Transcription profiling of human peripheral blood monocytes from acute lymphoblastic leukaemia patients to search for new biomarkers for the monitoring of the minimal residual disease of ALL
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Angel Lugo-Trampe
PROVIDER: E-GEOD-10820 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Abstract Purpose: There is a recognised need to develop new methods of high throughput, rapid and minimally invasive individual dose assessment for radiation exposure. The aim of this work is to establish a panel of highly radiation responsive genes suitable for biological dosimetry and to explore inter-individual variation in response to ionising radiation exposure.Materials and method: Analysis of gene expression in response to radiation was carried out using three independent techniques (microarray, Multiplex Quantitative RT-PCR and nCounter Analysis System) in human lymphocytes in culture and circulating blood exposed ex vivo from the same donors. Results: Variations in transcriptional response to exposure to ionising radiation analysed by microarray allowed the identification of genes which can be validated and measured accurately as biomarkers of radiation exposure using other techniques. We have identified genes which are consistently up-regulated following exposure at different time points to either 2 or 4 Gy of X-rays, for all individuals in blood and cultured lymphocytes. Most down-regulated genes including cyclins, centromeric and mitotic checkpoints proteins, particularly those associated with chromosome instability and cancer can only be detected in dividing cells. Conclusions: The data provides evidence that there are a number of genes which seem suitable for biological dosimetry, like SESN1, GADD45A, CDKN1A, CCNG1, FDXR, BBC3 and MDM2. ÊThese biomarkers could potentially be used for triage after large-scale radiological incidents. Variations in transcriptional response accurately measured by MQRT-PCRæ may allow the identification of biomarkers of radiation sensitivity and individual susceptibility and therefore being useful in radiation oncology.
2011-10-20 | E-TABM-1083 | biostudies-arrayexpress
Project description:Genomic analysis of DLBCL, FL and CLL. Genomic DNA from tumor samples analysed using Affymetrix 250K Sty Single Nucleotide Polymorphism microarrays.
2011-01-01 | E-GEOD-22082 | biostudies-arrayexpress
Project description:The bTB research programme is centred on identifying the genetic basis for resistance against bovine tuberculosis and towards diagnostics Agilent Whole Genome Bovine 8x60k Gene Expression (AMADID: 29411) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2016-10-25 | E-GEOD-74050 | biostudies-arrayexpress
Project description:In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based Rotating Wall Vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1g-incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichments in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death and regulation of cell proliferation. We identified the correlation between miR-9-3p, miR-155-5p, miR-150-3p and miR-378-3p expression with that of genes involved in immune/inflammatory response (eg. IFNG and IL17F), apoptosis (eg. PDCD4 and PTEN) and cell proliferation (eg. NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation. microRNA expression profiling were carried out on total RNA extracted from PBLs of twelve healthy donors at the end of 24h-incubation time in MMG and in 1g conditions. Analyses were performed by using the M-bM-^@M-^\Human miRNA Microarray kit (V2)M-bM-^@M-^] (Agilent Technologies), that allows the detection of 723 known human (miRBase v.10.1) and 76 human viral miRNAs.By comparing the expression profile of MMG-incubated vs. 1g-incubated PBLs of the same donor, we found 42 differentially expressed miRNAs, 25 up-regulated and 17 down-regulated.
2014-07-17 | E-GEOD-57400 | biostudies-arrayexpress
Project description:Gene expression profiles of human BM-MSC isolated form normal donor to elucidate potential molecular network for clinical application Fresh isolated BM-MSC cells were cultured on defined condition. Functional assay was performed prior to gene expression analysis
2010-10-02 | E-GEOD-19471 | biostudies-arrayexpress
Project description:In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based Rotating Wall Vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1g-incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichments in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death and regulation of cell proliferation. We identified the correlation between miR-9-3p, miR-155-5p, miR-150-3p and miR-378-3p expression with that of genes involved in immune/inflammatory response (eg. IFNG and IL17F), apoptosis (eg. PDCD4 and PTEN) and cell proliferation (eg. NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-07-17 | E-GEOD-57418 | biostudies-arrayexpress
Project description:In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition, simulated by a ground-based Rotating Wall Vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1g-incubated ones. Among these, miR-9-5p, miR-9-3p, miR-155-5p, miR-150-3p, and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichments in the biological processes of immune/inflammatory response, signal transduction, regulation of response to stress, regulation of programmed cell death and regulation of cell proliferation. We identified the correlation between miR-9-3p, miR-155-5p, miR-150-3p and miR-378-3p expression with that of genes involved in immune/inflammatory response (eg. IFNG and IL17F), apoptosis (eg. PDCD4 and PTEN) and cell proliferation (eg. NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation. Gene expression profiling was carried out in MMG-incubated PBLs vs. 1g-incubated PBLs on total RNA extracted from the same PBL samples assayed for miRNA profiling. We used the M-bM-^@M-^XM-bM-^@M-^XWhole Human Genome Oligo MicroarrayM-bM-^@M-^YM-bM-^@M-^Y (Agilent), consisting of ~41.000 (60-mer) oligonucleotide probes, which span conserved exons across the transcripts of the targeted full-length genes.
2014-07-17 | E-GEOD-57408 | biostudies-arrayexpress
Project description:TSLPR+ and TSLPR- monocytes were isolated form 3 adult healthy donors and stimulated with LPS. RNA-sequencing has been performed using Illumina technology.
2017-03-28 | E-MTAB-4996 | biostudies-arrayexpress
Project description:Low-grade chronic inflammation plays an important role in the development of obesity and obesity-associated disorders such as insulin resistance, type 2 diabetes, the metabolic syndrome and atherosclerosis. One possible link between obesity and inflammation is the enhanced activation of circulating monocytes making them more prone to infiltration into the adipose and vascular tissues of obese persons. Furthermore, weight loss after bariatric surgery is associated with less inflammation. Transcriptome analysis of circulating monocytes from control and obese patients before and after bariatric surgery will potentially provide insights into the pathophysiology of obesity and associated disorders and supply biomarkers for diagnostic purpose. The cohort comprised 6 lean age-matched controls (BMI: 20.3±0.5 kg/m2, mean±SEM) and 18 obese individuals without clinical symptoms of cardiovascular disease (BMI: 45.1±1.4 kg/m2, P<0.001 compared with lean controls). These 18 morbidly obese subjects were referred to our hospital for bariatric surgery. Before they were included, individuals were evaluated by an endocrinologist, an abdominal surgeon, a psychologist and a dietician. Only after multidisciplinary deliberation, the selected patients received a laparoscopic Roux-en-Y gastric bypass. CD14+ monocytes were collected before and three months after bariatric surgery (BMI: 37.5±1.3 kg/m2, P<0.001 compared with before weight loss), total RNA was extracted and subjected to genome-wide expression analysis. Samples consisted of CD14+ monocytes from 6 lean controls and 18 morbidly obese patients before and three months after bariatric surgery. The 6 lean controls were also used to make 6 control pools.
2012-05-23 | E-GEOD-32575 | biostudies-arrayexpress
Project description:Abstract: Bovine tuberculosis (bTB), caused by infection with Mycobacterium bovis, continues to cause significant issues for the global agriculture industry as well as for human health. An incomplete understanding of the host immune response contributes to the challenges of control and eradication of this zoonotic disease. In this study, high-throughput bulk RNA sequencing (RNA-seq) was used to characterize differential gene expression in γδ T cells – a subgroup of T cells which bridge innate and adaptive immunity and have specific anti-mycobacterial response mechanisms. γδ T cell subsets are classified on the basis of expression of a pathogen-recognition receptor known as Workshop Cluster 1 (WC1) and we hypothesised that bTB infection may alter the phenotype and function of specific γδ T cell subsets. Peripheral blood was collected from naturally M. bovis-infected (positive for single intradermal comparative tuberculin test (SICTT) and IFN-γ ELISA) and age- and sex-matched, non-infected control Holstein-Friesian cattle. γδ T subsets were isolated using fluorescence activated cell sorting (n = 10-12 per group) and high-quality RNA extracted from each purified lymphocyte subset (WC1.1+, WC1.2+, WC1- and γδ-) was used to generate transcriptomes using bulk RNA-seq (n = 6 per group, representing a total of 48 RNA-seq libraries). Relatively low numbers of differentially expressed genes (DEGs) were observed between most cell subsets; however, 163 genes were significantly differentially expressed in the M. bovis-infected compared to control groups for the WC1.1+ γδ T cell compartment (Log 2 FC ≥ 1.5 and FDR P adj ≤ 0.1). The majority of these DEGs (146) were significantly increased in expression in cells from the bTB+ cattle and included genes encoding transcription factor (TBX21 and EOMES), chemokine receptors (CCR5 and CCR7), granzymes (GZMA, GZMM and GZMH) and multiple killer cell immunoglobulin-like receptors (KIR) indicating cytotoxic functions. Biological pathway overrepresentation analysis revealed enrichment of genes with multiple immune functions including cell activation, proliferation, chemotaxis and cytotoxicity of lymphocytes. In conclusion, WC1.1+ γδ T cells have been proposed as major regulatory cell subset in cattle, and we provide evidence for preferential differential activation of this specific subset in cattle naturally infected with M. bovis. Understanding the role of these critical immune cells during mycobacterial infection contributes to our understanding of host immunity to bTB and identifies multiple novel cytotoxic functions of WC1.1+ γδ T cells.
2023-07-01 | E-MTAB-13111 | biostudies-arrayexpress