Spatially resolved transcriptomics reveals pro-inflammatory fibroblast involved in lymphocyte recruitment through CXCL8 and CXCL10

The interplay among different cells in a tissue is essential for maintaining homeostasis. Although disease states have been traditionally attributed to individual cell types, increasing evidence and new therapeutic options have demonstrated the primary role of multicellular functions to understand health and disease, opening new avenues to understand pathogenesis and develop new treatment strategies. We recently described the cellular composition and dynamics of the human oral mucosa; however, the spatial arrangement of cells is needed to better understand a morphologically complex tissue. Here, we link single-cell RNA sequencing, spatial transcriptomics, and high-resolution multiplex fluorescence in situ hybridisation to characterise human oral mucosa in health and oral chronic inflammatory disease. We deconvolved expression for resolution enhancement of spatial transcriptomic data and defined highly specialised epithelial and stromal compartments describing location-specific immune programs. Furthermore, we spatially mapped a rare pathogenic fibroblast population localised in a highly immunogenic region, responsible for lymphocyte recruitment through CXCL8 and CXCL10 and with a possible role in pathological angiogenesis through ALOX5AP. Collectively, our study provides a comprehensive reference for the study of oral chronic disease pathogenesis.

[1]  L. Nibali,et al.  Expression of periodontitis susceptibility genes in human gingiva using single-cell RNA sequencing. , 2022, Journal of periodontal research.

[2]  Q. Phan,et al.  Parallel single cell multi-omics analysis of neonatal skin reveals transitional fibroblast states that restricts differentiation into distinct fates. , 2021, The Journal of investigative dermatology.

[3]  B. Stockinger,et al.  Regulation of intestinal immunity and tissue repair by enteric glia , 2021, Nature.

[4]  K. Mishima,et al.  Structure of junctional epithelium is maintained by cell populations supplied from multiple stem cells , 2021, Scientific Reports.

[5]  N. Rosenthal,et al.  Fibroblasts: Origins, definitions, and functions in health and disease , 2021, Cell.

[6]  M. Haniffa,et al.  Human oral mucosa cell atlas reveals a stromal-neutrophil axis regulating tissue immunity , 2021, Cell.

[7]  Raphael Gottardo,et al.  Spatial transcriptomics at subspot resolution with BayesSpace , 2021, Nature Biotechnology.

[8]  G. Kollias,et al.  Fibroblasts as immune regulators in infection, inflammation and cancer , 2021, Nature Reviews Immunology.

[9]  Daniel S. Chertow,et al.  SARS-CoV-2 infection of the oral cavity and saliva , 2021, Nature Medicine.

[10]  Alison Simmons,et al.  Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution: Supplementary Data , 2021 .

[11]  N. Ashley,et al.  Spatiotemporal analysis of human intestinal development at single-cell resolution , 2021, Cell.

[12]  Guocheng Yuan,et al.  Giotto, a toolbox for integrative analysis and visualization of spatial expression data , 2020 .

[13]  J. Helms,et al.  The Junctional Epithelium Is Maintained by a Stem Cell Population , 2020, Journal of dental research.

[14]  P. Sharpe,et al.  Defining human mesenchymal and epithelial heterogeneity in response to oral inflammatory disease , 2020, bioRxiv.

[15]  I. Amit,et al.  Lgr5+ telocytes are a signaling source at the intestinal villus tip , 2020, Nature Communications.

[16]  Y. Saeys,et al.  NicheNet: modeling intercellular communication by linking ligands to target genes , 2019, Nature Methods.

[17]  O. Klein,et al.  Heterogeneity within Stratified Epithelial Stem Cell Populations Maintains the Oral Mucosa in Response to Physiological Stress. , 2019, Cell stem cell.

[18]  Aviv Regev,et al.  Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis , 2019, Cell.

[19]  S. Raychaudhuri,et al.  Distinct fibroblast subsets drive inflammation and damage in arthritis , 2019, Nature.

[20]  K. Divaris,et al.  What Is the Heritability of Periodontitis? A Systematic Review , 2019, Journal of dental research.

[21]  R. Satija,et al.  Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression , 2019, Genome Biology.

[22]  Allon M. Klein,et al.  Quantitative Clonal Analysis and Single-Cell Transcriptomics Reveal Division Kinetics, Hierarchy, and Fate of Oral Epithelial Progenitor Cells. , 2019, Cell stem cell.

[23]  Christoph Hafemeister,et al.  Comprehensive integration of single cell data , 2018, bioRxiv.

[24]  Quin F. Wills,et al.  Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease , 2018, Cell.

[25]  Marie-Liesse Asselin-Labat,et al.  Transcriptional signature primes human oral mucosa for rapid wound healing , 2018, Science Translational Medicine.

[26]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[27]  S. Itzkovitz,et al.  Subepithelial telocytes are an important source of Wnts that supports intestinal crypts , 2018, Nature.

[28]  David J. Jörg,et al.  Defining murine organogenesis at single cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation , 2018, Nature Cell Biology.

[29]  G. Kollias,et al.  Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions , 2017, Nature Communications.

[30]  N. Dutzan,et al.  Characterization of the human immune cell network at the gingival barrier , 2015, Mucosal Immunology.

[31]  Piero Carninci,et al.  A draft network of ligand–receptor-mediated multicellular signalling in human , 2015, Nature Communications.

[32]  Ruslan Medzhitov,et al.  Homeostasis, Inflammation, and Disease Susceptibility , 2015, Cell.

[33]  K. Brogden,et al.  Human oral mucosa , 2015 .

[34]  Z. Werb,et al.  Remodelling the extracellular matrix in development and disease , 2014, Nature Reviews Molecular Cell Biology.

[35]  L. Yin,et al.  The versatile functions of Sox9 in development, stem cells, and human diseases , 2014, Genes & diseases.

[36]  Angela Garding,et al.  Gene regulation and priming by topoisomerase IIα in embryonic stem cells , 2013, Nature Communications.

[37]  R. Shoemaker,et al.  An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype , 2013, Genome Medicine.

[38]  C. Reyes-Aldasoro,et al.  Cxcl8 (IL-8) Mediates Neutrophil Recruitment and Behavior in the Zebrafish Inflammatory Response , 2013, The Journal of Immunology.

[39]  Edward Y. Chen,et al.  Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.

[40]  David Haussler,et al.  The UCSC genome browser and associated tools , 2012, Briefings Bioinform..

[41]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[42]  A. Zlotnik,et al.  The chemokine superfamily revisited. , 2012, Immunity.

[43]  V. Hakim,et al.  Different cell fates from cell-cell interactions: core architectures of two-cell bistable networks. , 2012, Biophysical journal.

[44]  Z. Lee,et al.  CXCL10 and autoimmune diseases. , 2009, Autoimmunity reviews.

[45]  M. Rotondi,et al.  Role of chemokines in endocrine autoimmune diseases. , 2007, Endocrine reviews.

[46]  P. Sharpe,et al.  The cutting-edge of mammalian development; how the embryo makes teeth , 2004, Nature Reviews Genetics.

[47]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[48]  D. Ota,et al.  Angiogenic Effects of Interleukin 8 (CXCL8) in Human Intestinal Microvascular Endothelial Cells Are Mediated by CXCR2* , 2003, The Journal of Biological Chemistry.

[49]  A. Luster,et al.  Chemokines--chemotactic cytokines that mediate inflammation. , 1998, The New England journal of medicine.

[50]  W. Ketterl [Periodontal diseases]. , 1971, Der Zahnarzt; Colloquium med. dent.