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Yan-Yuan Xiao, Qing Zhang, Fei Huang, Lin Rao, Tian-Xiong Yao, Si-Yu Yang, Lei Xie, Xiao-Xiao Zou, Li-Ping Cai, Jia-Wen Yang, Bin Yang, Lu-Sheng Huang. Single-cell profiling of the pig cecum at various developmental stages. Zoological Research, 2024, 45(1): 55-68. doi: 10.24272/j.issn.2095-8137.2023.007
Citation: Yan-Yuan Xiao, Qing Zhang, Fei Huang, Lin Rao, Tian-Xiong Yao, Si-Yu Yang, Lei Xie, Xiao-Xiao Zou, Li-Ping Cai, Jia-Wen Yang, Bin Yang, Lu-Sheng Huang. Single-cell profiling of the pig cecum at various developmental stages. Zoological Research, 2024, 45(1): 55-68. doi: 10.24272/j.issn.2095-8137.2023.007

Single-cell profiling of the pig cecum at various developmental stages

doi: 10.24272/j.issn.2095-8137.2023.007
Datasets generated in this study were deposited in the Genome Sequence Archive (GSA) database (https://ngdc.cncb.ac.cn/gsa/) under accession number CRA010843, Science Data Bank (doi:10.57760/sciencedb.j00139.00082) and NCBI under BioProjectID PRJNA1036035.
Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
Experimental design and conception: L.S.H.; investigation: Y.Y.X., B.Y., Q.Z., F.H., L.R., T.X.Y., S.Y.Y., L.P.C., L.X., X.X.Z., and J.W.Y.; formal analysis: Y.Y.X.; writing-original draft: Y.Y.X.; writing-review & editing: L.S.H. and B.Y.; experimental organization and analysis supervision: L.S.H. All authors read and approved the final version of the manuscript.
Funds:  This work was supported by the National Natural Science Foundation of China (31790410, 32160781)
More Information
  • The gastrointestinal tract is essential for food digestion, nutrient absorption, waste elimination, and microbial defense. Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity, functional heterogeneity, and their importance in intestinal tract development and disease. Although such profiling has been extensively conducted in humans and mice, the single-cell gene expression landscape of the pig cecum remains unexplored. Here, single-cell RNA sequencing was performed on 45 572 cells obtained from seven cecal samples in pigs at four different developmental stages (days (D) 30, 42, 150, and 730). Analysis revealed 12 major cell types and 38 subtypes, as well as their distinctive genes, transcription factors, and regulons, many of which were conserved in humans. An increase in the relative proportions of CD8+ T and Granzyme A (low expression) natural killer T cells (GZMAlow NKT) cells and a decrease in the relative proportions of epithelial stem cells, Tregs, RHEX+ T cells, and plasmacytoid dendritic cells (pDCs) were noted across the developmental stages. Moreover, the post-weaning period exhibited an up-regulation in mitochondrial genes, COX2 and ND2, as well as genes involved in immune activation in multiple cell types. Cell-cell crosstalk analysis indicated that IBP6+ fibroblasts were the main signal senders at D30, whereas IBP6 fibroblasts assumed this role at the other stages. NKT cells established interactions with epithelial cells and IBP6+ fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs. This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.
  • Datasets generated in this study were deposited in the Genome Sequence Archive (GSA) database (https://ngdc.cncb.ac.cn/gsa/) under accession number CRA010843, Science Data Bank (doi:10.57760/sciencedb.j00139.00082) and NCBI under BioProjectID PRJNA1036035.
    Supplementary data to this article can be found online.
    The authors declare that they have no competing interests.
    Experimental design and conception: L.S.H.; investigation: Y.Y.X., B.Y., Q.Z., F.H., L.R., T.X.Y., S.Y.Y., L.P.C., L.X., X.X.Z., and J.W.Y.; formal analysis: Y.Y.X.; writing-original draft: Y.Y.X.; writing-review & editing: L.S.H. and B.Y.; experimental organization and analysis supervision: L.S.H. All authors read and approved the final version of the manuscript.
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