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一种用于研究雄性和雌性小鼠脊髓细胞间RNA差异表达的开源工具。

An Open-Source Tool for Investigation of Differential RNA Expression Between Spinal Cord Cells of Male and Female Mice.

作者信息

Bellavance Justin, David Laurence S, Hildebrand Michael E

机构信息

Department of Neuroscience, Carleton University, Ottawa, Ontario, Canada.

Department of Medicine, Université de Montréal, Montreal, Quebec, Canada.

出版信息

J Neurosci Res. 2024 Dec;102(12):e70008. doi: 10.1002/jnr.70008.

Abstract

Chronic pain is a highly debilitating condition that differs by type, prevalence, and severity between men and women. To uncover the molecular underpinnings of these differences, it is critical to analyze the transcriptomes of spinal cord pain-processing networks for both sexes. Despite several recently published single-nucleus RNA-sequencing (snRNA-seq) studies on the function and composition of the mouse spinal cord, a gene expression analysis investigating the differences between males and females has yet to be performed. Here, we combined data from three different large-scale snRNA-seq studies, which used sex-identified adult mice. Using SeqSeek, we classified more than 37,000 unique viable cells within predicted cell types with the use of machine learning. We then utilized DESeq2 to identify significant differentially expressed genes (DEGs) between males and females in a variety of cell populations, including superficial dorsal horn (SDH) neurons. We found a large number of DEGs between males and females in all cells, in neurons, and in SDH neurons of the mouse spinal cord, with a greater level of differential expression in inhibitory SDH neurons compared to excitatory SDH neurons. The results of these analyses are available on an open-source web-app: https://justinbellavance.shinyapps.io/snRNA_Visualization/. Lastly, we used gene set enrichment analysis to identify sex-enriched pathways from our previously identified DEGs. Through this, we have identified specific genetic players within the rodent spinal cord that diverge between males and females, which may underlie reported sex differences in spinal nociceptive mechanisms and pain processing.

摘要

慢性疼痛是一种极具致残性的病症,在男性和女性之间,其类型、患病率和严重程度存在差异。为了揭示这些差异的分子基础,分析两性脊髓疼痛处理网络的转录组至关重要。尽管最近发表了几项关于小鼠脊髓功能和组成的单细胞核RNA测序(snRNA-seq)研究,但尚未进行一项调查雄性和雌性之间差异的基因表达分析。在这里,我们整合了来自三项不同的大规模snRNA-seq研究的数据,这些研究使用了已鉴定性别的成年小鼠。我们使用SeqSeek,通过机器学习在预测的细胞类型中对超过37000个独特的活细胞进行了分类。然后,我们利用DESeq2来识别包括浅背角(SDH)神经元在内的多种细胞群体中雄性和雌性之间显著差异表达的基因(DEG)。我们在小鼠脊髓的所有细胞、神经元和SDH神经元中发现了大量雄性和雌性之间的DEG,与兴奋性SDH神经元相比,抑制性SDH神经元中的差异表达水平更高。这些分析结果可在一个开源网络应用程序上获取:https://justinbellavance.shinyapps.io/snRNA_Visualization/。最后,我们使用基因集富集分析从我们之前鉴定的DEG中识别性别富集途径。通过这项研究,我们在啮齿动物脊髓中确定了雄性和雌性之间存在差异的特定基因参与者,这可能是脊髓伤害性感受机制和疼痛处理中所报道的性别差异的基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c0ac/11645520/4a711cb25689/JNR-102-e70008-g006.jpg

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