Expression analysis of Epstein-Barr virus–transformed human lymphoblastoid cell lines (LCLs) between male and female.
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ABSTRACT: Investigation of human X-linked imprinted gene. Comparing pooled RNA of lymphoblastoid cell lines from normal human male and female, identify the genes expressed with sex spesific manner. Expression array study with total RNA extracted from pooled male and female LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts/variants.
Project description:Investigation of 5-aza-2'-cytidine and trichostatin A effect to gene expression of human LCLs. LCLs estabulished from patients with genetic dissease are commonly used for mRNA or protein analysis of disease related genes. However, ofen times the gene of interset is not expressed in LCL. Epigenetic modification could be overcome this problem. Expression array study with total RNA extracted from normal male derived LCLs with eight 60-mer probe per gene. 47633 exemplar genes representing a total of 63780 transcripts variants.
Project description:Adult polyglucosan body disease is a rare autosomal recessive neurologicla disorder with progressive paralysis, sensory deficits, and neurogenic bladder usually manifesting late in life. The disease is derived from glycogen branching enzyme deficiency that leads to aggregation of polyglucosan bodies in many cell types. This project focuses on delinating disease mechanisms in APBD through studying the proteomes of lymphoblasts of 3 patients with APBD and comparing them to several controls.
Project description:In internally fertilizing organisms, mating involves a series of highly coordinated molecular interactions between the sexes that occur within the female reproductive tract. In species with promiscuous mating systems, traits involved in postcopulatory interactions are expected to evolve rapidly, potentially leading to postmating-prezygotic (PMPZ) reproductive isolation between diverging populations. Here, we use a novel study design to investigate the postmating transcriptional response of Drosophila mojavensis female reproductive tracts following copulation with either conspecific or heterospecific (D. arizonae) males at three time points postmating. Relatively few genes (15 total) were transcriptionally regulated in the female lower reproductive tract in response to conspecific mating. Heterospecifically-mated females exhibited significant perturbations in the expression of the majority of these genes, and also downregulated transcription of a number of others, including several involved in mitochondrial function. These striking regulatory differences indicate failed postcopulatory molecular interactions between the sexes consistent with the strong PMPZ isolation observed for this cross. We also report, for the first time, the transfer of male mRNA transcripts to females during copulation. These included transcripts from male accessory-gland proteins (ACPs), a finding with potentially broad implications for understanding postcopulatory molecular interactions between the sexes. Dataset from Postmating transcriptional changes in reproductive tracts of con- and heterospecifically-mated Drosophila mojavensis females Bono, JM, Matzkin,LM, Kelleher, ES, and Markow, MA, Proceedings of the National Academy of Sciences, USA. The treatments were con- and heterospecific mated D. mojavensis females. Three different post-copulation times points were assayed, 15 minutes, 2 hours and 6 hours. For each time point there were two independent replicates. Additionally, two replicates of a virgin D. mojavensis female control were assayed. A total of 14 arrays. All RNA extractions were from the lower reproductive tract of females.
Project description:We show that traumatic stress experienced by males in early postnatal life impairs memory in their offspring, blocks long-term potentiation (LTP) and favors long-term depression (LTD). These effects are accompanied by suppression of key molecular pathways involved in neuronal plasticity both at rest and after acute stress. Male mice were exposed to chronic traumatic stress in early postnatal life and were later bred to naM-CM-/ve females to produce second-generation offspring. Memory performance was evaluated in the offspring, and synaptic plasticity was examined in the hippocampus and the amygdala, brain areas important for memory formation. The two groups tested were 1: offspring of fathers which were stressed (MSUS - maternal separation unpredictable stress) and 2: offspring of non-stressed fathers (control). Genome-wide gene expression in hippocampus of these two groups was assessed at rest and after acute stress (this study).
Project description:We show that traumatic stress experienced by males in early postnatal life impairs memory in their offspring, blocks long-term potentiation (LTP) and favors long-term depression (LTD). These effects are accompanied by suppression of key molecular pathways involved in neuronal plasticity both at rest and after acute stress. Male mice were exposed to chronic traumatic stress in early postnatal life and were later bred to naM-CM-/ve females to produce second-generation offspring. Memory performance was evaluated in the offspring, and synaptic plasticity was examined in the hippocampus and the amygdala, brain areas important for memory formation. The two groups tested were 1: offspring of fathers which were stressed (MSUS - maternal separation unpredictable stress) and 2: offspring of non-stressed fathers (control). Genome-wide gene expression in hippocampus of these two groups was assessed at rest (this study) and after acute stress.
Project description:HERC2 is a giant protein with E3 ubiquitin ligase activity and other known and suspected functions. Mutations of HERC2 are implicated in the pathogenesis of various cancers and result in various severe neurological conditions in Herc2-mutant mice. Recently, a pleotropic autosomal recessive HERC2-associated syndrome of intellectual disability, autism and variable neurological deficits was described; its pathogenetic basis is largely unknown. Using peripheral blood-derived lymphoblasts from 3 persons with homozygous HERC2 variants and 14 age- and gender-matched controls, we performed unbiased HPLC-tandem mass spectrometry-based proteomic analyses to provide insights into HERC2-mediated pathobiology. We found that out of 3427 detected proteins, there were 812 differentially expressed proteins between HERC2-cases vs. controls. 184 canonical pathways were enriched after FDR adjustment, including mitochondrial function, energy metabolism, EIF2 signaling, immune functions, ubiquitination and DNA repair. Ingenuity Pathway Analysis® identified 209 upstream regulators that could drive the differential expression, prominent amongst which were neurodegeneration-associated proteins. Differentially expressed protein interaction networks highlighted themes of immune function/dysfunction, regulation of cell cycle/cell death, and energy metabolism. Overall, the analysis of the HERC2-associated proteome revealed striking differential protein expression between cases and controls. The large number of differentially expressed proteins likely reflects HERC2’s multiple domains and numerous interacting proteins. Our canonical pathway and protein interaction network findings suggest derangements of multiple pathways in HERC2-associated disease.
Project description:Genetic variants that impact gene regulation are important contributors to human phenotypic variation. For this reason, considerable efforts have been made to identify genetic associations with differences in mRNA levels of nearby genes, namely, cis expression quantitative trait loci (eQTLs). The phenotypic consequences of eQTLs are presumably due, in most cases, to their ultimate effects on protein expression levels. Yet, only few studies have quantified the impact of genetic variation on proteins levels directly. It remains unclear how faithfully eQTLs are reflected at the protein level, and whether there is a significant layer of cis regulatory variation acting primarily on translation or steady state protein levels. To address these questions, we measured ribosome occupancy by high-throughput sequencing, and relative protein levels by high-resolution quantitative mass spectrometry, in a panel of lymphoblastoid cell lines (LCLs) in which we had previously measured transcript expression using RNA sequencing. We then mapped genetic variants that are associated with changes in transcript expression (eQTLs), ribosome occupancy (rQTLs), or protein abundance (pQTLs). Most of the QTLs we detected are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, we found that eQTLs tend to have significantly reduced effect sizes on protein levels, suggesting that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we confirmed the presence of a class of cis QTLs that specifically affect protein abundance with little or no effect on mRNA levels; most of these QTLs have little effect on ribosome occupancy, and hence may arise from differences in post-translational regulation.
Project description:Although the COVID-19 pandemic has ended, it is important to understand the pathology of severe SARS-CoV-2 infection associated with respiratory failure and high mortality. In this study, a proteomics approach using nano-HPLC-MS/MS (QExactive HF) was used to compare the plasma proteome of COVID-19 survivors (COVID-19; n=10) and deceased individuals (CovDeath; n=10) with that of healthy individuals (Ctr; n=10). The effects of SARS-CoV-2 infection on the alteration of plasma proteins by lipid peroxidation products such as 4-hydroxynonenal (4-HNE), malondialdehyde (MDA) and 15-deoxy-12,14-prostaglandin J2 (15d-PGJ2) were also examined. The results suggest that the development of COVID-19 strongly alters the expression of proteins involved in the regulation of exocytosis and platelet degranulation. These changes were most pronounced in the CovDeath group. In addition, a significant increase in proteins modified with reactive aldehydes was observed in all patients. In the COVID-19 and CovDeath groups, the levels of 4-HNE adducts increased 2- and 3-fold, respectively, whereas MDA adducts increased 7- and 2.5-fold, respectively. Signaling kinases and proinflammatory proteins were particularly affected by these modifications, and the amount of 4-HNE modifications confirmed previous findings on the relevance of 4-HNE in disease pathogenesis and lethal outcome. Protein adducts with 15d-PGJ2 were increased 2.5-fold in COVID-19 patients, including modifications of proteins such as p53 and STAT3, whereas CovDeath showed a decrease of approximately 60% compared with Ctr. It can be assumed that the observed changes in protein expression and modification in COVID-19 are unlikely to be used as prognostic biomarkers because they are also present in the other inflammatory diseases. However, larger studies may prove that the extent and the nature of protein modifications in plasma may be a predictor of the course of SARS-CoV-2 infection.
Project description:There are histological and functional differences between human deciduous and permanent pediodontal ligament (PDL) tissues. The purpose of this study was to determine the differences between these two types of tissue at the molecular level by comparative gene expression analysis. PDL samples were obtained from permanent premolars (n=38) and anterior deciduous teeth (n=31) extracted from 40 healthy persons. Comparative cDNA microarrary analysis revealed several differences in gene expression between the deciduous and permanent PDL tissues.