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Lötstedt B, Stražar M, Xavier R, Regev A, Vickovic S. Spatial host-microbiome sequencing reveals niches in the mouse gut. Nat Biotechnol 2023:10.1038/s41587-023-01988-1. [PMID: 37985876 DOI: 10.1038/s41587-023-01988-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/12/2023] [Indexed: 11/22/2023]
Abstract
Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host-microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host-microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host-bacteria interactions. SHM-seq should enhance the study of native host-microbe interactions in health and disease.
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Affiliation(s)
- Britta Lötstedt
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
- New York Genome Center, New York, NY, USA
| | | | - Ramnik Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts, General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Genentech, South San Francisco, CA, USA.
| | - Sanja Vickovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- New York Genome Center, New York, NY, USA.
- Department of Biomedical Engineering and Herbert Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA.
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Beijer Laboratory for Gene and Neuro Research, Uppsala University, Uppsala, Sweden.
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Blackburn JB, Schaff JA, Gutor S, Du RH, Nichols D, Sherrill T, Gutierrez AJ, Xin MK, Wickersham N, Zhang Y, Holtzman MJ, Ware LB, Banovich NE, Kropski JA, Blackwell TS, Richmond BW. Secretory Cells Are the Primary Source of pIgR in Small Airways. Am J Respir Cell Mol Biol 2022; 67:334-345. [PMID: 35687143 PMCID: PMC9447142 DOI: 10.1165/rcmb.2021-0548oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Loss of secretory IgA (SIgA) is common in chronic obstructive pulmonary disease (COPD) small airways and likely contributes to disease progression. We hypothesized that loss of SIgA results from reduced expression of pIgR (polymeric immunoglobulin receptor), a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium. pIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA in situ hybridization, immunostaining, and single-cell RNA sequencing. Complementary studies in mice used immunostaining, primary murine tracheal epithelial cell culture, and transgenic mice with secretory or ciliated cell-specific knockout of pIgR. SIgA degradation by human neutrophil elastase or secreted bacterial proteases from nontypeable Haemophilus influenzae was evaluated in vitro. We found that secretory cells are the predominant cell type responsible for pIgR expression in human and murine airways. Loss of SIgA in small airways was not associated with a reduction in secretory cells but rather a reduction in pIgR protein expression despite intact PIGR mRNA expression. Neutrophil elastase and nontypeable H. influenzae-secreted proteases are both capable of degrading SIgA in vitro and may also contribute to a deficient SIgA immunobarrier in COPD. Loss of the SIgA immunobarrier in small airways of patients with severe COPD is complex and likely results from both pIgR-dependent defects in IgA transcytosis and SIgA degradation.
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Affiliation(s)
- Jessica B. Blackburn
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Jacob A. Schaff
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Sergey Gutor
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Rui-Hong Du
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - David Nichols
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Taylor Sherrill
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | | | - Matthew K. Xin
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Nancy Wickersham
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Yong Zhang
- Division of Pulmonary and Critical Care Medicine, Washington University–St. Louis, St. Louis, Missouri
| | - Michael J. Holtzman
- Division of Pulmonary and Critical Care Medicine, Washington University–St. Louis, St. Louis, Missouri
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | | | - Jonathan A. Kropski
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Timothy S. Blackwell
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Bradley W. Richmond
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
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Abstract
The immune system in the large intestine is separated from commensal microbes and comparatively rare enteric pathogens by a monolayer of diverse epithelial cells overlaid with a compact and adherent inner mucus layer and a looser outer mucus layer. Microorganisms, collectively referred to as the mucus-associated (MA) microbiota, physically inhabit this mucus barrier, resulting in a dynamic and incessant dialog to maintain both spatial segregation and immune tolerance. Recent major findings reveal novel features of the crosstalk between the immune system and mucus-associated bacteria in health and disease, as well as disease-related peripheral immune signatures indicative of host responses to these organisms. In this brief review, we integrate these novel observations into our overall understanding of host-microbiota mutualism at the colonic mucosal border and speculate on the significance of this emerging knowledge for our understanding of the prevention, development, and progression of chronic intestinal inflammation.
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Affiliation(s)
- Qing Zhao
- Department of Medicine, University of Alabama at Birmingham, Birmingham, 35294, USA,CONTACT Qing Zhao University of Alabama at Birmingham, Birmingham, AL, 35294
| | - Craig L. Maynard
- Department of Medicine, University of Alabama at Birmingham, Birmingham, 35294, USA,Department of Pathology, University of Alabama at Birmingham, Birmingham, 35294, USA,Craig L. Maynard Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294
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The Fast Track for Intestinal Tumor Cell Differentiation and In Vitro Intestinal Models by Inorganic Topographic Surfaces. Pharmaceutics 2022; 14:pharmaceutics14010218. [PMID: 35057113 PMCID: PMC8781367 DOI: 10.3390/pharmaceutics14010218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 11/17/2022] Open
Abstract
Three-dimensional (3D) complex in vitro cell systems are well suited to providing meaningful and translatable results in drug screening, toxicity measurements, and biological studies. Reliable complex gastrointestinal in vitro models as a testbed for oral drug administration and toxicity are very valuable in achieving predictive results for clinical trials and reducing animal testing. However, producing these models is time-consuming due to the lengthy differentiation of HT29 or other cells into mucus-producing goblet cells or other intestinal cell lineages. In the present work, HT29 cells were grown on an inorganic topographic surface decorated with a periodic pattern of micrometre-sized amorphous SiO2 structures for up to 35 days. HT29 cells on topographic surfaces were compared to undifferentiated HT29 in glucose-containing medium on glass or culture dish and with HT29 cells differentiated for 30 days in the presence of methotrexate (HT29-MTX). The cells were stained with Alcian blue for mucus, antibodies for mucus 2 (goblet cells), villin (enterocytes), lysozyme (Paneth cells), and FITC-labeled lectins to identify different cells, glycomic profiles, and cell features. We observed that HT29 cells on topographic surfaces showed more similarities with the differentiated HT29-MTX than with undifferentiated HT29. They formed islands of cell clusters, as observed for HT29-MTX. Already after 2 days, the first mucus secretion was shown by Alcian blue stain and FITC-wheat germ agglutinin. After 4–6 days, mucus was observed on the cell surface and in the intercellular space. The cell layer was undulated, and in 3D reconstruction, the cells showed a clear polarisation with a strong actin signal to one membrane. The lectins and the antibody-staining confirmed the heterogeneous composition of differentiated HT29 cells on topographic surfaces after 6–8 days, or after 6–8 days following MTX differentiation (30 days).
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LaCourse KD, Johnston CD, Bullman S. The relationship between gastrointestinal cancers and the microbiota. Lancet Gastroenterol Hepatol 2021; 6:498-509. [PMID: 33743198 PMCID: PMC10773981 DOI: 10.1016/s2468-1253(20)30362-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
The contribution of the microbiota to disease progression and treatment efficacy is often neglected when determining who is at the highest risk of developing gastrointestinal cancers or designing treatment strategies for patients. We reviewed the current literature on the effect of the human microbiota on cancer risk, prognosis, and treatment efficacy. We highlight emerging research that seeks to identify microbial signatures as biomarkers for various gastrointestinal cancers, and discuss how we could harness knowledge of the microbiome to detect, prevent, and treat these cancers. Finally, we outline further research needed in the field of gastrointestinal cancers and the microbiota, and describe the efforts required to increase the accuracy and reproducibility of data linking the microbiome to cancer.
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Affiliation(s)
- Kaitlyn D LaCourse
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher D Johnston
- Vaccine and Infection Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Adade EE, Al Lakhen K, Lemus AA, Valm AM. Recent progress in analyzing the spatial structure of the human microbiome: distinguishing biogeography and architecture in the oral and gut communities. CURRENT OPINION IN ENDOCRINE AND METABOLIC RESEARCH 2021; 18:275-283. [PMID: 35936977 PMCID: PMC9351436 DOI: 10.1016/j.coemr.2021.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fueled by technological advances in methods for sample collection and preservation in sequencing studies, and in advances in computational analyses of high content image data, the spatial structure of the human microbiome is coming to light. In this mini-review, we summarize recent developments in our understanding of the structure of two human microbiomes: the lower gut and the oral cavity. We focus on only the most recent literature and we make an important distinction between two forms of spatial structure, governed by scale: biogeography and architecture. By segmenting the study of microbiome spatial structure into two categories, we demonstrate the potential to greatly advance our understanding of the mechanistic principles that link structure and function in the microbiome.
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Affiliation(s)
- Emmanuel E. Adade
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA
| | - Khalid Al Lakhen
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA
| | - Alex A. Lemus
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA
| | - Alex M. Valm
- Department of Biological Sciences, State University of New York at Albany, Albany, NY 12222 USA,Corresponding author.
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Marincola Smith P, Choksi YA, Markham NO, Hanna DN, Zi J, Weaver CJ, Hamaamen JA, Lewis KB, Yang J, Liu Q, Kaji I, Means AL, Beauchamp RD. Colon epithelial cell TGFβ signaling modulates the expression of tight junction proteins and barrier function in mice. Am J Physiol Gastrointest Liver Physiol 2021; 320:G936-G957. [PMID: 33759564 PMCID: PMC8285585 DOI: 10.1152/ajpgi.00053.2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Defective barrier function is a predisposing factor in inflammatory bowel disease (IBD) and colitis-associated cancer (CAC). Although TGFβ signaling defects have been associated with IBD and CAC, few studies have examined the relationship between TGFβ and intestinal barrier function. Here, we examine the role of TGFβ signaling via SMAD4 in modulation of colon barrier function. The Smad4 gene was conditionally deleted in the intestines of adult mice and intestinal permeability assessed using an in vivo 4 kDa FITC-Dextran (FD4) permeability assay. Mouse colon was isolated for gene expression (RNA-sequencing), Western blot, and immunofluorescence analysis. In vitro colon organoid culture was utilized to assess junction-related gene expression by qPCR and transepithelial resistance (TER). In silico analyses of human IBD and colon cancer databases were performed. Mice lacking intestinal expression of Smad4 demonstrate increased colonic permeability to FD4 without gross mucosal damage. mRNA/protein expression analyses demonstrate significant increases in Cldn2/Claudin 2 and Cldn8/Claudin 8, and decreases in Cldn3, Cldn4, and Cldn7/Claudin 7 with intestinal SMAD4 loss in vivo without changes in Claudin protein localization. TGFβ1/BMP2 treatment of polarized SMAD4+ colonoids increases TER. Cldn2, Cldn4, Cldn7, and Cldn8 are regulated by canonical TGFβ signaling, and TGFβ-dependent regulation of these genes is dependent on nascent RNA transcription (Cldn2, Cldn4, Cldn8) but not nascent protein translation (Cldn4, Cldn8). Human IBD/colon cancer specimens demonstrate decreased SMAD4, CLDN4, CLDN7, and CLDN8 and increased CLDN2 compared with healthy controls. Canonical TGFβ signaling modulates the expression of tight junction proteins and barrier function in mouse colon.NEW & NOTEWORTHY We demonstrate that canonical TGFβ family signaling modulates the expression of critical tight junction proteins in colon epithelial cells, and that expression of these tight junction proteins is associated with maintenance of colon epithelial barrier function in mice.
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Affiliation(s)
- Paula Marincola Smith
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee,2Graduate Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yash A. Choksi
- 3Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,4Veterans Affairs Hospital, Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Nicholas O. Markham
- 3Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,5Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee,6Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David N. Hanna
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jinghuan Zi
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Connie J. Weaver
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jalal A. Hamaamen
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Keeli B. Lewis
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jing Yang
- 7Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee,8Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qi Liu
- 7Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee,8Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Izumi Kaji
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee,5Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anna L. Means
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee,2Graduate Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,6Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee,9Vanderbilt Ingram Cancer Center, Vanderbilt University
Medical Center, Nashville, Tennessee,10Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - R. Daniel Beauchamp
- 1Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee,2Graduate Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee,5Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, Tennessee,6Digestive Disease Research Center, Vanderbilt University Medical Center, Nashville, Tennessee,9Vanderbilt Ingram Cancer Center, Vanderbilt University
Medical Center, Nashville, Tennessee,10Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
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