Transcriptomics of human multipotent mesenchymal stromal cells: Retrospective analysis and future prospects

Abstract

The plastic-adherent, fibroblast-like, clonogenic cells found in the human body now defined as multipotent "Mesenchymal Stromal Cells" (MSCs) hold immense potential for cell-based therapies. Recently, research and basic knowledge of these cells has fast-tracked, both from fundamental and translational perspectives. There have been important discoveries with respect to the available variety of tissue sources, the development of protocols for their easy isolation and in vitro expansion and for directed differentiation into various cell types. In addition, there has been discovery of novel abilities such as immune-modulation and further development of the use of biomaterials to aid isolation, expansion and differentiation together with improved delivery to the selected optimal tissue site. However, the molecular fingerprint of MSCs in these contexts remains imprecise and inadequate. Consequently, without this crucial knowledge it is difficult to achieve progress to determine with precision their practical developmental potentials. Detailed investigations on the global gene expression, or transcriptome, of MSCs could offer essential clues in this regard. In this article, we address the challenges associated with MSC transcriptome studies, the paradoxes observed in published experimental results and the need for careful transcriptomic analysis. We describe the exemplary applications with various transcriptome platforms that are used to address the variation in biomarkers and the identification of differentiation processes. The evolution and the potentials for adapting next-generation sequencing (NGS) technology in transcriptome analysis are discussed. Lastly, based on review of the existing understanding and published studies, we propose how NGS may be applied to promote further understanding of the biology of MSCs and their use in allied fields such as regenerative medicine.

Differential and Interactive Effects of Substrate Topography and Chemistry on Human Mesenchymal Stem Cell Gene Expression

“…In this regard, high-throughput assays such as microarray and next generation sequencing-based transcriptomics have advanced the field of stem cell biology and technology [36]. Particularly, whole transcriptome shotgun sequencing known as RNA-sequencing or RNA-seq for short, is currently being explored in order to understand the gene expression profile of MSCs in various contexts [36].…”

“…Particularly, whole transcriptome shotgun sequencing known as RNA-sequencing or RNA-seq for short, is currently being explored in order to understand the gene expression profile of MSCs in various contexts [36]. One of the areas of significant interest is in the expansion of MSCs.…”

Transcriptome profiles acquired during cell expansion and licensing validate mesenchymal stromal cell lineage genes

“…Recent advances in MSC therapies have revealed a need for reliable and accessible MSC identity tests to support cell production [ 20 ]. Two independent groups have proposed MSC transcriptomic signature profiles that purportedly distinguish MSCs from other stromal and stem cells [ 4 , 5 ], potential tools that could address this gap.…”

Improving characterisation of human Multipotent Stromal Cells cultured in 2D and 3D: Design and evaluation of primer sets for accurate gene expression normalisation

“…An alternative to microarray is RNA sequencing (RNAseq). Although a bit more expensive than microarray, the much broader dynamic range, possible discovery of new genes or splice variants and the ability to examine DNA variations are only some of the benefits [7]. These techniques require the extraction of RNA from MSCs cultured in 2D (on culture dish in monolayer) or 3D (cultured in a scaffold of any particular material).…”