Unknown,Transcriptomics,Genomics,Proteomics

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Comparative RNA-seq analysis of CD146⁺ pericyte transcriptomes from wild-type and mdx mice

ABSTRACT: The project aimed to investigate differences in the gene expression profile of pericytes expressing the CD146 marker (CD146+ pericytes) isolated from the skeletal muscles of wild-type (WT) mice and mdx mice, which serve as a fundamental research model for Duchenne muscular dystrophy. The aim was to understand the differences between two cell types and their potential role in the disease progression. Pericytes were isolated from the skeletal muscles of WT and mdx mice and subsequently enriched for the CD146+ population using magnetic column sorting. After five days of in vitro culture, cells were harvested, and total RNA was extracted. Next-generation sequencing (NGS) was performed at the Next Generation Sequencing Core Facility, Center for New Technologies.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Bartosz Mierzejewski

PROVIDER: E-MTAB-16523 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:A widely shared view reads that 'MSCs' are ubiquitous in human connective tissues, can be defined by a common in vitro phenotype, share a skeletogenic potential as assessed by in vitro differentiation assays, and coincide with the ubiquitous 'pericytes.' Using stringent in vivo differentiation assays and transcriptome analysis, we show here that human cell populations from different anatomical sources, which would all be regarded as 'MSCs' based on these criteria and assumptions, actually differ widely in their transcriptomic signature and in vivo differentiation potential. In contrast, they share the capacity to guide the assembly of functional microvessels in vivo, regardless of their anatomical source, or in situ identity as perivascular or circulating cells. This analysis further reveals that muscle 'pericytes,' which are not spontaneously osteo-chondrogenic as previously claimed, may indeed coincide with an ectopic perivascular subset of committed myogenic cells similar to satellite cells. Cord blood-derived stromal cells, on the other hand, display the unique capacity to form cartilage in vivo spontaneously, in addition to an assayable osteogenic capacity. These data suggest the need to revise current misconceptions on the origin and function of so-called 'MSCs,' with important applicative implications. The data also support the view that rather than a uniform class of 'MSCs,' different mesoderm derivatives include distinct classes of tissue-specific committed progenitors, likely of different developmental origin. The anatomical identity of 'mesenchymal stem cells', (MSCs) their phenotype, their distribution in the different tissues, their lineage, their physiological functions and biological properties represent one of the most controversial and confusing areas in stem cell biology. The definition of the origin, anatomy, function and biological properties of so-called MSCs has obvious implications both for understanding their biology and for their use in potential therapies. We have previously identified a minimal surface phenotype suited not only to enrich for the archetypal human 'MSCs' in uncultured bone marrow cell suspensions, but also to correlate their ex vivo-assayed clonogenic capacity with their in situ identity and in vivo fate following tranplantation (Sacchetti et al., 2007). Stromal cell strains were established from four different tissue sources: bone marrow (BM), skeletal muscle (MU), periosteum (PE), and perinatal blood-borne cord blood (CB) cells. For all post-natal tissue sources, clonogenic cells were prospectively isolated based on a minimal surface phenotype as previously described for human BMSCs (CD34-/CD45-/CD146+); colonies of CB-derived stromal cells were established as described (Kluth et al., 2010; Kogler et al., 2004). Of note, CD146 identified a clonogenic subset in MU (presented below) and PE (data not shown), as it does in BM. Multi-clonal strains derived from growth of the originally explanted cells were then expanded under identical culture conditions; all resulting cell strains exhibited the canonical in vitro cell surface markers regarded as characteristic of 'MSCs'. In order to characterize the specificity and functional significance of the cell surface phenotype of 'MSCs' that is widely regarded as a defining feature of 'MSCs' across tissues, we performed gene expression profiling using Affimetrix technology.

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Comparative RNA-seq analysis of CD146⁺ pericyte transcriptomes from wild-type and mdx mice

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