Spatially resolved transcriptomics reveals innervation-responsive functional cluster in skeletal muscle.. Spatially resolved transcriptomics reveals innervation-responsive functional cluster in skeletal muscle.

Striated muscle is a highly organized structure composed by well-defined anatomical domains with integrated but distinct assignments. Indeed, the lack of a direct correlation between tissue architecture and gene expression has thus far limited our understanding of how each unit responds to physio-pathologic contexts. Here, we show how the combined use of spatially resolved transcriptomics and immunofluorescence can bridge this gap by enabling the unbiased identification of such domains and the characterization of their response to external perturbations. Using a spatiotemporal analysis, we followed the changes in the transcriptomics profile of specific domains in muscle in a model of denervation. Furthermore, our approach allowed us to identify the spatial distribution and nerve dependence of atrophic signalling pathway and polyamine metabolism to glycolytic fibres. Indeed, we demonstrate a pronounced alteration of polyamine homeostasis upon denervation. Overall design: Spatial Transcriptomics analysis of wildtype murine Tibialis Anterior and Extensor digitorum longus prior and after Nerve Crush (3 days and 30 days )

横纹肌（Striated muscle）是一类高度有序的结构，由界定清晰的解剖区域构成，这些区域兼具整合性与独特的功能分工。此前，由于组织架构与基因表达之间缺乏直接关联，我们对各肌肉单元如何响应生理-病理（physio-pathologic）环境的认知一直受到限制。本研究表明，空间转录组学（spatially resolved transcriptomics）与免疫荧光（immunofluorescence）联合使用，能够通过无偏识别这类解剖区域，并表征其对外部扰动的响应，从而填补这一认知空白。我们通过时空分析，追踪了去神经支配（denervation）模型中肌肉特定区域的转录组谱变化。此外，本方法还帮助我们明确了萎缩信号通路与多胺代谢在糖酵解肌纤维中的空间分布特征及神经依赖性。研究证实，去神经支配后多胺稳态会发生显著改变。整体实验设计：对野生型小鼠胫骨前肌（Tibialis Anterior）及趾长伸肌（Extensor digitorum longus）在神经压迫（Nerve Crush）造模前，以及造模后3天、30天分别开展空间转录组学分析。