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Huang ZM, Kang JQ, Chen PZ, Deng LF, Li JX, He YX, Liang J, Huang N, Luo TY, Lan QW, Chen HK, Guo XG. Identifying the Interaction Between Tuberculosis and SARS-CoV-2 Infections via Bioinformatics Analysis and Machine Learning. Biochem Genet 2024; 62:2606-2630. [PMID: 37991568 DOI: 10.1007/s10528-023-10563-x] [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: 08/08/2023] [Accepted: 10/25/2023] [Indexed: 11/23/2023]
Abstract
The number of patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 is still increasing. In the case of COVID-19 and tuberculosis (TB), the presence of one disease affects the infectious status of the other. Meanwhile, coinfection may result in complications that make treatment more difficult. However, the molecular mechanisms underpinning the interaction between TB and COVID-19 are unclear. Accordingly, transcriptome analysis was used to detect the shared pathways and molecular biomarkers in TB and COVID-19, allowing us to determine the complex relationship between COVID-19 and TB. Two RNA-seq datasets (GSE114192 and GSE163151) from the Gene Expression Omnibus were used to find concerted differentially expressed genes (DEGs) between TB and COVID-19 to identify the common pathogenic mechanisms. A total of 124 common DEGs were detected and used to find shared pathways and drug targets. Several enterprising bioinformatics tools were applied to perform pathway analysis, enrichment analysis and networks analysis. Protein-protein interaction analysis and machine learning was used to identify hub genes (GAS6, OAS3 and PDCD1LG2) and datasets GSE171110, GSE54992 and GSE79362 were used for verification. The mechanism of protein-drug interactions may have reference value in the treatment of coinfection of COVID-19 and TB.
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Affiliation(s)
- Ze-Min Huang
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jia-Qi Kang
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The First Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Pei-Zhen Chen
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Lin-Fen Deng
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Jia-Xin Li
- Department of Clinical Medicine, The First Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Ying-Xin He
- Clinical Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510006, China
| | - Jie Liang
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Nan Huang
- Clinical Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510006, China
| | - Tian-Ye Luo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Qi-Wen Lan
- Department of Clinical Medicine, The Second Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Hao-Kai Chen
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
- Department of Clinical Medicine, The Third Clinical School of Guangzhou Medical University, Guangzhou, 511436, China
| | - Xu-Guang Guo
- Department of Clinical Laboratory Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Department of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, King Med School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510000, China.
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Uddin MN, Singh MV, Faiyaz A, Szczepankiewicz F, Nilsson M, Boodoo ZD, Sutton KR, Tivarus ME, Zhong J, Wang L, Qiu X, Weber MT, Schifitto G. Tensor-valued diffusion MRI detects brain microstructure changes in HIV infected individuals with cognitive impairment. RESEARCH SQUARE 2024:rs.3.rs-4482269. [PMID: 38946952 PMCID: PMC11213220 DOI: 10.21203/rs.3.rs-4482269/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Despite advancements, the prevalence of HIV-associated neurocognitive impairment remains at approximately 40%, attributed to factors like pre-cART (combination antiretroviral therapy) irreversible brain injury. People with HIV (PWH) treated with cART do not show significant neurocognitive changes over relatively short follow-up periods. However, quantitative neuroimaging may be able to detect ongoing subtle microstructural changes. This study aimed to investigate the sensitivity of tensor-valued diffusion encoding in detecting such changes in brain microstructural integrity in cART-treated PWH. Additionally, it explored relationships between these metrics, neurocognitive scores, and plasma levels of neurofilament light (NFL) chain and glial fibrillary acidic protein (GFAP). Using MRI at 3T, 24 PWH and 31 healthy controls underwent cross-sectional examination. The results revealed significant variations in b-tensor encoding metrics across white matter regions, with associations observed between these metrics, cognitive performance, and blood markers of neuronal and glial injury (NFL and GFAP). Moreover, a significant interaction between HIV status and imaging metrics was observed, particularly impacting total cognitive scores in both gray and white matter. These findings suggest that b-tensor encoding metrics offer heightened sensitivity in detecting subtle changes associated with axonal injury in HIV infection, underscoring their potential clinical relevance in understanding neurocognitive impairment in PWH.
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Woeller CF, Lim SA, Roztocil E, Yee M, Beier EE, Puzas JE, O'Reilly MA. Neonatal hyperoxia impairs adipogenesis of bone marrow-derived mesenchymal stem cells and fat accumulation in adult mice. Free Radic Biol Med 2021; 167:287-298. [PMID: 33757863 PMCID: PMC8096722 DOI: 10.1016/j.freeradbiomed.2021.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022]
Abstract
Preterm birth is a risk factor for growth failure and development of respiratory disease in children and young adults. Their early exposure to oxygen may contribute to lung disease because adult mice exposed to hyperoxia as neonates display reduced lung function, changes in the host response to respiratory viral infections, and develop pulmonary hypertension and heart failure that shortens their lifespan. Here, we provide new evidence that neonatal hyperoxia also impairs growth by inhibiting fat accumulation. Failure to accumulate fat may reflect a systemic defect in adipogenic potential of stem cells because bone marrow-derived mesenchymal cells (BMSCs) isolated from the mice grew slower and were more oxidized compared to controls. They also displayed reduced capacity to accumulate lipid and differentiate into adipocytes. BMSCs from adult mice exposed to neonatal hyperoxia express lower levels of peroxisome proliferator-activated receptor gamma (PPARγ), a transcription factor that drives adipocyte differentiation. The defect in adipogenesis was rescued by expressing PPARγ in these cells. These findings reveal early life exposure to high levels of oxygen may suppresses fat accumulation and impair adipogenic differentiation upstream of PPARγ signaling, thus potentially contributing to growth failure seen in people born preterm.
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Affiliation(s)
- Collynn F Woeller
- Departments of Ophthalmology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA.
| | - Sydney A Lim
- Departments of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - Elisa Roztocil
- Departments of Ophthalmology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - Min Yee
- Departments of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - Eric E Beier
- Departments of Orthopaedics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - J Edward Puzas
- Departments of Orthopaedics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - Michael A O'Reilly
- Departments of Ophthalmology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA; Departments of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA.
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Wang B, Cai W, Zhang Z, Zhang H, Tang K, Zhang Q, Wang X. Circulating microparticles in patients after ischemic stroke: a systematic review and meta-analysis. Rev Neurosci 2018; 32:/j/revneuro.ahead-of-print/revneuro-2017-0105/revneuro-2017-0105.xml. [PMID: 29750657 DOI: 10.1515/revneuro-2017-0105] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022]
Abstract
Microparticles (MPs), a class of cell products with biological activities, have been found to participate in a series of vascular activities. The aim of this article is to investigate the changes in the concentrations of MPs after ischemic stroke by meta-analysis. According to pre-established criteria, a strict screening of articles was performed through the Medline and Embase databases. Subsequently, the included studies were subjected to quality assessment and data extraction. Finally, a meta-analysis was performed on seven major outcomes from 985 noncerebrovascular disease controls and 988 ischemic stroke patients. The pooled concentrations of total MPs (TMPs), endotheliocyte-derived MPs (EMPs), platelet-derived MPs (PMPs), erythrocyte-derived MPs (RMPs), leukocyte-derived MPs (LMPs), and monocyte-derived MPs (MMPs) were significantly increased in the ischemic stroke patients compared to the noncerebrovascular disease controls, with the results as follows: TMPs [standardized mean difference (SMD), 1.12; 95% confidence interval (CI), 0.26-1.97; p=0.01], EMPs (SMD, 0.90; 95% CI, 0.67-1.13; p<0.00001), PMPs (SMD, 1.15; 95% CI, 0.69-1.60; p<0.00001), RMPs (SMD, 1.14; 95% CI, 0.57-1.71; p<0.0001), LMPs (SMD, 1.42; 95% CI, 0.74-2.10; p<0.0001), and MMPs (SMD, 1.09; 95% CI, 0.59-1.60; p<0.0001). However, the pooled concentration of lymphocyte-derived MPs (LyMPs) demonstrated no significant difference between the patients and the controls (SMD, 0.22; 95% CI, -0.19 to 0.63; p=0.29). The available data indicated that the circulating MPs, except for LyMPs, play an important role in the development and prognosis of ischemic stroke.
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Affiliation(s)
- Botao Wang
- Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
- Institute of Integrative Medicines for Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin 300100, China
| | - Wang Cai
- Department of Surgery, Tianjin Nankai Hospital, Tianjin 300100, China
| | - Zhen Zhang
- Nankai Clinical College, Tianjin Medical University, Tianjin 300100, China
- Institute of Integrative Medicines for Acute Abdominal Diseases, Tianjin Nankai Hospital, Tianjin 300100, China
| | - Hui Zhang
- Department of Oncology Surgery, Tianjin Nankai Hospital, Tianjin 300100, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qi Zhang
- Institute of Integrative Medicines for Acute Abdominal Diseases, Tianjin Nankai Hospital, 6 Changjiang Road, Tianjin 300100, China
| | - Ximo Wang
- Institute of Integrative Medicines for Acute Abdominal Diseases, Tianjin Nankai Hospital, 6 Changjiang Road, Tianjin 300100, China
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Baldari S, Di Rocco G, Piccoli M, Pozzobon M, Muraca M, Toietta G. Challenges and Strategies for Improving the Regenerative Effects of Mesenchymal Stromal Cell-Based Therapies. Int J Mol Sci 2017; 18:E2087. [PMID: 28974046 PMCID: PMC5666769 DOI: 10.3390/ijms18102087] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/18/2017] [Accepted: 09/28/2017] [Indexed: 12/11/2022] Open
Abstract
Cell-based therapies have the potential to revolutionize current treatments for diseases with high prevalence and related economic and social burden. Unfortunately, clinical trials have made only modest improvements in restoring normal function to degenerating tissues. This limitation is due, at least in part, to the death of transplanted cells within a few hours after transplant due to a combination of mechanical, cellular, and host factors. In particular, mechanical stress during implantation, extracellular matrix loss upon delivery, nutrient and oxygen deprivation at the recipient site, and host inflammatory response are detrimental factors limiting long-term transplanted cell survival. The beneficial effect of cell therapy for regenerative medicine ultimately depends on the number of administered cells reaching the target tissue, their viability, and their promotion of tissue regeneration. Therefore, strategies aiming at improving viable cell engraftment are crucial for regenerative medicine. Here we review the major factors that hamper successful cell engraftment and the strategies that have been studied to enhance the beneficial effects of cell therapy. Moreover, we provide a perspective on whether mesenchymal stromal cell-derived extracellular vesicle delivery, as a cell-free regenerative approach, may circumvent current cell therapy limitations.
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Affiliation(s)
- Silvia Baldari
- Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute, via E. Chianesi 53, Rome 00144, Italy.
| | - Giuliana Di Rocco
- Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute, via E. Chianesi 53, Rome 00144, Italy.
| | - Martina Piccoli
- Stem Cells and Regenerative Medicine Laboratory, Foundation Institute of Pediatric Research "Città della Speranza", corso Stati Uniti 4, Padova 35127, Italy.
| | - Michela Pozzobon
- Department of Women's and Children's Health, University of Padova, Via Giustiniani 3, Padova 35128, Italy.
| | - Maurizio Muraca
- Department of Women's and Children's Health, University of Padova, Via Giustiniani 3, Padova 35128, Italy.
| | - Gabriele Toietta
- Department of Research, Advanced Diagnostic, and Technological Innovation, Regina Elena National Cancer Institute, via E. Chianesi 53, Rome 00144, Italy.
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PPARγ and the Innate Immune System Mediate the Resolution of Inflammation. PPAR Res 2015; 2015:549691. [PMID: 26713087 PMCID: PMC4680113 DOI: 10.1155/2015/549691] [Citation(s) in RCA: 403] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/15/2015] [Indexed: 11/18/2022] Open
Abstract
The resolution of inflammation is an active and dynamic process, mediated in large part by the innate immune system. Resolution represents not only an increase in anti-inflammatory actions, but also a paradigm shift in immune cell function to restore homeostasis. PPARγ, a ligand activated transcription factor, has long been studied for its anti-inflammatory actions, but an emerging body of literature is investigating the role of PPARγ and its ligands (including thiazolidinediones, prostaglandins, and oleanolic acids) in all phases of resolution. PPARγ can shift production from pro- to anti-inflammatory mediators by neutrophils, platelets, and macrophages. PPARγ and its ligands further modulate platelet and neutrophil function, decreasing trafficking, promoting neutrophil apoptosis, and preventing platelet-leukocyte interactions. PPARγ alters macrophage trafficking, increases efferocytosis and phagocytosis, and promotes alternative M2 macrophage activation. There are also roles for this receptor in the adaptive immune response, particularly regarding B cells. These effects contribute towards the attenuation of multiple disease states, including COPD, colitis, Alzheimer's disease, and obesity in animal models. Finally, novel specialized proresolving mediators-eicosanoids with critical roles in resolution-may act through PPARγ modulation to promote resolution, providing another exciting area of therapeutic potential for this receptor.
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Lannan KL, Sahler J, Kim N, Spinelli SL, Maggirwar SB, Garraud O, Cognasse F, Blumberg N, Phipps RP. Breaking the mold: transcription factors in the anucleate platelet and platelet-derived microparticles. Front Immunol 2015; 6:48. [PMID: 25762994 PMCID: PMC4327621 DOI: 10.3389/fimmu.2015.00048] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/26/2015] [Indexed: 01/15/2023] Open
Abstract
Platelets are small anucleate blood cells derived from megakaryocytes. In addition to their pivotal roles in hemostasis, platelets are the smallest, yet most abundant, immune cells and regulate inflammation, immunity, and disease progression. Although platelets lack DNA, and thus no functional transcriptional activities, they are nonetheless rich sources of RNAs, possess an intact spliceosome, and are thus capable of synthesizing proteins. Previously, it was thought that platelet RNAs and translational machinery were remnants from the megakaryocyte. We now know that the initial description of platelets as "cellular fragments" is an antiquated notion, as mounting evidence suggests otherwise. Therefore, it is reasonable to hypothesize that platelet transcription factors are not vestigial remnants from megakaryocytes, but have important, if only partly understood functions. Proteins play multiple cellular roles to minimize energy expenditure for maximum cellular function; thus, the same can be expected for transcription factors. In fact, numerous transcription factors have non-genomic roles, both in platelets and in nucleated cells. Our lab and others have discovered the presence and non-genomic roles of transcription factors in platelets, such as the nuclear factor kappa β (NFκB) family of proteins and peroxisome proliferator-activated receptor gamma (PPARγ). In addition to numerous roles in regulating platelet activation, functional transcription factors can be transferred to vascular and immune cells through platelet microparticles. This method of transcellular delivery of key immune molecules may be a vital mechanism by which platelet transcription factors regulate inflammation and immunity. At the very least, platelets are an ideal model cell to dissect out the non-genomic roles of transcription factors in nucleated cells. There is abundant evidence to suggest that transcription factors in platelets play key roles in regulating inflammatory and hemostatic functions.
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Affiliation(s)
- Katie L Lannan
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA
| | - Julie Sahler
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA ; Department of Biological and Environmental Engineering, Cornell University , Ithaca, NY , USA
| | - Nina Kim
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA
| | - Sherry L Spinelli
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA
| | - Sanjay B Maggirwar
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA
| | - Olivier Garraud
- Faculté de Médecine, Université de Lyon , Saint-Etienne , France
| | - Fabrice Cognasse
- Faculté de Médecine, Université de Lyon , Saint-Etienne , France ; Etablissement Français du Sang Auvergne-Loire , Saint-Etienne , France
| | - Neil Blumberg
- Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA
| | - Richard P Phipps
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA ; Department of Pathology and Laboratory Medicine, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA ; Department of Environmental Medicine, University of Rochester School of Medicine and Dentistry , Rochester, NY , USA
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