic Sarcomatoid Urothelial Carcinoma with a Prolonged Response to Pembrolizumab - IMC data
<blockquote> <p>Sarcomatoid urothelial carcinoma (SUC) is a rare subtype of urothelial carcinoma (UC), that typically presents at an advanced stage compared to more common variants of UC. Locally advanced and metastatic UC have a poor long-term survival following progression on first-line platinum-based chemotherapy. Antibodies directed against the programmed cell death 1 protein (PD-1) or its ligand (PD-L1) are now approved to be used in these scenarios. The need for reliable biomarkers for treatment stratification is still under research. Here we present a novel case report of the first Image Mass Cytometry (IMC) analysis done in SUC to investigate the immune cell repertoire and PD-L1 expression in a patient who presented with metastatic SUC and experienced a prolonged response to the anti-PD1 immune checkpoint inhibitor pembrolizumab after progression on first line chemotherapy. This case report provides an important platform for translating these findings to a larger cohort of UC and UC variants.</p> </blockquote> <p>We make available TIFF files containing imaging mass cytometry data for 4 regions of interest of a sample of metastatic sarcomatoid urothelial carcinoma. The order of the axis in the image stacks is "CYX". The CSV files indicate the identity of the channels.</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>
Immunofluorescence of human metastatic lymph node
<p><strong>Description:</strong></p> <p>Immunofluorescence staining of a consecutive, 10 µm-thick section (IF section #1), consecutive to Open-ST metastatic lymph node section #2</p> <p>Data is provided as a standard, non-compressed pyramidal OME.TIFF file with 3 channels, converted with QuPath.</p> <p><strong>Channels:</strong></p> <p>0 (cyan): DAPI<br>1 (yellow): panCK<br>2 (magenta): VIM</p> <p><strong>Methods:</strong></p> <p>Immunofluorescent (IF) staining was performed on the first cryosection of the metastatic lymph node reserved for validations, as shown in the experimental setup in Figure 2D. This slide was reserved at -80°C for ~15 months, before proceeding to IF staining. Steps were performed at room temperature unless stated otherwise. Upon drying the slide, the OCT was removed in a 10-minute PBS wash. Next, the section was fixed with 4% formaldehyde (Sigma-Aldrich, F8775) for 15 minutes and then washed with DPBS (no calcium, no magnesium, Gibco™, 14190169) three times. Blocking and permeabilization was done by incubating in 0.25% Triton-X (Sigma-Aldrich, T8787) and 5% normal donkey serum (Biozol Diagnostica, SBA-0030-01) in DPBS for 1 hour. </p> <p>The section was incubated overnight at 4°C in the dark, with primary-conjugated antibodies diluted in a DPBS buffer with 0.1% Triton-X and 5% normal donkey serum, as follows: 1:100 for Pan Cytokeratin (mouse mAb, clones AE1and AE3, eFluor™ 570 conjugate, ThermoFisher, Cat# 41-9003-82), 1:50 for Vimentin (mouse mAb, clone V9, Alexa Fluor® 750 conjugate, Bio-Techne, Cat# NBP1-97670AF750). Following three 5-minute DPBS washes, DAPI staining was performed with 1 ug/mL DAPI (Bio-Trend, #40011) in DPBS for 10 min in the dark. After three DPBS rinses, the section was dried and then mounted with 85% glycerol. </p> <p>Images were acquired on the Leica Thunder DMi8 imager using a Leica DFC 9000GT sCMOS fluorescence camera, a 20X objective and the Leica Application Suite (LAS) X software (v.3.9.0.28093). Thunder instant computational clearing was performed on the image.</p>
Structural modelling results to accompany the paper "Uncommon mutational profiles of metastatic colorectal cancer detected during routine genotyping using next generation sequencing: an update"
<p>This repository contains the results of modelling missense mutants in KRAS, NRAS and BRAF observed in our study in the corresponding protein structures. Modelling was performed using FoldX.</p>
Dataset for "Overall Survival after Treatment for Metastatic Uveal Melanoma: A Systematic Review and Meta-Analysis"
<p>Raw data corresponding to the paper entitled: "<strong>Overall Survival after Treatment for Metastatic Uveal Melanoma: A Systematic Review and Meta-Analysis" </strong>published in <em>Melanoma Research</em> (2019) by Rantala <em>et al. </em></p>
The outcome of Childhood Adrenocortical Carcinoma in Developing Countries; Supplementary Table 2: Metastatic sites
<p>The outcome of Childhood Adrenocortical Carcinoma in Developing Countries; a scene for surgeons or a chance for medicines.</p> <p>Supplementary Table 2: Metastatic sites</p>
Dataset for "Validation of a Prognostic Staging for Metastatic Uveal Melanoma: A Collaborative Study of the European Ophthalmic Oncology Group"
<p>Raw data corresponding to the paper entitled: "<strong>Validation of a Prognostic Staging for Metastatic Uveal Melanoma: A Collaborative Study of the European Ophthalmic Oncology Group</strong><strong>" </strong>published in <em>Am. J. Ophthalmol.</em> 2016 Aug;168:217-226 by Kivelä <em>et al.</em></p>
Supporting data for "Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche"
<p>This data repository contains several datasets supplementing the paper “Dissecting the cellular architecture of neuroblastoma bone marrow metastasis using single-cell transcriptomics and epigenomics unravels the role of monocytes at the metastatic niche” by Fetahu, Esser-Skala, Dnyansagar et al. (2023).</p> <ul> <li>HOMER_Results.zip: detailed results of the HOMER analysis</li> <li>nblast_scopen_gene_activity_normalized_motifs_added.rds: Seurat object with scATAC-seq data</li> <li>snp_array.tgz: SNP array data</li> <li>R_data_generated.tgz: Files generated by the scRNA-seq analysis scripts in the GitHub repository associated with the publication.</li> </ul>
Dataset on prognostic factors in patients with metastatic castration-resistant prostate cancer undergoing radioligand therapy with [177Lu]Lu-PSMA-617
<p>This upload provides Open Data associated with the publication "Prognostic value of the De Ritis ratio for overall survival in patients with metastatic castration-resistant prostate cancer undergoing [<sup>177</sup>Lu]Lu-PSMA-617 radioligand therapy" by Gaal S <em>et al.</em> (2023).</p> <p>The upload contains the anonymized dataset of 91 patients analyzed in this publication with all variables that are required to reproduce the results.</p> <p>However, to fully comply with requirements for data anonymization, the patients' age was categorized into groups spanning 5 years each. A dataset with the age variable in exact years can be obtained from the corresponding author (julian.rogasch@charite.de) upon reasonable request.</p> <p>Besides the dataset, this upload provides a dictionary to explain all variables and their categories.</p>
Pazopanib Versus Sunitinib in the Treatment of Locally Advanced and/or Metastatic Renal Cell Carcinoma
ClinicalTrials.gov study NCT00720941. IPD Sharing: YES. Countries: 14. Publications: 10.
Study of DS-1062a in Advanced or Metastatic Non-small Cell Lung Cancer With Actionable Genomic Alterations (TROPION-Lung05)
ClinicalTrials.gov study NCT04484142. IPD Sharing: YES. Countries: 10. Publications: 1.
A Phase II Study to Evaluate the Efficacy and Safety of Oral Ceritinib in Patients With ALK-positive NSCLC Metastatic to the Brain and/or to Leptomeninges
ClinicalTrials.gov study NCT02336451. IPD Sharing: YES. Countries: 17. Publications: 1.
A Study of Dabrafenib in Combination With Trametinib in Chinese Patients With BRAF V600E Mutant Metastatic NSCLC
ClinicalTrials.gov study NCT04452877. IPD Sharing: YES. Countries: 1. Publications: 1.
ErbB2 Over-expressing Metastatic Breast Cancer Study Using Paclitaxel, Trastuzumab, and Lapatinib
ClinicalTrials.gov study NCT00272987. IPD Sharing: YES. Countries: 2. Publications: 1.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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.