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Kaneko T, Ezra S, Abdo R, Voss C, Zhong S, Liu X, Hovey O, Slessarev M, Van Nynatten LR, Ye M, Fraser DD, Li SSC. Kinome and phosphoproteome reprogramming underlies the aberrant immune responses in critically ill COVID-19 patients. Clin Proteomics 2024; 21:13. [PMID: 38389037 PMCID: PMC10882830 DOI: 10.1186/s12014-024-09457-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
SARS-CoV-2 infection triggers extensive host immune reactions, leading to severe diseases in certain individuals. However, the molecular basis underlying the excessive yet non-productive immune responses in severe COVID-19 remains incompletely understood. In this study, we conducted a comprehensive analysis of the peripheral blood mononuclear cell (PBMC) proteome and phosphoproteome in sepsis patients positive or negative for SARS-CoV-2 infection, as well as healthy subjects, using quantitative mass spectrometry. Our findings demonstrate dynamic changes in the COVID-19 PBMC proteome and phosphoproteome during disease progression, with distinctive protein or phosphoprotein signatures capable of distinguishing longitudinal disease states. Furthermore, SARS-CoV-2 infection induces a global reprogramming of the kinome and phosphoproteome, resulting in defective adaptive immune response mediated by the B and T lymphocytes, compromised innate immune responses involving the SIGLEC and SLAM family of immunoreceptors, and excessive cytokine-JAK-STAT signaling. In addition to uncovering host proteome and phosphoproteome aberrations caused by SARS-CoV-2, our work recapitulates several reported therapeutic targets for COVID-19 and identified numerous new candidates, including the kinases PKG1, CK2, ROCK1/2, GRK2, SYK, JAK2/3, TYK2, DNA-PK, PKCδ, and the cytokine IL-12.
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Affiliation(s)
- Tomonori Kaneko
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Sally Ezra
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Rober Abdo
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Courtney Voss
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Shanshan Zhong
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Xuguang Liu
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Owen Hovey
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada
| | - Marat Slessarev
- Departments of Medicine and Pediatrics, Western University, London, Canada
| | | | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Douglas D Fraser
- Departments of Medicine and Pediatrics, Western University, London, Canada
- Lawson Health Research Institute, 750 Base Line Rd E, London, ON, N6C 2R5, Canada
| | - Shawn Shun-Cheng Li
- Departments of Biochemistry, Western University, London, ON, N6A 5C1, Canada.
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Mazzaccara C, Lombardi R, Mirra B, Barretta F, Esposito MV, Uomo F, Caiazza M, Monda E, Losi MA, Limongelli G, D’Argenio V, Frisso G. Next-Generation Sequencing Gene Panels in Inheritable Cardiomyopathies and Channelopathies: Prevalence of Pathogenic Variants and Variants of Unknown Significance in Uncommon Genes. Biomolecules 2022; 12:1417. [PMID: 36291626 PMCID: PMC9599286 DOI: 10.3390/biom12101417] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 08/17/2023] Open
Abstract
The diffusion of next-generation sequencing (NGS)-based approaches allows for the identification of pathogenic mutations of cardiomyopathies and channelopathies in more than 200 different genes. Since genes considered uncommon for a clinical phenotype are also now included in molecular testing, the detection rate of disease-causing variants has increased. Here, we report the prevalence of genetic variants detected by using a NGS custom panel in a cohort of 133 patients with inherited cardiomyopathies (n = 77) or channelopathies (n = 56). We identified 82 variants, of which 50 (61%) were identified in genes without a strong or definitive evidence of disease association according to the NIH-funded Clinical Genome Resource (ClinGen; "uncommon genes"). Among these, 35 (70%) were variants of unknown significance (VUSs), 13 (26%) were pathogenic (P) or likely pathogenic (LP) mutations, and 2 (4%) benign (B) or likely benign (LB) variants according to American College of Medical Genetics (ACMG) classifications. These data reinforce the need for the screening of uncommon genes in order to increase the diagnostic sensitivity of the genetic testing of inherited cardiomyopathies and channelopathies by allowing for the identification of mutations in genes that are not usually explored due to a currently poor association with the clinical phenotype.
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Affiliation(s)
- Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
| | - Raffaella Lombardi
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131 Napoli, Italy
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bruno Mirra
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
| | - Ferdinando Barretta
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
| | | | - Fabiana Uomo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
| | - Martina Caiazza
- Monaldi Hospital, AO Colli, 80131 Napoli, Italy
- Department of Translational Medical Sciences, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy
| | - Emanuele Monda
- Monaldi Hospital, AO Colli, 80131 Napoli, Italy
- Department of Translational Medical Sciences, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy
| | - Maria Angela Losi
- Department of Advanced Biomedical Sciences, University of Naples Federico II, 80131 Napoli, Italy
| | - Giuseppe Limongelli
- Monaldi Hospital, AO Colli, 80131 Napoli, Italy
- Department of Translational Medical Sciences, University of Campania ‘Luigi Vanvitelli’, 81100 Caserta, Italy
| | - Valeria D’Argenio
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, 00166 Roma, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, 80131 Napoli, Italy
- CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy
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Borch JDS, Krag T, Holm-Yildiz SD, Cetin H, Solheim TA, Fornander F, Straub V, Duno M, Vissing J. Three novel FHL1 Variants cause a mild Phenotype of Emery-Dreifuss Muscular Dystrophy. Hum Mutat 2022; 43:1234-1238. [PMID: 35607917 PMCID: PMC9545859 DOI: 10.1002/humu.24415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/14/2022] [Accepted: 05/22/2022] [Indexed: 11/11/2022]
Abstract
Emery-Dreifuss muscular dystrophy (EDMD) is a hereditary muscle disease, characterized by the clinical triade of early-onset joint contractures, progressive muscle weakness and cardiac involvement. Pathogenic variants in FHL1 can cause a rare X-linked recessive form of EDMD, type 6. We report three men with novel variants in FHL1 leading to EDMD6. Onset of muscle symptoms was in late adulthood and muscle weakness was not prominent in either of the patients. All patients had hypertrophic cardiomyopathy and one of them also had cardiac arrhythmias. Western blot performed on muscle biopsies from two of the patients showed no FHL1 protein expression. We predict that the variant in the third patient also leads to absence of FHL1 protein. Complete loss of all FHL1 isoforms combined with mild muscle involvement supports the hypothesis that loss of all FHL1 isoforms is more benign than the cytotoxic effects of expressed FHL1 protein with pathogenic missense variants. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Josefine D S Borch
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark
| | - Thomas Krag
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark
| | - Sonja D Holm-Yildiz
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Austria
| | - Tuva A Solheim
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark
| | - Freja Fornander
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 3BZ, UK
| | - Morten Duno
- Department of Clinical Genetics, section 4062, Rigshospitalet, University of Copenhagen, Denmark
| | - John Vissing
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Denmark
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Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
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Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
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Micheu MM, Popa-Fotea NM, Oprescu N, Bogdan S, Dan M, Deaconu A, Dorobantu L, Gheorghe-Fronea O, Greavu M, Iorgulescu C, Scafa-Udriste A, Ticulescu R, Vatasescu RG, Dorobanțu M. Yield of Rare Variants Detected by Targeted Next-Generation Sequencing in a Cohort of Romanian Index Patients with Hypertrophic Cardiomyopathy. Diagnostics (Basel) 2020; 10:diagnostics10121061. [PMID: 33297573 PMCID: PMC7762332 DOI: 10.3390/diagnostics10121061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022] Open
Abstract
Background: The aim of this study was to explore the rare variants in a cohort of Romanian index cases with hypertrophic cardiomyopathy (HCM). Methods: Forty-five unrelated probands with HCM were screened by targeted next generation sequencing (NGS) of 47 core and emerging genes connected with HCM. Results: We identified 95 variants with allele frequency < 0.1% in population databases. MYBPC3 and TTN had the largest number of rare variants (17 variants each). A definite genetic etiology was found in 6 probands (13.3%), while inconclusive results due to either known or novel variants were established in 31 cases (68.9%). All disease-causing variants were detected in sarcomeric genes (MYBPC3 and MYH7 with two cases each, and one case in TNNI3 and TPM1 respectively). Multiple variants were detected in 27 subjects (60%), but no proband carried more than one causal variant. Of note, almost half of the rare variants were novel. Conclusions: Herein we reported for the first time the rare variants identified in core and putative genes associated with HCM in a cohort of Romanian unrelated adult patients. The clinical significance of most detected variants is yet to be established, additional studies based on segregation analysis being required for definite classification.
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Affiliation(s)
- Miruna Mihaela Micheu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Correspondence: (M.M.M.); (N.-M.P.-F.); Tel.: +4-072-245-1755 (M.M.M.); Tel: +4-072-438-1835 (N.-M.P.-F.)
| | - Nicoleta-Monica Popa-Fotea
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
- Correspondence: (M.M.M.); (N.-M.P.-F.); Tel.: +4-072-245-1755 (M.M.M.); Tel: +4-072-438-1835 (N.-M.P.-F.)
| | - Nicoleta Oprescu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
| | - Stefan Bogdan
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Monica Dan
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
| | - Alexandru Deaconu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Lucian Dorobantu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Monza Hospital, Tony Bulandra Street, No. 27, 021967 Bucharest, Romania; (M.G.); (R.T.)
| | - Oana Gheorghe-Fronea
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Maria Greavu
- Monza Hospital, Tony Bulandra Street, No. 27, 021967 Bucharest, Romania; (M.G.); (R.T.)
| | - Corneliu Iorgulescu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
| | - Alexandru Scafa-Udriste
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Razvan Ticulescu
- Monza Hospital, Tony Bulandra Street, No. 27, 021967 Bucharest, Romania; (M.G.); (R.T.)
| | - Radu Gabriel Vatasescu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
| | - Maria Dorobanțu
- Department of Cardiology, Clinical Emergency Hospital of Bucharest, Calea Floreasca 8, 014461 Bucharest, Romania; (N.O.); (S.B.); (M.D.); (A.D.); (L.D.); (O.G.-F.); (C.I.); (A.S.-U.); (R.G.V.); (M.D.)
- Department 4-Cardiothoracic Pathology, University of Medicine and Pharmacy Carol Davila, Eroii Sanitari Bvd. 8, 050474 Bucharest, Romania
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