Advanced Search
Turn off MathJax
Article Contents
Article Navigation >  Zoological Research  > 2024  > In Press
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
shu

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

doi: 10.24272/j.issn.2095-8137.2023.007
  • 1.

    National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China

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
    Abstract
  • 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.
    FullText(HTML)
  • loading
    • References(77)
  • [1]
    Agace WW, McCoy KD. 2017. Regionalized development and maintenance of the intestinal adaptive immune landscape. Immunity, 46(4): 532−548. doi: 10.1016/j.immuni.2017.04.004
    [2]
    Aibar S, González-Blas CB, Moerman T, et al. 2017. SCENIC: single-cell regulatory network inference and clustering. Nature Methods, 14(11): 1083−1086. doi: 10.1038/nmeth.4463
    [3]
    Ali A, Tan HY, Kaiko GE. 2020. Role of the intestinal epithelium and its interaction with the microbiota in food allergy. Frontiers in Immunology, 11: 604054. doi: 10.3389/fimmu.2020.604054
    [4]
    Aliluev A, Tritschler S, Sterr M, et al. 2021. Diet-induced alteration of intestinal stem cell function underlies obesity and prediabetes in mice. Nature Metabolism, 3(9): 1202−1216. doi: 10.1038/s42255-021-00458-9
    [5]
    Blavi L, Solà-Oriol D, Llonch P, et al. 2021. Management and feeding strategies in early life to increase piglet performance and welfare around weaning: a review. Animals, 11(2): 302. doi: 10.3390/ani11020302
    [6]
    Bohlson SS, O'Conner SD, Hulsebus HJ, et al. 2014. Complement, C1q, and C1q-related molecules regulate macrophage polarization. Frontiers in Immunology, 5: 402.
    [7]
    Boyd M, Bressendorff S, Møller J, et al. 2009. Mapping of HNF4α target genes in intestinal epithelial cells. BMC Gastroenterology, 9: 68. doi: 10.1186/1471-230X-9-68
    [8]
    Brown K, Abbott DW, Uwiera RRE, et al. 2018. Removal of the cecum affects intestinal fermentation, enteric bacterial community structure, and acute colitis in mice. Gut Microbes, 9(3): 218−235. doi: 10.1080/19490976.2017.1408763
    [9]
    Burclaff J, Bliton RJ, Breau KA, et al. 2022. A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics. Cellular and Molecular Gastroenterology and Hepatology, 13(5): 1554−1589. doi: 10.1016/j.jcmgh.2022.02.007
    [10]
    Campbell JM, Crenshaw JD, Polo J. 2013. The biological stress of early weaned piglets. Journal of Animal Science and Biotechnology, 4(1): 19. doi: 10.1186/2049-1891-4-19
    [11]
    Catalan E, Sanchez-Martinez D, Pardo J. 2012. GZMA (granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)). Atlas of Genetics and Cytogenetics in Oncology and Haematology, 16(2): 123−126.
    [12]
    Chassaing B, Kumar M, Baker MT, et al. 2014. Mammalian gut immunity. Biomedical Journal, 37(5): 246−258. doi: 10.4103/2319-4170.130922
    [13]
    Chen SF, Zhou YQ, Chen YR, et al. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17): i884−i890. doi: 10.1093/bioinformatics/bty560
    [14]
    Choi SH, Aid S, Bosetti F. 2009. The distinct roles of cyclooxygenase-1 and -2 in neuroinflammation: implications for translational research. Trends in Pharmacological Sciences, 30(4): 174−181. doi: 10.1016/j.tips.2009.01.002
    [15]
    Chowdhury D, Lieberman J. 2008. Death by a thousand cuts: granzyme pathways of programmed cell death. Annual Review of Immunology, 26: 389−420. doi: 10.1146/annurev.immunol.26.021607.090404
    [16]
    Cobaleda C, Schebesta A, Delogu A, et al. 2007. Pax5: the guardian of B cell identity and function. Nature Immunology, 8(5): 463−470. doi: 10.1038/ni1454
    [17]
    Dabareiner RM, White II NA. 1997. Diseases and surgery of the cecum. Veterinary Clinics of North America:Equine Practice, 13(2): 303−315. doi: 10.1016/S0749-0739(17)30241-9
    [18]
    Davis MB, Walens A, Hire R, et al. 2015. Distinct transcript isoforms of the atypical chemokine receptor 1 (ACKR1)/duffy antigen receptor for chemokines (DARC) gene are expressed in lymphoblasts and altered isoform levels are associated with genetic ancestry and the duffy-null allele. PLoS One, 10(10): e0140098. doi: 10.1371/journal.pone.0140098
    [19]
    Duval V, Alayrac P, Silvestre JS, et al. 2022. Emerging roles of the atypical chemokine receptor 3 (ACKR3) in cardiovascular diseases. Frontiers in Endocrinology, 13: 906586. doi: 10.3389/fendo.2022.906586
    [20]
    Elmentaite R, Kumasaka N, Roberts K, et al. 2021. Cells of the human intestinal tract mapped across space and time. Nature, 597(7875): 250−255. doi: 10.1038/s41586-021-03852-1
    [21]
    Fawkner-Corbett D, Antanaviciute A, Parikh K, et al. 2021. Spatiotemporal analysis of human intestinal development at single-cell resolution. Cell, 184(3): 810−826.e23. doi: 10.1016/j.cell.2020.12.016
    [22]
    Gerrits RJ, Lunney JK, Johnson LA, et al. 2005. Perspectives for artificial insemination and genomics to improve global swine populations. Theriogenology, 63(2): 283−299. doi: 10.1016/j.theriogenology.2004.09.013
    [23]
    González-Castillo C, Ortuño-Sahagún D, Guzmán-Brambila C, et al. 2015. Pleiotrophin as a central nervous system neuromodulator, evidences from the hippocampus. Frontiers in Cellular Neuroscience, 8: 443.
    [24]
    Grieb G, Merk M, Bernhagen J, et al. 2010. Macrophage migration inhibitory factor (MIF): a promising biomarker. Drug News & Perspectives, 23(4): 257−64.
    [25]
    Grondin JA, Kwon YH, Far PM, et al. 2020. Mucins in intestinal mucosal defense and inflammation: learning from clinical and experimental studies. Frontiers in Immunology, 11: 2054. doi: 10.3389/fimmu.2020.02054
    [26]
    Haber AL, Biton M, Rogel N, et al. 2017. A single-cell survey of the small intestinal epithelium. Nature, 551(7680): 333−339. doi: 10.1038/nature24489
    [27]
    Haghverdi L, Lun ATL, Morgan MD, et al. 2018. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nature Biotechnology, 36(5): 421−427. doi: 10.1038/nbt.4091
    [28]
    Han L, Wei XY, Liu CY, et al. 2022. Cell transcriptomic atlas of the non-human primate Macaca fascicularis. Nature, 604(7907): 723–731.
    [29]
    Han XP, Wang RY, Zhou YC, et al. 2018. Mapping the mouse cell atlas by microwell-seq. Cell, 172(5): 1091−1107.e17. doi: 10.1016/j.cell.2018.02.001
    [30]
    Han XP, Zhou ZM, Fei LJ, et al. 2020. Construction of a human cell landscape at single-cell level. Nature, 581(7808): 303−309. doi: 10.1038/s41586-020-2157-4
    [31]
    Ito G, Okamoto R, Murano T, et al. 2013. Lineage-specific expression of bestrophin-2 and bestrophin-4 in human intestinal epithelial cells. PLoS One, 8(11): e79693. doi: 10.1371/journal.pone.0079693
    [32]
    James KR, Elmentaite R, Teichmann SA, et al. 2022. Redefining intestinal immunity with single-cell transcriptomics. Mucosal Immunology, 15(4): 531−541. doi: 10.1038/s41385-021-00470-y
    [33]
    James KR, Gomes T, Elmentaite R, et al. 2020. Distinct microbial and immune niches of the human colon. Nature Immunology, 21(3): 343−353. doi: 10.1038/s41590-020-0602-z
    [34]
    James SP. 1993. The gastrointestinal mucosal immune system. Digestive Diseases, 11(3): 146−156. doi: 10.1159/000171407
    [35]
    Jin SQ, Guerrero-Juarez CF, Zhang LH, et al. 2021. Inference and analysis of cell-cell communication using CellChat. Nature Communications, 12(1): 1088. doi: 10.1038/s41467-021-21246-9
    [36]
    Kalucka J, de Rooij LPMH, Goveia J, et al. 2020. Single-cell transcriptome atlas of murine endothelial cells. Cell, 180(4): 764−779.e20. doi: 10.1016/j.cell.2020.01.015
    [37]
    Kong SS, Zhang YH, Zhang WQ. 2018. Regulation of intestinal epithelial cells properties and functions by amino acids. BioMed Research International, 2018: 2819154.
    [38]
    Korsunsky I, Millard N, Fan J, et al. 2019. Fast, sensitive and accurate integration of single-cell data with Harmony. Nature Methods, 16(12): 1289−1296. doi: 10.1038/s41592-019-0619-0
    [39]
    Kryuchkova-Mostacci N, Robinson-Rechavi M. 2017. A benchmark of gene expression tissue-specificity metrics. Briefings in Bioinformatics, 18(2): 205−214.
    [40]
    Li HJ, Janssens J, De Waegeneer M, et al. 2022. Fly cell atlas: a single-nucleus transcriptomic atlas of the adult fruit fly. Science, 375(6584): eabk2432. doi: 10.1126/science.abk2432
    [41]
    Liao DH, Zhao JB, Gregersen H. 2009. Gastrointestinal tract modelling in health and disease. World Journal of Gastroenterology, 15(2): 169−176. doi: 10.3748/wjg.15.169
    [42]
    Lin L, Yee SW, Kim RB, et al. 2015. SLC transporters as therapeutic targets: emerging opportunities. Nature Reviews Drug Discovery, 14(8): 543−560. doi: 10.1038/nrd4626
    [43]
    Lobo GP, Hessel S, Eichinger A, et al. 2010. ISX is a retinoic acid-sensitive gatekeeper that controls intestinal β, β-carotene absorption and vitamin A production. The FASEB Journal, 24(6): 1656−1666. doi: 10.1096/fj.09-150995
    [44]
    Lohela M, Bry M, Tammela T, et al. 2009. VEGFs and receptors involved in angiogenesis versus lymphangiogenesis. Current Opinion in Cell Biology, 21(2): 154−165. doi: 10.1016/j.ceb.2008.12.012
    [45]
    Lunney JK, Van Goor A, Walker KE, et al. 2021. Importance of the pig as a human biomedical model. Science Translational Medicine, 13(621): eabd5758. doi: 10.1126/scitranslmed.abd5758
    [46]
    Marques RE, Guabiraba R, Russo RC, et al. 2013. Targeting CCL5 in inflammation. Expert Opinion on Therapeutic Targets, 17(12): 1439−1460. doi: 10.1517/14728222.2013.837886
    [47]
    McKenna K, Beignon AS, Bhardwaj N. 2005. Plasmacytoid dendritic cells: linking innate and adaptive immunity. Journal of Virology, 79(1): 17−27. doi: 10.1128/JVI.79.1.17-27.2005
    [48]
    Medvedovic J, Ebert A, Tagoh H, et al. 2011. Pax5: a master regulator of B cell development and leukemogenesis. Advances in Immunology, 111: 179−206.
    [49]
    Mowat AM, Agace WW. 2014. Regional specialization within the intestinal immune system. Nature Reviews Immunology, 14(10): 667−685. doi: 10.1038/nri3738
    [50]
    Parikh K, Antanaviciute A, Fawkner-Corbett D, et al. 2019. Colonic epithelial cell diversity in health and inflammatory bowel disease. Nature, 567(7746): 49−55. doi: 10.1038/s41586-019-0992-y
    [51]
    Ricciotti E, Fitzgerald GA. 2011. Prostaglandins and inflammation. Arteriosclerosis, Thrombosis, and Vascular Biology, 31(5): 986−1000. doi: 10.1161/ATVBAHA.110.207449
    [52]
    Rodriguez PC, Ochoa AC, Al-Khami AA. 2017. Arginine metabolism in myeloid cells shapes innate and adaptive immunity. Frontiers in Immunology, 8: 93.
    [53]
    Seino Y, Miki T, Kiyonari H, et al. 2008. Isx participates in the maintenance of vitamin A metabolism by regulation of β-carotene 15, 15'-monooxygenase (Bcmo1) expression. Journal of Biological Chemistry, 283(8): 4905−4911. doi: 10.1074/jbc.M707928200
    [54]
    Shroyer NF, Wallis D, Venken KJT, et al. 2005. Gfi1 functions downstream of Math1 to control intestinal secretory cell subtype allocation and differentiation. Genes & Development, 19(20): 2412−2417.
    [55]
    Sicard JF, Le Bihan G, Vogeleer P, et al. 2017. Interactions of intestinal bacteria with components of the intestinal mucus. Frontiers in Cellular and Infection Microbiology, 7: 387. doi: 10.3389/fcimb.2017.00387
    [56]
    Smillie CS, Biton M, Ordovas-Montanes J, et al. 2019. Intra- and inter-cellular rewiring of the human colon during ulcerative colitis. Cell, 178(3): 714−730.e22. doi: 10.1016/j.cell.2019.06.029
    [57]
    Snoeck V, Goddeeris B, Cox E. 2005. The role of enterocytes in the intestinal barrier function and antigen uptake. Microbes and Infection, 7(7-8): 997−1004. doi: 10.1016/j.micinf.2005.04.003
    [58]
    Song J, Heijink IH, Kistemaker LEM, et al. 2017. Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD. Clinical Epigenetics, 9: 42. doi: 10.1186/s13148-017-0341-7
    [59]
    Specian RD, Oliver MG. 1991. Functional biology of intestinal goblet cells. American Journal of Physiology-Cell Physiology, 260(2 Pt 1): C183–C193.
    [60]
    Stokes CR, Bailey M, Haverson K, et al. 2004. Postnatal development of intestinal immune system in piglets: implications for the process of weaning. Animal Research, 53(4): 325−334. doi: 10.1051/animres:2004020
    [61]
    Stumpff F, Manneck D, Martens H. 2019. Unravelling the secrets of the caecum. Pflügers Archiv - European Journal of Physiology, 471(7): 925−926.
    [62]
    Su XM, Xu YL, Fox GC, et al. 2021. Breast cancer-derived GM-CSF regulates arginase 1 in myeloid cells to promote an immunosuppressive microenvironment. Journal of Clinical Investigation, 131(20): e145296. doi: 10.1172/JCI145296
    [63]
    Tang XP, Xiong KN, Fang RJ, et al. 2022. Weaning stress and intestinal health of piglets: a review. Frontiers in Immunology, 13: 1042778. doi: 10.3389/fimmu.2022.1042778
    [64]
    Topham NJ, Hewitt EW. 2009. Natural killer cell cytotoxicity: how do they pull the trigger?. Immunology, 128(1): 7−15. doi: 10.1111/j.1365-2567.2009.03123.x
    [65]
    Tunçer S, Sade-Memişoğlu A, Keşküş AG, et al. 2020. Enhanced expression of HNF4αduring intestinal epithelial differentiation is involved in the activation of ER stress. The FEBS Journal, 287(12): 2504−2523. doi: 10.1111/febs.15152
    [66]
    Van de Sande B, Flerin C, Davie K, et al. 2020. A scalable SCENIC workflow for single-cell gene regulatory network analysis. Nature Protocols, 15(7): 2247−2276. doi: 10.1038/s41596-020-0336-2
    [67]
    van der Flier LG, Haegebarth A, Stange DE, et al. 2009. OLFM4 is a robust marker for stem cells in human intestine and marks a subset of colorectal cancer cells. Gastroenterology, 137(1): 15−17. doi: 10.1053/j.gastro.2009.05.035
    [68]
    Wan WZ, Liu Q, Lionakis MS, et al. 2015. Atypical chemokine receptor 1 deficiency reduces atherogenesis in ApoE-knockout mice. Cardiovascular Research, 106(3): 478−487. doi: 10.1093/cvr/cvv124
    [69]
    Wang YL, Song WL, Wang JL, et al. 2020. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. Journal of Experimental Medicine, 217(2): e20191130. doi: 10.1084/jem.20191130
    [70]
    Wiertsema SP, van Bergenhenegouwen J, Garssen J, et al. 2021. The Interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies. Nutrients, 13(3): 886. doi: 10.3390/nu13030886
    [71]
    Wolf FA, Hamey FK, Plass M, et al. 2019. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology, 20(1): 59. doi: 10.1186/s13059-019-1663-x
    [72]
    Yang L, Yang HY, Chu YX, et al. 2021. CREPT is required for murine stem cell maintenance during intestinal regeneration. Nature Communications, 12(1): 270. doi: 10.1038/s41467-020-20636-9
    [73]
    Yao YC, Yao JY, Boström KI. 2019. SOX transcription factors in endothelial differentiation and endothelial-mesenchymal transitions. Frontiers in Cardiovascular Medicine, 6: 30. doi: 10.3389/fcvm.2019.00030
    [74]
    Zhang MM, Wu CC. 2020. The relationship between intestinal goblet cells and the immune response. Bioscience Reports, 40(10): BSR20201471. doi: 10.1042/BSR20201471
    [75]
    Zheng L, Duarte ME, Sevarolli Loftus A, et al. 2021. Intestinal health of pigs upon weaning: challenges and nutritional intervention. Frontiers in Veterinary Science, 8: 628258. doi: 10.3389/fvets.2021.628258
    [76]
    Zhu YL, Zhou ZM, Huang T, et al. 2022. Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs. Science China Life Sciences, 65(8): 1517−1534. doi: 10.1007/s11427-021-2034-5
    [77]
    Zorn AM, Wells JM. 2009. Vertebrate endoderm development and organ formation. Annual Review of Cell and Developmental Biology, 25: 221−251. doi: 10.1146/annurev.cellbio.042308.113344
    • Relative Articles
    • Supplements(1)
  • ZR-2023-007-Supplementary Materials.pdf
    • Cited By
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(7)

    Get Citation
    PDF
    XML

    Article Metrics

    Article views (402) PDF downloads(45) Cited by()
    Proportional views
    Related

    Content

    For Authors

    About ZR

    Copyright © 2016 Editorial Office of ZOOLOGICAL RESEARCH

    滇ICP备05000723号-2滇公网安备 53010202000944号

    Supported by: Beijing Renhe Information Technology Co. Ltd  

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return