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Yan Q, Zhao Z, Liu D, Li J, Pan S, Duan J, Liu Z. Novel immune cross-talk between inflammatory bowel disease and IgA nephropathy. Ren Fail 2024; 46:2337288. [PMID: 38628140 PMCID: PMC11025414 DOI: 10.1080/0886022x.2024.2337288] [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: 09/15/2023] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
The mechanisms underlying the complex correlation between immunoglobulin A nephropathy (IgAN) and inflammatory bowel disease (IBD) remain unclear. This study aimed to identify the optimal cross-talk genes, potential pathways, and mutual immune-infiltrating microenvironments between IBD and IgAN to elucidate the linkage between patients with IBD and IgAN. The IgAN and IBD datasets were obtained from the Gene Expression Omnibus (GEO). Three algorithms, CIBERSORTx, ssGSEA, and xCell, were used to evaluate the similarities in the infiltrating microenvironment between the two diseases. Weighted gene co-expression network analysis (WGCNA) was implemented in the IBD dataset to identify the major immune infiltration modules, and the Boruta algorithm, RFE algorithm, and LASSO regression were applied to filter the cross-talk genes. Next, multiple machine learning models were applied to confirm the optimal cross-talk genes. Finally, the relevant findings were validated using histology and immunohistochemistry analysis of IBD mice. Immune infiltration analysis showed no significant differences between IBD and IgAN samples in most immune cells. The three algorithms identified 10 diagnostic genes, MAPK3, NFKB1, FDX1, EPHX2, SYNPO, KDF1, METTL7A, RIDA, HSDL2, and RIPK2; FDX1 and NFKB1 were enhanced in the kidney of IBD mice. Kyoto Encyclopedia of Genes and Genomes analysis showed 15 mutual pathways between the two diseases, with lipid metabolism playing a vital role in the cross-talk. Our findings offer insights into the shared immune mechanisms of IgAN and IBD. These common pathways, diagnostic cross-talk genes, and cell-mediated abnormal immunity may inform further experimental studies.
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Affiliation(s)
- Qianqian Yan
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
| | - Zihao Zhao
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
| | - Dongwei Liu
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Jia Li
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Shaokang Pan
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Jiayu Duan
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
| | - Zhangsuo Liu
- Department of Integrated Traditional and Western Nephrology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, P. R. China
- Henan Province Research Center for Kidney Disease, Zhengzhou, P. R. China
- Key Laboratory of Precision Diagnosis and Treatment for Chronic Kidney Disease in Henan Province, Zhengzhou, P. R. China
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Luo M, He N, Xu Q, Wen Z, Wang Z, Zhao J, Liu Y. Roles of prostaglandins in immunosuppression. Clin Immunol 2024; 265:110298. [PMID: 38909972 DOI: 10.1016/j.clim.2024.110298] [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: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 06/25/2024]
Abstract
Prostaglandins (PGs) play a crucial and multifaceted role in various physiological processes such as intercellular signaling, inflammation regulation, neurotransmission, vasodilation, vasoconstriction, and reproductive functions. The diversity and biological significance of these effects are contingent upon the specific types or subtypes of PGs, with each PG playing a crucial role in distinct physiological and pathological processes. Particularly within the immune system, PGs are essential in modulating the function of immune cells and the magnitude and orientation of immune responses. Hence, a comprehensive comprehension of the functions PG signaling pathways in immunosuppressive regulation holds substantial clinical relevance for disease prevention and treatment strategies. The manuscript provides a review of recent developments in PG signaling in immunosuppressive regulation. Furthermore, the potential clinical applications of PGs in immunosuppression are also discussed. While research into the immunosuppressive effects of PGs required further exploration, targeted therapies against their immunosuppressive pathways might open new avenues for disease prevention and treatment.
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Affiliation(s)
- Minjie Luo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China
| | - Nina He
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China
| | - Qing Xu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China
| | - Zhongchi Wen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China
| | - Ziqin Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China
| | - Jie Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China.
| | - Ying Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha 410008, Hunan, China; Sepsis Translational Medicine Key Lab of Hunan Province, Changsha 410008, Hunan, China; National Medicine Functional Experimental Teaching Center, Changsha 410008, Hunan, China.
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Ren R, Jiang J, Li X, Zhang G. Research progress of autoimmune diseases based on induced pluripotent stem cells. Front Immunol 2024; 15:1349138. [PMID: 38720903 PMCID: PMC11076788 DOI: 10.3389/fimmu.2024.1349138] [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: 12/04/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Autoimmune diseases can damage specific or multiple organs and tissues, influence the quality of life, and even cause disability and death. A 'disease in a dish' can be developed based on patients-derived induced pluripotent stem cells (iPSCs) and iPSCs-derived disease-relevant cell types to provide a platform for pathogenesis research, phenotypical assays, cell therapy, and drug discovery. With rapid progress in molecular biology research methods including genome-sequencing technology, epigenetic analysis, '-omics' analysis and organoid technology, large amount of data represents an opportunity to help in gaining an in-depth understanding of pathological mechanisms and developing novel therapeutic strategies for these diseases. This paper aimed to review the iPSCs-based research on phenotype confirmation, mechanism exploration, drug discovery, and cell therapy for autoimmune diseases, especially multiple sclerosis, inflammatory bowel disease, and type 1 diabetes using iPSCs and iPSCs-derived cells.
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Affiliation(s)
| | | | | | - Guirong Zhang
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [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: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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Pérez-Jeldres T, Magne F, Ascui G, Alvares D, Orellana M, Alvarez-Lobos M, Hernandez-Rocha C, Azocar L, Aguilar N, Espino A, Estela R, Escobar S, Zazueta A, Baez P, Silva V, De La Vega A, Arriagada E, Pavez-Ovalle C, Díaz-Asencio A, Travisany D, Miquel JF, Villablanca EJ, Kronenberg M, Bustamante ML. Amerindian ancestry proportion as a risk factor for inflammatory bowel diseases: results from a Latin American Andean cohort. Front Med (Lausanne) 2023; 10:1258395. [PMID: 37964883 PMCID: PMC10642057 DOI: 10.3389/fmed.2023.1258395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
Background and aims Latin American populations remain underrepresented in genetic studies of inflammatory bowel diseases (IBDs). Most genetic association studies of IBD rely on Caucasian, African, and Asian individuals. These associations have yet to be evaluated in detail in the Andean region of South America. We explored the contribution of IBD-reported genetic risk variants to a Chilean cohort and the ancestry contribution to IBD in this cohort. Methods A total of 192 Chilean IBD patients were genotyped using Illumina's Global Screening Array. Genotype data were combined with similar information from 3,147 Chilean controls. The proportions of Aymara, African, European, and Mapuche ancestries were estimated using the software ADMIXTURE. We calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for gender, age, and ancestry proportions. We also explored associations with previously reported IBD-risk variants independently and in conjunction with genetic ancestry. Results The first and third quartiles of the proportion of Mapuche ancestry in IBD patients were 24.7 and 34.2%, respectively, and the corresponding OR was 2.30 (95%CI 1.52-3.48) for the lowest vs. the highest group. Only one variant (rs7210086) of the 180 reported IBD-risk SNPs was associated with IBD risk in the Chilean cohort (adjusted P = 0.01). This variant is related to myeloid cells. Conclusion The type and proportion of Native American ancestry in Chileans seem to be associated with IBD risk. Variants associated with IBD risk in this Andean region were related to myeloid cells and the innate immune response.
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Affiliation(s)
- Tamara Pérez-Jeldres
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Fabien Magne
- Department of Microbiology, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Gabriel Ascui
- La Jolla Institute for Immunology, San Diego, CA, United States
| | - Danilo Alvares
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | - Matias Orellana
- Department of Computer Science, Faculty of Physical Sciences and Mathematics, Universidad de Chile, Santiago, Chile
| | - Manuel Alvarez-Lobos
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristian Hernandez-Rocha
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azocar
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nataly Aguilar
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto Espino
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ricardo Estela
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Sergio Escobar
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Alejandra Zazueta
- Department of Microbiology, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Pablo Baez
- Center of Medical Informatics and Telemedicine, University of Chile, Santiago, Chile
| | - Verónica Silva
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Andres De La Vega
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Elizabeth Arriagada
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Carolina Pavez-Ovalle
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Dante Travisany
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago, Chile
| | - Juan Francisco Miquel
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo J. Villablanca
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Mitchell Kronenberg
- La Jolla Institute for Immunology, San Diego, CA, United States
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, United States
| | - María Leonor Bustamante
- Department of Human Genetic, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
- Fundación Diagnosis, Santiago, Chile
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