Project description:The objective of this analysis was to identify trans-eQTLs. Samples were collected from control participants of the Heart and Vascular Health (HVH) study that constitutes a group of population based case control studies of myocardial infarction (MI), stroke, venous thromboembolism (VTE), and atrial fibrillation (AF) conducted among 30-79 year old members of Group Health, a large integrated health care organization in Washington State. Total RNA was isolated from peripheral collected using PAXgene tubes and gene expression was profiled using the Illumina platform.
Project description:The objective of this analysis was to identify trans-eQTLs. Samples were collected from control participants of the Heart and Vascular Health (HVH) study that constitutes a group of population based case control studies of myocardial infarction (MI), stroke, venous thromboembolism (VTE), and atrial fibrillation (AF) conducted among 30-79 year old members of Group Health, a large integrated health care organization in Washington State. Total RNA was isolated from peripheral collected using PAXgene tubes and gene expression was profiled using the Illumina platform.
Project description:Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people. Total RNA was extracted from whole-blood lysates obtained from individuals immediately prior to vaccination against seasonal influenza, followed by depletion of globin messenger RNA. The goal was to evaluate potential gene expression signatures at Day 0 associated with immune senescence.
Project description:Systems biology approach to examine effects of seasonal flu vaccination in adults of different ages on gene expression, cytokine stimulation and serum cytokines with parameters such as immune senescence to uncover new markers and mechanisms behind failure of immune function in many older people. Total RNA was extracted from whole-blood lysates obtained from individuals immediately prior to vaccination against seasonal influenza, followed by depletion of globin messenger RNA. The goal was to evaluate potential gene expression signatures at Day 0 associated with immune senescence.
Project description:Spinal muscular atrophy (SMA) is a common genetic motor neuron (MN) disease caused by low levels of the ubiquitously expressed housekeeping survival motor neuron (SMN) protein, whereas concomitant overexpression of plastin 3 (PLS3) protects from SMA. Here we identify neurocalcin delta (NCALD), a neuronal calcium sensor, as a second fully protective SMA modifier, which counteracts SMA pathology when downregulated. We show reduced Ca2+ influx and impaired endocytosis in SMA, which are crucial processes in synaptic vesicle recycling and neurotransmission. Remarkably, both reduced NCALD or increased PLS3 restore endocytosis in cell culture and MN function across species in zebrafish, worm and mouse SMA models, whereas Ca2+ influx remains disturbed. Furthermore, NCALD physically binds clathrin in a Ca2+-dependent manner. We propose that NCALD acts as a Ca2+-regulated inhibitor of endocytosis, and that endocytosis is critically affected in SMA. This finding opens new therapeutic avenues for SMA. Multifactorial design comparing affected patients and unaffected disease carriers against severly affected control group to identify disease modifying transcripts
Project description:Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology. Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified â 2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel. In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown. HUVEC were exposed to normoxia or 24 and 48 hours of hypoxia (1% oxygen). For each time point and condition was performed in duplicate was produced Total RNAs of six samples were extracted and analysed.
Project description:Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for some lncRNAs a relevant role in hypoxic endothelium has been shown, the regulation and function of lncRNAs is still largely unknown in the vascular physio-pathology. Taking advantage of next-generation sequencing techniques, transcriptomic changes induced by endothelial cell exposure to hypoxia were investigated. Paired-end sequencing of polyadenylated RNA derived from human umbilical vein endothelial cells (HUVECs) exposed to 1% O2 or normoxia was performed. Bioinformatics analysis identified â 2000 differentially expressed genes, including 122 lncRNAs. Extensive validation was performed by both microarray and qPCR. Among the validated lncRNAs, H19, MIR210HG, MEG9, MALAT1 and MIR22HG were also induced in a mouse model of hindlimb ischemia. To test the functional relevance of lncRNAs in endothelial cells, knockdown of H19 expression was performed. H19 inhibition decreased HUVEC growth, inducing their accumulation in G1 phase of the cell cycle; accordingly, p21 (CDKN1A) expression was increased. Additionally, H19 knockdown also diminished HUVEC ability to form capillary like structures when plated on matrigel. In conclusion, a high-confidence signature of lncRNAs modulated by hypoxia in HUVEC was identified and a significant impact of H19 lncRNA was shown. For H19 knock-down, 50 nM of antisense LNA⢠GapmeRs customer-designed for H19 or Negative control A (Exiqon) were transfected by siRNA transfection reagent (Santa Cruz Biotechnology) in 40% confluent HAOEC according to the manufacturerâs manual.
Project description:This study aims at identifying genes whose expression at baseline predicts the immune response to seasonal influenza vaccination. Blood samples were collected from healthy volunteers before their vaccination 91 Samples
Project description:Analysis of the genes involved in the metastasis of head and neck squamous cell carcinoma (HNSCC). We hypothesized that there would be overexpression of certain genes in the highly metastatic USC-HN1-GFP-G1 and USC-HN1-GFP-G2 cell lines compared to the parental USC-HN1-GFP cell line. We used the USC-HN1 cell line stably transfected with H2B-GFP and developed an immortal cell line (USC-HN1-GFP), which was injected into the tongues of SCID/nude mice. The metastatic cells were collected at the LN, separated and cultured, forming an immortal USC-HN1-GFP-G1 cell line. These cells were reinjected into the tongues of mice and the USC-HN1-GFP-G2 cell line was formed by the same LN collection method. The gene expression in these three cell lines were compared using Illumina microarray chips.