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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq performed on sarcomas to identify various alterations

ABSTRACT: We validated the technological and material transfers of the CINSARC signature. We performed both microarray and RNA-seq analysis and compared prognostic values based on the CINSARC classification. We measure significant metastasis-free survivals with both approaches. Additionally, depending on RNA degradation, transcriptomic analysis from FFPE blocks show similar CINSARC classification.

ORGANISM(S): Homo sapiens

SUBMITTER: Tom Lesluyes

PROVIDER: E-GEOD-71119 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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RNA sequencing validation of the Complexity INdex in SARComas prognostic signature.

Lesluyes Tom T Pérot Gaëlle G Largeau Marine Roxane MR Brulard Céline C Lagarde Pauline P Dapremont Valérie V Lucchesi Carlo C Neuville Agnès A Terrier Philippe P Vince-Ranchère Dominique D Mendez-Lago Maria M Gut Marta M Gut Ivo I Coindre Jean-Michel JM Chibon Frédéric F

European journal of cancer (Oxford, England : 1990) 20160223

<h4>Background</h4>Prognosis of metastatic outcome in soft tissue sarcomas is an important clinical challenge since these tumours can be very aggressive (up to 50% of recurring events). A gene expression signature, Complexity INdex in SARComas (CINSARC), has been identified as a better prognostic factor compared to the current international grading system defined by the Fédération Nationale des Centres de Lutte Contre le Cancer. Since CINSARC has been established on frozen tumours analysed by mi ...[more]

PMID: 26916546

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RNA-seq performed on FFPE sarcoma blocks

Project description:We validated the technological and material transfers of the CINSARC signature. We performed both microarray and RNA-seq analysis and compared prognostic values based on the CINSARC classification. We measure significant metastasis-free survivals with both approaches. Additionally, depending on RNA degradation, transcriptomic analysis from FFPE blocks show similar CINSARC classification.

2016-03-03 | E-GEOD-71120 | biostudies-arrayexpress

Expression data (micro-array and RNA-seq, frozen tumors and FFPE blocks) from various sarcomas

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-03 | E-GEOD-71121 | biostudies-arrayexpress

Expression data (micro-array, frozen tumors) from various sarcomas

2016-03-03 | E-GEOD-71118 | biostudies-arrayexpress

Effects on adult testis of Sertoli cell-specific ablation of miR-17-92 in mouse embryos

Project description:We induced specific deletion of miR-17-92 in Sertoli cells at the time of Amh expression in mouse embryos. We analyzed the effect of this deletion in the long term in adult testis. The transcriptome of mutant testis was consistently altered but do not produce a phenotype due to the testis homeostasis.

2018-05-10 | E-MTAB-5914 | biostudies-arrayexpress

RNA-Seq analysis of Gestational Trophoblastic Diseases

Project description:Purpose was to determine whether varying gestational trophoblastic disease samples exhibit differences in RNA expression and fusion transcripts.

2021-04-14 | E-MTAB-10321 | biostudies-arrayexpress

Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague

Project description:During pneumonic plague, the bacterium Yersinia pestis elicits the development of inflammatory lung lesions that continue to expand throughout infection. This lesion development and persistence is poorly understood. Here, we examine spatially distinct regions of lung lesions using laser capture microdissection and RNAseq analysis to identify transcriptional differences between lesion microenvironments. We show that cellular pathways involved in leukocyte migration and apoptosis are down regulated in the center of lung lesions compared to the periphery. Probing for the bacterial factor(s) important for the alteration in neutrophil survival, we show both in vitro and in vivo that Y. pestis increases neutrophil survival in a manner that is dependent on the type-III secretion system effector YopM. This research explores the complexity of spatially distinct host - microbe interactions and emphasizes the importance of cell relevance in assays in order to fully understand Y. pestis virulence. We examine spatially distinct regions of lung lesions using laser capture microdissection and RNAseq analysis to identify transcriptional differences between lesion microenvironments. Sample types: uninfected BM-PMN, infected BM-PMN, lesion periphery, lesion center.

2015-07-13 | E-GEOD-70819 | biostudies-arrayexpress

Transcriptome sequencing of porcine liver samples

Project description:Identification of genes and causal mutations regulating growth and fatness traits in pig. Transcriptome sequencing of 10 liver samples of two groups of divergent pigs for growth and fatness.

2016-06-01 | E-GEOD-75850 | biostudies-arrayexpress

Transcriptome regulating differentiation from the early human embryonic distal foregut

Project description:To interrogate the alternative fates of pancreas and liver in the earliest stages of human organogenesis, we developed laser capture, RNA amplification, and computational analysis of deep sequencing. Pancreas-enriched gene expression was less conserved between human and mouse than for liver. The dorsal pancreatic bud was enriched for components of Notch, Wnt, BMP, and FGF signaling, almost all genes known to cause pancreatic agenesis or hypoplasia, and over 30 unexplored transcription factors. SOX9 and RORA were imputed as key regulators in pancreas compared with EP300, HNF4A, and FOXA family members in liver. Analyses implied that current in vitro human stem cell differentiation follows a dorsal rather than a ventral pancreatic program and pointed to additional factors for hepatic differentiation. In summary, we provide the transcriptional codes regulating the start of human liver and pancreas development to facilitate stem cell research and clinical interpretation without inter-species extrapolation.

2017-11-07 | E-MTAB-3259 | biostudies-arrayexpress

Next generation sequencing profiling identifies miR-574-3p and miR-660-5p as potential novel prognostic markers for breast cancer

Project description:Prognostication of Breast Cancer (BC) relies largely on traditional markers such as hormone or growth factors but due to their suboptimal specificities, it is challenging to identify the subset of patients who are likely to undergo recurrence and markers of higher specificity are sought to guide therapies. MicroRNAs (miRNAs) are small non-coding RNAs which function as post-transcriptional regulators of gene expression and have shown promise as potential prognostic markers in several cancer types including BC. In our study, we sequenced 104 breast tumor tissue samples and 11 apparently healthy normal breast tissues for miRNAs. Two widely used approaches were adopted to identify prognostic markers â Case-control and Case-only. For both the approaches, Cox-proportional hazards regression model and risk score analysis was performed to identify miRNA signature independent of potential confounders. Representative miRNAs were validated using qRT-PCR. Gene ontology terms were identified for miRNAs significant in survival analysis. A total of 1,423 miRNAs were captured from the tissues, of which 126 were retained with predetermined criteria for good read counts. In the case-control approach, 80 miRNAs were differentially expressed, from which four and two miRNAs were significant for OS and RFS respectively. In the case-only approach, from 147 miRNAs, 11 and four miRNAs were significant for OS and RFS respectively, in which miR-574-3p and miR-660-5p were novel and were not previously found to be associated with BC prognosis. Multivariate Cox analysis indicated that the risk scores calculated in both the approaches were potential independent prognostic factors for BC. Targets for the identified miRNAs were enriched for cell proliferation, invasion and migration. Identification of miRNAs as prognostic markers for breast cancer

2016-03-02 | E-GEOD-68085 | biostudies-arrayexpress

Platelets favor the outgrowth of established metastases

Project description:Despite abundant evidence demonstrating that platelets foster metastasis, anti- platelet agents have low therapeutic potential due to the risk of hemorrhages. In addition, whether platelets can regulate metastasis at the late stages of the disease remains unknown. In this study, we subjected syngeneic models of metastasis to various thrombocytopenic regimes to show that platelets provide a biphasic contribution to metastasis. While potent intravascular binding of platelets to tumor cells efficiently promotes metastasis, platelets further support the outgrowth of established metastases via immune suppression. Genetic depletion and pharmacological targeting of the platelet-specific receptor GPVI in humanized mouse models efficiently reduced the growth of established metastases, independently of active platelet binding to tumor cells in the bloodstream. Our study is the first to demonstrate therapeutic efficacy when targeting animals bearing growing metastases. It further identifies GPVI as the first molecular target whose inhibition can impair metastasis without inducing collateral hemostatic perturbations.

2024-03-10 | E-MTAB-13864 | biostudies-arrayexpress

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