AI Article Synopsis
- Systemic lupus erythematosus (SLE) is an autoimmune disorder where anti-RNP antibodies show unique gene expression and immune responses, prompting a study of gene profiles in affected patients.
- The study analyzed gene expression data from 79 anti-RNP-positive SLE patients and 30 healthy controls, identifying 1891 differentially expressed genes (DEGs) and conducting various enrichment analyses to understand immune tissue involvement.
- Results indicated significant dysregulation in antiviral and immune regulation pathways in anti-RNP-positive patients, suggesting a distinct immune profile influenced by altered gene expression, which provides valuable insights into their condition.
Article Abstract
Background: Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by immune dysregulation and chronic inflammation across various organ systems. While anti-dsDNA and anti-Sm antibodies are commonly associated with SLE, the presence of anti-RNP antibodies is often linked to unique gene expression profiles and immune responses. This study aims to investigate the gene expression profiles in ribonucleoprotein (RNP) autoantibody-positive SLE patients by analyzing publicly available transcriptomic data.
Methods: This study analyzed transcriptomic data from the GEO dataset GSE61635, which includes gene expression profiles from 79 anti-RNP-positive SLE patients and 30 healthy controls. Differentially expressed genes (DEGs) were identified using the GEO2R tool with a -value < 0.05 and |log2fold change| > 1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Tissue-specific and cell-type enrichment analyses highlighted the involvement of immune tissues.
Results: A total of 1891 DEGs were identified between anti-RNP-positive SLE patients and healthy controls. Among the identified DEGs, and were notably downregulated, while was highly upregulated. Enrichment analyses revealed significant dysregulation in antiviral response and immune regulation pathways. PPI network analysis highlighted key hub genes, suggesting a heightened antiviral state in these patients. Tissue-specific enrichment and cell-type enrichment identified the bone marrow and immune tissues as being highly affected by the altered gene expression. Additionally, gene frequency analysis highlighted as being recurrently significant across multiple studies.
Conclusions: The findings suggest that anti-RNP-positive SLE patients exhibit distinct gene expression and immune dysregulation profiles, particularly in antiviral and immune regulation pathways. These results provide insights into the molecular mechanisms driving SLE in this patient subset and may guide future therapeutic interventions.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11593874 | PMC |
| http://dx.doi.org/10.3390/genes15111353 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Heterogeneity analysis and prognostic model construction of HPV negative oral squamous cell carcinoma T cells using ScRNA-seq and bulk-RNA analysis.
Funct Integr Genomics
January 2025
Department of Oncology, the First People's Hospital of Qujing City/the Qujing Affiliated Hospital of Kunming Medical University, 1 Yuanlin Road, Qujing, Yunnan, China.
Background: T cells are involved in every stage of tumor development and significantly influence the tumor microenvironment (TME). Our objective was to assess T-cell marker gene expression profiles, develop a predictive risk model for human papilloma virus (HPV)-negative oral squamous cell carcinoma (OSCC) utilizing these genes, and examine the correlation between the risk score and the immunotherapy response.
Methods: We acquired scRNA-seq data for HPV-negative OSCC from the GEO datasets.
Rapid human oogonia-like cell specification via transcription factor-directed differentiation.
EMBO Rep
January 2025
Department of Biomedical Engineering, Duke University, Durham, NC, USA.
The generation of germline cells from human induced pluripotent stem cells (hiPSCs) represents a milestone toward in vitro gametogenesis. Methods to recapitulate germline development beyond primordial germ cells in vitro have relied on long-term cell culture, such as 3-dimensional organoid co-culture for ~four months. Using a pipeline with highly parallelized screening, this study identifies combinations of TFs that directly and rapidly convert hiPSCs to induced oogonia-like cells (iOLCs).
View Article and Find Full Text PDFGenome-wide analysis of TCP family genes and their constitutive expression pattern analysis in the melon (Cucumis melo).
Genes Genomics
January 2025
Plant Molecular Breeding and Bioinformatics Laboratory, Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
Background: TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done.
Objective: The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions.
Advances in cancer genomics and precision oncology.
Genes Genomics
January 2025
Department of Smart Farm and Agricultural Industry, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Background: Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division.
View Article and Find Full Text PDFMitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies.
Funct Integr Genomics
January 2025
National Agri-Food and Biomanufacturing Institute, Sector-81, SAS Nagar, Knowledge City, Punjab, India.
Mitochondria, the cellular powerhouses, are pivotal to neuronal function and health, particularly through their role in regulating synaptic structure and function. Spine reprogramming, which underlies synapse development, depends heavily on mitochondrial dynamics-such as biogenesis, fission, fusion, and mitophagy as well as functions including ATP production, calcium (Ca) regulation, and retrograde signaling. Mitochondria supply the energy necessary for assisting synapse development and plasticity, while also regulating intracellular Ca homeostasis to prevent excitotoxicity and support synaptic neurotransmission.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!