1
|
Kwon G, Wiedemann A, Steinheuer LM, Stefanski AL, Szelinski F, Racek T, Frei AP, Hatje K, Kam-Thong T, Schubert D, Schindler T, Dörner T, Thurley K. Transcriptional profiling upon T cell stimulation reveals down-regulation of inflammatory pathways in T and B cells in SLE versus Sjögren's syndrome. NPJ Syst Biol Appl 2023; 9:62. [PMID: 38102122 PMCID: PMC10724199 DOI: 10.1038/s41540-023-00319-z] [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: 05/25/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) share clinical as well as pathogenic similarities. Although previous studies suggest various abnormalities in different immune cell compartments, dedicated cell-type specific transcriptomic signatures are often masked by patient heterogeneity. Here, we performed transcriptional profiling of isolated CD4, CD8, CD16 and CD19 lymphocytes from pSS and SLE patients upon T cell stimulation, in addition to a steady-state condition directly after blood drawing, in total comprising 581 sequencing samples. T cell stimulation, which induced a pronounced inflammatory response in all four cell types, gave rise to substantial re-modulation of lymphocyte subsets in the two autoimmune diseases compared to healthy controls, far exceeding the transcriptomic differences detected at steady-state. In particular, we detected cell-type and disease-specific down-regulation of a range of pro-inflammatory cytokine and chemokine pathways. Such differences between SLE and pSS patients are instrumental for selective immune targeting by future therapies.
Collapse
Affiliation(s)
- Gino Kwon
- Systems Biology of Inflammation, German Rheumatism Research Center, a Leibniz-Institute, Berlin, Germany
| | - Annika Wiedemann
- Rheumatology and Clinical Immunology, Department of Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lisa M Steinheuer
- Biomathematics Division, Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany
| | - Ana-Luisa Stefanski
- Rheumatology and Clinical Immunology, Department of Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Franziska Szelinski
- Rheumatology and Clinical Immunology, Department of Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tomas Racek
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Andreas Philipp Frei
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Klas Hatje
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Tony Kam-Thong
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - David Schubert
- Roche Pharma Research and Early Development, Immunology, Infectious Diseases and Ophthalmology (I2O) Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Thomas Schindler
- Product Development Immunology, F. Hoffmann-La Roche AG, Basel, Switzerland
| | - Thomas Dörner
- Rheumatology and Clinical Immunology, Department of Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Kevin Thurley
- Systems Biology of Inflammation, German Rheumatism Research Center, a Leibniz-Institute, Berlin, Germany.
- Biomathematics Division, Institute of Experimental Oncology, University Hospital Bonn, Bonn, Germany.
| |
Collapse
|
2
|
Li J, Li J, Teng P, Yang F, Zhang J, Sun B, Chen W. Long noncoding RNA 1392 regulates MDA5 by interaction with ELAVL1 to inhibit coxsackievirus B5 infection. Virol Sin 2023; 38:699-708. [PMID: 37543144 PMCID: PMC10590689 DOI: 10.1016/j.virs.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 07/21/2023] [Indexed: 08/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) modulate many aspects of biological and pathological processes. Recent studies have shown that host lncRNAs participate in the antiviral immune response, but functional lncRNAs in coxsackievirus B5 (CVB5) infection remain unknown. Here, we identified a novel cytoplasmic lncRNA, LINC1392, which was highly inducible in CVB5 infected RD cells in a time- and dose-dependent manner, and also can be induced by the viral RNA and IFN-β. Further investigation showed that LINC1392 promoted several important interferon-stimulated genes (ISGs) expression, including IFIT1, IFIT2, and IFITM3 by activating MDA5, thereby inhibiting the replication of CVB5 in vitro. Mechanistically, LINC1392 bound to ELAV like RNA binding protein 1 (ELAVL1) and blocked ELAVL1 interaction with MDA5. Functional study revealed that the 245-835 nt locus of LINC1392 exerted the antiviral effect and was also an important site for ELAVL1 binding. In mice, LINC1392 could inhibit CVB5 replication and alleviated the histopathological lesions of intestinal and brain tissues induced by viral infection. Our findings collectively reveal that the novel LINC1392 acts as a positive regulator in the IFN-I signaling pathway against CVB5 infection. Elucidating the underlying mechanisms on how lncRNA regulats the host innate immunity response towards CVB5 infection will lay the foundation for antiviral drug research.
Collapse
Affiliation(s)
- Jing Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jinwei Li
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Peiying Teng
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Fan Yang
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Jihong Zhang
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Bo Sun
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Wei Chen
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China.
| |
Collapse
|
3
|
Interaction between Long Noncoding RNAs and Syncytin-1/Syncytin-2 Genes and Transcripts: How Noncoding RNAs May Affect Pregnancy in Patients with Systemic Lupus Erythematosus. Int J Mol Sci 2023; 24:ijms24032259. [PMID: 36768581 PMCID: PMC9917164 DOI: 10.3390/ijms24032259] [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] [Received: 12/06/2022] [Revised: 12/27/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Patients with systemic lupus erythematosus (SLE) often suffer from obstetric complications not necessarily associated with the antiphospholipid syndrome. These events may potentially result from the reduced placental synthesis of the fusogenic proteins syncytin-1 and syncytin-2, observed in women with pregnancy-related disorders. SLE patients have an aberrant noncoding (nc)RNA signature that may in turn dysregulate the expression of syncytin-1 and syncytin-2 during placentation. The aim of this research is to computationally evaluate and characterize the interaction between syncytin-1 and syncytin-2 genes and human ncRNAs and to discuss the potential implications for SLE pregnancy adverse outcomes. METHODS The FASTA sequences of the syncytin-1 and syncytin-2 genes were used as inputs to the Ensembl.org library to find any alignments with human ncRNA genes and their transcripts, which were characterized for their tissue expression, regulatory activity on adjacent genes, biological pathways, and potential association with human disease. RESULTS BLASTN analysis revealed a total of 100 hits with human long ncRNAs (lncRNAs) for the syncytin-1 and syncytin-2 genes, with median alignment scores of 151 and 66.7, respectively. Only lncRNAs TP53TG1, TTTY14, and ENSG00000273328 were reported to be expressed in placental tissue. Dysregulated expression of lncRNAs TP53TG1, LINC01239, and LINC01320 found in this analysis has previously been described in SLE patients as well as in women with a high-risk pregnancy. In addition, some of the genes adjacent to lncRNAs aligned with syncytin-1 or syncytin-2 in a regulatory region might increase the risk of pregnancy complications or SLE. CONCLUSIONS This is the first computational study showing alignments between syncytin-1 and syncytin-2 genes and human lncRNAs. Whether this mechanism affects syncytiotrophoblast morphogenesis in SLE females is unknown and requires further investigation.
Collapse
|
4
|
Zhang XX, You JP, Liu XR, Zhao YF, Cui Y, Zhao ZZ, Qi YY. PRDX6AS1 gene polymorphisms and SLE susceptibility in Chinese populations. Front Immunol 2022; 13:987385. [PMID: 36311744 PMCID: PMC9601311 DOI: 10.3389/fimmu.2022.987385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a complex, multisystem autoimmune disease that is characterized by the production of autoantibodies. Although accumulated evidence suggests that the dysregulation of long non-coding RNAs (lncRNAs) is involved in the pathogenesis of SLE, the genetic contributions of lncRNA coding genes to SLE susceptibility remain largely unknown. Here, we aimed to provide more evidence for the role of lncRNA coding genes to SLE susceptibility. Methods The genetic association analysis was first adopted from the previous genome-wide association studies (GWAS) and was then validated in an independent cohort. PRDX6-AS1 is located at chr1:173204199-173446294. It spans a region of approximately 240 kb, and 297 single nucleotide polymorphisms (SNPs) were covered by the previous GWAS. Differential expression at the mRNA level was analyzed based on the ArrayExpress Archive database. Results A total of 33 SNPs were associated with SLE susceptibility, with a P<1.68×10-4. The strongest association signal was detected at rs844649 (P=2.12×10-6), according to the previous GWAS. Combining the results from the GWAS Chinese cohort and our replication cohort, we pursued a meta-analysis approach and found a pronounced genetic association between PRDX6-AS1 rs844649 and SLE susceptibility (pmeta=1.24×10-13, OR 1.50, 95% CI: 1.34–1.67). The mRNA expression of PRDX6 was elevated in peripheral blood cells, peripheral blood mononuclear cells (PBMCs), and multiple cell subpopulations, such as B cells, CD4+ T cells, CD3+ cells, and monocytes in patients with SLE. The PRDX6 protein expression level was also increased in patients with SLE compared with healthy donors. Conclusion Our study provides new evidence that variants located in lncRNA coding genes are associated with SLE susceptibility.
Collapse
Affiliation(s)
- Xiao-Xue Zhang
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jun-Peng You
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xin-Ran Liu
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Ya-Fei Zhao
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yan Cui
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Department of Nephrology, Wuhan Fourth Hospital, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhan-Zheng Zhao
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Yuan-Yuan Qi, ; Zhan-Zheng Zhao,
| | - Yuan-Yuan Qi
- Nephrology Hospital, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- *Correspondence: Yuan-Yuan Qi, ; Zhan-Zheng Zhao,
| |
Collapse
|
5
|
Alghazali MW, Al-Hetty HRAK, Ali ZMM, Saleh MM, Suleiman AA, Jalil AT. Non-coding RNAs, another side of immune regulation during triple-negative breast cancer. Pathol Res Pract 2022; 239:154132. [PMID: 36183439 DOI: 10.1016/j.prp.2022.154132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/23/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancer (TNBC) is considered about 12-24 % of all breast cancer cases. Patients experience poor overall survival, high recurrence rate, and distant metastasis compared to other breast cancer subtypes. Numerous studies have highlighted the crucial roles of non-coding RNAs (ncRNAs) in carcinogenesis and proliferation, migration, and metastasis of tumor cells in TNBC. Recent research has demonstrated that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play a role in the regulation of the immune system by affecting the tumor microenvironment, the epithelial-mesenchymal transition, the regulation of dendritic cells and myeloid-derived stem cells, and T and B cell activation and differentiation. Immune-related miRNAs and lncRNAs, which have been established as predictive markers for various cancers, are strongly linked to immune cell infiltration and could be a viable therapeutic target for TNBC. In the current review, we discuss the recent updates of ncRNAs, including miRNAs and lncRNAs in TNBC, including their biogenesis, target genes, and biological function of their targets, which are mostly involved in the immune response.
Collapse
Affiliation(s)
| | | | - Zahraa Muhsen M Ali
- Department of Medical Laboratory Techniques, Al-Rafidain University College, Iraq
| | - Marwan Mahmood Saleh
- Department of Biophysics, College of Applied Sciences, University of Anbar, Iraq; Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | | | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla 51001, Iraq.
| |
Collapse
|