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Beltran JVB, Lin FP, Chang CL, Ko TM. Single-Cell Meta-Analysis of Neutrophil Activation in Kawasaki Disease and Multisystem Inflammatory Syndrome in Children Reveals Potential Shared Immunological Drivers. Circulation 2023; 148:1778-1796. [PMID: 37905415 DOI: 10.1161/circulationaha.123.064734] [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: 04/21/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023]
Abstract
BACKGROUND Kawasaki disease (KD) and multisystem inflammatory syndrome in children (MIS-C) share similar clinical manifestations, including cardiovascular complications, suggesting similar underlying immunopathogenic processes. Aberrant neutrophil activation may play a crucial role in the shared pathologies of KD and MIS-C; however, the associated pathogenic mechanisms and molecular drivers remain unknown. METHODS We performed a single-cell meta-analysis of neutrophil activation with 103 pediatric single-cell transcriptomic peripheral blood mononuclear cell data across 9 cohorts, including healthy controls, KD, MIS-C, compared with dengue virus infection, juvenile idiopathic arthritis, and pediatric celiac disease. We used a series of computational analyses to investigate the shared neutrophil transcriptional programs of KD and MIS-C that are linked to systemic damage and cardiac pathologies, and suggested Food and Drug Administration-approved drugs to consider as KD and MIS-C treatment. RESULTS We meta-analyzed 521 950 high-quality cells. We found that blood signatures associated with risks of cardiovascular events are enriched in neutrophils of KD and MIS-C. We revealed the expansion of CD177+ neutrophils harboring hyperactivated effector functions in both KD and MIS-C, but not in healthy controls or in other viral-, inflammatory-, or immune-related pediatric diseases. KD and MIS-C CD177+ neutrophils had highly similar transcriptomes, marked by conserved signatures and pathways related to molecular damage. We found the induction of a shared neutrophil expression program, potentially regulated by SPI1 (Spi-1 proto-oncogene), which confers enhanced effector functions, especially neutrophil degranulation. CD177 and shared neutrophil expression program expressions were associated with acute stages and attenuated during KD intravenous immunoglobulin treatment and MIS-C recovery. Network analysis identified hub genes that correlated with the high activation of CD177+ neutrophils. Disease-gene association analysis revealed that the KD and MIS-C CD177+ neutrophils' shared expression program was associated with the development of coronary and myocardial disorders. Last, we identified and validated TSPO (translocator protein) and S100A12 (S100 calcium-binding protein A12) as main molecular targets, for which the Food and Drug Administration-approved drugs methotrexate, zaleplon, metronidazole, lorazepam, clonazepam, temazepam, and zolpidem, among others, are primary candidates for drug repurposing. CONCLUSIONS Our findings indicate that CD177+ neutrophils may exert systemic pathological damage contributing to the shared morbidities in KD and MIS-C. We uncovered potential regulatory drivers of CD177+ neutrophil hyperactivation and pathogenicity that may be targeted as a single therapeutic strategy for either KD or MIS-C.
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Affiliation(s)
- Jan Vincent B Beltran
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
| | - Fang-Ping Lin
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan (F.-P.L., C.-L.C., T.-M.K.)
| | - Chaw-Liang Chang
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan (F.-P.L., C.-L.C., T.-M.K.)
- Department of Pediatrics, Cathay General Hospital, Hsinchu, Taiwan (C.-L.C.)
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan (C.-L.C.)
| | - Tai-Ming Ko
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan (J.V.B.B., T.-M.K.)
- Department of Biological Sciences and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan (F.-P.L., C.-L.C., T.-M.K.)
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan (T.-M.K.)
- School of Pharmacy, College of Pharmacy, Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan (T.-M.K.)
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Gromadziński L, Paukszto Ł, Lepiarczyk E, Skowrońska A, Lipka A, Makowczenko KG, Łopieńska-Biernat E, Jastrzębski JP, Holak P, Smoliński M, Majewska M. Pulmonary artery embolism: comprehensive transcriptomic analysis in understanding the pathogenic mechanisms of the disease. BMC Genomics 2023; 24:10. [PMID: 36624378 PMCID: PMC9830730 DOI: 10.1186/s12864-023-09110-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 01/02/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Pulmonary embolism (PE) is a severe disease that usually originates from deep vein thrombosis (DVT) of the lower extremities. This study set out to investigate the changes in the transcriptome of the pulmonary artery (PA) in the course of the PE in the porcine model. METHODS The study was performed on 11 male pigs: a thrombus was formed in each right femoral vein in six animals, and then was released to induce PE, the remaining five animals served as a control group. In the experimental animals total RNA was isolated from the PA where the blood clot lodged, and in the control group, from the corresponding PA segments. High-throughput RNA sequencing was used to analyse the global changes in the transcriptome of PA with induced PE (PA-E). RESULTS Applied multistep bioinformatics revealed 473 differentially expressed genes (DEGs): 198 upregulated and 275 downregulated. Functional Gene Ontology annotated 347 DEGs into 27 biological processes, 324 to the 11 cellular components and 346 to the 2 molecular functions categories. In the signaling pathway analysis, KEGG 'protein processing in endoplasmic reticulum' was identified for the mRNAs modulated during PE. The same KEGG pathway was also exposed by 8 differentially alternative splicing genes. Within single nucleotide variants, the 61 allele-specific expression variants were localised in the vicinity of the genes that belong to the cellular components of the 'endoplasmic reticulum'. The discovered allele-specific genes were also classified as signatures of the cardiovascular system. CONCLUSIONS The findings of this research provide the first thorough investigation of the changes in the gene expression profile of PA affected by an embolus. Evidence from this study suggests that the disturbed homeostasis in the biosynthesis of proteins in the endoplasmic reticulum plays a major role in the pathogenesis of PE.
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Affiliation(s)
- Leszek Gromadziński
- grid.412607.60000 0001 2149 6795Department of Cardiology and Internal Medicine, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Warszawska Str 30, 10-082 Olsztyn, Poland
| | - Łukasz Paukszto
- grid.412607.60000 0001 2149 6795Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Ewa Lepiarczyk
- grid.412607.60000 0001 2149 6795Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Warszawska Str 30, 10-082 Olsztyn, Poland
| | - Agnieszka Skowrońska
- grid.412607.60000 0001 2149 6795Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Warszawska Str 30, 10-082 Olsztyn, Poland
| | - Aleksandra Lipka
- grid.412607.60000 0001 2149 6795Department of Gynecology, and Obstetrics, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Żołnierska Str 18, 10-561 Olsztyn, Poland
| | - Karol G. Makowczenko
- grid.412607.60000 0001 2149 6795Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Elżbieta Łopieńska-Biernat
- grid.412607.60000 0001 2149 6795Department of Biochemistry, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn, Poland
| | - Jan P. Jastrzębski
- grid.412607.60000 0001 2149 6795Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 1A, 10-719 Olsztyn-Kortowo, Poland
| | - Piotr Holak
- grid.412607.60000 0001 2149 6795Department of Surgery and Radiology With Clinic, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Oczapowskiego Str 14, 10-719 Olsztyn, Poland
| | - Michał Smoliński
- grid.460107.4Clinic of Cardiology and Internal Diseases, University Clinical Hospital in Olsztyn, Warszawska Str 30, 10-082 Olsztyn, Poland
| | - Marta Majewska
- grid.412607.60000 0001 2149 6795Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Warszawska Str 30, 10-082 Olsztyn, Poland
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Jacintho BC, Mazetto Fonseca BDM, Hounkpe BW, Oliveira JD, dos Santos APR, Vaz CDO, de Paula EV, Orsi FA. Evaluation of a gene signature related to thrombotic manifestations in antiphospholipid syndrome. Front Med (Lausanne) 2023; 10:1139906. [PMID: 37035297 PMCID: PMC10076702 DOI: 10.3389/fmed.2023.1139906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/03/2023] [Indexed: 04/11/2023] Open
Abstract
Thrombotic primary antiphospholipid syndrome (t-PAPS) is an acquired condition characterized by heterogeneous thrombotic manifestations, which is intriguing since venous and arterial thrombosis appear to have distinct pathogenesis. Gene expression analysis may constitute a new approach to evaluate potential similarities or differences between the clinical manifestations of t-PAPS. Recently, dysregulation of the ANXA3, TNFAIP6, TXK, BACH2, and SERPINB2 genes has been associated with both arterial and venous thrombosis in the general population. Therefore, the aim of this study was to examine whether ANXA3, TNFAIP6, TXK, BACH2, and SERPINB2 expression was associated with t-PAPS. Gene expression was quantified by qPCR of total leukocyte mRNA. In this case-control study, 102 t-PAPS patients, 17 asymptomatic antiphospholipid (aPL) carriers and 100 controls were evaluated. Increased expression of ANXA3 (P = 0.008) and TNFAIP6 (P = 0.001) and decreased expression of the TXK gene (P = 0.0001) were associated with an increased risk of t-PAPS compared to the control. ANXA3 upregulation was more evident in cases of arterial thrombosis and multiple thrombotic events. There was no difference in the expression of these genes between triple and non-triple aPL positivity. ANXA3, TNFAIP6, TXK, BACH2, and SERPINB2 expression levels were also similar between aPL carriers and controls (P = 0.77; P = 0.48; P = 0.08; P = 0.73, and P = 0.13, respectively). In conclusion, our results showed that genes related to hemostasis (ANXA3) and immunity (TNFAIP6, TXK) are dysregulated in t-PAPS compared to controls. Gene dysregulation was not detected in aPL carriers and was not related to the aPL profile, suggesting that this gene signature is related to thrombotic manifestations rather than to aPL burden. Our results suggest that innate immunity and hemostasis pathways are associated with t-PAPS at a molecular level and may play a role in disease severity.
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Affiliation(s)
| | - Bruna de Moraes Mazetto Fonseca
- School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Jose Diogo Oliveira
- School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Erich Vinicius de Paula
- School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Andrade Orsi
- Hematology and Hemotherapy Center, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Pathology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Fernanda Andrade Orsi,
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de Guimarães JA, Hounpke BW, Duarte B, Boso ALM, Viturino MGM, de Carvalho Baptista L, de Melo MB, Alves M. Transcriptomics and network analysis highlight potential pathways in the pathogenesis of pterygium. Sci Rep 2022; 12:286. [PMID: 34997134 PMCID: PMC8741985 DOI: 10.1038/s41598-021-04248-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 11/09/2022] Open
Abstract
Pterygium is a common ocular surface condition frequently associated with irritative symptoms. The precise identity of its critical triggers as well as the hierarchical relationship between all the elements involved in the pathogenesis of this disease are not yet elucidated. Meta-analysis of gene expression studies represents a novel strategy capable of identifying key pathogenic mediators and therapeutic targets in complex diseases. Samples from nine patients were collected during surgery after photo documentation and clinical characterization of pterygia. Gene expression experiments were performed using Human Clariom D Assay gene chip. Differential gene expression analysis between active and atrophic pterygia was performed using limma package after adjusting variables by age. In addition, a meta-analysis was performed including recent gene expression studies available at the Gene Expression Omnibus public repository. Two databases including samples from adults with pterygium and controls fulfilled our inclusion criteria. Meta-analysis was performed using the Rank Production algorithm of the RankProd package. Gene set analysis was performed using ClueGO and the transcription factor regulatory network prediction was performed using appropriate bioinformatics tools. Finally, miRNA-mRNA regulatory network was reconstructed using up-regulated genes identified in the gene set analysis from the meta-analysis and their interacting miRNAs from the Brazilian cohort expression data. The meta-analysis identified 154 up-regulated and 58 down-regulated genes. A gene set analysis with the top up-regulated genes evidenced an overrepresentation of pathways associated with remodeling of extracellular matrix. Other pathways represented in the network included formation of cornified envelopes and unsaturated fatty acid metabolic processes. The miRNA-mRNA target prediction network, also reconstructed based on the set of up-regulated genes presented in the gene ontology and biological pathways network, showed that 17 target genes were negatively correlated with their interacting miRNAs from the Brazilian cohort expression data. Once again, the main identified cluster involved extracellular matrix remodeling mechanisms, while the second cluster involved formation of cornified envelope, establishment of skin barrier and unsaturated fatty acid metabolic process. Differential expression comparing active pterygium with atrophic pterygium using data generated from the Brazilian cohort identified differentially expressed genes between the two forms of presentation of this condition. Our results reveal differentially expressed genes not only in pterygium, but also in active pterygium when compared to the atrophic ones. New insights in relation to pterygium's pathophysiology are suggested.
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Affiliation(s)
- Juliana Albano de Guimarães
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo. Cidade Universitária, Campinas, São Paulo, 13083887, Brazil
| | | | - Bruna Duarte
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo. Cidade Universitária, Campinas, São Paulo, 13083887, Brazil
| | - Ana Luiza Mylla Boso
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo. Cidade Universitária, Campinas, São Paulo, 13083887, Brazil
| | - Marina Gonçalves Monteiro Viturino
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo. Cidade Universitária, Campinas, São Paulo, 13083887, Brazil
| | | | - Mônica Barbosa de Melo
- Center for Molecular Biology and Genetic Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Monica Alves
- Department of Ophthalmology and Otorhinolaryngology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo. Cidade Universitária, Campinas, São Paulo, 13083887, Brazil.
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Jales Neto LH, Hounkpe BW, Fernandes GH, Takayama L, Caparbo VF, Lopes NH, Pereira AC, Pereira RM. Transcriptomic analysis of elderly women with low muscle mass: association with immune system pathway. Aging (Albany NY) 2021; 13:20992-21008. [PMID: 34493690 PMCID: PMC8457609 DOI: 10.18632/aging.203505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Despite the well-established association of gene expression deregulation with low muscle mass (LMM), the associated biological mechanisms remain unclear. Transcriptomic studies are capable to identify key mediators in complex diseases. We aimed to identify relevant mediators and biological mechanisms associated with age-related LMM. LMM-associated genes were detected by logistic regression using microarray data of 20 elderly women with LMM and 20 age and race-matched controls extracted from our SPAH Study (GSE152073). We performed weighted gene co-expression analysis (WGCNA) that correlated the identified gene modules with laboratorial characteristics. Gene enrichment analysis was performed and an LMM predictive model was constructed using Support Vector Machine (SVM). Overall, 821 discriminating transcripts clusters were identified (|beta coefficient| >1; p-value <0.01). From this list, 45 predictors of LMM were detected by SVM and validated with 0.7 of accuracy. Our results revealed that the well-described association of inflammation, immunity and metabolic alterations is also relevant at transcriptomic level. WGCNA highlighted a correlation of genes modules involved in immunity pathways with vitamin D level (R = 0.63, p = 0.004) and the Agatston score (R = 0.51, p = 0.02). Our study generated a predicted regulatory network and revealed significant metabolic pathways related to aging processes, showing key mediators that warrant further investigation.
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Affiliation(s)
- Levi H. Jales Neto
- Bone Metabolism Laboratory, Rheumatology Division Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Bidossessi W. Hounkpe
- Bone Metabolism Laboratory, Rheumatology Division Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Georgea H. Fernandes
- Bone Metabolism Laboratory, Rheumatology Division Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Liliam Takayama
- Bone Metabolism Laboratory, Rheumatology Division Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Valéria F. Caparbo
- Bone Metabolism Laboratory, Rheumatology Division Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Neuza H.M. Lopes
- Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Instituto do Coração (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Rosa M.R. Pereira
- Bone Metabolism Laboratory, Rheumatology Division Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
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