Small fruit flies, great achievements: Li Hongjie/Luo Liqun and others completed the whole body single-cell transcriptome atlas of fruit flies

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Article source: BioArt | Author: November

Fig. 1 White-eyed drosophila versus red-eyed wild-type drosophila

Speaking of fruit flies, The white-eyed fruit fly of Morgan in morgan's most impressive textbook (Figure 1), "... The fruit fly was weak. Morgan took it home at night, left it in a bottle next to the bed, and brought it back to the lab during the day. In the lab, it shook its spirits before dying, mated with a red-eyed fruit fly, and passed on the mutant gene." From this, Morgan discovered the third law of genetics.

Drosophila melanogaster's biological research history is linked to a variety of key biological discoveries, and the high degree of collaboration among scientists within the Drosophila melanogaster has led to the development of multiple resources, including high-quality genomic, genetic, and molecular biology tools, as well as important databases such as Flybase, FlyMine, FlyLight, VirtualFlyBrain, etc. [1-3]. However, there is currently a lack of databases on cell type resolution. The development of single-cell technology has made multicellular transcriptome analysis possible, and there have been some studies that apply single-cell scRNA-seq technology to the analysis of multiple tissues and different stages of development in Drosophila [4], but these databases are generated by different laboratories based on different genetic backgrounds, different experimental methods, and different sequencing platforms, thus hindering systematic analysis of gene expression between cells and tissues.

To this end, the Li Hongjie Research Group of Baylor Medical School (0608 alumni of the University of Science and Technology of China), the Stein Aerts Research Group of the University of Leuven in Belgium, the Luo Liqun Research Group of Stanford University (81 young alumni of the University of Science and Technology of China), the Stephen R. Quake Research Group, the Bart Deplancke Research Group of the Lausanne Polytechnic Institute in Switzerland, and the Norbert of harvard medical school in the United States Perrimon's research group published an article in Science entitled Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly, which establishes a drosophila cell atlas (www.flycellatlas.org) through gene function and cell type at single-cell nucleus resolution, and the data in this database can be obtained through multiple portals. This facilitates the analysis and research of the entire scientific research community.

The genome of Drosophila contains about 14,000 protein-coding genes, of which about 63% are homologous to humans. Therefore, the study of drosophila genome and single-cell omics is also very important for the study of human genes and diseases. The authors' goal is to build a complete cell profile of adult Drosophila with the same genetic background, sorting protocol, and sequencing platform to obtain comprehensive cell classification, integrate single-cell transcriptome data with information on gene expression and cell type, systematically compare differences in gene expression in adult drosophila and male and female drosophila, and identify and establish specific markers for different cell types in Drosophila.

To achieve full sampling, the authors dissected 12 individual tissues of female and male Drosophila and three sex-specific tissues. For tissues that cannot be dissected throughout the body, the authors performed single-cell nucleus snRNA-seq using specific GAL4-driven nuclear green fluorescent protein, labeling and collecting nuclei using fluorescently activated cell sorting methods[5]. In addition, the authors used Smart-seq2 to sequence two rare cellular insulin-producing cells and Corpora cardiaca cells (Figure 2). These two complementary strategies achieved unprecedented cell type coverage, with the authors obtaining a total of 580,000 high-quality nuclei, of which 570,000 were from the 10x Genomics platform and 10,000 from Smart-seq2.

Figure 2 Drosophila cell mapping workflow and tissue types covered by the analysis

After obtaining the Drosophila cell atlas, the authors analyzed the results and annotated the cell types in detail through collaboration in more than forty laboratories. For example, in the head of Fruit Fly, the authors identified a total of 81 nerve cell types found. In the body of Drosophila, there are mainly 33 cell types, including muscle cells, endothelial cells, fat cells, pigment cells, germ cells, glial cells and tracheal cells. The atlases created by the authors can be used to compare the same cells across tissues. In addition, the authors counted cell markers for each cell type, of which 14,240 genes were found to appear in at least one type of cell, with a median of 638 markers for each cell type, of which 94 were visceral muscle cells with the least cell markers, and 7736 cell markers were included in spermblasts. In addition, the authors identified and calculated tissue-specific transcription factors to derive specific transcription factor markers for one or a few types.

Subsequently, the authors analyzed sex-dependent gene expression and sex-specific tissues. The key signaling pathway in somatic cells that determines sex leading to gender differences is doublesex (dsx), and the authors' genetic atlas provides a comprehensive overview of sex difference memory expression, and also identifies differential cell types in female and male flies.

Figure 3 Working model - Drosophila cell atlas

Large-scale identification and characterization of cell types by single-cell nuclear sequencing has been studied in nematodes, mice, and human cells [6-8]. In this work, the authors comprehensively covered the cells in the adult Drosophila body through a unified sequencing method, sequencing platform, and analysis process, made detailed gene annotations on a variety of cells, and established cell type-specific markers and transcription factors to build a large-scale gene regulation network (Figure 3). In addition, the atlases established by the authors analyzed sex dimorphism with Drosophila and studied the histological dynamics of sex-specific cell differentiation trajectories. This atlas has been integrated into multiple platforms and provides an important resource for research and development in the research community.

At present, The Research Group of Li Hongjie of Baylor Medical College is recruiting postdoctoral fellows, and dr. Li Hongjie can be contacted directly if you are willing to contact dr. Li Hongjie directly, and the details https://hongjielilab.org/

Original link:

https://doi.org/10.1126/science.abk2432

bibliography

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8. J. Cao et al., A human cell atlas of fetal gene expression. Science 370, eaba7721 (2020). doi: 10.1126/science.aba7721; pmid: 33184181

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