Analysis of deep sequencing microRNA expression profile from human embryonic stem cells derived mesenchymal stem cells reveals possible role of let-7 microRNA family in downstream targeting of Hepatic Nuclear Factor 4 Alpha

Abstract

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-MSCwith 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.

Microvesicles Derived from Human Umbilical Cord Mesenchymal Stem Cells Stimulated by Hypoxia Promote Angiogenesis Both In Vitro and In Vivo

“…The proangiogenic activity of MVs derived from brain tumor cells was also reported [37], and MSC-MVs were found to protect the kidneys in a rat ischemia-reperfusion model [25]. Previous data have also demonstrated that MVs derived from other cell types, including platelets [32], endothelial progenitors [38][39][40][41], tumor cells [37,42], and ES-derived MSCs [43], have the proangiogenic activity both in vitro and in vivo.…”

Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA

“…Since the observation that various types of RNAs are part of the cargo of extracellular vesicles (EVs) (Ratajczak et al 2006;Valadi et al 2007;Skog et al 2008), numerous efforts have been made to catalog RNA cargos and determine whether these RNAs are biologically functional (Luo et al 2009;Koh et al 2010;Nolte-'t Hoen et al 2012;Zhou et al 2012). The question of the functionality of the RNA cargos has been made complicated by the observation that a large proportion of the detected RNA biotypes are represented by a mixture of full-length and shorter fragments (Tuck and Tollervey 2011;Dhahbi et al 2013a,b;Vojtech et al 2014).…”

Los exosomas de las células presentadoras de antígeno y su papel en la regulación de las respuestas inmunológicas

“…17 Dichas variantes incluyen RNA mensajeros y RNA reguladores tales como microRNA (miRNA) y RNA nocodificantes largos. 3,18,20 Los estudios de secuenciación de RNA de macrófagos (en reposo comparados con células activadas) demuestran que la inflamación altera importantemente el transcriptoma de dichas células. 21 De forma interesante, estudios del mismo tipo llevados a cabo comparando RNA exosomal derivado de macrófagos naïve y estimulados con lipopolisacárido (LPS) indican también alteraciones en el transcriptoma exosomal inducidas por la inflamación.…”