Increased levels of aneuploidy and deregulation of ploidy controlling genes are associated with maintained cultures of hMSC
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ABSTRACT: Human mesenchymal stem cells (hMSC) are being successfully evaluated for the treatment of a wide range of pathological conditions, including graft versus host disease (GVHD), bone and cartilage degeneration, complex fistula and myocardial infarction. Many of these clinical trials use hMSC, which have been previously expanded in vitro for 8-12 weeks under pro-oxidative M-bM-^@M-^\standardM-bM-^@M-^] cell culture conditions. These conditions could have negative effects over genetic stability and promote mutations and chromosomal abnormalities. Our FISH (Fluorescence in situ hybridization) analysis shows that aneuploidy is not unusual phenomenon in conventional cultures of hMSC and that it progressively increases with the passages. We further demonstrate that senescence is linked to transcriptional deregulation of a set of genes that have been previously implicated in cancer and ploidy control. Overexpression of hTERT reversed the deregulation of these ploidy control genes and maintained the basal levels of ploidy even during long-term culture, through its canonical function of telomere elongation and by reducing the levels of oxidative stress. We propose that the high levels of aneuploidy and deregulation of these genes would be relevant biomarkers of senescence in standard cultures of hMSC. We compared the RNA expression profiles of adipose tissue-derived human mesenchymal stem cells cultured in standard cell culture condition at passages 2 with the same primary cell lines cultured by 21 passages. A total of four independent samples were used.
Project description:Human mesenchymal stem cells (hMSC) are being successfully evaluated for the treatment of a wide range of pathological conditions, including graft versus host disease (GVHD), bone and cartilage degeneration, complex fistula and myocardial infarction. Many of these clinical trials use hMSC, which have been previously expanded in vitro for 8-12 weeks under pro-oxidative “standard” cell culture conditions. These conditions could have negative effects over genetic stability and promote mutations and chromosomal abnormalities. Our FISH (Fluorescence in situ hybridization) analysis shows that aneuploidy is not unusual phenomenon in conventional cultures of hMSC and that it progressively increases with the passages. We further demonstrate that senescence is linked to transcriptional deregulation of a set of genes that have been previously implicated in cancer and ploidy control. Overexpression of hTERT reversed the deregulation of these ploidy control genes and maintained the basal levels of ploidy even during long-term culture, through its canonical function of telomere elongation and by reducing the levels of oxidative stress. We propose that the high levels of aneuploidy and deregulation of these genes would be relevant biomarkers of senescence in standard cultures of hMSC.
Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5M-bM-^@M-^Y untranslated region (5M-bM-^@M-^Y UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway. Monitor the translational status of transcriptome in mammalian cells under different conditions
Project description:Linker histones are essential components of chromatin but the distributions and functions of many during cellular differentiation is not well understood. Here, we show that H1.5 binds to genic and intergenic regions, forming blocks of enrichment, in differentiated human cells from all three embryonic germ layers but not in embryonic stem cells. In differentiated cells, H1.5, but not H1.3, binds preferentially to genes that encode membrane and membrane-related proteins. Strikingly, 37% of H1.5 target genes belong to gene family clusters, groups of homologous genes that are located in proximity to each other on chromosomes. H1.5 binding is associated with gene repression and is required for SIRT1 binding, H3K9me2 enrichment and chromatin compaction. Depletion of H1.5 results in loss of SIRT1 and H3K9me2, increased chromatin accessibility, deregulation of gene expression and decreased cell growth. Our data reveal for the first time a specific and novel function for linker histone subtype H1.5 in maintenance of condensed chromatin at defined gene families in differentiated human cells. Examine mRNA expression in control and H1.5 knockdown IMR90 cells
Project description:Using an RNA interference-based genetic screen in mouse F9 cells we identify the transcriptional corepressor CTBP2 as a coactivator critically required for retinoic acid (RA)-induced transcription. Here we perfom a whole genome transcriptome analysis in F9 cells expressing shRNA for Ctbp2 and Rxr in the absence or presence of retinoic acid (RA). A total of 2,754 genes were found to be upregulated (>2 fold) and 1518 genes were downregulated (>2 fold) in response to RA treatment in the control cells. We find that around 52% and 55% of upregulated genes are dependent on Ctbp2 and Rxr for activation respectively suggesting that Ctbp2 is a coactivator of RA signaling. Whole genome RNA-sequencing in F9 cells expressing shGFP or shCtbp2 or shRxr
Project description:The transcriptome of hMSC in late passages was compared to hMSC in early passages. Both hMSC were obtained from the umbilical vein of three donors, two of hMSC have a normal karyotype (MSC/n) and another has a constitutional paracentric chromosomal inversion (hMSC/inv).
Project description:RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here we used a reverse-engineering approach in an ovarian cancer model to reconstruct KRAS oncogene-dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT-PCR and Western Blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions we analysed growth parameters and transcriptional deregulation in the KRAS-transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype. RAS-ROSE cells and ROSE cells treated with Scrambled siRNA
Project description:RAS mutations are highly relevant for progression and therapy response of human tumours, but the genetic network that ultimately executes the oncogenic effects is poorly understood. Here we used a reverse-engineering approach in an ovarian cancer model to reconstruct KRAS oncogene-dependent cytoplasmic and transcriptional networks from perturbation experiments based on gene silencing and pathway inhibitor treatments. We measured mRNA and protein levels in manipulated cells by microarray, RT-PCR and Western Blot analysis, respectively. The reconstructed model revealed complex interactions among the transcriptional and cytoplasmic components, some of which were confirmed by double pertubation experiments. Interestingly, the transcription factors decomposed into two hierarchically arranged groups. To validate the model predictions we analysed growth parameters and transcriptional deregulation in the KRAS-transformed epithelial cells. As predicted by the model, we found two functional groups among the selected transcription factors. The experiments thus confirmed the predicted hierarchical transcription factor regulation and showed that the hierarchy manifests itself in downstream gene expression patterns and phenotype. RAS-ROSE cells were treated with siRNA against 7 transcription factors or controls,
Project description:Linker histones are essential components of chromatin but the distributions and functions of many during cellular differentiation is not well understood. Here, we show that H1.5 binds to genic and intergenic regions, forming blocks of enrichment, in differentiated human cells from all three embryonic germ layers but not in embryonic stem cells. In differentiated cells, H1.5, but not H1.3, binds preferentially to genes that encode membrane and membrane-related proteins. Strikingly, 37% of H1.5 target genes belong to gene family clusters, groups of homologous genes that are located in proximity to each other on chromosomes. H1.5 binding is associated with gene repression and is required for SIRT1 binding, H3K9me2 enrichment and chromatin compaction. Depletion of H1.5 results in loss of SIRT1 and H3K9me2, increased chromatin accessibility, deregulation of gene expression and decreased cell growth. Our data reveal for the first time a specific and novel function for linker histone subtype H1.5 in maintenance of condensed chromatin at defined gene families in differentiated human cells. Examine human linker histone H1.5 (HIST1H1B) binding pattern in H1 hESCs and IMR90 fibroblasts