Cell transcriptomic atlas of the non-human primate Macaca fascicularis

Han, Lei; Wei, Xiaoyü; Liu, Chuanyu; Volpe, Giacomo; Zhuang, Zhenkun; Zou, Xudong; Wang, Zhifeng; Pan, Tao; Yuan, Yue; Zhang, Xiao; Fan, Peng; Guo, Pengcheng; Lai, Yiwei; Lei, Ying; Liu, Xingyuan; Yu, Feng; Shangguan, Shuncheng; Lai, Guangyao; Deng, Qiuting; Liu, Ya; Wu, Liang; Shi, Qiong; Yu, Hao; Huang, Yunting; Cheng, Mengnan; Xu, Jiangshan; Liu, Yang; Wang, Mingyue; Wang, Chunqing; Zhang, Yuanhang; Xie, Duo; Yang, Yunzhi; Yu, Yeya; Zheng, Huiwen; Wei, Yanrong; Huang, Fubaoqian; Lei, Jie; Huang, Waidong; Zhu, Zhiyong; Lu, Haorong; Wang, Bo; Wei, Xiaofeng; Chen, Fengzhen; Yang, Tao; Du, Wensi; Chen, Jing; Xu, Shi-Bo; An, Juan; Ward, Carl; Wang, Zongren; Pei, Zhong; Wong, Chi‐Wai; Liu, Xiaolei; Zhang, Huafeng; Liu, Mingyuan; Qin, Baoming; Schambach, Axel; Isern, Joan; Feng, Liqiang; Liu, Yan; Guo, Xiangyu; Liu, Zhen; Sun, Qiang; Maxwell, Patrick H.; Barker, Nick; Muñoz‐Cánoves, Pura; Gu, Ying; Mulder, Jan; Uhlén, Mathias; Tan, Tao; Liu, Shi Ping; Yang, Huanming; Wang, Jian; Hou, Yong; Xu, Xun; Esteban, Miguel A.; Liu, Longqi

doi:10.1038/s41586-022-04587-3

Cited by 94 publications

(91 citation statements)

References 87 publications

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“…Importantly, extensive clinical and histopathological metadata should be collected from each donor and tissue to mitigate against complexities arising from genetic and environmental differences, as this can provide insight into individual-specific features of the atlas, as we exploit in the accompanying paper (Tabula Microcebus manuscript 2). Application of this strategy to a wide variety of organisms [76][77][78][79] will rapidly expand our cellular, genetic, and molecular understanding of biology that has been dominated for a half century by a small number of model organisms.…”

Section: Discussionmentioning

confidence: 99%

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

Ezran

Liu

Chang

et al. 2021

Preprint

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Mouse lemurs are the smallest, fastest reproducing, and among the most abundant primates, and an emerging model organism for primate biology, behavior, health and conservation. Although much has been learned about their physiology and their Madagascar ecology and phylogeny, little is known about their cellular and molecular biology. Here we used droplet- and plate-based single cell RNA-sequencing to profile 226,000 cells from 27 mouse lemur organs and tissues opportunistically procured from four donors clinically and histologically characterized. Using computational cell clustering, integration, and expert cell annotation, we defined and biologically organized over 750 mouse lemur molecular cell types and their full gene expression profiles. These include cognates of most classical human cell types, including stem and progenitor cells, and the developmental programs for spermatogenesis, hematopoiesis, and other adult tissues. We also described dozens of previously unidentified or sparsely characterized cell types and subtypes. We globally compared cell type expression profiles to define the molecular relationships of cell types across the body, and explored primate cell type evolution by comparing mouse lemur cell profiles to those of the homologous cells in human and mouse. This revealed cell type specific patterns of primate cell specialization even within a single tissue compartment, as well as many cell types for which lemur provides a better human model than mouse. The atlas provides a cellular and molecular foundation for studying this primate model organism, and establishes a general approach for other emerging model organisms.

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Section: Discussionmentioning

confidence: 99%

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

Ezran

Liu

Chang

et al. 2021

Preprint

Self Cite

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“…Although some analysis platforms for scRNA-seq can provide functions such as data expression, pseudo-time analysis, and cell interaction, they are often complicated to operate [14]. In addition, many scRNA databases contain millions of cells and all major tissues and organs, but their cell annotation methods are not focused on the male genitourinary system and are often not monitored by trained investigators in andrology or urology [2, 4, 7]. To our knowledge, there is no convenient tool for the targeted analysis of scRNA-seq data for the male genitourinary system.…”

Section: Discussionmentioning

confidence: 99%

“…For example, spermatogenesis is a complex and continuous cellular developmental process, which comprises mitotic spermatogonia, meiotic spermatocytes, and post-meiotic spermiogenesis from round spermatids to spermatozoa, and spans dozens of cell subtypes [6]. The early stages of meiosis alone can be divided into at least four stages, however, comprehensive databases often simply define meiosis as one to three germ cell clusters [5, 7]. Researchers in reproductive medicine often cannot gain useful information from such rudimentary analysis.…”

Section: Introductionmentioning

confidence: 99%

MHA, an interactive website for scRNA-seq data of male genitourinary development and disease

Zhao

Yao

et al. 2022

Preprint

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The development of single-cell sequencing technology has expanded the understanding of cell heterogeneity and disease progression in the male genitourinary system. However, complex processing processes and unprofessional analytical annotations limit the daily use and wildly sharing of published datasets. Here, we describe the Male Health Atlas (MHA), an easy-to-operate online visual website focused on the male genitourinary system, allowing researchers to quickly search for expression patterns of one or multiple genes, and dynamic changes of gene expression during tissue development or under pathological states. At present, the MHA includes nine objects, two species, five types of male genitourinary tissues/organs, and 258,777 single-cell profiles. Compared with other single-cell databases, the MHA has the following advantages: (1) It is easy to operate, and users can complete retrieval and output of results within 5 min without any bioinformatics skills; (2) The selection and analysis of data are under professional supervision of researchers in the male genitourinary field; (3) It contains most of the main male-specific organs and will continue to be updated; (4) MHA provides multi-dimensional output patterns, including tSNE/UMAP, violin, and bubble plot output for displaying single or multiple genes. MHA is the first single-cell database website in the field of andrology and male reproduction, providing researchers with scRNA-seq resources and an accessible tool. MHA is freely available at http://malehealthatlas.cn/.

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“…We assembled a set of 55 human proteins known from the literature (taken from two recent papers (Han et al, 2022;Wang et al, 2021) and several manual additions) -see Table S4 for the list of these receptors. We tested the occurrence of these receptors in our various protein categories (see Figures S7B-S7E for more details).…”

Section: Acknowledgmentsmentioning

confidence: 99%

Cell transcriptomic atlas of the non-human primate Macaca fascicularis

Cited by 94 publications

References 87 publications

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

Tabula Microcebus: A transcriptomic cell atlas of mouse lemur, an emerging primate model organism

MHA, an interactive website for scRNA-seq data of male genitourinary development and disease

Rapidly evolving viral motifs mostly target biophysically constrained binding pockets of host proteins

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