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van Wijck RTA, Sharma HS, Swagemakers SMA, Dik WA, IJspeert H, Dalm VASH, van Daele PLA, van Hagen PM, van der Spek PJ. Bioinformatic meta-analysis reveals novel differentially expressed genes and pathways in sarcoidosis. Front Med (Lausanne) 2024; 11:1381031. [PMID: 38938383 PMCID: PMC11208482 DOI: 10.3389/fmed.2024.1381031] [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: 02/02/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
Introduction Sarcoidosis is a multi-system inflammatory disease of unknown origin with heterogeneous clinical manifestations varying from a single organ non-caseating granuloma site to chronic systemic inflammation and fibrosis. Gene expression studies have suggested several genes and pathways implicated in the pathogenesis of sarcoidosis, however, due to differences in study design and variable statistical approaches, results were frequently not reproducible or concordant. Therefore, meta-analysis of sarcoidosis gene-expression datasets is of great importance to robustly establish differentially expressed genes and signalling pathways. Methods We performed meta-analysis on 22 published gene-expression studies on sarcoidosis. Datasets were analysed systematically using same statistical cut-offs. Differentially expressed genes were identified by pooling of p-values using Edgington's method and analysed for pathways using Ingenuity Pathway Analysis software. Results A consistent and significant signature of novel and well-known genes was identified, those collectively implicated both type I and type II interferon mediated signalling pathways in sarcoidosis. In silico functional analysis showed consistent downregulation of eukaryotic initiation factor 2 signalling, whereas cytokines like interferons and transcription factor STAT1 were upregulated. Furthermore, we analysed affected tissues to detect differentially expressed genes likely to be involved in granuloma biology. This revealed that matrix metallopeptidase 12 was exclusively upregulated in affected tissues, suggesting a crucial role in disease pathogenesis. Discussion Our analysis provides a concise gene signature in sarcoidosis and expands our knowledge about the pathogenesis. Our results are of importance to improve current diagnostic approaches and monitoring strategies as well as in the development of targeted therapeutics.
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Affiliation(s)
- Rogier T. A. van Wijck
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hari S. Sharma
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Sigrid M. A. Swagemakers
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Willem A. Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Hanna IJspeert
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Virgil A. S. H. Dalm
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Paul L. A. van Daele
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - P. Martin van Hagen
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Peter J. van der Spek
- Department of Pathology & Clinical Bioinformatics, Erasmus MC University Medical Center, Rotterdam, Netherlands
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Lower EE, Baughman RP. Hematologic and Oncologic Aspects of Sarcoidosis: Some of the Least Studied but Most Common Dilemmas. Clin Chest Med 2024; 45:119-129. [PMID: 38245361 DOI: 10.1016/j.ccm.2023.08.008] [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] [Indexed: 01/22/2024]
Abstract
The hematologic system is frequently involved in sarcoidosis. Lymphopenia is the most common hematologic manifestation noted, although anemia and thrombocytopenia also occur. The etiology of these common manifestations can be direct granulomatous infiltration of bone marrow, lymph nodes, or spleen or related to immunologic dysfunction. Although not life threatening, these problems can lead to cytopenias requiring close monitoring in patients receiving a variety of disease treatments. The relationship between sarcoidosis and malignancy remains complex. However, some sarcoidosis patients are at increased risk for the development of malignancies, particularly lymphomas and gastrointestinal cancers. Conversely, cancer patients can experience an increase in the likelihood for the development of breast cancer and lymphomas.
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Affiliation(s)
- Elyse E Lower
- Department of Medicine, University of Cincinnati Medical Center, 200 Eden Avenue, Cincinnati, OH 45219, USA.
| | - Robert P Baughman
- Department of Medicine, University of Cincinnati Medical Center, 200 Eden Avenue, Cincinnati, OH 45219, USA
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Alnaimat F, Sweis JJG, Jansz J, Modi Z, Prasad S, AbuHelal A, Vagts C, Hanson HA, Ascoli C, Novak RM, Papanikolaou IC, Rubinstein I, Sweiss N. Vaccination in the Era of Immunosuppression. Vaccines (Basel) 2023; 11:1446. [PMID: 37766123 PMCID: PMC10537746 DOI: 10.3390/vaccines11091446] [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: 07/20/2023] [Revised: 08/20/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Patients with autoimmune inflammatory rheumatic diseases (AIIRDs) are at increased risk for severe infections. Vaccine responses and safety profiles may differ between AIIRD patients and the general population. While patients with autoimmune inflammatory rheumatic diseases (AIIRDs) often experience diminished humoral responses and reduced vaccine efficacy, factors such as the type of immunosuppressant medications used and the specific vaccine employed contribute to these outcomes. Notably, individuals undergoing B cell depletion therapy tend to have poor vaccine immunogenicity. However, despite these considerations, vaccine responses are generally considered clinically sufficient. Ideally, immunosuppressed AIIRD patients should receive vaccinations at least two weeks before commencing immunosuppressive treatment. However, it is common for many patients to already be on immunosuppressants during the immunization process. Vaccination rarely triggers flares in AIIRDs; if flares occur, they are typically mild. Despite the heightened infection risk, including COVID-19, among AIIRD patients with rheumatoid arthritis, systemic lupus erythematosus, sarcoidosis, and other diseases on immunosuppressants, the vaccination rates remain suboptimal. The future directions of vaccination in the era of immunosuppression will likely involve customized vaccines with enhanced adjuvants and alternative delivery methods. By addressing the unique challenges faced by immunosuppressed individuals, we may improve vaccine efficacy, reduce the risk of infections, and ultimately enhance the health outcomes. Additionally, clinical trials to evaluate the safety and efficacy of temporarily discontinuing immunosuppressants during vaccination in various AIIRDs are crucial.
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Affiliation(s)
- Fatima Alnaimat
- Department of Internal Medicine, Division of Rheumatology, School of Medicine, University of Jordan, Amman 11942, Jordan
| | | | - Jacqueline Jansz
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (J.J.); (Z.M.); (S.P.)
| | - Zeel Modi
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (J.J.); (Z.M.); (S.P.)
| | - Supritha Prasad
- Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA; (J.J.); (Z.M.); (S.P.)
| | | | - Christen Vagts
- Department of Medicine, Division of Pulmonary Critical Care Sleep and Allergy, University of Illinois Chicago, Chicago, IL 60612, USA; (C.V.); (C.A.); (I.R.)
| | - Hali A. Hanson
- College of Pharmacy, University of Illinois Hospital & Health Sciences System, Chicago, IL 60612, USA;
| | - Christian Ascoli
- Department of Medicine, Division of Pulmonary Critical Care Sleep and Allergy, University of Illinois Chicago, Chicago, IL 60612, USA; (C.V.); (C.A.); (I.R.)
| | - Richard M. Novak
- Division of Infectious Diseases, University of Illinois, Chicago, IL 60612, USA;
| | - Ilias C. Papanikolaou
- Department of Respiratory Medicine, Sarcoidosis Clinic, Corfu General Hospital, 49100 Corfu, Greece;
| | - Israel Rubinstein
- Department of Medicine, Division of Pulmonary Critical Care Sleep and Allergy, University of Illinois Chicago, Chicago, IL 60612, USA; (C.V.); (C.A.); (I.R.)
| | - Nadera Sweiss
- Division of Rheumatology, Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA;
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Shao K, Wang Z, Fan X, Sun R, Tang C. Comprehensive Analysis of the miRNA-mRNA Pathological Regulatory Network of Intestinal CD4 + T Cells in Parkinson's Disease. J Mol Neurosci 2023; 73:529-538. [PMID: 37354355 DOI: 10.1007/s12031-023-02132-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: 04/08/2023] [Accepted: 05/27/2023] [Indexed: 06/26/2023]
Abstract
Infiltration of CD4 + T cells was found in brain tissue samples from PD patients, suggesting their involvement in developing central nervous system (CNS) disease. The idea of the gut-brain axis further corroborates intestinal T cells' activation as the central immune response initiation. However, the specific factors and molecular pathways regulating intestinal T-cell activation are unclear. We used the GSE156287 and GSE145814 datasets from the GEO database to analyze and obtain the miRNAs, which are aberrantly expressed in intestinal CD4 + T cells in PD patients and predict their regulatory target mRNAs. Further, combined with the GSE174473 dataset of CD4 + T cells sequencing in PD patients, we finally clarified the aberrant genes expressed in CD4 + T cells from the intestine of PD patients and constructed a miRNA-mRNA regulatory network. The highlight of our findings showed pathways, networks, biological functions, and key molecules potentially involved in the miRNA-mediated functional effects in CD4 + T cell from the intestine of PD patients. The hsa-miR-3180-3p mediated CBX8, etc. were determined as most effective in enhancing T cell survival. PEG10, etc. regulated by hsa-miR-20a-3p targets were possibly involved in T cell differentiation. The JPT2 regulated by hsa-miR-1281 were involved in influencing T cell infiltration. The discovery of this interaction between miRNA and mRNA in CD4 + T cell has important implications for understanding the intestinal initial of PD pathological molecular and anti-inflammation of T cell activation.
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Affiliation(s)
- Kaiquan Shao
- Department of Neurobiology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou , Jiangsu, 221004, China
| | - Zipeng Wang
- Department of Neurology, The Affiliated Huai'an Hospital of Xuzhou Medical Universityand, The Second People's Hospital of Huai'an , Jiangsu, 223022, Huai, China
| | - Xinyu Fan
- Department of Neurobiology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou , Jiangsu, 221004, China
| | - Ruiao Sun
- Department of Neurobiology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou , Jiangsu, 221004, China
| | - Chuanxi Tang
- Department of Neurobiology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou , Jiangsu, 221004, China.
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Vagts C, Sweis JJG, Sweis NWG, Ascoli C, Rottoli P, Martone FM, Wells AU, Judson MA, Sweiss NJ, Lower EE, Baughman RP. Initial behaviors and attitudes towards the COVID-19 vaccine in sarcoidosis patients: results of a self-reporting questionnaire. SARCOIDOSIS, VASCULITIS, AND DIFFUSE LUNG DISEASES : OFFICIAL JOURNAL OF WASOG 2023; 40:e2023012. [PMID: 37382069 PMCID: PMC10494750 DOI: 10.36141/svdld.v40i2.14388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Individuals with self-declared sarcoidosis are at increased risk of COVID-19 related morbidity and mortality for which vaccination can be lifesaving. Despite this, vaccine hesitancy remains a large barrier to global acceptance of vaccination against COVID-19. We aimed to identify individuals with sarcoidosis who had and had not been vaccinated against COVID-19 vaccine to 1) establish a safety profile of COVID-19 vaccination in those with sarcoidosis and 2) to elucidate factors that contribute to COVID-19 vaccine hesitancy. METHODS A questionnaire inquiring about COVID-19 vaccination status, vaccination side effects, and willingness for future vaccination was distributed from December 2020 to May 2021 to individuals with sarcoidosis living in the US and European countries. Details regarding sarcoidosis manifestations and treatment were solicited. Vaccine attitudes were classified as pro or anti-COVID-19 vaccination for subgroup analysis. RESULTS At the time of questionnaire administration, 42% of respondents had already received a COVID-19 vaccination, most of whom either denied side effects or reported a local reaction only. Those off sarcoidosis therapy were more likely to report systemic side effects. Among subjects who had not yet received a COVID-19 vaccine, 27% of individuals reported they would not receive one once available. Reasons against vaccination were overwhelmingly related to the lack of confidence in vaccine safety and/or efficacy and less related to concerns associated with convenience or complacency. Black individuals, women, and younger adults were more likely to decline vaccination. CONCLUSIONS Among individuals with sarcoidosis, COVID-19 vaccination is well-accepted and well-tolerated. Subjects on sarcoidosis therapy reported significantly less vaccination side effects, and thus the correlation between side effects, vaccine type, and vaccine efficacy requires further investigation. Strategies to improve vaccination should focus on improving knowledge and education regarding vaccine safety and efficacy, as well as targeting sources of misinformation, particularly in young, black, and female subpopulations.
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Affiliation(s)
- Christen Vagts
- Division of Pulmonary Critical Care Sleep and Allergy, Department of Medicine, University of Illinois Chicago, Chicago IL, USA.
| | | | | | - Christian Ascoli
- Division of Pulmonary Critical Care Sleep and Allergy, Department of Medicine, University of Illinois Chicago, Chicago IL, USA.
| | - Paola Rottoli
- Specialization School of Respiratory Diseases, Department of Medical, Surgical and Neurological Sciences, Siena University, Italy.
| | | | - Athol U Wells
- Royal Brompton and Harefield National Health Service Foundation Trust, Interstitial Lung Disease Unit, London, UK.
| | - Marc A Judson
- Department of Medicine, Albany Medical College, Albany NY, USA.
| | - Nadera J Sweiss
- Division of Rheumatology and Medical Director of the Arthritis Clinic and Bernie Mac Sarcoidosis Translational Advanced Research (STAR) Center.
| | - Elyse E Lower
- University of Cincinnati Medical Center, Department of Medicine, Cincinnati, OH, USA.
| | - Robert P Baughman
- University of Cincinnati Medical Center, Department of Medicine, Cincinnati, OH, USA.
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Agidigbi TS, Kwon HK, Knight JR, Zhao D, Lee FY, Oh I. Transcriptomic identification of genes expressed in invasive S. aureus diabetic foot ulcer infection. Front Cell Infect Microbiol 2023; 13:1198115. [PMID: 37434783 PMCID: PMC10332306 DOI: 10.3389/fcimb.2023.1198115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Infection in diabetic foot ulcers (DFUs) is one of the major complications associated with patients with diabetes. Staphylococcus aureus is the most common offending pathogen in patients with infected DFU. Previous studies have suggested the application of species-specific antibodies against S. aureus for diagnosis and monitoring treatment response. Early and accurate identification of the main pathogen is critical for management of DFU infection. Understanding the host immune response against species-specific infection may facilitate diagnosis and may suggest potential intervention options to promote healing infected DFUs. We sought to investigate evolving host transcriptome associated with surgical treatment of S. aureus- infected DFU. Methods This study compared the transcriptome profile of 21 patients with S. aureus- infected DFU who underwent initial foot salvage therapy with irrigation and debridement followed by intravenous antibiotic therapy. Blood samples were collected at the recruitment (0 weeks) and 8 weeks after therapy to isolate peripheral blood mononuclear cells (PBMCs). We analyzed the PBMC expression of transcriptomes at two different time points (0 versus 8 weeks). Subjects were further divided into two groups at 8 weeks: healed (n = 17, 80.95%) versus non-healed (n = 4, 19.05%) based on the wound healing status. DESeq2 differential gene analysis was performed. Results and discussion An increased expression of IGHG1, IGHG2, IGHG3, IGLV3-21, and IGLV6-57 was noted during active infection at 0 weeks compared with that at 8 weeks. Lysine- and arginine-rich histones (HIST1H2AJ, HIST1H2AL, HIST1H2BM, HIST1H3B, and HIST1H3G) were upregulated at the initial phase of active infection at 0 weeks. CD177 and RRM2 were also upregulated at the initial phase of active infection (0 weeks) compared with that at 8 weeks of follow-up. Genes of heat shock protein members (HSPA1A, HSPE1, and HSP90B1) were high in not healed patients compared with that in healed patients 8 weeks after therapy. The outcome of our study suggests that the identification of genes evolution based on a transcriptomic profiling could be a useful tool for diagnosing infection and assessing severity and host immune response to therapies.
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Affiliation(s)
- Taiwo Samuel Agidigbi
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Hyuk-Kwon Kwon
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
- Division of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - James R. Knight
- Yale Center for Genome Analysis, Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Dejian Zhao
- Yale Center for Genome Analysis, Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Francis Y. Lee
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
| | - Irvin Oh
- Department of Orthopedics and Rehabilitation, Yale School of Medicine, New Haven, CT, United States
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Wu Z, Hu Z, Gao Y, Xia Y, Zhang X, Jiang Z. A computational approach based on weighted gene co-expression network analysis for biomarkers analysis of Parkinson's disease and construction of diagnostic model. Front Comput Neurosci 2023; 16:1095676. [PMID: 36704228 PMCID: PMC9873349 DOI: 10.3389/fncom.2022.1095676] [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: 11/11/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Background Parkinson's disease (PD) is a common age-related chronic neurodegenerative disease. There is currently no affordable, effective, and less invasive test for PD diagnosis. Metabolite profiling in blood and blood-based gene transcripts is thought to be an ideal method for diagnosing PD. Aim In this study, the objective is to identify the potential diagnostic biomarkers of PD by analyzing microarray gene expression data of samples from PD patients. Methods A computational approach, namely, Weighted Gene Co-expression Network Analysis (WGCNA) was used to construct co-expression gene networks and identify the key modules that were highly correlated with PD from the GSE99039 dataset. The Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was performed to identify the hub genes in the key modules with strong association with PD. The selected hub genes were then used to construct a diagnostic model based on logistic regression analysis, and the Receiver Operating Characteristic (ROC) curves were used to evaluate the efficacy of the model using the GSE99039 dataset. Finally, Reverse Transcription-Polymerase Chain Reaction (RT-PCR) was used to validate the hub genes. Results WGCNA identified two key modules associated with inflammation and immune response. Seven hub genes, LILRB1, LSP1, SIPA1, SLC15A3, MBOAT7, RNF24, and TLE3 were identified from the two modules and used to construct diagnostic models. ROC analysis showed that the diagnostic model had a good diagnostic performance for PD in the training and testing datasets. Results of the RT-PCR experiments showed that there were significant differences in the mRNA expression of LILRB1, LSP1, and MBOAT7 among the seven hub genes. Conclusion The 7-gene panel (LILRB1, LSP1, SIPA1, SLC15A3, MBOAT7, RNF24, and TLE3) will serve as a potential diagnostic signature for PD.
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Affiliation(s)
- Zhaoping Wu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiping Hu
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yunchun Gao
- Department of Neurology, The First People’s Hospital of Changde City, Changde, Hunan, China
| | - Yuechong Xia
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China
| | - Xiaobo Zhang
- Department of Neurology, The First People’s Hospital of Changde City, Changde, Hunan, China
| | - Zheng Jiang
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Zheng Jiang,
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