Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome analysis of human, IPSC-derived cardiomyocytes transfected with siRNA against frataxin vs cells transfect with control siRNA.

ABSTRACT: Friedreich ataxia is a neuro and cardio degenerative disease, caused by progressive, decreased expression of the frataxin gene (FXN). Hyperthrophic cardiomyopathy is the major cause of early mortality. We used four different lines of human, Induced Pluripotent Stem Cells derived- cardiomyocytes which were transfected with an siRNA against frataxin post-differentiation. Trascriptome analysis of cells in which frataxin was knocked down vs cells transfected with a si control RNA allowed the identification of novel pathways that may contribute to the pathogenesis of the disease.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Grazia Cotticelli

PROVIDER: E-MTAB-11296 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Transcriptome analysis of human, IPSC-derived cardiomyocytes transfected with siRNA against frataxin vs cells transfect with control siRNA.

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