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Differential MicroRNA Expression Profile of Human Embryonic Stem Cell-Derived Cardiac Lineage Cells.

ABSTRACT: MicroRNAs (miRNAs) are small non-coding RNA molecules that participate in transcriptional and post-transcriptional regulation of gene expression. miRNAs have numerous roles in cellular function including embryonic development. Human embryonic stem cells (hESCs) are capable of self-renewal and can differentiate into most of cell types including cardiomyocytes (CMs). These characteristics of hESCs make them considered as an important model for studying human embryonic development and tissue specific differentiation. In this study, we tried to demonstrate the profile of miRNA expression in cardiac differentiation from hESCs. To induce differentiation, we differentiated hESCs into CMs by direct differentiation method and characterized differentiated cells. To analyze the expression of miRNAs, we distinguished (days 4, 8, 12, 16, 20, 24, 28) and isolated RNAs from each differentiation stage. miRNA specific RT-qPCR was performed and the expression profile of miR-1, -30d, -133a, -143, -145, -378a, -499a was evaluated. The expression of all miRs was up-regulated at day 8. miR-143 and -145 expression was also up-regulated at the later stage of differentiation. Only miR-378a expression returned to undifferentiated hESC levels at the other stages of differentiation. In conclusion, we elucidated the expression profile of miRNAs during differentiation into cardiomyocytes from hESCs. Our findings demonstrate the expression of miRNAs was stage-dependent during differentiation and suggest that the differentiation into CMs can be regulated by miRNAs through direct or indirect pathway.

SUBMITTER: Kim YY

PROVIDER: S-EPMC6171578 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Differential MicroRNA Expression Profile of Human Embryonic Stem Cell-Derived Cardiac Lineage Cells.

Kim Yoon Young YY Min Harry H Kim Hoon H Choi Young Min YM Liu Hung Ching HC Ku Seung-Yup SY

Tissue engineering and regenerative medicine 20170315 2

MicroRNAs (miRNAs) are small non-coding RNA molecules that participate in transcriptional and post-transcriptional regulation of gene expression. miRNAs have numerous roles in cellular function including embryonic development. Human embryonic stem cells (hESCs) are capable of self-renewal and can differentiate into most of cell types including cardiomyocytes (CMs). These characteristics of hESCs make them considered as an important model for studying human embryonic development and tissue specif ...[more]

PMID: 30603473

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Project description:BACKGROUND:Commitment of pluripotent stem cells into differentiated cells and associated gene expression necessitate specific epigenetic mechanisms that modify the DNA and corresponding histone proteins to render the chromatin in an open or closed state. This in turn dictates the associated genetic machinery, including transcription factors, acknowledging the cellular signals provided. Activating histone methyltransferases represent crucial enzymes in the epigenetic machinery that cause transcription initiation by delivering the methyl mark on histone proteins. A number of studies have evidenced the vital role of one such histone modifier, DOT1L, in transcriptional regulation. Involvement of DOT1L in differentiating pluripotent human embryonic stem (hES) cells into the cardiac lineage has not yet been investigated. METHODS:The study was conducted on in-house derived (KIND1) and commercially available (HES3) human embryonic stem cell lines. Chromatin immunoprecipitation (ChIP) was performed followed by sequencing to uncover the cardiac genes harboring the DOT1L specific mark H3K79me2. Following this, dual immunofluorescence was employed to show the DOT1L co-occupancy along with the cardiac progenitor specific marker. DOT1L was knocked down by siRNA to further confirm its role during cardiac differentiation. RESULTS:ChIP sequencing revealed a significant number of peaks characterizing H3K79me2 occupancy in the proximity of the transcription start site. This included genes like MYOF, NR2F2, NKX2.5, and HAND1 in cardiac progenitors and cardiomyocytes, and POU5F1 and NANOG in pluripotent hES cells. Consistent with this observation, we also show that DOT1L co-localizes with the master cardiac transcription factor NKX2.5, suggesting its direct involvement during gene activation. Knockdown of DOT1L did not alter the pluripotency of hES cells, but it led to the disruption of cardiac differentiation observed morphologically as well as at transcript and protein levels. CONCLUSIONS:Collectively, our data suggests the crucial role of H3K79me2 methyltransferase DOT1L for activation of NKX2.5 during the cardiac differentiation of hES cells.

Project description:BackgroundRecent literature has revealed that genetic exchange of microRNA between cells can be essential for cell-cell communication, tissue-specificity and developmental processes. In stem cells, as in other cells, this can be accomplished through microvesicles or exosome mediated transfer. However, molecular profiles and functions of microRNAs within the cells and in their exosomes are poorly studied. Next generation sequencing technologies could provide a broad-spectrum of microRNAs and their expression and identify possible microRNA targets. In this work, we performed deep sequencing of microRNAs to understand the profile and expression of the microRNAs in microvesicles and intracellular environment of human embryonic stem cells derived mesenchymal stem cells (hES-MSC). We outline a workflow pertaining to visualizing, statistical analysis and interpreting deep sequencing data of known intracellular and extracellular microRNAs from hES-MSC). We utilized these results of which directed our attention towards establishing hepatic nuclear factor 4 alpha (HNF4A) as a downstream target of let-7 family of microRNAs.ResultsIn our study, significant differences in expression profile of microRNAs were found in the intracellular and extracellular environment of hES-MSC. However, a high level of let-7 family of microRNAs is predominant in both intra- and extra- cellular samples of hES-MSC. Further results derived from visualization of our alignment data and network analysis showed that let-7 family microRNAs could affect the downstream target HNF4A, which is a known endodermal differentiation marker. The elevated presence of let-7 microRNA in both intracellular and extra cellular environment further suggests a possible intercellular signalling mechanism through microvesicles transfer. We suggest that let-7 family microRNAs might play a signalling role via such a mechanism amongst populations of stem cells in maintaining self renewal property by suppressing HNF4A expression. This is in line with recent paradigm where microRNAs regulate self-renewal and differentiation pathways of embryonic stem cells by forming an integral biological network with transcription factors.ConclusionIn summary, our study using a combination of alignment, statistical and network analysis tools to examine deep sequencing data of microRNAs in hES-MSC has led to a result that (i) identifies intracellular and exosome microRNA expression profiles of hES-MSC with a possible mechanism of miRNA mediated intercellular regulation by these cells and (ii) placed HNF4A within the cross roads of regulation by the let-7 family of microRNAs.

Project description:BackgroundCells of the oligodendrocyte (OL) lineage play a vital role in the production and maintenance of myelin, a multilamellar membrane which allows for saltatory conduction along axons. These cells may provide immense therapeutic potential for lost sensory and motor function in demyelinating conditions, such as spinal cord injury, multiple sclerosis, and transverse myelitis. However, the molecular mechanisms controlling OL differentiation are largely unknown. MicroRNAs (miRNAs) are considered the "micromanagers" of gene expression with suggestive roles in cellular differentiation and maintenance. Although unique patterns of miRNA expression in various cell lineages have been characterized, this is the first report documenting their expression during oligodendrocyte maturation from human embryonic stem (hES) cells. Here, we performed a global miRNA analysis to reveal and identify characteristic patterns in the multiple stages leading to OL maturation from hES cells including those targeting factors involved in myelin production.Methodology/principal findingsWe isolated cells from 8 stages of OL differentiation. Total RNA was subjected to miRNA profiling and validations preformed using real-time qRT-PCR. A comparison of miRNAs from our cultured OLs and OL progenitors showed significant similarities with published results from equivalent cells found in the rat and mouse central nervous system. Principal component analysis revealed four main clusters of miRNA expression corresponding to early, mid, and late progenitors, and mature OLs. These results were supported by correlation analyses between adjacent stages. Interestingly, the highest differentially-expressed miRNAs demonstrated a similar pattern of expression throughout all stages of differentiation, suggesting that they potentially regulate a common target or set of targets in this process. The predicted targets of these miRNAs include those with known or suspected roles in oligodendrocyte development and myelination including C11Orf9, CLDN11, MYTL1, MBOP, MPZL2, and DDR1.Conclusions/significanceWe demonstrate miRNA profiles during distinct stages in oligodendroglial differentiation that may provide key markers of OL maturation. Our results reveal pronounced trends in miRNA expression and their potential mRNA target interactions that could provide valuable insight into the molecular mechanisms of differentiation.

Dataset Information

Differential MicroRNA Expression Profile of Human Embryonic Stem Cell-Derived Cardiac Lineage Cells.

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Differential MicroRNA Expression Profile of Human Embryonic Stem Cell-Derived Cardiac Lineage Cells.

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