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10,694 results for “carcinoma,”
GeoMx DSP dataset of "Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma"
<p>This data set is linked to the paper "Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma". It contains datasets and images from GeoMx DSP analysis. </p>
Fully annotated Human Breast carcinoma cells for 3D segmentation training
<p>Fully annotated dataset for training of 3D segmentation models. We provide the Raw image patches in the Raw directory and instance segmentation labels in the RealMask directory, the semantic segmentation masks are provided in the BinaryMask directory. Manually curated from originally published dataset over here: http://celltrackingchallenge.net/3d-datasets/ by team at Kapoorlabs.</p>
Expression of CDCA2 in hepatocellular carcinoma by immunohistochemistry and patients' information
<p>Cohort of hepatocellular carcinoma patients enrolled in the study entitled "Cell division cycle associated 2 (CDCA2) upregulation promotes the progression of hepatocellular carcinoma in a p53-dependant mannar". CDCA2 expression in paraffin-embedded liver cancer tissue sections was evaluated by immunohistochemistry. Patients' clinicopathological information was collected.</p>
Cell recognition in clear cell renal cell carcinoma tissue
<p>This dataset contains a set of 426 PNG images extracted from clear cell renal cell carcinoma samplers of the Cancer Genome Atlas. A JSON file included contains the bounding boxes and classes of each cell found in the PNG images. The label 2 is utilized for lymphocytes and the label 1 for cells other than lymphocytes.</p> <p> </p> <p>The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.</p>
miRNA profiling of human nasopharyngeal carcinoma cell lines HONE1 and CNE2 after X-ray therapy
<p>The package contains two file:</p> <p>Supplementary Table 1. Kruskal Wallis test for cell viability rate</p> <p>Supplementary Table 2. Kruskal Wallis test for apoptosis rate</p> <p>The HONE1 and CNE2 cells were irradiated with X-rays at doses of 4 Gy, 8 Gy, 16 Gy and 20 Gy for 24 h. The cell viability rate and apoptosis rate were compared.</p>
Raw Data for the article: HCV Interplay With Mir34a: Implications in Hepatocellular Carcinoma
<p>Since its identification, HCV has been considered one of the main causes of hepatitis and liver cancer. Currently, the molecular mechanisms of HCC development induced by HCV infection have not been sufficiently clarified. The recent discovery of novel treatments that inhibit HCV replication gave rise to new questions concerning HCC mechanisms. In particular, the HCV eradication mediated by new direct-acting antiviral (DAAs) drugs does not exclude the possibility of <em>de novo</em> HCC development; this finding opened more questions on the interplay between liver cells and the virus. Different groups have investigated the pathways leading to cancer recurrence in patients treated with DAAs. For this reason, we tried to gain molecular insights into the changes induced by HCV infection in the target liver cells. In particular, we observed an increase in microRNA34a (miR34a) expression following HCV infection of HCC cell line Huh7.5. In addition, Huh7.5 treated with extracellular vesicles (EVs) from the previously HCV-infected Huh7.5 underwent apoptosis. Since miR34 expression was increased in Huh7.5 EVs, we hypothesized a paracrine mechanism of viral infection mediated by miR34a cargo of EVs. The balance between viral infection and cell transformation may raise some questions on the possible use of antiviral drugs in association with antineoplastic treatment.</p>
Raw Data for the article: Clinical and Molecular-Based Approach in the Evaluation of Hepatocellular Carcinoma Recurrence after Radical Liver Resection
<p><strong>Background: </strong>Hepatic resection remains the treatment of choice for patients with early-stage HCC with preserved liver function. Unfortunately, however, the majority of patients develop tumor recurrence. While several clinical factors were found to be associated with tumor recurrence, HCC pathogenesis is a complex process of accumulation of somatic genomic alterations, which leads to a huge molecular heterogeneity that has not been completely understood. The aim of this study is to complement potentially predictive clinical and pathological factors with next-generation sequencing genomic profiling and loss of heterozygosity analysis.</p> <p><strong>Methods: </strong>124 HCC patients, who underwent a primary hepatic resection from January 2016 to December 2019, were recruited for this study. Next-generation sequencing (NGS) analysis and allelic imbalance assessment in a case-control subgroup analysis were performed. A time-to-recurrence analysis was performed as well by means of Kaplan-Meier estimators.</p> <p><strong>Results: </strong>Cumulative number of HCC recurrences were 26 (21%) and 32 (26%), respectively, one and two years after surgery. Kaplan-Meier estimates for the probability of recurrence amounted to 37% (95% C.I.: 24-47) and to 51% (95% C.I.: 35-62), after one and two years, respectively. Multivariable analysis identified as independent predictors of HCC recurrence: hepatitis C virus (HCV) infection (HR: 1.96, 95%C.I.: 0.91-4.24, <em>p</em> = 0.085), serum bilirubin levels (HR: 5.32, 95%C.I.: 2.07-13.69, <em>p</em> = 0.001), number of nodules (HR: 1.63, 95%C.I.: 1.12-2.38, <em>p</em> = 0.011) and size of the larger nodule (HR: 1.11, 95%C.I.: 1.03-1.18, <em>p</em> = 0.004). Time-to-recurrence analysis showed that loss of heterozygosity in the <em>PTEN</em> loci (involved in the PI3K/AKT/mTOR signaling pathway) was significantly associated with a lower risk of HCC recurrence (HR: 0.35, 95%C.I.: 0.13-0.93, <em>p</em> = 0.036).</p> <p><strong>Conclusions: </strong>multiple alterations of cancer genes are associated with HCC progression. In particular, the evidence of a specific AI mutation presented in 20 patients seemed to have a protective effect on the risk of HCC recurrence.</p>
Hormone receptors AR, ER, PR and growth factor receptor Her-2 expression in oral squamous cell carcinoma: Correlation with overall survival, disease-free survival and 10-year survival in a high-risk population
<p>Oral squamous cell carcinoma (OSCC) comprises most of head and neck neoplasms and is one of the highest-ranking and lethal cancers in Pakistan due to prevailing mouth habits. Growth and hormonal receptors act as prognostic markers and targets for therapy in some cancers, but their application in OSCC is largely unexplored. This study aimed to evaluate the expression of growth and hormonal receptors in OSCC patients and correlate it with 10-year, overall and disease-free survival. To achieve this objective, immunohistochemistry for Her-2, AR, ER and PR was performed on 100 formalin-fixed paraffin-embedded primary OSCC specimens. Receptor expression was correlated with mouth habits and clinicopathological features and patient survival was analyzed using Kaplan-Meier method and Cox regression univariate analysis. We observed that in 100 patients, there were 57 males and 43 females. Immunopositive Her-2 expression was observed in 21% of patients, AR in 13%, ER in 3% and 0% for PR. Patients with betel quid/areca nut mouth habits had significantly absent Her-2 expression (P=0.035). Also, Her-2 negative patients were also negative for AR expression (P=0.002). Her-2 positive patients had poor 10-year survival (P=0.041). A trend of low survival and high recurrence rate was observed in AR positive patients, but this was not significant (P=0.072). No statistically relevant correlations were seen in the case of ER and PR. In conclusion, Her-2 may be a valuable marker for predicting long-term prognosis of OSCC patients.</p>
Distinct mechanisms of mismatch repair deficiency delineate two modes of response to PD-1 immunotherapy in endometrial carcinoma
<p>Responses to immune checkpoint blockade (ICB) are variable even among mismatch repair deficient (MMRd) cancers. We completed a phase 2 clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared to epigenetic MMRd; however, within each category of MMRd, mutation burden was not associated with ICB response. Notably, JAK1 mutations did not confer resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of anti-tumor immunity against mutational and epigenetic MMRd tumors. Whereas effector CD8+ T cell responses correlated with mutational MMRd, highly active CD16+ NK cells were associated with epigenetic MMRd tumors responsive to ICB. These data highlight factors beyond neoantigen burden that influence ICB response.</p>
The role of Cornulin (CRNN) in the progression of cutaneous squamous cell carcinoma involving AKT activation in SCL-1
<p>Cutaneous squamous cell carcinoma (cSCC) is a prevalent type of skin cancer that has been on the rise in recent times, particularly among older individuals. Cornulin (CRNN) is increasingly recognized as an oncogene involved in developing various types of tumors. However, the precise contribution to cSCC remains unclear. Our study observed a significant increase in CRNN expression in cSCC samples compared to healthy skin. CRNN expression in the SCL-1 cell line derived from cSCC was reduced, leading to a halt in cell growth during the transition from the G1 phase to the S phase. This reduction inhibits cell division, promotes cell death, and decreases cell invasion and migration. CRNN overexpression has been found to enhance cell growth and prevent cells from undergoing natural cell death, and the cancer-promoting effects of CRNN are linked to AKT activation. Using a mouse xenograft model, we demonstrated that the inhibition of CRNN led to a decline in cSCC tumor growth in a living organism, providing evidence of CRNN’s involvement in cSCC occurrence and development. This study establishes a foundation for evaluating the effectiveness of CRNN in treating cSCC, enabling further investigation in this area</p>
Source data for publication "A multimodal atlas of hepatocellular carcinoma reveals convergent evolutionary paths and 'bad apple' effect on clinical trajectory" in Journal of Hepatology
<p>Processed genomic and transcriptomic data for the publication <a href="https://doi.org/10.1016/j.jhep.2024.05.017">https://doi.org/10.1016/j.jhep.2024.05.017</a>.</p> <p>cnv_segmentation.tsv: CNV segmentation file from Sequenza.</p> <p>cnv_arm.tsv: Significant arm level CNV events called by GISTIC, from broad_values_by_arm.txt file.</p> <p>cnv_gene.tsv: Gene level CNV events called by GISTIC, from all_threshold_by_genes.txt file. </p> <p>RNA_raw_counts.tsv: Raw RNA-seq read counts from featureCounts.</p> <p>snv_indel.tsv: All SNV and Indel called with annotation from Funcotator.</p> <p> </p>
The effect of extracellular vesicles derived from oral squamous cell carcinoma on the metabolic profile of oral fibroblasts
<p><span>Oral cancer is one of the most common forms of head and neck cancers. Oral squamous cell carcinoma (OSCC) accounts for more than 90% of the oral malignancies. The molecular pathogenesis of OSCC is complex as it involves altered expression of specific genes and proteins, but also comprises changes in metabolic processes. It is suggested that extracellular vesicles (EVs) released by cancer cells may contribute to cancer development and metastasis by recruiting and changing phenotype of normal cells that surround the tumor. The aim of the project was to characterize the effect of OSCC EVs on the metabolic profile of normal oral fibroblasts (NOFs). Targeted </span><span>liquid chromatography-mass spectrometry metabolic profiling was performed on control cells and NOFs exposed to OSCC EVs for 24 and 48 h. Analysis of detected metabolites revealed that OSCC EVs affected NOFs the most after 24 h of exposure. Among metabolites that were significantly altered at 24 h, </span><span>pyruvate, ATP, UTP, coenzyme A, and dihydroxyacetone phosphate were upregulated, while fatty acids such as nervonic acid, linoleate, oleate, palmitoleic acid, and docosahexaenoic acid were downregulated. These findings were supported by Western blotting of pyruvate kinase M2 (PKM2). The metabolic pathways of glycolysis, </span><span>citric acid cycle, and </span><span>amino acid metabolism were enriched, suggesting that OSCC EVs cause phenotype switch in NOFs that may contribute to </span><span>acquiring</span><span> a pro-tumorigenic phenotype.</span></p>
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Nanostring CosMx SMI Data
<p>Data export from Nanostring CosMx SMI, directly from Nanostring, in Seurat Object format for use in R. Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</p>
Exploring NSD3 Driven Gene Expression Profiles in Lung Squamous Cell Carcinoma
<p><strong>SGC Open Notebook Project to Characterize the HMTase NSD3</strong></p> <p><strong>Exp026 Objective:</strong> NSD3 is frequently amplified as part of the 8p11-12 focal amplification in several types of cancer. Here we set out to explore the gene expression profiles of NSD3 amplified versus non-amplified lung squamous cancer samples from the TCGA. However, because this event takes place in the context of a focal amplification we will also compare samples with high versus low NSD3 expression. The goal of this experiment is to identify putative oncogenic signalling pathways NSD3 may regulate, as well as inform on the biological role of this protein in the context of gene expression. </p>
Supplemental Material from: Immune Profiling of Thyroid Carcinomas Suggests the Existence of Two Major Phenotypes: an ATC-like and a PDTC-like
<p>Supplemental Material from: Immune Profiling of Thyroid Carcinomas Suggests the Existence of Two Major Phenotypes: an ATC-like and a PDTC-like</p>
Assessment of changes in circRNA expression based on transcripts of genes encoding ADAMTS proteins in patients with non-small cell lung carcinoma compared to normal tissue
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Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma
<p>This repository contains imaging mass cytometry (IMC) data and associated files for the publication "Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma". Code used to analyze these data can be found at https://github.com/FertigLab/HCCTLS. Raw IMC data have been uploaded as .mcd files (n=10). The file "IMCpanel.xlsx" indicates the antibodies used for each IMC channel. In addition, we have uploaded .tiff files (n=38) generated from each .mcd, which were used to identify and annotate individual tertiary lymphoid structures (TLS) as some ROI had multiple TLS. The file "Updated Catalogue of TLS with S numbers.xlsx" indicates which TLS correspond to each ROI in the .mcd files. To determine the area of each TLS, .tiff files were annotated using ImageJ and the area of each TLS was exported and stored in the file, "TLS_selection_area_pixels.csv". The XY coordinates of individual TLS were obtained by using FlowJo software to annotate .fcs files resulting from single cell segmentation of each ROI. </p>
Test Dataset for 3D semantic image segmentation of the Breast, Fibrograndular Tissue, and Breast Carcinoma
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Validation of urine p-cresol glucuronide as renal cell carcinoma non-invasive biomarker
<p><strong>Description of the study</strong>: Renal cell carcinoma (RCC) stands among the most lethal urological malignancies. Most RCCs are incidentally diagnosed as initial symptoms are unspecific. Novel, minimally-invasive diagnostic and prognostic methods for RCC are needed, ideally in urine.</p> <p>Using UPLC-Q-ToF MS untargeted metabolomic analysis in urine, we previously revealed p-cresol glucuronide as potential RCC diagnostic marker. Additionally, urine samples one-year post-nephrectomy revealed isobutyryl-L-carnitine and L-proline betaine as potential RCC prognostic markers. Our present aim was to validate these differences in an independent cohort of RCC patients and healthy controls to strengthen their value as non-invasive biomarkers.</p> <p>In an independent cohort of 69 RCC patients and 52 controls we validated an increase in p-cresol glucuronide in urine from patients at diagnosis compared to controls (<em>P</em>=0.0043). It remained increased one-year post-nephrectomy (<em>P</em>=0.0288). The value of p-cresol glucuronide for RCC diagnosis was assessed with ROC curves analysis (AUC=0.66, 95% Confidence Interval 0.56-0.76). The role of isobutyryl-L-carnitine and <a name="_Hlk172707445"></a>L-proline betaine as prognostic markers could not be validated and will require a larger cohort.</p> <p>Our findings confirm the value of p-cresol glucuronide in urine as diagnostic marker for RCC in an independent cohort. This non-invasive method holds promise for enhancing patient care by reducing the need for potentially risky diagnostic procedures. Further metaproteomics-oriented approaches towards the tyrosine oxidation pathway and microbiota metagenomics studies may promote a holistic management of RCC.</p> <p><strong>Description of the data:</strong></p> <p>We provided data in .d format adquired with Agilent.</p> <p> </p> <p> </p>
Tackling hepatocellular carcinoma with individual or combinatorial immunotherapy approaches
<p>Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer globally. Indeed, there is a single drug approved as first-line systemic therapy in advanced unresectable HCC, providing a very limited survival benefit. In earlier stages, 5-year survival rates after surgical and loco-regional therapies are extremely variable depending on the stage of disease.</p> <p>Nevertheless, HCC is considered an immunogenic tumor arising in chronically inflamed livers. </p> <p>In such a scenario, immunotherapy strategies for HCC, in particular combinations including cancer vaccines, may represent a key therapeutic tool to improve clinical outcome in HCC patients. However, a lot of improvement is needed given the disappointing results obtained so far.</p>
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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.