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Katsuki S, K. Jha P, Lupieri A, Nakano T, Passos LS, Rogers MA, Becker-Greene D, Le TD, Decano JL, Ho Lee L, Guimaraes GC, Abdelhamid I, Halu A, Muscoloni A, V. Cannistraci C, Higashi H, Zhang H, Vromman A, Libby P, Keith Ozaki C, Sharma A, Singh SA, Aikawa E, Aikawa M. Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Promotes Macrophage Activation via LDL Receptor-Independent Mechanisms. Circ Res 2022; 131:873-889. [PMID: 36263780 PMCID: PMC9973449 DOI: 10.1161/circresaha.121.320056] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Activated macrophages contribute to the pathogenesis of vascular disease. Vein graft failure is a major clinical problem with limited therapeutic options. PCSK9 (proprotein convertase subtilisin/kexin 9) increases low-density lipoprotein (LDL)-cholesterol levels via LDL receptor (LDLR) degradation. The role of PCSK9 in macrophage activation and vein graft failure is largely unknown, especially through LDLR-independent mechanisms. This study aimed to explore a novel mechanism of macrophage activation and vein graft disease induced by circulating PCSK9 in an LDLR-independent fashion. METHODS We used Ldlr-/- mice to examine the LDLR-independent roles of circulating PCSK9 in experimental vein grafts. Adeno-associated virus (AAV) vector encoding a gain-of-function mutant of PCSK9 (rAAV8/D377Y-mPCSK9) induced hepatic PCSK9 overproduction. To explore novel inflammatory targets of PCSK9, we used systems biology in Ldlr-/- mouse macrophages. RESULTS In Ldlr-/- mice, AAV-PCSK9 increased circulating PCSK9, but did not change serum cholesterol and triglyceride levels. AAV-PCSK9 promoted vein graft lesion development when compared with control AAV. In vivo molecular imaging revealed that AAV-PCSK9 increased macrophage accumulation and matrix metalloproteinase activity associated with decreased fibrillar collagen, a molecular determinant of atherosclerotic plaque stability. AAV-PCSK9 induced mRNA expression of the pro-inflammatory mediators IL-1β (interleukin-1 beta), TNFα (tumor necrosis factor alpha), and MCP-1 (monocyte chemoattractant protein-1) in peritoneal macrophages underpinned by an in vitro analysis of Ldlr-/- mouse macrophages stimulated with endotoxin-free recombinant PCSK9. A combination of unbiased global transcriptomics and new network-based hyperedge entanglement prediction analysis identified the NF-κB (nuclear factor-kappa B) signaling molecules, lectin-like oxidized LOX-1 (LDL receptor-1), and SDC4 (syndecan-4) as potential PCSK9 targets mediating pro-inflammatory responses in macrophages. CONCLUSIONS Circulating PCSK9 induces macrophage activation and vein graft lesion development via LDLR-independent mechanisms. PCSK9 may be a potential target for pharmacologic treatment for this unmet medical need.
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Affiliation(s)
- Shunsuke Katsuki
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Prabhash K. Jha
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Adrien Lupieri
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Toshiaki Nakano
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Livia S.A. Passos
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Maximillian A. Rogers
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Dakota Becker-Greene
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Thanh-Dat Le
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Julius L. Decano
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Lang Ho Lee
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Gabriel C. Guimaraes
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Ilyes Abdelhamid
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Arda Halu
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alessandro Muscoloni
- The Biomedical Cybernetics Group, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Center for Systems Biology Dresden, Cluster of Excellence Physics of Life, Department of Physics, Technical University Dresden, Dresden, Germany (A.M., C.V.C)
- Center for Complex Network Intelligence at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China (A.M., C.V.C.)
| | - Carlo V. Cannistraci
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
- Center for Complex Network Intelligence at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China (A.M., C.V.C.)
| | - Hideyuki Higashi
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Hengmin Zhang
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Amélie Vromman
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - Peter Libby
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
| | - C. Keith Ozaki
- Center for Complex Network Intelligence at the Tsinghua Laboratory of Brain and Intelligence, Department of Bioengineering, Tsinghua University, Beijing, China (A.M., C.V.C.)
| | - Amitabh Sharma
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sasha A. Singh
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Elena Aikawa
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
| | - Masanori Aikawa
- The Center for Excellence in Vascular Biology, Cardiovascular Division (S.K., P.K.J., A.L., T.N., L.S.A.P., D.B.-G., T.-D.L., G.C.G., A.V., P.L., E.A., M.A.)
- The Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division (M.A.R., J.L.D., L.H.L., I.A., A.H., H.H., H.Z., A.S., S.A.S., E.A., M.A.)
- Channing Division of Network Medicine (I.A., A.H., A.S., M.A.), Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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2
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Ammirati E, Lupi L, Palazzini M, Hendren NS, Grodin JL, Cannistraci CV, Schmidt M, Hekimian G, Peretto G, Bochaton T, Hayek A, Piriou N, Leonardi S, Guida S, Turco A, Sala S, Uribarri A, Van de Heyning CM, Mapelli M, Campodonico J, Pedrotti P, Barrionuevo Sánchez MI, Ariza Sole A, Marini M, Matassini MV, Vourc'h M, Cannatà A, Bromage DI, Briguglia D, Salamanca J, Diez-Villanueva P, Lehtonen J, Huang F, Russel S, Soriano F, Turrini F, Cipriani M, Bramerio M, Di Pasquale M, Grosu A, Senni M, Farina D, Agostoni P, Rizzo S, De Gaspari M, Marzo F, Duran JM, Adler ED, Giannattasio C, Basso C, McDonagh T, Kerneis M, Combes A, Camici PG, de Lemos JA, Metra M. Prevalence, Characteristics, and Outcomes of COVID-19-Associated Acute Myocarditis. Circulation 2022; 145:1123-1139. [PMID: 35404682 PMCID: PMC8989611 DOI: 10.1161/circulationaha.121.056817] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Acute myocarditis (AM) is thought to be a rare cardiovascular complication of COVID-19, although minimal data are available beyond case reports. We aim to report the prevalence, baseline characteristics, in-hospital management, and outcomes for patients with COVID-19–associated AM on the basis of a retrospective cohort from 23 hospitals in the United States and Europe. Methods: A total of 112 patients with suspected AM from 56 963 hospitalized patients with COVID-19 were evaluated between February 1, 2020, and April 30, 2021. Inclusion criteria were hospitalization for COVID-19 and a diagnosis of AM on the basis of endomyocardial biopsy or increased troponin level plus typical signs of AM on cardiac magnetic resonance imaging. We identified 97 patients with possible AM, and among them, 54 patients with definite/probable AM supported by endomyocardial biopsy in 17 (31.5%) patients or magnetic resonance imaging in 50 (92.6%). We analyzed patient characteristics, treatments, and outcomes among all COVID-19–associated AM. Results: AM prevalence among hospitalized patients with COVID-19 was 2.4 per 1000 hospitalizations considering definite/probable and 4.1 per 1000 considering also possible AM. The median age of definite/probable cases was 38 years, and 38.9% were female. On admission, chest pain and dyspnea were the most frequent symptoms (55.5% and 53.7%, respectively). Thirty-one cases (57.4%) occurred in the absence of COVID-19–associated pneumonia. Twenty-one (38.9%) had a fulminant presentation requiring inotropic support or temporary mechanical circulatory support. The composite of in-hospital mortality or temporary mechanical circulatory support occurred in 20.4%. At 120 days, estimated mortality was 6.6%, 15.1% in patients with associated pneumonia versus 0% in patients without pneumonia (P=0.044). During hospitalization, left ventricular ejection fraction, assessed by echocardiography, improved from a median of 40% on admission to 55% at discharge (n=47; P<0.0001) similarly in patients with or without pneumonia. Corticosteroids were frequently administered (55.5%). Conclusions: AM occurrence is estimated between 2.4 and 4.1 out of 1000 patients hospitalized for COVID-19. The majority of AM occurs in the absence of pneumonia and is often complicated by hemodynamic instability. AM is a rare complication in patients hospitalized for COVID-19, with an outcome that differs on the basis of the presence of concomitant pneumonia.
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Affiliation(s)
- Enrico Ammirati
- De Gasperis Cardio Center and Transplant Center, Niguarda Hospital, Milano, Italy (E.A., M.P., P.P. F.S., M.C., C.G.)
| | - Laura Lupi
- Institute of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy (L.L., M.D.P., M. Metra)
| | - Matteo Palazzini
- De Gasperis Cardio Center and Transplant Center, Niguarda Hospital, Milano, Italy (E.A., M.P., P.P. F.S., M.C., C.G.)
| | - Nicholas S Hendren
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas (N.S.H., J.L.G., J.A.d.L.)
| | - Justin L Grodin
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas (N.S.H., J.L.G., J.A.d.L.)
| | - Carlo V Cannistraci
- Center for Complex Network Intelligence, Tsinghua Laboratory of Brain and Intelligence, Department of Computer Science, Department of Biomedical Engineering, Tsinghua University, Beijing, China (C.V.C.).,Center for Systems Biology Dresden, Germany (C.V.C.)
| | - Matthieu Schmidt
- Sorbonne Université, UMRS 1166, Institute of Cardiometabolism and Nutrition, Service de Médecine Intensive-Réanimation, Institut de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, France (M. Schmidt, G.H., A. Combes)
| | - Guillaume Hekimian
- Sorbonne Université, UMRS 1166, Institute of Cardiometabolism and Nutrition, Service de Médecine Intensive-Réanimation, Institut de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, France (M. Schmidt, G.H., A. Combes)
| | - Giovanni Peretto
- San Raffaele Hospital and Vita Salute University, Milano, Italy (G.P., S.S., P.G.C.)
| | - Thomas Bochaton
- Urgences et Soins Critiques Cardiologiques, Hôpital Cardiologique, Hospices Civils de Lyon, Bron, France (T.B., A.H.)
| | - Ahmad Hayek
- Urgences et Soins Critiques Cardiologiques, Hôpital Cardiologique, Hospices Civils de Lyon, Bron, France (T.B., A.H.)
| | - Nicolas Piriou
- Université Nantes, CHU Nantes, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, l'Institut du Thorax, France (N.P.)
| | - Sergio Leonardi
- University of Pavia and Fondazione Istituto di Ricovero e Cura a Carattere Scientificio Policlinico S. Matteo, Italy (S.L., S.G., A.T.)
| | - Stefania Guida
- University of Pavia and Fondazione Istituto di Ricovero e Cura a Carattere Scientificio Policlinico S. Matteo, Italy (S.L., S.G., A.T.)
| | - Annalisa Turco
- University of Pavia and Fondazione Istituto di Ricovero e Cura a Carattere Scientificio Policlinico S. Matteo, Italy (S.L., S.G., A.T.)
| | - Simone Sala
- San Raffaele Hospital and Vita Salute University, Milano, Italy (G.P., S.S., P.G.C.)
| | - Aitor Uribarri
- Departamento de Cardiología, Hospital Clínico Universitario, Valladolid, Spain (A.U.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Instituto de Salud Carlos III, Madrid, Spain (A.U.)
| | - Caroline M Van de Heyning
- Department of Cardiology, Antwerp University Hospital, and Genetics, Pharmacology and Physiopathology of Heart, Blood Vessels and Skeleton Research Group, Antwerp University, Belgium (C.M.V.d.H.)
| | - Massimo Mapelli
- Centro Cardiologico Monzino Istituto di Ricovero e Cura a Carattere Scientificio, Milano, Italy (M. Mapelli, J.C., P.A.).,Department of Clinical Sciences and Community Health, Cardiovascular Section, University of Milano, Italy (M. Mapelli, J.C., P.A.)
| | - Jeness Campodonico
- Centro Cardiologico Monzino Istituto di Ricovero e Cura a Carattere Scientificio, Milano, Italy (M. Mapelli, J.C., P.A.).,Department of Clinical Sciences and Community Health, Cardiovascular Section, University of Milano, Italy (M. Mapelli, J.C., P.A.)
| | - Patrizia Pedrotti
- De Gasperis Cardio Center and Transplant Center, Niguarda Hospital, Milano, Italy (E.A., M.P., P.P. F.S., M.C., C.G.)
| | - Maria Isabel Barrionuevo Sánchez
- Cardiology Department, Bellvitge University Hospital, Bioheart, Grup de Malalties Cardiovasculars, Institut d'Investigació Biomèdica de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge, L'Hospotalet del Llobregat, Barcelona, Spain (M.I.B.S., A.A.S.)
| | - Albert Ariza Sole
- Cardiology Department, Bellvitge University Hospital, Bioheart, Grup de Malalties Cardiovasculars, Institut d'Investigació Biomèdica de Bellvitge, Institut d'Investigació Biomèdica de Bellvitge, L'Hospotalet del Llobregat, Barcelona, Spain (M.I.B.S., A.A.S.)
| | - Marco Marini
- Cardiology Division, Cardiovascular Department, Azienda Ospedaliero Universitaria Ospedali Riuniti di Ancona Umberto I-GM Lancisi-G Salesi, Ancona, Italy (M. Marini, M.V.M.)
| | - Maria Vittoria Matassini
- Cardiology Division, Cardiovascular Department, Azienda Ospedaliero Universitaria Ospedali Riuniti di Ancona Umberto I-GM Lancisi-G Salesi, Ancona, Italy (M. Marini, M.V.M.)
| | - Mickael Vourc'h
- Department of Anesthesiology and Surgical Intensive Care, Hôpital Laennec, University Hospital of Nantes, France (M.V.).,School of Medicine, UPRES EA 3826, Thérapeutiques Cliniques et Expérimentales des Infections, IRS2 Nantes Biotech, France (M.V.)
| | - Antonio Cannatà
- School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre of Excellence, James Black Centre, United Kingdom (A. Cannatà, D.I.B., T.M.).,Department of Cardiology, King's College Hospital London, United Kingdom (A. Cannatà, D.I.B., T.M.)
| | - Daniel I Bromage
- School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre of Excellence, James Black Centre, United Kingdom (A. Cannatà, D.I.B., T.M.).,Department of Cardiology, King's College Hospital London, United Kingdom (A. Cannatà, D.I.B., T.M.)
| | | | - Jorge Salamanca
- Cardiology Department, Hospital Universitario De La Princesa, Madrid, Spain (J.S., P.D.-V.)
| | - Pablo Diez-Villanueva
- Cardiology Department, Hospital Universitario De La Princesa, Madrid, Spain (J.S., P.D.-V.)
| | - Jukka Lehtonen
- Heart and Lung Center, Department of Cardiology, Helsinki University Hospital, Finland (J.L.)
| | - Florent Huang
- Service de Cardiologie, Hôpital Foch, Suresnes, France (F.H., S. Russel)
| | - Stéphanie Russel
- Service de Cardiologie, Hôpital Foch, Suresnes, France (F.H., S. Russel)
| | - Francesco Soriano
- De Gasperis Cardio Center and Transplant Center, Niguarda Hospital, Milano, Italy (E.A., M.P., P.P. F.S., M.C., C.G.)
| | | | - Manlio Cipriani
- De Gasperis Cardio Center and Transplant Center, Niguarda Hospital, Milano, Italy (E.A., M.P., P.P. F.S., M.C., C.G.)
| | - Manuela Bramerio
- Department of Histopathology, Niguarda Hospital, Milano, Italy (M.B.)
| | - Mattia Di Pasquale
- Institute of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy (L.L., M.D.P., M. Metra)
| | - Aurelia Grosu
- Cardiovascular Department, ASST Papa Giovanni XXIII, Bergamo, Italy (A.G., M. Senni)
| | - Michele Senni
- Cardiovascular Department, ASST Papa Giovanni XXIII, Bergamo, Italy (A.G., M. Senni)
| | - Davide Farina
- Institute of Radiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy (D.F.)
| | - Piergiuseppe Agostoni
- Centro Cardiologico Monzino Istituto di Ricovero e Cura a Carattere Scientificio, Milano, Italy (M. Mapelli, J.C., P.A.).,Department of Clinical Sciences and Community Health, Cardiovascular Section, University of Milano, Italy (M. Mapelli, J.C., P.A.)
| | - Stefania Rizzo
- Cardiovascular Pathology Unit, Azienda Ospedaliera, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, Italy (S. Rizzo, M.D.G., C.B.)
| | - Monica De Gaspari
- Cardiovascular Pathology Unit, Azienda Ospedaliera, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, Italy (S. Rizzo, M.D.G., C.B.)
| | - Francesca Marzo
- Department of Cardiology, Infermi Hospital, Rimini, Italy (F.M.)
| | - Jason M Duran
- Division of Cardiology, Department of Medicine, University of California San Diego (J.M.D., E.D.A.)
| | - Eric D Adler
- Division of Cardiology, Department of Medicine, University of California San Diego (J.M.D., E.D.A.)
| | - Cristina Giannattasio
- De Gasperis Cardio Center and Transplant Center, Niguarda Hospital, Milano, Italy (E.A., M.P., P.P. F.S., M.C., C.G.).,Department of Health Sciences, University of Milano-Bicocca, Monza, Italy (C.G.)
| | - Cristina Basso
- Cardiovascular Pathology Unit, Azienda Ospedaliera, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padua, Italy (S. Rizzo, M.D.G., C.B.)
| | - Theresa McDonagh
- School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre of Excellence, James Black Centre, United Kingdom (A. Cannatà, D.I.B., T.M.).,Department of Cardiology, King's College Hospital London, United Kingdom (A. Cannatà, D.I.B., T.M.)
| | - Mathieu Kerneis
- Sorbonne Université, ACTION Study Group, Institut National de la Santé et de la Recherche Médicale UMRS1166, Institute of CardioMetabolism and Nutrition, Institut de Cardiologie, Hôpital Pitié-Salpêtrière (AP-HP), Paris, France (M.K.)
| | - Alain Combes
- Sorbonne Université, UMRS 1166, Institute of Cardiometabolism and Nutrition, Service de Médecine Intensive-Réanimation, Institut de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, France (M. Schmidt, G.H., A. Combes)
| | - Paolo G Camici
- San Raffaele Hospital and Vita Salute University, Milano, Italy (G.P., S.S., P.G.C.)
| | - James A de Lemos
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas (N.S.H., J.L.G., J.A.d.L.)
| | - Marco Metra
- Institute of Cardiology, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Italy (L.L., M.D.P., M. Metra)
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3
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Xia X, Chen X, Wu G, Li F, Wang Y, Chen Y, Chen M, Wang X, Chen W, Xian B, Chen W, Cao Y, Xu C, Gong W, Chen G, Cai D, Wei W, Yan Y, Liu K, Qiao N, Zhao X, Jia J, Wang W, Kennedy BK, Zhang K, Cannistraci CV, Zhou Y, Han JDJ. Three-dimensional facial-image analysis to predict heterogeneity of the human ageing rate and the impact of lifestyle. Nat Metab 2020; 2:946-957. [PMID: 32895578 DOI: 10.1038/s42255-020-00270-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022]
Abstract
Not all individuals age at the same rate. Methods such as the 'methylation clock' are invasive, rely on expensive assays of tissue samples and infer the ageing rate by training on chronological age, which is used as a reference for prediction errors. Here, we develop models based on convoluted neural networks through training on non-invasive three-dimensional (3D) facial images of approximately 5,000 Han Chinese individuals that achieve an average difference between chronological or perceived age and predicted age of ±2.8 and 2.9 yr, respectively. We further profile blood transcriptomes from 280 individuals and infer the molecular regulators mediating the impact of lifestyle on the facial-ageing rate through a causal-inference model. These relationships have been deposited and visualized in the Human Blood Gene Expression-3D Facial Image (HuB-Fi) database. Overall, we find that humans age at different rates both in the blood and in the face, but do so coherently and with heterogeneity peaking at middle age. Our study provides an example of how artificial intelligence can be leveraged to determine the perceived age of humans as a marker of biological age, while no longer relying on prediction errors of chronological age, and to estimate the heterogeneity of ageing rates within a population.
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Affiliation(s)
- Xian Xia
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xingwei Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gang Wu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yiyang Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yang Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingxu Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Weiyang Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bo Xian
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Weizhong Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chi Xu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wenxuan Gong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoyu Chen
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Donghong Cai
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wenxin Wei
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Yizhen Yan
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kangping Liu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Nan Qiao
- Accenture China Artificial Intelligence Lab, Shenzhen, China
| | - Xiaohui Zhao
- Accenture China Artificial Intelligence Lab, Shenzhen, China
| | - Jin Jia
- Accenture China Artificial Intelligence Lab, Shenzhen, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth, Western Australia, Australia
| | - Brian K Kennedy
- Departments of Biochemistry and Physiology, National University of Singapore, Singapore, Singapore
- Centre for Healthy Ageing, National University Health System, Singapore, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, Singapore, Singapore
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Carlo V Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Cluster of Excellence Physics of Life (PoL), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI) and Department of Bioengineering, Tsinghua University, Beijing, China
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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4
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Gerl MJ, Klose C, Surma MA, Fernandez C, Melander O, Männistö S, Borodulin K, Havulinna AS, Salomaa V, Ikonen E, Cannistraci CV, Simons K. Machine learning of human plasma lipidomes for obesity estimation in a large population cohort. PLoS Biol 2019; 17:e3000443. [PMID: 31626640 PMCID: PMC6799887 DOI: 10.1371/journal.pbio.3000443] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [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: 05/31/2019] [Accepted: 09/04/2019] [Indexed: 01/05/2023] Open
Abstract
Obesity is associated with changes in the plasma lipids. Although simple lipid quantification is routinely used, plasma lipids are rarely investigated at the level of individual molecules. We aimed at predicting different measures of obesity based on the plasma lipidome in a large population cohort using advanced machine learning modeling. A total of 1,061 participants of the FINRISK 2012 population cohort were randomly chosen, and the levels of 183 plasma lipid species were measured in a novel mass spectrometric shotgun approach. Multiple machine intelligence models were trained to predict obesity estimates, i.e., body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR), and body fat percentage (BFP), and validated in 250 randomly chosen participants of the Malmö Diet and Cancer Cardiovascular Cohort (MDC-CC). Comparison of the different models revealed that the lipidome predicted BFP the best (R2 = 0.73), based on a Lasso model. In this model, the strongest positive and the strongest negative predictor were sphingomyelin molecules, which differ by only 1 double bond, implying the involvement of an unknown desaturase in obesity-related aberrations of lipid metabolism. Moreover, we used this regression to probe the clinically relevant information contained in the plasma lipidome and found that the plasma lipidome also contains information about body fat distribution, because WHR (R2 = 0.65) was predicted more accurately than BMI (R2 = 0.47). These modeling results required full resolution of the lipidome to lipid species level, and the predicting set of biomarkers had to be sufficiently large. The power of the lipidomics association was demonstrated by the finding that the addition of routine clinical laboratory variables, e.g., high-density lipoprotein (HDL)- or low-density lipoprotein (LDL)- cholesterol did not improve the model further. Correlation analyses of the individual lipid species, controlled for age and separated by sex, underscores the multiparametric and lipid species-specific nature of the correlation with the BFP. Lipidomic measurements in combination with machine intelligence modeling contain rich information about body fat amount and distribution beyond traditional clinical assays.
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Affiliation(s)
| | | | - Michal A. Surma
- Lipotype GmbH, Dresden, Germany
- Łukasiewicz Research Network—PORT Polish Center for Technology Development, Wroclaw, Poland
| | | | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Emergency and Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Satu Männistö
- Public Health Promotion Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katja Borodulin
- National Institute for Health and Welfare, Helsinki, Finland
| | - Aki S. Havulinna
- National Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland (FIMM-HiLife), Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Elina Ikonen
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland
| | - Carlo V. Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Department of Physics, Technische Universität Dresden, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Complex Network Intelligence Lab, Tsinghua Laboratory of Brain and Intelligence, Tsinghua University, Beijing, China
| | - Kai Simons
- Lipotype GmbH, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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5
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Onesto V, Villani M, Narducci R, Malara N, Imbrogno A, Allione M, Costa N, Coppedè N, Zappettini A, Cannistraci CV, Cancedda L, Amato F, Di Fabrizio E, Gentile F. Cortical-like mini-columns of neuronal cells on zinc oxide nanowire surfaces. Sci Rep 2019; 9:4021. [PMID: 30858456 PMCID: PMC6411964 DOI: 10.1038/s41598-019-40548-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 10/26/2018] [Accepted: 02/18/2019] [Indexed: 11/25/2022] Open
Abstract
A long-standing goal of neuroscience is a theory that explains the formation of the minicolumns in the cerebral cortex. Minicolumns are the elementary computational units of the mature neocortex. Here, we use zinc oxide nanowires with controlled topography as substrates for neural-cell growth. We observe that neuronal cells form networks where the networks characteristics exhibit a high sensitivity to the topography of the nanowires. For certain values of nanowires density and fractal dimension, neuronal networks express small world attributes, with enhanced information flows. We observe that neurons in these networks congregate in superclusters of approximately 200 neurons. We demonstrate that this number is not coincidental: the maximum number of cells in a supercluster is limited by the competition between the binding energy between cells, adhesion to the substrate, and the kinetic energy of the system. Since cortical minicolumns have similar size, similar anatomical and topological characteristics of neuronal superclusters on nanowires surfaces, we conjecture that the formation of cortical minicolumns is likewise guided by the interplay between energy minimization, information optimization and topology. For the first time, we provide a clear account of the mechanisms of formation of the minicolumns in the brain.
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Affiliation(s)
- V Onesto
- Center for Advanced Biomaterials for HealthCare, Istituto Italiano di Tecnologia, 80125, Naples, Italy.,Department of Experimental and Clinical Medicine, University of Magna Graecia, 88100, Catanzaro, Italy
| | - M Villani
- IMEM-CNR Parco Area delle Scienze 37/A, 43124, Parma, Italy
| | - R Narducci
- Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - N Malara
- Department of Experimental and Clinical Medicine, University of Magna Graecia, 88100, Catanzaro, Italy
| | - A Imbrogno
- Tyndall National Institute, Cork, T12 R5CP, Ireland
| | - M Allione
- PSE division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - N Costa
- Health Department, University of Magna Graecia, 88100, Catanzaro, Italy
| | - N Coppedè
- IMEM-CNR Parco Area delle Scienze 37/A, 43124, Parma, Italy
| | - A Zappettini
- IMEM-CNR Parco Area delle Scienze 37/A, 43124, Parma, Italy
| | - C V Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, 98124, Italy
| | - L Cancedda
- Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.,Dulbecco Telethon Institute, Rome, Italy
| | - F Amato
- Department of Electrical Engineering and Information Technology, University Federico II, Naples, Italy
| | - Enzo Di Fabrizio
- PSE division, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - F Gentile
- Department of Electrical Engineering and Information Technology, University Federico II, Naples, Italy.
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6
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Miendlarzewska EA, Ciucci S, Cannistraci CV, Bavelier D, Schwartz S. Reward-enhanced encoding improves relearning of forgotten associations. Sci Rep 2018; 8:8557. [PMID: 29867116 PMCID: PMC5986818 DOI: 10.1038/s41598-018-26929-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 09/05/2017] [Accepted: 05/18/2018] [Indexed: 12/16/2022] Open
Abstract
Research on human memory has shown that monetary incentives can enhance hippocampal memory consolidation and thereby protect memory traces from forgetting. However, it is not known whether initial reward may facilitate the recovery of already forgotten memories weeks after learning. Here, we investigated the influence of monetary reward on later relearning. Nineteen healthy human participants learned object-location associations, for half of which we offered money. Six weeks later, most of these associations had been forgotten as measured by a test of declarative memory. Yet, relearning in the absence of any reward was faster for the originally rewarded associations. Thus, associative memories encoded in a state of monetary reward motivation may persist in a latent form despite the failure to retrieve them explicitly. Alternatively, such facilitation could be analogous to the renewal effect observed in animal conditioning, whereby a reward-associated cue can reinstate anticipatory arousal, which would in turn modulate relearning. This finding has important implications for learning and education, suggesting that even when learned information is no longer accessible via explicit retrieval, the enduring effects of a past prospect of reward could facilitate its recovery.
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Affiliation(s)
- Ewa A Miendlarzewska
- Department of Neuroscience, University of Geneva, Geneva, Switzerland. .,Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland. .,Geneva Finance Research Institute, University of Geneva, Geneva, Switzerland.
| | - Sara Ciucci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Lipotype GmbH, Tatzberg 47, 01307, Dresden, Germany
| | - Carlo V Cannistraci
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.,Brain Bio-Inspired Computing (BBC) Lab, IRCCS Centro Neurolesi "Bonino Pulejo", Messina, 98124, Italy
| | - Daphne Bavelier
- Psychology Section, FPSE, University of Geneva, Geneva, Switzerland.,Brain & Cognitive Sciences, University of Rochester, Rochester, NY, United States
| | - Sophie Schwartz
- Department of Neuroscience, University of Geneva, Geneva, Switzerland. .,Swiss Center for Affective Sciences, University of Geneva, Geneva, Switzerland. .,Geneva Neuroscience Center, University of Geneva, Geneva, Switzerland.
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7
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Mavromatis CH, Bokil NJ, Totsika M, Kakkanat A, Schaale K, Cannistraci CV, Ryu T, Beatson SA, Ulett GC, Schembri MA, Sweet MJ, Ravasi T. The co-transcriptome of uropathogenic Escherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions. Cell Microbiol 2015; 17:730-46. [PMID: 25410299 PMCID: PMC4950338 DOI: 10.1111/cmi.12397] [Citation(s) in RCA: 54] [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: 08/31/2014] [Revised: 11/01/2014] [Accepted: 11/11/2014] [Indexed: 12/26/2022]
Abstract
Urinary tract infections (UTI) are among the most common infections in humans. Uropathogenic Escherichia coli (UPEC) can invade and replicate within bladder epithelial cells, and some UPEC strains can also survive within macrophages. To understand the UPEC transcriptional programme associated with intramacrophage survival, we performed host–pathogen co‐transcriptome analyses using RNA sequencing. Mouse bone marrow‐derived macrophages (BMMs) were challenged over a 24 h time course with two UPEC reference strains that possess contrasting intramacrophage phenotypes: UTI89, which survives in BMMs, and 83972, which is killed by BMMs. Neither of these strains caused significant BMM cell death at the low multiplicity of infection that was used in this study. We developed an effective computational framework that simultaneously separated, annotated and quantified the mammalian and bacterial transcriptomes. Bone marrow‐derived macrophages responded to the two UPEC strains with a broadly similar gene expression programme. In contrast, the transcriptional responses of the UPEC strains diverged markedly from each other. We identified UTI89 genes up‐regulated at 24 h post‐infection, and hypothesized that some may contribute to intramacrophage survival. Indeed, we showed that deletion of one such gene (pspA) significantly reduced UTI89 survival within BMMs. Our study provides a technological framework for simultaneously capturing global changes at the transcriptional level in co‐cultures, and has generated new insights into the mechanisms that UPEC use to persist within the intramacrophage environment.
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Affiliation(s)
- Charalampos Harris Mavromatis
- Division of Biological and Environmental Sciences and Engineering, Division of Computer, Electrical and Mathematical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia; Division of Medical Genetics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, USA
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8
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Bayer K, Moitinho-Silva L, Brümmer F, Cannistraci CV, Ravasi T, Hentschel U. GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater. FEMS Microbiol Ecol 2014; 90:832-43. [PMID: 25318900 DOI: 10.1111/1574-6941.12441] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 07/16/2014] [Revised: 09/30/2014] [Accepted: 10/06/2014] [Indexed: 12/12/2022] Open
Abstract
The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.
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Affiliation(s)
- Kristina Bayer
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany
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9
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Conti A, Riva N, Pesca M, Iannaccone S, Cannistraci CV, Corbo M, Previtali SC, Quattrini A, Alessio M. Increased expression of Myosin binding protein H in the skeletal muscle of amyotrophic lateral sclerosis patients. Biochim Biophys Acta Mol Basis Dis 2014; 1842:99-106. [DOI: 10.1016/j.bbadis.2013.10.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 10/18/2013] [Accepted: 10/24/2013] [Indexed: 12/31/2022]
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10
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Moitinho-Silva L, Bayer K, Cannistraci CV, Giles EC, Ryu T, Seridi L, Ravasi T, Hentschel U. Specificity and transcriptional activity of microbiota associated with low and high microbial abundance sponges from the Red Sea. Mol Ecol 2013; 23:1348-1363. [DOI: 10.1111/mec.12365] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/16/2013] [Accepted: 04/18/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas Moitinho-Silva
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germany
| | - Kristina Bayer
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germany
| | - Carlo V. Cannistraci
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Emily C. Giles
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Taewoo Ryu
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Loqmane Seridi
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Timothy Ravasi
- Division of Biological and Environmental Sciences & Engineering and Division of Applied Mathematics and Computer Science; Computational Biosciences Research Center; King Abdullah University of Science and Technology; Thuwal 23955-6900 Kingdom of Saudi Arabia
| | - Ute Hentschel
- Department of Botany II; Julius-von-Sachs Institute for Biological Sciences; University of Wuerzburg; Julius-von-Sachs Platz 3 97082 Wuerzburg Germany
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11
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Ammirati E, Maseri A, Cannistraci CV. Still Need for Compelling Evidence to Support the Circadian Dependence of Infarct Size After ST-Elevation Myocardial Infarction. Circ Res 2013; 113:e43-4. [DOI: 10.1161/circresaha.113.301908] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Enrico Ammirati
- Cardiovascular Department, San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy
| | | | - Carlo V. Cannistraci
- Computational Bioscience Research Center, King Abdullah University for Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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12
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Ammirati E, Cristell N, Cianflone D, Vermi AC, Marenzi G, De Metrio M, Uren NG, Hu D, Ravasi T, Maseri A, Cannistraci CV. Questing for Circadian Dependence in ST-Segment–Elevation Acute Myocardial Infarction. Circ Res 2013; 112:e110-4. [DOI: 10.1161/circresaha.112.300778] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Rationale:
Four monocentric studies reported that circadian rhythms can affect left ventricular infarct size after ST-segment–elevation acute myocardial infarction (STEMI).
Objective:
To further validate the circadian dependence of infarct size after STEMI in a multicentric and multiethnic population.
Methods and Results:
We analyzed a prospective cohort of subjects with first STEMI from the First Acute Myocardial Infarction study that enrolled 1099 patients (ischemic time <6 hours) in Italy, Scotland, and China. We confirmed a circadian variation of STEMI incidence with an increased morning incidence (from 6:00 am till noon). We investigated the presence of circadian dependence of infarct size plotting the peak creatine kinase against time onset of ischemia. In addition, we studied the patients from the 3 countries separately, including 624 Italians; all patients were treated with percutaneous coronary intervention. We adopted several levels of analysis with different inclusion criteria consistent with previous studies. In all the analyses, we did not find a clear-cut circadian dependence of infarct size after STEMI.
Conclusions:
Although the circadian dependence of infarct size supported by previous studies poses an intriguing hypothesis, we were unable to converge toward their conclusions in a multicentric and multiethnic setting. Parameters that vary as a function of latitude could potentially obscure the circadian variations observed in monocentric studies. We believe that, to assess whether circadian rhythms can affect the infarct size, future study design should not only include larger samples but also aim to untangle the molecular time–dynamic mechanisms underlying such a relation.
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Affiliation(s)
- Enrico Ammirati
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Nicole Cristell
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Domenico Cianflone
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Anna-Chiara Vermi
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Giancarlo Marenzi
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Monica De Metrio
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Neal G. Uren
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Dayi Hu
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Timothy Ravasi
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Attilio Maseri
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
| | - Carlo V. Cannistraci
- From the San Raffaele Scientific Institute and Vita-Salute University, Milan, Italy (E.A., N.C., D.C., A.C.V.); Heart Transplantation Division, Azienda Ospedaliera Ospedale Niguarda Ca' Granda, Milan, Italy (E.A.); Heart Care Foundation, Florence, Italy (A.M.); Centro Cardiologico Monzino, IRCCS and University of Milan, Milan, Italy (G.M., M.D.M.); Department of Cardiology, Royal Infirmary of Edinburgh, United Kingdom (N.G.U.); The Heart Center, People’s Hospital of Peking University, Beijing, China
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13
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Miendlarzewska EA, van Elswijk G, Cannistraci CV, van Ee R. Working memory load attenuates emotional enhancement in recognition memory. Front Psychol 2013; 4:112. [PMID: 23515565 PMCID: PMC3600573 DOI: 10.3389/fpsyg.2013.00112] [Citation(s) in RCA: 17] [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: 10/29/2012] [Accepted: 02/20/2013] [Indexed: 11/13/2022] Open
Abstract
Emotionally arousing stimuli are perceived and remembered better than neutral stimuli. Under threat, this negativity bias is further increased. We investigated whether working memory (WM) load can attenuate incidental memory for emotional images. Two groups of participants performed the N-back task with two WM load levels. In one group, we induced anxiety using a threat of shock paradigm to increase attentional processing of negative information. During task performance we incidentally and briefly flashed emotional distracter images which prolonged response times in both load conditions. A subsequent unannounced immediate recognition memory test revealed that when load at exposure had been low, recognition was better for negative items in both participant groups. This enhancement, however, was attenuated under high load, leaving performance on neutral items unchanged regardless of the threat of shock manipulation. We conclude that both in threat and in normal states WM load at exposure can attenuate immediate emotional memory enhancement.
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Affiliation(s)
- Ewa A Miendlarzewska
- Department of Fundamental Neurosciences, Centre Médical Universitaire, University of Geneva Geneva, Switzerland
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14
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Cannistraci CV, Ogorevc J, Zorc M, Ravasi T, Dovc P, Kunej T. Pivotal role of the muscle-contraction pathway in cryptorchidism and evidence for genomic connections with cardiomyopathy pathways in RASopathies. BMC Med Genomics 2013; 6:5. [PMID: 23410028 PMCID: PMC3626861 DOI: 10.1186/1755-8794-6-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 02/14/2012] [Accepted: 02/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryptorchidism is the most frequent congenital disorder in male children; however the genetic causes of cryptorchidism remain poorly investigated. Comparative integratomics combined with systems biology approach was employed to elucidate genetic factors and molecular pathways underlying testis descent. METHODS Literature mining was performed to collect genomic loci associated with cryptorchidism in seven mammalian species. Information regarding the collected candidate genes was stored in MySQL relational database. Genomic view of the loci was presented using Flash GViewer web tool (http://gmod.org/wiki/Flashgviewer/). DAVID Bioinformatics Resources 6.7 was used for pathway enrichment analysis. Cytoscape plug-in PiNGO 1.11 was employed for protein-network-based prediction of novel candidate genes. Relevant protein-protein interactions were confirmed and visualized using the STRING database (version 9.0). RESULTS The developed cryptorchidism gene atlas includes 217 candidate loci (genes, regions involved in chromosomal mutations, and copy number variations) identified at the genomic, transcriptomic, and proteomic level. Human orthologs of the collected candidate loci were presented using a genomic map viewer. The cryptorchidism gene atlas is freely available online: http://www.integratomics-time.com/cryptorchidism/. Pathway analysis suggested the presence of twelve enriched pathways associated with the list of 179 literature-derived candidate genes. Additionally, a list of 43 network-predicted novel candidate genes was significantly associated with four enriched pathways. Joint pathway analysis of the collected and predicted candidate genes revealed the pivotal importance of the muscle-contraction pathway in cryptorchidism and evidence for genomic associations with cardiomyopathy pathways in RASopathies. CONCLUSIONS The developed gene atlas represents an important resource for the scientific community researching genetics of cryptorchidism. The collected data will further facilitate development of novel genetic markers and could be of interest for functional studies in animals and human. The proposed network-based systems biology approach elucidates molecular mechanisms underlying co-presence of cryptorchidism and cardiomyopathy in RASopathies. Such approach could also aid in molecular explanation of co-presence of diverse and apparently unrelated clinical manifestations in other syndromes.
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Affiliation(s)
- Carlo V Cannistraci
- Integrative Systems Biology Laboratory, Biological and Environmental Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University for Science and Technology, Thuwal, Saudi Arabia.
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15
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Ammirati E, Cannistraci CV, Cristell NA, Vecchio V, Palini AG, Tornvall P, Paganoni AM, Miendlarzewska EA, Sangalli LM, Monello A, Pernow J, Björnstedt Bennermo M, Marenzi G, Hu D, Uren NG, Cianflone D, Ravasi T, Manfredi AA, Maseri A. Identification and Predictive Value of Interleukin-6
+
Interleukin-10
+
and Interleukin-6
−
Interleukin-10
+
Cytokine Patterns in ST-Elevation Acute Myocardial Infarction. Circ Res 2012; 111:1336-48. [DOI: 10.1161/circresaha.111.262477] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Rationale:
At the onset of ST-elevation acute myocardial infarction (STEMI), patients can present with very high circulating interleukin-6 (IL-6
+
) levels or very low-IL-6
–
levels.
Objective:
We compared these 2 groups of patients to understand whether it is possible to define specific STEMI phenotypes associated with outcome based on the cytokine response.
Methods and Results:
We compared 109 patients with STEMI in the top IL-6 level (median, 15.6 pg/mL; IL-6
+
STEMI) with 96 in the bottom IL-6 level (median, 1.7 pg/mL; IL-6
−
STEMI) and 103 matched controls extracted from the multiethnic First Acute Myocardial Infarction study. We found minimal clinical differences between IL-6
+
STEMI and IL-6
−
STEMI. We assessed the inflammatory profiles of the 2 STEMI groups and the controls by measuring 18 cytokines in blood samples. We exploited clustering analysis algorithms to infer the functional modules of interacting cytokines. IL-6
+
STEMI patients were characterized by the activation of 2 modules of interacting signals comprising IL-10, IL-8, macrophage inflammatory protein-1α, and C-reactive protein, and monocyte chemoattractant protein-1, macrophage inflammatory protein-1β, and monokine induced by interferon-γ. IL-10 was increased both in IL-6
+
STEMI and IL-6
−
STEMI patients compared with controls. IL-6
+
IL-10
+
STEMI patients had an increased risk of systolic dysfunction at discharge and an increased risk of death at 6 months in comparison with IL-6
−
IL-10
+
STEMI patients. We combined IL-10 and monokine induced by interferon-γ (derived from the 2 identified cytokine modules) with IL-6 in a formula yielding a risk index that outperformed any single cytokine in the prediction of systolic dysfunction and death.
Conclusions:
We have identified a characteristic circulating inflammatory cytokine pattern in STEMI patients, which is not related to the extent of myocardial damage. The simultaneous elevation of IL-6 and IL-10 levels distinguishes STEMI patients with worse clinical outcomes from other STEMI patients. These observations could have potential implications for risk-oriented patient stratification and immune-modulating therapies.
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Affiliation(s)
- Enrico Ammirati
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Carlo V. Cannistraci
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Nicole A. Cristell
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Viviana Vecchio
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Alessio G. Palini
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Per Tornvall
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Anna M. Paganoni
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Ewa A. Miendlarzewska
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Laura M. Sangalli
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Alberto Monello
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - John Pernow
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Marie Björnstedt Bennermo
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Giancarlo Marenzi
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Dayi Hu
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Neal G. Uren
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Domenico Cianflone
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Timothy Ravasi
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Angelo A. Manfredi
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
| | - Attilio Maseri
- From the Clinical Cardiovascular Biology Centre (E.A., N.A.C., A.M., D.C.), Proteome Biochemistry Unit (C.V.C.), Flow Cytometry Resource Analytical Cytology Technical Applications Laboratory (V.V., A.G.P.), and Autoimmunity and Vascular Inflammation Unit (A.A.M.), San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy; MOX, Politecnico di Milano, Milan, Italy (A.M.P., L.M.S.); Department of Cardiovascular Sciences, Centro Cardiologico Monzino, IRCCS University of Milan,
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16
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Fanucchi F, Alpi E, Olivieri S, Cannistraci CV, Bachi A, Alpi A, Alessio M. Acclimation increases freezing stress response of Arabidopsis thaliana at proteome level. Biochim Biophys Acta 2012; 1824:813-25. [PMID: 22510494 DOI: 10.1016/j.bbapap.2012.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 03/28/2012] [Accepted: 03/30/2012] [Indexed: 12/28/2022]
Abstract
This study used 2DE to investigate how Arabidopsis thaliana modulates protein levels in response to freezing stress after sub-lethal exposure at -10°C, both in cold-acclimated and in non-acclimated plants. A map was implemented in which 62 spots, corresponding to 44 proteins, were identified. Twenty-two spots were modulated upon treatments, and the corresponding proteins proved to be related to photosynthesis, energy metabolism, and stress response. Proteins demonstrated differences between control and acclimation conditions. Most of the acclimation-responsive proteins were either not further modulated or they were down-modulated by freezing treatment, indicating that the levels reached during acclimation were sufficient to deal with freezing. Anabolic metabolism appeared to be down-regulated in favor of catabolic metabolism. Acclimated plants and plants submitted to freezing after acclimation showed greater reciprocal similarity in protein profiles than either showed when compared both to control plants and to plants frozen without acclimation. The response of non-acclimated plants was aimed at re-modulating photosynthetic apparatus activity, and at increasing the levels of proteins with antioxidant-, molecular chaperone-, or post-transcriptional regulative functions. These changes, even less effective than the acclimation strategy, might allow the injured plastids to minimize the production of non-useful metabolites and might counteract photosynthetic apparatus injuries.
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17
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Cannistraci CV, Montevecchi FM, Alessio M. Median-modified Wiener filter provides efficient denoising, preserving spot edge and morphology in 2-DE image processing. Proteomics 2009; 9:4908-19. [PMID: 19862762 DOI: 10.1002/pmic.200800538] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Denoising is a fundamental early stage in 2-DE image analysis strongly influencing spot detection or pixel-based methods. A novel nonlinear adaptive spatial filter (median-modified Wiener filter, MMWF), is here compared with five well-established denoising techniques (Median, Wiener, Gaussian, and Polynomial-Savitzky-Golay filters; wavelet denoising) to suggest, by means of fuzzy sets evaluation, the best denoising approach to use in practice. Although median filter and wavelet achieved the best performance in spike and Gaussian denoising respectively, they are unsuitable for contemporary removal of different types of noise, because their best setting is noise-dependent. Vice versa, MMWF that arrived second in each single denoising category, was evaluated as the best filter for global denoising, being its best setting invariant of the type of noise. In addition, median filter eroded the edge of isolated spots and filled the space between close-set spots, whereas MMWF because of a novel filter effect (drop-off-effect) does not suffer from erosion problem, preserves the morphology of close-set spots, and avoids spot and spike fuzzyfication, an aberration encountered for Wiener filter. In our tests, MMWF was assessed as the best choice when the goal is to minimize spot edge aberrations while removing spike and Gaussian noise.
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Corti V, Sanchez-Ruiz Y, Piccoli G, Bergamaschi A, Cannistraci CV, Pattini L, Cerutti S, Bachi A, Alessio M, Malgaroli A. Protein fingerprints of cultured CA3-CA1 hippocampal neurons: comparative analysis of the distribution of synaptosomal and cytosolic proteins. BMC Neurosci 2008; 9:36. [PMID: 18402664 PMCID: PMC2324106 DOI: 10.1186/1471-2202-9-36] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [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: 02/01/2008] [Accepted: 04/10/2008] [Indexed: 11/21/2022] Open
Abstract
Background All studies aimed at understanding complex molecular changes occurring at synapses face the problem of how a complete view of the synaptic proteome and of its changes can be efficiently met. This is highly desirable when synaptic plasticity processes are analyzed since the structure and the biochemistry of neurons and synapses get completely reshaped. Because most molecular studies of synapses are nowadays mainly or at least in part based on protein extracts from neuronal cultures, this is not a feasible option: these simplified versions of the brain tissue on one hand provide an homogeneous pure population of neurons but on the other yield only tiny amounts of proteins, many orders of magnitude smaller than conventional brain tissue. As a way to overcome this limitation and to find a simple way to screen for protein changes at cultured synapses, we have produced and characterized two dimensional electrophoresis (2DE) maps of the synaptic proteome of CA3-CA1 hippocampal neurons in culture. Results To obtain 2D maps, hippocampal cultures were mass produced and after synaptic maturation, proteins were extracted following subfractionation procedures and separated by 2D gel electrophoresis. Similar maps were obtained for the crude cytosol of cultured neurons and for synaptosomes purified from CA3-CA1 hippocampal tissue. To efficiently compare these different maps some clearly identifiable reference points were molecularly identified by mass spectrometry and immunolabeling methods. This information was used to run a differential analysis and establish homologies and dissimilarities in these 2D protein profiles. Conclusion Because reproducible fingerprints of cultured synapses were clearly obtained, we believe that our mapping effort could represent a simple tool to screen for protein expression and/or protein localization changes in CA3-CA1 hippocampal neurons following plasticity.
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Affiliation(s)
- Valeria Corti
- Proteome Biochemistry, San Raffaele Scientific Institute, Milan, Italy.
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