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Cheng X, Meng X, Chen R, Song Z, Li S, Wei S, Lv H, Zhang S, Tang H, Jiang Y, Zhang R. The molecular subtypes of autoimmune diseases. Comput Struct Biotechnol J 2024; 23:1348-1363. [PMID: 38596313 PMCID: PMC11001648 DOI: 10.1016/j.csbj.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
Autoimmune diseases (ADs) are characterized by their complexity and a wide range of clinical differences. Despite patients presenting with similar symptoms and disease patterns, their reactions to treatments may vary. The current approach of personalized medicine, which relies on molecular data, is seen as an effective method to address the variability in these diseases. This review examined the pathologic classification of ADs, such as multiple sclerosis and lupus nephritis, over time. Acknowledging the limitations inherent in pathologic classification, the focus shifted to molecular classification to achieve a deeper insight into disease heterogeneity. The study outlined the established methods and findings from the molecular classification of ADs, categorizing systemic lupus erythematosus (SLE) into four subtypes, inflammatory bowel disease (IBD) into two, rheumatoid arthritis (RA) into three, and multiple sclerosis (MS) into a single subtype. It was observed that the high inflammation subtype of IBD, the RA inflammation subtype, and the MS "inflammation & EGF" subtype share similarities. These subtypes all display a consistent pattern of inflammation that is primarily driven by the activation of the JAK-STAT pathway, with the effective drugs being those that target this signaling pathway. Additionally, by identifying markers that are uniquely associated with the various subtypes within the same disease, the study was able to describe the differences between subtypes in detail. The findings are expected to contribute to the development of personalized treatment plans for patients and establish a strong basis for tailored approaches to treating autoimmune diseases.
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Affiliation(s)
| | | | | | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Siyu Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongchao Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuhao Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hao Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Ren H, Lv W, Shang Z, Li L, Shen Q, Li S, Song Z, Cheng X, Meng X, Chen R, Zhang R. Identifying functional subtypes of IgA nephropathy based on three machine learning algorithms and WGCNA. BMC Med Genomics 2024; 17:61. [PMID: 38395835 PMCID: PMC10893719 DOI: 10.1186/s12920-023-01702-9] [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: 05/08/2023] [Accepted: 10/14/2023] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND IgA nephropathy (IgAN) is one of the most common primary glomerulonephritis, which is a significant cause of renal failure. At present, the classification of IgAN is often limited to pathology, and its molecular mechanism has not been established. Therefore we aim to identify subtypes of IgAN at the molecular level and explore the heterogeneity of subtypes in terms of immune cell infiltration, functional level. METHODS Two microarray datasets (GSE116626 and GSE115857) were downloaded from GEO. Differential expression genes (DEGs) for IgAN were screened with limma. Three unsupervised clustering algorithms (hclust, PAM, and ConsensusClusterPlus) were combined to develop a single-sample subtype random forest classifier (SSRC). Functional subtypes of IgAN were defined based on functional analysis and current IgAN findings. Then the correlation between IgAN subtypes and clinical features such as eGFR and proteinuria was evaluated by using Pearson method. Subsequently, subtype heterogeneity was verified by subtype-specific modules identification based on weighted gene co-expression network analysis(WGCNA) and immune cell infiltration analysis based on CIBERSORT algorithm. RESULTS We identified 102 DEGs as marker genes for IgAN and three functional subtypes namely: viral-hormonal, bacterial-immune and mixed type. We screened seventeen genes specific to viral hormonal type (ATF3, JUN and FOS etc.), and seven genes specific to bacterial immune type (LIF, C19orf51 and SLPI etc.). The subtype-specific genes showed significantly high correlation with proteinuria and eGFR. The WGCNA modules were in keeping with functions of the IgAN subtypes where the MEcyan module was specific to the viral-hormonal type and the MElightgreen module was specific to the bacterial-immune type. The results of immune cell infiltration revealed subtype-specific cell heterogeneity which included significant differences in T follicular helper cells, resting NK cells between viral-hormone type and control group; significant differences in eosinophils, monocytes, macrophages, mast cells and other cells between bacterial-immune type and control. CONCLUSION In this study, we identified three functional subtypes of IgAN for the first time and specific expressed genes for each subtype. Then we constructed a subtype classifier and classify IgAN patients into specific subtypes, which may be benefit for the precise treatment of IgAN patients in future.
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Affiliation(s)
- Hongbiao Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Zhenwei Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Liangshuang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Qi Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Shuai Li
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Zerun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Xiangshu Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Xin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Rui Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, 150086, Harbin, China.
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Leventhal EL, Daamen AR, Grammer AC, Lipsky PE. An interpretable machine learning pipeline based on transcriptomics predicts phenotypes of lupus patients. iScience 2023; 26:108042. [PMID: 37860757 PMCID: PMC10582499 DOI: 10.1016/j.isci.2023.108042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/03/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Machine learning (ML) has the potential to identify subsets of patients with distinct phenotypes from gene expression data. However, phenotype prediction using ML has often relied on identifying important genes without a systems biology context. To address this, we created an interpretable ML approach based on blood transcriptomics to predict phenotype in systemic lupus erythematosus (SLE), a heterogeneous autoimmune disease. We employed a sequential grouped feature importance algorithm to assess the performance of gene sets, including immune and metabolic pathways and cell types, known to be abnormal in SLE in predicting disease activity and organ involvement. Gene sets related to interferon, tumor necrosis factor, the mitoribosome, and T cell activation were the best predictors of phenotype with excellent performance. These results suggest potential relationships between the molecular pathways identified in each model and manifestations of SLE. This ML approach to phenotype prediction can be applied to other diseases and tissues.
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Affiliation(s)
- Emily L. Leventhal
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Andrea R. Daamen
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Amrie C. Grammer
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
| | - Peter E. Lipsky
- AMPEL BioSolutions LLC, and the RILITE Research Institute, Charlottesville, VA 22902, USA
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Shen M, Duan C, Xie C, Wang H, Li Z, Li B, Wang T. Identification of key interferon-stimulated genes for indicating the condition of patients with systemic lupus erythematosus. Front Immunol 2022; 13:962393. [PMID: 35967341 PMCID: PMC9365928 DOI: 10.3389/fimmu.2022.962393] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with highly heterogeneous clinical symptoms and severity. There is complex pathogenesis of SLE, one of which is IFNs overproduction and downstream IFN-stimulated genes (ISGs) upregulation. Identifying the key ISGs differentially expressed in peripheral blood mononuclear cells (PBMCs) of patients with SLE and healthy people could help to further understand the role of the IFN pathway in SLE and discover potential diagnostic biomarkers.The differentially expressed ISGs (DEISG) in PBMCs of SLE patients and healthy persons were screened from two datasets of the Gene Expression Omnibus (GEO) database. A total of 67 DEISGs, including 6 long noncoding RNAs (lncRNAs) and 61 messenger RNAs (mRNAs) were identified by the “DESeq2” R package. According to Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, those DEISGs were mainly concentrated in the response to virus and immune system processes. Protein-protein interaction (PPI) network showed that most of these DEISGs could interact strongly with each other. Then, IFIT1, RSAD2, IFIT3, USP18, ISG15, OASL, MX1, OAS2, OAS3, and IFI44 were considered to be hub ISGs in SLE by “MCODE” and “Cytohubba” plugins of Cytoscape, Moreover, the results of expression correlation suggested that 3 lncRNAs (NRIR, FAM225A, and LY6E-DT) were closely related to the IFN pathway.The lncRNA NRIR and mRNAs (RSAD2, USP18, IFI44, and ISG15) were selected as candidate ISGs for verification. RT-qPCR results showed that PBMCs from SLE patients had substantially higher expression levels of 5 ISGs compared to healthy controls (HCs). Additionally, statistical analyses revealed that the expression levels of these ISGs were strongly associated to various clinical symptoms, including thrombocytopenia and facial erythema, as well as laboratory indications, including the white blood cell (WBC) count and levels of autoantibodies. The Receiver Operating Characteristic (ROC) curve demonstrated that the IFI44, USP18, RSAD2, and IFN score had good diagnostic capabilities of SLE.According to our study, SLE was associated with ISGs including NRIR, RSAD2, USP18, IFI44, and ISG15, which may contribute to the future diagnosis and new personalized targeted therapies.
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Affiliation(s)
- Mengjia Shen
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
| | - Congcong Duan
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
| | - Changhao Xie
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
| | - Hongtao Wang
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
| | - Zhijun Li
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
| | - Baiqing Li
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
| | - Tao Wang
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Bengbu Medical College, Bengbu, China
- *Correspondence: Tao Wang,
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Predicted Immune-Related Genes and Subtypes in Systemic Lupus Erythematosus Based on Immune Infiltration Analysis. DISEASE MARKERS 2022; 2022:8911321. [PMID: 35864995 PMCID: PMC9296307 DOI: 10.1155/2022/8911321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/07/2022]
Abstract
Objective The present investigation is aimed at identifying key immune-related genes linked with SLE and their roles using integrative analysis of publically available gene expression datasets. Methods Four gene expression datasets pertaining to SLE, 2 from whole blood and 2 experimental PMBC, were sourced from GEO. Shared differentially expressed genes (DEG) were determined as SLE-related genes. Immune cell infiltration analysis was performed using CIBERSORT, and case samples were subjected to k-means cluster analysis using high-abundance immune cells. Key immune-related SLE genes were identified using correlation analysis with high-abundance immune cells and subjected to functional enrichment analysis for enriched Gene Ontology Biological Processes and KEGG pathways. A PPI network of genes interacting with the key immune-related SLE genes was constructed. LASSO regression analysis was performed to identify the most significant key immune-related SLE genes, and correlation with clinicopathological features was examined. Results 309 SLE-related genes were identified and found functionally enriched in several pathways related to regulation of viral defenses and T cell functions. k-means cluster analysis identified 2 sample clusters which significantly differed in monocytes, dendritic cell resting, and neutrophil abundance. 65 immune-related SLE genes were identified, functionally enriched in immune response-related signaling, antigen receptor-mediated signaling, and T cell receptor signaling, along with Th17, Th1, and Th2 cell differentiation, IL-17, NF-kappa B, and VEGF signaling pathways. LASSO regression identified 9 key immune-related genes: DUSP7, DYSF, KCNA3, P2RY10, S100A12, SLC38A1, TLR2, TSR2, and TXN. Imputed neutrophil percentage was consistent with their expression pattern, whereas anti-Ro showed the inverse pattern as gene expression. Conclusions Comprehensive bioinformatics analyses revealed 9 key immune-related genes and their associated functions highly pertinent to SLE pathogenesis, subtypes, and identified valuable candidates for experimental research.
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Diaz-Gallo LM, Oke V, Lundström E, Elvin K, Ling Wu Y, Eketjäll S, Zickert A, Gustafsson JT, Jönsen A, Leonard D, Birmingham DJ, Nordmark G, Bengtsson AA, Rönnblom L, Gunnarsson I, Yu CY, Padyukov L, Svenungsson E. Four Systemic Lupus Erythematosus Subgroups, Defined by Autoantibodies Status, Differ Regarding HLA-DRB1 Genotype Associations and Immunological and Clinical Manifestations. ACR Open Rheumatol 2021; 4:27-39. [PMID: 34658170 PMCID: PMC8754019 DOI: 10.1002/acr2.11343] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022] Open
Abstract
Objective The heterogeneity of systemic lupus erythematosus (SLE) constitutes clinical and therapeutical challenges. We therefore studied whether unrecognized disease subgroups can be identified by using autoantibody profiling together with HLA‐DRB1 alleles and immunological and clinical data. Methods An unsupervised cluster analysis was performed based on detection of 13 SLE‐associated autoantibodies (double‐stranded DNA, nucleosomes, ribosomal P, ribonucleoprotein [RNP] 68, RNPA, Smith [Sm], Sm/RNP, Sjögren's syndrome antigen A [SSA]/Ro52, SSA/Ro60, Sjögren's syndrome antigen B [SSB]/La, cardiolipin [CL]‐Immunoglobulin G [IgG], CL–Immunoglobulin M [IgM], and β2 glycoprotein I [β2GPI]–IgG) in 911 patients with SLE from two cohorts. We evaluated whether each SLE subgroup is associated with HLA‐DRB1 alleles, clinical manifestations (n = 743), and cytokine levels in circulation (n = 446). Results Our analysis identified four subgroups among the patients with SLE. Subgroup 1 (29.3%) was dominated by anti‐SSA/Ro60/Ro52/SSB autoantibodies and was strongly associated with HLA‐DRB1*03 (odds ratio [OR] = 4.73; 95% confidence interval [CI] = 4.52‐4.94). Discoid lesions were more common for this disease subgroup (OR = 1.71, 95% CI = 1.18‐2.47). Subgroup 2 (28.7%) was dominated by anti‐nucleosome/SmRNP/DNA/RNPA autoantibodies and associated with HLA‐DRB1*15 (OR = 1.62, 95% CI = 1.41‐1.84). Nephritis was most common in this subgroup (OR = 1.61, 95% CI = 1.14‐2.26). Subgroup 3 (23.8%) was characterized by anti‐ß2GPI‐IgG/anti‐CL–IgG/IgM autoantibodies and a higher frequency of HLA‐DRB1*04 compared with the other patients with SLE. Vascular events were more common in Subgroup 3 (OR = 1.74, 95% CI = 1.2‐2.5). Subgroup 4 (18.2%) was negative for the investigated autoantibodies, and this subgroup was not associated with HLA‐DRB1. Additionally, the levels of eight cytokines significantly differed among the disease subgroups. Conclusion Our findings suggest that four fairly distinct subgroups can be identified on the basis of the autoantibody profile in SLE. These four SLE subgroups differ regarding associations with HLA‐DRB1 alleles and immunological and clinical features, suggesting dissimilar disease pathways.
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Affiliation(s)
- Lina-Marcela Diaz-Gallo
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vilija Oke
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Emeli Lundström
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kerstin Elvin
- Department of Clinical Immunology and Transfusion Medicine, Unit of Clinical Immunology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Yee Ling Wu
- The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Department of Microbiology and Immunology, Loyola University Chicago, lk, Illinois
| | - Susanna Eketjäll
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Agneta Zickert
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden
| | - Johanna T Gustafsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences, Section of Rheumatology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | | | - Gunnel Nordmark
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Anders A Bengtsson
- Department of Clinical Sciences, Section of Rheumatology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden
| | - Chack-Yung Yu
- The Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinksa University Hospital, Stockholm, Sweden
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