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.

在人体中发现的塑料粘附，成纤维细胞样克隆形成细胞现在被定义为多能“间质基质细胞”（MSC），具有用于基于细胞的疗法的巨大潜力。最近，无论是从基础角度还是从转化角度来看，这些细胞的研究和基础知识都已快速发展。关于可用的各种组织来源，易于分离和体外的实验方案的开发方面，已有重要发现。扩增并定向分化成各种细胞类型。另外，已经发现了诸如免疫调节之类的新能力，并进一步发展了生物材料的使用，以帮助分离，扩增和分化以及改善向选定的最佳组织部位的递送。但是，在这些情况下，MSC的分子指纹仍然不够精确和不足。因此，如果没有这些关键的知识，就很难在准确确定其实际发展潜力方面取得进展。对MSC的整体基因表达或转录组的详细研究可能会提供这方面的重要线索。在本文中，我们将解决与MSC转录组研究相关的挑战，在已发表的实验结果中观察到的悖论，以及对仔细的转录组学分析的需求。我们描述了具有各种转录组平台的示例性应用程序，这些平台用于解决生物标志物的变异和分化过程的鉴定。讨论了转录组分析中适应下一代测序（NGS）技术的发展和潜力。最后，在回顾现有理解和发表的研究的基础上，我们提出了如何应用NGS来促进对MSC生物学及其在相关领域（如再生医学）中的应用的进一步理解。讨论了转录组分析中适应下一代测序（NGS）技术的发展和潜力。最后，在回顾现有理解和发表的研究的基础上，我们提出了如何应用NGS来促进对MSC生物学及其在相关领域（如再生医学）中的应用的进一步理解。讨论了转录组分析中适应下一代测序（NGS）技术的发展和潜力。最后，在回顾现有理解和发表的研究的基础上，我们提出了如何应用NGS来促进对MSC生物学及其在相关领域（如再生医学）中的应用的进一步理解。