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Yue C, Xue H. Identification and immune landscape of sarcopenia-related molecular clusters in inflammatory bowel disease by machine learning and integrated bioinformatics. Sci Rep 2024; 14:17603. [PMID: 39079987 PMCID: PMC11289443 DOI: 10.1038/s41598-024-68198-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Sarcopenia, a prevalent comorbidity of inflammatory bowel disease (IBD), is characterized by diminished skeletal muscle mass and strength. Nevertheless, the underlying interconnected mechanisms remain elusive. This study identified distinct expression patterns of sarcopenia-associated genes (SRGs) across individuals with IBD and in samples of normal tissue. By analyzing SRG expression profiles, we effectively segregated 541 IBD samples into three distinct clusters, each marked by its unique immune landscape. To unravel the transcriptional disruptions underlying these clusters, the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm was employed to spotlight key genes linked to each cluster. A diagnostic model based on four key genes (TIMP1, PLAU, PHLDA1, TGFBI) was established using Random Forest and LASSO (least absolute shrinkage and selection operator) algorithms, and validated with the GSE179285 dataset. Moreover, the GSE112366 dataset facilitated the exploration of gene expression dynamics within the ileum mucosa of UC patients pre- and post-Ustekinumab treatment. Additionally, insights into the intricate relationship between immune cells and these pivotal genes were gleaned from the single-cell RNA dataset GSE162335. In conclusion, our findings collectively underscored the pivotal role of sarcopenia-related genes in the pathogenesis of IBD. Their potential as robust biomarkers for future diagnostic and therapeutic strategies is particularly promising, opening avenues for a deeper understanding and improved management of these interconnected conditions.
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Affiliation(s)
- Chongkang Yue
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Middle Shandong Road, Shanghai, 200001, China
- Department of Gastroenterology, Shanghai Punan Hospital of Pudong New District, Shanghai, China, 200120
| | - Huiping Xue
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Middle Shandong Road, Shanghai, 200001, China.
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Cao S, Nguyen K, Ma K, Du X, Liu X, Antonova AU, Rood RP, Gremida A, Chen CH, Gutierrez A, Rubin DC, Gregory MH, Gergely M, Escudero GO, Huang K, Jaeger N, Cella M, Newberry RD, Davidson NO, Ciorba MA, Deepak P, Colonna M. Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets. Gastroenterology 2024:S0016-5085(24)05284-3. [PMID: 39084267 DOI: 10.1053/j.gastro.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/11/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND & AIMS The pathophysiology of Crohn's-like disease of the pouch (CDP) in patients with a history of ulcerative colitis (UC) is unknown. We examined mucosal cells from patients with and without CDP using single-cell analyses. METHODS Endoscopic samples were collected from pouch body and prepouch ileum (pouch/ileum) of 50 patients with an ileal pouch-anal anastomosis. Single-cell RNA sequencing was performed on pouch/ileal tissues of patients with normal pouch/ileum and CDP. Mass cytometry was performed on mucosal immune cells from patients with UC with normal pouch/ileum, CDP, pouchitis, and those with familial adenomatous polyposis after pouch formation. Findings were independently validated using immunohistochemistry. RESULTS The cell populations/states in the pouch body differed from those in the prepouch ileum, likely secondary to increased microbial burden. Compared with the familial adenomatous polyposis pouch, the UC pouch was enriched in colitogenic immune cells even without inflammation. CDP was characterized by increases in T helper 17 cells, inflammatory fibroblasts, inflammatory monocytes, TREM1+ monocytes, clonal expansion of effector T cells, and overexpression of T helper 17 cells-inducing cytokine genes such as IL23, IL1B, and IL6 by mononuclear phagocytes. Ligand-receptor analysis further revealed a stromal-mononuclear phagocytes-lymphocyte circuit in CDP. Integrated analysis showed that up-regulated immune mediators in CDP were similar to those in CD and pouchitis, but not UC. Additionally, CDP pouch/ileum exhibited heightened endoplasmic reticulum stress across all major cell compartments. CONCLUSIONS CDP likely represents a distinct entity of inflammatory bowel disease with heightened endoplasmic reticulum stress in both immune and nonimmune cells, which may become a novel diagnostic biomarker and therapeutic target for CDP.
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Affiliation(s)
- Siyan Cao
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri.
| | - Khai Nguyen
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Kaiming Ma
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Xiaotang Du
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Xiuli Liu
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Richard P Rood
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Anas Gremida
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Chien-Huan Chen
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Alexandra Gutierrez
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Deborah C Rubin
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Martin H Gregory
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Mate Gergely
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Guadalupe Oliva Escudero
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Katherine Huang
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marina Cella
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Rodney D Newberry
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Nicholas O Davidson
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Matthew A Ciorba
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Parakkal Deepak
- Division of Gastroenterology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri.
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Deka A, Kumar N, Basu S, Chawla M, Bhattacharya N, Ali SA, Bhawna, Madan U, Kumar S, Das B, Sengupta D, Awasthi A, Basak S. Non-canonical NF-κB signaling limits the tolerogenic β-catenin-Raldh2 axis in gut dendritic cells to exacerbate intestinal pathologies. EMBO J 2024:10.1038/s44318-024-00182-6. [PMID: 39060515 DOI: 10.1038/s44318-024-00182-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/12/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Dendritic cell (DC) dysfunction is known to exacerbate intestinal pathologies, but the mechanisms compromising DC-mediated immune regulation in this context remain unclear. Here, we show that intestinal dendritic cells from a mouse model of experimental colitis exhibit significant levels of noncanonical NF-κB signaling, which activates the RelB:p52 heterodimer. Genetic inactivation of this pathway in DCs alleviates intestinal pathologies in mice suffering from colitis. Deficiency of RelB:p52 diminishes transcription of Axin1, a critical component of the β-catenin destruction complex, reinforcing β-catenin-dependent expression of Raldh2, which imparts tolerogenic DC attributes by promoting retinoic acid synthesis. DC-specific impairment of noncanonical NF-κB signaling leads to increased colonic numbers of Tregs and IgA+ B cells, which promote luminal IgA production and foster eubiosis. Experimentally introduced β-catenin haploinsufficiency in DCs with deficient noncanonical NF-κB signaling moderates Raldh2 activity, reinstating colitogenic sensitivity in mice. Finally, inflammatory bowel-disease patients also display a deleterious noncanonical NF-κB signaling signature in intestinal DCs. In sum, we establish how noncanonical NF-κB signaling in dendritic cells can subvert retinoic acid synthesis to fuel intestinal inflammation.
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Affiliation(s)
- Alvina Deka
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Kumar
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swapnava Basu
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Meenakshi Chawla
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Namrata Bhattacharya
- Indraprastha Institute of Information Technology Delhi, New Delhi, India
- Australian Prostate Cancer Research Centre-Queensland, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Sk Asif Ali
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhawna
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Upasna Madan
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Shakti Kumar
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Bhabatosh Das
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Debarka Sengupta
- Indraprastha Institute of Information Technology Delhi, New Delhi, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Soumen Basak
- Systems Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Li ZY, Sun YH, Qian-Hua, Wang HY, Wang YJ, Miao-Jiang. Single-cell analysis of Crohn's disease: Unveiling heterogeneity and evaluating ustekinumab outcomes. J Gene Med 2024; 26:e3715. [PMID: 38962887 DOI: 10.1002/jgm.3715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND The present study aimed to dissect the cellular complexity of Crohn's disease (CD) using single-cell RNA sequencing, focusing on identifying key cell populations and their transcriptional profiles in inflamed tissue. METHODS We applied scRNA-sequencing to compare the cellular composition of CD patients with healthy controls, utilizing Seurat for clustering and annotation. Differential gene expression analysis and protein-protein interaction networks were constructed to identify crucial genes and pathways. RESULTS Our study identified eight distinct cell types in CD, highlighting crucial fibroblast and T cell interactions. The analysis revealed key cellular communications and identified significant genes and pathways involved in the disease's pathology. The role of fibroblasts was underscored by elevated expression in diseased samples, offering insights into disease mechanisms and potential therapeutic targets, including responses to ustekinumab treatment, thus enriching our understanding of CD at a molecular level. CONCLUSIONS Our findings highlight the complex cellular and molecular interplay in CD, suggesting new biomarkers and therapeutic targets, offering insights into disease mechanisms and treatment implications.
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Affiliation(s)
- Zheng-Yang Li
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Yong-Hong Sun
- Department of Gastroenterology, Dalian Friendship Hospital, Dalian, Liaoning, China
| | - Qian-Hua
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Hai-Yan Wang
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Ya-Jie Wang
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Miao-Jiang
- Department of Gastroenterology, Jinshan Hospital of Fudan University, Shanghai, China
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Abstract
Pouchitis is an acute or chronic inflammatory disease of the ileal reservoir. It is common after restorative proctocolectomy with ileal pouch-anal anastomosis, and treatment of chronic antibiotic-refractory pouchitis has proven challenging. Most cases of acute pouchitis evolve into chronic pouchitis. The aetiology of acute pouchitis is likely to be partly related to the gut microbiota, whereas the pathophysiology of chronic pouchitis involves abnormal interactions between genetic disposition, faecal stasis, the gut microbiota, dysregulated host immunity, surgical techniques, ischaemia and mesentery-related factors. Pouchoscopy with biopsy is the most valuable modality for diagnosis, disease monitoring, assessment of treatment response, dysplasia surveillance and delivery of endoscopic therapy. Triggering or risk factors, such as Clostridioides difficile infection and use of non-steroidal anti-inflammatory drugs, should be modified or eradicated. In terms of treatment, acute pouchitis usually responds to oral antibiotics, whereas chronic antibiotic-refractory pouchitis often requires induction and maintenance therapy with integrin, interleukin or tumour necrosis factor inhibitors. Chronic pouchitis with ischaemic features, fistulae or abscesses can be treated with hyperbaric oxygen therapy.
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Affiliation(s)
- Bo Shen
- Center for Inflammatory Bowel Diseases and the Global Center for Integrated Colorectal Surgery and IBD Interventional Endoscopy, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, NY, USA.
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6
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Felício R, Franco A, Corrêa-Moreira D, Martinez de Carvalho F, Guimarães A, Vargas FR. Humoral immune transcriptome signature in myelomeningocele patients. J Reprod Immunol 2024; 163:104224. [PMID: 38479055 DOI: 10.1016/j.jri.2024.104224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 06/03/2024]
Abstract
INTRODUCTION Myelomeningocele (MMC) results from incomplete closure of the neural tube, and has a complex multifactorial etiology, including an inflammatory microenvironment. OBJECTIVE We evaluated the contribution of humoral immune response for development of inflammatory milieu. METHODS Using public repository Gene Expression Omnibus (GEO), we retrieve dataset transcriptome from the amniotic fluid of ten fetuses with myelomeningocele and ten healthy control fetuses to found differential gene expression associated with disturbances and inflammatory signatures in MMC. The identified DEGs were submitted to enrichment, network, and matrix correlation analyses. RESULTS Our initial analysis revealed 90 DEGs in MMC, mainly associated with signaling pathways of inflammation, including the immune modules, humoral immune response and IFN-type I signatures. Protein-protein analysis (PPI) revealed an association with three protein networks; positive regulation of B cell proliferation constituted the largest network. Matrix correlation analyses showed that MMC alters the co-expression of genes related to inflammatory processes that promote microenvironment inflammation. CONCLUSION These results revealed an altered humoral immune response in MMC patients, contributing to an inflammatory profile and providing opportunities for identifying potential biomarkers in myelomeningocele disease.
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Affiliation(s)
- Rfm Felício
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Almm Franco
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Ciências Biológicas (Genética), Universidade Federal do Rio de Janeiro, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - D Corrêa-Moreira
- Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Laboratory of Taxonomy, Biochesmistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - F Martinez de Carvalho
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Programa de Pós-Graduação em Ciências Biológicas (Genética), Universidade Federal do Rio de Janeiro, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Acr Guimarães
- Laboratory of Taxonomy, Biochesmistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - F R Vargas
- Birth Defects Epidemiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Rede de Atenção à Saúde nas Anomalias Congênitas do Sistema Nervoso Central, Instituo Oswaldo Cruz, Fundação Oswaldo Cruz, Brazil; Programa de Pós-Graduação em Ciências Biológicas (Genética), Universidade Federal do Rio de Janeiro, Brazil; Laboratory for Applied Genomics and Bioinnovations, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil; Departamento de Genética e Biologia Molecular, Universidade Federal do Estado do Rio de Janeiro, Brazil.
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Puca P, Capobianco I, Coppola G, Di Vincenzo F, Trapani V, Petito V, Laterza L, Pugliese D, Lopetuso LR, Scaldaferri F. Cellular and Molecular Determinants of Biologic Drugs Resistance and Therapeutic Failure in Inflammatory Bowel Disease. Int J Mol Sci 2024; 25:2789. [PMID: 38474034 DOI: 10.3390/ijms25052789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The advent of biologic drugs has revolutionized the treatment of Inflammatory Bowel Disease, increasing rates of response and mucosal healing in comparison to conventional therapies by allowing the treatment of corticosteroid-refractory cases and reducing corticosteroid-related side effects. However, biologic therapies (anti-TNFα inhibitors, anti-α4β7 integrin and anti-IL12/23) are still burdened by rates of response that hover around 40% (in biologic-naïve patients) or lower (for biologic-experienced patients). Moreover, knowledge of the mechanisms underlying drug resistance or loss of response is still scarce. Several cellular and molecular determinants are implied in therapeutic failure; genetic predispositions, in the form of single nucleotide polymorphisms in the sequence of cytokines or Human Leukocyte Antigen, or an altered expression of cytokines and other molecules involved in the inflammation cascade, play the most important role. Accessory mechanisms include gut microbiota dysregulation. In this narrative review of the current and most recent literature, we shed light on the mentioned determinants of therapeutic failure in order to pave the way for a more personalized approach that could help avoid unnecessary treatments and toxicities.
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Affiliation(s)
- Pierluigi Puca
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Ivan Capobianco
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gaetano Coppola
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Federica Di Vincenzo
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Valentina Trapani
- Alleanza Contro il Cancro, Istituto Superiore di Sanità, 00144 Rome, Italy
| | - Valentina Petito
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Lucrezia Laterza
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Daniela Pugliese
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Loris Riccardo Lopetuso
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medicine and Ageing Sciences, "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
- Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, 66100 Chieti, Italy
| | - Franco Scaldaferri
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- IBD Unit, UOC CEMAD Centro Malattie dell'Apparato Digerente, Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
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Barnes EL, Dunn MS, Ashburn J, Barto A, Bloomfeld R, Cairns A, Mehta K, Patel P, Dziwis J, Esckilsen S, Rahbar R, Sadiq TS, Hanson JS, Herfarth HH. Extraintestinal Manifestations and Family History of Inflammatory Bowel Disease Increase the Risk of Pouchitis in a State-Level Epidemiology Study. Clin Transl Gastroenterol 2024; 15:e00670. [PMID: 38146854 PMCID: PMC10887435 DOI: 10.14309/ctg.0000000000000670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023] Open
Abstract
INTRODUCTION Our understanding of the epidemiology of inflammatory conditions of the pouch and effectiveness of treatment is largely based on selected populations. We created a state-level registry to evaluate the incidence of pouchitis and the effectiveness of treatments used in an initial episode of pouchitis. METHODS In a state-level retrospective cohort of all patients undergoing proctocolectomy with ileal pouch-anal anastomosis (IPAA) for ulcerative colitis between January 1, 2018, and December 31, 2020, we evaluated the incidence of pouchitis and compared the proportion of patients developing recurrent pouchitis and chronic antibiotic-dependent pouchitis according to initial antibiotic therapy. RESULTS A total of 177 patients underwent surgery with 49 (28%) developing pouchitis within the 12 months after the final stage of IPAA. Patients with extraintestinal manifestations of inflammatory bowel disease (IBD) were significantly more likely to develop pouchitis within the first 12 months after IPAA (adjusted odds ratio 2.45, 95% confidence interval 1.03-5.81) after adjusting for family history of IBD (adjusted odds ratio 3.50, 95% 1.50-8.18). When comparing the proportion of patients who developed recurrent pouchitis or chronic antibiotic-dependent pouchitis with those who experienced an isolated episode of pouchitis, there were no significant differences among the initial antibiotic regimens used. DISCUSSION In a state-level examination of outcomes after IPAA for ulcerative colitis, patients with extraintestinal manifestations of IBD were more likely to develop pouchitis; however, the initial antibiotic regimen chosen did not seem to affect long-term outcomes.
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Affiliation(s)
- Edward L. Barnes
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael S. Dunn
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jean Ashburn
- Division of Colon and Rectal Surgery, Atrium Health at Wake Forest Baptist, Winston-Salem, North Carolina, USA
| | - Amy Barto
- Division of Gastroenterology and Hepatology, Duke University, Durham, North Carolina, USA
| | - Richard Bloomfeld
- Section of Gastroenterology, Atrium Health at Wake Forest Baptist, Winston-Salem, North Carolina, USA
| | - Ashley Cairns
- Division of Colon and Rectal Surgery, Atrium Health at Wake Forest Baptist, Winston-Salem, North Carolina, USA
| | - Kurren Mehta
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Pooja Patel
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Jennifer Dziwis
- Section of Gastroenterology, Atrium Health at Wake Forest Baptist, Winston-Salem, North Carolina, USA
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Scott Esckilsen
- University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Reza Rahbar
- North Carolina Surgery, Raleigh, North Carolina, USA
| | | | - John S. Hanson
- Division of Gastroenterology and Hepatology, Atrium Health, Charlotte, North Carolina, USA
| | - Hans H. Herfarth
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
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Xu J, Zheng B, Xie C, Zhao Y, Wu H, Wang Y, Guan X, Lei X, Liu D, Lou X, Chen X, Huang Y. Inhibition of FABP5 attenuates inflammatory bowel disease by modulating macrophage alternative activation. Biochem Pharmacol 2024; 219:115974. [PMID: 38081366 DOI: 10.1016/j.bcp.2023.115974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/26/2023]
Abstract
Fatty acid binding protein 5 (FABP5) is an intracellular chaperone of fatty acid molecules that regulates lipid metabolism and cell growth. However, its role in intestinal inflammation remains enigmatic. Through examination of human tissue samples and single-cell data, we observed a significant upregulation of FABP5 within the mucosa of patients afflicted with ulcerative colitis (UC) and Crohn's disease (CD), predominantly localized in intestinal macrophages. Herein, we investigate the regulation of FABP5-IN-1, a FABP5 inhibitor, on various cells of the gut in an inflammatory environment. Our investigations confirmed that FABP5 ameliorates DSS-induced colitis in mice by impeding the differentiation of macrophages into M1 macrophages in vitro and in vivo. Furthermore, following FABP5-IN-1 intervention, we observed a notable restoration of intestinal goblet cells and tuft cells, even under inflammatory conditions. Additionally, FABP5-IN-1 exhibits a protective effect against DSS-induced colitis by promoting the polarization of macrophages towards the M2 phenotype in vivo. In summary, FABP5-IN-1 confers protection against DSS-induced acute colitis through a multifaceted approach, encompassing the reduction of inflammatory macrophage infiltration, macrophage polarization, regulating Th17/Treg cells to play an anti-inflammatory role in IBD. The implications for IBD are underscored by the comprehensive in vivo and in vitro experiments presented in this article, thereby positioning FABP5 as a promising and novel therapeutic target for the treatment of IBD.
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Affiliation(s)
- Jingping Xu
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China
| | - Bolin Zheng
- Department of Radiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, PR China
| | - Chunlan Xie
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen 361102, PR China
| | - Yao Zhao
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China
| | - Hailun Wu
- First Affiliated Hospital, Nanchang University, Nanchang 330000, Jiangxi Province, PR China
| | - Yiting Wang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China
| | - Xiaoli Guan
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China
| | - Xintao Lei
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China
| | - Dexin Liu
- Department of Radiology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, PR China
| | - Xiaoying Lou
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China
| | - Xiaohui Chen
- Department of Orthopedic Surgery, The First Affiliated Hospital of Xiamen University, Xiamen 361003, PR China.
| | - Yan Huang
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, PR China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University,Guangzhou, Guangdong 510655, PR China.
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10
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Jiang T, Zheng J, Li N, Li X, He J, Zhou J, Sun B, Chi Q. Dissecting the Mechanisms of Intestinal Immune Homeostasis by Analyzing T-Cell Immune Response in Crohn's Disease and Colorectal Cancer. Curr Gene Ther 2024; 24:422-440. [PMID: 38682449 DOI: 10.2174/0115665232294568240201073417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 05/01/2024]
Abstract
INTRODUCTION Crohn's disease (CD) and colorectal cancer (CRC) represent a group of intestinal disorders characterized by intricate pathogenic mechanisms linked to the disruption of intestinal immune homeostasis. Therefore, comprehending the immune response mechanisms in both categories of intestinal disorders is of paramount significance in the prevention and treatment of these debilitating intestinal ailments. METHOD IIn this study, we conducted single-cell analysis on paired samples obtained from primary colorectal tumors and individuals with Crohn's disease, which was aimed at deciphering the factors influencing the composition of the intestinal immune microenvironment. By aligning T cells across different tissues, we identified various T cell subtypes, such as γδ T cell, NK T cell, and regulatory T (Treg) cell, which maintained immune system homeostasis and were confirmed in enrichment analyses. Subsequently, we generated pseudo-time trajectories for subclusters of T cells in both syndromes to delineate their differentiation patterns and identify key driver genes Result: Furthermore, cellular communication and transcription factor regulatory networks are all essential components of the intricate web of mechanisms that regulate intestinal immune homeostasis. The identified complex cellular interaction suggested potential T-lineage immunotherapeutic targets against epithelial cells with high copy number variation (CNV) levels in CD and CRC. CONCLUSION Finally, the analysis of regulon networks revealed several promising candidates for cell-specific transcription factors (TFs). This study focused on the immune molecular mechanism under intestinal diseases. It contributed to the novel insight of depicting a detailed immune landscape and revealing T-cell responding mechanisms in CD and CRC.
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Affiliation(s)
- Tianming Jiang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jie Zheng
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT06510, USA
| | - Nana Li
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaodong Li
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jixing He
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Junde Zhou
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Boshi Sun
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
- Division of Surgical Oncology, Department of Surgery, Yale University School of Medicine, New Haven, CT06510, USA
| | - Qiang Chi
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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11
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Karmele EP, Moldoveanu AL, Kaymak I, Jugder BE, Ursin RL, Bednar KJ, Corridoni D, Ort T. Single cell RNA-sequencing profiling to improve the translation between human IBD and in vivo models. Front Immunol 2023; 14:1291990. [PMID: 38179052 PMCID: PMC10766350 DOI: 10.3389/fimmu.2023.1291990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024] Open
Abstract
Inflammatory bowel disease (IBD) is an umbrella term for two conditions (Crohn's Disease and Ulcerative Colitis) that is characterized by chronic inflammation of the gastrointestinal tract. The use of pre-clinical animal models has been invaluable for the understanding of potential disease mechanisms. However, despite promising results of numerous therapeutics in mouse colitis models, many of these therapies did not show clinical benefits in patients with IBD. Single cell RNA-sequencing (scRNA-seq) has recently revolutionized our understanding of complex interactions between the immune system, stromal cells, and epithelial cells by mapping novel cell subpopulations and their remodeling during disease. This technology has not been widely applied to pre-clinical models of IBD. ScRNA-seq profiling of murine models may provide an opportunity to increase the translatability into the clinic, and to choose the most appropriate model to test hypotheses and novel therapeutics. In this review, we have summarized some of the key findings at the single cell transcriptomic level in IBD, how specific signatures have been functionally validated in vivo, and highlighted the similarities and differences between scRNA-seq findings in human IBD and experimental mouse models. In each section of this review, we highlight the importance of utilizing this technology to find the most suitable or translational models of IBD based on the cellular therapeutic target.
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Affiliation(s)
- Erik P. Karmele
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Ana Laura Moldoveanu
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Irem Kaymak
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Bat-Erdene Jugder
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, United States
| | - Rebecca L. Ursin
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Waltham, MA, United States
| | - Kyle J. Bednar
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Daniele Corridoni
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Tatiana Ort
- Bioscience Immunology, Research and Early Development, Respiratory and Immunology, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
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Kayal M, Posner H, Milwidsky HM, Plietz M, Khaitov S, Sylla P, Greenstein A, Dubinsky MC, Mehandru S, Colombel JF. Acute Severe Ulcerative Colitis Is Associated With an Increased Risk of Acute Pouchitis. Inflamm Bowel Dis 2023; 29:1907-1911. [PMID: 36939632 DOI: 10.1093/ibd/izad039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Indexed: 03/21/2023]
Abstract
BACKGROUND Pouchitis occurs in up to 80% of patients after total proctocolectomy (TPC) with ileal pouch-anal anastomosis (IPAA) and has been associated with microbial and host-related immunological factors. We hypothesized that a more robust immune response at the time of colectomy, manifested by acute severe ulcerative colitis (ASUC), may be associated with subsequent acute pouchitis. METHODS This was a retrospective cohort analysis of all patients with UC or indeterminate colitis complicated by medically refractory disease or dysplasia who underwent TPC with IPAA at Mount Sinai Hospital between 2008 and 2017 and at least 1 subsequent pouchoscopy. Acute pouchitis was defined according to the Pouchitis Disease Activity Index. Cox regression was used to assess unadjusted relationships between hypothesized risk factors and acute pouchitis. RESULTS A total of 416 patients met inclusion criteria. Of the 165 (39.7%) patients who underwent urgent colectomy, 77 (46.7%) were admitted with ASUC. Acute pouchitis occurred in 228 (54.8%) patients a median of 1.3 (interquartile range, 0.6-3.1) years after the final surgical stage. On multivariable analysis, ASUC (hazard ratio [HR], 1.50; 95% confidence interval [CI], 1.04-2.17) and a greater number of biologics precolectomy (HR, 1.57; 95% CI, 1.06-2.31) were associated with an increased probability of acute pouchitis, while older age at colectomy (HR, 0.98; 95% CI, 0.97-0.99) was associated with a decreased probability. Time to pouchitis was significantly less in patients admitted with ASUC compared with those not (P = .002). CONCLUSION A severe UC disease phenotype at the time of colectomy was associated with an increased probability of acute pouchitis.
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Affiliation(s)
- Maia Kayal
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hannah Posner
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadar Meringer Milwidsky
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Plietz
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sergey Khaitov
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patricia Sylla
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Greenstein
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Saurabh Mehandru
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Zhao Y, Zhou R, Xie B, Liu CY, Kalski M, Cham CM, Koval J, Weber CR, Rubin DT, Sogin M, Crosson S, Huang J, Fiebig A, Dalal S, Chang EB, Basu A, Pott S. Multiomic analysis reveals cellular and epigenetic plasticity in intestinal pouches of ulcerative colitis patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.11.23298309. [PMID: 38014192 PMCID: PMC10680893 DOI: 10.1101/2023.11.11.23298309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Background & Aims Total proctocolectomy with ileal pouch anal anastomosis (IPAA) is the standard of care for patients with severe treatment resistant ulcerative colitis (UC). Despite improvements in patient outcomes, about 50% of patients will develop inflammation of the pouch within 1-2 years following surgery. Establishment of UC pouches is associated with profound histological changes of the mucosa. A detailed characterization of these changes on a cellular and molecular level is crucial for an improved understanding of pouch physiology and diseases management. Methods We generated cell-type-resolved transcriptional and epigenetic atlases of UC pouches using scRNA-seq and scATAC-seq data from paired biopsy samples from the ileal pouch and ileal segment above the pouch (pre-pouch) of UC-IPAA patients (n=6, female=2) without symptoms. We also collected data from paired biopsies of the terminal ileum (TI) and ascending colon (AC) from healthy controls (n=6, female=3). Results We identified novel populations of colon-like absorptive and secretory epithelial cells, constituting a significant proportion of the epithelial cell fraction in the pouch but not in matched pre-pouch samples. Pouch-specific enterocytes expressed colon-specific genes, including CEACAM5, CA2. However, in contrast to normal colonic epithelium, these cells also expressed a range of inflammatory and secretory genes, similar to previously detected gene expression signatures in IBD patients. Comparison to longitudinal bulk RNA-seq data from UC pouches demonstrated that colon-like epithelial cells are present early after pouch functionalization and independently of subsequent pouchitis. Finally, single cell chromatin accessibility revealed activation colonic transcriptional regulators, including CDX1, NFIA, and EHF. Conclusion UC pouches are characterized by partial colonic metaplasia of the epithelium. These data constitute a resource of transcriptomic and epigenetic signatures of cell populations in the pouch and provide an anchor for understanding the underlying molecular mechanisms of pouchitis.
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Affiliation(s)
- Yu Zhao
- University of Chicago, Pritzker School of Molecular Engineering, Chicago, IL
| | - Ran Zhou
- University of Chicago, Department of Medicine, Chicago, IL
| | - Bingqing Xie
- University of Chicago, Department of Medicine, Chicago, IL
| | - Cambrian Y Liu
- University of Chicago, Department of Medicine, Chicago, IL
| | - Martin Kalski
- University of Chicago, Department of Medicine, Chicago, IL
| | - Candace M Cham
- University of Chicago, Department of Medicine, Chicago, IL
| | - Jason Koval
- University of Chicago, Department of Medicine, Chicago, IL
| | | | - David T Rubin
- University of Chicago, Department of Medicine, Chicago, IL
- University of Chicago, Department of Pathology, Chicago, IL
| | - Mitch Sogin
- Marine Biological Laboratory, Woods Hole, MA
| | | | - Jun Huang
- University of Chicago, Pritzker School of Molecular Engineering, Chicago, IL
| | | | - Sushila Dalal
- University of Chicago, Department of Medicine, Chicago, IL
| | - Eugene B Chang
- University of Chicago, Department of Medicine, Chicago, IL
| | - Anindita Basu
- University of Chicago, Department of Medicine, Chicago, IL
| | - Sebastian Pott
- University of Chicago, Department of Medicine, Chicago, IL
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14
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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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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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Hong S, Wang H, Chan S, Zhang J, Chen B, Ma X, Chen X. Identifying Macrophage-Related Genes in Ulcerative Colitis Using Weighted Coexpression Network Analysis and Machine Learning. Mediators Inflamm 2023; 2023:4373840. [PMID: 38633005 PMCID: PMC11023725 DOI: 10.1155/2023/4373840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/23/2023] [Accepted: 09/27/2023] [Indexed: 04/19/2024] Open
Abstract
Ulcerative colitis (UC) is an inflammatory bowel disease of unknown cause that typically affects the colon and rectum. Innate intestinal immunity, including macrophages, plays a significant role in the pathological development of UC. Using the CIBERSORT algorithm, we observed elevated levels of 22 types of immune cell infiltrates, as well as increased M1 and decreased M2 macrophages in UC compared to normal colonic mucosa. Weighted gene coexpression network analysis (WGCNA) was used to identify modules associated with macrophages and UC, resulting in the identification of 52 macrophage-related genes (MRGs) that were enriched in macrophages at single-cell resolution. Consensus clustering based on these 52 MRGs divided the integrated UC cohorts into three subtypes. Machine learning algorithms were used to identify ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), sodium- and chloride-dependent neutral and basic amino acid transporter B(0+) (SLC6A14), and 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2) in the training set, and their diagnostic value was validated in independent validation sets. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) revealed the main biological effects, and that interleukin-17 was one of several signaling pathways enriched by the three genes. We also constructed a competitive endogenous RNA (CeRNA) network reflecting a potential posttranscriptional regulatory mechanism. Expression of diagnostic markers was validated in vivo and in biospecimens, and our immunohistochemistry (IHC) results confirmed that HMGCS2 gradually decreased during the transformation of UC to colorectal cancer. In conclusion, ENPP1, SLC6A14, and HMGCS2 are associated with macrophages and the progression of UC pathogenesis and have good diagnostic value for patients with UC.
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Affiliation(s)
- Shaocheng Hong
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Anhui Provincial Key Laboratory of Digestive Diseases, Hefei, China
| | - Hongqian Wang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Anhui Provincial Key Laboratory of Digestive Diseases, Hefei, China
| | - Shixin Chan
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Jiayi Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Anhui Provincial Key Laboratory of Digestive Diseases, Hefei, China
| | - Bangjie Chen
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Xiaohan Ma
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Anhui Provincial Key Laboratory of Digestive Diseases, Hefei, China
| | - Xi Chen
- Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
- Anhui Provincial Key Laboratory of Digestive Diseases, Hefei, China
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Yao Y, Yang L, Zhang Z, Wang B, Feng B, Liu Z. Identification of Targets for Subsequent Treatment of Crohn's Disease Patients After Failure of Anti-TNF Therapy. J Inflamm Res 2023; 16:4617-4631. [PMID: 37868830 PMCID: PMC10590116 DOI: 10.2147/jir.s422881] [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: 05/25/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
Background Anti-TNF medications are the first-line treatment for Crohn's Disease (CD), despite the fact that a significant portion of the population continues to be ineffectively treated. This research aims to discover accurate intervention targets for the follow-up of anti-TNF non-responders using bioinformatics technology. Methods GSE16879, GSE111761, and GSE52746 retrieved from the GEO database. Unbiased differentially expressed genes (DEGs) were discovered utilizing the limma and RobustRankAggreg (RRA) tools. Then, we used weighted gene co-expression network analysis (WGCNA) to identify the module most strongly associated with non responders and subjected this module to Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis with overlapping genes of the DEGs. GSEA analysis applied to check the results of GO and KEGG. Using the Cytoscape program, the protein-protein interaction (PPI) network was constructed. The software's MCODE addon and CytoHubba addon was used to find the most important modules and the hub genes. Subsequently, we employed reverse transcription-polymerase chain reaction (RT-PCR) to confirm hub gene expression from mucosal biopsy specimens. Results There were a total of 142 genes co-upregulated and 65 genes co-downregulated. According to the WGCNA analysis, 42 genes were duplicated inside the light cyan module. GO and KEGG enrichment analyses of overlapped genes in nonresponders demonstrated an increase in the expression of genes associated with inflammation and immune response, consistent with GSEA results. The PPI network was constructed using 41 protein nodes and 177 edges. After validation, 8 of the top 10 genes were verified to be differentially expressed. Conclusion Our investigation is the first to integrate three CD databases after the anti-TNF medication treatment. We identified IL1B, CCL4, CXCL1, CXCL10, CCL3, CSF3, TREM1, and IL1RN as potential therapeutic targets for patients whose anti-TNF treatment failed.
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Affiliation(s)
- Yao Yao
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Liu Yang
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Zhe Zhang
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Binbin Wang
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Baisui Feng
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
| | - Zhanju Liu
- Department of Gastroenterology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, People’s Republic of China
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital of Tongji University, Shanghai, 200072, People’s Republic of China
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Hsu P, Choi, EJ, Patel, SA, Wong, WH, Olvera, JG, Yao, P, Liu YC, Tsai MS, Wang W, Boland BS, Chang JT. Responsiveness to Vedolizumab Therapy in Ulcerative Colitis is Associated With Alterations in Immune Cell-Cell Communications. Inflamm Bowel Dis 2023; 29:1602-1612. [PMID: 37235748 PMCID: PMC10547234 DOI: 10.1093/ibd/izad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 05/28/2023]
Abstract
BACKGROUND Ulcerative colitis (UC) and Crohn's disease are 2 types of inflammatory bowel disease (IBD), a group of chronic digestive disorders caused by aberrant immune responses to intestinal microbes. Although changes in the composition of immune cell subsets in the context of IBD have been previously described, the interactions and communication among cells are less well understood. Moreover, the precise mechanisms of action underlying many biologic therapies, including the anti-α4β7 integrin antagonist vedolizumab, remain incompletely understood. Our study aimed to explore possible additional mechanisms through which vedolizumab acts. METHODS We performed cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) on peripheral blood and colon immune cells derived from patients with ulcerative colitis treated with the anti-α4β7 integrin antagonist vedolizumab. We applied a previously published computational approach, NicheNet, to predict immune cell-cell interactions, revealing putative ligand-receptor pairs and key transcriptional changes downstream of these cell-cell communications (CCC). RESULTS We observed decreased proportions of T helper 17 (TH17) cells in UC patients who responded to vedolizumab and therefore focused the study on identifying cell-cell communications and signals of TH17 cells with other immune cells. For example, we observed that colon TH17 cells from vedolizumab nonresponders were predicted to have a greater degree of interactions with classical monocytes compared with responders, whereas colon TH17 cells from vedolizumab responders exhibited more interactions with myeloid dendritic cells compared with nonresponders. CONCLUSIONS Overall, our results indicate that efforts to elucidate cell-cell communications among immune and nonimmune cell types may increase the mechanistic understanding of current and investigational therapies for IBD.
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Affiliation(s)
- Paul Hsu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Eunice J Choi,
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Shefali A Patel,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - William H Wong,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Jocelyn G Olvera,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Priscilla Yao,
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Yi Chia Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Matthew S Tsai
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - John T Chang
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Medicine, Jennifer Moreno Department of Veteran Affairs Medical Center, San Diego, CA, 92161, USA
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19
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Huang B, Gui M, An H, Shen J, Ye F, Ni Z, Zhan H, Che L, Lai Z, Zeng J, Peng J, Lin J. Babao Dan alleviates gut immune and microbiota disorders while impacting the TLR4/MyD88/NF-кB pathway to attenuate 5-Fluorouracil-induced intestinal injury. Biomed Pharmacother 2023; 166:115387. [PMID: 37643486 DOI: 10.1016/j.biopha.2023.115387] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
Adjuvant chemotherapy based on 5-fluorouracil (5-FU), such as FOLFOX, is suggested as a treatment for gastrointestinal cancer. Yet, intestinal damage continues to be a prevalent side effect for which there are no practical prevention measures. We investigated whether Babao Dan (BBD), a Traditional Chinese Medicine, protects against intestinal damage induced by 5-FU by controlling immune response and gut microbiota. 5-FU was injected intraperitoneally to establish the mice model, then 250 mg/kg BBD was gavaged for five days straight. 5-FU led to marked weight loss, diarrhea, fecal blood, and histopathologic intestinal damage. Administration of BBD reduced these symptoms, inhibited proinflammatory cytokine (IL-6, IL-1β, IFN-γ, TNF-α) secretion, and upregulated the ratio of CD3(+) T cells and the CD4(+)/CD8(+) ratio. According to 16S rRNA sequencing, BBD dramatically repaired the disruption of the gut microbiota caused in a time-dependent way, and increased the Firmicutes/Bacteroidetes (F/B) ratio. Transcriptomic results showed that the mechanism is mainly concentrated on the NF-κB pathway, and we found that BBD reduced the concentration of LPS in the fecal suspension and serum, and inhibited TLR4/MyD88/NF-κB pathway activation. Furthermore, at the genus level on the fifth day, BBD upregulated the abundance of unidentified_Corynebacteriaceae, Aerococcus, Blautia, Jeotgalicoccus, Odoribacter, Roseburia, Rikenella, Intestinimonas, unidentified_Lachnospiraceae, Enterorhabdus, Ruminiclostridium, and downregulated the abundance of Bacteroides, Parabacteroides, Parasutterella, Erysipelatoclostridium, which were highly correlated with intestinal injury or the TLR4/MyD88/NF-κB pathway. In conclusion, we established a network involving 5-FU, BBD, the immune response, gut microbiota, and key pathways to explain the pharmacology of oral BBD in preventing 5-FU-induced intestinal injury.
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Affiliation(s)
- Bin Huang
- Academy of Integrative Medicine of Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China; Key Laboratory of Integrative Medicine of Fujian Province University, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Mengxuan Gui
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Honglin An
- Key Laboratory of Integrative Medicine of Fujian Province University, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Jiayu Shen
- Key Laboratory of Integrative Medicine of Fujian Province University, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Feimin Ye
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Zhuona Ni
- Academy of Integrative Medicine of Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Hanzhang Zhan
- Key Laboratory of Integrative Medicine of Fujian Province University, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Li Che
- Xiamen Traditional Chinese Medicine Co., Ltd., Xiamen 361100, PR China
| | - Zhicheng Lai
- Xiamen Traditional Chinese Medicine Co., Ltd., Xiamen 361100, PR China
| | - Jiahan Zeng
- Xiamen Traditional Chinese Medicine Co., Ltd., Xiamen 361100, PR China
| | - Jun Peng
- Academy of Integrative Medicine of Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China; Key Laboratory of Integrative Medicine of Fujian Province University, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China
| | - Jiumao Lin
- Academy of Integrative Medicine of Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China; Key Laboratory of Integrative Medicine of Fujian Province University, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350122, PR China.
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20
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Mondini M, Guipaud O, François A, Mathieu N, Deutsch É, Milliat F. [Interactions between vascular endothelium and immune cells: A key control point of radiation-induced digestive lesions]. Cancer Radiother 2023; 27:643-647. [PMID: 37516639 DOI: 10.1016/j.canrad.2023.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 07/31/2023]
Abstract
Radiation-induced toxicity of the digestive tract is a major clinical concern as many cancer survivors have received radiotherapy for tumours of the abdominopelvic area. The coordination and orchestration of a tissue's response to stress depend not only on the phenotype of the cells that make up the tissue but also on cell-cell interactions. The digestive system, i.e., the intestine/colon/rectum, is made up of a range of different cell populations: epithelial cells, stromal cells, i.e. endothelial cells and mesenchymal lineages, immune cells and nerve cells. Moreover, each of these populations is heterogeneous and presents very significant plasticity and differentiation states. The pathogenesis of radiation-induced digestive lesions is an integrated process that involves multiple cellular compartments interacting in a complex sequence of events. Understanding all the cellular events and communication networks that contribute to the tissue's response to stress is therefore a major conceptual and methodological scientific challenge. The study of heterogeneous populations of cells in a tissue is now possible thanks to "single cell' RNA sequencing and spatial transcriptomics techniques, which enable a comprehensive study of the transcriptomic profiles of individual cells in an integrated system. In addition, the mathematical and bioinformatics tools that are now available for the large-scale analysis of data allow the inference of cell-cell communication networks. Such approaches have become possible through advances in bioinformatics algorithms for the analysis and deciphering of interaction networks. Interactions influence the tissue regeneration process through expression of various molecules, including metabolites, integrins, junction proteins, ligands, receptors and proteins secreted into the extracellular space. The vascular network is viewed as a key player in the progression of digestive lesions, which are characterised by infiltration of a range of immune cells. A better characterisation of endothelium/immune cell interactions in suitable preclinical models, as well as in humans, may help to identify some promising therapeutic targets for the prediction, prevention or treatment of digestive toxicity after radiotherapy.
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Affiliation(s)
- M Mondini
- Gustave-Roussy, Inserm U1030, université Paris-Saclay, Villejuif, France
| | - O Guipaud
- Institut de radioprotection et de sûreté nucléaire (IRSN), PSE-Sante/Seramed/LRMed, 92260 Fontenay-aux-Roses, France
| | - A François
- Institut de radioprotection et de sûreté nucléaire (IRSN), PSE-Sante/Seramed/LRMed, 92260 Fontenay-aux-Roses, France
| | - N Mathieu
- Institut de radioprotection et de sûreté nucléaire (IRSN), PSE-Sante/Seramed/LRMed, 92260 Fontenay-aux-Roses, France
| | - É Deutsch
- Gustave-Roussy, Inserm U1030, université Paris-Saclay, Villejuif, France; Service de radiothérapie oncologique, Gustave-Roussy, Villejuif, France
| | - F Milliat
- Institut de radioprotection et de sûreté nucléaire (IRSN), PSE-Sante/Seramed/LRMed, 92260 Fontenay-aux-Roses, France.
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21
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Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023; 20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
Abstract
The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.
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Affiliation(s)
- Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- University Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Cambridge, UK.
| | - Kylie R James
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mandeep Kaur
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sebastian Pott
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhixin Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert Burger
- Department of Computer Science, Heriot-watt University, Edinburgh, UK
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frode L Jahnsen
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Francesca Perrone
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Nathalie Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Tomohisa Sujino
- Center for the Diagnostic and Therapeutic Endoscopy, School of Medicine, Keio University, Tokyo, Japan
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Raquel Bartolome-Casado
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, UK
| | - Espen S Bækkevold
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ran Zhou
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shahida Din
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qiuming Yao
- Department of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Semir Beyaz
- Cold Spring Harbour Laboratory, Cold Spring Harbour, New York, NY, USA
| | - Mark Arends
- Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Institute of Cancer and Genetics, University of Edinburgh, Edinburgh, UK
| | - Alexandre Denadai-Souza
- Laboratory of Mucosal Biology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | | | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK
| | - Aviv Regev
- Genentech, San Francisco, CA, USA
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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22
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Kim H, Kim HK, Hong D, Kim M, Jang S, Yang CS, Yoon S. Identification of ulcerative colitis-specific immune cell signatures from public single-cell RNA-seq data. Genes Genomics 2023; 45:957-967. [PMID: 37133723 DOI: 10.1007/s13258-023-01390-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/13/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Single-cell RNA-seq enabled microscopic studies on tissue microenvironment of many diseases. Inflammatory bowel disease, an autoimmune disease, is involved with various dysfunction of immune cells, for which single-cell RNA-seq may provide us a deeper insight into the causes and mechanism of this complex disease. OBJECTIVE In this work, we used public single-cell RNA-seq data to study tissue microenvironment around ulcerative colitis, an inflammatory bowel disease causing chronic inflammation and ulcers in large intestine. METHODS Since not all the datasets provide cell-type annotations, we first identified cell identities to select cell populations of our interest. Differentially expressed genes and gene set enrichment analysis was then performed to infer the polarization/activation state of macrophages and T cells. Cell-to-cell interaction analysis was also performed to discover distinct interactions in ulcerative colitis. RESULTS Differentially expressed genes analysis of the two datasets confirmed the regulation of CTLA4, IL2RA, and CCL5 genes in the T cell subset and regulation of S100A8/A9, CLEC10A genes in macrophages. Cell-to-cell interaction analysis showed CD4+ T cells and macrophages interact actively to each other. We also identified IL-18 pathway activation in inflammatory macrophages, evidence that CD4+ T cells induce Th1 and Th2 differentiation, and also found that macrophages regulate T cell activation through different ligand-receptor pairs, viz. CD86-CTL4, LGALS9-CD47, SIRPA-CD47, and GRN-TNFRSF1B. CONCLUSION Analysis of these immune cell subsets may suggest novel strategies for the treatment of inflammatory bowel disease.
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Affiliation(s)
- Hanbyeol Kim
- Dept of Computer Science, College of SW Convergence, Dankook Univ, Yongin-si, 16890, Korea
| | - Hyo Keun Kim
- Dept of Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, 15588, Korea
| | - Dawon Hong
- Dept of Molecular Biology, Graduate Department of Bioconvergence Engineering, Dankook University, Yongin-si, 16890, Korea
| | - Minsu Kim
- Dept of Computer Science, College of SW Convergence, Dankook Univ, Yongin-si, 16890, Korea
| | - Sein Jang
- Dept of Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, 15588, Korea
| | - Chul-Su Yang
- Dept of Medicinal/Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, 15588, Korea
| | - Seokhyun Yoon
- Dept of Electronics & Electrical Eng, College of Engineering, Dankook Univ, Yongin-si, 16890, Korea.
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23
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Lai W, Xian C, Chen M, Luo D, Zheng J, Zhao S, Li XG. Single-cell and bulk transcriptomics reveals M2d macrophages as a potential therapeutic strategy for mucosal healing in ulcerative colitis. Int Immunopharmacol 2023; 121:110509. [PMID: 37369160 DOI: 10.1016/j.intimp.2023.110509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/31/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Mucosal healing is essential for treating ulcerative colitis (UC), which results from imbalanced macrophage polarization and dysregulated inflammatory responses. However, the mechanisms of cellular communication and signal transduction that regulate mucosal healing among macrophage subtypes require further investigation. We use bulk and single-cell RNA sequencing analysis to reveal that macrophage subtypes vary in different UC states. At the same time, chemokine and angiogenesis signaling is strongly associated with M2 macrophage's infiltrated proportion. To get more insight into subtypes of macrophages in mucosal healing, we divided macrophages into M1, M2b, and M2d macrophages. Based on the differentially expressed genes (DEGs) between M2d and M1 macrophages, KEGG and GO analysis highlights M2d macrophages' ability to alleviate inflammation and promote epithelial healing. Trajectory analysis revealed opposite differentiation of macrophage subsets between UC and healthy groups, with M1 and M2d macrophages coexisting in the same differentiation branch under UC conditions. Along the pseudotime axis, CCL3 and VEGFA expression increased in UC, while IL10RA remained stable in UC but increased in healthy controls. CellChat identified CCL3-CCR1 has strong communication between M1 and M2d macrophages, while the IL10 signaling pathway is activated explicitly in M2d macrophages to mitigate inflammation and promote epithelial healing. We also speculate that high levels of VEGFA activate endothelial cells expressing VEGFR and worsen inflammation. To conclude, we suggested IL10 and VEGF signaling in M2d macrophages as potential therapeutic targets for mucosal healing. However, it is necessary to establish reliable methods for isolating and purifying M2d macrophages before these targets can be effectively utilized.
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Affiliation(s)
- Weiming Lai
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Changxiu Xian
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Mingxia Chen
- College of Animal Science and Technology, Guangdong Polytechnic of Science and Trade, 510640 Guangzhou, China
| | - Ding Luo
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510120, China
| | - Junxia Zheng
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Suqing Zhao
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Xiang-Guang Li
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
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24
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Peng Z, Ren Z, Tong Z, Zhu Y, Zhu Y, Hu K. Interactions between MFAP5 + fibroblasts and tumor-infiltrating myeloid cells shape the malignant microenvironment of colorectal cancer. J Transl Med 2023; 21:405. [PMID: 37344903 DOI: 10.1186/s12967-023-04281-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND The therapeutic targeting of the tumor microenvironment (TME) in colorectal cancer (CRC) has not yet been fully developed and utilized because of the complexity of the cell-cell interactions within the TME. The further exploration of these interactions among tumor-specific clusters would provide more detailed information about these communication networks with potential curative value. METHODS Single-cell RNA sequencing, spatial transcriptomics, and bulk RNA sequencing datasets were integrated in this study to explore the biological properties of MFAP5 + fibroblasts and their interactions with tumor-infiltrating myeloid cells in colorectal cancer. Immunohistochemistry and multiplex immunohistochemistry were performed to confirm the results of these analyses. RESULTS We profiled heterogeneous single-cell landscapes across 27,414 cells obtained from tumors and adjacent tissues. We mainly focused on the pro-tumorigenic functions of the identified MFAP5 + fibroblasts. We demonstrated that tumor-resident MFAP5 + fibroblasts and myeloid cells (particularly C1QC + macrophages) were positively correlated in both spatial transcriptomics and bulk RNA-seq public cohorts. These cells and their interactions might shape the malignant behavior of CRC. Intercellular interaction analysis suggested that MFAP5 + fibroblasts could reciprocally communicate with C1QC + macrophages and other myeloid cells to remodel unfavorable conditions via MIF/CD74, IL34/CSF1R, and other tumor-promoting signaling pathways. CONCLUSION Our study has elucidated the underlying pro-tumor mechanisms of tumor-resident MFAP5 + fibroblasts and provided valuable targets for the disruption of their properties.
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Affiliation(s)
- Zhiwei Peng
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Zihao Ren
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Zhiwei Tong
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Yinan Zhu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China
| | - Yansong Zhu
- School of Life Science, Anhui Medical University, Hefei, 230022, Anhui, China
| | - Kongwang Hu
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, Anhui, China.
- Department of General Surgery, Fuyang Affiliated Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China.
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25
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Nie H, Lin P, Zhang Y, Wan Y, Li J, Yin C, Zhang L. Single-cell meta-analysis of inflammatory bowel disease with scIBD. NATURE COMPUTATIONAL SCIENCE 2023; 3:522-531. [PMID: 38177426 DOI: 10.1038/s43588-023-00464-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/09/2023] [Indexed: 01/06/2024]
Abstract
Understanding the heterogeneous intestinal microenvironment is critical to uncover the pathogenesis of inflammatory bowel disease (IBD). Recent advances in single-cell RNA sequencing (scRNA-seq) have identified certain cell types and genes that could contribute to IBD; however, a comprehensively integrated analysis of these scRNA-seq datasets is not yet available. Here we introduce scIBD, a platform for single-cell meta-analysis of IBD with interactive and visualization features, which combines highly curated single-cell datasets in a uniform workflow, enabling identifying rare or less-characterized cell types in IBD and dissecting the commonalities, as well as the differences between ulcerative colitis and Crohn's disease. scIBD also incorporates multifunctional information-including regulon activity, GWAS-implicated risk genes and genes targeted by therapeutics-to infer clinically relevant cell-type specificity. Collectively, scIBD is a user-friendly web-based platform for the community to analyze the transcriptome features and gene regulatory networks associated with the pathogenesis and treatment of IBD at single-cell resolution.
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Affiliation(s)
- Hu Nie
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Peilu Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yu Zhang
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yihong Wan
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Jiesheng Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Chengqian Yin
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China
| | - Lei Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, China.
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Dai Z, Zhang J, Xu W, Du P, Wang Z, Liu Y. Single-Cell Sequencing-Based Validation of T Cell-Associated Diagnostic Model Genes and Drug Response in Crohn's Disease. Int J Mol Sci 2023; 24:ijms24076054. [PMID: 37047025 PMCID: PMC10093907 DOI: 10.3390/ijms24076054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Crohn's disease is a highly heterogeneous autoimmune disease with a unique inflammatory phenotype of T cells at the lesion site. We aim to further explore the diagnosis of Crohn's disease and drug prediction of T cell marker gene expression. We obtained single-cell expression profile data from 22 CDs or normal samples and performed cell annotation and cellular communication analysis. Through the intersection of T cell marker genes, differential genes, and WGCNA results, we identified T cell-specific key genes and their immune landscapes and potential pathogenesis, and validated them across multiple datasets and patient tissue samples. We also explored the differentiation characteristics of genes by pseudo-temporal analysis and assessed their diagnostic performance and drug sensitivity by molecular docking. Finally, we extended this study to the prognosis of IBD-associated colon cancer. TNF-centered 5-gene diagnostic model not only has excellent diagnostic efficacy, but is also closely associated with KRAS, P53, and IL6/JAK/STAT3 pathways and physiological processes, such as EMT, coagulation, and apoptosis. In addition, this diagnostic model may have potential synergistic immunotherapeutic effects, with positive correlations with immune checkpoints such as CTLA4, CD86, PDCD1LG2, and CD40. Molecular docking demonstrated that BIRC3 and ANXA1 have strong binding properties to Azathioprine and Glucoocorticoid. Furthermore, the 5-gene model may suggest antagonism to IFX and prognosis for colon cancer associated with inflammatory bowel disease. Single-cell sequencing targeting T cell-related features in patients with Crohn's disease may aid in new diagnostic decisions, as well as the initial exploration of high-potential therapies.
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Affiliation(s)
- Zhujiang Dai
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Jie Zhang
- Department of Gastroenterology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Weimin Xu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Zhongchuan Wang
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
| | - Yun Liu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Shanghai Colorectal Cancer Research Center, Shanghai 200092, China
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Xiao S, Xie W, Zhang Y, Pan Y, Lei L. The Immune Landscape and Molecular Subtypes of Pediatric Crohn's Disease: Results from In Silico Analysis. J Pers Med 2023; 13:jpm13040571. [PMID: 37108957 PMCID: PMC10142949 DOI: 10.3390/jpm13040571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 04/29/2023] Open
Abstract
Pediatric Crohn's disease (CD) presents a distinct phenotype from adult-onset disease. A dysregulated immune response is critical in CD pathogenesis; thus, it is clinically important to describe immune cell alterations and to identify a new molecular classification for pediatric CD. To this end, in this study, a RNA-seq derived dataset GSE101794-which contains the expression profiles of 254 treatment-naïve pediatric CD samples, including CIBERSORTx and weighted gene-co-expression network analysis (WGCNA)-were performed to estimate the ratio of immune cells and to identify modules and genes related to specific immune cell infiltration, respectively. Hub genes derived from WGCNA were further employed to create a molecular classification using unsupervised K-means clustering. In the pediatric CD samples, it was found that M2 macrophages, CD4+ memory resting T cells, CD8+ T cells, and resting mast cells were the most prominent immune cells in intestinal tissues. Then, 985 up-regulated genes and 860 down-regulated genes were identified in samples with high immune cell infiltration. Of these differential genes, 10 hub genes (APOA1, CYB5A, XPNPEP2, SLC1A7, SLC4A6, LIPE, G6PC, AGXT2, SLC13A1, and SOAT2) were associated with CD8+T cell infiltration. Clinically, the higher expression of these 10 hub genes was strongly associated with an earlier age of CD onset and colonic-type CD. Furthermore, based on these key genes, pediatric CD could be classified into three molecular subtypes, displaying a different immune landscape. Altogether, this in silico analysis provides a novel insight into the immune signature of pediatric CD, and a new classification of pediatric CD is presented, which may help us develop more personalized disease management and treatments for pediatric CD.
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Affiliation(s)
- Shiyu Xiao
- Department of Gastroenterology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 100034, China
| | - Wenhui Xie
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing 100034, China
| | - Yinghui Zhang
- Department of Gastroenterology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 100034, China
| | - Yan Pan
- Department of Gastroenterology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 100034, China
| | - Lei Lei
- Department of Gastroenterology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610072, China
- School of Medicine, University of Electronic Science and Technology of China, Chengdu 100034, China
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Ma S, Yang Q, Chen N, Zheng A, Abbasi N, Wang G, Patel PR, Cho BS, Yee BA, Zhang L, Chu H, Evans SM, Yeo GW, Zheng Y, Huang WJM. RNA binding protein DDX5 restricts RORγt + T reg suppressor function to promote intestine inflammation. SCIENCE ADVANCES 2023; 9:eadd6165. [PMID: 36724232 PMCID: PMC9891705 DOI: 10.1126/sciadv.add6165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
Retinoid-related orphan receptor (RAR) gamma (RORγt)-expressing regulatory T cells (RORγt+ Tregs) play pivotal roles in preventing T cell hyperactivation and maintaining tissue homeostasis, in part by secreting the anti-inflammation cytokine interleukin-10 (IL-10). Here, we report that hypoxia-induced factor 1α (HIF1α) is the master transcription factor for Il10 in RORγt+ Tregs. This critical anti-inflammatory pathway is negatively regulated by an RNA binding protein DEAD box helicase 5 (DDX5). As a transcriptional corepressor, DDX5 restricts the expression of HIF1α and its downstream target gene Il10 in RORγt+ Tregs. T cell-specific Ddx5 knockout (DDX5ΔT) mice have augmented RORγt+ Treg suppressor activities and are better protected from intestinal inflammation. Genetic ablation or pharmacologic inhibition of HIF1α restores enteropathy susceptibility in DDX5ΔT mice. The DDX5-HIF1α-IL-10 pathway is conserved in mice and humans. These findings reveal potential therapeutic targets for intestinal inflammatory diseases.
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Affiliation(s)
- Shengyun Ma
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qiyuan Yang
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicholas Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anna Zheng
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Nazia Abbasi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gaowei Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Parth R. Patel
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin S. Cho
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lunfeng Zhang
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Hiutung Chu
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Chiba University–UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (cMAV), University of California San Diego, La Jolla, CA, USA
| | - Sylvia M. Evans
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ye Zheng
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Wendy Jia Men Huang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
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Kayal M, Kohler D, Colombel JF, Dubinsky MC, Ungaro RC. Early Biologic Initiation After Chronic Pouch Inflammation Diagnosis Does Not Impact Clinical Outcomes. Clin Gastroenterol Hepatol 2023; 21:541-542.e1. [PMID: 35123095 PMCID: PMC11273368 DOI: 10.1016/j.cgh.2022.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/05/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
Approximately 20% of patients with ulcerative colitis (UC) who undergo total proctocolectomy (TPC) with ileal pouch-anal anastomosis (IPAA) develop chronic pouch inflammation (CPI).1 Given the involvement of the small bowel in CPI, there is no consensus on whether it should be managed more like UC or Crohn's disease (CD). Despite limited evidence, biologics are often used for CPI with clinical response rates of 20%-60% with adalimumab and infliximab, 50%-80% with ustekinumab, and 30%-70% with vedolizumab.2,3 Earlier biologic therapy has been associated with greater rates of response and favorable long-term outcomes in patients with CD, however not UC.4-7 The impact of earlier initiation of biologic therapy on CPI clinical outcomes has not been elucidated. The aim of this study was to assess whether timing of biologic initiation relative to CPI diagnosis impacts clinical and endoscopic remission.
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Affiliation(s)
- Maia Kayal
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - David Kohler
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marla C Dubinsky
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C Ungaro
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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Gomez-Bris R, Saez A, Herrero-Fernandez B, Rius C, Sanchez-Martinez H, Gonzalez-Granado JM. CD4 T-Cell Subsets and the Pathophysiology of Inflammatory Bowel Disease. Int J Mol Sci 2023; 24:2696. [PMID: 36769019 PMCID: PMC9916759 DOI: 10.3390/ijms24032696] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is an umbrella term for the chronic immune-mediated idiopathic inflammation of the gastrointestinal tract, manifesting as Crohn's disease (CD) or ulcerative colitis (UC). IBD is characterized by exacerbated innate and adaptive immunity in the gut in association with microbiota dysbiosis and the disruption of the intestinal barrier, resulting in increased bacterial exposure. In response to signals from microorganisms and damaged tissue, innate immune cells produce inflammatory cytokines and factors that stimulate T and B cells of the adaptive immune system, and a prominent characteristic of IBD patients is the accumulation of inflammatory T-cells and their proinflammatory-associated cytokines in intestinal tissue. Upon antigen recognition and activation, CD4 T-cells differentiate towards a range of distinct phenotypes: T helper(h)1, Th2, Th9, Th17, Th22, T follicular helper (Tfh), and several types of T-regulatory cells (Treg). T-cells are generated according to and adapt to microenvironmental conditions and participate in a complex network of interactions among other immune cells that modulate the further progression of IBD. This review examines the role of the CD4 T-cells most relevant to IBD, highlighting how these cells adapt to the environment and interact with other cell populations to promote or inhibit the development of IBD.
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Affiliation(s)
- Raquel Gomez-Bris
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Angela Saez
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria (UFV), 28223 Pozuelo de Alarcón, Spain
| | - Beatriz Herrero-Fernandez
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- Departamento de Fisiología, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Cristina Rius
- Department of History of Science and Information Science, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
- UISYS Research Unit, University of Valencia, 46010 Valencia, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Hector Sanchez-Martinez
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Jose M. Gonzalez-Granado
- LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain
- CIBER de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
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31
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Pang X, Song H, Li X, Xu F, Lei B, Wang F, Xu J, Qi L, Wang L, Tan G. Transcriptomic analyses of treatment-naïve pediatric ulcerative colitis patients and exploration of underlying disease pathogenesis. J Transl Med 2023; 21:30. [PMID: 36647141 PMCID: PMC9843999 DOI: 10.1186/s12967-023-03881-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/08/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a form of chronic inflammatory bowel disease of nonspecific origin. This study used an RNA-Sequencing (RNA-Seq) approach to evaluate the transcriptomic landscape of a well-stratified treatment-naïve pediatric UC patient population by comparing them with healthy control children. The data were analyzed to evaluate the mechanisms driving UC-related intestinal inflammation and fibrosis. METHODS Intestinal mucosal samples from five pediatric UC patients and five healthy controls were analyzed by RNA-Seq, and results were verified by qPCR. A CRISPR/Cas9 approach was used to knock out the expression of HLA-DRB5, and molecular biology techniques were used for additional mechanistic studies. RESULTS In these analyses, 2290 genes were found to be differentially expressed between the UC and control samples, of which 1258 and 1032 were upregulated and downregulated, respectively. Gene Ontology analysis showed that these genes were enriched in extracellular matrix (ECM)-related processes and that 7 of 8 differentially expressed genes of interest (PIK3CD, IL1β, IL1α, TIMP1, MMP1, MMP12, COL6A3, and HLADRB5) were upregulated and involved in ECM-receptor interaction and inflammatory bowel disease-related pathways. Increased HLA-DRB5 expression driven by intestinal bacteria was found to promote IL-1α secretion, leading to intestinal inflammation and fibrosis, suggesting a possible target for the treatment of UC. CONCLUSION These data suggest that intestinal inflammation is present in pediatric UC patients for extended periods before the onset of symptoms, and intestinal fibrosis begins even during the early stages of UC. Intestinal bacteria were also found to trigger intestinal inflammation and fibrosis, with HLA-DRB5 playing a central role in this process.
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Affiliation(s)
- Xiaoli Pang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Hongxiao Song
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Xiaolu Li
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Fengchao Xu
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Bingxun Lei
- grid.430605.40000 0004 1758 4110Department of Anesthesia, The First Hospital of Jilin University, Changchun, China
| | - Fei Wang
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
| | - Jing Xu
- grid.430605.40000 0004 1758 4110Health Examination Center, The First Hospital of Jilin University, Changchun, China
| | - Lingli Qi
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Libo Wang
- grid.430605.40000 0004 1758 4110Department of Pediatric Gastroenterology, The First Hospital of Jilin University, Changchun, China
| | - Guangyun Tan
- grid.430605.40000 0004 1758 4110Department of Hepatology, Center for Pathogen Biology and Infectious Diseases, Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, Jilin China
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Zeng L, Yang K, Zhang T, Zhu X, Hao W, Chen H, Ge J. Research progress of single-cell transcriptome sequencing in autoimmune diseases and autoinflammatory disease: A review. J Autoimmun 2022; 133:102919. [PMID: 36242821 DOI: 10.1016/j.jaut.2022.102919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/07/2022]
Abstract
Autoimmunity refers to the phenomenon that the body's immune system produces antibodies or sensitized lymphocytes to its own tissues to cause an immune response. Immune disorders caused by autoimmunity can mediate autoimmune diseases. Autoimmune diseases have complicated pathogenesis due to the many types of cells involved, and the mechanism is still unclear. The emergence of single-cell research technology can solve the problem that ordinary transcriptome technology cannot be accurate to cell type. It provides unbiased results through independent analysis of cells in tissues and provides more mRNA information for identifying cell subpopulations, which provides a novel approach to study disruption of immune tolerance and disturbance of pro-inflammatory pathways on a cellular basis. It may fundamentally change the understanding of molecular pathways in the pathogenesis of autoimmune diseases and develop targeted drugs. Single-cell transcriptome sequencing (scRNA-seq) has been widely applied in autoimmune diseases, which provides a powerful tool for demonstrating the cellular heterogeneity of tissues involved in various immune inflammations, identifying pathogenic cell populations, and revealing the mechanism of disease occurrence and development. This review describes the principles of scRNA-seq, introduces common sequencing platforms and practical procedures, and focuses on the progress of scRNA-seq in 41 autoimmune diseases, which include 9 systemic autoimmune diseases and autoinflammatory diseases (rheumatoid arthritis, systemic lupus erythematosus, etc.) and 32 organ-specific autoimmune diseases (5 Skin diseases, 3 Nervous system diseases, 4 Eye diseases, 2 Respiratory system diseases, 2 Circulatory system diseases, 6 Liver, Gallbladder and Pancreas diseases, 2 Gastrointestinal system diseases, 3 Muscle, Bones and joint diseases, 3 Urinary system diseases, 2 Reproductive system diseases). This review also prospects the molecular mechanism targets of autoimmune diseases from the multi-molecular level and multi-dimensional analysis combined with single-cell multi-omics sequencing technology (such as scRNA-seq, Single cell ATAC-seq and single cell immune group library sequencing), which provides a reference for further exploring the pathogenesis and marker screening of autoimmune diseases and autoimmune inflammatory diseases in the future.
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Tianqing Zhang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaofei Zhu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Chen
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China; Hunan Academy of Chinese Medicine, Changsha, China.
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Colon-Targeted eNAMPT-Specific Peptide Systems for Treatment of DSS-Induced Acute and Chronic Colitis in Mouse. Antioxidants (Basel) 2022; 11:antiox11122376. [PMID: 36552583 PMCID: PMC9774280 DOI: 10.3390/antiox11122376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/07/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
Nicotinamide phosphoribosyl transferase (NAMPT) is required to maintain the NAD+ pool, among which extracellular (e) NAMPT is associated with inflammation, mainly mediated by macrophages. However, the role of (e) NAMPT in inflammatory macrophages in ulcerative colitis is insufficiently understood. Here our analyses of single-cell RNA-seq data revealed that the levels of NAMPT and CYBB/NOX2 in macrophages were elevated in patients with colitis and in mouse models of acute and chronic colitis. These findings indicate the clinical significance of NAMPT and CYBB in colitis. Further, we found that eNAMPT directly binds the extracellular domains of CYBB and TLR4 in activated NLRP3 inflammasomes. Moreover, we developed a recombinant 12-residue TK peptide designated colon-targeted (CT)-conjugated multifunctional NAMPT (rCT-NAMPT), comprising CT as the colon-targeting moiety, which harbors the minimal essential residues required for CYBB/TLR4 binding. rCT-NAMPT effectively suppressed the severity of disease in DSS-induced acute and chronic colitis models through targeting the colon and inhibiting the interaction of NAMPT with CYBB or TLR4. Together, our data show that rCT-NAMPT may serve as an effective novel candidate therapeutic for colitis by modulating the NLRP3 inflammasome-mediated immune signaling system.
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Dai YC, Qiao D, Fang CY, Chen QQ, Que RY, Xiao TG, Zheng L, Wang LJ, Zhang YL. Single-cell RNA-sequencing combined with bulk RNA-sequencing analysis of peripheral blood reveals the characteristics and key immune cell genes of ulcerative colitis. World J Clin Cases 2022; 10:12116-12135. [PMID: 36483809 PMCID: PMC9724533 DOI: 10.12998/wjcc.v10.i33.12116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/27/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affects mucosal homeostasis and triggers an inappropriate immune response. Single-cell RNA sequencing (scRNA-seq) can be used to rapidly obtain the precise gene expression patterns of thousands of cells in the intestine, analyze the characteristics of cells with the same phenotype, and provide new insights into the growth and development of intestinal organs, the clonal evolution of cells, and immune cell changes. These findings can provide new ideas for the diagnosis and treatment of intestinal diseases.
AIM To identify clinical phenotypes and biomarkers that can predict the response of UC patients to specific therapeutic drugs and thus aid the diagnosis and treatment of UC.
METHODS Using the Gene Expression Omnibus (GEO) database, we analyzed peripheral blood cell subtypes of patients with UC by scRNA-seq combined with bulk RNA sequencing (RNA-seq) to reveal the core genes of UC. We then combined weighted gene correlation network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) analysis to reveal diagnostic markers of UC.
RESULTS After processing the scRNA-seq data, we obtained data from approximately 24340 cells and identified 17 cell types. Through intercellular communication analysis, we selected monocyte marker genes as the candidate gene set for the prediction model. Construction of a WGCNA coexpression network identified RhoB, cathepsin D (CTSD) and zyxin (ZYX) as core genes. Immune infiltration analysis showed that these three core genes were strongly correlated with immune cells. Functional enrichment analysis showed that the differentially expressed genes were closely related to immune and inflammatory responses, which are associated with many challenges in the diagnosis and treatment of UC.
CONCLUSION Through scRNA-seq analysis, LASSO diagnostic model building and WGCNA, we identified RhoB, CTSD and ZYX as core genes of UC that are closely related to monocyte infiltration that may serve as diagnostic markers and molecular targets for UC therapeutic intervention.
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Affiliation(s)
- Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Dan Qiao
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Chen-Ye Fang
- Department of Gastroenterology, Traditional Chinese Medicine Hospital of Ningbo, Ningbo 315000, Zhejiang Province, China
| | - Qiu-Qin Chen
- Department of Pathology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Ren-Ye Que
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Tie-Gang Xiao
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Lie Zheng
- Department of Gastroenterology, Traditional Chinese Medicine Hospital of Xi’an 730000, Shaanxi Province, China
| | - Li-Juan Wang
- Experimental Education Center, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ya-Li Zhang
- Institute of Digestive Diseases, LongHua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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Chen K, Shang S, Yu S, Cui L, Li S, He N. Identification and exploration of pharmacological pyroptosis-related biomarkers of ulcerative colitis. Front Immunol 2022; 13:998470. [PMID: 36311726 PMCID: PMC9606687 DOI: 10.3389/fimmu.2022.998470] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/26/2022] [Indexed: 11/25/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD). Its etiology is unclear. Much evidence suggests that the death of abnormal intestinal epithelial cells (IECs) leads to intestinal barrier disruption, and the subsequent inflammatory response plays a vital role in UC. Pyroptosis is a form of programmed inflammatory cell death, and the role of pyroptosis in UC etiology remains to be explored. This study identified 10 hub genes in pyroptosis by gene expression profiles obtained from the GSE87466 dataset. Meanwhile, the biomarkers were screened based on gene significance (GS) and module membership (MM) through the Weighted Gene Co-Expression Network Analysis (WGCNA). The following analysis indicated that hub genes were closely associated with the UC progression and therapeutic drug response. The single-cell RNA (scRNA) sequencing data from UC patients within the GSE162335 dataset indicated that macrophages were most related to pyroptosis. Finally, the expression of hub genes and response to the therapeutic drug [5-aminosalicylic acid (5-ASA)] were verified in dextran sulfate sodium (DSS)-induced colitis mice. Our study identified IL1B as the critical pyroptosis-related biomarker in UC. The crosstalk between macrophage pyroptosis and IEC pyroptosis may play an essential role in UC, deserving further exploration.
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Affiliation(s)
| | | | | | | | | | - Ningning He
- *Correspondence: Shangyong Li, ; Ningning He,
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36
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Wang Y, Song W, Yu S, Liu Y, Chen YG. Intestinal cellular heterogeneity and disease development revealed by single-cell technology. CELL REGENERATION 2022; 11:26. [PMID: 36045190 PMCID: PMC9433512 DOI: 10.1186/s13619-022-00127-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/15/2022] [Indexed: 11/10/2022]
Abstract
The intestinal epithelium is responsible for food digestion and nutrient absorption and plays a critical role in hormone secretion, microorganism defense, and immune response. These functions depend on the integral single-layered intestinal epithelium, which shows diversified cell constitution and rapid self-renewal and presents powerful regeneration plasticity after injury. Derailment of homeostasis of the intestine epithelium leads to the development of diseases, most commonly including enteritis and colorectal cancer. Therefore, it is important to understand the cellular characterization of the intestinal epithelium at the molecular level and the mechanisms underlying its homeostatic maintenance. Single-cell technologies allow us to gain molecular insights at the single-cell level. In this review, we summarize the single-cell RNA sequencing applications to understand intestinal cell characteristics, spatiotemporal evolution, and intestinal disease development.
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PFKFB3 Increases IL-1β and TNF-α in Intestinal Epithelial Cells to Promote Tumorigenesis in Colitis-Associated Colorectal Cancer. JOURNAL OF ONCOLOGY 2022; 2022:6367437. [PMID: 36016583 PMCID: PMC9398832 DOI: 10.1155/2022/6367437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 01/17/2023]
Abstract
Colorectal cancer (CRC) is significantly correlated with inflammatory bowel disease, which usually manifests as chronic relapsing-remitting colitis. Phosphofructo-2-kinase/fructose-2,6-biophosphatase 3 (PFKFB3) can catalyze to produce fructose-2,6-bisphosphate and function as an oncogene. In this study, we revealed the function of PFKFB3 in colitis-associated CRC (CAC) and the potential mechanism. RT-qPCR and Western blot were utilized to detect the level of PFKFB3 expression. Increased PFKFB3 expression was observed in the mouse CAC model and CAC patient samples. We identified that overexpression of PFKFB3 in intestinal epithelial cells (IECs) could increase the proliferation, migration, and invasion of CRC cells by the coculture system. Mechanistically, overexpression of PFKFB3 induced phospho-p65 and promoted the expression of IL-1β and tumor necrosis factor alpha (TNF-α) in the development of colitis and CAC. In addition, PFK158, the PFKFB3 inhibitor, could reduce the CRC cell viability, migration, and invasion caused by PFKFB3 overexpression. In conclusion, overexpression of PFKFB3 promoted tumorigenesis in CAC by inducing phospho-p65 and expression of IL-1β and TNF-α. Our study suggested that PFKFB3 acted as a potential treatment target for CAC.
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38
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Loke P, Lee SC, Oyesola OO. Effects of helminths on the human immune response and the microbiome. Mucosal Immunol 2022; 15:1224-1233. [PMID: 35732819 DOI: 10.1038/s41385-022-00532-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023]
Abstract
Helminths have evolved sophisticated immune regulating mechanisms to prevent rejection by their mammalian host. Our understanding of how the human immune system responds to these parasites remains poor compared to mouse models of infection and this limits our ability to develop vaccines as well as harness their unique properties as therapeutic strategies against inflammatory disorders. Here, we review how recent studies on human challenge infections, self-infected individuals, travelers, and endemic populations have improved our understanding of human type 2 immunity and its effects on the microbiome. The heterogeneity of responses between individuals and the limited access to tissue samples beyond the peripheral blood are challenges that limit human studies on helminths, but also provide opportunities to transform our understanding of human immunology. Organoids and single-cell sequencing are exciting new tools for immunological analysis that may aid this pursuit. Learning about the genetic and immunological basis of resistance, tolerance, and pathogenesis to helminth infections may thus uncover mechanisms that can be utilized for therapeutic purposes.
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Affiliation(s)
- P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Soo Ching Lee
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oyebola O Oyesola
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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Chen M, Lin W, Gan J, Lu W, Wang M, Wang X, Yi J, Zhao Z. Transcriptomic Mapping of Human Parotid Gland at Single-Cell Resolution. J Dent Res 2022; 101:972-982. [PMID: 35220796 DOI: 10.1177/00220345221076069] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
As the largest salivary gland in oral cavity, the parotid gland plays an important role in initial digesting and lubricating food. The abnormal secretory function of the parotid gland can lead to dental caries and oral mucosal inflammation. In recent years, single-cell RNA sequencing (scRNA-seq) has been used to explore the heterogeneity and diversity of cells in various organs and tissues. However, the transcription profile of the human parotid gland at single-cell resolution has not been reported yet. In this study, we constructed the cell atlas of human parotid gland using the 10× Genomics platform. Characteristic gene analysis identified the biological functions of serous acinar cell populations in secreting digestive enzymes and antibacterial proteins. We revealed the specificity and similarity of the parotid gland compared to other digestive glands through comparative analyses of other published scRNA-seq data sets. We also identified the cell-specific expression of hub genes for Sjögren syndrome in the human parotid gland by integrating the results of genome-wide association studies and bulk RNA-seq, which highlighted the importance of immune cell dysfunction in parotid Sjögren syndrome pathogenesis.
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Affiliation(s)
- M. Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - W. Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - J. Gan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - W. Lu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - M. Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - X. Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - J. Yi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z. Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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40
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Verdonk F, Einhaus J, Tsai AS, Hedou J, Choisy B, Gaudilliere D, Kin C, Aghaeepour N, Angst MS, Gaudilliere B. Measuring the human immune response to surgery: multiomics for the prediction of postoperative outcomes. Curr Opin Crit Care 2021; 27:717-725. [PMID: 34545029 PMCID: PMC8585713 DOI: 10.1097/mcc.0000000000000883] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW Postoperative complications including infections, cognitive impairment, and protracted recovery occur in one-third of the 300 million surgeries performed annually worldwide. Complications cause personal suffering along with a significant economic burden on our healthcare system. However, the accurate prediction of postoperative complications and patient-targeted interventions for their prevention remain as major clinical challenges. RECENT FINDINGS Although multifactorial in origin, the dysregulation of immunological mechanisms that occur in response to surgical trauma is a key determinant of postoperative complications. Prior research, primarily focusing on inflammatory plasma markers, has provided important clues regarding their pathogenesis. However, the recent advent of high-content, single-cell transcriptomic, and proteomic technologies has considerably improved our ability to characterize the immune response to surgery, thereby providing new means to understand the immunological basis of postoperative complications and to identify prognostic biological signatures. SUMMARY The comprehensive and single-cell characterization of the human immune response to surgery has significantly advanced our ability to predict the risk of postoperative complications. Multiomic modeling of patients' immune states holds promise for the discovery of preoperative predictive biomarkers, ultimately providing patients and surgeons with actionable information to improve surgical outcomes. Although recent studies have generated a wealth of knowledge, laying the foundation for a single-cell atlas of the human immune response to surgery, larger-scale multiomic studies are required to derive robust, scalable, and sufficiently powerful models to accurately predict the risk of postoperative complications in individual patients.
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Affiliation(s)
- Franck Verdonk
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Julien Hedou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Benjamin Choisy
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | | | - Cindy Kin
- Department of Surgery, Stanford University School of Medicine
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
- Department of Biomedical Data Science, Stanford University
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine
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Rabbenou W, Chang S. Medical treatment of pouchitis: a guide for the clinician. Therap Adv Gastroenterol 2021; 14:17562848211023376. [PMID: 34249146 PMCID: PMC8239975 DOI: 10.1177/17562848211023376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/18/2021] [Indexed: 02/04/2023] Open
Abstract
Pouchitis is the most common complication in patients who have undergone restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA). Up to 81% of IPAA patients experience pouchitis, with 40% of patients presenting within the first year of surgery. Common risk factors include genetic mutations, extensive colitis, rheumatologic disorders, and primary sclerosing cholangitis. Currently, there are no medications with approved indications for pouchitis. As such, the conventional treatment of pouchitis is entirely off-label. This paper is intended to be a practical and up-to-date review of available therapies used for the management of pouchitis. The mainstay of treatment for acute pouchitis remains antibiotics, but newer therapeutics have also shown promise in the treatment of chronic pouchitis. Common lifestyle considerations that may play a role in pouchitis are also reviewed. PLAIN LANGUAGE SUMMARY Medical treatment of pouchitis: a guide for the clinician The ileal pouch-anal anastomosis ("pouch") is the most common way patients who require surgery to remove their colon are able to avoid a permanent ileostomy ("ostomy"). This pouch, created from the small intestines, serves as a reservoir to hold stool. The most common complication after pouch surgery is pouchitis. Pouchitis symptoms include more frequent bowel movements, urgency to defecate, blood in the stool, incontinence, and abdominal pain. This paper is intended to be a practical review of available therapies including medications and lifestyle changes that can be considered for the management of acute pouchitis, chronic pouchitis, and cuffitis.
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Affiliation(s)
- Wendy Rabbenou
- Division of Gastroenterology and Hepatology, New York University Langone Medical Center, New York, NY, USA
| | - Shannon Chang
- Division of Gastroenterology and Hepatology, New York University Langone Medical Center, 305 E 33rd Street, New York, NY 10016, USA
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