Integrative Bioinformatics Analysis Identifies DDX60 as a Potential Biomarker for Systemic Lupus Erythematosus

Deciphering the potential ability of DExD/H-box helicase 60 (DDX60) on the proliferation, diagnostic and prognostic biomarker in pancreatic cancer: a research based on silico, RNA-seq and molecular biology experiment

BACKGROUND

Pancreatic cancer is one of the most malignant abdominal tumors. DDX60 has been shown to be associated with a variety of tumor biological processes. However, DDX60 in pancreatic cancer has not been reported. Our study confirmed that DDX60 can serve as a novel biomarker for diagnosis and treatment of pancreatic cancer.

MATERIALS AND METHODS

We downloaded pancreatic cancer datasets from GEO and TCGA databases, respectively. To investigate the relationship between DDX60 expression and prognosis in pancreatic cancer. GSEA analysis was performed on DDX60. We performed RNA-seq to further explore the downstream biological targets of DDX60 and the signaling pathways that may be involved in pancreatic cancer. Finally, we tested it through molecular biology experiments. First, we constructed the plasmid and tested the plasmid effect by WB. Then MTT assay was performed to explore the effect of DDX60 knockout on the proliferation of pancreatic cancer cells. LDH assay was performed to explore the effect of DDX60 on the release of lactate dehydrogenase from tumor cells. The effect of DDX60 on cell proliferation was further explored by clonal formation experiment. Continue to explore clinical therapeutic drugs sensitive to DDX60 targets.

RESULTS

By analyzing the GSE71729, GSE183795, GSE16515, GSE28735 and GSE62452 data sets, we found that DDX60 was highly expressed in pancreatic cancer. And is associated with poorer outcomes for pancreatic patients. The mRNA expression level of DDX60 was correlated with lymph node metastasis and grade in clinical pancreatic patients. Through the results of RNA-seq analysis, GO and KEGG analysis showed that DDX60 may be associated with cell cycle in pancreatic cancer. Through molecular biology experiments (MTT, LDH, and clonal formation experiment), we found that When DDX60 is knocked down in pancreatic cancer cells, the proliferation ability of tumor cells is significantly decreased. Several drugs targeting about DDX60 have been found, such as JW-7-52-1, this could provide direction for drug therapy against the DDX60 target.

CONCLUSION

In summary, DDX60 can be used as a novel biomarker related to the diagnosis and treatment of pancreatic cancer, participate in tumor proliferation, and is associated with poor prognosis in patients.

Biomarkers for systemic lupus erythematosus: A scoping review

BACKGROUND

In recent years, newly discovered potential biomarkers have great research potential in the diagnosis, disease activity prediction, and treatment of systemic lupus erythematosus (SLE).

OBJECTIVE

In this study, a scoping review of potential biomarkers for SLE over several years has identified the extent to which studies on biomarkers for SLE have been conducted, the specificity, sensitivity, and diagnostic value of potential biomarkers of SLE, the research potential of these biomarkers in disease diagnosis, and activity detection is discussed.

METHODS

In PubMed and Google Scholar databases, "SLE," "biomarkers," "predictor," "autoimmune diseases," "lupus nephritis," "neuropsychiatric SLE," "diagnosis," "monitoring," and "disease activity" were used as keywords to systematically search for SLE molecular biomarkers published from 2020 to 2024. Analyze and summarize the literature that can guide the article.

CONCLUSIONS

Recent findings suggest that some potential biomarkers may have clinical application prospects. However, to date, many of these biomarkers have not been subjected to repeated clinical validation. And no single biomarker has sufficient sensitivity and specificity for SLE. It is not scientific to choose only one or several biomarkers to judge the complex disease of SLE. It may be a good direction to carry out a meta-analysis of various biomarkers to find SLE biomarkers suitable for clinical use, or to evaluate SLE by combining multiple biomarkers through mathematical models. At the same time, advanced computational methods are needed to analyze large data sets and discover new biomarkers, and strive to find biomarkers that are sensitive and specific enough to SLE and can be used in clinical practice, rather than only staying in experimental research and data analysis.

Predicting autoimmune diseases: A comprehensive review of classic biomarkers and advances in artificial intelligence

Autoimmune diseases comprise a spectrum of disorders characterized by the dysregulation of immune tolerance, resulting in tissue or organ damage and inflammation. Their prevalence has been on the rise, significantly impacting patients' quality of life and escalating healthcare costs. Consequently, the prediction of autoimmune diseases has recently garnered substantial interest among researchers. Despite their wide heterogeneity, many autoimmune diseases exhibit a consistent pattern of paraclinical findings that hold predictive value. From serum biomarkers to various machine learning approaches, the array of available methods has been continuously expanding. The emergence of artificial intelligence (AI) presents an exciting new range of possibilities, with notable advancements already underway. The ultimate objective should revolve around disease prevention across all levels. This review provides a comprehensive summary of the most recent data pertaining to the prediction of diverse autoimmune diseases and encompasses both traditional biomarkers and the latest innovations in AI.

Decoding the connection between SLE and DNA Sensors: A comprehensive review

Systemic lupus erythematosus (SLE) is recognized as a prevalent autoimmune disorder characterized by a multifaceted pathogenesis potentially influenced by a combination of environmental factors, genetic predisposition, and hormonal regulation. The continuous study of immune system activation is especially intriguing. Analysis of blood samples from individuals with SLE reveals an abnormal increase in interferon levels, along with the existence of anti-double-stranded DNA antibodies. This evidence suggests that the development of SLE may be initiated by innate immunity. The presence of abnormal dsDNA fragments can activate DNA sensors within cells, particularly immune cells, leading to the initiation of downstream signaling cascades that result in the upregulation of relevant cytokines and the subsequent initiation of adaptive immune responses, such as B cell differentiation and T cell activation. The intricate pathogenesis of SLE results in DNA sensors exhibiting a wide range of functions in innate immune responses that are subject to variation based on cell types, developmental processes, downstream effector signaling pathways and other factors. The review aims to reorganize how DNA sensors influence signaling pathways and contribute to the development of SLE according to current studies, with the aspiration of furnishing valuable insights for future investigations into the pathological mechanisms of SLE and potential treatment approaches.

Possible involvement of DExD/H box helicase 60 in synovial inflammation of rheumatoid arthritis: role of toll-like receptor 3 signaling

BACKGROUND

Innate immunity is known to be implicated in the etiology of synovitis in rheumatoid arthritis (RA). However, details of the molecular mechanisms have not been fully clarified. DExD/H-box helicase 60 (DDX60), a putative RNA helicase, is of consequence in anti-viral innate immune reactions followed by inflammation. Although DDX60 is involved in the pathogenesis of autoimmune diseases such as systemic lupus nephritis, the role of DDX60 in RA has not been elucidated. The objective of this study was to examine the expression and the role of DDX60 in RA synovial inflammation.

METHODS AND RESULTS

DDX60 protein expression was investigated by immunohistochemistry in synovial tissues resected from 4 RA and 4 osteoarthritis (OA) patients. We found that synovial DDX60 expression was more intense in RA than in OA. Treatment of human rheumatoid fibroblast-like synoviocytes in culture with polyinosinic-polycytidylic acid, a Toll-like receptor 3 (TLR3) ligand, increased DDX60 protein and mRNA expression. A knockdown experiment of DDX60 using RNA interference revealed a decrease in the expression of poly IC-induced C-X-C motif chemokine ligand 10 (CXCL10) which induces lymphocyte chemotaxis.

CONCLUSIONS

The synovial DDX60 was more expressed in RA patients than in OA. In human RFLS, DDX60 stimulated by TLR3 signaling affected CXCL10 expression. DDX60 may contribute to synovial inflammation in RA.