Single-cell atlas of domestic pig cerebral cortex and hypothalamus

Zhu, Jiacheng; Chen, Fang; Luo, Lihua; Wu, Weiying; Dai, Jinxia; Zhong, Junyan; Lin, Xiaofeng; Chai, Chaochao; Ding, Peiwen; Liang, Langchao; Wang, Shiyou; Ding, Xiangning; Chao, Yin; Wang, Haoyu; Qiu, Jiaying; Wang, Fei‐Yue; Sun, Chengcheng; Zeng, Yuying; Fang, Jian; Jiang, Xiaoying; Liu, Ping; Tang, Gen; Qiu, Xin; Zhang, Xingliang; Ruan, Yetian; Jiang, Sanjie; Li, Jiankang; Zhu, Shida; Xu, Xun; Li, Fang; Liu, Zhongmin; Cui, Gang; Chen, Dongsheng

doi:10.1016/j.scib.2021.04.002

Cited by 22 publications

(24 citation statements)

References 78 publications

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“…Fifteen tissues, including nine brain regions, retina, kidney, heart, spleen, liver, and lung, were analyzed by single-nuclei RNA sequencing (snRNA-seq). Among the nine different brain regions, four regions (area postrema, cerebellum, subfornical organ, and the vascular organ of lamina terminalis (OVoLT)) were generated by this study, and the other five brain regions (frontal lobe, hypothalamus, occipital lobe, parietal lobe, and temporal lobe) were from a study we had previously published using snRNA-seq 28 . Both scRNA-seq and snRNA-seq techniques were used for single-cell transcriptome analysis, which had both technical strengths and limitations 31 .…”

Section: Resultsmentioning

confidence: 99%

“…Since the completion of the first porcine reference genome, technological breakthroughs in gene editing and cloning allow precise manipulation of the pig genome in living animals 23 – 25 and applications of pigs in biomedical research have been greatly expanded. Previous scRNA-seq studies in pigs were restricted to a few tissues or a single organ 26 – 28 . Recently, the pig BodyMap atlas with the conventional bulk RNA-seq method has been reported 29 .…”

Section: Introductionmentioning

confidence: 99%

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Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

et al. 2022

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Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-β, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

et al. 2022

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“…All the literatures of the studies generating the above scRNA-seq datasets were manually confirmed by a group of experienced researchers and all the scRNA-seq dataset were processed with a unified analyzing pipeline (Figure 1B ). Briefly, they are processed with steps composed of both utilities packaged in Seurat v3.0 and in-house scripts according to previously study ( 21 , 22 ). Firstly, we conduct the quality control by filtering out cells with expressed genes <200 and genes those expressed in <1 cell for each dataset.…”

Section: Data Collection and Database Contentmentioning

confidence: 99%

VThunter: a database for single-cell screening of virus target cells in the animal kingdom

Chen

Tan

Ding

et al. 2021

Nucleic Acids Research

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Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.

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“…Single-cell RNA-seq (scRNA-seq) has been utilized to describe porcine immune cell transcriptomes at granularity unparalleled by bulk RNA-seq or microarray approaches, including in peripheral blood (Herrera-Uribe & Wiarda et al, 2021), lung (Zhang et al, 2021b), skin (Han et al, 2021), brain (Chen et al, 2019; Zhu et al, 2021), and embryos (Kong et al, 2020; Liu et al, 2021; Ramos-Ibeas et al, 2019). Additionally, epithelial cells in the porcine intestine were recently queried via scRNA-seq, and results provide new insight into biological development and epithelial cell functions (Meng et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing

Wiarda

Trachsel

Sivasankaran

et al. 2022

Preprint

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Intestinal lymphocytes are crucial members of the mucosal immune system with impact over outcomes of intestinal health versus dysbiosis. Resolving intestinal lymphocyte complexity and function is a challenge, as the intestine provides cellular snapshots of a diverse spectrum of immune states. In pigs, intestinal lymphocytes are poorly described relative to humans or traditional model species. Enhanced understanding of porcine intestinal lymphocytes will promote food security and improve utility of pigs as a biomedical model for intestinal research. Single-cell RNA sequencing (scRNA-seq) was performed to provide transcriptomic profiles of lymphocytes in the porcine ileum, with 31,983 cells annotated into 26 cell types. Deeper interrogation revealed previously undescribed cells in porcine ileum, including SELLhi γδ T cells, group 1 and group 3 innate lymphoid cells (ILCs), and four subsets of B cells. Single-cell transcriptomes in ileum were compared to those in porcine blood, and subsets of activated lymphocytes were detected in ileum but not periphery. Comparison to scRNA-seq human and murine ileum data revealed a general consensus of ileal lymphocytes across species. Lymphocyte spatial context in porcine ileum was conferred through differential tissue dissection prior to scRNA-seq. Antibody-secreting cells, B cells, follicular αβ T cells, and cycling T/ILCs were enriched in ileum with Peyer's patches, while non-cycling γδ T, CD8 αβ T, and group 1 ILCs were enriched in ileum without Peyer's patches. scRNA-seq findings were leverages to develop advanced toolsets for further identification of ILCs in porcine ileum via flow cytometry and in situ staining. Porcine ileal ILCs identified via scRNA-seq did not transcriptionally mirror peripheral ILCs (corresponding to natural killer cells) but instead had gene signatures indicative of tissue- and activation-specific functions, indicating potentially similar roles to intestinal ILCs identified in humans. Overall, the data serve as a highly-resolved transcriptomic atlas of the porcine intestinal immune landscape and will be useful in further understanding intestinal immune cell function.

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Single-cell atlas of domestic pig cerebral cortex and hypothalamus

Cited by 22 publications

References 78 publications

Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

VThunter: a database for single-cell screening of virus target cells in the animal kingdom

Porcine intestinal innate lymphoid cells and lymphocyte spatial context revealed through single-cell RNA sequencing

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