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Hua R, Qiao G, Chen G, Sun Z, Jia H, Li P, Zhang B, Qi F. Single-Cell RNA-Sequencing Analysis of Colonic Lamina Propria Immune Cells Reveals the Key Immune Cell-Related Genes of Ulcerative Colitis. J Inflamm Res 2023; 16:5171-5188. [PMID: 38026254 PMCID: PMC10649030 DOI: 10.2147/jir.s440076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Background Ulcerative colitis (UC) is a severe threat to humans worldwide. Single-cell RNA sequencing (scRNA-seq) can be used to screen gene expression patterns of each cell in the intestine, provide new insights into the potential mechanism of UC, and analyze the development of immune cell changes. These findings can provide new ideas for the diagnosis and treatment of intestinal diseases. In this study, bioinformatics analysis combined with experiments applied in dextran sulfate sodium (DSS)-induced colitis mice was used to explore new diagnostic genes for UC and their potential relationship with immune cells. Methods We downloaded microarray datasets (GSE75214, GSE87473, GSE92415) from the Gene Expression Omnibus and used these datasets to screen differentially expressed genes (DEGs) and conduct Weighted Gene Co-expression Network Analysis (WGCNA) after quality control. The hub genes were screened, and ROC curves were drawn to verify the reliability of the results in both training set (GSE75214, GSE87473, GSE92415) and validation cohort (GSE87466). Also, we explored the relation of diagnostic genes and immune cells by CIBERSORT algorithm and single-cell analysis. Finally, the expression of hub genes and their relation with immune cells were verified in DSS-induced colitis mice. Results Diagnostic genes (ANXA5, MMP7, NR1H4, CYP3A4, ABCG2) were identified. In addition, we found these five genes firmly related to immune infiltration. The DSS-induced colitis mice confirm that the expression of ANXA5 mainly increased in the intestinal macrophages and had a strong negative correlation with M2 macrophages, which indicated its possible influence on the polarization of macrophages in UC patients. Conclusion We identified ANXA5, MMP7, NR1H4, CYP3A4, and ABCG2 as diagnostic genes of UC that are closely related to immune infiltration and ANXA5 maintains a negative correlation with M2 macrophages which indicated its possible influence on the polarization of macrophage in UC patients.
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Affiliation(s)
- Run Hua
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Gangjie Qiao
- Department of Colorectal Surgery, Shanxi Provincial People’s Hospital, Shanxi, People’s Republic of China
| | - Guoshan Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Zhaonan Sun
- General Surgery Department, Tianjin Medical University General Hospital Airport Hospital, Tianjin, People’s Republic of China
| | - Haowen Jia
- General Surgery Department, Tianjin Medical University General Hospital Airport Hospital, Tianjin, People’s Republic of China
| | - Peiyuan Li
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Baotong Zhang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Feng Qi
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
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2
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Gu M, Samuelson DR, de la Rua NM, Charles TP, Taylor CM, Luo M, Siggins RW, Shellito JE, Welsh DA. Host innate and adaptive immunity shapes the gut microbiota biogeography. Microbiol Immunol 2022; 66:330-341. [PMID: 35067963 DOI: 10.1111/1348-0421.12963] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
The gut microbiota has a fundamental role in the development and the maturation of the host immune system. Both innate and adaptive immune cells have critical functions in microbial pathogen containment and clearance, but the regulation of the commensal microbiome ecosystem in the gastrointestinal tract by these major immune cell populations is incompletely defined. We investigated the role of specific innate and adaptive immune cell in the regulation of the microbiota in the intestinal tract biogeographically. Dendritic cells, macrophages, CD4+ T-cells, CD8+ T-cells, and B-cells were depleted using monoclonal antibodies and clodronate liposomes, and the microbial communities was determined by 16S rRNA gene sequencing. With specific immune cell depletion, distinct microbiota changes were observed. In general, immune cell depleted mice had higher microbiota richness and evenness at all gut anatomical sites. At each gut segment, samples from immune cell-depleted animals clustered away from the Isotype/Liposome control mice. This was especially dramatic for small intestinal microbiota. Specifically, Enterobacteriaceae, Bacteroides acidifaciens and Mucispirillum schaedleri were highly enriched in the mucosa and lumen of the small intestine in immune cell-deficient animals. Further, the mucosal microbiota had higher microbiota evenness compared to luminal microbiota at all gut segments, and the UniFrac distance between B cell depleted and isotype control mice was the largest in duodenum followed by ileum and colon. Taken together, our data suggest that innate and adaptive immune cells specifically contribute to the regulation of the gut microbiota's biogeographical distribution along the gastrointestinal tract, and microbiota in duodenum mucosa are more responsive to host immune changes compared to other anatomical sites. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Min Gu
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Derrick R Samuelson
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Internal Medicine, Division of Pulmonary, Critical Care, & Sleep, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicholas M de la Rua
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Tysheena P Charles
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Meng Luo
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Robert W Siggins
- Department of Physiology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Judd E Shellito
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - David A Welsh
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
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Koscsó B, Kurapati S, Rodrigues RR, Nedjic J, Gowda K, Shin C, Soni C, Ashraf AZ, Purushothaman I, Palisoc M, Xu S, Sun H, Chodisetti SB, Lin E, Mack M, Kawasawa YI, He P, Rahman ZSM, Aifantis I, Shulzhenko N, Morgun A, Bogunovic M. Gut-resident CX3CR1 hi macrophages induce tertiary lymphoid structures and IgA response in situ. Sci Immunol 2020; 5:5/46/eaax0062. [PMID: 32276965 DOI: 10.1126/sciimmunol.aax0062] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 12/27/2019] [Accepted: 02/28/2020] [Indexed: 12/12/2022]
Abstract
Intestinal mononuclear phagocytes (MPs) are composed of heterogeneous dendritic cell (DC) and macrophage subsets necessary for the initiation of immune response and control of inflammation. Although MPs in the normal intestine have been extensively studied, the heterogeneity and function of inflammatory MPs remain poorly defined. We performed phenotypical, transcriptional, and functional analyses of inflammatory MPs in infectious Salmonella colitis and identified CX3CR1+ MPs as the most prevalent inflammatory cell type. CX3CR1+ MPs were further divided into three distinct populations, namely, Nos2 +CX3CR1lo, Ccr7 +CX3CR1int (lymph migratory), and Cxcl13 +CX3CR1hi (mucosa resident), all of which were transcriptionally aligned with macrophages and derived from monocytes. In follow-up experiments in vivo, intestinal CX3CR1+ macrophages were superior to conventional DC1 (cDC1) and cDC2 in inducing Salmonella-specific mucosal IgA. We next examined spatial organization of the immune response induced by CX3CR1+ macrophage subsets and identified mucosa-resident Cxcl13 +CX3CR1hi macrophages as the antigen-presenting cells responsible for recruitment and activation of CD4+ T and B cells to the sites of Salmonella invasion, followed by tertiary lymphoid structure formation and the local pathogen-specific IgA response. Using mice we developed with a floxed Ccr7 allele, we showed that this local IgA response developed independently of migration of the Ccr7 +CX3CR1int population to the mesenteric lymph nodes and contributed to the total mucosal IgA response to infection. The differential activity of intestinal macrophage subsets in promoting mucosal IgA responses should be considered in the development of vaccines to prevent Salmonella infection and in the design of anti-inflammatory therapies aimed at modulating macrophage function in inflammatory bowel disease.
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Affiliation(s)
- Balázs Koscsó
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sravya Kurapati
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.,Biomedical Sciences PhD Program, Penn State University College of Medicine, Hershey, PA, USA
| | | | - Jelena Nedjic
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Kavitha Gowda
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Changsik Shin
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Chetna Soni
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Azree Zaffran Ashraf
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Indira Purushothaman
- PhD Program in Anatomy at Penn State College of Medicine, Penn State University College of Medicine, Hershey, PA, USA
| | - Maryknoll Palisoc
- MD/PhD Medical Scientist Training Program, Penn State University College of Medicine, Hershey, PA, USA
| | - Sulei Xu
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Haoyu Sun
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Sathi Babu Chodisetti
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Eugene Lin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Matthias Mack
- Department of Internal Medicine/Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Yuka Imamura Kawasawa
- Department of Pharmacology and Biochemistry and Molecular Biology, Institute of Personalized Medicine, Penn State University College of Medicine, Hershey, PA, USA
| | - Pingnian He
- Department of Cellular and Molecular Physiology, Penn State University College of Medicine, Hershey, PA, USA
| | - Ziaur S M Rahman
- Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY, USA
| | - Natalia Shulzhenko
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Milena Bogunovic
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Microbiology and Immunology, Penn State University College of Medicine, Hershey, PA, USA.,Inflammatory Bowel Disease Center, Milton S. Hershey Medical Center, Hershey, PA, USA
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4
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Chulkina MM, Pichugin AV, Ataullakhanov RI. Pharmaceutical grade synthetic peptide Thr-Glu-Lys-Lys-Arg-Arg-Glu-Thr-Val-Glu-Arg-Glu-Lys-Glu ameliorates DSS-induced murine colitis by reducing the number and pro-inflammatory activity of colon tissue-infiltrating Ly6G + granulocytes and Ly6C + monocytes. Peptides 2020; 132:170364. [PMID: 32621844 DOI: 10.1016/j.peptides.2020.170364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023]
Abstract
A pharmaceutical grade synthetic tetradecapeptide Thr-Glu-Lys-Lys-Arg-Arg-Glu-Thr-Val-Glu-Arg-Glu-Lys-Glu (GEPON) that mimics the ezrin protein hinge region was studied in dextran sodium sulphate-induced murine experimental colitis (DSS colitis). We report that GEPON intraperitoneal injections significantly attenuated DSS-induced pathological manifestations in the large intestine, bloody diarrhoea, and body weight loss in C57BL/6 mice. GEPON markedly inhibited the transcription rate of pro-inflammatory Il1b, Il6, and Nos2 genes in the colon tissue, in contrast with those encoding anti-inflammatory factors, such as Tgfb1, I10, and Arg1, whose transcription rate did not change significantly. Using flow cytometry, we found that GEPON treatment significantly reduced the accumulation of Ly6G+ granulocytes and Ly6C+ monocytes in the colon infiltrate of DSS colitis mice. Analysis of the mRNA level in myeloid cells sorted from the colon tissue revealed that GEPON had decreased the expression of pro-inflammatory genes in both colon-infiltrating Ly6G+ granulocytes and Ly6C+ monocytes, but not in Ly6C-CD64+ macrophages of DSS-treated mice. The direct anti-inflammatory impact of GEPON was shown in an in vitro culture of Ly6C+ monocytes, as evidenced by an inhibition of IL-1 beta and IL-6 mRNA expression. Taken together, our results demonstrated that GEPON had a pronounced therapeutic effect on ulcerative colitis in a laboratory mice model and provided evidence of its curative efficacy via inhibition of colon tissue inflammation by decreasing Ly6G+ granulocyte and Ly6C+ monocyte infiltration and by reducing their pro-inflammatory activities.
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Affiliation(s)
- M M Chulkina
- National Research Center - Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russia.
| | - A V Pichugin
- National Research Center - Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - R I Ataullakhanov
- National Research Center - Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, Russia.
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5
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D'Orazio SEF. Innate and Adaptive Immune Responses during Listeria monocytogenes Infection. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0065-2019. [PMID: 31124430 PMCID: PMC11086964 DOI: 10.1128/microbiolspec.gpp3-0065-2019] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 12/15/2022] Open
Abstract
It could be argued that we understand the immune response to infection with Listeria monocytogenes better than the immunity elicited by any other bacteria. L. monocytogenes are Gram-positive bacteria that are genetically tractable and easy to cultivate in vitro, and the mouse model of intravenous (i.v.) inoculation is highly reproducible. For these reasons, immunologists frequently use the mouse model of systemic listeriosis to dissect the mechanisms used by mammalian hosts to recognize and respond to infection. This article provides an overview of what we have learned over the past few decades and is divided into three sections: "Innate Immunity" describes how the host initially detects the presence of L. monocytogenes and characterizes the soluble and cellular responses that occur during the first few days postinfection; "Adaptive Immunity" discusses the exquisitely specific T cell response that mediates complete clearance of infection and immunological memory; "Use of Attenuated Listeria as a Vaccine Vector" highlights the ways that investigators have exploited our extensive knowledge of anti-Listeria immunity to develop cancer therapeutics.
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Affiliation(s)
- Sarah E F D'Orazio
- University of Kentucky, Microbiology, Immunology & Molecular Genetics, Lexington, KY 40536-0298
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6
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Qiu Z, Sheridan BS. Isolating Lymphocytes from the Mouse Small Intestinal Immune System. J Vis Exp 2018. [PMID: 29553537 DOI: 10.3791/57281] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The intestinal immune system plays an essential role in maintaining the barrier function of the gastrointestinal tract by generating tolerant responses to dietary antigens and commensal bacteria while mounting effective immune responses to enteropathogenic microbes. In addition, it has become clear that local intestinal immunity has a profound impact on distant and systemic immunity. Therefore, it is important to study how an intestinal immune response is induced and what the immunologic outcome of the response is. Here, a detailed protocol is described for the isolation of lymphocytes from small intestine inductive sites like the gut-associated lymphoid tissue Peyer's patches and the draining mesenteric lymph nodes and effector sites like the lamina propria and the intestinal epithelium. This technique ensures isolation of a large numbers of lymphocytes from small intestinal tissues with optimal purity and viability and minimal cross compartmental contamination within acceptable time constraints. The technical capability to isolate lymphocytes and other immune cells from intestinal tissues enables the understanding of immune responses to gastrointestinal infections, cancers, and inflammatory diseases.
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Affiliation(s)
- Zhijuan Qiu
- Center for Infectious Diseases, Department of Molecular Genetics and Microbiology, Stony Brook University
| | - Brian S Sheridan
- Center for Infectious Diseases, Department of Molecular Genetics and Microbiology, Stony Brook University;
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