Identification of Potential Biomarkers and Biological Pathways in Juvenile Dermatomyositis Based on miRNA-mRNA Network

Identifying potential pathogenesis and immune infiltration in diabetic foot ulcers using bioinformatics and in vitro analyses

BACKGROUND

Diabetic foot ulcers (DFU) are among the fastest-growing diseases worldwide. Recent evidence has emphasized the critical role of microRNA (miRNA)-mRNA networks in various chronic wounds, including DFU. In this study, we aimed to clarify the miRNA-mRNA axes associated with the occurrence of DFU.

METHODS

Expression profiles of miRNAs and mRNAs were extracted from the Gene Expression Omnibus. Differentially expressed genes and differentially expressed miRNAs were identified, and miRNA-mRNA regulatory axes were constructed through integrated bioinformatics analyses. We validated the miRNA-mRNA axes using quantitative real-time PCR (qPCR) and dual-luciferase reporter assays. We conducted an immune infiltration analysis and confirmed the bioinformatics results using immunofluorescence staining. Single-sample gene set enrichment analysis (ssGSEA) was used to analyze the metabolic mechanisms.

RESULTS

miR-182-5p-CHL1/MITF and miR-338-3p-NOVA1 interactions were identified using in silico analysis. The qPCR results showed apparent dysregulation of these miRNA-mRNA axes in DFU. The dual-luciferase reporter assay confirmed that miR-182-5p targeted CHL1 and MITF, and miR-338-3p targeted NOVA1. We conducted an immune infiltration analysis and observed that key genes correlated with decreased infiltration of M1 macrophages and resting mast cells in DFU. Immunofluorescence staining verified the co-localization of CHL1 and tryptase, while MITF and CD68 showed weak positive correlations. Metabolic pathways related to these three genes were identified using ssGSEA.

CONCLUSIONS

In summary, the miR-182-5p-CHL1/MITF and miR-338-3p-NOVA1 pathway interactions and decreased infiltration of M1 macrophages and resting mast cells may provide novel clues to the pathogenesis of DFU.

TRIAL REGISTRATION

The clinical trial included in this study was registered in the Chinese Clinical Trial Registry ( ChiCTR2200066660 ) on December 13, 2022.

Idiopathic inflammatory myopathy and non-coding RNA

Idiopathic inflammatory myopathies (IIMs) are common autoimmune diseases that affect skeletal muscle quality and function. The lack of an early diagnosis and treatment can lead to irreversible muscle damage. Non-coding RNAs (ncRNAs) play an important role in inflammatory transfer, muscle regeneration, differentiation, and regulation of specific antibody levels and pain in IIMs. ncRNAs can be detected in blood and hair; therefore, ncRNAs detection has great potential for diagnosing, preventing, and treating IIMs in conjunction with other methods. However, the specific roles and mechanisms underlying the regulation of IIMs and their subtypes remain unclear. Here, we review the mechanisms by which micro RNAs and long non-coding RNA-messenger RNA networks regulate IIMs to provide a basis for ncRNAs use as diagnostic tools and therapeutic targets for IIMs.

Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis

Dermatomyositis is an autoimmune disease characterized by severe symmetrical muscle dysfunction and pain. This study was aimed at discovering vital hub genes and potential molecular pathways of DM through bioinformatics analysis, which contributes to identifying potential diagnostic or therapeutic biomarkers and targets. In this study, a total of 915 DEGs in DM samples including 167 upregulated genes and 748 downregulated genes were screened out by the limma package based on the GSE142807 dataset from the Gene Expression Omnibus (GEO) database. Furthermore, the results of Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that these downregulated genes were highly associated with the immune-related biological processes and pathways. Therefore, 41 genes closely related to DM were extracted for further study based on the subcluster analysis through the Molecular Complex Detection (MCODE) software plugin in Cytoscape. Ultimately, 10 hub genes (including ISG15, DDX58, IFIT3, CXCL10, and STAT1) were identified as the potential candidate biomarkers and targets. Besides, we found that the identified hub genes directly or indirectly communicated with each other via molecular signaling pathways on the protein and transcription level. In general, under the guidance of bioinformatics analysis, 10 vital hub genes and molecular mechanisms in DM were identified and the expression of proinflammatory factors and interferon family proteins and genes showed high association with DM, which might help provide a theoretical foundation for the development of point-to-point targeted therapy in the future treatment of DM.

Polishing the crystal ball: mining multi-omics data in dermatomyositis

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.

Juvenile Dermatomyositis: Advances in Pathogenesis, Assessment, and Management

BACKGROUND

Juvenile dermatomyositis is the most common inflammatory myopathy in the pediatric age group and a major cause of mortality and morbidity in individuals with childhood rheumatic diseases. Mounting evidence suggests that early diagnosis and timely aggressive treatment are associated with better outcomes.

OBJECTIVE

The purpose of this article is to provide readers with an update on the evaluation, diagnosis, and the treatment of juvenile dermatomyositis.

METHODS

A PubMed search was performed in Clinical Queries using the key term "juvenile dermatomyositis" in the search engine. The search strategy included meta-analyses, randomized controlled trials, clinical trials, observational studies, and reviews. The search was restricted to English literature. The information retrieved from the above search was used in the compilation of the present article.

RESULTS

Juvenile dermatomyositis is a chronic autoimmune inflammatory condition characterized by systemic capillary vasculopathy that primarily affects the skin and muscles with possible involvement of other organs. In 2017, the European League Against Rheumatism (EULAR) and the American College of Rheumatology (ACR) developed diagnostic criteria for juvenile idiopathic inflammatory myopathies and juvenile dermatomyositis. In the absence of muscle biopsies which are infrequently performed in children, scores (in brackets) are assigned to four variables related to muscle weakness, three variables related to skin manifestations, one variable related to other clinical manifestations, and two variables related to laboratory measurements to discriminate idiopathic inflammatory myopathies from non-idiopathic inflammatory myopathies as follows: objective symmetric weakness, usually progressive, of the proximal upper extremities (0.7); objective symmetric weakness, usually progressive, of the proximal lower extremities (0.8); neck flexors relatively weaker than neck extensors (1.9); leg proximal muscles relatively weaker than distal muscles (0.9); heliotrope rash (3.1); Gottron papules (2.1); Gottron sign (3.3); dysphagia or esophageal dysmotility (0.7); the presence of anti-Jo-1 autoantibody (3.9); and elevated serum levels of muscle enzymes (1.3). In the absence of muscle biopsy, a definite diagnosis of idiopathic inflammatory myopathy can be made if the total score is ≥7.5. Patients whose age at onset of symptoms is less than 18 years and who meet the above criteria for idiopathic inflammatory myopathy and have a heliotrope rash, Gottron papules or Gottron sign are deemed to have juvenile dermatomyositis. The mainstay of therapy at the time of diagnosis is a high-dose corticosteroid (oral or intravenous) in combination with methotrexate.

CONCLUSION

For mild to moderate active muscle disease, early aggressive treatment with high-dose oral prednisone alone or in combination with methotrexate is the cornerstone of management. Pulse intravenous methylprednisolone is often preferred to oral prednisone in more severely affected patients, patients who respond poorly to oral prednisone, and those with gastrointestinal vasculopathy. Other steroid-sparing immunosuppressive agents such as cyclosporine and cyclophosphamide are reserved for patients with contraindications or intolerance to methotrexate and for refractory cases, as the use of these agents is associated with more adverse events. Various biological agents have been used in the treatment of juvenile dermatomyositis. Data on their efficacy are limited, and their use in the treatment of juvenile dermatomyositis is considered investigational.

Aberrant expression of the UPF1 RNA surveillance gene disturbs keratinocyte homeostasis by stabilizing AREG

The up-frameshift suppressor 1 homolog (UPF1) RNA surveillance gene is a core element in the nonsense-mediated RNA decay (NMD) pathway, which impacts a broad spectrum of biological processes in a cell-specific manner. In the present study, the contribution of the NMD pathway to psoriasis lesions and its moderating effects on the biological processes of keratinocytes was reported. Sanger sequencing for skin scales from two patients with psoriasis identified two mRNA mutations (c.2935_2936insA and c.2030-2081del) in the UPF1 gene. The somatic mutants produced truncated UPF1 proteins and perturbed the NMD pathway in cells, leading to the upregulation of NMD substrates. As the most abundant epidermal growth factor receptor ligand in keratinocytes, it was concluded that amphiregulin (AREG) mRNA is a natural NMD substrate, that is dependent on its 3′ untranslated region sequence. Perturbed NMD modulated keratinocyte homeostasis in an AREG-dependent but nonidentical manner, which highlighted the unique characteristics of NMD in keratinocytes. By targeting AREG mRNA post-transcriptionally, the UPF1-NMD pathway contributed to an imbalance between proliferation on the one hand, and apoptosis and abnormal differentiation, migration and inflammatory response on the other, in keratinocytes, which indicated a role of the NMD pathway in the full development of keratinocyte-related morbidity and skin diseases.