1
|
Talotta R. Sequence Alignment between TRIM33 Gene and Human Noncoding RNAs: A Potential Explanation for Paraneoplastic Dermatomyositis. J Pers Med 2024; 14:628. [PMID: 38929849 PMCID: PMC11204533 DOI: 10.3390/jpm14060628] [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: 05/25/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND This computational analysis investigated sequence complementarities between the TRIM33 gene and human noncoding (nc)RNAs and characterized their interactions in the context of paraneoplastic dermatomyositis. METHODS TRIM33 FASTA sequence (NCBI Reference Sequence: NC_000001.11) was used for BLASTN analysis against Human GRCh38 in the Ensembl.org database. Retrieved ncRNAs showing hits to TRIM33 were searched in the GeneCards.org database and further analyzed through RNAInter, QmRLFS-finder, Spliceator, and NcPath enrichment analysis. RESULTS A total of 100 hits were found, involving the lncRNAs NNT-AS1, MKLN1-AS, LINC01206, and PAXBP1-AS1, whose dysregulation has been reported in either cancer or dermatomyositis. Additionally, the lncRNAs NNT-AS1 and PAXBP1-AS1 may interact with microRNA-142-3p, reducing its expression and increasing that of TRIM33. Sequence complementarity affected only TRIM33 intron 1, possibly resulting in alternatively spliced isoforms of TIF1γ with increased immunogenicity. The results also revealed nucleotide alignment between TRIM33 and the gene regulatory elements of 28 ncRNA genes involved in immune pathways. CONCLUSIONS This pivotal study demonstrates sequence complementarity between TRIM33 and human ncRNAs dysregulated in cancer and dermatomyositis. This scenario may lead to the overproduction of more immunogenic TIF1γ variants in tumors and the stimulation of autoimmunity. Further experimental analyses using targeted methods such as Western blot or Chip-Seq are required to confirm these data.
Collapse
Affiliation(s)
- Rossella Talotta
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University Hospital "Gaetano Martino", 98124 Messina, Italy
| |
Collapse
|
2
|
Shi J, Zhou S, Zhao J, Xu D, Huang H, Li M, Tian X, He L, Wu C, Wang Q, Zhao Y, Zeng X. Microarray analysis of microrna expression in peripheral blood mononuclear cells of patients with polymyositis and dermatomyositis. J Transl Int Med 2024; 12:170-176. [PMID: 38779122 PMCID: PMC11107181 DOI: 10.2478/jtim-2022-0055] [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] [Indexed: 05/25/2024] Open
Abstract
Background and Objectives MicroRNAs (miRNAs) represent a new class of biomarkers in the context of connective tissue disorders. The miRNA expression profiles in peripheral blood mononuclear cells (PBMCs) of patients with polymyositis (PM) and dermatomyositis (DM) have not been fully elucidated. The objective is to investigate miRNAs expression profile in PBMCs of patients with PM/DM. Methods Microarray technology was used to identify differentially expressed miRNAs in PBMCs obtained from 6 untreated PM/DM patients and 3 healthy controls (HCs). TaqMan-based stem-loop real-time PCR detection was used for validation in a cohort of 34 PM/DM patients and 20 HCs. Results Microarray analysis revealed 38 differentially expressed miRNAs (24 up-regulated and 14 down-regulated) in PM/DM patients compared to HCs. Four miRNAs (miR-320a, miR-335-3p, miR-34a-5p and miR-454-3p) were chosen for real-time PCR validation. The expression of miR-34a-5p was significantly upregulated in PM/DM group (P < 0.05). In subgroup analysis, miR-34a-5p was significantly upregulated in interstitial lung disease (ILD) group and DM group (P < 0.001). The level of SIRT1, a validated target of miR-34a, was significantly lower in PBMCs of PM/DM patients compared with HCs. Conclusions MiR-34a-5p may potentially participate in the pathogenesis of PM/DM through SIRT1, and may serve as a potential new biomarker for PM/DM-ILD.
Collapse
Affiliation(s)
- Jia Shi
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Shuang Zhou
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Dong Xu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Hui Huang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100730, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Xinping Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Linrong He
- China-Japan Friendship Hospital, Yinghua East Road, Chaoyang District, Beijing100029, China
| | - Chanyuan Wu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Yan Zhao
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| |
Collapse
|
3
|
Muñoz-Braceras S, Pinal-Fernandez I, Casal-Dominguez M, Pak K, Milisenda JC, Lu S, Gadina M, Naz F, Gutierrez-Cruz G, Dell’Orso S, Torres-Ruiz J, Grau-Junyent JM, Selva-O’Callaghan A, Paik JJ, Albayda J, Christopher-Stine L, Lloyd TE, Corse AM, Mammen AL. Identification of Unique microRNA Profiles in Different Types of Idiopathic Inflammatory Myopathy. Cells 2023; 12:2198. [PMID: 37681930 PMCID: PMC10487266 DOI: 10.3390/cells12172198] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
Dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotizing myopathy (IMNM), and inclusion body myositis (IBM) are four major types of idiopathic inflammatory myopathy (IIM). Muscle biopsies from each type of IIM have unique transcriptomic profiles. MicroRNAs (miRNAs) target messenger RNAs (mRNAs), thereby regulating their expression and modulating transcriptomic profiles. In this study, 18 DM, 12 IMNM, 6 AS, 6 IBM, and 6 histologically normal muscle biopsies underwent miRNA profiling using the NanoString nCounter system. Eleven miRNAs were exclusively differentially expressed in DM compared to controls, seven miRNAs were only differentially expressed in AS, and nine miRNAs were specifically upregulated in IBM. No differentially expressed miRNAs were identified in IMNM. We also analyzed miRNA-mRNA associations to identify putative targets of differentially expressed miRNAs. In DM and AS, these were predominantly related to inflammation and cell cycle progression. Moreover, our analysis showed an association between miR-30a-3p, miR-30e-3p, and miR-199b-5p downregulation in DM and the upregulation of target genes induced by type I interferon. In conclusion, we show that muscle biopsies from DM, AS, and IBM patients have unique miRNA signatures and that these miRNAs might play a role in regulating the expression of genes known to be involved in IIM pathogenesis.
Collapse
Affiliation(s)
- Sandra Muñoz-Braceras
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
| | - Iago Pinal-Fernandez
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Maria Casal-Dominguez
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Katherine Pak
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
| | - José César Milisenda
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Muscle Research Unit, Internal Medicine Service, Hospital Clinic de Barcelona, 08036 Barcelona, Spain;
- CIBERER, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Shajia Lu
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (S.L.); (M.G.)
| | - Massimo Gadina
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (S.L.); (M.G.)
| | - Faiza Naz
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.N.); (G.G.-C.)
| | - Gustavo Gutierrez-Cruz
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.N.); (G.G.-C.)
| | - Stefania Dell’Orso
- Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (F.N.); (G.G.-C.)
| | - Jiram Torres-Ruiz
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Josep Maria Grau-Junyent
- Muscle Research Unit, Internal Medicine Service, Hospital Clinic de Barcelona, 08036 Barcelona, Spain;
- CIBERER, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Albert Selva-O’Callaghan
- Systemic Autoimmune Diseases Unit, Vall d’Hebron General Hospital, Universitat Autònoma de Barcelona, 08035 Barcelona, Spain;
| | - Julie J. Paik
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| | - Jemima Albayda
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| | - Lisa Christopher-Stine
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| | - Thomas E. Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Andrea M. Corse
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
| | - Andrew L. Mammen
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (I.P.-F.); (M.C.-D.); (K.P.); (J.C.M.); (J.T.-R.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (L.C.-S.); (T.E.L.); (A.M.C.)
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (J.J.P.); (J.A.)
| |
Collapse
|
4
|
Oxidative stress, mitochondrial dysfunction, and respiratory chain enzyme defects in inflammatory myopathies. Autoimmun Rev 2023; 22:103308. [PMID: 36822387 DOI: 10.1016/j.autrev.2023.103308] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
We investigated the relationship between oxidative stress and inflammatory myopathies. We searched in the current literature the role of mitochondria and respiratory chain defects as sources of oxidative stress and reactive oxygen species production that led to muscle weakness and fatigue. Different molecules and pathways contribute to redox milieu, reactive oxygen species generation, accumulation of misfolded and carbonylated proteins that lose their ability to fulfil cellular activities. Small peptides and physical techniques proved, in mice models, to reduce oxidative stress. We focused on inclusion body myositis, as a major expression of myopathy related to oxidative stress, where mitochondrial abnormalities are causative agents as well. We described the effect of physical exercise in inclusion body myositis that showed to increase strength and to reduce beta amyloid accumulation with subsequent improvement of the mitochondrial functions. We illustrated the influence of epigenetic control on the immune system by non-coding genetic material in the interaction between oxidative stress and inflammatory myopathies.
Collapse
|
5
|
Lu Z, Chen Y, Chen S, Zhu X, Wang C, Wang Z, Yao Q. Comprehensive Prognostic Analysis of Immune Implication Value and Oxidative Stress Significance of NECAP2 in Low-Grade Glioma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1494520. [PMID: 36531205 PMCID: PMC9750773 DOI: 10.1155/2022/1494520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 12/07/2023]
Abstract
Adaptin ear-binding coat-associated protein 2 (NECAP2) belongs to the family of proteins encoding adaptin-ear-binding coat-associated proteins. However, its immune effect on tumors and its microenvironment are still unclear. Here, we systematically evaluated the differences (variations) in NECAP2 expression for low-grade glioma (LGG) and pan-cancer in the LGG dataset of The Cancer Genome Atlas (TCGA) utilizing bioinformatics methods. We found for the first time that NECAP2 level was elevated in gliomas and that this upregulation increased as the tumor grade increased. In addition, Pearson correlations of NECAP2 with five immune pathways and significant gene mutations associated with NECAP2 were also analyzed. Univariate survival and multivariate Cox analyses were used to compare the clinical characteristics and survival of the patients. Glioma patients with NECAP2 overexpression have a remarkably higher risk of developing malignant behavior and a worse prognosis. The correlation between the expression levels of NECAP2 and the prognosis of glioma patients was identified. Kaplan-Meier curves showed that patients with upregulated NECAP2 expression exhibited an unfavorable prognosis. Western blotting showed that NECAP2 was overexpressed in glioma patients. IHC staining results illustrated an elevation in the NECAP2 protein expression level with the development of tumor malignancy. Additionally, qRT-PCR verified that oxidative stress in glioma tissues reduced the expression of stress-related genes and oxidative stress capacity compared to normal tissues, which may be associated with tumor evasion of immune surveillance and tumor progression. In vitro wound-healing and Transwell assay confirmed that NECAP2 promotes glioma cell migration and invasion. Our study also thoroughly examined the immune significance of NECAP2 in the TCGA-LGG samples, using CIBERSORT and ESTIMATE to explore the correlation between NECAP2 and cancer immune infiltration. The NECAP2 expression levels were correlated with the infiltration degree of immune cells such as neutrophils, CD4+ T cells, macrophages, CD8+ T cells, and B cells. Therefore, our results indicate that NECAP2 strongly correlates with the overall immune infiltration level of glioma and could independently serve as a prognostic biological marker for glioma patients.
Collapse
Affiliation(s)
- Zhichao Lu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yixun Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Siqi Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Xingjia Zhu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Chenxing Wang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Ziheng Wang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Qi Yao
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| |
Collapse
|
6
|
Chen J, Zhang R, Xie M, Luan C, Li X. Transcriptome Sequencing Identifies PLAUR as an Important Player in Patients With Dermatomyositis-Associated Interstitial Lung Disease. Front Genet 2021; 12:784215. [PMID: 34938325 PMCID: PMC8685457 DOI: 10.3389/fgene.2021.784215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/03/2021] [Indexed: 11/15/2022] Open
Abstract
Dermatomyositis (DM), an inflammatory disorder, is often associated with interstitial lung disease (ILD). However, the underlying mechanism remains unclear. Our study performed RNA sequencing (RNA-seq) and integrative bioinformatics analysis of differentially expressed genes (DEGs) in patients with dermatomyositis-associated interstitial lung disease (DM-ILD) and healthy controls. A total of 2,018 DEGs were identified between DM-ILD and healthy blood samples. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that DEGs were mainly involved in immune- and inflammatory-related biological processes and pathways. Disease ontology (DO) enrichment analysis identified 35 candidate key genes involved in both skin and lung diseases. Meanwhile, a total of 886 differentially expressed alternative splicing (AS) events were found between DM-ILD and healthy blood samples. After overlapping DEGs with differential AS genes, the plasminogen activator and urokinase receptor (PLAUR) involved in immune-related biological processes and complement and coagulation cascades was screened and identified as the most important gene associated with DM-ILD. The protein–protein interaction (PPI) network revealed that PLAUR had interactions with multiple candidate key genes. Moreover, we observed that there were significantly more neutrophils and less naive B cells in DM-ILD samples than in healthy samples. And the expression of PLAUR was significantly positively correlated with the abundance of neutrophils. Significant higher abundance of PLAUR in DM-ILD patients than healthy controls was validated by RT-qPCR. In conclusion, we identified PLAUR as an important player in regulating DM-ILD by neutrophil-associated immune response. These findings enrich our understanding, which may benefit DM-ILD patients.
Collapse
Affiliation(s)
- Juan Chen
- Department of Rheumatology and Clinical Immunology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruixian Zhang
- The Center for Disease Control and Prevention of Yunnan Province, Kunming, China
| | - Min Xie
- Department of Rheumatology and Clinical Immunology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chunyan Luan
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolan Li
- Department of Dermatology and Venereology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| |
Collapse
|
7
|
Li L, Zuo X, Liu D, Luo H, Zhu H. The Functional Roles of RNAs Cargoes Released by Neutrophil-Derived Exosomes in Dermatomyositis. Front Pharmacol 2021; 12:727901. [PMID: 34603043 PMCID: PMC8484304 DOI: 10.3389/fphar.2021.727901] [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] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/20/2021] [Indexed: 12/28/2022] Open
Abstract
Dermatomyositis (DM) is an idiopathic inflammatory myopathy characterized by cutaneous manifestations. We first identified the profiles of noncoding RNAs (lncRNAs and miRNAs) in peripheral neutrophil exosomes (EXOs) of DM patients and explored their potential functional roles. Bioinformatics analyses were performed with R packages. Real-time quantitative PCR was used to validate the altered RNAs in DM neutrophil EXO-stimulated human dermal microvascular endothelial cells (HDMECs) and human skeletal muscle myoblasts (HSkMCs). In DM neutrophil EXOs, 124 upregulated lncRNAs (with 1,392 target genes), 255 downregulated lncRNAs (with 1867 target genes), 17 upregulated miRNAs (with 2,908 target genes), and 15 downregulated miRNAs (with 2,176 target genes) were identified. GO analysis showed that the differentially expressed (DE) lncRNAs and DE miRNAs participated in interleukin-6 and interferon-beta production, skeletal muscle cell proliferation and development, and endothelial cell development and differentiation. KEGG analysis suggested that DE lncRNAs and DE miRNAs were enriched in the PI3K–Akt, MAPK, AMPK and FoxO signalling pathways. Many novel and valuable DE lncRNAs and DE miRNAs interacted and cotargeted in the PI3K–Akt, MAPK, AMPK and FoxO signalling pathways. Our study suggests that neutrophil EXOs participate in DM pathogenesis through lncRNAs and miRNAs in the PI3K–Akt, MAPK, AMPK and FoxO signalling pathways.
Collapse
Affiliation(s)
- Liya Li
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, China.,The Department of Rheumatology and Immunology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxia Zuo
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, China.,Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Di Liu
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, China
| | - Hui Luo
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, China.,Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| | - Honglin Zhu
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, China.,Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
| |
Collapse
|
8
|
Castillo RL, Femia AN. Polishing the crystal ball: mining multi-omics data in dermatomyositis. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:435. [PMID: 33842656 PMCID: PMC8033302 DOI: 10.21037/atm-20-5319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Precision medicine, which recognizes and upholds the uniqueness of each individual patient and the importance of discerning these inter-individual differences on a molecular scale in order to provide truly personalized medical care, is a revolutionary approach that relies on the discovery of clinically-relevant biomarkers derived from the massive amounts of data generated by epigenomic, genomic, transcriptomic, proteomic, microbiomic, and metabolomic studies, collectively known as multi-omics. If harnessed and mined appropriately with the help of ever-evolving computational and analytic methods, the collective data from omics studies has the potential to accelerate delivery of targeted medical treatment that maximizes benefit, minimizes harm, and eliminates the “fortune-telling” inextricably linked to the prevailing trial-and-error approach. For a disease such as dermatomyositis (DM), which is characterized by remarkable phenotypic heterogeneity and varying degrees of multi-organ involvement, an individualized approach that incorporates big data derived from multi-omics studies with the results of currently available serologic, histopathologic, radiologic, and electrophysiologic tests, and, most importantly, with clinical findings obtained from a thorough history and physical examination, has immense diagnostic, therapeutic, and prognostic value. In this review, we discuss omics-based research studies in DM and describe their practical applications and promising roles in guiding clinical decisions and optimizing patient outcomes.
Collapse
Affiliation(s)
- Rochelle L Castillo
- Department of Medicine, Division of Rheumatology, NYU Grossman School of Medicine, New York, NY, USA
| | - Alisa N Femia
- Ronald O. Perelman Department of Dermatology, NYU Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
9
|
Reolid A, Muñoz-Aceituno E, Abad-Santos F, Ovejero-Benito MC, Daudén E. Epigenetics in Non-tumor Immune-Mediated Skin Diseases. Mol Diagn Ther 2021; 25:137-161. [PMID: 33646564 DOI: 10.1007/s40291-020-00507-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 02/08/2023]
Abstract
Epigenetics is the study of the mechanisms that regulate gene expression without modifying DNA sequences. Knowledge of and evidence about how epigenetics plays a causative role in the pathogenesis of many skin diseases is increasing. Since the epigenetic changes present in tumor diseases have been thoroughly reviewed, we believe that knowledge of the new epigenetic findings in non-tumor immune-mediated dermatological diseases should be of interest to the general dermatologist. Hence, the purpose of this review is to summarize the recent literature on epigenetics in most non-tumor dermatological pathologies, focusing on psoriasis. Hyper- and hypomethylation of DNA methyltransferases and methyl-DNA binding domain proteins are the most common and studied methylation mechanisms. The acetylation and methylation of histones H3 and H4 are the most frequent and well-characterized histone modifications and may be associated with disease severity parameters and serve as therapeutic response markers. Many specific microRNAs dysregulated in non-tumor dermatological disease have been reviewed. Deepening the study of how epigenetic mechanisms influence non-tumor immune-mediated dermatological diseases might help us better understand the role of interactions between the environment and the genome in the physiopathogenesis of these diseases.
Collapse
Affiliation(s)
- Alejandra Reolid
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Diego de León, 62, 28006, Madrid, Spain.
| | - E Muñoz-Aceituno
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), Diego de León, 62, 28006, Madrid, Spain
| | - F Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - M C Ovejero-Benito
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - E Daudén
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| |
Collapse
|
10
|
Construction and validation of an immunity-related prognostic signature for breast cancer. Aging (Albany NY) 2020; 12:21597-21612. [PMID: 33216733 PMCID: PMC7695418 DOI: 10.18632/aging.103952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/08/2020] [Indexed: 12/24/2022]
Abstract
Breast cancer is one of the most lethal malignancies among women, and understanding the effects of host immunity on disease progression offers the potential to improve immunotherapies against it. Here, we constructed an immunity-related gene (IRG)-based prognostic signature to stratify breast cancer patients and predict their survival. We identified differentially-expressed genes by analyzing the breast cancer transcriptome data from The Cancer Genome Atlas. Univariate Cox regression revealed 179 survival-correlated IRGs, 12 of which we used to construct an immunity-based prognostic signature that stratified breast cancer patients into high- and low-risk groups. The signature was an independent predictor for survival and was validated in an independent dataset. We also investigated the correlations between our prognostic signature and immune infiltrates and found that signature-derived risk scores correlated negatively with infiltration of B cells, CD4+ T cells, CD8+ T cells, neutrophils and dendritic cells. Our results show that the proposed prognostic signature reflects the tumor immune microenvironment, which makes it a potential indicator for survival that warrants further research to assess its clinical utility.
Collapse
|
11
|
Casares-Marfil D, Martín J, Acosta-Herrera M. Genomic opportunities for drug repositioning in systemic seropositive rheumatic diseases. Expert Rev Clin Immunol 2020; 16:343-346. [DOI: 10.1080/1744666x.2020.1738926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain
| | | |
Collapse
|
12
|
Dermatomyositis: Clinical features and pathogenesis. J Am Acad Dermatol 2020; 82:267-281. [DOI: 10.1016/j.jaad.2019.06.1309] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/22/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022]
|
13
|
Abstract
Autoimmune diseases, such as rheumatoid arthritis, systematic lupus erythematosus and Sjögren's syndrome, are a group of diseases characterized by the activation of immune cells and excessive production of autoantibodies. Although the pathogenesis of these diseases is still not completely understood, studies have shown that multiple factors including genetics, environment and immune responses play important roles in the development and progression of the diseases. In China, there are great achievements in the mechanisms of autoimmune diseases during the last decades. These studies provide new insight to understand the diseases and also shed light on the development of novel therapy.
Collapse
Affiliation(s)
- Ru Li
- Department of Rheumatology & Immunology, Peking University People's Hospital, Beijing, China; Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China.
| | - Xing Sun
- Department of Rheumatology & Immunology, Peking University People's Hospital, Beijing, China; Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Xu Liu
- Department of Rheumatology & Immunology, Peking University People's Hospital, Beijing, China; Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Yue Yang
- Department of Rheumatology & Immunology, Peking University People's Hospital, Beijing, China; Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Zhanguo Li
- Department of Rheumatology & Immunology, Peking University People's Hospital, Beijing, China; Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| |
Collapse
|