Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
Quantitative Life Sciences Program, McGill University, Montreal, QC, H3A 0G4, Canada.
Biol Sex Differ. 2020 Nov 5;11(1):61. doi: 10.1186/s13293-020-00335-2.
It is a long established fact that sex is an important factor that influences the transcriptional regulatory processes of an organism. However, understanding sex-based differences in gene expression has been limited because existing studies typically sequence and analyze bulk tissue from female or male individuals. Such analyses average cell-specific gene expression levels where cell-to-cell variation can easily be concealed. We therefore sought to utilize data generated by the rapidly developing single cell RNA sequencing (scRNA-seq) technology to explore sex dimorphism and its functional consequences at the single cell level.
Our study included scRNA-seq data of ten well-defined cell types from the brain and heart of female and male young adult mice in the publicly available tissue atlas dataset, Tabula Muris. We combined standard differential expression analysis with the identification of differential distributions in single cell transcriptomes to test for sex-based gene expression differences in each cell type. The marker genes that had sex-specific inter-cellular changes in gene expression formed the basis for further characterization of the cellular functions that were differentially regulated between the female and male cells. We also inferred activities of transcription factor-driven gene regulatory networks by leveraging knowledge of multidimensional protein-to-genome and protein-to-protein interactions and analyzed pathways that were potential modulators of sex differentiation and dimorphism.
For each cell type in this study, we identified marker genes with significantly different mean expression levels or inter-cellular distribution characteristics between female and male cells. These marker genes were enriched in pathways that were closely related to the biological functions of each cell type. We also identified sub-cell types that possibly carry out distinct biological functions that displayed discrepancies between female and male cells. Additionally, we found that while genes under differential transcriptional regulation exhibited strong cell type specificity, six core transcription factor families responsible for most sex-dimorphic transcriptional regulation activities were conserved across the cell types, including ASCL2, EGR, GABPA, KLF/SP, RXRα, and ZF.
We explored novel gene expression-based biomarkers, functional cell group compositions, and transcriptional regulatory networks associated with sex dimorphism with a novel computational pipeline. Our findings indicated that sex dimorphism might be widespread across the transcriptomes of cell types, cell type-specific, and impactful for regulating cellular activities.
性是影响生物体转录调控过程的一个重要因素，这是一个长期确立的事实。然而，由于现有研究通常对来自女性或男性个体的批量组织进行测序和分析，因此对性别相关的基因表达差异的理解一直受到限制。这种分析平均了细胞特异性基因表达水平，而细胞间的差异很容易被掩盖。因此，我们试图利用快速发展的单细胞 RNA 测序 (scRNA-seq) 技术生成的数据来探索单细胞水平的性别二态性及其功能后果。
我们的研究包括来自大脑和心脏的十个定义明确的细胞类型的 scRNA-seq 数据，这些数据来自于公开的组织图谱数据集 Tabula Muris 中的雌性和雄性年轻成年小鼠。我们将标准差异表达分析与单细胞转录组中差异分布的识别相结合，以测试每种细胞类型中的性别相关基因表达差异。具有细胞间基因表达差异的标记基因构成了进一步描述雌性和雄性细胞之间差异调节的细胞功能的基础。我们还通过利用多维蛋白质-基因组和蛋白质-蛋白质相互作用的知识来推断转录因子驱动的基因调控网络的活性，并分析可能调节性别分化和二态性的途径。
对于本研究中的每一种细胞类型，我们都鉴定出了具有显著不同的平均表达水平或细胞间分布特征的标记基因。这些标记基因在与每个细胞类型的生物学功能密切相关的途径中富集。我们还鉴定出了可能执行不同生物学功能的亚细胞类型，这些功能在雌性和雄性细胞之间存在差异。此外，我们发现，虽然差异转录调控的基因表现出很强的细胞类型特异性，但负责大多数性别二态性转录调控活动的六个核心转录因子家族在细胞类型之间是保守的，包括 ASCL2、EGR、GABPA、KLF/SP、RXRα 和 ZF。
我们使用一种新的计算管道探索了与性别二态性相关的新型基于基因表达的生物标志物、功能细胞群组成和转录调控网络。我们的研究结果表明，性别二态性可能在细胞类型的转录组中广泛存在，具有细胞类型特异性，并且对调节细胞活动具有重要影响。
