Meeting report: Signal transduction meets systems biology

Louis-Dit-Sully, Christine; Kubatzky, Katharina F.; Lindquist, Jonathan A.; Blattner, Christine; Janßen, Ottmar; Schamel, Wolfgang W. A.

doi:10.1186/1478-811x-10-11

Cited by 4 publications

(3 citation statements)

References 57 publications

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“…In the majority of cancers, overexpression of FOXM1 induces the progression of the disease [ 21 , 37 , 38 ]. LYN is a tyrosine kinase which is deregulated in a variety of cancers like breast, prostate, melanoma, and cervix [ 39 – 42 ]. β -Arrestin 2 (ARRB2) belongs to the arrestin family, which helps to modulate the desensitization and trafficking of G protein-coupled receptors (GPCRs).…”

Section: Discussionmentioning

confidence: 99%

Identification of Differentially Expressed Genes in Cervical Cancer Patients by Comparative Transcriptome Analysis

Annapurna

Pasumarthi

Pasha

et al. 2021

BioMed Research International

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Cervical cancer is one of the most malignant reproductive diseases seen in women worldwide. The identification of dysregulated genes in clinical samples of cervical cancer may pave the way for development of better prognostic markers and therapeutic targets. To identify the dysregulated genes (DEGs), we have retrospectively collected 10 biopsies, seven from cervical cancer patients and three from normal subjects who underwent a hysterectomy. Total RNA isolated from biopsies was subjected to microarray analysis using the human Clariom D Affymetrix platform. Based on the results of principal component analysis (PCA), only eight samples are qualified for further studies; GO and KEGG were used to identify the key genes and were compared with TCGA and GEO datasets. Identified genes were further validated by quantitative real-time PCR and receiver operating characteristic (ROC) curves, and the highest Youden index was calculated in order to evaluate cutoff points (COPs) that allowed distinguishing of tissue samples of cervical squamous carcinoma patients from those of healthy individuals. By comparative microarray analysis, a total of 108 genes common across the six patients’ samples were chosen; among these, 78 genes were upregulated and 26 genes were downregulated. The key genes identified were SPP1, LYN, ARRB2, COL6A3, FOXM1, CCL21, TTK, and MELK. Based on their relative expression, the genes were ordered as follows: TTK > ARRB2 > SPP1 > FOXM1 > LYN > MELK > CCL21 > COL6A3; this generated data is in sync with the TCGA datasets, except for ARRB2. Protein-protein interaction network analysis revealed that TTK and MELK are closely associated with SMC4, AURKA, PLK4, and KIF18A. The candidate genes SPP1, FOXM1, LYN, COL6A3, CCL21, TTK and MELK at mRNA level, emerge as promising candidate markers for cervical cancer prognosis and also emerge as potential therapeutic drug targets.

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Section: Discussionmentioning

confidence: 99%

Identification of Differentially Expressed Genes in Cervical Cancer Patients by Comparative Transcriptome Analysis

Annapurna

Pasumarthi

Pasha

et al. 2021

BioMed Research International

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“…Systems wide investigations of platelet signalling are currently at an early stage; mathematical modelling of intracellular events is more advanced in other cell types. Vigorous research efforts to understand T cell signalling (Systems Biology of T‐cell Activation in Health and Disease (SYBILLA – http://www.sybilla-t-cell.de)) . Part of this work includes MS‐based strategies which aim to provide a systematic and quantitative analysis of protein interactome and phospho‐proteome changes observed upon T cell stimulation.…”

Section: Integrating Proteomics and Systems Approaches To Model Platementioning

confidence: 99%

The integration of proteomics and systems approaches to map regulatory mechanisms underpinning platelet function

Wright

Stanley

Kaiser

et al. 2013

Proteomics Clinical Apps

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Platelets in the circulation are triggered by vascular damage to activate, aggregate and form a thrombus that prevents excessive blood loss. Platelet activation is stringently regulated by intracellular signalling cascades, which when activated inappropriately lead to myocardial infarction and stroke. Strategies to address platelet dysfunction have included proteomics approaches which have lead to the discovery of a number of novel regulatory proteins of potential therapeutic value. Global analysis of platelet proteomes may enhance the outcome of these studies by arranging this information in a contextual manner that recapitulates established signalling complexes and predicts novel regulatory processes. Platelet signalling networks have already begun to be exploited with interrogation of protein datasets using in silico methodologies that locate functionally feasible protein clusters for subsequent biochemical validation. Characterization of these biological systems through analysis of spatial and temporal organization of component proteins is developing alongside advances in the proteomics field. This focused review highlights advances in platelet proteomics data mining approaches that complement the emerging systems biology field. We have also highlighted nucleated cell types as key examples that can inform platelet research. Therapeutic translation of these modern approaches to understanding platelet regulatory mechanisms will enable the development of novel anti-thrombotic strategies.

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“…To foster interactions between researchers working on γδ or αβ T cells, the organisers invited the EU FP7 consortium SYBILLA (systems biology on T‐cell activation) to participate in this meeting. SYBILLA uses systems biology approaches to understand the early steps of αβ T‐cell activation and differentiation . Wolfgang Schamel (Freiburg, Germany) addressed the question of how αβ T cells are able to distinguish peptide‐MHC (pMHC) ligands of different affinity.…”

Section: Insights From αβ T‐cell Activation and Differentiationmentioning

confidence: 99%

γδ T‐cell conference 2012: Close encounters for the fifth time

et al. 2012

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The fifth international γδ T-cell conference was held in Freiburg, Germany, from May 31 to June 2, 2012, bringing together approximately 170 investigators from all over the world. The scientific program covered topics such as thymic development and the mechanisms of ligand recognition and activation, the interaction of γδ T cells with other immune and non-immune cells and its implications for homeostasis, infection, tissue repair and autoimmunity, and the role of γδ T cells in malignancy and their potential for novel immunotherapies. Here we discuss a selection of the oral communications at the conference, and summarise exciting new findings in the field regarding the development, mode of antigen recognition, and responses to microorganisms, viruses and tumours by human and mouse γδ T cells.

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Meeting report: Signal transduction meets systems biology

Cited by 4 publications

References 57 publications

Identification of Differentially Expressed Genes in Cervical Cancer Patients by Comparative Transcriptome Analysis

Identification of Differentially Expressed Genes in Cervical Cancer Patients by Comparative Transcriptome Analysis

The integration of proteomics and systems approaches to map regulatory mechanisms underpinning platelet function

γδ T‐cell conference 2012: Close encounters for the fifth time

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