Department of Dermatology, Huashan Hospital, Fudan University, Shanghai Institute of Dermatology, Shanghai, China.
Department of Allergy and Rheumatology, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.
J Dermatol Sci. 2023 Aug;111(2):22-31. doi: 10.1016/j.jdermsci.2023.06.005. Epub 2023 Jun 20.
Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of skin biology, but its utility is restricted by the requirement of fresh samples, inadequate dissociation-induced cell loss or death, and activation during tissue digestion. Single-nucleus RNA sequencing (snRNA-seq) can use frozen, hard-to-dissociate materials, which might be a promising method to circumvent the limitations of scRNA-seq for the skin tissue.
To profile skin cells using snRNA-seq in parallel with scRNA-seq.
We performed snRNA-seq in parallel with scRNA-seq for the bisected skin sample of one person and integrated previously published scRNA-seq data for analysis. We comparatively analyzed the differences in cell proportions and gene expression between the two methods. The differentiation trajectories of keratinocytes and fibroblasts were analyzed by Slingshot analysis.
snRNA-seq was less susceptible to contamination from mitochondrial and ribosomal RNA, and exhibited a greater capacity to detect transcription factors. snRNA-seq identified more spatially and functionally relevant keratinocyte clusters that constitute cell trajectories with expected differentiation dynamics. Novel markers, e.g., LYPD3, EMP2, and CSTB, were revealed for different differentiation stages of keratinocytes, and NFIB and GRHL1 were identified as transcription factors involving in the proliferation and functional differentiation of keratinocytes. Fibroblasts were found in a state of activation in scRNA-seq. And scRNA-seq detected a greater number of immune cells.
We generated an updated atlas of the skin transcriptome based on the reciprocal contribution of scRNA-seq and snRNA-seq.
单细胞 RNA 测序 (scRNA-seq) 提高了我们对皮肤生物学的认识，但它的应用受到新鲜样本的要求、分离诱导的细胞损失或死亡以及组织消化过程中的激活的限制。单核 RNA 测序 (snRNA-seq) 可以使用冷冻的、难以分离的材料，这可能是一种有前途的方法，可以规避 scRNA-seq 对皮肤组织的限制。
使用 snRNA-seq 与 scRNA-seq 并行对皮肤细胞进行分析。
我们对一个人的皮肤样本进行了 snRNA-seq 和 scRNA-seq 的并行分析，并整合了先前发表的 scRNA-seq 数据进行分析。我们比较分析了两种方法在细胞比例和基因表达上的差异。通过 Slingshot 分析分析了角质形成细胞和成纤维细胞的分化轨迹。
snRNA-seq 不易受到线粒体和核糖体 RNA 的污染，并且能够更好地检测转录因子。snRNA-seq 鉴定出更多的空间和功能相关的角质形成细胞簇，构成具有预期分化动力学的细胞轨迹。新的标记物，如 LYPD3、EMP2 和 CSTB，被揭示用于角质形成细胞的不同分化阶段，而 NFIB 和 GRHL1 被鉴定为涉及角质形成细胞增殖和功能分化的转录因子。在 scRNA-seq 中发现成纤维细胞处于激活状态。并且 scRNA-seq 检测到更多的免疫细胞。
我们基于 scRNA-seq 和 snRNA-seq 的相互贡献生成了一个更新的皮肤转录组图谱。
