Science

Nature

White adipose tissue, once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic and heterogenous, and is involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control and host defence. High-fat feeding and other metabolic stressors cause marked changes in adipose morphology, physiology and cellular composition, and alterations in adiposity are associated with insulin resistance, dyslipidemia and type 2 diabetes. Here we provide detailed cellular atlases of human and mouse subcutaneous and visceral white fat at single-cell resolution across a range of body weight. We identify subpopulations of adipocytes, adipose stem and progenitor cells, vascular and immune cells and demonstrate commonalities and differences across species and dietary conditions. We link specific cell types to increased risk of metabolic disease and provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity. These data comprise an extensive resource for the exploration of genes, traits and cell types in the function of white adipose tissue across species, depots and nutritional conditions.

Science

果绳是生物学研究极其重要的动物模型之一，结合多种当前非常成熟的RNA测序技术，作者对整个成年果绳身体进行单细胞测序，获得了果绳细胞图谱（FCA）数据库。作者首先分别提取了雌雄两性的12种组织和3种性别特异性组织，做单细胞核转录RNA测序（snRNA-seq），并针对两个特殊的细胞类型：胰岛素分泌细胞和心脏CC（corpora cardiaca）细胞，做Smart-Seq2测序，从而得到覆盖全身不同组织的580,000个细胞。来自全世界的40个实验室的科研人员参与了随后的注释工作，标注了与FlyBase数据库对应的251种细胞类型，并与对果绳整个头部和躯干分别做snRNA-seq的结果进行对应。在以上测序结果基础上，作者分别做了常见细胞类型的跨组织分析、转录因子的多效性和特异性分析、性别偏好的基因表达和性别特异组织的谱系分析等等，为后续研究提供了很多重要的工作点。

随着测序技术的不断成熟和成本降低，近年来科学界一直在致力于提供不同模式动物的单细胞转录图谱数据库，已经完成的包括完整成年线虫、小鼠部分组织和人的部分组织。本篇文章发表了来自多个国家研究组组成的联合团队的成果，为科学界提供了又一模式动物——果绳的完整转录图谱，并与已有果绳数据库相关联，是十分重要的免费科学资源。

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed tissues as well as the entire head and body, annotated to >250 distinct cell types. We provide an in-depth analysis of cell type–related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types between tissues, such as blood and muscle cells, reveals rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the Drosophila community and serves as a reference to study genetic perturbations and disease models at single-cell resolution.

Nature Biotechnology

Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in health and disease, but comprehensive mapping of cell types in situ remains a challenge. Here we present сell2location, a Bayesian model that can resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Cell2location accounts for technical sources of variation and borrows statistical strength across locations, thereby enabling the integration of single-cell and spatial transcriptomics with higher sensitivity and resolution than existing tools. We assessed cell2location in three different tissues and show improved mapping of fine-grained cell types. In the mouse brain, we discovered fine regional astrocyte subtypes across the thalamus and hypothalamus. In the human lymph node, we spatially mapped a rare pre-germinal center B cell population. In the human gut, we resolved fine immune cell populations in lymphoid follicles. Collectively, our results present сell2location as a versatile analysis tool for mapping tissue architectures in a comprehensive manner.