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Rai MF, Collins KH, Lang A, Maerz T, Geurts J, Ruiz-Romero C, June RK, Ramos Y, Rice SJ, Ali SA, Pastrello C, Jurisica I, Thomas Appleton C, Rockel JS, Kapoor M. Three decades of advancements in osteoarthritis research: insights from transcriptomic, proteomic, and metabolomic studies. Osteoarthritis Cartilage 2024; 32:385-397. [PMID: 38049029 DOI: 10.1016/j.joca.2023.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is a complex disease involving contributions from both local joint tissues and systemic sources. Patient characteristics, encompassing sociodemographic and clinical variables, are intricately linked with OA rendering its understanding challenging. Technological advancements have allowed for a comprehensive analysis of transcripts, proteomes and metabolomes in OA tissues/fluids through omic analyses. The objective of this review is to highlight the advancements achieved by omic studies in enhancing our understanding of OA pathogenesis over the last three decades. DESIGN We conducted an extensive literature search focusing on transcriptomics, proteomics and metabolomics within the context of OA. Specifically, we explore how these technologies have identified individual transcripts, proteins, and metabolites, as well as distinctive endotype signatures from various body tissues or fluids of OA patients, including insights at the single-cell level, to advance our understanding of this highly complex disease. RESULTS Omic studies reveal the description of numerous individual molecules and molecular patterns within OA-associated tissues and fluids. This includes the identification of specific cell (sub)types and associated pathways that contribute to disease mechanisms. However, there remains a necessity to further advance these technologies to delineate the spatial organization of cellular subtypes and molecular patterns within OA-afflicted tissues. CONCLUSIONS Leveraging a multi-omics approach that integrates datasets from diverse molecular detection technologies, combined with patients' clinical and sociodemographic features, and molecular and regulatory networks, holds promise for identifying unique patient endophenotypes. This holistic approach can illuminate the heterogeneity among OA patients and, in turn, facilitate the development of tailored therapeutic interventions.
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Affiliation(s)
- Muhammad Farooq Rai
- Department of Anatomy and Cellular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Kelsey H Collins
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Annemarie Lang
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jeroen Geurts
- Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR), Unidad de Proteómica, INIBIC -Hospital Universitario A Coruña, SERGAS, Spain
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, USA
| | - Yolande Ramos
- Dept. Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shabana Amanda Ali
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
| | - C Thomas Appleton
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Jason S Rockel
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, ON, Canada.
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2
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Clotet-Freixas S, Zaslaver O, Kotlyar M, Pastrello C, Quaile AT, McEvoy CM, Saha AD, Farkona S, Boshart A, Zorcic K, Neupane S, Manion K, Allen M, Chan M, Chen X, Arnold AP, Sekula P, Steinbrenner I, Köttgen A, Dart AB, Wicklow B, McGavock JM, Blydt-Hansen TD, Barrios C, Riera M, Soler MJ, Isenbrandt A, Lamontagne-Proulx J, Pradeloux S, Coulombe K, Soulet D, Rajasekar S, Zhang B, John R, Mehrotra A, Gehring A, Puhka M, Jurisica I, Woo M, Scholey JW, Röst H, Konvalinka A. Sex differences in kidney metabolism may reflect sex-dependent outcomes in human diabetic kidney disease. Sci Transl Med 2024; 16:eabm2090. [PMID: 38446901 DOI: 10.1126/scitranslmed.abm2090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/24/2024] [Indexed: 03/08/2024]
Abstract
Diabetic kidney disease (DKD) is the main cause of chronic kidney disease (CKD) and progresses faster in males than in females. We identify sex-based differences in kidney metabolism and in the blood metabolome of male and female individuals with diabetes. Primary human proximal tubular epithelial cells (PTECs) from healthy males displayed increased mitochondrial respiration, oxidative stress, apoptosis, and greater injury when exposed to high glucose compared with PTECs from healthy females. Male human PTECs showed increased glucose and glutamine fluxes to the TCA cycle, whereas female human PTECs showed increased pyruvate content. The male human PTEC phenotype was enhanced by dihydrotestosterone and mediated by the transcription factor HNF4A and histone demethylase KDM6A. In mice where sex chromosomes either matched or did not match gonadal sex, male gonadal sex contributed to the kidney metabolism differences between males and females. A blood metabolomics analysis in a cohort of adolescents with or without diabetes showed increased TCA cycle metabolites in males. In a second cohort of adults with diabetes, females without DKD had higher serum pyruvate concentrations than did males with or without DKD. Serum pyruvate concentrations positively correlated with the estimated glomerular filtration rate, a measure of kidney function, and negatively correlated with all-cause mortality in this cohort. In a third cohort of adults with CKD, male sex and diabetes were associated with increased plasma TCA cycle metabolites, which correlated with all-cause mortality. These findings suggest that differences in male and female kidney metabolism may contribute to sex-dependent outcomes in DKD.
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Affiliation(s)
- Sergi Clotet-Freixas
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Olga Zaslaver
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Andrew T Quaile
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Caitriona M McEvoy
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
- Division of Nephrology, Tallaght University Hospital, Dublin D24, Ireland
- Trinity Kidney Centre, Trinity College Dublin, Dublin D8, Ireland
| | - Aninda D Saha
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Alex Boshart
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Katarina Zorcic
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Slaghaniya Neupane
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Kieran Manion
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Maya Allen
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Michael Chan
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Xuqi Chen
- Department of Integrative Biology & Physiology, University of California, Los Angeles, CA 90095, USA
| | - Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, CA 90095, USA
| | - Peggy Sekula
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79085, Germany
| | - Inga Steinbrenner
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79085, Germany
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79085, Germany
| | - Allison B Dart
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba Research Team, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Brandy Wicklow
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba Research Team, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Jon M McGavock
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba Research Team, Children's Hospital Research Institute of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Tom D Blydt-Hansen
- Department of Pediatrics, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Clara Barrios
- Kidney Research Group, Hospital del Mar Medical Research Institute, IMIM, Barcelona 08003, Spain
| | - Marta Riera
- Kidney Research Group, Hospital del Mar Medical Research Institute, IMIM, Barcelona 08003, Spain
| | - María José Soler
- Hospital Universitari Vall d'Hebron, Division of Nephrology Autonomous University of Barcelona, Barcelona 08035, Spain
| | - Amandine Isenbrandt
- Neurosciences Axis, CHU de Quebec Research Center - Université Laval, Québec, QC G1V 4G2, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC G1V 0A6, Canada
| | - Jérôme Lamontagne-Proulx
- Neurosciences Axis, CHU de Quebec Research Center - Université Laval, Québec, QC G1V 4G2, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC G1V 0A6, Canada
| | - Solène Pradeloux
- Neurosciences Axis, CHU de Quebec Research Center - Université Laval, Québec, QC G1V 4G2, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC G1V 0A6, Canada
| | - Katherine Coulombe
- Neurosciences Axis, CHU de Quebec Research Center - Université Laval, Québec, QC G1V 4G2, Canada
| | - Denis Soulet
- Neurosciences Axis, CHU de Quebec Research Center - Université Laval, Québec, QC G1V 4G2, Canada
- Faculty of Pharmacy, Université Laval, Québec, QC G1V 0A6, Canada
| | - Shravanthi Rajasekar
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Boyang Zhang
- Department of Chemical Engineering, McMaster University, Hamilton, ON L8S 4L8, Canada
- School of Biomedical Engineering, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Rohan John
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aman Mehrotra
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Adam Gehring
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M5G 2C4, Canada
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1X3, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava 845 10, Slovakia
| | - Minna Woo
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Department of Medicine, Division of Endocrinology, University Health Network, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - James W Scholey
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON M5S 3H2, Canada
| | - Hannes Röst
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON M5G 2C4, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON M5G 2C4, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON M5S 3H2, Canada
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3
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Ramos YFM, Rice SJ, Ali SA, Pastrello C, Jurisica I, Rai MF, Collins KH, Lang A, Maerz T, Geurts J, Ruiz-Romero C, June RK, Thomas Appleton C, Rockel JS, Kapoor M. Evolution and advancements in genomics and epigenomics in OA research: How far we have come. Osteoarthritis Cartilage 2024:S1063-4584(24)00054-2. [PMID: 38428513 DOI: 10.1016/j.joca.2024.02.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/29/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most prevalent musculoskeletal disease affecting articulating joint tissues, resulting in local and systemic changes that contribute to increased pain and reduced function. Diverse technological advancements have culminated in the advent of high throughput "omic" technologies, enabling identification of comprehensive changes in molecular mediators associated with the disease. Amongst these technologies, genomics and epigenomics - including methylomics and miRNomics, have emerged as important tools to aid our biological understanding of disease. DESIGN In this narrative review, we selected articles discussing advancements and applications of these technologies to OA biology and pathology. We discuss how genomics, deoxyribonucleic acid (DNA) methylomics, and miRNomics have uncovered disease-related molecular markers in the local and systemic tissues or fluids of OA patients. RESULTS Genomics investigations into the genetic links of OA, including using genome-wide association studies, have evolved to identify 100+ genetic susceptibility markers of OA. Epigenomic investigations of gene methylation status have identified the importance of methylation to OA-related catabolic gene expression. Furthermore, miRNomic studies have identified key microRNA signatures in various tissues and fluids related to OA disease. CONCLUSIONS Sharing of standardized, well-annotated omic datasets in curated repositories will be key to enhancing statistical power to detect smaller and targetable changes in the biological signatures underlying OA pathogenesis. Additionally, continued technological developments and analysis methods, including using computational molecular and regulatory networks, are likely to facilitate improved detection of disease-relevant targets, in-turn, supporting precision medicine approaches and new treatment strategies for OA.
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Affiliation(s)
- Yolande F M Ramos
- Dept. Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Sarah J Rice
- Biosciences Institute, International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Shabana Amanda Ali
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada; Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Muhammad Farooq Rai
- Department of Biological Sciences, Center for Biotechnology, College of Medicine & Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Kelsey H Collins
- Department of Orthopaedic Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Annemarie Lang
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Tristan Maerz
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jeroen Geurts
- Rheumatology, Department of Musculoskeletal Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR), Unidad de Proteómica, INIBIC -Hospital Universitario A Coruña, SERGAS, A Coruña, Spain
| | - Ronald K June
- Department of Mechanical & Industrial Engineering, Montana State University, Bozeman, MT, USA
| | - C Thomas Appleton
- Department of Medicine, University of Western Ontario, London, Ontario, Canada
| | - Jason S Rockel
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.
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Plaça DR, Fonseca DLM, Marques AHC, Zaki Pour S, Usuda JN, Baiocchi GC, Prado CADS, Salgado RC, Filgueiras IS, Freire PP, Rocha V, Camara NOS, Catar R, Moll G, Jurisica I, Calich VLG, Giil LM, Rivino L, Ochs HD, Cabral-Miranda G, Schimke LF, Cabral-Marques O. Immunological signatures unveiled by integrative systems vaccinology characterization of dengue vaccination trials and natural infection. Front Immunol 2024; 15:1282754. [PMID: 38444851 PMCID: PMC10912564 DOI: 10.3389/fimmu.2024.1282754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Introduction Dengue virus infection is a global health problem lacking specific therapy, requiring an improved understanding of DENV immunity and vaccine responses. Considering the recent emerging of new dengue vaccines, here we performed an integrative systems vaccinology characterization of molecular signatures triggered by the natural DENV infection (NDI) and attenuated dengue virus infection models (DVTs). Methods and results We analyzed 955 samples of transcriptomic datasets of patients with NDI and attenuated dengue virus infection trials (DVT1, DVT2, and DVT3) using a systems vaccinology approach. Differential expression analysis identified 237 common differentially expressed genes (DEGs) between DVTs and NDI. Among them, 28 and 60 DEGs were up or downregulated by dengue vaccination during DVT2 and DVT3, respectively, with 20 DEGs intersecting across all three DVTs. Enriched biological processes of these genes included type I/II interferon signaling, cytokine regulation, apoptosis, and T-cell differentiation. Principal component analysis based on 20 common DEGs (overlapping between DVTs and our NDI validation dataset) distinguished dengue patients by disease severity, particularly in the late acute phase. Machine learning analysis ranked the ten most critical predictors of disease severity in NDI, crucial for the anti-viral immune response. Conclusion This work provides insights into the NDI and vaccine-induced overlapping immune response and suggests molecular markers (e.g., IFIT5, ISG15, and HERC5) for anti-dengue-specific therapies and effective vaccination development.
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Affiliation(s)
- Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M. Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
| | - Alexandre H. C. Marques
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Shahab Zaki Pour
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Júlia Nakanishi Usuda
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Gabriela Crispim Baiocchi
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ranieri Coelho Salgado
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology and Cell Therapy, Hospital das Clínicas, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Fundação Pró-Sangue-Hemocentro de São Paulo, São Paulo, Brazil
- Department of Hematology, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Niels Olsen Saraiva Camara
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
- Berlin Institute of Health (BIH) Center for Regenerative Therapies (BCRT) and Berlin-Brandenburg School for Regenerative Therapies (BSRT), Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vera Lúcia Garcia Calich
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lasse M. Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Laura Rivino
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Emerging Infectious Diseases, Duke-National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Hans D. Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children’s Research Institute, Seattle, WA, United States
| | - Gustavo Cabral-Miranda
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Lena F. Schimke
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, SP, Brazil
- Departament of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
- Instituto D’Or de Ensino e Pesquisa, São Paulo, Brazil
- Department of Medicine, Division of Molecular Medicine, Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, Berlin, Germany
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, SP, Brazil
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5
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Vosberg DE, Jurisica I, Pausova Z, Paus T. Intrauterine growth and the tangential expansion of the human cerebral cortex in times of food scarcity and abundance. Nat Commun 2024; 15:1205. [PMID: 38350995 PMCID: PMC10864407 DOI: 10.1038/s41467-024-45409-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Tangential growth of the human cerebral cortex is driven by cell proliferation during the first and second trimester of pregnancy. Fetal growth peaks in mid-gestation. Here, we explore how genes associated with fetal growth relate to cortical growth. We find that both maternal and fetal genetic variants associated with higher birthweight predict larger cortical surface area. The relative dominance of the maternal vs. fetal variants in these associations show striking variations across birth years (1943 to 1966). The birth-year patterns vary as a function of the epigenetic status near genes differentially methylated in individuals exposed (or not) to famine during the Dutch Winter of 1944/1945. Thus, it appears that the two sets of molecular processes contribute to early cortical development to a different degree in times of food scarcity or its abundance.
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Affiliation(s)
- Daniel E Vosberg
- Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
- Research Institute of the Hospital for Sick Children, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics and Computer Science, and the Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Zdenka Pausova
- Research Institute of the Hospital for Sick Children, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
- ECOGENE-21, Chicoutimi, Quebec, Canada
| | - Tomáš Paus
- Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada.
- Department of Neuroscience, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.
- ECOGENE-21, Chicoutimi, Quebec, Canada.
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.
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Koussiouris J, Looby N, Kotlyar M, Kulasingam V, Jurisica I, Chandran V. Classifying patients with psoriatic arthritis according to their disease activity status using serum metabolites and machine learning. Metabolomics 2024; 20:17. [PMID: 38267619 PMCID: PMC10810020 DOI: 10.1007/s11306-023-02079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Psoriatic arthritis (PsA) is a heterogeneous inflammatory arthritis, affecting approximately a quarter of patients with psoriasis. Accurate assessment of disease activity is difficult. There are currently no clinically validated biomarkers to stratify PsA patients based on their disease activity, which is important for improving clinical management. OBJECTIVES To identify metabolites capable of classifying patients with PsA according to their disease activity. METHODS An in-house solid-phase microextraction (SPME)-liquid chromatography-high resolution mass spectrometry (LC-HRMS) method for lipid analysis was used to analyze serum samples obtained from patients classified as having low (n = 134), moderate (n = 134) or high (n = 104) disease activity, based on psoriatic arthritis disease activity scores (PASDAS). Metabolite data were analyzed using eight machine learning methods to predict disease activity levels. Top performing methods were selected based on area under the curve (AUC) and significance. RESULTS The best model for predicting high disease activity from low disease activity achieved AUC 0.818. The best model for predicting high disease activity from moderate disease activity achieved AUC 0.74. The best model for classifying low disease activity from moderate and high disease activity achieved AUC 0.765. Compounds confirmed by MS/MS validation included metabolites from diverse compound classes such as sphingolipids, phosphatidylcholines and carboxylic acids. CONCLUSION Several lipids and other metabolites when combined in classifying models predict high disease activity from both low and moderate disease activity. Lipids of key interest included lysophosphatidylcholine and sphingomyelin. Quantitative MS assays based on selected reaction monitoring, are required to quantify the candidate biomarkers identified.
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Affiliation(s)
- John Koussiouris
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopaedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Institute, University Health Network, Toronto, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, Canada.
- Institute of Medical Science, University of Toronto, Toronto, Canada.
- Krembil Research Institute, University Health Network, Toronto, Canada.
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7
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Pastrello C, Kotlyar M, Abovsky M, Lu R, Jurisica I. PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. Nucleic Acids Res 2024; 52:D663-D671. [PMID: 37994706 PMCID: PMC10767947 DOI: 10.1093/nar/gkad1027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023] Open
Abstract
Pathway Data Integration Portal (PathDIP) is an integrated pathway database that was developed to increase functional gene annotation coverage and reduce bias in pathway enrichment analysis. PathDIP 5 provides multiple improvements to enable more interpretable analysis: users can perform enrichment analysis using all sources, separate sources or by combining specific pathway subsets; they can select the types of sources to use or the types of pathways for the analysis, reducing the number of resulting generic pathways or pathways not related to users' research question; users can use API. All pathways have been mapped to seven representative types. The results of pathway enrichment can be summarized through knowledge-based pathway consolidation. All curated pathways were mapped to 53 pathway ontology-based categories. In addition to genes, pathDIP 5 now includes metabolites. We updated existing databases, included two new sources, PathBank and MetabolicAtlas, and removed outdated databases. We enable users to analyse their results using Drugst.One, where a drug-gene network is created using only the user's genes in a specific pathway. Interpreting the results of any analysis is now improved by multiple charts on all the results pages. PathDIP 5 is freely available at https://ophid.utoronto.ca/pathDIP.
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Affiliation(s)
- Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, Toronto, Ontario M5T 0S8, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON M5T 0S8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, Toronto, Ontario M5T 0S8, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON M5T 0S8, Canada
| | - Mark Abovsky
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, Toronto, Ontario M5T 0S8, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON M5T 0S8, Canada
| | - Richard Lu
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, Toronto, Ontario M5T 0S8, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON M5T 0S8, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, Toronto, Ontario M5T 0S8, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1L7, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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Muniz-Santos R, Magno-França A, Jurisica I, Cameron LC. From Microcosm to Macrocosm: The -Omics, Multiomics, and Sportomics Approaches in Exercise and Sports. OMICS 2023; 27:499-518. [PMID: 37943554 DOI: 10.1089/omi.2023.0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
This article explores the progressive integration of -omics methods, including genomics, metabolomics, and proteomics, into sports research, highlighting the development of the concept of "sportomics." We discuss how sportomics can be used to comprehend the multilevel metabolism during exercise in real-life conditions faced by athletes, enabling potential personalized interventions to improve performance and recovery and reduce injuries, all with a minimally invasive approach and reduced time. Sportomics may also support highly personalized investigations, including the implementation of n-of-1 clinical trials and the curation of extensive datasets through long-term follow-up of athletes, enabling tailored interventions for athletes based on their unique physiological responses to different conditions. Beyond its immediate sport-related applications, we delve into the potential of utilizing the sportomics approach to translate Big Data regarding top-level athletes into studying different human diseases, especially with nontargeted analysis. Furthermore, we present how the amalgamation of bioinformatics, artificial intelligence, and integrative computational analysis aids in investigating biochemical pathways, and facilitates the search for various biomarkers. We also highlight how sportomics can offer relevant information about doping control analysis. Overall, sportomics offers a comprehensive approach providing novel insights into human metabolism during metabolic stress, leveraging cutting-edge systems science techniques and technologies.
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Affiliation(s)
- Renan Muniz-Santos
- Laboratory of Protein Biochemistry, The Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Magno-França
- Laboratory of Protein Biochemistry, The Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - L C Cameron
- Laboratory of Protein Biochemistry, The Federal University of the State of Rio de Janeiro, Rio de Janeiro, Brazil
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Tavasolian F, Lively S, Pastrello C, Tang M, Lim M, Pacheco A, Qaiyum Z, Yau E, Baskurt Z, Jurisica I, Kapoor M, Inman RD. Proteomic and genomic profiling of plasma exosomes from patients with ankylosing spondylitis. Ann Rheum Dis 2023; 82:1429-1443. [PMID: 37532285 DOI: 10.1136/ard-2022-223791] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
INTRODUCTION Recent advances in understanding the biology of ankylosing spondylitis (AS) using innovative genomic and proteomic approaches offer the opportunity to address current challenges in AS diagnosis and management. Altered expression of genes, microRNAs (miRNAs) or proteins may contribute to immune dysregulation and may play a significant role in the onset and persistence of inflammation in AS. The ability of exosomes to transport miRNAs across cells and alter the phenotype of recipient cells has implicated exosomes in perpetuating inflammation in AS. This study reports the first proteomic and miRNA profiling of plasma-derived exosomes in AS using comprehensive computational biology analysis. METHODS Plasma samples from patients with AS and healthy controls (HC) were isolated via ultracentrifugation and subjected to extracellular vesicle flow cytometry analysis to characterise exosome surface markers by a multiplex immunocapture assay. Cytokine profiling of plasma-derived exosomes and cell culture supernatants was performed. Next-generation sequencing was used to identify miRNA populations in exosomes enriched from plasma fractions. CD4+ T cells were sorted, and the frequency and proliferation of CD4+ T-cell subsets were analysed after treatment with AS-exosomes using flow cytometry. RESULTS The expression of exosome marker proteins CD63 and CD81 was elevated in the patients with AS compared with HC (q<0.05). Cytokine profiling in plasma-derived AS-exosomes demonstrated downregulation of interleukin (IL)-8 and IL-10 (q<0.05). AS-exosomes cocultured with HC CD4+ T cells induced significant upregulation of IFNα2 and IL-33 (q<0.05). Exosomes from patients with AS inhibited the proliferation of regulatory T cells (Treg), suggesting a mechanism for chronically activated T cells in this disease. Culture of CD4+ T cells from healthy individuals in the presence of AS-exosomes reduced the proliferation of FOXP3+ Treg cells and decreased the frequency of FOXP3+IRF4+ Treg cells. miRNA sequencing identified 24 differentially expressed miRNAs found in circulating exosomes of patients with AS compared with HC; 22 of which were upregulated and 2 were downregulated. CONCLUSIONS Individuals with AS have different immunological and genetic profiles, as determined by evaluating the exosomes of these patients. The inhibitory effect of exosomes on Treg in AS suggests a mechanism contributing to chronically activated T cells in this disease.
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Affiliation(s)
- Fataneh Tavasolian
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Starlee Lively
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
| | - Chiara Pastrello
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
- Krembil Research Institute, - Data Science Discovery Centre for Chronic Diseases, University Health Network, Toronto, Ontario, Canada
| | - Michael Tang
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Melissa Lim
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Addison Pacheco
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Zoya Qaiyum
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Enoch Yau
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Zeynep Baskurt
- Department of Biostatistics, Princess Margaret Cancer Center, 610 University Ave, Toronto, Ontario, Canada
| | - Igor Jurisica
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
- Krembil Research Institute, - Data Science Discovery Centre for Chronic Diseases, University Health Network, Toronto, Ontario, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mohit Kapoor
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, Division of Orthopaedic Surgery and Department of Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Robert D Inman
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Spondylitis Program, Division of Rheumatology, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
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Choksi H, Li S, Looby N, Kotlyar M, Jurisica I, Kulasingam V, Chandran V. Identifying Serum Metabolomic Markers Associated with Skin Disease Activity in Patients with Psoriatic Arthritis. Int J Mol Sci 2023; 24:15299. [PMID: 37894979 PMCID: PMC10607811 DOI: 10.3390/ijms242015299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Psoriatic arthritis (PsA) is a chronic, systemic, immune-mediated inflammatory disease causing cutaneous and musculoskeletal inflammation that affects 25% of patients with psoriasis. Current methods for evaluating PsA disease activity are not accurate enough for precision medicine. A metabolomics-based approach can elucidate psoriatic disease pathogenesis, providing potential objective biomarkers. With the hypothesis that serum metabolites are associated with skin disease activity, we aimed to identify serum metabolites associated with skin activity in PsA patients. We obtained serum samples from patients with PsA (n = 150) who were classified into mild, moderate and high disease activity groups based on the Psoriasis Area Severity Index. We used solid-phase microextraction (SPME) for sample preparation, followed by data acquisition via an untargeted liquid chromatography-mass spectrometry (LC-MS) approach. Disease activity levels were predicted using identified metabolites and machine learning algorithms. Some metabolites tentatively identified include eicosanoids with anti- or pro-inflammatory properties, like 12-Hydroxyeicosatetraenoic acid, which was previously implicated in joint disease activity in PsA. Other metabolites of interest were associated with dysregulation of fatty acid metabolism and belonged to classes such as bile acids, oxidized phospholipids, and long-chain fatty acids. We have identified potential metabolites associated with skin disease activity in PsA patients.
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Affiliation(s)
- Hani Choksi
- Schroeder Arthritis Program, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (H.C.); (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Shenghan Li
- Schroeder Arthritis Program, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (H.C.); (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Nikita Looby
- Schroeder Arthritis Program, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (H.C.); (S.L.); (N.L.)
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada; (M.K.); (I.J.)
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada; (M.K.); (I.J.)
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON M5S 1A1, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravská cesta 9, 845 10 Bratislava, Slovakia
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vinod Chandran
- Schroeder Arthritis Program, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (H.C.); (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
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11
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Muniz-Santos R, Watt P, Jurisica I, Cameron LC. Editorial: Metabolic response: nexus or nemesis for the understanding of sports nutrition and doping. Front Nutr 2023; 10:1306052. [PMID: 37899835 PMCID: PMC10602773 DOI: 10.3389/fnut.2023.1306052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023] Open
Affiliation(s)
- Renan Muniz-Santos
- Laboratory of Protein Biochemistry, The Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Peter Watt
- Environmental Extremes Lab, Sport and Exercise Science and Medicine Research and Enterprise Group, University of Brighton, Brighton, United Kingdom
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
| | - L. C. Cameron
- Laboratory of Protein Biochemistry, The Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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van Gogh M, Glaus Garzon JF, Sahin D, Knopfova L, Benes P, Boyman O, Jurisica I, Borsig L. Tumor Cell-Intrinsic c-Myb Upregulation Stimulates Antitumor Immunity in a Murine Colorectal Cancer Model. Cancer Immunol Res 2023; 11:1432-1444. [PMID: 37478172 PMCID: PMC10548106 DOI: 10.1158/2326-6066.cir-22-0912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/08/2023] [Accepted: 07/20/2023] [Indexed: 07/23/2023]
Abstract
The transcription factor c-Myb is overexpressed in many different types of solid tumors, including colorectal cancer. However, its exact role in tumorigenesis is unclear. In this study, we show that tumor-intrinsic c-Myb expression in mouse models of colon cancer and melanoma suppresses tumor growth. Although no differences in proliferation, apoptosis, and angiogenesis of tumors were evident in tumors with distinct levels of c-Myb expression, we observed changes in intratumoral immune cell infiltrates. MC38 tumors with upregulated c-Myb expression showed increased numbers of CD103+ dendritic cells and eosinophils, but decreased tumor-associated macrophages (TAM). Concomitantly, an increase in the number of activated cytotoxic CD8+ T cells upon c-Myb upregulation was observed, which correlated with a pro-inflammatory tumor microenvironment and increased numbers of M1 polarized TAMs. Mechanistically, c-Myb upregulation in immunogenic MC38 colon cancer cells resulted in enhanced expression of immunomodulatory genes, including those encoding β2-microglobulin and IFNβ, and decreased expression of the gene encoding the chemokine receptor CCR2. The increased numbers of activated cytotoxic CD8+ T cells contributed to tumor growth attenuation. In poorly immunogenic CT26, LLC, and B16-BL6 tumor cells, c-Myb upregulation did not affect the immunomodulatory gene expression. Despite this, c-Myb upregulation led to reduced B16-BL6 tumor growth but it did not affect tumor growth of CT26 and LLC tumors. Altogether, we postulate that c-Myb functions as a tumor suppressor in a tumor cell-type specific manner and modulates antitumor immunity.
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Affiliation(s)
- Merel van Gogh
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Dilara Sahin
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Lucia Knopfova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Petr Benes
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and, Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital (UHN), Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Faculty of Dentistry, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lubor Borsig
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, University Hospital of Zurich, Zurich, Switzerland
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Khan S, Chakraborty M, Wu F, Chen N, Wang T, Chan YT, Sayad A, Vásquez JDS, Kotlyar M, Nguyen K, Huang Y, Alibhai FJ, Woo M, Li RK, Husain M, Jurisica I, Gehring AJ, Ohashi PS, Furman D, Tsai S, Winer S, Winer DA. B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters. bioRxiv 2023:2023.09.12.556363. [PMID: 38529494 PMCID: PMC10962733 DOI: 10.1101/2023.09.12.556363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A dysregulated adaptive immune system is a key feature of aging, and is associated with age-related chronic diseases and mortality. Most notably, aging is linked to a loss in the diversity of the T cell repertoire and expansion of activated inflammatory age-related T cell subsets, though the main drivers of these processes are largely unknown. Here, we find that T cell aging is directly influenced by B cells. Using multiple models of B cell manipulation and single-cell omics, we find B cells to be a major cell type that is largely responsible for the age-related reduction of naive T cells, their associated differentiation towards pathogenic immunosenescent T cell subsets, and for the clonal restriction of their T cell receptor (TCR). Accordingly, we find that these pathogenic shifts can be therapeutically targeted via CD20 monoclonal antibody treatment. Mechanistically, we uncover a new role for insulin receptor signaling in influencing age-related B cell pathogenicity that in turn induces T cell dysfunction and a decline in healthspan parameters. These results establish B cells as a pivotal force contributing to age-associated adaptive immune dysfunction and healthspan outcomes, and suggest new modalities to manage aging and related multi-morbidity.
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Affiliation(s)
- Saad Khan
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Mainak Chakraborty
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Fei Wu
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Nan Chen
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
| | - Tao Wang
- Department of Physiology, University of Toronto, ON M5S 1A8, Canada
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON, M5G 1X8, Canada
| | - Yi Tao Chan
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2C1, Canada
| | - Juan Diego Sánchez Vásquez
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
| | - Khiem Nguyen
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Yingxiang Huang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Faisal J. Alibhai
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
| | - Minna Woo
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, University Health Network, University of Toronto, ON M5G 1L7, Canada
| | - Ren-Ke Li
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Division of Cardiac Surgery, University Health Network, University of Toronto, ON M5G IL7, Canada
| | - Mansoor Husain
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
- Department of Physiology, University of Toronto, ON M5S 1A8, Canada
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON, M5G 1X8, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, ON M5S 2E4, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Adam J. Gehring
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Toronto Center for Liver Disease & Schwartz Reisman Liver Research Centre, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Pamela S. Ohashi
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2C1, Canada
| | - David Furman
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Sue Tsai
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2RS, Canada
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Daniel A. Winer
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
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14
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Taibi A, Tokar T, Tremblay J, Gargari G, Streutker CJ, Li B, Pierro A, Guglielmetti S, Tompkins TA, Jurisica I, Comelli EM. Intestinal microRNAs and bacterial taxa in juvenile mice are associated, modifiable by allochthonous lactobacilli, and affect postnatal maturation. mSystems 2023; 8:e0043123. [PMID: 37462361 PMCID: PMC10469672 DOI: 10.1128/msystems.00431-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/07/2023] [Indexed: 07/22/2023] Open
Abstract
The interplay between the intestinal microbiota and host is critical to intestinal ontogeny and homeostasis. MicroRNAs (miRNAs) may be an underlying link. Intestinal miRNAs are microbiota-dependent and, when shed in the lumen, affect resident microorganisms. Yet, longitudinal relationships between intestinal tissue miRNAs, luminal miRNAs, and luminal microorganisms have not been elucidated, especially in early life. Here, we investigated the postnatal cecal miRNA and microbiota populations, their relationship, and their impact on intestinal maturation in specific pathogen-free mice; we also assessed if they can be modified by intervention with allochthonous probiotic lactobacilli. We report that cecal and cecal content miRNA and microbiota signatures are temporally regulated, correlated, and modifiable by probiotics with implications for intestinal maturation. These findings help understand causal relationships within the gut ecosystem and provide a basis for preventing and managing their alterations in diseases throughout life. IMPORTANCE The gut microbiota affects intestinal microRNA (miRNA) signatures and is modified by host-derived luminal miRNA. This suggests the existence of close miRNA-microbiota relationships that are critical to intestinal homeostasis. However, an integrative analysis of these relationships and their evolution during intestinal postnatal maturation is lacking. We provide a system-level longitudinal analysis of miRNA-microbiota networks in the intestine of mice at the weaning transition, including tissue and luminal miRNA and luminal microbiota. To address causality and move toward translational applications, we used allochthonous probiotic lactobacilli to modify these longitudinal relationships and showed that they are critical for intestinal maturation in early life. These findings contribute to understand mechanisms that underlie the maturation of the intestinal ecosystem and suggest that interventions aiming at maintaining, or restoring, homeostasis cannot prescind from considering relationships among its components.
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Affiliation(s)
- Amel Taibi
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Tomas Tokar
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montréal, Quebec, Canada
| | - Giorgio Gargari
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Catherine J. Streutker
- Department of Laboratory Medicine and Pathobiology, Unity Health Toronto: St. Michael’s Hospital, Toronto, Ontario, Canada
| | - Bo Li
- Division of General and Thoracic Surgery, Physiology and Experimental Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Agostino Pierro
- Division of General and Thoracic Surgery, Physiology and Experimental Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Simone Guglielmetti
- Department of Food Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
| | - Elena M. Comelli
- Department of Nutritional Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Joannah and Brian Lawson Centre for Child Nutrition, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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15
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Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I. USNAP: fast unique dense region detection and its application to lung cancer. Bioinformatics 2023; 39:btad477. [PMID: 37527019 PMCID: PMC10425186 DOI: 10.1093/bioinformatics/btad477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/09/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
MOTIVATION Many real-world problems can be modeled as annotated graphs. Scalable graph algorithms that extract actionable information from such data are in demand since these graphs are large, varying in topology, and have diverse node/edge annotations. When these graphs change over time they create dynamic graphs, and open the possibility to find patterns across different time points. In this article, we introduce a scalable algorithm that finds unique dense regions across time points in dynamic graphs. Such algorithms have applications in many different areas, including the biological, financial, and social domains. RESULTS There are three important contributions to this manuscript. First, we designed a scalable algorithm, USNAP, to effectively identify dense subgraphs that are unique to a time stamp given a dynamic graph. Importantly, USNAP provides a lower bound of the density measure in each step of the greedy algorithm. Second, insights and understanding obtained from validating USNAP on real data show its effectiveness. While USNAP is domain independent, we applied it to four non-small cell lung cancer gene expression datasets. Stages in non-small cell lung cancer were modeled as dynamic graphs, and input to USNAP. Pathway enrichment analyses and comprehensive interpretations from literature show that USNAP identified biologically relevant mechanisms for different stages of cancer progression. Third, USNAP is scalable, and has a time complexity of O(m+mc log nc+nc log nc), where m is the number of edges, and n is the number of vertices in the dynamic graph; mc is the number of edges, and nc is the number of vertices in the collapsed graph. AVAILABILITY AND IMPLEMENTATION The code of USNAP is available at https://www.cs.utoronto.ca/~juris/data/USNAP22.
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Affiliation(s)
- Serene W H Wong
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
| | - Christos Faloutsos
- Department of Computer Science, GHC 7003 Carnegie, Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213-3891, United States
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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16
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Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J. Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing. ArXiv 2023:arXiv:2305.15453v2. [PMID: 37332567 PMCID: PMC10274948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research.
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Affiliation(s)
- Andreas Maier
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Mark Abovsky
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | - Klaudia Adamowicz
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Sylvie Baier
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - David B Blumenthal
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
| | - Jing Chen
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Maria L Elkjaer
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Mohamed Helmy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Markus Hoffmann
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Igor Jurisica
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Max Kotlyar
- Division of Orthopaedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre, Osteoarthritis Research Program, Krembil Research Institute, UHN, Toronto, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, 60 Leonard Avenue, 5KD-407, Toronto, ON, M5T 0S8, Canada
| | - Olga Lazareva
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Junior Clinical Cooperation Unit Multiparametric methods for early detection of prostate cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Hagai Levi
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Sebastian Lobentanzer
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Quirin Manz
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Julian Matschinske
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Miles Mee
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, 1650 Owens Street, San Francisco, 94158, California, USA
| | - Rudolf T Pillich
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Julian M Poschenrieder
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Dexter Pratt
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nataša Pržulj
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Department of Computer Science, University College London, London WC1E 6BT, UK
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Sepideh Sadegh
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany
| | - Suryadipto Sarkar
- Department Artificial Intelligence in Biomedical Engineering (AIBE), Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91052 Erlangen, Germany
| | - Gideon Shaked
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
| | - Nico Trummer
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ugur Turhan
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Ruisheng Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Olga Zolotareva
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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Dantas-Komatsu RCS, Cruz MS, Freire PP, Diniz RVZ, Bortolin RH, Cabral-Marques O, Souza KBDS, Hirata MH, Hirata RDC, Reis BZ, Jurisica I, Silbiger VN, Luchessi AD. The let-7b-5p, miR-326, and miR-125a-3p are associated with left ventricular systolic dysfunction in post-myocardial infarction. Front Cardiovasc Med 2023; 10:1151855. [PMID: 37252118 PMCID: PMC10218134 DOI: 10.3389/fcvm.2023.1151855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Background Acute ST-elevation myocardial infarction (STEMI) can lead to adverse cardiac remodeling, resulting in left ventricular systolic dysfunction (LVSd) and heart failure. Epigenetic regulators, such as microRNAs, may be involved in the physiopathology of LVSd. Objective This study explored microRNAs in peripheral blood mononuclear cells (PBMC) of post-myocardial infarction patients with LVSd. Methods Post-STEMI patients were grouped as having (LVSd, n = 9) or not LVSd (non-LVSd, n = 16). The expression of 61 microRNAs was analyzed in PBMC by RT-qPCR and the differentially expressed microRNAs were identified. Principal Component Analysis stratified the microRNAs based on the development of dysfunction. Predictive variables of LVSd were investigated through logistic regression analysis. A system biology approach was used to explore the regulatory molecular network of the disease and an enrichment analysis was performed. Results The let-7b-5p (AUC: 0.807; 95% CI: 0.63-0.98; p = 0.013), miR-125a-3p (AUC: 0.800; 95% CI: 0.61-0.99; p = 0.036) and miR-326 (AUC: 0.783; 95% CI: 0.54-1.00; p = 0.028) were upregulated in LVSd (p < 0.05) and discriminated LVSd from non-LVSd. Multivariate logistic regression analysis showed let-7b-5p (OR: 16.00; 95% CI: 1.54-166.05; p = 0.020) and miR-326 (OR: 28.00; 95% CI: 2.42-323.70; p = 0.008) as predictors of LVSd. The enrichment analysis revealed association of the targets of these three microRNAs with immunological response, cell-cell adhesion, and cardiac changes. Conclusion LVSd alters the expression of let-7b-5p, miR-326, and miR-125a-3p in PBMC from post-STEMI, indicating their potential involvement in the cardiac dysfunction physiopathology and highlighting these miRNAs as possible LVSd biomarkers.
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Affiliation(s)
| | - Marina Sampaio Cruz
- Postgraduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
- Division of Cardiology, Department of Medicine, UC San Diego, San Diego, CA, United States
| | - Paula Paccielli Freire
- Postgraduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rosiane Viana Zuza Diniz
- Department of Clinical Medicine, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Raul Hernandes Bortolin
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
- Department of Cardiology, Boston Children’s Hospital/Harvard Medical School, Boston, MA, United States
| | - Otávio Cabral-Marques
- Postgraduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
- Division of Molecular Medicine, Departmentof Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
- Laboratory of Medical Investigation, University of São Paulo School of Medicine, São Paulo, Brazil
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Rosario Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Bruna Zavarize Reis
- Department of Nutrition, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Igor Jurisica
- Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
- Slovak Academy of Sciences, Institute of Neuroimmunology, Bratislava, Slovakia
| | - Vivian Nogueira Silbiger
- Department of Clinical and Toxicology Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
- Translational Medicine, The Hospital for Sick Children (SickKids), Toronto, ON, Canada
| | - Andre Ducati Luchessi
- Postgraduate Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, Brazil
- Translational Medicine, The Hospital for Sick Children (SickKids), Toronto, ON, Canada
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18
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Cente M, Perackova J, Peracek P, Majdan M, Toth I, Mikulic M, Hanes J, Porubska S, Spajdel M, Kazickova B, Jurisica I, Filipcik P. Association of Nonconcussive Repetitive Head Impacts and Intense Physical Activity With Levels of Phosphorylated Tau181 and Total Tau in Plasma of Young Elite Soccer Players. JAMA Netw Open 2023; 6:e236101. [PMID: 36995709 PMCID: PMC10064253 DOI: 10.1001/jamanetworkopen.2023.6101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Importance Head impacts resulting in traumatic brain injury (TBI) lead to the elevation of phosphorylated tau protein (p-tau181) in plasma. To our knowledge, this study is the first to investigate dynamics of p-tau181 levels and the ratio of p-tau181 to total tau in individuals after nonconcussive head impacts. Objective To determine the association of repetitive low-intensity head impacts on p-tau181 and total tau protein levels in the plasma of young adult elite soccer players and assess the possible association of head impacts with focused attention and cognitive flexibility. Design, Setting, and Participants In this cohort study, young elite soccer players performed intense physical activity with and without heading the ball. The study was conducted at a university facility in Slovakia from October 1, 2021, to May 31, 2022. Eligible participants were selected based on similarities in demographic variables, excluding those with a history of TBI. Main Outcomes and Measures The primary study outcomes were the levels of total tau protein and p-tau181 in plasma samples and the cognitive status of the study participants. Results A total of 37 male athletes participated in the study (mean [SD] age: exercise group, 21.6 [1.6] years; heading group, 21.2 [1.5] years). We found significantly elevated levels of total tau and p-tau181 in the plasma of soccer players 1 hour after physical exercise (tau, 1.4-fold; 95% CI, 1.2-1.5; P < .001; p-tau181, 1.4-fold; 95% CI, 1.3-1.5, P < .001) and repetitive head impacts (tau, 1.3-fold; 95% CI, 1.2-1.4; P < .001; p-tau181, 1.5-fold; 95% CI, 1.4-1.7 P < .001). The ratio of p-tau181 to tau was significantly higher 1 hour after exercise and heading training, and remained elevated specifically in the heading group even after 24 hours (1.2-fold; 95% CI, 1.1-1.3; P = .002). Performance in cognitive tests revealed a significant decline in focused attention and cognitive flexibility after physical exercise and heading training; physical exercise of higher intensity without heading training was associated with a greater negative cognitive performance than heading only. Conclusions and Relevance In this cohort study of young elite soccer players, the elevation of p-tau181 and tau was observed after acute intense physical activity and nonconcussive repetitive head impacts. The increase of p-tau181 levels relative to tau after 24 hours indicated an acute enrichment of phosphorylated tau fraction in the periphery when compared with preimpact levels; an imbalance of tau proteins may have long-lasting consequences in the brain of head-impacted individuals.
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Affiliation(s)
- Martin Cente
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Janka Perackova
- Department of Sport Science in Educology and Humanities, Faculty of Physical Education and Sport, Comenius University in Bratislava, Bratislava, Slovakia
| | - Pavol Peracek
- Department of Sports Games, Faculty of Physical Education and Sport, Comenius University in Bratislava, Bratislava, Slovakia
| | - Marek Majdan
- Institute for Global Health and Epidemiology, Department of Public Health, Faculty of Health Sciences and Social Work, Trnava University, Trnava, Slovakia
| | - Igor Toth
- Department of Sports Games, Faculty of Physical Education and Sport, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martin Mikulic
- Department of Sports Games, Faculty of Physical Education and Sport, Comenius University in Bratislava, Bratislava, Slovakia
| | - Jozef Hanes
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Sara Porubska
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Marian Spajdel
- Department of Psychology, Faculty of Philosophy and Arts, Trnava University, Trnava, Slovakia
| | - Barbora Kazickova
- Department of Psychology, Faculty of Philosophy and Arts, Trnava University, Trnava, Slovakia
| | - Igor Jurisica
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Ontario, Canada
| | - Peter Filipcik
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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D'Angelo E, Pastrello C, Biccari A, Marangio A, Sensi F, Crotti S, Fassan M, Jurisica I, Pucciarelli S, Agostini M. An integrated multiomics analysis of rectal cancer patients identified POU2F3 as a putative druggable target and entinostat as a cytotoxic enhancer of 5-fluorouracil. Int J Cancer 2023; 153:437-449. [PMID: 36815540 DOI: 10.1002/ijc.34478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/24/2023]
Abstract
Rectal cancer (RC) accounts for one-third of colorectal cancers (CRC), and 40% of these are locally advanced rectal cancers (LARC). The use of neoadjuvant chemoradiotherapy (nCRT) significantly reduces the rate of local recurrence compared to adjuvant therapy or surgery alone. However, after nCRT, up to 40%-60% of patients show a poor pathological response, while only about 20% achieve a pathological complete response. In this scenario, the identification of novel predictors of tumor response to nCRT is urgently needed to reduce LARC mortality and to spare poorly responding patients from unnecessary treatments. Therefore, by combining gene and microRNA expression datasets with proteomic data from LARC patients, we developed an integrated network centered on seven hub-genes putatively involved in the response to nCRT. In an independent validation cohort of LARC patients, we confirmed that differential expression of NFKB1, TRAF6 and STAT3 is correlated with the response to nCRT. In addition, the functional enrichment analysis also revealed that these genes are strongly related to hallmarks of cancer and inflammation, whose dysfunction may causatively affect LARC patient's response to nCRT. Furthermore, by constructing the transcription factor-module network, we hypothesized a protective role of POU2F3 gene, which could be used as a new drug target in LARC patients. Finally, we identified and tested in vitro entinostat, a histone deacetylase inhibitor, as a chemical compound that could be combined with a classical therapeutic regimen in order to design more efficient therapeutic strategies in LARC management.
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Affiliation(s)
- Edoardo D'Angelo
- General Surgery 3, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- LIFELAB Program, Consorzio per la Ricerca Sanitaria-CORIS, Padova, Italy
- NanoInspired biomedicine lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Andrea Biccari
- General Surgery 3, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- LIFELAB Program, Consorzio per la Ricerca Sanitaria-CORIS, Padova, Italy
| | - Asia Marangio
- General Surgery 3, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Francesca Sensi
- NanoInspired biomedicine lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
- Department of Women and Children's Health, University of Padova, Padua, Italy
| | - Sara Crotti
- NanoInspired biomedicine lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| | - Matteo Fassan
- Department of Medicine, University of Padua, Padova, Italy
- Veneto Institute of Oncology-Institute for Hospitalization and Care Scientific, Padova, Italy
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Salvatore Pucciarelli
- General Surgery 3, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Marco Agostini
- General Surgery 3, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- LIFELAB Program, Consorzio per la Ricerca Sanitaria-CORIS, Padova, Italy
- NanoInspired biomedicine lab, Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
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20
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Prado CADS, Fonseca DLM, Singh Y, Filgueiras IS, Baiocchi GC, Plaça DR, Marques AHC, Dantas-Komatsu RCS, Usuda JN, Freire PP, Salgado RC, Napoleao SMDS, Ramos RN, Rocha V, Zhou G, Catar R, Moll G, Camara NOS, de Miranda GC, Calich VLG, Giil LM, Mishra N, Tran F, Luchessi AD, Nakaya HI, Ochs HD, Jurisica I, Schimke LF, Cabral-Marques O. Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity. J Med Virol 2023; 95:e28450. [PMID: 36597912 PMCID: PMC10107240 DOI: 10.1002/jmv.28450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/24/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023]
Abstract
Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenance proteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients' blood leukocytes (B, T, and natural killer cells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.
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Affiliation(s)
- Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Dennyson Leandro M Fonseca
- Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil
| | - Youvika Singh
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H C Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Júlia N Usuda
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ranieri Coelho Salgado
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Rodrigo Nalio Ramos
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, Hospital São Luiz, São Paulo, Brazil
| | - Vanderson Rocha
- Laboratory of Medical Investigation in Pathogenesis and Directed Therapy in Onco-Immuno-Hematology (LIM-31), Departament of Hematology and Cell Therapy, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil.,Instituto D'Or de Ensino e Pesquisa, Hospital São Luiz, São Paulo, Brazil.,Fundação Pró-Sangue-Hemocentro de São Paulo, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil.,Department of Hematology, Churchill Hospital, University of Oxford, Oxford, UK
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Rusan Catar
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Internal Intensive Care Medicine, Charité University Hospital, Berlin, Germany.,Berlin Institute of Health (BIH) and Berlin Center for Regenerative Therapies (BCRT), Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin-Brandenburg School for Regenerative Therapies (BSRT), all Charité Universitätsmedizin Berlin, Berlin, Germany
| | | | - Gustavo Cabral de Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Vera Lúcia Garcia Calich
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany.,Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andre Ducati Luchessi
- Department of Clinical and Toxicology Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Instituto Israelita de Ensino e Pesquisa Albert Einstein, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Research Institute, Seattle, Washington, USA
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN, Toronto, Ontario, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.,Departments of Medical Biophysics and Computer Science, Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada.,Krembil Research Institute, UHN, Data Science Discovery Centre, Toronto, Ontario, Canada
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Otavio Cabral-Marques
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo (USP), Sao Paulo, Brazil.,Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Pharmacy and Postgraduate Program of Health and Science, Federal University of Rio Grande do Norte, Natal, Brazil.,Department of Medicine, Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil.,Laboratory of Medical Investigation 29, University of São Paulo School of Medicine, São Paulo, Brazil
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21
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Tavasolian F, Pastrello C, Ahmed Z, Jurisica I, Inman RD. Vesicular traffic-mediated cell-to-cell signaling at the immune synapse in Ankylosing Spondylitis. Front Immunol 2023; 13:1102405. [PMID: 36741392 PMCID: PMC9889860 DOI: 10.3389/fimmu.2022.1102405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
The chronic inflammatory disease ankylosing spondylitis (AS) is marked by back discomfort, spinal ankylosis, and extra-articular symptoms. In AS, inflammation is responsible for both pain and spinal ankylosis. However, the processes that sustain chronic inflammation remain unknown. Despite the years of research conducted to decipher the intricacy of AS, little progress has been made in identifying the signaling events that lead to the development of this disease. T cells, an immune cell type that initiates and regulates the body's response to infection, have been established to substantially impact the development of AS. T lymphocytes are regarded as a crucial part of adaptive immunity for the control of the immune system. A highly coordinated interaction involving antigen-presenting cells (APCs) and T cells that regulate T cell activation constitutes an immunological synapse (IS). This first phase leads to the controlled trafficking of receptors and signaling mediators involved in folding endosomes to the cellular interface, which allows the transfer of information from T cells to APCs through IS formation. Discrimination of self and nonself antigen is somatically learned in adaptive immunity. In an autoimmune condition such as AS, there is a disturbance of self/nonself antigen discrimination; available findings imply that the IS plays a preeminent role in the adaptive immune response. In this paper, we provide insights into the genesis of AS by evaluating recent developments in the function of vesicular trafficking in IS formation and the targeted release of exosomes enriched microRNAs (miRNA) at the synaptic region in T cells.
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Affiliation(s)
- Fataneh Tavasolian
- Spondylitis Program, Division of Rheumatology, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada,Departments of Medical Biophysics and Computer Science, and the Faculty of Dentistry, University of Toronto, Toronto, ON, Canada,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Robert D. Inman
- Spondylitis Program, Division of Rheumatology, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada,Krembil Research Institute, University Health Network, Toronto, ON, Canada,Departments of Medicine and Immunology, University of Toronto, Toronto, ON, Canada,*Correspondence: Robert D. Inman,
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22
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Sidhu K, Kim D, Lebel D, Alshammari A, Photopoulos G, Duarte MP, Provost M, Nielsen C, Oitment C, Cowley R, Dumas E, Dea N, Versteeg A, Eltit F, Rampersaud YR, Dandurand C, Grassner L, Alduwaisan A, Kennedy C, Christie S, Toobaie A, Algarni N, El-Mughayyar D, Pahuta M, Grassner L, Pelletier-Roy R, Bak AB, Singh S, Abbas A, Abbas A, Abbas A, Ajisebutu A, Aldahamsheh O, Martin S, Baron N, Basiratzadeh S, Beresford-Cleary N, Good C, Thomson A, Bhatt F, Bhatt F, Good C, Thomson A, Blake N, Briand MM, Shah V, Chen T, Cherry A, Rocos B, Cherry A, Chua R, Chua R, Cotter T, Coyle MJ, Dandurand C, Dandurand C, Dandurand C, Dauphinee E, Dionne A, El Bojairami I, Duarte MP, Duarte MP, Elahi MT, Ellingwood N, Ells B, Fallah N, Fernandes R, Fernandes R, Fleury C, Flórez-Jiménez S, Li P, Gennari A, Georgiopoulos M, Greene R, Yu C, Werthmann N, Hakimjavadi R, Hakimjavadi R, Heard B, Hutchison C, Kemna C, Kennedy C, Laflamme M, Laskin J, MacLean M, Mac-Thiong JM, Manson N, Manson N, Manson N, Urquhart J, Kuepper E, Pahuta M, Pahuta M, Parker E, Persad A, Phan K, Rachevitz M, Ridha B, Dhaliwal P, Sakoto S, Sarraj M, Sarraj M, Hache P, Singh S, Slosar P, Sun M, Sundararajan K, Sundararajan K, Thornley P, Thornley P, Thornley P, Thornley P, Thorogood N, Toobaie A, Belhouari S, Olotu O, Du JT, Saleh I, Varga A, Varshney V, Versteeg A, Visnjevac O, Wang Z, Wasim A, Wasim A, Wu J, Filezio M, Singh V, Ferri-de-Barros F, Dermott J, Lebel D, Machida M, Bath N, Levin D, Campbell F, Koyle M, Isaac L, Ruskin D, Brennenstuh S, Stinson J, Navarro-Ramirez R, Rabau O, Ouellet JA, Hurry J, Brooks J, Fitzgerald R, Louer C, Murphy J, Shaw KA, Smit K, El-Hawary R, Joncas J, Parent S, Duval M, Chèmaly O, Brassard F, Mac-Thiong JM, Barchi S, Labelle H, Beauséjour M, Ishimo MC, Joncas J, Labelle H, Le May S, Lewis L, Arnold K, Oitment C, Jentzsch T, Lewis S, Rienmuller A, Jentzsch T, Yashuv HS, Martin A, Nielsen C, Berven S, Ludwig T, Coyle M, Asmussen M, Edwards B, Nicholls F, Bigney E, Fleury C, El-Mughayyar D, Cherry A, Vanderwint A, Richardson E, Kerr J, McPhee R, Abraham E, Manson N, Attabib N, Small C, Couture J, Goulet J, Bédard S, Lebel K, LaRue B, Investigators CSORN, Gal R, Verlaan JJ, Charest-Morin R, Fisher CG, Wessels H, Verkooijen L, Ng T, Gokaslan Z, Fisher C, Dea N, Charest-Morin R, Urquhart J, Glennie A, Fisher C, Bailey C, Mcintosh G, Fisher C, Paquet J, Abraham E, Bailey C, Weber M, Johnson M, Nataraj A, Glennie A, Attabib N, Kelly A, Hall H, Rampersaud R, Manson N, Phan P, Thomas K, Dea N, Thomé C, Kögl N, Vo AK, Kramer JLK, Petr O, Visva S, Phan K, Nguyen-Luu T, Stratton A, Kingwell S, Wai E, Phan P, Puskas D, Pahuta M, Marion T, Greene R, Kehler S, Rockwood K, Urquhart J, Thornley P, Rasoulinejad P, Glennie A, Rampersaud R, Manson N, Abraham E, Fisher C, Charest-Morin R, Paquette S, Gélinas-Phaneuf N, Thomas K, Dea N, Dvorak M, Kwon B, Street J, Ailon T, Christie S, Bailey C, McIntosh G, Dea N, Charest-Morin R, Adams T, Bigney E, Cunningham E, Richardson E, Vandewint A, Attabib N, Abraham E, Manson N, Small C, LeRoux A, Kolyvas G, Investigators CSORN, Hebert J, Jiang E, Fisk F, Taliaferro K, Stukas S, Cooper J, Gill J, Fallah N, Skinnider MA, Belanger L, Ritchie L, Tsang A, Dong K, Streijger F, Street J, Paquette S, Ailon T, Dea N, Charest-Morin R, Fisher CG, Dvorak MF, Wellington C, Kwon BK, Dionne A, Richard-Denis A, Briand MM, Bourassa-Moreau É, Mac-Thiong JM, Moghaddamjou A, Fehlings MG, Nadeau M, Fisher C, Toor J, Larouche J, Finkelstein J, Whyne C, Yee A, Toor J, Du JT, Versteeg A, Yee N, Finkelstein J, Abouali J, Nousiainen MT, Kreder H, Whyne C, Larouche J, Toor J, Lewis S, Finkelstein J, Larouche J, Yee A, Whyne C, Dhaliwal P, Hasan M, Berrington N, Johnson M, Burger L, Nicholls F, Evaniew N, Cobetto N, Aubin CE, Larson AN, Cheng Y, Fourney D, Hakimjavadi R, Michalowski W, Viktor H, Baddour N, Wai E, Stratton A, Kingwell S, Phan P, Dandurand C, Mawhinney G, Reynolds J, Orosz L, Thomson A, Bhatt F, Guth M, Allen B, Boyd D, Grigorian J, Schuler T, Jazini E, Haines C, Orosz L, Bhatt F, Allen B, Sabet A, Schuler T, Haines C, Jazini E, Orosz L, Thomson A, Namian S, Bharara N, Jazini E, Good C, Schuler T, Haines C, Orosz L, Tewari A, Roy R, Good C, Schuler T, Haines C, Jazini E, Orosz L, Thomson A, Bhatt F, Grigorian J, Schuler T, Haines C, Merril J, Roy R, Jazini E, Wang M, Orosz L, Haines C, Jazini E, Bhatt F, Sabet A, Roy R, Schuler T, Good C, Greene R, Schmidt M, Christie S, Richard-Denis A, Le MT, Lim V, Mac-Thiong JM, Gallagher M, Cheung A, Brown J, Chaudhry H, Yee C, McIntosh G, Christie S, Fisher C, Jarzem P, Roy JF, Bouchard J, Yee A, Eseonu K, Ahn H, Cherry A, Rampersaud R, Davidson B, Rabinovitch L, Nielsen C, Jiang F, Vaisman A, Lewis S, Canizares M, Rampersaud R, Investigators CSORN, Avila M, Burket A, Aguilar-Salinas P, Mongrain R, Ouellet J, Driscoll M, Schmidt-Braekling T, Dobransky J, Kreviazuk C, Gofton W, Phan P, Beaule P, Grammatopoulos G, Street J, Fisher C, Jacobs B, Johnson M, Paquet J, Wilson J, Hall H, Bailey CS, Christie S, Nataraj A, Manson N, Phan P, Rampersaud R, Thomas K, Mcintosh G, Rasoulinejad P, Charest-Morin R, Hindi M, Farimani PL, Mashayekhi MS, Ailon T, Boyd M, Charest-Morin R, Dea N, Dvorak M, Fisher C, Kwon B, Paquette S, Street J, Urquhart J, Ailon T, Bailey C, Boyd M, Charest-Morin R, Dea N, Dvorak M, Glennie A, Kwon B, Paquette S, Rampersaud R, Street J, Fisher C, Vandewint A, Bigney E, El-Mughayyar D, Richardson E, Edward A, Manson N, Attabib N, Kolyvas G, Small C, Investigators CSORN, Mac-Thiong JM, Barthélémy D, Lim V, Richard-Denis A, Driscoll M, Aubin CE, Cobetto N, Roy-Beaudry M, Bellefleur C, Turgeon I, Labelle H, Barchi S, Parent S, Joncas J, Parent S, Labelle H, Barchi S, Mac-Thiong JM, Lee W, Phan P, Bigney E, Richardson E, El-Mughayyar D, Vandewint A, Abraham E, Manson N, Small C, Alugo T, Leroux A, Kolyvas G, Investigators CSORN, Attabib N, McIntosh G, Oxner W, Dunning PC, Glennie A, Wang D, Humphreys S, Noonan V, Urquhart J, Siddiqi F, Rasoulinejad P, Bailey C, Urquhart J, Thornley P, Rampersaud R, Glennie A, Rasoulinejad P, Fisher C, Bailey C, Investigators CSORN, Bigney E, Dumas E, El-Mughayyar D, Cherry A, Vanderwint A, Richardson E, Kerr J, McPhee R, Abraham E, Manson N, Attabib N, Small C, Couture J, Goulet J, Bédard S, LaRue B, Investigators CSORN, Macthiong JM, Bourassa-Moreau E, Ogden C, Gallagher M, Cheung A, Huong VT, Tarabay B, Al-Shakfa F, Yuh SJ, Shedid D, Boubez G, Wang Z, Gueziri HE, Santaguida C, Collins DL, Hall A, Alant J, Barry S, Weise L, Glennie A, Oxner B, Etchegary H, Christie S, Carreon L, Glassman S, Brown M, Daniels C, Polly D, Gum J, Gum J, Glassman S, Brown M, Daniels C, Carreon L, Hong HA, Fallah N, Humphreys S, Walden K, Noonan VK, Phan P, Basiratzadeh S, Wai EK, Phan P, Salo P, Krawetz R, Hart D, Bains I, Swamy G, Yang Q, Godoy A, Smith S, Lin C, Nataraj A, Puskas D, Pahuta M, Marion T, Dea N, Waheed Z, Thorogood N, Nightingale T, Noonan V, Touchette C, Duda T, Almojuela A, Bergeron D, Aljoghaiman M, Sader N, Kameda-Smith M, Alant J, Christie S, Hresko MT, Alzakri A, Parent S, Sucato DJ, Lenke LG, Marks M, Labelle H, Pereira P, Charles YP, Krutko A, Santos C, Park Y, Arzoglou V, Park SW, Franke J, Fuentes S, He S, Hosszu T, Varanda P, Mlyavykh S, Vanhauwaert D, Senker W, Franke J, Park Y, Charles YP, Santos C, Arzoglou V, Song Y, He S, Bhagat S, Hong JY, Vanhauwaert D, Senker W, Pereira P, Senker W, Charles YP, Pereira P, Santos C, Park Y, Arzoglou V, Park SW, Bordon G, Fuentes S, Song Y, Vialle E, Bhagat S, Krutko A, Franke J, Thornley P, Rampersaud R, Glennie A, Rasoulinejad P, Abraham E, Ailon T, Charest-Morin R, Dea N, Dvorak M, Gélinas-Phaneuf N, Kwon B, Manson N, Paquette S, Street J, Thomas K, Fisher C, Bailey C, Mishreky A, Hurry J, El-Hawary R, Jiang E, Fisk F, Taliaferro K, Dea N, Investigators CSORN, Al Anazi M, El-Hawary R, Kindrachuk M, Noyes E, Wu A, Fourney D, Pratt M, Wai E, Stratton A, Kingwell S, Wang Z, Phan P, Robarts S, Razmjou H, Yee A, Larouche J, Finkelstein J, Persad A, Huschi Z, Cheng Y, Fourney D, Rossong H, Zhang H, Johnson M, Goytan M, Zarrabian M, Berrington N, Zeiler F, Charles A, Roy-Beaudy, Parent S, Duong L, Marion T, Guha D, Pahuta M, Hache P, Oitment C, Guha D, Pahuta M, Sarraj M, Oitment C, Guha D, Pahuta M, Miyanji F, McAnany S, Cheung A, Dewitt D, Street J, Jurisica I, Perruccio AV, Rampersaud YR, Niu Y, Perruccio AV, Jurisica I, Rampersaud YR, Glennie A, Alahmari A, Al-Jahdali F, Fisher C, Rampersaud R, Urquhart J, Bailey C, Urquhart J, Bailey C, Urquhart J, Rampersaud R, Glennie A, Fisher C, Bailey C, Urquhart J, Rampersaud R, Glennie A, Fisher C, Bailey C, Harback K, Akpinar I, Adjetey C, Tindall D, Chernesky J, Noonan V, Fernandes RJR, Bailey C, Siddiqi F, Rasoulinejad P, Toor J, Abbas A, Brooks H, Larouche J, Abbas A, Bhatia A, Selimovic D, Larouche J, Yee A, Lewis S, Finkelstein J, Toor J, Abbas A, Toor J, Versteeg A, Finkelstein J, Toor J, Abbas A, Ahn H, Larouche J, Finkelstein J, Whyne C, Yee A, Slomp F, Thiessen E, Lastivnyak N, Maclean LS, Ritchie V, Hockley A, Osborn J, Paquette S, Sahjpaul R, Gal R, Charest-Morin R, Verlaan JJ, Wessels H, Fisher CG, Verkooijen L, Pastrak M, Truong VT, Liberman M, Al-Shakfa F, Yuh SJ, Soder SA, Wu J, Sunna T, Renaud-Charest É, Boubez G, Shedid D, Balasuberamaniam P, Shrikumar M, Chen T, Anthony T, Phillips A, Nathens A, Chapman M, Crawford E, Stark R, Schwartz C, Finkelstein J, Small C, Rampersaud R. Canadian Spine SocietyAbstract 57. Radiographic reporting in adolescent idiopathic scoliosis: Is there a discrepancy comparing radiologists’ reports and surgeons’ assessments?Abstract 74. How useful is prereferral spine imaging? A quality improvement projectAbstract 82. Early recovery after surgery, predictors of shorter length of stayAbstract 68. Gliding screws on early-onset scoliosis: a 5-year experienceAbstract 66. Reliability of radiographic assessment of growth modulation from anterior vertebral body tethering surgery in pediatric scoliosisAbstract 16. A dangerous curve: impact of the COVID-19 pandemic on brace treatment in adolescent idiopathic scoliosisAbstract 24. Development of a model of interprofessional support interventions to enhance brace adherence in adolescents with idiopathic scoliosisAbstract 94. Recognizing the importance of self-image in adult spinal deformity: results from the Prospective Evaluation of Elderly Deformity Surgery (PEEDS)Abstract 25. Assessing pain as a primary factor in the surgical treatment of adult spinal deformity surgery in patients over 60 years of ageAbstract 72. Application of the Ames-International Spine Study Group (AMES) radiographic modifiers to an asymptomatic population. Are the thresholds for “normal” appropriate?Abstract 109. Exploring the relationship between cannabis and narcotic use on preoperative health considerations in Canadian thoracolumbar patients: a CSORN studyAbstract 36. Metastatic spine disease: Should patients with short life expectancy be denied surgical care? An international retrospective cohort studyAbstract 91. What do patients expect of palliative treatment for symptomatic spinal metastases? A qualitative studyAbstract 44. Denosumab for giant cell tumours of the spine: molecular predictors of clinical response — a pilot studyAbstract 89. Surgical management and outcomes from “stable” degenerative spondylolisthesis (DS) from the CSORN prospective DS study: What the @#$ % are we doing?Abstract 33. Economic consequences of waiting for lumbar disc herniation surgeryAbstract 108. Motor recovery depends on timing of surgery in patients with lumbar disc herniationAbstract 106. Outcomes following revision decompression for lumbar spinal stenosis when compared to primary decompression: a matched cohort analysis using the Canadian Spine Outcomes and Research Network registryAbstract 64. Patient engagement, remote monitoring and virtual care — a pilot project in rural and remote patients undergoing elective lumbar surgeryAbstract 84. Development of a frailty index from the Canadian Spine Outcomes and Research Network (CSORN) to predict long-term success of surgery for patients with degenerative pathologies of the spineAbstract 102. Posterolateral versus posterior interbody fusion for the management of lumbar degenerative spondylolisthesis: analysis from the CSORN prospective LDS propensity score matched studyAbstract 31. Impact on patient-reported outcomes of ending the posterior construct proximally at C2 versus C3 in degenerative cervical myelopathy patientsAbstract 42. Perioperative factors predict 2-year trajectories of pain and disability following anterior cervical discectomy and fusionAbstract 61. Calculating utilities from the modified Japanese Orthopaedic Association score: a prerequisite for quantifying the value of care for cervical myelopathyAbstract 119. Serum neurofilament light (NF-L) and glial fibrillary acidic protein (GFAP) biomarkers and their association with MRI findings in human acute traumatic spinal cord injuryAbstract 95. The Montreal Acute Classification of Spinal Cord Injury (MAC-SCI): a new tool to detect and characterize spinal cord injury in the trauma patientAbstract 118. Mechanism of injury is associated with neurologic outcomes after cervical sensorimotor complete acute traumatic spinal cord injuryAbstract 13. Patient perspective: diagnosis and prognosis of acute spinal cord injuriesAbstract 136. Predictive analytics to improve dedicated spine trauma operating room resource allocationAbstract 138. Machine learning models to predict surgical resident workload at a level 1 trauma centreAbstract 139. Machine learning to predict duration of surgery and length of stay for single-level discectomy proceduresAbstract 9. Outpatient spinal surgery in ManitobaAbstract 131. Unexpected positive culture in presumed aseptic revision spine surgery: a systematic review and meta-analysisAbstract 50. Lumbar anterior vertebral body tethering: biomechanical assessment of the surgical decision factors influencing the immediate and 2 years postoperative correctionAbstract 145. Does prolonged symptom duration influence surgical outcomes for cervical radiculopathy?Abstract 147. A data-driven cluster analysis approach to create homogenous subgroups for traumatic spine injury: toward improving traditional classificationAbstract 41. The use of neo-adjuvant denosumab in treatment of giant cell tumours of the spineAbstract 5. Complications, revision rates and accuracy of robotic-guided S2 alar-iliac screw placementAbstract 6. Opioid use after spine surgery: How much are we over-prescribing?Abstract 7. Intradiscal injection of autologous bone marrow aspirate concentrate improves low back pain at 1 yearAbstract 8. Augmented reality–assisted spine surgery: an early experience demonstrating safety and accuracy with 218 screwsAbstract 22. Comparison of complications, revision rates and fluoroscopy time using the latest technology in robotic-guided surgery with historical fluoroscopic-guided controlsAbstract 23. Robotic-guided thoracolumbar fusion experience: a multi-surgeon, single-centre study of 628 patients and 3874 robotic-guided screws from 2012 to 2020Abstract 86. A province-wide assessment of the appropriateness of lumbar spine MRIAbstract 134. Concomitant traumatic spinal cord injury and brain injury diagnoses are more frequent and impactful than expectedAbstract 45. Spatial and depth mapping of nascent mineralization on Ti6Al4V surfaces demonstrating hierarchical macro-micro-nanoscale surface featuresAbstract 111. Propensity-matched outcomes comparing lumbar interbody fusion and total disk arthroplasty: a Canadian Spine Outcomes and Research Network (CSORN) studyAbstract 30. A Canadian-based pilot study of current surgical practice and implant preferences in lumbar fusion surgeryAbstract 32. Local contamination is a major cause of early deep wound infections following open posterior lumbosacral fusionsAbstract 99. Comparing patient preoperative expectations and postoperative expectation fulfillment between minimally invasive versus open fusion surgeryAbstract 146. Outpatient robotic-assisted lumbar spinal fusion using the Mazor X Stealth EditionAbstract 149. Lessons learned from my first 100 robotic-assisted lumbar fusions using the Mazor X Stealth Edition: surgical synergy with MIS, surgical navigation and roboticsAbstract 151. Freehand biomechanical testing for use in lumbar discectomy trainingAbstract 48. Spinal pathology and outcome post-THA: Does segment of arthrodesis matter?Abstract 27. Patient, surgical and institutional factors associated with length of stay in degenerative lumbar spine surgery: national multicentre cohort analysis from the Canadian Spine Outcomes and Research Network (CSORN)Abstract 28. The impact of the increasing proportion of degenerative spine emergency admissionsAbstract 51. Patient’s expectations of surgery for degenerative spondylolisthesis: analysis by site and type of surgery from the Canadian Spine Outcomes and Research Network (CSORN)Abstract 60. The impact of sex on thoracolumbar surgery outcomes in patients with diabetes — a CSORN studyAbstract 81. The impact of older age on rehabilitation outcomes following functional motor-incomplete traumatic spinal cord injuryAbstract 47. Devise and investigate a novel, intramuscular pressure based, muscle activation strategy in a spine stability modelAbstract 17. 3D radiologic outcomes for patients with moderate idiopathic scoliosis curves treated with internal (anterior vertebral growth modulation) versus external bracing: a 2-year observational studyAbstract 18. Is quality of life affected by concomitant isthmic spondylolisthesis when undergoing surgery for adolescent idiopathic scoliosis and nonsurgical management of the spondylolisthesis?Abstract 128. Toward macrostructural and microstructural investigation of the cervical spinal cord through quantitative analysis of T2-weighted and diffusion-weighted imagingAbstract 26. Minimally invasive versus open thoracolumbar spine surgery for patients who have lumbar spinal stenosis and an ASA score of 3 or above: a CSORN studyAbstract 101. Association between surgeon age and outcomes of spine surgery: a population-based retrospective cohort studyAbstract 77. Utilizing machine learning methodology to create a short form of the Multi-Morbidity Index in spinal cord injuryAbstract 70. Ten-year reoperation rate and clinical outcome in patients treated surgically for lumbar spinal stenosisAbstract 105. Assessing the importance of radiographic and clinical parameters when choosing decompression without fusion for LDS: results from the CSORN prospective DS studyAbstract 104. Preoperative cannabis use in Canadian thoracolumbar spine surgery patients: a CSORN studyAbstract 142. Post-traumatic ascending myelitis, about 2 cases, etiologic analysis and treatmentAbstract 55. NanoLOCK surfaces enhance osteoblast activities at the cellular levelAbstract 76. Which scoring system is the most accurate for predicting survival in patients undergoing surgery for spinal metastases from lung cancer?Abstract 11. Pedicle screw insertion using ultrasound-based navigation without intraoperative radiation: feasibility study on porcine cadaversAbstract 85. What barriers prevent patients being discharged from hospital following elective spine surgery?Abstract 15. Propensity-matched comparison of 90-day complications in robotic-assisted versus non-robotic-assisted lumbar fusionAbstract 56. No-tap (2-step) robotic-assisted cortical bone trajectory (RA-CBT) screw insertion is safe and efficient: comparative analysis of 179 patients and 924 RA-CBT screwsAbstract 124. Developing a Web-based application to promote the adoption of a clinical prediction model for independent walking in people with traumatic spinal cord injury — a protocolAbstract 125. Multivariable prediction models for prognostication after traumatic spinal cord injury — a systematic reviewAbstract 148. Expression of blood serum cytokines in the presentation of acute sciaticaAbstract 150. Do patient-reported outcome scores (PROs) correlate with bundled payment plan performance for elective spine surgeries?Abstract 46. Effects of delayed neurosurgery on anxiety, depression and economic burdenAbstract 69. Care close to home — a retrospective analysis of patients undergoing elective lumbar surgery in a rural satellite hospitalAbstract 110. Surgical adverse events for primary tumours of the spine and their impact on prognosis and outcomes: a PTRON studyAbstract 80. Spinal cord stimulation research in the restoration of function for individuals living with spinal cord injuries: a scoping reviewAbstract 132. Workup and management of asymptomatic extracranial traumatic vertebral artery injury: a Canadian Neurosurgery Resident Research Collaborative studyAbstract 12. A surgical treatment algorithm for restoring pelvic balance and health-related quality of life in high-grade lumbosacral spondylolisthesisAbstract 38. Effectiveness of 6 surgical approaches for minimally invasive lumbar interbody fusion: 1-year follow-up results from a global multicentre studyAbstract 39. Clinical outcomes and fusion success in patients with degenerative lumbar disease without spondylolisthesis: comparing anterolateral to posterior MIS approaches from a global multicentre studyAbstract 40. Anterolateral versus posterior approaches to minimally invasive interbody fusion for patients with spondylolisthesis: results at 1-year follow-up from a global multicentre studyAbstract 73. Benefit of minimally invasive lumbar interbody fusion versus traditional interbody fusion versus posterolateral spinal fusion in lumbar degenerative spondylolisthesis: a propensity-matched analysis from the CSORN prospective LDS studyAbstract 67. The effect of fusionless pediatric scoliosis surgery on 3D radiographic spinopelvic alignmentAbstract 62. Calculating utilities from the Neck Disability Index: a prerequisite for quantifying the value of cervical spine careAbstract 63. The psychometric properties of the mJOA for quality-of-life assessments in cervical myelopathyAbstract 59. Low radius of curvature growth friendly implants increases the risk of developing clinically significant proximal junctional kyphosisAbstract 144. Very long–term outcome of single-level minimally invasive lumbar microdiscectomy with a tubular retractorAbstract 112. Metal implant hypersensitivity in patients undergoing spinal surgery: a literature review and case reportAbstract 43. Diagnostic value of the lumbar spinal stenosis (SSHQ) survey in virtual care provided at a tertiary spine programAbstract 54. Is the Calgary Postoperative Pain After Spine Surgery (CAPPS) score correlated with long-term outcomes after lumbar fusion?Abstract 4. Development of a single-entry referral pathway for patients with spinal conditions in Manitoba: a cross-sectional review of impact and potential way forward for Canadian spine programsAbstract 113. Automatization of bone age calculationAbstract 123. An effectiveness and quality-of-life analysis of conservative care versus surgery for moderate and severe cervical myelopathyAbstract 133. Long-term survivorship of cervical spine procedures: a survivorship meta-analysis and meta-regressionAbstract 137. Natural history of degenerative cervical myelopathy: a meta-analysis and neurologic deterioration survival curve synthesisAbstract 14. Does intraoperative vancomycin powder affect postoperative infections in adolescent idiopathic scoliosis?Abstract 37. The clinical impact of nano-surface technology on postoperative opioid consumption in patients undergoing anterior lumbar interbody fusionAbstract 130. Design and implementation of a comprehensive perioperative complex spine communication toolAbstract 87. Stratifying low back pain patients in an inter-professional education and self-management model of care: results of a latent class analysisAbstract 88. Cohort accuracy versus confidence at the patient level: clinical challenges for AI-based prediction of low back pain outcomesAbstract 96. Preoperative disc angle is an important predictor of segmental lordosis after degenerative spondylolisthesis fusionAbstract 97. Preoperative depression, functional and radiographic outcomes after surgery for degenerative lumbar spondylolisthesisAbstract 116. A CSORN study of functional outcomes after surgery for lumbar degenerative spondylolisthesisAbstract 121. A CSORN study of the effect on radiographic alignment outcomes with different surgery type for degenerative lumbar spondylolisthesisAbstract 79. Spinal cord stimulation to restore neurological function: a costing analysisAbstract 107. Biomechanical properties of a novel morselized bone graft cageAbstract 93. Optimizing spine surgery instrument trays to immediately increase efficiency and reduce costs in the operating roomAbstract 103. Machine learning models can predict subsequent publication of North American Spine Society Annual General Meeting abstractsAbstract 117. The use of primary sacroiliac joint fusion for lower back pain due to sacroiliac joint pathology: a systematic review and meta-analysisAbstract 141. How to make the most of your operative time by optimizing surgical schedulingAbstract 126. Altering physician referral practices remains a challenge: a spine assessment clinic quality improvement studyAbstract 152. Outcomes of workers’ compensation patients undergoing neuromodulation for persistent neuropathic pain conditionsAbstract 90. Expectations of treatment outcomes in patients with spinal metastases: What do we tell our patients? A qualitative studyAbstract 52. Fluoroscopically guided radiofrequency ablation of the superior cluneal nerve: preliminary outcomes data for a minimally invasive approach for treating superior cluneal neuralgiaAbstract 21. Single-stage posterior approach for en bloc resection and spinal reconstruction of T4 Pancoast tumour invading spineAbstract 34. Predictors of sacral ulcers in patients with complete spinal cord injuryAbstract 135. Targeting geographic wait time disparities in Canada: a rapid review of domestic and international strategies to reduce orthopedic wait times in the MaritimesAbstract 143. The influence of coronal plane parameters on patient-reported outcome measures in patients undergoing decompression for lumbar spinal stenosis. Can J Surg 2022. [DOI: 10.1503/cjs.011622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Tavallaee G, Lively S, Rockel JS, Ali SA, Im M, Sarda C, Mitchell GM, Rossomacha E, Nakamura S, Potla P, Gabrial S, Matelski J, Ratneswaran A, Perry K, Hinz B, Gandhi R, Jurisica I, Kapoor M. Contribution of MicroRNA-27b-3p to Synovial Fibrotic Responses in Knee Osteoarthritis. Arthritis Rheumatol 2022; 74:1928-1942. [PMID: 35791923 PMCID: PMC10946865 DOI: 10.1002/art.42285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 05/18/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Synovial fibrosis contributes to osteoarthritis (OA) pathology, but the underlying mechanisms remain unknown. We have observed increased microRNA-27b-3p (miR-27b-3p) levels in synovial fluid of patients with late-stage radiographic knee OA. Here, we investigated the contribution of miR-27b-3p to synovial fibrosis in patients with severe knee OA and in a mouse model of knee OA. METHODS We stained synovium sections obtained from patients with radiographic knee OA scored according to the Kellgren/Lawrence scale and mice that underwent destabilization of the medial meniscus (DMM) for miR-27b-3p using in situ hybridization. We examined the effects of intraarticular injection of miR-27b-3p mimic into naive mouse knee joints and intraarticular injection of a miR-27b-3p inhibitor into mouse knee joints after DMM. We performed transfection with miR-27b-3p mimic and miR-27b-3p inhibitor in human OA fibroblast-like synoviocytes (FLS) using reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) array, RNA sequencing, RT-qPCR, Western blotting, immunofluorescence, and migration assays. RESULTS We observed increased miR-27b-3p expression in the synovium from patients with knee OA and in mice with DMM-induced arthritis. Injection of the miR-27b-3p mimic in mouse knee joints induced a synovial fibrosis-like phenotype, increased synovitis scores, and increased COL1A1 and α-smooth muscle actin (α-SMA) expression. In the mouse model of DMM-induced arthritis, injection of the miR-27b-3p inhibitor decreased α-SMA but did not change COL1A1 expression levels or synovitis scores. Transfection with the miR-27b-3p mimic in human OA FLS induced profibrotic responses, including increased migration and expression of key extracellular matrix (ECM) genes, but transfection with the miR-27b-3p inhibitor had the opposite effects. RNA sequencing identified a PPARG/ADAMTS8 signaling axis regulated by miR-27b-3p in OA FLS. Human OA FLS transfected with miR-27b-3p mimic and then treated with the PPARG agonist rosiglitazone or with ADAMTS8 small interfering RNA exhibited altered expression of select ECM genes. CONCLUSION Our findings demonstrate that miR-27b-3p has a key role in ECM regulation associated with synovial fibrosis during OA.
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Affiliation(s)
- Ghazaleh Tavallaee
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Krembil Research Institute, University Health Network, and Department of Laboratory Medicine and Pathobiology, University of TorontoTorontoOntarioCanada
| | - Starlee Lively
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Jason S. Rockel
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Shabana Amanda Ali
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada, and Bone & Joint Center, Department of Orthopaedic Surgery, Henry Ford Health SystemDetroitMichigan
| | - Michelle Im
- Faculty of Dentistry, University of TorontoTorontoOntarioCanada
| | - Clementine Sarda
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Greniqueca M. Mitchell
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Evgeny Rossomacha
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Sayaka Nakamura
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Pratibha Potla
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Sarah Gabrial
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - John Matelski
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Anusha Ratneswaran
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Kim Perry
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, and Krembil Research Institute, University Health NetworkTorontoOntarioCanada
| | - Boris Hinz
- Faculty of Dentistry, University of Toronto, and Laboratory of Tissue Repair and Regeneration, Keenan Research Centre for Biomedical Science of the St. Michael's HospitalTorontoOntarioCanada
| | - Rajiv Gandhi
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Krembil Research Institute, University Health Network, and Departments of Medical Biophysics and Computer Science, University of TorontoTorontoOntarioCanada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Krembil Research Institute, University Health Network, Toronto, Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada, and Institute of Neuroimmunology, Slovak Academy of SciencesBratislavaSlovakia
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Krembil Research Institute, University Health Network, Department of Laboratory Medicine and Pathobiology, University of Toronto, and Division of Orthopaedic Surgery, Department of Surgery, University of TorontoTorontoOntarioCanada
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Hauschild AC, Pastrello C, Ekaputeri G, Bethune-Waddell D, Abovsky M, Ahmed Z, Kotlyar M, Lu R, Jurisica I. MirDIP 5.2: tissue context annotation and novel microRNA curation. Nucleic Acids Res 2022; 51:D217-D225. [PMID: 36453996 PMCID: PMC9825511 DOI: 10.1093/nar/gkac1070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/16/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
MirDIP is a well-established database that aggregates microRNA-gene human interactions from multiple databases to increase coverage, reduce bias, and improve usability by providing an integrated score proportional to the probability of the interaction occurring. In version 5.2, we removed eight outdated resources, added a new resource (miRNATIP), and ran five prediction algorithms for miRBase and mirGeneDB. In total, mirDIP 5.2 includes 46 364 047 predictions for 27 936 genes and 2734 microRNAs, making it the first database to provide interactions using data from mirGeneDB. Moreover, we curated and integrated 32 497 novel microRNAs from 14 publications to accelerate the use of these novel data. In this release, we also extend the content and functionality of mirDIP by associating contexts with microRNAs, genes, and microRNA-gene interactions. We collected and processed microRNA and gene expression data from 20 resources and acquired information on 330 tissue and disease contexts for 2657 microRNAs, 27 576 genes and 123 651 910 gene-microRNA-tissue interactions. Finally, we improved the usability of mirDIP by enabling the user to search the database using precursor IDs, and we integrated miRAnno, a network-based tool for identifying pathways linked to specific microRNAs. We also provide a mirDIP API to facilitate access to its integrated predictions. Updated mirDIP is available at https://ophid.utoronto.ca/mirDIP.
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Affiliation(s)
| | | | - Gitta Kirana Anindya Ekaputeri
- Department of Medical Informatics, University Medical Center Göttingen, Georg-August University, Göttingen, Lower Saxony 37075, Germany
| | - Dylan Bethune-Waddell
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Mark Abovsky
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Richard Lu
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto M5T 0S8, Canada
| | - Igor Jurisica
- To whom correspondence should be addressed. Tel: +1 416 581 7437;
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Bassini A, Sartoretto S, Jurisica L, Magno-França A, Anderson L, Pearson T, Razavi M, Chandran V, Martin L, Jurisica I, Cameron LC. Sportomics method to assess acute phase proteins in Olympic level athletes using dried blood spots and multiplex assay. Sci Rep 2022; 12:19824. [PMID: 36400821 PMCID: PMC9672598 DOI: 10.1038/s41598-022-23300-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 10/29/2022] [Indexed: 11/19/2022] Open
Abstract
Sportomics is a subject-centered holistic method similar to metabolomics focusing on sports as the metabolic challenge. Dried blood spot is emerging as a technique due to its simplicity and reproducibility. In addition, mass spectrometry and integrative computational biology enhance our ability to understand exercise-induced modifications. We studied inflammatory blood proteins (Alpha-1-acid glycoprotein-A1AG1; Albumin; Cystatin C; C-reactive protein-CRP; Hemoglobin-HBA; Haptoglobin-HPT; Insulin-like growth factor 1; Lipopolysaccharide binding protein-LBP; Mannose-binding lectin-MBL2; Myeloperoxidase-PERM and Serum amyloid A1-SAA1), in 687 samples from 97 World-class and Olympic athletes across 16 sports in nine states. Data were analyzed with Spearman's rank-order correlation. Major correlations with CRP, LBP; MBL2; A1AG1, and SAA1 were found. The pairs CRP-SAA1 and CRP-LBP appeared with a robust positive correlation. Other pairs, LBP-SAA1; A1AG1-CRP; A1AG1-SAA1; A1AG1-MBL, and A1AG1-LBP, showed a broader correlation across the sports. The protein-protein interaction map revealed 1500 interactions with 44 core proteins, 30 of them linked to immune system processing. We propose that the inflammation follow-up in exercise can provide knowledge for internal cargo management in training, competition, recovery, doping control, and a deeper understanding of health and disease.
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Affiliation(s)
- Adriana Bassini
- grid.467095.90000 0001 2237 7915Laboratory of Protein Biochemistry, Federal University of State of Rio de Janeiro, Av. Pasteur, 296 – Urca, Rio de Janeiro, R.J. 22290-350 Brazil ,SOmics, Vila Velha, ES Brazil
| | - Silvia Sartoretto
- grid.467095.90000 0001 2237 7915Laboratory of Protein Biochemistry, Federal University of State of Rio de Janeiro, Av. Pasteur, 296 – Urca, Rio de Janeiro, R.J. 22290-350 Brazil
| | - Lukas Jurisica
- grid.467095.90000 0001 2237 7915Laboratory of Protein Biochemistry, Federal University of State of Rio de Janeiro, Av. Pasteur, 296 – Urca, Rio de Janeiro, R.J. 22290-350 Brazil ,grid.34428.390000 0004 1936 893XSchool of Computer Science, Carleton University, Ottawa, Canada ,grid.17063.330000 0001 2157 2938Department of Computer Science, University of Toronto, Toronto, Canada
| | - Alexandre Magno-França
- grid.467095.90000 0001 2237 7915Laboratory of Protein Biochemistry, Federal University of State of Rio de Janeiro, Av. Pasteur, 296 – Urca, Rio de Janeiro, R.J. 22290-350 Brazil
| | | | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Washington, DC USA
| | - Morty Razavi
- SISCAPA Assay Technologies, Inc., Washington, DC USA
| | - Vinod Chandran
- grid.231844.80000 0004 0474 0428Arthritis Program, Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Faculty of Medicine, University of Toronto, Toronto, ON Canada
| | - LeRoy Martin
- grid.433801.d0000 0004 0580 039XWaters Technologies, Milford, MA USA
| | - Igor Jurisica
- grid.231844.80000 0004 0474 0428Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Canada ,grid.17063.330000 0001 2157 2938Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON Canada ,grid.419303.c0000 0001 2180 9405Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - L. C. Cameron
- grid.467095.90000 0001 2237 7915Laboratory of Protein Biochemistry, Federal University of State of Rio de Janeiro, Av. Pasteur, 296 – Urca, Rio de Janeiro, R.J. 22290-350 Brazil
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Pathmanathan S, Yao Z, Coelho P, Valla R, Drecun L, Benz C, Snider J, Saraon P, Grozavu I, Kotlyar M, Jurisica I, Park M, Stagljar I. B cell linker protein (BLNK) is a regulator of Met receptor signaling and trafficking in non-small cell lung cancer. iScience 2022; 25:105419. [DOI: 10.1016/j.isci.2022.105419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
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Sotzny F, Filgueiras IS, Kedor C, Freitag H, Wittke K, Bauer S, Sepúlveda N, Mathias da Fonseca DL, Baiocchi GC, Marques AHC, Kim M, Lange T, Plaça DR, Luebber F, Paulus FM, De Vito R, Jurisica I, Schulze-Forster K, Paul F, Bellmann-Strobl J, Rust R, Hoppmann U, Shoenfeld Y, Riemekasten G, Heidecke H, Cabral-Marques O, Scheibenbogen C. Dysregulated autoantibodies targeting vaso- and immunoregulatory receptors in Post COVID Syndrome correlate with symptom severity. Front Immunol 2022; 13:981532. [PMID: 36238301 PMCID: PMC9552223 DOI: 10.3389/fimmu.2022.981532] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Most patients with Post COVID Syndrome (PCS) present with a plethora of symptoms without clear evidence of organ dysfunction. A subset of them fulfills diagnostic criteria of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Symptom severity of ME/CFS correlates with natural regulatory autoantibody (AAB) levels targeting several G-protein coupled receptors (GPCR). In this exploratory study, we analyzed serum AAB levels against vaso- and immunoregulatory receptors, mostly GPCRs, in 80 PCS patients following mild-to-moderate COVID-19, with 40 of them fulfilling diagnostic criteria of ME/CFS. Healthy seronegative (n=38) and asymptomatic post COVID-19 controls (n=40) were also included in the study as control groups. We found lower levels for various AABs in PCS compared to at least one control group, accompanied by alterations in the correlations among AABs. Classification using random forest indicated AABs targeting ADRB2, STAB1, and ADRA2A as the strongest classifiers (AABs stratifying patients according to disease outcomes) of post COVID-19 outcomes. Several AABs correlated with symptom severity in PCS groups. Remarkably, severity of fatigue and vasomotor symptoms were associated with ADRB2 AAB levels in PCS/ME/CFS patients. Our study identified dysregulation of AAB against various receptors involved in the autonomous nervous system (ANS), vaso-, and immunoregulation and their correlation with symptom severity, pointing to their role in the pathogenesis of PCS.
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Affiliation(s)
- Franziska Sotzny
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Claudia Kedor
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Helma Freitag
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Kirsten Wittke
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Sandra Bauer
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Nuno Sepúlveda
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
- CEAUL – Centro de Estatística e Aplicações da Universidade de Lisboa, Lisbon, Portugal
| | | | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandre H. C. Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Myungjin Kim
- Data Science Initiative, Brown University, Providence, RI, United States
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Finn Luebber
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Frieder M. Paulus
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Roberta De Vito
- Department of Biostatistics and the Data Science Initiative, Brown University, Providence, RI, United States
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Friedemann Paul
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- NeuroCure Clinical Research Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Judith Bellmann-Strobl
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Rebekka Rust
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Uta Hoppmann
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Affiliated with the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Hashomer, Israel
- Ariel University, Ariel, Israel
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | | | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Interunit PostGraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo, Sao Paulo, Brazil
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sao Paulo, Brazil
- Department of Pharmacy, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- *Correspondence: Franziska Sotzny, ; Igor Salerno Filgueiras, ; Otavio Cabral-Marques, ; Carmen Scheibenbogen,
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Ali S, Espin-Garcia O, Wong A, Potla P, Pastrello C, Mcintyre M, Lively S, Jurisica I, Gandhi R, Kapoor M. POS0230 THE miR-320 FAMILY IS UPREGULATED IN FAST-PROGRESSING RADIOGRAPHIC KNEE OSTEOARTHRITIS: DATA FROM THE OSTEOARTHRITIS INITIATIVE. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.2970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BackgroundThere is an outstanding need for prognostic biomarkers to reliably detect fast-progressing knee osteoarthritis (OA) such that preventative interventions can be targeted to this patient population. MicroRNA-sequencing is an unbiased approach for comprehensive profiling of circulating microRNAs in liquid biopsies to discover novel biomarkers of disease. As negative regulators of gene expression, microRNAs hold potential not only as biomarkers, but also as mechanistic drivers of knee OA.ObjectivesTo apply microRNA-sequencing to identify unique circulating microRNAs as potential biomarkers that distinguish fast-progressing radiographic knee OA from both slow- and non-progressing radiographic knee OA.MethodsLeveraging the Osteoarthritis Initiative (OAI) longitudinal cohort, we applied our customized microRNA-sequencing pipeline [1] to blood plasma samples collected at both baseline and 4-year follow-up from 106 participants. The disease trajectory for each participant was constructed by plotting their Kellgren-Lawrence (KL) grades over an 8-year follow-up period. Based on these trajectories, we defined fast-progression as an increase from KL 0/1 at baseline to KL 3/4 by 4-year follow-up, slow-progression as an increase from KL 0/1 at baseline to KL 2/3/4 by 8-year follow-up, and non-progression as no increase from KL0/1 at baseline throughout the 8-year follow-up. Following differential expression analysis, we assessed predictive performance and identified putative gene targets for prioritized microRNAs.ResultsComparing fast-progressors to both slow-progressors and non-progressors, we identified differentially expressed microRNAs within timepoints (i.e., 48 microRNAs at baseline and 2 microRNAs at 4-year follow-up) and across timepoints. Among these microRNAs were four members of the miR-320 family, with miR-320d showing an increase in fast-progressors at both timepoints, compared to both slow- and non-progressors. The predictive models we constructed included miR-320 members and had good accuracy (area under the receiver operating characteristic curves ranging from 82.6 to 91.9) in distinguishing fast-progressors. Putative gene targets of the miR-320 family included members of the 14-3-3 gene family (Table 1), including YWHAE, whose downregulation in OA cartilage was reported to promote deterioration [2].Table 1.Predicted gene targets of the miR-320 family include members of the 14-3-3 gene family.14-3-3 gene family memberhsa-miR-320bhsa-miR-320chsa-miR-320dhsa-miR-320eSFNMMMLYWHABMMMMYWHAEVVVHYWHAGVVVMYWHAHVVVMYWHAQVVVMYWHAZVVVMAll mirDIP results with bold text indicating the prediction was among the top 1% for that microRNA/gene target pair. Letters denote the mirDIP score class with V=very high, H=high, M=medium, and L=low.ConclusionThis microRNA-sequencing study is the first of its kind, profiling circulating microRNAs at two timepoints in 106 participants with data-driven construction of knee OA trajectories. We identify the miR-320 family of microRNAs to be associated with fast-progressing radiographic knee OA over time. While our data suggest this microRNA family could have applications as prognostic biomarkers for knee OA, and could be regulating gene targets to impact OA severity, validation of these findings in independent longitudinal cohorts is required.References[1]Potla P, Ali SA, Kapoor M. A bioinformatics approach to microRNA-sequencing analysis. Osteoarthritis and Cartilage Open. 2021;3(1):100131. doi: https://doi.org/10.1016/j.ocarto.2020.100131.[2]Fu W, Hettinghouse A, Chen Y, Hu W, Ding X, Chen M, Ding Y, Mundra J, Song W, Liu R, Yi YS, Attur M, Samuels J, Strauss E, Leucht P, Schwarzkopf R, Liu CJ. 14-3-3 epsilon is an intracellular component of TNFR2 receptor complex and its activation protects against osteoarthritis. Ann Rheum Dis. 2021 Dec;80(12):1615-1627. doi: 10.1136/annrheumdis-2021-220000.Disclosure of InterestsNone declared
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Ali SA, Espin-Garcia O, Wong AK, Potla P, Pastrello C, McIntyre M, Lively S, Jurisica I, Gandhi R, Kapoor M. Circulating microRNAs differentiate fast-progressing from slow-progressing and non-progressing knee osteoarthritis in the Osteoarthritis Initiative cohort. Ther Adv Musculoskelet Dis 2022; 14:1759720X221082917. [PMID: 35321117 PMCID: PMC8935408 DOI: 10.1177/1759720x221082917] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 02/07/2022] [Indexed: 02/02/2023] Open
Abstract
Introduction: The objective of this study is to identify circulating microRNAs that distinguish fast-progressing radiographic knee osteoarthritis (OA) in the Osteoarthritis Initiative cohort by applying microRNA-sequencing. Methods: Participants with Kellgren–Lawrence (KL) grade 0/1 at baseline were included (N = 106). Fast-progressors were defined by an increase to KL 3/4 by 4-year follow-up (N = 20), whereas slow-progressors showed an increase to KL 2/3/4 only at 8-year follow-up (N = 35). Non-progressors remained at KL 0/1 by 8-year follow-up (N = 51). MicroRNA-sequencing was performed on plasma collected at baseline and 4-year follow-up from the same participants. Negative binomial models were fitted to identify differentially expressed (DE) microRNAs. Penalized logistic regression (PLR) analyses were performed to select combinations of DE microRNAs that distinguished fast-progressors. Area under the receiver operating characteristic curves (AUC) were constructed to evaluate predictive ability. Results: DE analyses revealed 48 microRNAs at baseline and 2 microRNAs at 4-year follow-up [false discovery rate (FDR) < 0.05] comparing fast-progressors with both slow-progressors and non-progressors. Among these were hsa-miR-320b, hsa-miR-320c, hsa-miR-320d, and hsa-miR-320e, which were predicted to target gene families, including members of the 14-3-3 gene family, involved in signal transduction. PLR models included miR-320 members as top predictors of fast-progressors and yielded AUC ranging from 82.6 to 91.9, representing good accuracy. Conclusion: The miR-320 family is associated with fast-progressing radiographic knee OA and merits further investigation as potential biomarkers and mechanistic drivers of knee OA.
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Affiliation(s)
- Shabana Amanda Ali
- Bone and Joint Center, Henry Ford Health System, 6135 Woodward Avenue, Detroit, MI, 48202, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Osvaldo Espin-Garcia
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Andy K. Wong
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Pratibha Potla
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Madison McIntyre
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Starlee Lively
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Departments of Medical Biophysics, Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Rajiv Gandhi
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, 60 Leonard Avenue, Toronto, ON, M5T 2R1, Canada
- Krembil Research Institute, University Health Network, Toronto, Canada
- Departments of Surgery and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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Cabral-Marques O, Halpert G, Schimke LF, Ostrinski Y, Vojdani A, Baiocchi GC, Freire PP, Filgueiras IS, Zyskind I, Lattin MT, Tran F, Schreiber S, Marques AHC, Plaça DR, Fonseca DLM, Humrich JY, Müller A, Giil LM, Graßhoff H, Schumann A, Hackel A, Junker J, Meyer C, Ochs HD, Lavi YB, Scheibenbogen C, Dechend R, Jurisica I, Schulze-Forster K, Silverberg JI, Amital H, Zimmerman J, Heidecke H, Rosenberg AZ, Riemekasten G, Shoenfeld Y. Autoantibodies targeting GPCRs and RAS-related molecules associate with COVID-19 severity. Nat Commun 2022; 13:1220. [PMID: 35264564 PMCID: PMC8907309 DOI: 10.1038/s41467-022-28905-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/27/2022] Open
Abstract
COVID-19 shares the feature of autoantibody production with systemic autoimmune diseases. In order to understand the role of these immune globulins in the pathogenesis of the disease, it is important to explore the autoantibody spectra. Here we show, by a cross-sectional study of 246 individuals, that autoantibodies targeting G protein-coupled receptors (GPCR) and RAS-related molecules associate with the clinical severity of COVID-19. Patients with moderate and severe disease are characterized by higher autoantibody levels than healthy controls and those with mild COVID-19 disease. Among the anti-GPCR autoantibodies, machine learning classification identifies the chemokine receptor CXCR3 and the RAS-related molecule AGTR1 as targets for antibodies with the strongest association to disease severity. Besides antibody levels, autoantibody network signatures are also changing in patients with intermediate or high disease severity. Although our current and previous studies identify anti-GPCR antibodies as natural components of human biology, their production is deregulated in COVID-19 and their level and pattern alterations might predict COVID-19 disease severity.
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Affiliation(s)
- Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil.
- Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sao Paulo, Brazil.
| | - Gilad Halpert
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University, Saint-Petersburg, Russia
| | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Yuri Ostrinski
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Saint Petersburg State University, Saint-Petersburg, Russia
- Ariel University, Ariel, Israel
| | - Aristo Vojdani
- Department of Immunology, Immunosciences Laboratory, Inc., Los Angeles, CA, United States
- Cyrex Laboratories, LLC 2602S. 24th St., Phoenix, AZ, 85034, USA
| | - Gabriela Crispim Baiocchi
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Paula Paccielli Freire
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Igor Salerno Filgueiras
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA
- Maimonides Medical Center, Brooklyn, NY, USA
| | - Miriam T Lattin
- Department of Biology, Yeshiva University, Manhatten, NY, USA
| | - Florian Tran
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Alexandre H C Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Dennyson Leandro M Fonseca
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Jens Y Humrich
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Antje Müller
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Hanna Graßhoff
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Anja Schumann
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Alexander Hackel
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Juliane Junker
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Carlotta Meyer
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA
| | - Yael Bublil Lavi
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Carmen Scheibenbogen
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ralf Dechend
- Experimental and Clinical Research Center, a collaboration of Max Delbruck Center for Molecular Medicine and Charité Universitätsmedizin, and HELIOS Clinic, Department of Cardiology and Nephrology, Berlin, 13125, Germany
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, UHN; Data Science Discovery Centre, Krembil Research Institute, UHN, Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Kai Schulze-Forster
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Jonathan I Silverberg
- School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Howard Amital
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Department of Medicine B, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Harry Heidecke
- CellTrend Gesellschaft mit beschränkter Haftung (GmbH), Luckenwalde, Germany
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriela Riemekasten
- Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lübeck, Lübeck, Germany.
| | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel.
- Saint Petersburg State University, Saint-Petersburg, Russia.
- Ariel University, Ariel, Israel.
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Schimke LF, Marques AHC, Baiocchi GC, de Souza Prado CA, Fonseca DLM, Freire PP, Rodrigues Plaça D, Salerno Filgueiras I, Coelho Salgado R, Jansen-Marques G, Rocha Oliveira AE, Peron JPS, Cabral-Miranda G, Barbuto JAM, Camara NOS, Calich VLG, Ochs HD, Condino-Neto A, Overmyer KA, Coon JJ, Balnis J, Jaitovich A, Schulte-Schrepping J, Ulas T, Schultze JL, Nakaya HI, Jurisica I, Cabral-Marques O. Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States. Cells 2022; 11:cells11050847. [PMID: 35269470 PMCID: PMC8909161 DOI: 10.3390/cells11050847] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Severe COVID-19 patients present a clinical and laboratory overlap with other hyperinflammatory conditions such as hemophagocytic lymphohistiocytosis (HLH). However, the underlying mechanisms of these conditions remain to be explored. Here, we investigated the transcriptome of 1596 individuals, including patients with COVID-19 in comparison to healthy controls, other acute inflammatory states (HLH, multisystem inflammatory syndrome in children [MIS-C], Kawasaki disease [KD]), and different respiratory infections (seasonal coronavirus, influenza, bacterial pneumonia). We observed that COVID-19 and HLH share immunological pathways (cytokine/chemokine signaling and neutrophil-mediated immune responses), including gene signatures that stratify COVID-19 patients admitted to the intensive care unit (ICU) and COVID-19_nonICU patients. Of note, among the common differentially expressed genes (DEG), there is a cluster of neutrophil-associated genes that reflects a generalized hyperinflammatory state since it is also dysregulated in patients with KD and bacterial pneumonia. These genes are dysregulated at the protein level across several COVID-19 studies and form an interconnected network with differentially expressed plasma proteins that point to neutrophil hyperactivation in COVID-19 patients admitted to the intensive care unit. scRNAseq analysis indicated that these genes are specifically upregulated across different leukocyte populations, including lymphocyte subsets and immature neutrophils. Artificial intelligence modeling confirmed the strong association of these genes with COVID-19 severity. Thus, our work indicates putative therapeutic pathways for intervention.
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Affiliation(s)
- Lena F. Schimke
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Correspondence: (L.F.S.); (O.C.-M.); Tel.: +55-11-943661555 (L.F.S.); +55-11-974642022 (O.C.-M.)
| | - Alexandre H. C. Marques
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gabriela Crispim Baiocchi
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Dennyson Leandro M. Fonseca
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Paula Paccielli Freire
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Igor Salerno Filgueiras
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Ranieri Coelho Salgado
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gabriel Jansen-Marques
- Information Systems, School of Arts, Sciences and Humanities, University of Sao Paulo, São Paulo 03828-000, Brazil;
| | - Antonio Edson Rocha Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Jean Pierre Schatzmann Peron
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gustavo Cabral-Miranda
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - José Alexandre Marzagão Barbuto
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Laboratory of Medical Investigation in Pathogenesis, Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo 05403-000, Brazil
| | - Niels Olsen Saraiva Camara
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Vera Lúcia Garcia Calich
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Hans D. Ochs
- Department of Pediatrics, Seattle Children’s Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA;
| | - Antonio Condino-Neto
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; (K.A.O.); (J.J.C.)
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; (K.A.O.); (J.J.C.)
- Morgridge Institute for Research, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; (J.B.); (A.J.)
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; (J.B.); (A.J.)
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Jonas Schulte-Schrepping
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; (J.S.-S.); (J.L.S.)
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; (J.S.-S.); (J.L.S.)
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, University of Bonn, 53127 Bonn, Germany
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo 05508-020, Brazil
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada;
- Departments of Medical Biophysics and Computer Science, Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1L7, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Otávio Cabral-Marques
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo 05508-000, Brazil
- Correspondence: (L.F.S.); (O.C.-M.); Tel.: +55-11-943661555 (L.F.S.); +55-11-974642022 (O.C.-M.)
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Sandmo SB, Matyasova K, Filipcik P, Cente M, Koerte IK, Pasternak O, Andersen TE, Straume-Næsheim TM, Bahr R, Jurisica I. Changes in circulating microRNAs following head impacts in soccer. Brain Inj 2022; 36:560-571. [PMID: 35172120 DOI: 10.1080/02699052.2022.2034042] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AIM To explore the short-term effects of accidental head impacts and repetitive headers on circulating microRNAs, accounting for the effects of high-intensity exercise alone. METHODS Blood samples were collected from professional soccer players at rest. Repeat samples were drawn 1 h and 12 h after three conditions: (1) accidental head impacts in a match, (2) repetitive headers during training, and (3) high-intensity exercise. 89 samples were screened to detect microRNAs expressed after each exposure. Identified microRNAs were then validated in 98 samples to determine consistently deregulated microRNAs. Deregulated microRNAs were further explored using bioinformatics to identify target genes and characterize their involvement in biological pathways. RESULTS Accidental head impacts led to deregulation of eight microRNAs that were unaffected by high-intensity exercise; target genes were linked to 12 specific signaling pathways, primarily regulating chromatin organization, Hedgehog and Wnt signaling. Repetitive headers led to deregulation of six microRNAs that were unaffected by high-intensity exercise; target genes were linked to one specific signaling pathway (TGF-β). High-intensity exercise led to deregulation of seven microRNAs; target genes were linked to 31 specific signaling pathways. CONCLUSION We identified microRNAs specific to accidental head impacts and repetitive headers in soccer, potentially being useful as brain injury biomarkers.
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Affiliation(s)
- Stian Bahr Sandmo
- Oslo Sports Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Katarina Matyasova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Peter Filipcik
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martin Cente
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Inga Katharina Koerte
- cBRAIN, Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, Ludwig-Maximilians-Universität, Munich, Germany.,Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ofer Pasternak
- Department of Psychiatry, Psychiatry Neuroimaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thor Einar Andersen
- Oslo Sports Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway
| | - Truls Martin Straume-Næsheim
- Oslo Sports Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway.,Department of Orthopedic Surgery, Akershus University Hospital, Lørenskog, Norway.,Department of Orthopedic Surgery, Haugesund Rheumatism Hospital, Haugesund, Norway
| | - Roald Bahr
- Oslo Sports Trauma Research Center, Department of Sports Medicine, Norwegian School of Sport Sciences, Oslo, Norway
| | - Igor Jurisica
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.,Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
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Eder L, Li Q, Rahmati S, Rahman P, Jurisica I, Chandran V. Defining imaging sub-phenotypes of psoriatic arthritis: integrative analysis of imaging data and gene expression in a PsA patient cohort. Rheumatology (Oxford) 2022; 61:4952-4961. [PMID: 35157043 PMCID: PMC9707284 DOI: 10.1093/rheumatology/keac078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/07/2022] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES To define imaging sub-phenotypes in patients with PsA; determine their association with whole blood gene expression and identify biological pathways characterizing the sub-phenotypes. METHODS Fifty-five patients with PsA ready to initiate treatment for active disease were prospectively recruited. We performed musculoskeletal ultrasound assessment of the extent of inflammation in the following domains: synovitis, peritenonitis, tenosynovitis and enthesitis. Peripheral whole blood was profiled with RNAseq, and gene expression data were obtained. First, unsupervised cluster analysis was performed to define imaging sub-phenotypes that reflected the predominant tissue involved. Subsequently, principal component analysis was used to determine the association between imaging-defined sub-phenotypes and peripheral blood gene expression profile. Pathway enrichment analysis was performed to identify underlying mechanisms that characterize individual sub-phenotypes. RESULTS Cluster analysis revealed three imaging sub-phenotypes: (i) synovitis predominant [n = 31 (56%)]; (ii) enthesitis predominant [n = 13 (24%)]; (iii) peritenonitis predominant [n = 11 (20%)]. The peritenonitis-predominant sub-phenotype had the most severe clinical joint involvement, whereas the enthesitis-predominant sub-phenotype had the highest tender entheseal count. Unsupervised clustering of gene expression data identified three sub-phenotypes that partially overlapped with the imaging sub-phenotypes suggesting biological and clinical relevance of these sub-phenotypes. We therefore characterized enriched differential pathways, which included: immune system (innate system, B cells and neutrophil degranulation), complement system, platelet activation and coagulation function. CONCLUSIONS We identified three sub-phenotypes based on the predominant tissue involved in patients with active PsA. Distinct biological pathways may underlie these imaging sub-phenotypes seen in PsA, suggesting their biological and clinical importance.
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Affiliation(s)
- Lihi Eder
- Correspondence to: Lihi Eder, Women’s College Research Institute, Room 6326, Women’s College Hospital, 76 Grenville Street, Toronto, Ontario M5S 1B2, Canada. E-mail:
| | - Quan Li
- Princess Margaret Cancer Centre, University Health Network, University of Toronto
| | - Sara Rahmati
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON
| | - Proton Rahman
- Rheumatology Division, Department of Medicine, Memorial University, St. John’s, NL
| | - Igor Jurisica
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON,Departments of Medical Biophysics and Computer Science, Faculty of Dentistry University of Toronto, ON, Canada,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vinod Chandran
- Rheumatology Division, Department of Medicine,Institute of Medical Science,Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON,Rheumatology Division, Department of Medicine, Memorial University, St. John’s, NL,Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada
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Lim SH, Snider J, Birimberg‐Schwartz L, Ip W, Serralha JC, Botelho HM, Lopes‐Pacheco M, Pinto MC, Moutaoufik MT, Zilocchi M, Laselva O, Esmaeili M, Kotlyar M, Lyakisheva A, Tang P, López Vázquez L, Akula I, Aboualizadeh F, Wong V, Grozavu I, Opacak‐Bernardi T, Yao Z, Mendoza M, Babu M, Jurisica I, Gonska T, Bear CE, Amaral MD, Stagljar I. CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system. Mol Syst Biol 2022; 18:e10629. [PMID: 35156780 PMCID: PMC8842165 DOI: 10.15252/msb.202110629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/16/2022] [Accepted: 01/19/2022] [Indexed: 12/19/2022] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel in secretory epithelia with a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. While remarkable treatment advances have been made recently in the form of modulator drugs directly rescuing CFTR dysfunction, there is still considerable scope for improvement of therapeutic effectiveness. Here, we report the application of a high‐throughput screening variant of the Mammalian Membrane Two‐Hybrid (MaMTH‐HTS) to map the protein–protein interactions of wild‐type (wt) and mutant CFTR (F508del), in an effort to better understand CF cellular effects and identify new drug targets for patient‐specific treatments. Combined with functional validation in multiple disease models, we have uncovered candidate proteins with potential roles in CFTR function/CF pathophysiology, including Fibrinogen Like 2 (FGL2), which we demonstrate in patient‐derived intestinal organoids has a significant effect on CFTR functional expression.
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Affiliation(s)
- Sang Hyun Lim
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | - Jamie Snider
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Liron Birimberg‐Schwartz
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Wan Ip
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
| | - Joana C Serralha
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
- Faculty of Life Sciences and Medicine School of Bioscience Education King’s College London London UK
| | - Hugo M Botelho
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Miquéias Lopes‐Pacheco
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Madalena C Pinto
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Mohamed Taha Moutaoufik
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Mara Zilocchi
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Onofrio Laselva
- Department of Physiology University of Toronto Toronto ON Canada
| | - Mohsen Esmaeili
- Program in Genetics and Genome Biology The Hospital for Sick Children Toronto ON Canada
| | - Max Kotlyar
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
| | | | | | | | - Indira Akula
- Donnelly Centre University of Toronto Toronto ON Canada
| | | | - Victoria Wong
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Ingrid Grozavu
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
| | | | - Zhong Yao
- Donnelly Centre University of Toronto Toronto ON Canada
| | - Meg Mendoza
- Department of Molecular Genetics University of Toronto Toronto ON Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre University of Regina Regina SK Canada
| | - Igor Jurisica
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute University Health Network Toronto ON Canada
- Data Science Discovery Centre for Chronic Diseases Krembil Research Institute University Health Network Toronto ON Canada
- Departments of Medical Biophysics and Computer Science University of Toronto Toronto ON Canada
- Institute of Neuroimmunology Slovak Academy of Sciences Bratislava Slovakia
| | - Tanja Gonska
- Programme in Translational Medicine The Hospital for Sick Children Toronto ON Canada
- Division of Gastroenterology, Hepatology and Nutrition Department of Pediatrics University of Toronto Toronto ON Canada
| | - Christine E Bear
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Physiology University of Toronto Toronto ON Canada
| | - Margarida D Amaral
- Faculty of Sciences BioISI‐Biosystems and Integrative Sciences Institute University of Lisboa Lisboa Portugal
| | - Igor Stagljar
- Donnelly Centre University of Toronto Toronto ON Canada
- Department of Biochemistry University of Toronto Toronto ON Canada
- Department of Molecular Genetics University of Toronto Toronto ON Canada
- Mediterranean Institute for Life Sciences Split Croatia
- School of Medicine University of Split Split Croatia
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Tokar T, Pastrello C, Abovsky M, Rahmati S, Jurisica I. miRAnno-network-based functional microRNA annotation. Bioinformatics 2022; 38:592-593. [PMID: 34297061 DOI: 10.1093/bioinformatics/btab527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 06/16/2021] [Accepted: 07/16/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Functional annotation is a common part of microRNA (miRNA)-related research, typically carried as pathway enrichment analysis of the selected miRNA targets. Here, we propose miRAnno, a fast and easy-to-use web application for miRNA annotation. RESULTS miRAnno uses comprehensive molecular interaction network and random walks with restart to measure the association between miRNAs and individual pathways. Independent validation shows that miRAnno achieves higher signal-to-noise ratio compared to the standard enrichment analysis. AVAILABILITY AND IMPLEMENTATION miRAnno is freely available at https://ophid.utoronto.ca/miRAnno/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tomas Tokar
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Mark Abovsky
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Sara Rahmati
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program Division of Orthopedic Surgery Schroeder Arthritis Institute, and Data Science Discovery Centre for Chronic Diseases Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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Pastrello C, Abovsky M, Lu R, Ahmed Z, Kotlyar M, Veillette C, Jurisica I. Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database. Osteoarthritis and Cartilage Open 2022; 4:100237. [DOI: 10.1016/j.ocarto.2022.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022] Open
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Pastrello C, Niu Y, Jurisica I. Pathway Enrichment Analysis of Microarray Data. Methods Mol Biol 2022; 2401:147-159. [PMID: 34902127 DOI: 10.1007/978-1-0716-1839-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Microarray analyses usually result in a list of differential genes that need to be annotated to link them the phenotype being studied, help planning validation experiments and interpretation of the results. Pathway enrichment analyses are frequently used for such purpose, where pathways are human created models of molecular activities and processes. While different types of pathway enrichment are available, we focus this protocol on the most frequent type-overrepresentation analysis. Many databases collect different sets of pathways and curate different sets of genes for the same pathways, so it is important to carefully choose the most suitable pathway source to perform enrichment analysis. To provide a comprehensive pathway analysis, in this protocol we will use pathDIP, which supports comprehensive enrichment analysis by integrating 22 main pathway databases. We will also describe the steps needed to visualize the enriched pathways using GSOAP.
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Affiliation(s)
- Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Yun Niu
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada.
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Kotlyar M, Wong SWH, Pastrello C, Jurisica I. Improving Analysis and Annotation of Microarray Data with Protein Interactions. Methods Mol Biol 2022; 2401:51-68. [PMID: 34902122 DOI: 10.1007/978-1-0716-1839-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gene expression microarrays are one of the most widely used high-throughput technologies in molecular biology, with applications such as identification of disease mechanisms and development of diagnostic and prognostic gene signatures. However, the success of these tasks is often limited because microarray analysis does not account for the complex relationships among genes, their products, and overall signaling and regulatory cascades. Incorporating protein-protein interaction data into microarray analysis can help address these challenges. This chapter reviews how protein-protein interactions can help with microarray analysis, leading to benefits such as better explanations of disease mechanisms, more complete gene annotations, improved prioritization of genes for future experiments, and gene signatures that generalize better to new data.
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Affiliation(s)
- Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Serene W H Wong
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
- Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada.
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia.
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Passalent L, Cyr A, Jurisica I, Mathur S, Inman RD, Haroon N. Motivators, Barriers, and Opportunity for E-Health to Encourage Physical Activity in Axial Spondyloarthritis: A Qualitative Descriptive Study. Arthritis Care Res (Hoboken) 2021; 74:50-58. [PMID: 34928533 DOI: 10.1002/acr.24788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Physical activity is fundamental in the management of axial spondyloarthritis (SpA); however, evidence suggests that patients with axial SpA are not adhering to physical activity recommendations. E-health technology (e.g., telephone reminders and mobile text messaging) can increase participation in physical activity. The aims of this study were as follows: 1) to understand perspectives of the importance of physical activity in the management of axial SpA; 2) to describe factors associated with physical activity adherence; and 3) to explore the role of e-health technology to facilitate physical activity in patients with axial SpA. METHODS Semistructured interviews were conducted with axial SpA patients attending an urban academic rheumatology clinic. Interviews were audio recorded and transcribed verbatim. Data were analyzed using thematic principles. Systematic labeling of the data set was completed using an inductive approach until saturation of emergent themes. RESULTS Twelve patient interviews were completed. Most respondents were male (83.3%) with a mean ± SD age of 45.5 ± 12.5 years and a mean ± SD disease duration of 21.5 ± 14.9 years. Participants defined physical as any activity involving physical exertion. The role of physical activity in axial SpA management was well recognized and included symptom relief, pharmacologic synergy, and impact on general health. Motivators included a growth mindset, social support networks, and facility access. Barriers included fear of disease progression, life demands, and environmental restrictions. Feedback, electronic reminders, and virtual support networks were key components of e-health technology to facilitate engagement in physical activity. CONCLUSION The results of this study provide a foundation to guide development of patient-centered e-health technology interventions to increase physical activity uptake in patients with axial SpA.
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Affiliation(s)
- Laura Passalent
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, and University of Toronto, Toronto, Ontario, Canada
| | - Alaina Cyr
- University Health Network, Toronto, Ontario, Canada
| | - Igor Jurisica
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, and University of Toronto, Toronto, Ontario, Canada, and Slovak Academy of Sciences, Bratislava, Slovakia
| | | | - Robert D Inman
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, and University of Toronto, Toronto, Ontario, Canada
| | - Nigil Haroon
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, and University of Toronto, Toronto, Ontario, Canada
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Matyasova K, Csicsatkova N, Filipcik P, Jurisica I, Cente M. Peripheral microRNA alteration and pathway signaling after mild traumatic brain injury. Gen Physiol Biophys 2021; 40:523-539. [PMID: 34897024 DOI: 10.4149/gpb_2021038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/20/2021] [Indexed: 11/08/2022]
Abstract
Discovering novel diagnostic biomarkers and signatures for traumatic brain injury (TBI) represents a major challenge in the brain trauma research. Detailed analysis of post-concussive molecular pathways based on experimental data could provide a new insight into the pathophysiological sequelae and mapping of recovery mechanisms involved in TBI. MicroRNAs (miRNAs) detectable in peripheral body fluids after TBI are promising carriers of this missing knowledge. In order to define the signature of peripheral miRNAs signaling associated with mild TBI (mTBI), we performed a comprehensive meta-analysis of miRNA profiles in mTBI patients using multiple curated pathway databases. Using a bioinformatic pipeline with integrated data analysis we identified a set of genes that are connected to deregulated circulating miRNAs following the mTBI. Identified genes belong to specific pathways of MAPK, TGF-β, WNT, TLR2/4, PI3K/AKT, insulin, and growth factor signaling. Since the enriched pathways markedly overlap among the various biological fluids, signaling associated with mTBI that is concomitantly reflected in serum, plasma and saliva is robust and unique. Furthermore, we identified a network of 33 validated interacting proteins and their regulatory miRNAs that link the post-mTBI signaling in peripheral fluids with neurodegeneration-associated interaction pathways. Presented data provide a comprehensive insight into molecular events following mTBI, and the top predicted genes represent a group of novel candidate targets to be validated in connection with mTBI.
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Affiliation(s)
- Katarina Matyasova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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Bhat M, Pasini E, Pastrello C, Angeli M, Baciu C, Abovsky M, Coffee A, Adeyi O, Kotlyar M, Jurisica I. Estrogen Receptor 1 Inhibition of Wnt/β-Catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis. Front Oncol 2021; 11:777834. [PMID: 34881186 PMCID: PMC8645636 DOI: 10.3389/fonc.2021.777834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/01/2021] [Indexed: 01/10/2023] Open
Abstract
Background Hepatocellular Carcinoma (HCC) is a sexually dimorphic cancer, with female sex being independently protective against HCC incidence and progression. The aim of our study was to understand the mechanism of estrogen receptor signaling in driving sex differences in hepatocarcinogenesis. Methods We integrated 1,268 HCC patient sample profiles from publicly available gene expression data to identify the most differentially expressed genes (DEGs). We mapped DEGs into a physical protein interaction network and performed network topology analysis to identify the most important proteins. Experimental validation was performed in vitro on HCC cell lines, in and in vivo, using HCC mouse model. Results We showed that the most central protein, ESR1, is HCC prognostic, as increased ESR1 expression was protective for overall survival, with HR=0.45 (95%CI 0.32-0.64, p=4.4E-06), and was more pronounced in women. Transfection of HCC cell lines with ESR1 and exposure to estradiol affected expression of genes involved in the Wnt/β-catenin signaling pathway. ER-α (protein product of ESR1) agonist treatment in a mouse model of HCC resulted in significantly longer survival and decreased tumor burden (p<0.0001), with inhibition of Wnt/β-Catenin signaling. In vitro experiments confirmed colocalization of β-catenin with ER-α, leading to inhibition of β-catenin-mediated transcription of target genes c-Myc and Cyclin D1. Conclusion Combined, the centrality of ESR1 and its inhibition of the Wnt/β-catenin signaling axis provide a biological rationale for protection against HCC incidence and progression in women.
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Affiliation(s)
- Mamatha Bhat
- Ajmera Transplant Program, University Health Network, Toronto, ON, Canada.,Division of Gastroenterology & Hepatology, University of Toronto, Toronto, ON, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada.,Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Elisa Pasini
- Ajmera Transplant Program, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.,Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Marc Angeli
- Ajmera Transplant Program, University Health Network, Toronto, ON, Canada
| | - Cristina Baciu
- Ajmera Transplant Program, University Health Network, Toronto, ON, Canada
| | - Mark Abovsky
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.,Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Angella Coffee
- Department of Pathology and University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, United States
| | - Oyedele Adeyi
- Department of Pathology and University of Minnesota Medical Center, University of Minnesota, Minneapolis, MN, United States
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.,Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.,Krembil Research Institute, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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Aboualizadeh F, Yao Z, Guan J, Drecun L, Pathmanathan S, Snider J, Umapathy G, Kotlyar M, Jurisica I, Palmer R, Stagljar I. Mapping the Phospho-dependent ALK Interactome to Identify Novel Components in ALK Signaling. J Mol Biol 2021; 433:167283. [PMID: 34606829 DOI: 10.1016/j.jmb.2021.167283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 10/25/2022]
Abstract
Protein-protein interactions (PPIs) play essential roles in Anaplastic Lymphoma Kinase (ALK) signaling. Systematic characterization of ALK interactors helps elucidate novel ALK signaling mechanisms and may aid in the identification of novel therapeutics targeting related diseases. In this study, we used the Mammalian Membrane Two-Hybrid (MaMTH) system to map the phospho-dependent ALK interactome. By screening a library of 86 SH2 domain-containing full length proteins, 30 novel ALK interactors were identified. Many of their interactions are correlated to ALK phosphorylation activity: oncogenic ALK mutations potentiate the interactions and ALK inhibitors attenuate the interactions. Among the novel interactors, NCK2 was further verified in neuroblastoma cells using co-immunoprecipitation. Modulation of ALK activity by addition of inhibitors lead to concomitant changes in the tyrosine phosphorylation status of NCK2 in neuroblastoma cells, strongly supporting the functionality of the ALK/NCK2 interaction. Our study provides a resource list of potential novel ALK signaling components for further study.
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Affiliation(s)
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Ontario, Canada
| | | | - Jamie Snider
- Donnelly Centre, University of Toronto, Ontario, Canada
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Max Kotlyar
- Krembil Research Institute, University Health Network, Ontario, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Ontario, Canada; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Ruth Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-40530, Sweden
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Ontario, Canada; Mediterranean Institute for Life Sciences, Meštrovićevo Šetalište 45, Split, Croatia; School of Medicine, University of Split, Split, Croatia. https://twitter.com/stagljar
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Kotlyar M, Pastrello C, Ahmed Z, Chee J, Varyova Z, Jurisica I. IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. Nucleic Acids Res 2021; 50:D640-D647. [PMID: 34755877 PMCID: PMC8728267 DOI: 10.1093/nar/gkab1034] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/13/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
Improved bioassays have significantly increased the rate of identifying new protein-protein interactions (PPIs), and the number of detected human PPIs has greatly exceeded early estimates of human interactome size. These new PPIs provide a more complete view of disease mechanisms but precise understanding of how PPIs affect phenotype remains a challenge. It requires knowledge of PPI context (e.g. tissues, subcellular localizations), and functional roles, especially within pathways and protein complexes. The previous IID release focused on PPI context, providing networks with comprehensive tissue, disease, cellular localization, and druggability annotations. The current update adds developmental stages to the available contexts, and provides a way of assigning context to PPIs that could not be previously annotated due to insufficient data or incompatibility with available context categories (e.g. interactions between membrane and cytoplasmic proteins). This update also annotates PPIs with conservation across species, directionality in pathways, membership in large complexes, interaction stability (i.e. stable or transient), and mutation effects. Enrichment analysis is now available for all annotations, and includes multiple options; for example, context annotations can be analyzed with respect to PPIs or network proteins. In addition to tabular view or download, IID provides online network visualization. This update is available at http://ophid.utoronto.ca/iid.
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Affiliation(s)
- Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Zuhaib Ahmed
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Justin Chee
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Zofia Varyova
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON M5S 1A4, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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Ali SA, Peffers MJ, Ormseth MJ, Jurisica I, Kapoor M. The non-coding RNA interactome in joint health and disease. Nat Rev Rheumatol 2021; 17:692-705. [PMID: 34588660 DOI: 10.1038/s41584-021-00687-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
Non-coding RNAs have distinct regulatory roles in the pathogenesis of joint diseases including osteoarthritis (OA) and rheumatoid arthritis (RA). As the amount of high-throughput profiling studies and mechanistic investigations of microRNAs, long non-coding RNAs and circular RNAs in joint tissues and biofluids has increased, data have emerged that suggest complex interactions among non-coding RNAs that are often overlooked as critical regulators of gene expression. Identifying these non-coding RNAs and their interactions is useful for understanding both joint health and disease. Non-coding RNAs regulate signalling pathways and biological processes that are important for normal joint development but, when dysregulated, can contribute to disease. The specific expression profiles of non-coding RNAs in various disease states support their roles as promising candidate biomarkers, mediators of pathogenic mechanisms and potential therapeutic targets. This Review synthesizes literature published in the past 2 years on the role of non-coding RNAs in OA and RA with a focus on inflammation, cell death, cell proliferation and extracellular matrix dysregulation. Research to date makes it apparent that 'non-coding' does not mean 'non-essential' and that non-coding RNAs are important parts of a complex interactome that underlies OA and RA.
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Affiliation(s)
- Shabana A Ali
- Bone and Joint Center, Department of Orthopaedic Surgery, Henry Ford Health System, Detroit, MI, USA. .,Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA.
| | - Mandy J Peffers
- Department of Musculoskeletal Biology, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Michelle J Ormseth
- Department of Research and Development, Veterans Affairs Medical Center, Nashville, TN, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada.,Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Mohit Kapoor
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, Ontario, Canada. .,Department of Surgery and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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Nakamura A, Zeng F, Nakamura S, Reid KT, Gracey E, Lim M, Leng L, Jo S, Park YS, Kusuda M, Machhar R, Boroojeni SF, Wu B, Rossomacha E, Kim TH, Ciccia F, Rockel JS, Kapoor M, Inman RD, Jurisica I, Crome SQ, Bucala R, Haroon N. Macrophage migration inhibitory factor drives pathology in a mouse model of spondyloarthritis and is associated with human disease. Sci Transl Med 2021; 13:eabg1210. [PMID: 34669443 DOI: 10.1126/scitranslmed.abg1210] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Akihiro Nakamura
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario M5T 2S8, Canada.,Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Fanxing Zeng
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Sayaka Nakamura
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Kyle T Reid
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2C4, Canada
| | - Eric Gracey
- Unit Molecular Immunology and Inflammation, Inflammation Research Institute, VIB-Ghent University, 9000 Ghent, Belgium.,Department of Rheumatology, Universitair Ziekenhuis Ghent, University of Gent, 9000 Ghent, Belgium
| | - Melissa Lim
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Lin Leng
- Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sungsin Jo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Republic of Korea
| | - Ye-Soo Park
- Department of Orthopaedic Surgery, Guri Hospital, Hanyang University College of Medicine, Guri 11293, Republic of Korea
| | - Masaki Kusuda
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Rohan Machhar
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Shaghayegh F Boroojeni
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Brian Wu
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Evgeny Rossomacha
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Republic of Korea
| | - Francesco Ciccia
- Department of Precision Medicine, University della Campania L. Vanvitelli, 80131 Naples, Italy
| | - Jason S Rockel
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Mohit Kapoor
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Robert D Inman
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario M5T 2S8, Canada.,Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Igor Jurisica
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, 85410 Bratislava, Slovakia
| | - Sarah Q Crome
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2C4, Canada
| | - Richard Bucala
- Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nigil Haroon
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada.,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario M5T 2S8, Canada.,Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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França TT, Al-Sbiei A, Bashir G, Mohamed YA, Salgado RC, Barreiros LA, Maria da Silva Napoleão S, Weber CW, Fernandes Severo Ferreira J, Aranda CS, Prando C, de Barros Dorna MB, Jurisica I, Fernandez-Cabezudo MJ, Ochs HD, Condino-Neto A, Al-Ramadi BK, Cabral-Marques O. CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. JCI Insight 2021; 6:e148652. [PMID: 34255742 PMCID: PMC8410015 DOI: 10.1172/jci.insight.148652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Neutrophils are produced in the BM in a process called granulopoiesis, in which progenitor cells sequentially develop into mature neutrophils. During the developmental process, which is finely regulated by distinct transcription factors, neutrophils acquire the ability to exit the BM, properly distribute throughout the body, and migrate to infection sites. Previous studies have demonstrated that CD40 ligand (CD40L) influences hematopoiesis and granulopoiesis. Here, we investigate the effect of CD40L on neutrophil development and trafficking by performing functional and transcriptome analyses. We found that CD40L signaling plays an essential role in the early stages of neutrophil generation and development in the BM. Moreover, CD40L modulates transcriptional signatures, indicating that this molecule enables neutrophils to traffic throughout the body and to migrate in response to inflammatory signals. Thus, our study provides insights into the complex relationships between CD40L signaling and granulopoiesis, and it suggests a potentially novel and nonredundant role of CD40L signaling in neutrophil development and function.
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Affiliation(s)
- Tábata Takahashi França
- Department of Immunology, Institute of Biomedical Science, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ashraf Al-Sbiei
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Ghada Bashir
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Yassir Awad Mohamed
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Ranieri Coelho Salgado
- Department of Immunology, Institute of Biomedical Science, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Lucila Akune Barreiros
- Department of Immunology, Institute of Biomedical Science, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Cristina Worm Weber
- Pediatric Allergy & Immunology Clinic, Caxias do Sul, Rio Grande do Sul, Brazil
| | | | - Carolina Sanchez Aranda
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Federal University of São Paulo, São Paulo, São Paulo, Brazil
| | - Carolina Prando
- Faculdades Pequeno Príncipe, Pelé Pequeno Principe Research Intitute, Curitiba, Paraná, Brazil.,Hospital Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Mayra B de Barros Dorna
- Division of Allergy and Immunology, Department of Pediatrics, Children's Institute, Hospital das Clínicas, São Paulo, São Paulo, Brazil
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Krembil Research Institute, University Health Network, Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Ontaro, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Maria J Fernandez-Cabezudo
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, UAE University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, Washington, USA
| | - Antonio Condino-Neto
- Department of Immunology, Institute of Biomedical Science, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Basel K Al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates (UAE) University, Al Ain, Abu Dhabi, United Arab Emirates.,Zayed Center for Health Sciences, UAE University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Science, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo, São Paulo, Brazil
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Li L, Guturi KKN, Gautreau B, Patel PS, Saad A, Morii M, Mateo F, Palomero L, Barbour H, Gomez A, Ng D, Kotlyar M, Pastrello C, Jackson HW, Khokha R, Jurisica I, Affar EB, Raught B, Sanchez O, Alaoui-Jamali M, Pujana MA, Hakem A, Hakem R. Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis. J Clin Invest 2021; 131:e152424. [PMID: 34196309 DOI: 10.1172/jci152424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Rahman P, Li Q, Codner D, O’Rielly D, Dohey A, Jenkins K, Gladman DD, Chandran V, Jurisica I. POS0406 miRNAs DEREGULATED IN RESPONSE TO IL17A INHIBITORS IN PSORIATIC ARTHRITIS REGULATE GENE PRODUCTS IN Rho-GTPase PATHWAYS. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.1434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:Using transcriptomic data at initiation of therapy, we recently identified differentially expressed genes (DEGs) that separated IL-17Ai response from non-response1. Integration of cell-type-specific DEGs with protein-protein interactions (PPIs) and further comprehensive pathway enrichment analysis revealed Rho GTPase signaling pathway exhibited a strong signal specific to IL-17Ai response and particularly the genes, RAC1 and ROCKs.Objectives:To characterize microRNA (miR) profiles among IL-17Ai responders and non-responders, as it relates to RHO GTPase pathway.Methods:We interrogated 20 psoriatic arthritis (PsA) patients initiating IL-17Ai. Patients achieving at least low disease activity according to the Disease Activity Index for PsA (DAPSA) at three months were classified as responders. There were seven responders (35%) and thirteen non-responders (65%) in the IL-17Ai group, with biologic treatment naïve (bio-naïve) and previously-exposed (bio-exposed) patients exhibiting a 50% (4/8) and a 25% (3/12) response rate, respectively. For the miR analysis, CD4 positive T cells were isolated from peripheral blood mononuclear cells using DynabeadsTM CD4 beads (ThermoFisher). Total RNA was extracted from the CD4+ T cells using Lexogen’s Split RNA Extraction Kit (D-Mark Biosciences). Libraries were prepared from 200ng total RNA with the NEXTFLEX Small RNA-Seq Kit v3 with UDIs (Bioo Scientific) and sequenced on the Illumina NovaSeq 6000. Raw sequencing fastq data assessed the quality using FastQC. The miRDeep2 was used to trim the adapter, align and quantify human mature miRs from miRbase (Release 22). The abundance of miRs was converted to read counts per million, normalized and limma R package was used to identify pre- and post-differentially expressed miRs.Results:We obtained 2,889 miRs. After removing miRs with low reads in >90% of samples, 1902 high quality miRs remained for further analysis. Using mirDIP v4.1 we identified gene targets for differential miRs, and focused on recently identified DEGs related to RHO GTPase pathway. The miRs on the left of the figure 1 are those deregulated in pre-treatment, and the miRs on the right of the figure 1 show the post-treatment deregulated miRs. hsa-miR-3691-5p and hsa-miR-3161 represent the miRs that were deregulated in both conditions. The red highlighted nodes represent the most connected miRs and genes; thus, representing miRs that are the most RHO-pathway centric regulators (hsa-miR-495-3p, 16-5p, 129-5p, 520h, 520g-3p), and genes representing the most strongly regulated RHO-pathway gene products (ROCK1, RHOQ, PFN2, TAOK1, DYNC1L12, MAPRE1, PAFAH1B1, ARHGAP5, MAPK1, CALM1, DIAPH2, PKN2, ITSN1).Conclusion:Pre- and post-treatment differential miRs related to IL-17Ai response regulate multiple genes from RHO GTPase pathway.References:[1]Rahmati S, O’Rielly DD, Li Q, Codner D, Dohey A, Jenkins K, Jurisica I, Gladman DD, Chandran V, Rahman P. Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis. Sci Rep. 2020 Dec 10;10(1):21703.Figure 1.Disclosure of Interests:Proton Rahman Speakers bureau: AbbVie, Amgen, BMS, Celgene, Eli Lily, Janssen, Merck, Novartis, Pfizer, UCB, Consultant of: AbbVie, Amgen, BMS, Celgene, Eli Lily, Janssen, Merck, Novartis, Pfizer, UCB, Grant/research support from: Janssen, Novartis, Quan Li: None declared, Dianne Codner: None declared, Darren O’Rielly: None declared, Amanda Dohey: None declared, Kari Jenkins: None declared, Dafna D Gladman Speakers bureau: AbbVie, Amgen, BMS, Eli Lily, Galapagos, Gilead, Janssen, Novartis, Pfizer, UCB, Consultant of: AbbVie, Amgen, BMS, Eli Lily, Galapagos, Gilead, Janssen, Novartis, Pfizer, UCB, Grant/research support from: AbbVie, Amgen, Eli Lily, Janssen, Novartis, Pfizer, UCB, Vinod Chandran Speakers bureau: AbbVie, Amgen, BMS, Eli Lily, Janssen, Novartis, Pfizer, UCB, Paid instructor for: AbbVie, Amgen, BMS, Eli Lily, Janssen, Novartis, Pfizer, UCB, Grant/research support from: AbbVie, Amgen, Eli Lily, Employee of: Spousal Employment Eli Lilly, Igor Jurisica: None declared
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Cohn DE, Barros-Filho MC, Minatel BC, Pewarchuk ME, Marshall EA, Vucic EA, Sage AP, Telkar N, Stewart GL, Jurisica I, Reis PP, Robinson WP, Lam WL. Reactivation of Multiple Fetal miRNAs in Lung Adenocarcinoma. Cancers (Basel) 2021; 13:2686. [PMID: 34072436 PMCID: PMC8199175 DOI: 10.3390/cancers13112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) play vital roles in the regulation of normal developmental pathways. However, cancer cells can co-opt these miRNAs, and the pathways that they regulate, to drive pro-tumourigenic phenotypes. Characterization of the miRNA transcriptomes of fetal organs is essential for identifying these oncofetal miRNAs, but it has been limited by fetal sample availability. As oncofetal miRNAs are absent from healthy adult lungs, they represent ideal targets for developing diagnostic and therapeutic strategies. We conducted small RNA sequencing of a rare collection of 25 human fetal lung (FL) samples and compared them to two independent cohorts (n = 140, n = 427), each comprised of adult non-neoplastic lung (ANL) and lung adenocarcinoma (LUAD) samples. We identified 13 oncofetal miRNAs that were expressed in FL and LUAD but not in ANL. These oncofetal miRNAs are potential biomarkers for LUAD detection (AUC = 0.963). Five of these miRNAs are derived from the imprinted C14MC miRNA cluster at the 14q32 locus, which has been associated with cancer development and abnormal fetal and placental development. Additionally, we observed the pulmonary expression of 44 previously unannotated miRNAs. The sequencing of these fetal lung samples also provides a baseline resource against which aberrant samples can be compared.
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Affiliation(s)
- David E. Cohn
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Mateus C. Barros-Filho
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
- International Research Center, A.C. Camargo Cancer Center, São Paulo, SP 01525-001, Brazil
| | - Brenda C. Minatel
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Michelle E. Pewarchuk
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Erin A. Marshall
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Emily A. Vucic
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
- NYU Langone Medical Center, New York, NY 10016, USA
| | - Adam P. Sage
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Nikita Telkar
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Greg L. Stewart
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada;
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Patricia P. Reis
- Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil;
| | - Wendy P. Robinson
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Wan L. Lam
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
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Freire PP, Marques AH, Baiocchi GC, Schimke LF, Fonseca DL, Salgado RC, Filgueiras IS, Napoleao SM, Plaça DR, Akashi KT, Hirata TDC, El Khawanky N, Giil LM, Cabral-Miranda G, Carvalho RF, Ferreira LCS, Condino-Neto A, Nakaya HI, Jurisica I, Ochs HD, Camara NOS, Calich VLG, Cabral-Marques O. The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2-infected patients by sex and age. JCI Insight 2021; 6:147535. [PMID: 34027897 PMCID: PMC8262322 DOI: 10.1172/jci.insight.147535] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/07/2021] [Indexed: 01/11/2023] Open
Abstract
The fact that the COVID-19 fatality rate varies by sex and age is poorly understood. Notably, the outcome of SARS-CoV-2 infections mostly depends on the control of cytokine storm and the increasingly recognized pathological role of uncontrolled neutrophil activation. Here, we used an integrative approach with publicly available RNA-Seq data sets of nasopharyngeal swabs and peripheral blood leukocytes from patients with SARS-CoV-2, according to sex and age. Female and young patients infected by SARS-CoV-2 exhibited a larger number of differentially expressed genes (DEGs) compared with male and elderly patients, indicating a stronger immune modulation. Among them, we found an association between upregulated cytokine/chemokine- and downregulated neutrophil-related DEGs. This was correlated with a closer relationship between female and young subjects, while the relationship between male and elderly patients was closer still. The association between these cytokine/chemokines and neutrophil DEGs is marked by a strongly correlated interferome network. Here, female patients exhibited reduced transcriptional levels of key proinflammatory/neutrophil-related genes, such as CXCL8 receptors (CXCR1 and CXCR2), IL-1β, S100A9, ITGAM, and DBNL, compared with male patients. These genes are well known to be protective against inflammatory damage. Therefore, our work suggests specific immune-regulatory pathways associated with sex and age of patients infected with SARS-CoV-2 and provides a possible association between inverse modulation of cytokine/chemokine and neutrophil transcriptional signatures.
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Affiliation(s)
- Paula P Freire
- Department of Immunology, Institute of Biomedical Sciences, and
| | | | | | - Lena F Schimke
- Department of Immunology, Institute of Biomedical Sciences, and
| | | | | | | | | | - Desirée R Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Karen T Akashi
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thiago Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nadia El Khawanky
- Department of Hematology and Oncology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lasse M Giil
- Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway
| | | | - Robson F Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, São Paulo
| | - Luis Carlos S Ferreira
- Vaccine Development Laboratory, Institute of Biomedical Sciences, Department of Microbiology, University of São Paulo, São Paulo, Brazil
| | | | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, and Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, Canada
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, Washington
| | | | | | - Otavio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, and.,Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil.,Network of Immunity in Infection, Malignancy, and Autoimmunity, Universal Scientific Education and Research Network, São Paulo, Brazil
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