ABSTRACT: The PDE12 gene codes for the poly(A)-specific exoribonuclease, involved in the quality control of mitochondrial non-coding RNAs. Here, we report that disease-causing PDE12 variants in three unrelated families are associated with mitochondrial respiratory chain deficiencies. Clinically, they presented in utero and within the neonatal period with muscle and brain involvement leading to marked cytochrome c oxidase (COX) deficiency in muscle and severe lactic acidosis. To analyze perturbations in specific cellular pathways contributing to pathogenesis in our patient cohort, we used Affymetrix Clariom D transcriptome arrays to study the RNA levels in fibroblasts derived from two patient (Patient 2 and patient 3), comparing these to age-matched controls.
Project description:The experiment was performed to reveal transcriptomic alterations in melanoma cells caused by dacarbazine (DTIC) treatment. Two primary cell cultures were exposed to dacarbazine at a final concentration of 1 mg/mL. The whole transcriptome was investigated in the cells treated with DTIC compared to a negative control group.
Project description:Human pluripotent stem cells hold great potential for regenerative medicine, but available cell types have important limitations. While embryonic stem cells derived from fertilized embryos (IVF-ESCs) are considered the "gold standard" of pluripotency, they are allogeneic to potential recipients. Autologous induced pluripotent stem cells (iPSCs) are prone to epigenetic and transcriptional aberrations. To determine whether accumulation of such aberrations is intrinsic to somatic cell reprogramming or secondary to the reprogramming method, we generated a genetically matched collection of human IVF-ESCs, iPSCs, and ESCs derived by somatic cell nuclear transfer (SCNT; NT-ESCs), and subjected them to genome-wide genetic, epigenetic and transcriptional analyses. SCNT-based reprogramming is mediated by the full complement of oocyte cytoplasmic factors, thus closely recapitulating early embryogenesis. NT-ESCs and iPSCs derived from the same somatic donor cells contained comparable numbers of de novo copy number variations (CNVs), suggesting that the two reprogramming methods may not differ significantly in mutagenic or selective pressure. On the other hand, the DNA methylation and transcriptome profiles of NT-ESCs corresponded very closely to those of IVF-ESCs, while iPSCs differed markedly from IVF-ESCs and harbored residual DNA methylation patterns typical of parental fibroblasts, suggesting incomplete reprogramming. We conclude that human somatic cells can be faithfully reprogrammed to pluripotency by SCNT and are therefore ideal candidates for cell replacement therapies. 16 matched samples, two IVF-ESCs, five sendai produced iPSC lines, two retro-virus produced iPSC lines, four NT-ESCs, the parental fibroblast line, and the sperm and oocyte donor were genotyped using the Illumina Omni5, which interrogates 4.3 million SNPs across the human genome. Additionally, matched samples from a patient with Leigh syndrome, a NT-ESC line, three iPSC lines, and the parental fibroblast line were genotyped using the Illumina Omni5.
Project description:Maple syrup urine disease (MSUD) is a rare inherited metabolic disorder characterised by deficient activity of the branched-chain alpha-ketoacid dehydrogenase complex, required to metabolise the amino acids leucine, isoleucine and valine. Despite its profound metabolic implications, the molecular alterations underlying this metabolic impairment had not yet been elucidated. Here we performed a comprehensive epigenomic analysis including fibroblasts derived from a cohort of MSUD patients (9) and unaffected controls (5) using the Infinium HumanMethylation EPIC platform.
Project description:Analysis of platelet-derived growth factor (PDGF)-stimulated fibroblasts. Results provide insight into novel pro-tumorigenic factors induced by PDGF-activation of fibroblasts. 1.2 x 10e6 BJ-hTERT fibroblasts were cultured in 10cm dish with Dulbecco's Modified Eagle Medium (DMEM; Gibco Life Technologies, Gergy-Pontoise, France) containing 1% heat-inactivated fetal calf serum (FCS), 2 mM L-glutamine, penicillin (100 units/ml) and streptomycin (100 ng/ml) at 37ºC in a 5% CO2 humidified atmosphere during 24h. Cultures were stimulated with or without 20ng/mL PDGF-BB (Peprotech, New Jersey, USA) for another 24h prior to harvest. Unstimulated fibroblasts were used as control samples. Cultures of both unstimulated and stimulated fibroblasts were done in triplicate.
Project description:Mesothelial cells, which interact with endothelial cells, are widely used in research including cancer and drug development, have not been comprehensively profiled. We therefore performed RNA sequencing of polarized, primary peritoneal (HPMC) and immortalized pleural mesothelial cells (MeT-5A), and compared it to endothelial cells from umbilical vein (HUVEC) and cardiac capillaries (HCMEC).
Project description:To probe into the potential mechanisms contributing to the strong synergistic interaction between gefitinib and pemetrexed, gene expression profiles of PC-9 cells exposed to gefitinib, pemetrexed or combined treatment were analyzed using microarray technique.
Project description:The uploaded datasets contains raw data from our research: columns represent patients, rows represent meta data (patients response, type of sarcoma, etc ...) + the raw gene counts.
Project description:Phenotypic variability in cultured mammalian cell lines has long been recognized and known to be driven by passaging and culture conditions. Yet, the effect these variations have on the production of gene therapy viral vectors has been largely overlooked. In this work we evaluated the impact of using MDCK parental cells from ATCC or ECACC for the production of canine adenoviral vectors type 2 (CAV-2) in adherent and suspension cultures. Additionally, we conducted whole-genome transcriptome analysis to further explore the differences between cells. Our results indicate that ECACC parental cells are a less heterogeneous population, relatively to ATCC’s, more difficult to adapt to suspension and serum-free culture conditions, but more permissive to CAV-2 replication progression enabling higher yields. Transcriptome data indicates that this increased permissiveness is due to a general down-regulation of biological networks of innate immunity in ECACC cells.
Project description:The three isoenzymes of iodothyronine deiodinases (DIO1-3) are membrane-anchored homo-dimeric selenoproteins which share the thioredoxin fold structure. Several questions regarding their catalytic mechanisms still remain open. Here, we addressed the roles of several cysteines which are conserved among deiodinase isoenzymes and asked whether they may contribute to dimerization and reduction of the oxidized enzyme with physiological reductants. We also asked whether amino acids previously identified in DIO3 play the same role in DIO1. Human DIO1 and 2 were recombinantly expressed in insect cells with selenocysteine replaced with cysteine (DIO1U126C), or in COS7 cells as selenoprotein. Enzyme activities were studied by radioactive deiodination assays with physiological reducing agents and recombinant proteins were characterized by mass-spectrometry. Mutation of Cys124 in DIO1 prevented reduction by glutathione, while 20 mM dithiothreitol still regenerated the enzyme. Protein thiol reductants, thioredoxin and glutaredoxin, did not reduce DIO1U126C. Mass-spectrometry demonstrated the formation of an intracellular disulfide between the side-chains of Cys124 and Cys(Sec)126. We conclude that the proximal Cys124 forms a selenenyl-sulfide with the catalytic Sec126 during catalysis, which is the substrate of the physiological reductant glutathione. Mutagenesis studies support the idea of a proton-relay pathway from solvent to substrate that is shared between DIO1 and DIO3.
Project description:In animal models and human trials, intramyocardial injection of adult bone-marrow derived mesenchymal stem cells (BM-MSC) provides beneficial effects in failing hearts. These effects are mainly mediated through paracrine mechanisms. Mesenchymal stem cells of fetal origin (hAMC) can be isolated from the amniotic membrane of human placenta. Our results provide evidence that hAMC exert remarkable cardioprotective effects through paracrine mechanisms. However, the complete nature and scope of the paracrine mediators of cardioprotection have not been investigated yet. We compared the gene expression profiling of hAMC (n=8), BM-MSC (n=10) and dermal fibroblasts (n=6) to shed light onto the identity of putative cardioprotective factors secreted by fetal MSC. Total RNA was extracted from cultured hAMC (n=8), BM-MSC (n=10) and dermal fibroblasts (n=6) and analyzed with HumanHT-12 v3 Expression BeadChips