We performed gene expression profiling of total RNA from brain samples derived from BSE-infected versus non-infected cynomolgus macaques (Macaca fascicularis).
Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques.
Sex, Age, Specimen part
View SamplesThe leading cause of death in human patients with metastatic renal cell carcinoma (RCC) and malignant cancer in general is the dissemination of the primary tumor to secondary sites. The mechanisms by which RCC colonize the lung microenvironment during metastasis remain largely unknown. To investigate the mechanisms of lung colonization by tumor cells, we grafted human RCC cells with different lung metastatic activities in mice. Gene expression profiling of the mouse lung stromal compartment revealed a gene signature enriched for neutrophil-specific functions, induced preferentially by poorly metastatic cells. Analysis of the gene expression patterns in tumor cells and clinical specimens showed an inverse correlation between metastatic activity and the levels of a number of chemokines, including CXL5 ad IL8. Enforced depletion of CXCL5 and IL8 in tumor cells allowed us to establish a functional link between lung neutrophil infiltration, the secretion of chemokines by cancer cells and metastatic activity. Finally, we showed that human neutrophils displayed a higher cytotoxic activity toward poorly metastatic cells relative to highly metastatic cells. Together, these results support a model in which neutrophils recruited to the lung by tumor-secreted chemokines build an antimetastatic barrier and loss of those neutrophil chemokines in tumor cells is a critical rate-limiting step during lung metastatic seeding.
Neutrophil chemokines secreted by tumor cells mount a lung antimetastatic response during renal cell carcinoma progression.
Specimen part
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Genomic deregulation during metastasis of renal cell carcinoma implements a myofibroblast-like program of gene expression.
Specimen part, Disease, Disease stage, Cell line
View SamplesThis study investigates the molecular signatures that drive Renal Cell Carcinoma (RCC) metastatic conversion using the 16 paired Human tumor samples.
Genomic deregulation during metastasis of renal cell carcinoma implements a myofibroblast-like program of gene expression.
Specimen part, Disease
View SamplesThis study investigates the molecular signatures that drive Renal Cell Carcinoma (RCC) metastatic conversion using the metastatic (LM2) and non-metastatic (SN12C) RCC cell lines.
Genomic deregulation during metastasis of renal cell carcinoma implements a myofibroblast-like program of gene expression.
Cell line
View SamplesRenal cell carcinomas with unclassified histology (uRCC) constitute a significant portion of aggressive non-clear cell RCC (nccRCC) that have no standard therapy. The oncogenic drivers in these tumors are unknown. We performed a molecular analysis of 62 high-grade primary uRCC, incorporating targeted cancer gene sequencing, RNA sequencing, Single Nucleotide Polymorphism array, fluorescence in-situ hybridization, immunohistochemistry, and cell-based assays. We identified recurrent somatic mutations in 29 genes, including NF2 (18%), SETD2 (18%), BAP1 (13%), KMT2C (10%), and MTOR (8%). Integrated analysis revealed distinct molecular subsets, including a subset of 26% uRCC characterized by NF2-loss, dysregulated Hippo-YAP pathway and worse survival. Overall design: Analysis of RNA from uRCC with or without NF2-loss
Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets.
Specimen part, Subject
View SamplesTotal, nascent and unlabeled RNA were prepared following 1h of labeling with 100 M 4-thiouridine and 3 replicates analyzed by Affymetrix Gene ST 1.0 arrays
Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay.
Cell line
View SamplesRIP-Chip was performed on DG75-eGFP, DG75-10/12, BCBL-1, BL41, BL41 B95.8 and Jijoye using anti-human Ago2 (11A9) antibodies. Anti-BrdU antibodies were used as controls for DG75-eGFP, DG75-10/12 and BCBL-1. Total RNA was used as control for BL41, BL41 B95.8 and Jijoye. Samples were analyzed on Affymetrix Gene ST 1.0 Arrays (2 independent biological replicates / sample)
Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay.
No sample metadata fields
View SamplesThe intracellular pathogen Trypanosoma cruzi secretes an activity that blocks TGF--dependent induction of connective tissue growth factor (CTGF/CCN2). Here, we address the mechanistic basis for T. cruzi-mediated interference of
A soluble factor from Trypanosoma cruzi inhibits transforming growth factor-ß-induced MAP kinase activation and gene expression in dermal fibroblasts.
Specimen part
View SamplesOncogenic transformation in Ewing sarcoma tumors is driven by the fusion oncogene EWS-FLI1. The inducible expression of EWS-FLI1 (EF) in embryoid bodies, or collections of differentiating stem cells, generates cells with properties of Ewing sarcoma tumors, including characteristics of transformation. These cell lines exhibit anchorage-independent growth, a lack of contact inhibition and a strong Ewing sarcoma gene expression signature. These cells also demonstrate a requirement for the persistent expression of EWS-FLI1 for cell survival and growth.
Modeling the initiation of Ewing sarcoma tumorigenesis in differentiating human embryonic stem cells.
Specimen part
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