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14,866
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14,866 results for “cancer cell”
Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites
GEO Series GSE223350. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Regulation of gene expression by AR agonism and AR antagonism in prostate cancer cells
GEO Series GSE279660. Homo sapiens. 29 samples. Type: Expression profiling by array.
Evolution of a transplantable cancer by adaptation [CTVT_RNAseq_cells]
GEO Series GSE288897. Mus musculus. 40 samples. Type: Expression profiling by high throughput sequencing.
Small cell lung cancer induces synaptic scaling to alter neuronal excitability
GEO Series GSE305403. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Deconvolution of drug screening data delineates drug sensitivity of stem-like cancer cells in Acute Myeloid Leukemia [RNA-Seq]
GEO Series GSE217919. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Effect of matrix deprivation on breast cancer cells Part-1
GEO Series GSE108817. Homo sapiens. 8 samples. Type: Expression profiling by array.
NOTCH signaling is activated in and contributes to resistance in enzalutamide-resistant prostate cancer cells
GEO Series GSE123379. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Next generation seuquencing of 3D breast cancer cell culture in synthetic hydrogels presenting either a collagen mimic or laminin mimic with low and high mechanical properties
GEO Series GSE145696. Homo sapiens. 26 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome changes after knocking out MYEOV in two human pancreatic cancer cell lines
GEO Series GSE143827. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
Role of LINC01235 on transcriptional output in HCC1954 HER2 positive breast cancer cells
GEO Series GSE271688. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profile at single cell level of mouse lung cancer cell-line tumors grown subcutaneously in adult male C57BL/6 mice with and without high-fat diet-induced obesity
GEO Series GSE280717. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Dataset related to article "Nivolumab in disadvantaged subgroups of metastatic non-small-cell lung cancer patients: a single-institution experience."
<p><strong>Aim:</strong> Immunotherapy opened new frontiers in metastatic non-small-cell lung cancer treatment, but not all patients benefit from it. <strong>Methods:</strong> We retrospectively evaluated 65 metastatic non-small-cell lung cancer patients, treated with nivolumab, considering as disadvantaged subgroups those with poor performance status, elderly, patients with brain metastases at baseline, with high disease burden and refractory to platinum. <strong>Results:</strong> No differences in overall survival or time to treatment failure were found according to performance status, age, presence of brain metastases at baseline or high disease burden. Conversely, patients refractory to platinum had a statistically significant shorter overall survival and time to treatment failure. At multivariate analysis only platinum resistance was confirmed as an independent predictive factor. <strong>Conclusion:</strong> Our study suggests that only refractoriness to platinum salts influence the efficacy of nivolumab.</p>
Dataset related to article "Chemotherapy accelerates immune-senescence and functional impairments of Vδ2pos T cells in elderly patients affected by liver metastatic colorectal cancer."
<p>Human (gamma delta) γδ T cells are unconventional innate-like lymphocytes displaying a broad array of anti-tumor activities with promising perspectives in cancer immunotherapy. In this context, Vδ2<sup>pos</sup> T cells represent the preferential target of several immunotherapy protocols against solid tumors. However, the impact of both aging and chemotherapy (CHT) on Vδ2<sup>pos</sup> T cells is still unknown. The present study evaluates with multi-parametric flow cytometry the frequencies, terminal differentiation, senescence and effector-functions of peripheral blood and tumor infiltrating Vδ2<sup>pos</sup> T cells purified from liver metastases (CLM) of patients affected by colorectal cancer (CRC) compared to those of sex- and age-matched healthy donors. The peripheral blood of CLM patients underwent CHT is characterized by decreased amounts of Vδ2<sup>pos</sup> T cells showing a relative increase of terminally-differentiated CD27<sup>neg</sup>/CD45RA<sup>pos</sup> (T<sub>EMRA</sub>) cells. The enrichment of this latter subset is associated with an increased expression of the senescent marker CD57. The acquisition of CD57 on T<sub>EMRA</sub> Vδ2<sup>pos</sup> T cells is also coupled with impairments in cytotoxicity and production of TNF-α and IFN-γ. These features resemble the acquisition of an immune-senescent profile by Vδ2<sup>pos</sup> T cells from CLM patients that received CHT, a phenomenon that is also associated with the loss of the co-stimulatory marker CD28 and with the induced expression of CD16. The group of CLM patients underwent CHT and older than 60 years old showed higher frequencies of CD57<sup>pos</sup> and T<sub>EMRA</sub> Vδ2<sup>pos</sup> T cells. Similar results were found for tumor infiltrating Vδ2<sup>pos</sup> T cell subset purified from CLM specimens of patients treated with CHT. The toxicity of CHT regimens also affects the homeostasis of Vδ2<sup>pos</sup> T cells by inducing higher frequencies of circulating CD57<sup>pos</sup> T<sub>EMRA</sub> subset in CLM underwent CHT and younger than 60 years old. Taken together, our data demonstrate that the enrichment of senescent Vδ2<sup>pos</sup> T cells in CLM patients is not only induced by patients' aging but also by the toxicity of CHT that further accelerates the accumulation of CD57<sup>pos</sup> T<sub>EMRA</sub> cells highly dysfunctional in their anti-tumor activities. These results are important to both predict the clinical outcome of CLM and to optimize those protocols of cell cancer immunotherapy employing unconventional Vδ2<sup>pos</sup> T cells.</p>
Dataset related to article "Survival outcome of tyrosine kinase inhibitors beyond progression in association to radiotherapy in oligoprogressive EGFR-mutant non-small-cell lung cancer."
<p><strong>Aim:</strong> The association of tyrosine kinase inhibitors (TKIs) and local radiotherapy in <em>EGFR</em>-mutated non-small-cell lung cancer patients experiencing disease progression under TKIs could be a valid an option. <strong>Patients & methods:</strong> We included 131 patients experiencing disease progression during first-line TKI. In group A, patients received TKI beyond progression and site(s) of progression were irradiated; in group B, patients remained on TKI alone beyond progression; and group C stopped TKI at first disease progression. <strong>Results:</strong> Median overall survival resulted longer in group A versus B and C (p < 0.0001). Group A had a trend toward a longer second progression-free survival (measured from the time of first progression until second progression) versus group B (p = 0.06). <strong>Conclusion:</strong> TKI beyond progression in association with local ablative treatment is a valid treatment option in oligoprogressive patients.</p> <p> </p> <p> </p>
Link to dataset related to article "FOXA2 controls the cis-regulatory networks of pancreatic cancer cells in a differentiation grade-specific manner."
<p>Differentiation of normal and tumor cells is controlled by regulatory networks enforced by lineage-determining transcription factors (TFs). Among them, TFs such as FOXA1/2 bind naïve chromatin and induce its accessibility, thus establishing new gene regulatory networks. Pancreatic ductal adenocarcinoma (PDAC) is characterized by the coexistence of well- and poorly differentiated cells at all stages of disease. How the transcriptional networks determining such massive cellular heterogeneity are established remains to be determined. We found that FOXA2, a TF controlling pancreas specification, broadly contributed to the cis-regulatory networks of PDACs. Despite being expressed in both well- and poorly differentiated PDAC cells, FOXA2 displayed extensively different genomic distributions and controlled distinct gene expression programs. Grade-specific functions of FOXA2 depended on its partnership with TFs whose expression varied depending on the differentiation grade. These data suggest that FOXA2 contributes to the regulatory networks of heterogeneous PDAC cells via interactions with alternative partner TFs.</p>
Dataset related to article "Independent expression of circulating and tissue levels of PD-L1: correlation of clusters with tumor metabolism and outcome in patients with non-small cell lung cancer."
<p>PURPOSE:</p> <p>To evaluate the clinical-pathological and prognostic significance of the circulating PD-L1 level in patients with surgically treated NSCLC, by combining data for PD-L1 expression with other immune-related markers and tumor metabolism.</p> <p>METHODS:</p> <p>Overall, 40 patients with resected NSCLC (stage Ia-IIIa) who had preoperative blood storage and underwent staging PET/CT were enrolled for the study. In all cases, we determined plasma levels of PD-L1 (pg/ml), immune-reactive areas (IRA %) covered by CD3, CD68, CD20, CD8, PD-1, and PD-L1 in the tumor specimen, and metabolic parameters on PET, i.e., SUV<sub>max</sub>, SUV<sub>peak</sub>, metabolic tumor volume (MTV), and total lesion glycolysis (TLG). Variables were statistically analyzed to establish their association with disease-free survival (DFS).</p> <p>RESULTS:</p> <p>The circulating levels of PD-L1 in the bloodstream could be determined in 38/40 (95%) samples. The mean and median expression levels were 34.86 pg/ml and 24.83 pg/ml, respectively. We did not find any statistically significant correlation between circulating PD-L1 and tissue expression of PD-L1/PD-1. Some mild degree of positive correlation was determined between tissue PD-L1 and SUV<sub>max</sub> (ρ =&thinsp;0.390; p =&thinsp;0.0148). Hierarchical clustering combining circulating, tissue, and metabolic parameters identified clusters with high metabolic tumor burden or high expression of plasma PD-L1 levels (Z score ≥ 2) as having a poor DFS (p =&thinsp;0.033). The multivariate analysis detected stage and metabolism (i.e., SUV<sub>max</sub> and SUV<sub>peak</sub>) as independent prognostic factors for DFS.</p> <p>CONCLUSION:</p> <p>Plasma levels of PD-L1 are independent of the expression of PD-1/PD-L1 in NSCLC tumor tissue and, when combined with other clinical-pathological parameters, allow for the identification of clusters with different outcomes.</p>
Dataset related to article "Immune infiltrating cells in duodenal cancers"
<p>This record contains data related to article "Immune infiltrating cells in duodenal cancers"</p> <p> </p> <p>Abstract.</p> <p> Background: Duodenal adenocarcinoma (DA) is a rare yet aggressive malignancy, with increasing incidence in the</p> <p>last decades. Its low frequency has hampered a thorough understanding of the pathogenesis of the disease and of</p> <p>its biology, limiting the identification of tailored therapeutic options. A large body of evidence has clearly shown the</p> <p>clinical relevance of immune cells in solid tumors, correlating immune features with post-surgical prognosis. The aim</p> <p>of this study was to analyze the immune contexture in a cohort of duodenal adenocarcinomas surgically resected at</p> <p>our Institution and define its correlation with clinical variables.</p> <p> Methods: Tissue slides from paraffin-embedded tumor specimens of 15 consecutive DA and 3 adenomas that</p> <p>underwent a pancreaticoduodenectomy in our center between 2010 to 2018 were immunohistochemically stained.</p> <p>The density (percentage of immune reactive area, IRA%) of immune markers CD45RO, CD8, CD20, IL-17, PD-1, CD68</p> <p>was quantified by computer-assisted image analysis. Demographic, clinical, histopathological data were collected.</p> <p> Results: In our population, median IRA % (IQR) of immune subsets was respectively CD45RO-TILs 2.19 (2.14), CD8-TIL</p> <p>0.42 (0.81), CD20-TILs 0.22 (0.51), CD20-TLT 2.84 (4.64), CD68-TAM 2.19 (1.56), IL17+</p> <p>cells 0.39 (0.39), PD1-TILs 0.19 (0.41).</p> <p>The median follow-up was 47.5 (22.4–63.3) months. At statistical analysis, the density of CD8-TILs inversely correlated</p> <p>with lymph node ratio (p = 0.013), number of metastatic lymph nodes (p = 0.019), and was lower in N+ adenocarcinomas</p> <p>compared to N0 (1.07 vs 0.29; p = 0.093), albeit not significantly. Stratifying patients for the N status, the density of</p> <p>CD8-TILs decreased with the increasing of the N stage (p = 0.065) and was lower in patients who experienced recurrence</p> <p>and died for the disease (0.276 vs 0.641; p = 0.044). Notably, also CD68-TAM distribution was different in patients</p> <p>who had recurrence versus patients who did not (1.028 vs 2.276; p = 0.036).</p> <p> Conclusions: Immune cells showed variable expression in correlation with common prognostic factors, suggesting</p> <p>T cell infiltration may play a protective role towards lymphatic spread of disease and nodal metastatization. Furthermore,</p> <p>T cell density and macrophage infiltration were associated to a lower risk of recurrence and disease related</p> <p>death. A multicentric approach may be indicated to allow analysis of larger cohorts of patients, potentially increasing</p> <p>the power of our observations.</p>
Dataset related to article "Metabolome of Pancreatic Juice Delineates Distinct Clinical Profiles of Pancreatic Cancer and Reveals a Link between Glucose Metabolism and PD-1+ Cells"
<p>This record contains data related to the article "Metabolome of Pancreatic Juice Delineates Distinct Clinical Profiles of Pancreatic Cancer and Reveals a Link between Glucose Metabolism and PD-1+ Cells".</p> <p>Better understanding of pancreatic diseases, including pancreatic ductal adenocarcinoma (PDAC), is an urgent medical need, with little advances in preoperative differential diagnosis, preventing rational selection of therapeutic strategies. The clinical management of pancreatic cancer patients would benefit from the identification of variables distinctively associated with the multiplicity of pancre- atic disorders. We investigated, by 1H nuclear magnetic resonance, the metabolomic fingerprint of pancreatic juice (the biofluid that collects pancreatic products) in 40 patients with different pancreatic diseases. Metabolic variables discriminated PDAC from other less aggressive pancreatic diseases and identified metabolic clusters of patients with distinct clinical behaviors. PDAC specimens were overtly glycolytic, with significant accumulation of lactate, which was probed as a disease-specific variable in pancreatic juice from a larger cohort of 106 patients. In human PDAC sections, high expression of the glucose transporter GLUT-1 correlated with tumor grade and a higher density of PD-1+ T cells, suggesting their accumulation in glycolytic tumors. In a preclinical model, PD-1+ CD8 tumor–infiltrating lymphocytes differentially infiltrat- ed PDAC tumors obtained from cell lines with different metabolic consumption, and tumors metabolically rewired by knocking down the phosphofructokinase (Pfkm) gene displayed a decrease in PD-1+ cell infiltration. Collectively, we introduced pancreatic juice as a valuable source of metabolic variables that could contri- bute to differential diagnosis. The correlation of metabolic markers with immune infiltration suggests that upfront evaluation of the metabolic profile of PDAC patients could foster the introduction of immunotherapeutic approaches for pancreatic cancer.</p> <p> </p>
Dataset related to article "Post-biopsy cell-free DNA from blood: an open window on primary prostate cancer genetics and biology"
<p>This record contains data related to article "Post-biopsy cell-free DNA from blood: an open window on primary prostate cancer genetics and biology".</p> <p>Circulating cell-free DNA (ccfDNA), released from normal and cancerous cells, is a promising biomarker for cancer detection as in neoplastic patients it is enriched in tumor-derived DNA (ctDNA). ctDNA contains cancer-specific mutations and epigenetic modifications, which can have diagnostic/prognostic value. However, in primary tumors, and in particular in localized prostate cancer (PCa), the fraction of ctDNA is very low and conventional strategies to study ccfDNA are unsuccessful. Here we demonstrate that prostate biopsy, by causing multiple injuries to the organ, leads to a significant increase in plasma concentration of ccfDNA (P<0.0024) in primary PCa patients. By calculating the minor allele fraction at patient-specific somatic mutations pre- and post-biopsy, we show that ctDNA is significantly enriched (from 3.9 to 164 fold) after biopsy, representing a transient “molecular window” to access and analyze ctDNA. Moreover, we show that newly released ccfDNA contains a larger fraction of di-, tri- and multi-nucleosome associated DNA fragments. This feature could be exploited to further enrich prostate-derived ccfDNA and to analyze epigenetic markers. Our data represent a proof-of-concept that liquid tumor profiling from peripheral blood performed just after the biopsy procedure can open a “valuable molecular metastatic window” giving access to the tumor genetic asset, thus providing an opportunity for early cancer detection and individual genomic profiling in the view of PCa precision medicine.</p>
Dataset related to article"Integrating single-cell and spatial transcriptomics to elucidate the crosstalk between cancer-associated fibroblasts and cancer cells in hepatocellular carcinoma with spleen-deficiency syndrome"
<p>Most patients with hepatocellular carcinoma (HCC) in China have been diagnosed with spleen deficiency syndrome (SDS), which accelerates the progression of HCC by disrupting the tumor microenvironment (TME) homeostasis. However, the underlying mechanism remains to be explored. By integrating single-cell and spatial transcriptomics, we found that the crosstalk between CAFs and cancer cells is crucial for the tumor-promoting effect of SDS. CAFs recruited by HCC via PDGFA may lead to ECM remodeling through activation of the TGF-β pathway, thereby forming a physical barrier to block immune cell infiltration under SDS. </p>
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.