Majd Homa, Cesiulis Andrius, Samuel Ryan M, Richter Mikayla N, Elder Nicholas, Guyer Richard A, Hao Marlene M, Stamp Lincon A, Goldstein Allan M, Fattahi Faranak
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94143, USA.
bioRxiv. 2024 Feb 5:2024.01.15.575794. doi: 10.1101/2024.01.15.575794.
The enteric nervous system (ENS) is a tantalizing frontier in neuroscience. With the recent emergence of single cell transcriptomic technologies, this rare and poorly understood tissue has begun to be better characterized in recent years. A precise functional mapping of enteric neuron diversity is critical for understanding ENS biology and enteric neuropathies. Nonetheless, this pursuit has faced considerable technical challenges. By leveraging different methods to compare available primary mouse and human ENS datasets, we underscore the urgent need for careful identity annotation, achieved through the harmonization and advancements of wet lab and computational techniques. We took different approaches including differential gene expression, module scoring, co-expression and correlation analysis, unbiased biological function hierarchical clustering, data integration and label transfer to compare and contrast functional annotations of several independently reported ENS datasets. These analyses highlight substantial discrepancies stemming from an overreliance on transcriptomics data without adequate validation in tissues. To achieve a comprehensive understanding of enteric neuron identity and their functional context, it is imperative to expand tissue sources and incorporate innovative technologies such as multiplexed imaging, electrophysiology, spatial transcriptomics, as well as comprehensive profiling of epigenome, proteome, and metabolome. Harnessing human pluripotent stem cell (hPSC) models provides unique opportunities for delineating lineage trees of the human ENS, and offers unparalleled advantages, including their scalability and compatibility with genetic manipulation and unbiased screens. We encourage a paradigm shift in our comprehension of cellular complexity and function in the ENS by calling for large-scale collaborative efforts and research investments.
肠神经系统（ENS）是神经科学中一个诱人的前沿领域。随着单细胞转录组技术的近期出现，这个罕见且了解甚少的组织近年来已开始得到更好的表征。对肠神经元多样性进行精确的功能图谱绘制对于理解肠神经系统生物学和肠道神经病变至关重要。尽管如此，这一追求面临着相当大的技术挑战。通过利用不同方法比较现有的原发性小鼠和人类肠神经系统数据集，我们强调了通过湿实验室和计算技术的协调与进步来实现仔细的身份注释的迫切需求。我们采用了不同的方法，包括差异基因表达、模块评分、共表达和相关性分析、无偏生物学功能层次聚类、数据整合和标签转移，以比较和对比几个独立报告的肠神经系统数据集的功能注释。这些分析突出了由于过度依赖转录组学数据而在组织中缺乏充分验证所导致的重大差异。为了全面了解肠神经元身份及其功能背景，必须扩大组织来源并纳入创新技术，如多重成像、电生理学、空间转录组学，以及表观基因组、蛋白质组和代谢组的全面分析。利用人类多能干细胞（hPSC）模型为描绘人类肠神经系统的谱系树提供了独特的机会，并提供了无与伦比的优势，包括其可扩展性以及与基因操作和无偏筛选的兼容性。我们呼吁进行大规模的合作努力和研究投资，以推动我们对肠神经系统中细胞复杂性和功能的理解发生范式转变。
