1
|
Rusu EC, Monfort-Lanzas P, Bertran L, Barrientos-Riosalido A, Solé E, Mahmoudian R, Aguilar C, Briansó S, Mohamed F, Garcia S, Camaron J, Auguet T. Towards understanding post-COVID-19 condition: A systematic meta-analysis of transcriptomic alterations with sex-specific insights. Comput Biol Med 2024; 175:108507. [PMID: 38657468 DOI: 10.1016/j.compbiomed.2024.108507] [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: 11/24/2023] [Revised: 03/26/2024] [Accepted: 04/21/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Post COVID-19 Condition (PCC), characterized by lingering symptoms post-acute COVID-19, poses clinical challenges, highlighting the need to understand its underlying molecular mechanisms. This meta-analysis aims to shed light on the transcriptomic landscapes and sex-specific molecular dynamics intrinsic to PCC. METHODS A systematic review identified three studies suitable for comprehensive meta-analysis, encompassing 135 samples (57 PCC subjects and 78 recovered subjects). We performed meta-analysis on differential gene expression, a gene set enrichment analysis of Reactome pathways, and weighted gene co-expression network analysis (WGCNA). We performed a drug and disease enrichment analysis and also assessed sex-specific differences in expression patterns. KEY FINDINGS A clear difference was observed in the transcriptomic profiles of PCC subjects, with 530 differentially expressed genes (DEGs) identified. Enrichment analysis revealed that the altered pathways were predominantly implicated in cell cycle processes, immune dysregulation and histone modifications. Antioxidant compounds such as hesperitin were predominantly linked to the hub genes of the DEGs. Sex-specific analyses highlighted disparities in DEGs and altered pathways in male and female PCC patients, revealing a difference in the expression of ribosomal proteins. PCC in men was mostly linked to neuro-cardiovascular disorders, while women exhibited more diverse disorders, with a high index of respiratory conditions. CONCLUSION Our study reveals the intricate molecular processes underlying PCC, highlighting that the differences in molecular dynamics between males and females could be key to understanding and effectively managing the varied symptomatology of this condition.
Collapse
Affiliation(s)
- Elena Cristina Rusu
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain; Institute for Integrative Systems Biology (I2SysBio), University of Valencia and the Spanish National Research Council (CSIC), 46980, Valencia, Spain.
| | - Pablo Monfort-Lanzas
- Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria; Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Laia Bertran
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Andrea Barrientos-Riosalido
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Emilia Solé
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Razieh Mahmoudian
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Carmen Aguilar
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain.
| | - Silvia Briansó
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Fadel Mohamed
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Susana Garcia
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Javier Camaron
- Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| | - Teresa Auguet
- GEMMAIR Research Unit (AGAUR) - Applied Medicine (URV), Department of Medicine and Surgery. University Rovira i Virgili (URV), Health Research Institute Pere Virgili (IISPV), 43007, Tarragona, Spain; Internal Medicine Unit, Joan XXIII University Hospital of Tarragona, 43007, Tarragona, Spain.
| |
Collapse
|
2
|
Tanaka Y, Ikeda K, Kaneko Y, Ishiguro N, Takeuchi T. Why does malaise/fatigue occur? Underlying mechanisms and potential relevance to treatments in rheumatoid arthritis. Expert Rev Clin Immunol 2024; 20:485-499. [PMID: 38224064 DOI: 10.1080/1744666x.2024.2306220] [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: 08/13/2023] [Accepted: 01/12/2024] [Indexed: 01/16/2024]
Abstract
INTRODUCTION Fatigue and malaise are commonly associated with a wide range of medical conditions, including rheumatoid arthritis (RA). Evidence suggests that fatigue and malaise can be overwhelming for patients, yet these symptoms remain inadequately-managed, largely due to an incomplete elucidation of the underlying causes. AREAS COVERED In this assessment of the published literature relating to the pathogenesis of fatigue or malaise in chronic conditions, four key mechanistic themes were identified. Each theme (inflammation, hypothalamic-pituitary-adrenal axis, dysautonomia, and monoamines) is discussed, as well as the complex network of interconnections between themes which suggests a key role for inflammatory cytokines in the development and persistence of fatigue. EXPERT OPINION Fatigue is multifaceted, poorly defined, and imperfectly comprehended. Moreover, the cause and severity of fatigue may change over time, as a consequence of the natural disease course or pharmacologic treatment. This detailed synthesis of available evidence permits us to identify avenues for current treatment optimization and future research, to improve the management of fatigue and malaise in RA. Within the development pipeline, several new anti-inflammatory therapies are currently under investigation, and we anticipate that the next five years will herald much-needed progress to reduce the debilitating nature of fatigue in patients with RA.
Collapse
Affiliation(s)
- Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kei Ikeda
- Department of Rheumatology, Dokkyo Medical University, Mibu, Tochigi, Japan
| | - Yuko Kaneko
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | | |
Collapse
|
3
|
Liu S, Zhong M, Wu H, Su W, Wang Y, Li P. Potential Beneficial Effects of Naringin and Naringenin on Long COVID-A Review of the Literature. Microorganisms 2024; 12:332. [PMID: 38399736 PMCID: PMC10892048 DOI: 10.3390/microorganisms12020332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused a severe epidemic due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Recent studies have found that patients do not completely recover from acute infections, but instead, suffer from a variety of post-acute sequelae of SARS-CoV-2 infection, known as long COVID. The effects of long COVID can be far-reaching, with a duration of up to six months and a range of symptoms such as cognitive dysfunction, immune dysregulation, microbiota dysbiosis, myalgic encephalomyelitis/chronic fatigue syndrome, myocarditis, pulmonary fibrosis, cough, diabetes, pain, reproductive dysfunction, and thrombus formation. However, recent studies have shown that naringenin and naringin have palliative effects on various COVID-19 sequelae. Flavonoids such as naringin and naringenin, commonly found in fruits and vegetables, have various positive effects, including reducing inflammation, preventing viral infections, and providing antioxidants. This article discusses the molecular mechanisms and clinical effects of naringin and naringenin on treating the above diseases. It proposes them as potential drugs for the treatment of long COVID, and it can be inferred that naringin and naringenin exhibit potential as extended long COVID medications, in the future likely serving as nutraceuticals or clinical supplements for the comprehensive alleviation of the various manifestations of COVID-19 complications.
Collapse
Affiliation(s)
- Siqi Liu
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Mengli Zhong
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Hao Wu
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Weiwei Su
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Yonggang Wang
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| | - Peibo Li
- Guangdong Engineering and Technology Research Center for Quality and Efficacy Re-Evaluation of Post-Market Traditional Chinese Medicine, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.L.); (M.Z.); (H.W.); (W.S.); (Y.W.)
| |
Collapse
|
4
|
Liu X, Xiong W, Ye M, Lu T, Yuan K, Chang S, Han Y, Wang Y, Lu L, Bao Y. Non-coding RNAs expression in SARS-CoV-2 infection: pathogenesis, clinical significance, and therapeutic targets. Signal Transduct Target Ther 2023; 8:441. [PMID: 38057315 PMCID: PMC10700414 DOI: 10.1038/s41392-023-01669-0] [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: 12/09/2022] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 12/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has been looming globally for three years, yet the diagnostic and treatment methods for COVID-19 are still undergoing extensive exploration, which holds paramount importance in mitigating future epidemics. Host non-coding RNAs (ncRNAs) display aberrations in the context of COVID-19. Specifically, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) exhibit a close association with viral infection and disease progression. In this comprehensive review, an overview was presented of the expression profiles of host ncRNAs following SARS-CoV-2 invasion and of the potential functions in COVID-19 development, encompassing viral invasion, replication, immune response, and multiorgan deficits which include respiratory system, cardiac system, central nervous system, peripheral nervous system as well as long COVID. Furthermore, we provide an overview of several promising host ncRNA biomarkers for diverse clinical scenarios related to COVID-19, such as stratification biomarkers, prognostic biomarkers, and predictive biomarkers for treatment response. In addition, we also discuss the therapeutic potential of ncRNAs for COVID-19, presenting ncRNA-based strategies to facilitate the development of novel treatments. Through an in-depth analysis of the interplay between ncRNA and COVID-19 combined with our bioinformatic analysis, we hope to offer valuable insights into the stratification, prognosis, and treatment of COVID-19.
Collapse
Affiliation(s)
- Xiaoxing Liu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Wandi Xiong
- Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, 570228, Haikou, China
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, 650204, Kunming, Yunnan, China
| | - Tangsheng Lu
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China
| | - Kai Yuan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Suhua Chang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China
| | - Ying Han
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China
| | - Yongxiang Wang
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, China.
- Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
| | - Lin Lu
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), 100191, Beijing, China.
- Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China.
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China.
| | - Yanping Bao
- National Institute on Drug Dependence and Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, 100191, China.
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, China.
- School of Public Health, Peking University, 100191, Beijing, China.
| |
Collapse
|
5
|
Li J, Zhou Y, Ma J, Zhang Q, Shao J, Liang S, Yu Y, Li W, Wang C. The long-term health outcomes, pathophysiological mechanisms and multidisciplinary management of long COVID. Signal Transduct Target Ther 2023; 8:416. [PMID: 37907497 PMCID: PMC10618229 DOI: 10.1038/s41392-023-01640-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/04/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
There have been hundreds of millions of cases of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the growing population of recovered patients, it is crucial to understand the long-term consequences of the disease and management strategies. Although COVID-19 was initially considered an acute respiratory illness, recent evidence suggests that manifestations including but not limited to those of the cardiovascular, respiratory, neuropsychiatric, gastrointestinal, reproductive, and musculoskeletal systems may persist long after the acute phase. These persistent manifestations, also referred to as long COVID, could impact all patients with COVID-19 across the full spectrum of illness severity. Herein, we comprehensively review the current literature on long COVID, highlighting its epidemiological understanding, the impact of vaccinations, organ-specific sequelae, pathophysiological mechanisms, and multidisciplinary management strategies. In addition, the impact of psychological and psychosomatic factors is also underscored. Despite these crucial findings on long COVID, the current diagnostic and therapeutic strategies based on previous experience and pilot studies remain inadequate, and well-designed clinical trials should be prioritized to validate existing hypotheses. Thus, we propose the primary challenges concerning biological knowledge gaps and efficient remedies as well as discuss the corresponding recommendations.
Collapse
Affiliation(s)
- Jingwei Li
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yun Zhou
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jiechao Ma
- AI Lab, Deepwise Healthcare, Beijing, China
| | - Qin Zhang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- Department of Postgraduate Student, West China Hospital, West China School of Medicine, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Shufan Liang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yizhou Yu
- Department of Computer Science, The University of Hong Kong, Hong Kong, China.
| | - Weimin Li
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, Med-X Center for Manufacturing, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.
| |
Collapse
|
6
|
Liu Y, Si D, Bai P, Zhu L, Zhang L, Chen Q, Qi Y. CXCL10 May Be Responsible for Susceptibility to Pulmonary Embolism in COVID-19 Patients. J Inflamm Res 2023; 16:4913-4924. [PMID: 37927958 PMCID: PMC10625331 DOI: 10.2147/jir.s431212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023] Open
Abstract
Background Although the potential of coronavirus disease 2019 (COVID-19) patients to develop pulmonary embolism (PE) is widely recognized, the underlying mechanism has not been completely elucidated. This study aimed to identify genes common to COVID-19 and PE to reveal the underlying pathogenesis of susceptibility to PE in COVID-19 patients. Methods COVID-19 genes were obtained from the GEO database and the OMIM, CTD, GeneCards, and DisGeNET databases; PE genes were obtained from the OMIM, CTD, GeneCards, and DisGeNET databases. We overlapped the genes of COVID-19 and PE to obtain common genes for additional analysis, including functional enrichment, protein-protein interaction, and immune infiltration analysis. Hub genes were identified using cytoHubba, a plugin of Cytoscape, and validated using the independent datasets GSE167000 and GSE13535. The genes validated by the above datasets were further validated in clinical samples. Results We obtained 36 genes shared by PE and COVID-19. Functional enrichment and immune infiltration analyses revealed the involvement of cytokines and immune activation. Five genes (CCL2, CXCL10, ALB, EGF, and MKI67) were identified as hub genes common to COVID-19 and PE. CXCL10 was validated in both independent datasets (GSE167000 and GSE13535). Serum levels of CXCL10 in the COVID-19 group and the COVID-19 combined with PE group were significantly higher than those in the healthy control group (P<0.001). In addition, there were significant differences between the COVID-19 group and the COVID-19 combined with PE group (P<0.01). Conclusion Our study reveals common genes shared by PE and COVID-19 and identifies CXCL10 as a possible cause of susceptibility to PE in COVID-19 patients.
Collapse
Affiliation(s)
- Yingli Liu
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, 450003, People’s Republic of China
| | - Dan Si
- Department of Pulmonary and Critical Care Medicine, Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, Henan, 451464, People’s Republic of China
| | - Pingping Bai
- Department of Health Management, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Zhengzhou, Henan, 450003, People’s Republic of China
| | - Li Zhu
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan, 450003, People’s Republic of China
| | - Lili Zhang
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, 450003, People’s Republic of China
| | - Qi Chen
- Department of Pulmonary and Critical Care Medicine, Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, Henan, 450003, People’s Republic of China
| | - Yong Qi
- Department of Pulmonary and Critical Care Medicine, Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Henan University People’s Hospital, Zhengzhou, Henan, 450003, People’s Republic of China
| |
Collapse
|
7
|
Cui Y, Zhang H, Wang Z, Gong B, Al-Ward H, Deng Y, Fan O, Wang J, Zhu W, Sun YE. Exploring the shared molecular mechanisms between systemic lupus erythematosus and primary Sjögren's syndrome based on integrated bioinformatics and single-cell RNA-seq analysis. Front Immunol 2023; 14:1212330. [PMID: 37614232 PMCID: PMC10442653 DOI: 10.3389/fimmu.2023.1212330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023] Open
Abstract
Background Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) are common systemic autoimmune diseases that share a wide range of clinical manifestations and serological features. This study investigates genes, signaling pathways, and transcription factors (TFs) shared between SLE and pSS. Methods Gene expression profiles of SLE and pSS were obtained from the Gene Expression Omnibus (GEO). Weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) analysis were conducted to identify shared genes related to SLE and pSS. Overlapping genes were then subject to Gene Ontology (GO) and protein-protein interaction (PPI) network analyses. Cytoscape plugins cytoHubba and iRegulon were subsequently used to screen shared hub genes and predict TFs. In addition, gene set variation analysis (GSVA) and CIBERSORTx were used to calculate the correlations between hub genes and immune cells as well as related pathways. To confirm these results, hub genes and TFs were verified in microarray and single-cell RNA sequencing (scRNA-seq) datasets. Results Following WGCNA and limma analysis, 152 shared genes were identified. These genes were involved in interferon (IFN) response and cytokine-mediated signaling pathway. Moreover, we screened six shared genes, namely IFI44L, ISG15, IFIT1, USP18, RSAD2 and ITGB2, out of which three genes, namely IFI44L, ISG15 and ITGB2 were found to be highly expressed in both microarray and scRNA-seq datasets. IFN response and ITGB2 signaling pathway were identified as potentially relevant pathways. In addition, STAT1 and IRF7 were identified as common TFs in both diseases. Conclusion This study revealed IFI44L, ISG15 and ITGB2 as the shared genes and identified STAT1 and IRF7 as the common TFs of SLE and pSS. Notably, the IFN response and ITGB2 signaling pathway played vital roles in both diseases. Our study revealed common pathogenetic characteristics of SLE and pSS. The particular roles of these pivotal genes and mutually overlapping pathways may provide a basis for further mechanistic research.
Collapse
Affiliation(s)
- Yanling Cui
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Huina Zhang
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhen Wang
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bangdong Gong
- Division of Rheumatology, Tongji Hospital of Tongji University School of Medicine, Shanghai, China
| | - Hisham Al-Ward
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yaxuan Deng
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Orion Fan
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Junbang Wang
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Wenmin Zhu
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yi Eve Sun
- Stem Cell Translational Research Center, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| |
Collapse
|
8
|
Cai Y, Zuo X, Zuo Y, Wu S, Pang W, Ma K, Yi Q, Tan L, Deng H, Qu X, Chen X. Transcriptomic analysis reveals shared gene signatures and molecular mechanisms between obesity and periodontitis. Front Immunol 2023; 14:1101854. [PMID: 37063877 PMCID: PMC10090675 DOI: 10.3389/fimmu.2023.1101854] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/24/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundBoth obesity (OB) and periodontitis (PD) are chronic non-communicable diseases, and numerous epidemiological studies have demonstrated the association between these two diseases. However, the molecular mechanisms that could explain the association between OB and PD are largely unclear. This study aims to investigate the common gene signatures and biological pathways in OB and PD through bioinformatics analysis of publicly available transcriptome datasets.MethodsThe RNA expression profile datasets of OB (GSE104815) and PD (GSE106090) were used as training data, and GSE152991 and GSE16134 as validation data. After screening for differentially expressed genes (DEGs) shared by OB and PD, gene enrichment analysis, protein-protein interaction (PPI) network construction, GeneMANIA analysis, immune infiltration analysis and gene set enrichment analysis (GSEA) were performed. In addition, receiver operating characteristic (ROC) curves were used to assess the predictive accuracy of the hub gene. Finally, we constructed the hub gene-associated TF-miRNA-mRNA regulatory network.ResultsWe identified a total of 147 DEGs shared by OB and PD (38 down-regulated and 109 up-regulated). Functional analysis showed that these genes were mainly enriched in immune-related pathways such as B cell receptor signalling, leukocyte migration and cellular defence responses. 14 hub genes (FGR, MNDA, NCF2, FYB1, EVI2B, LY86, IGSF6, CTSS, CXCR4, LCK, FCN1, CXCL2, P2RY13, MMP7) showed high sensitivity and specificity in the ROC curve analysis. The results of immune infiltration analysis showed that immune cells such as macrophages, activated CD4 T cells and immune B cells were present at high infiltration levels in both OB and PD samples.The results of GeneMANIA analysis and GSEA analysis suggested that five key genes (FGR, LCK, FYB1, LY86 and P2RY13) may be strongly associated with macrophages. Finally, we constructed a TF-miRNA-mRNA regulatory network consisting of 233 transcription factors (TFs), 8 miRNAs and 14 mRNAs based on the validated information obtained from the database.ConclusionsFive key genes (FGR, LCK, FYB1, LY86, P2RY13) may be important biomarkers of OB and PD. These genes may play an important role in the pathogenesis of OB and PD by affecting macrophage activity and participating in immune regulation and inflammatory responses.
Collapse
Affiliation(s)
- Yisheng Cai
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xuemei Zuo
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yuyang Zuo
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shuang Wu
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Weiwei Pang
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Keqiang Ma
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qiaorong Yi
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Lijun Tan
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Hongwen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Xiaochao Qu
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Xiaochao Qu, ; Xiangding Chen,
| | - Xiangding Chen
- Laboratory of Molecular and Statistical Genetics and Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Xiaochao Qu, ; Xiangding Chen,
| |
Collapse
|
9
|
Xu Z, Yu Z, Li S, Tian Z, Yuan J, You F. Exploration of the core gene signatures and mechanisms between NAFLD and sarcopenia through transcriptomic level. Front Endocrinol (Lausanne) 2023; 14:1140804. [PMID: 36967768 PMCID: PMC10033966 DOI: 10.3389/fendo.2023.1140804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
INTRODUCTION The increased prevalence of non-alcoholic fatty liver disease (NAFLD) and sarcopenia among the elderly are facing a significant challenge to the world's health systems. Our study aims to identify the coexpressed genes in NAFLD and sarcopenia patients. METHODS We downloaded the transcriptome data of NAFLD tissue from patients, as well as muscle tissues from sarcopenia patients, from the GEO database in order to investigate the shared transcriptional regulation mechanisms between these two diseases. Then, focusing on the genes that were frequently expressed in these diseases, together with GSVA and WGCNA, we utilized a range of analysis methods to identify the main co-expressed genes in both diseases by taking intersections. We investigated these changes after learning that they mostly affected lipid metabolism and oxidative stress injury pathways. RESULTS By analyzing these genes and their interactions with transcription factors and proteins, we were able to identify 8 genes that share common patterns. From these 8 genes, we were possible to forecast potential future medicines. Our research raises the possibility of NAFLD and sarcopenia transcriptome regulatory pathways in aging populations. DISCUSSION In conclusion, a complete transcription pattern mapping was carried out in order to identify the core genes, underlying biological mechanisms, and possible therapeutic targets that regulate aging in NAFLD and sarcopenia patients. It provides novel insights and proof in favor of decreasing the increased prevalence of sarcopenia in the elderly caused by NAFLD.
Collapse
Affiliation(s)
- Ziying Xu
- School of Basic Medical Sciences, Peking University, Beijing, China
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shang Li
- Department of Orthopedics, General Hospital of Chinese People's Liberation Army of China (PLA), Beijing, China
- National Clinical Research Center for Orthopedics, Sports Medicine & Rehabilitation, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- School of Basic Medical Sciences, Peking University, Beijing, China
- *Correspondence: Jing Yuan, ; Fuping You,
| | - Fuping You
- School of Basic Medical Sciences, Peking University, Beijing, China
- *Correspondence: Jing Yuan, ; Fuping You,
| |
Collapse
|