Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Science, University of Oxford, Oxford, UK.
Department of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA.
J Orthop Res. 2022 May;40(5):993-1005. doi: 10.1002/jor.25315. Epub 2022 Mar 16.
Tendon transcriptomics is a rapidly growing field in musculoskeletal biology. The ultimate aim of many current tendon transcriptomic studies is characterization of in vitro, ex vivo, or in vivo, healthy, and diseased tendon microenvironments to identify the underlying pathways driving human tendon pathology. The transcriptome interfaces between genomic, proteomic, and metabolomic signatures of the tendon cellular niche and the response of this niche to stimuli. Some of the greatest bottlenecks in tendon transcriptomics relate to the availability and quality of human tendon tissue, hence animal tissues are frequently used even though human tissue is most translationally relevant. Here, we review the variability associated with human donor and procurement factors, such as whether the tendon is cadaveric or a clinical remnant, and how these variables affect the quality and relevance of the transcriptomes obtained. Moreover, age, sex, and health demographic variables impact the human tendon transcriptome. Tendons present tissue-specific challenges for cell, nuclei, and RNA extraction that include a dense extracellular matrix, low cellularity, and therefore low RNA yield of variable quality. Consideration of these factors is particularly important for single-cell and single-nuclei resolution transcriptomics due to the necessity for unbiased and representative cell or nuclei populations. Different cell, nuclei, and RNA extraction methods, library preparation, and quality control methods are used by the tendon research community and attention should be paid to these when designing and reporting studies. We discuss the different components and challenges of human tendon transcriptomics, and propose pipelines, quality control, and reporting guidelines for future work in the field.
肌腱转录组学是肌肉骨骼生物学中一个快速发展的领域。许多当前肌腱转录组学研究的最终目标是描述体外、离体或体内、健康和患病的肌腱微环境，以确定驱动人类肌腱病理学的潜在途径。转录组学介于肌腱细胞生态位的基因组、蛋白质组和代谢组学特征及其对刺激的反应之间。肌腱转录组学的一些最大瓶颈与人类肌腱组织的可用性和质量有关，因此尽管人类组织最具转化相关性，但仍经常使用动物组织。在这里，我们回顾了与人类供体和采集因素相关的变异性，例如肌腱是尸体还是临床残余物，以及这些变量如何影响获得的转录组的质量和相关性。此外，年龄、性别和健康人口统计学变量会影响人类肌腱转录组。肌腱为细胞、核和 RNA 提取带来了组织特异性挑战，包括致密的细胞外基质、低细胞密度，因此 RNA 产量和质量可变。由于需要无偏倚和代表性的细胞或核群体，因此在单细胞和单核分辨率转录组学中应特别考虑这些因素。肌腱研究界使用不同的细胞、核和 RNA 提取方法、文库制备和质量控制方法，在设计和报告研究时应注意这些方法。我们讨论了人类肌腱转录组学的不同组成部分和挑战，并为该领域的未来工作提出了管道、质量控制和报告指南。
