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Song S, Zeng L, Xu J, Shi L, Lu L, Ling Y, Zhang L. Proteomic lung analysis revealed hyper-activation of neutrophil extracellular trap formation in cases of fatal COVID-19. Heliyon 2024; 10:e31878. [PMID: 38882332 PMCID: PMC11177151 DOI: 10.1016/j.heliyon.2024.e31878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024] Open
Abstract
The molecular pathology of lung injury in patients with Corona Virus Disease 2019 (COVID-19) remain unclear. In this study, we performed a proteomic study of lung tissues from seven patients with COVID-19, and eight without. Lung parenchymal tissues with COVID-19 were obtained from autopsy samples, while control samples were obtained from paracancerous tissues. Proteins were extracted using phenol extraction. A tandem mass tag-based quantitative proteomic approach combined with bioinformatic analysis was used to detect proteomic changes in the SARS-CoV-2-infected lung tissues. A total of 6,602, and 6,549 proteins were identified in replicates 1 and 2, respectively. Of these, 307, and 278, respectively, were identified as differentially expressed proteins (DEPs). In total, 216 DEPs were identified in this study. These proteins were enriched in 189 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The downregulated proteins are mainly involved in focal adhesion (n = 5), and the PI3K-Akt signaling pathway (n = 4). The upregulated proteins were related to neutrophil extracellular trap (NET) formation (n = 16), and the phagosome pathway (n = 11). The upregulated proteins in these two pathways interact with one another. Further immunohistochemistry verified NET enrichment in the tissues with COVID-19 compared to the controls. Our results systematically outlined the proteomic profiles of the lung's response to SARS-CoV-2 infection and indicated that NET formation was hyper-activated. These results will hopefully provide new evidence for understanding the mechanism behind fatal COVID-19.
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Affiliation(s)
- Shu Song
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Liyan Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Jingjing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lei Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lingqing Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Yun Ling
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
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2
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Weber L, Torres A, Realini O, Bendek MJ, Mizgier ML, Brizuela C, Herrera D, González FE, Chaparro A. Proteomic Analysis of Salivary Extracellular Vesicles from COVID-19 Patients Reveals a Specific Anti-COVID-19 Response Protein Signature. Int J Mol Sci 2024; 25:3704. [PMID: 38612515 PMCID: PMC11011897 DOI: 10.3390/ijms25073704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
Despite the understanding of the coronavirus disease-19 (COVID-19), the role of salivary extracellular vesicles (sEVs) in COVID-19 remains unclear. Exploring the proteomic cargo of sEVs could prove valuable for diagnostic and prognostic purposes in assessing COVID-19. The proteomic cargo of sEVs from COVID-19(+) subjects and their healthy close contacts (HCC) was explored. sEVs were isolated by ultracentrifugation from unstimulated saliva samples, and subsequently characterized through nanoparticle tracking, transmission electron microscopy, and Western blot analyses. The proteomic cargo of sEVs was processed by LC-MS/MS. sEVs were morphologically compatible with EVs, with the presence of Syntenin-1 and CD81 EV markers. The sEV pellet showed 1417 proteins: 1288 in COVID-19(+) cases and 1382 in HCC. In total, 124 proteins were differentially expressed in sEVs from COVID-19(+) subjects. "Coronavirus-disease response", "complement and coagulation cascades", and "PMN extracellular trap formation" were the most enriched KEGG pathways in COVID-19(+) cases. The most represented biological processes were "Hemoglobin and haptoglobin binding" and "oxygen carrier activity", and the best-denoted molecular functions were "regulated exocytosis and secretion" and "leucocyte and PMN mediated immunity". sEV proteomic cargo in COVID-19(+) suggests activity related to immune response processes, oxygen transport, and antioxidant mechanisms. In contrast, in HCC, sEV signature profiles are mainly associated with epithelial homeostasis.
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Affiliation(s)
- Laura Weber
- Department of Pathology and Conservative Dentistry, Faculty of Dentistry, Universidad de los Andes, Santiago 7620060, Chile; (L.W.); (M.J.B.); (M.L.M.); (C.B.)
| | - Alfredo Torres
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, Universidad de Chile, Santiago 8380492, Chile;
- Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago 8380492, Chile
| | - Ornella Realini
- Centre for Biomedical Research and Innovation (CIIB), Periodontal Research Laboratory, Universidad de los Andes, Santiago 7620060, Chile;
| | - María José Bendek
- Department of Pathology and Conservative Dentistry, Faculty of Dentistry, Universidad de los Andes, Santiago 7620060, Chile; (L.W.); (M.J.B.); (M.L.M.); (C.B.)
- Centre for Biomedical Research and Innovation (CIIB), Periodontal Research Laboratory, Universidad de los Andes, Santiago 7620060, Chile;
| | - María Luisa Mizgier
- Department of Pathology and Conservative Dentistry, Faculty of Dentistry, Universidad de los Andes, Santiago 7620060, Chile; (L.W.); (M.J.B.); (M.L.M.); (C.B.)
- Centre for Biomedical Research and Innovation (CIIB), Periodontal Research Laboratory, Universidad de los Andes, Santiago 7620060, Chile;
| | - Claudia Brizuela
- Department of Pathology and Conservative Dentistry, Faculty of Dentistry, Universidad de los Andes, Santiago 7620060, Chile; (L.W.); (M.J.B.); (M.L.M.); (C.B.)
| | - David Herrera
- Department of Periodontology, Faculty of Dentistry, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - Fermín E. González
- Laboratory of Experimental Immunology & Cancer, Faculty of Dentistry, Universidad de Chile, Santiago 8380492, Chile;
- Department of Conservative Dentistry, Faculty of Dentistry, Universidad de Chile, Santiago 8380492, Chile
| | - Alejandra Chaparro
- Department of Pathology and Conservative Dentistry, Faculty of Dentistry, Universidad de los Andes, Santiago 7620060, Chile; (L.W.); (M.J.B.); (M.L.M.); (C.B.)
- Centre for Biomedical Research and Innovation (CIIB), Periodontal Research Laboratory, Universidad de los Andes, Santiago 7620060, Chile;
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3
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Harriott NC, Ryan AL. Proteomic profiling identifies biomarkers of COVID-19 severity. Heliyon 2024; 10:e23320. [PMID: 38163173 PMCID: PMC10755324 DOI: 10.1016/j.heliyon.2023.e23320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
SARS-CoV-2 infection remains a major public health concern, particularly for the aged and those individuals with co-morbidities at risk for developing severe COVID-19. Understanding the pathogenesis and biomarkers associated with responses to SARS-CoV-2 infection remain critical components in developing effective therapeutic approaches, especially in cases of severe and long-COVID-19. In this study blood plasma protein expression was compared in subjects with mild, moderate, and severe COVID-19 disease. Evaluation of an inflammatory protein panel confirms upregulation of proteins including TNFβ, IL-6, IL-8, IL-12, already associated with severe cytokine storm and progression to severe COVID-19. Importantly, we identify several proteins not yet associated with COVID-19 disease, including mesothelin (MSLN), that are expressed at significantly higher levels in severe COVID-19 subjects. In addition, we find a subset of markers associated with T-cell and dendritic cell responses to viral infection that are significantly higher in mild cases and decrease in expression as severity of COVID-19 increases, suggesting that an immediate and effective activation of T-cells is critical in modulating disease progression. Together, our findings identify new targets for further investigation as therapeutic approaches for the treatment of SARS-CoV-2 infection and prevention of complications of severe COVID-19.
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Affiliation(s)
- Noa C. Harriott
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City IA 52240, USA
| | - Amy L. Ryan
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles CA 90033, USA
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City IA 52240, USA
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4
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Lipman D, Safo SE, Chekouo T. Integrative multi-omics approach for identifying molecular signatures and pathways and deriving and validating molecular scores for COVID-19 severity and status. BMC Genomics 2023; 24:319. [PMID: 37308820 PMCID: PMC10259816 DOI: 10.1186/s12864-023-09410-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND There is still more to learn about the pathobiology of COVID-19. A multi-omic approach offers a holistic view to better understand the mechanisms of COVID-19. We used state-of-the-art statistical learning methods to integrate genomics, metabolomics, proteomics, and lipidomics data obtained from 123 patients experiencing COVID-19 or COVID-19-like symptoms for the purpose of identifying molecular signatures and corresponding pathways associated with the disease. RESULTS We constructed and validated molecular scores and evaluated their utility beyond clinical factors known to impact disease status and severity. We identified inflammation- and immune response-related pathways, and other pathways, providing insights into possible consequences of the disease. CONCLUSIONS The molecular scores we derived were strongly associated with disease status and severity and can be used to identify individuals at a higher risk for developing severe disease. These findings have the potential to provide further, and needed, insights into why certain individuals develop worse outcomes.
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Affiliation(s)
- Danika Lipman
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Sandra E Safo
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, USA.
| | - Thierry Chekouo
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada.
- Division of Biostatistics, School of Public Health, University of Minnesota, Minnesota, USA.
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5
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer's and coronary disease pathways. iScience 2023; 26:106408. [PMID: 36974157 PMCID: PMC10010831 DOI: 10.1016/j.isci.2023.106408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/21/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Identification of proteins dysregulated by COVID-19 infection is critically important for better understanding of its pathophysiology, building prognostic models, and identifying new targets. Plasma proteomic profiling of 4,301 proteins was performed in two independent datasets and tested for the association for three COVID-19 outcomes (infection, ventilation, and death). We identified 1,449 proteins consistently associated in both datasets with any of these three outcomes. We subsequently created highly accurate models that distinctively predict infection, ventilation, and death. These proteins were enriched in specific biological processes including cytokine signaling, Alzheimer's disease, and coronary artery disease. Mendelian randomization and gene network analyses identified eight causal proteins and 141 highly connected hub proteins including 35 with known drug targets. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes, reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R. Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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6
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Omenn GS, Lane L, Overall CM, Pineau C, Packer NH, Cristea IM, Lindskog C, Weintraub ST, Orchard S, Roehrl MH, Nice E, Liu S, Bandeira N, Chen YJ, Guo T, Aebersold R, Moritz RL, Deutsch EW. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project. J Proteome Res 2023; 22:1024-1042. [PMID: 36318223 PMCID: PMC10081950 DOI: 10.1021/acs.jproteome.2c00498] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, "A Function for Each Protein".
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Affiliation(s)
- Gilbert S. Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland
| | | | - Charles Pineau
- French Institute of Health and Medical Research, 35042 RENNES Cedex, France
| | - Nicolle H. Packer
- Macquarie University, Sydney, NSW 2109, Australia
- Griffith University’s Institute for Glycomics, Sydney, NSW 2109, Australia
| | | | | | - Susan T. Weintraub
- University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States
| | - Sandra Orchard
- EMBL-EBI, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Michael H.A. Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York, 10065, United States
| | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Tiannan Guo
- Westlake University Guomics Laboratory of Big Proteomic Data, Hangzhou 310024, Zhejiang Province, China
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W. Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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7
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Towards precision medicine: Omics approach for COVID-19. BIOSAFETY AND HEALTH 2023; 5:78-88. [PMID: 36687209 PMCID: PMC9846903 DOI: 10.1016/j.bsheal.2023.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic had a devastating impact on human society. Beginning with genome surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the development of omics technologies brought a clearer understanding of the complex SARS-CoV-2 and COVID-19. Here, we reviewed how omics, including genomics, proteomics, single-cell multi-omics, and clinical phenomics, play roles in answering biological and clinical questions about COVID-19. Large-scale sequencing and advanced analysis methods facilitate COVID-19 discovery from virus evolution and severity risk prediction to potential treatment identification. Omics would indicate precise and globalized prevention and medicine for the COVID-19 pandemic under the utilization of big data capability and phenotypes refinement. Furthermore, decoding the evolution rule of SARS-CoV-2 by deep learning models is promising to forecast new variants and achieve more precise data to predict future pandemics and prevent them on time.
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8
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Dos Santos F, Li JB, Juocys N, Mazor R, Beretta L, Coufal NG, Lam MTY, Odish MF, Irigoyen MC, O’Donoghue AJ, Aletti F, Kistler EB. Plasma enzymatic activity, proteomics and peptidomics in COVID-19-induced sepsis: A novel approach for the analysis of hemostasis. Front Mol Biosci 2023; 9:1051471. [PMID: 36710882 PMCID: PMC9874325 DOI: 10.3389/fmolb.2022.1051471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Introduction: Infection by SARS-CoV-2 and subsequent COVID-19 can cause viral sepsis. We investigated plasma protease activity patterns in COVID-19-induced sepsis with bacterial superinfection, as well as plasma proteomics and peptidomics in order to assess the possible implications of enhanced proteolysis on major protein systems (e.g., coagulation). Methods: Patients (=4) admitted to the intensive care units (ICUs) at the University of California, San Diego (UCSD) Medical Center with confirmed positive test for COVID-19 by real-time reverse transcription polymerase chain reaction (RT-PCR) were enrolled in a study approved by the UCSD Institutional Review Board (IRB# 190699, Protocol #20-0006). Informed consent was obtained for the collection of blood samples and de-identified use of the data. Blood samples were collected at multiple time points and analyzed to quantify a) the circulating proteome and peptidome by mass spectrometry; b) the aminopeptidase activity in plasma; and c) the endopeptidase activity in plasma using fluorogenic substrates that are cleaved by trypsin-like endopeptidases, specific clotting factors and plasmin. The one patient who died was diagnosed with bacterial superinfection on day 7 after beginning of the study. Results: Spikes in protease activity (factor VII, trypsin-like activity), and corresponding increases in the intensity of peptides derived by hydrolysis of plasma proteins, especially of fibrinogen degradation products and downregulation of endogenous protease inhibitors were detected on day 7 for the patient who died. The activity of the analyzed proteases was stable in survivors. Discussion: The combination of multiomics and enzymatic activity quantification enabled to i) hypothesize that elevated proteolysis occurs in COVID-19-induced septic shock with bacterial superinfection, and ii) provide additional insight into malfunctioning protease-mediated systems, such as hemostasis.
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Affiliation(s)
- Fernando Dos Santos
- Department of Anesthesiology, School of Medicine, University of California, San Diego, CA, United States
| | - Joyce B. Li
- Department of Bioengineering, University of California, San Diego, CA, United States
| | - Nathalia Juocys
- Department of Anesthesiology, School of Medicine, University of California, San Diego, CA, United States
- Instituto do Coração, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (InCor-FMUSP), São Paulo, Brazil
| | - Rafi Mazor
- Department of Anesthesiology, School of Medicine, University of California, San Diego, CA, United States
| | - Laura Beretta
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Nicole G. Coufal
- Department of Pediatrics, School of Medicine, University of California, San Diego, CA, United States
| | - Michael T. Y. Lam
- Department of Medicine, School of Medicine, University of California, San Diego, CA, United States
| | - Mazen F. Odish
- Department of Medicine, School of Medicine, University of California, San Diego, CA, United States
| | - Maria Claudia Irigoyen
- Instituto do Coração, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (InCor-FMUSP), São Paulo, Brazil
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Federico Aletti
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São Josê dos Campos, Brazil
| | - Erik B. Kistler
- Department of Anesthesiology, School of Medicine, University of California, San Diego, CA, United States
- Department of Anesthesiology and Critical Care, VA San Diego Healthcare System, San Diego, CA, United States
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9
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A two-gene marker for the two-tiered innate immune response in COVID-19 patients. PLoS One 2023; 18:e0280392. [PMID: 36649304 PMCID: PMC9844909 DOI: 10.1371/journal.pone.0280392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
For coronavirus disease 2019 (COVID-19), a pandemic disease characterized by strong immune dysregulation in severe patients, convenient and efficient monitoring of the host immune response is critical. Human hosts respond to viral and bacterial infections in different ways, the former is characterized by the activation of interferon stimulated genes (ISGs) such as IFI27, while the latter is characterized by the activation of anti-bacterial associated genes (ABGs) such as S100A12. This two-tiered innate immune response has not been examined in COVID-19. In this study, the activation patterns of this two-tiered innate immune response represented by IFI27 and S100A12 were explored based on 1421 samples from 17 transcriptome datasets derived from the blood of COVID-19 patients and relevant controls. It was found that IFI27 activation occurred in most of the symptomatic patients and displayed no correlation with disease severity, while S100A12 activation was more restricted to patients under severe and critical conditions with a stepwise activation pattern. In addition, most of the S100A12 activation was accompanied by IFI27 activation. Furthermore, the activation of IFI27 was most pronounced within the first week of symptom onset, but generally waned after 2-3 weeks. On the other hand, the activation of S100A12 displayed no apparent correlation with disease duration and could last for several months in certain patients. These features of the two-tiered innate immune response can further our understanding on the disease mechanism of COVID-19 and may have implications to the clinical triage. Development of a convenient two-gene protocol for the routine serial monitoring of this two-tiered immune response will be a valuable addition to the existing laboratory tests.
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10
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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11
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Molinero M, Gómez S, Benítez ID, Vengoechea JJ, González J, Polanco D, Gort-Paniello C, Moncusí-Moix A, García-Hidalgo MC, Perez-Pons M, Belmonte T, Torres G, Caballero J, Barberà C, Ayestarán Rota JI, Socías Crespí L, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Lorente-Balanza JÁ, Menéndez R, Motos A, Peñuelas O, Riera J, Torres A, Barbé F, de Gonzalo-Calvo D. Multiplex protein profiling of bronchial aspirates reveals disease-, mortality- and respiratory sequelae-associated signatures in critically ill patients with ARDS secondary to SARS-CoV-2 infection. Front Immunol 2022; 13:942443. [PMID: 35967328 PMCID: PMC9373836 DOI: 10.3389/fimmu.2022.942443] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction Bronchial aspirates (BAS) obtained during invasive mechanical ventilation (IMV) constitutes a useful tool for molecular phenotyping and decision making. Aim To identify the proteomic determinants associated with disease pathogenesis, all-cause mortality and respiratory sequelae in BAS samples from critically ill patients with SARS-CoV-2-induced ARDS. Methods Multicenter study including 74 critically ill patients with COVID-19 and non-COVID-19 ARDS. BAS were obtained by bronchoaspiration after IMV initiation. Three hundred sixty-four proteins were quantified using proximity extension assay (PEA) technology. Random forest models were used to assess predictor importance. Results After adjusting for confounding factors, CST5, NADK, SRPK2 and TGF-α were differentially detected in COVID-19 and non-COVID-19 patients. In random forest models for COVID-19, CST5, DPP7, NADK, KYAT1 and TYMP showed the highest variable importance. In COVID-19 patients, reduced levels of ENTPD2 and PTN were observed in nonsurvivors of ICU stay, even after adjustment. AGR2, NQO2, IL-1α, OSM and TRAIL showed the strongest associations with in-ICU mortality and were used to construct a protein-based prediction model. Kaplan-Meier curves revealed a clear separation in mortality risk between subgroups of PTN, ENTPD2 and the prediction model. Cox regression models supported these findings. In survivors, the levels of FCRL1, NTF4 and THOP1 in BAS samples obtained during the ICU stay correlated with lung function (i.e., DLCO levels) 3 months after hospital discharge. Similarly, Flt3L and THOP1 levels were correlated with radiological features (i.e., TSS). These proteins are expressed in immune and nonimmune lung cells. Poor host response to viral infectivity and an inappropriate reparative mechanism seem to be linked with the pathogenesis of the disease and fatal outcomes, respectively. Conclusion BAS proteomics identified novel factors associated with the pathology of SARS-CoV-2-induced ARDS and its adverse outcomes. BAS-based protein testing emerges as a novel tool for risk assessment in the ICU.
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Affiliation(s)
- Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Silvia Gómez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - J J Vengoechea
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Dinora Polanco
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Thalía Belmonte
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Jose Ignacio Ayestarán Rota
- Intensive Care Unit, Son Espases University Hospital, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | | | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca VHIR), Barcelona, Spain
| | | | - Jose Ángel Lorente-Balanza
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari. SODIR Research Group, Vall d'Hebron Institut de Recerca VHIR), Barcelona, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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12
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Zhang N, Wang S, Wong CC. Proteomics research of SARS-CoV-2 and COVID-19 disease. MEDICAL REVIEW (BERLIN, GERMANY) 2022; 2:427-445. [PMID: 37724330 PMCID: PMC10388787 DOI: 10.1515/mr-2022-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/06/2022] [Indexed: 09/20/2023]
Abstract
Currently, coronavirus disease 2019 (COVID-19) is still spreading in a global scale, exerting a massive health and socioeconomic crisis. Deep insights into the molecular functions of the viral proteins and the pathogenesis of this infectious disease are urgently needed. In this review, we comprehensively describe the proteome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and summarize their protein interaction map with host cells. In the protein interaction network between the virus and the host, a total of 787 host prey proteins that appeared in at least two studies or were verified by co-immunoprecipitation experiments. Together with 29 viral proteins, a network of 1762 proximal interactions were observed. We also review the proteomics results of COVID-19 patients and proved that SARS-CoV-2 hijacked the host's translation system, post-translation modification system, and energy supply system via viral proteins, resulting in various immune disorders, multiple cardiomyopathies, and cholesterol metabolism diseases.
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Affiliation(s)
- Nan Zhang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, OH, USA
- Center for Cancer Metabolism, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Siyuan Wang
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Catherine C.L. Wong
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, P. R. China
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13
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Wang L, Western D, Timsina J, Repaci C, Song WM, Norton J, Kohlfeld P, Budde J, Climer S, Butt OH, Jacobson D, Garvin M, Templeton AR, Campagna S, O’Halloran J, Presti R, Goss CW, Mudd PA, Ances BM, Zhang B, Sung YJ, Cruchaga C. Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer and coronary disease pathways. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.07.25.22278025. [PMID: 35923315 PMCID: PMC9347279 DOI: 10.1101/2022.07.25.22278025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Identification of the plasma proteomic changes of Coronavirus disease 2019 (COVID-19) is essential to understanding the pathophysiology of the disease and developing predictive models and novel therapeutics. We performed plasma deep proteomic profiling from 332 COVID-19 patients and 150 controls and pursued replication in an independent cohort (297 cases and 76 controls) to find potential biomarkers and causal proteins for three COVID-19 outcomes (infection, ventilation, and death). We identified and replicated 1,449 proteins associated with any of the three outcomes (841 for infection, 833 for ventilation, and 253 for death) that can be query on a web portal ( https://covid.proteomics.wustl.edu/ ). Using those proteins and machine learning approached we created and validated specific prediction models for ventilation (AUC>0.91), death (AUC>0.95) and either outcome (AUC>0.80). These proteins were also enriched in specific biological processes, including immune and cytokine signaling (FDR ≤ 3.72×10 -14 ), Alzheimer's disease (FDR ≤ 5.46×10 -10 ) and coronary artery disease (FDR ≤ 4.64×10 -2 ). Mendelian randomization using pQTL as instrumental variants nominated BCAT2 and GOLM1 as a causal proteins for COVID-19. Causal gene network analyses identified 141 highly connected key proteins, of which 35 have known drug targets with FDA-approved compounds. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes (ventilation and death), reveal their relationship to Alzheimer's disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.
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Affiliation(s)
- Lihua Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Dan Western
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Jigyasha Timsina
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Charlie Repaci
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Won-Min Song
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Pat Kohlfeld
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - John Budde
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlee Climer
- Department of Computer Science, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Omar H. Butt
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alan R Templeton
- Department of Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shawn Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN, USA
| | - Jane O’Halloran
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel Presti
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Beau M. Ances
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St Louis, MO, USA
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14
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Ward B, Yombi JC, Balligand JL, Cani PD, Collet JF, de Greef J, Dewulf JP, Gatto L, Haufroid V, Jodogne S, Kabamba B, Pyr dit Ruys S, Vertommen D, Elens L, Belkhir L. HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach. Viruses 2022; 14:v14071373. [PMID: 35891354 PMCID: PMC9318602 DOI: 10.3390/v14071373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
More than two years on, the COVID-19 pandemic continues to wreak havoc around the world and has battle-tested the pandemic-situation responses of all major global governments. Two key areas of investigation that are still unclear are: the molecular mechanisms that lead to heterogenic patient outcomes, and the causes of Post COVID condition (AKA Long-COVID). In this paper, we introduce the HYGIEIA project, designed to respond to the enormous challenges of the COVID-19 pandemic through a multi-omic approach supported by network medicine. It is hoped that in addition to investigating COVID-19, the logistics deployed within this project will be applicable to other infectious agents, pandemic-type situations, and also other complex, non-infectious diseases. Here, we first look at previous research into COVID-19 in the context of the proteome, metabolome, transcriptome, microbiome, host genome, and viral genome. We then discuss a proposed methodology for a large-scale multi-omic longitudinal study to investigate the aforementioned biological strata through high-throughput sequencing (HTS) and mass-spectrometry (MS) technologies. Lastly, we discuss how a network medicine approach can be used to analyze the data and make meaningful discoveries, with the final aim being the translation of these discoveries into the clinics to improve patient care.
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Affiliation(s)
- Bradley Ward
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
| | - Jean Cyr Yombi
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-Luc Balligand
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Pole of Pharmacology and Therapeutics (FATH), Institut de Recherche Experimentale et Clinique (IREC), Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Patrice D. Cani
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Jean-François Collet
- WELBIO (Walloon Excellence in Life Sciences and Biotechnology), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Julien de Greef
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Joseph P. Dewulf
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Department of Biochemistry, de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Laurent Gatto
- Computational Biology and Bioinformatics Unit (CBIO), de Duve Institute, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Vincent Haufroid
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Sébastien Jodogne
- Computer Science and Engineering Department (INGI), Institute of Information and Communication Technologies, Electronics and Applied Mathematics (ICTEAM), UCLouvain, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Benoît Kabamba
- Department of Laboratory Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Pôle de Microbiologie, Institut de Recherche Expérimentale et Clinique, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Sébastien Pyr dit Ruys
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
| | - Didier Vertommen
- De Duve Institute, and MASSPROT Platform, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
| | - Laure Elens
- Integrated Pharmacometrics, Pharmacogenomics and Pharmacokinetics Group (PMGK), Louvain Drug Research Institute (LDRI), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (B.W.); (S.P.d.R.)
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Correspondence: (L.E.); (L.B.)
| | - Leïla Belkhir
- Louvain Center for Toxicology and Applied Pharmacology (LTAP), Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium; (J.d.G.); (J.P.D.); (V.H.)
- Department of Internal Medicine, Cliniques Universitaires Saint-Luc, UCLouvain, Université Catholique de Louvain, 1200 Brussels, Belgium;
- Correspondence: (L.E.); (L.B.)
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15
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Beltrán-Camacho L, Eslava-Alcón S, Rojas-Torres M, Sánchez-Morillo D, Martinez-Nicolás MP, Martín-Bermejo V, de la Torre IG, Berrocoso E, Moreno JA, Moreno-Luna R, Durán-Ruiz MC. The serum of COVID-19 asymptomatic patients up-regulates proteins related to endothelial dysfunction and viral response in circulating angiogenic cells ex-vivo. Mol Med 2022; 28:40. [PMID: 35397534 PMCID: PMC8994070 DOI: 10.1186/s10020-022-00465-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has already caused 6 million deaths worldwide. While asymptomatic individuals are responsible of many potential transmissions, the difficulty to identify and isolate them at the high peak of infection constitutes still a real challenge. Moreover, SARS-CoV-2 provokes severe vascular damage and thromboembolic events in critical COVID-19 patients, deriving in many related deaths and long-hauler symptoms. Understanding how these processes are triggered as well as the potential long-term sequelae, even in asymptomatic individuals, becomes essential.
Methods We have evaluated, by application of a proteomics-based quantitative approach, the effect of serum from COVID-19 asymptomatic individuals over circulating angiogenic cells (CACs). Healthy CACs were incubated ex-vivo with the serum of either COVID-19 negative (PCR −/IgG −, n:8) or COVID-19 positive asymptomatic donors, at different infective stages: PCR +/IgG − (n:8) and PCR −/IgG + (n:8). Also, a label free quantitative approach was applied to identify and quantify protein differences between these serums. Finally, machine learning algorithms were applied to validate the differential protein patterns in CACs.
Results Our results confirmed that SARS-CoV-2 promotes changes at the protein level in the serum of infected asymptomatic individuals, mainly correlated with altered coagulation and inflammatory processes (Fibrinogen, Von Willebrand Factor, Thrombospondin-1). At the cellular level, proteins like ICAM-1, TLR2 or Ezrin/Radixin were only up-regulated in CACs treated with the serum of asymptomatic patients at the highest peak of infection (PCR + /IgG −), but not with the serum of PCR −/IgG + individuals. Several proteins stood out as significantly discriminating markers in CACs in response to PCR or IgG + serums. Many of these proteins particiArticle title: Kindly check and confirm the edit made in the article
title.pate in the initial endothelial response against the virus. Conclusions The ex vivo incubation of CACs with the serum of asymptomatic COVID-19 donors at different stages of infection promoted protein changes representative of the endothelial dysfunction and inflammatory response after viral infection, together with activation of the coagulation process. The current approach constitutes an optimal model to study the response of vascular cells to SARS-CoV-2 infection, and an alternative platform to test potential inhibitors targeting either the virus entry pathway or the immune responses following SARS-CoV-2 infection. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00465-w.
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16
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Acharjee A, Stephen Kingsly J, Kamat M, Kurlawala V, Chakraborty A, Vyas P, Vaishnav R, Srivastava S. Rise of the SARS-CoV-2 Variants: can proteomics be the silver bullet? Expert Rev Proteomics 2022; 19:197-212. [PMID: 35655386 DOI: 10.1080/14789450.2022.2085564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION The challenges posed by emergent strains of SARS-CoV-2 need to be tackled by contemporary scientific approaches, with proteomics playing a significant role. AREAS COVERED In this review, we provide a brief synthesis of the impact of proteomics technologies in elucidating disease pathogenesis and classifiers for the prognosis of COVID-19 and propose proteomics methodologies that could play a crucial role in understanding emerging variants and their altered disease pathology. From aiding the design of novel drug candidates to facilitating the identification of T cell vaccine targets, we have discussed the impact of proteomics methods in COVID-19 research. Techniques varied as mass spectrometry, single-cell proteomics, multiplexed ELISA arrays, high-density proteome arrays, surface plasmon resonance, immunopeptidomics, and in silico docking studies that have helped augment the fight against existing diseases were useful in preparing us to tackle SARS-CoV-2 variants. We also propose an action plan for a pipeline to combat emerging pandemics using proteomics technology by adopting uniform standard operating procedures and unified data analysis paradigms. EXPERT OPINION The knowledge about the use of diverse proteomics approaches for COVID-19 investigation will provide a framework for future basic research, better infectious disease prevention strategies, improved diagnostics, and targeted therapeutics.
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Affiliation(s)
- Arup Acharjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Madhura Kamat
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | - Vishakha Kurlawala
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be University), Mumbai, India
| | | | - Priyanka Vyas
- Department of Biotechnology and Botany, Mahila PG Mahavidyalaya, J. N. V University, Jodhpur, India
| | - Radhika Vaishnav
- Department of Life Sciences, Ivy Tech Community College, Indianapolis, Indiana, USA
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Reverté L, Yeregui E, Olona M, Gutiérrez‐Valencia A, Buzón MJ, Martí A, Gómez‐Bertomeu F, Auguet T, López‐Cortés LF, Burgos J, Benavent‐Bofill C, Boqué C, García‐Pardo G, Ruiz‐Mateos E, Mestre MT, Vidal F, Viladés C, Peraire J, Rull A. Fetuin‐A, inter‐α‐trypsin inhibitor, glutamic acid and ChoE (18:0) are key biomarkers in a panel distinguishing mild from critical coronavirus disease 2019 outcomes. Clin Transl Med 2022; 12:e704. [PMID: 35075803 PMCID: PMC8787095 DOI: 10.1002/ctm2.704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022] Open
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Beimdiek J, Janciauskiene S, Wrenger S, Volland S, Rozy A, Fuge J, Olejnicka B, Pink I, Illig T, Popov A, Chorostowska J, Buettner FFR, Welte T. Plasma markers of COVID-19 severity: a pilot study. Respir Res 2022; 23:343. [PMID: 36514048 PMCID: PMC9745704 DOI: 10.1186/s12931-022-02272-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND SARS-CoV-2 infected patients show heterogeneous clinical presentations ranging from mild symptoms to severe respiratory failure and death. Consequently, various markers reflect this wide spectrum of disease presentations. METHODS Our pilot cohort included moderate (n = 10) and severe (n = 10) COVID-19 patients, and 10 healthy controls. We determined plasma levels of nine acute phase proteins (APPs) by nephelometry, and full-length (M65), caspase-cleaved (M30) cytokeratin 18, and ADAMTS13 (a disintegrin-like and metalloprotease with thrombospondin type-1 motif 13) by ELISA. In addition, we examined whole plasma N-glycosylation by capillary gel electrophoresis coupled to laser-induced fluorescence detection (CGE-LIF). RESULTS When compared to controls, COVID-19 patients had significantly lower concentrations of ADAMTS13 and albumin (ALB) but higher M30, M65, α1-acid glycoprotein (AGP), α1-antitrypsin (AAT), ceruloplasmin (CP), haptoglobin (HP), and high-sensitivity C-reactive protein (hs-CRP). The concentrations of α1-antichymotrypsin (ACT), α2-macroglobulin (A2MG) and serum amyloid A (SAA) proteins did not differ. We found significantly higher levels of AAT and M65 but lower ALB in severe compared to moderate COVID-19 patients. N-glycan analysis of the serum proteome revealed increased levels of oligomannose- and sialylated di-antennary glycans and decreased non-sialylated di-antennary glycan A2G2 in COVID-19 patients compared to controls. CONCLUSIONS COVID-19-associated changes in levels and N-glycosylation of specific plasma proteins highlight complexity of inflammatory process and grant further investigations.
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Affiliation(s)
- Julia Beimdiek
- grid.10423.340000 0000 9529 9877Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Sabina Janciauskiene
- grid.10423.340000 0000 9529 9877Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL) Hannover University School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Sabine Wrenger
- grid.10423.340000 0000 9529 9877Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL) Hannover University School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Sonja Volland
- grid.10423.340000 0000 9529 9877Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Str. 15, 30625 Hannover, Germany
| | - Adriana Rozy
- grid.419019.40000 0001 0831 3165Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01138 Warsaw, Poland
| | - Jan Fuge
- grid.10423.340000 0000 9529 9877Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL) Hannover University School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Beata Olejnicka
- grid.10423.340000 0000 9529 9877Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL) Hannover University School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Isabell Pink
- grid.10423.340000 0000 9529 9877Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL) Hannover University School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Thomas Illig
- grid.10423.340000 0000 9529 9877Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Str. 15, 30625 Hannover, Germany
| | - Alexander Popov
- grid.10423.340000 0000 9529 9877Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Str. 15, 30625 Hannover, Germany
| | - Joanna Chorostowska
- grid.419019.40000 0001 0831 3165Department of Genetics and Clinical Immunology, National Institute of Tuberculosis and Lung Diseases, 26 Plocka St., 01138 Warsaw, Poland
| | - Falk F. R. Buettner
- grid.10423.340000 0000 9529 9877Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Tobias Welte
- grid.10423.340000 0000 9529 9877Department of Pulmonary and Infectious Diseases, Hannover Medical School, BREATH German Center for Lung Research (DZL) Hannover University School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Pinto G, Illiano A, Ferrucci V, Quarantelli F, Fontanarosa C, Siciliano R, Di Domenico C, Izzo B, Pucci P, Marino G, Zollo M, Amoresano A. Identification of SARS-CoV-2 Proteins from Nasopharyngeal Swabs Probed by Multiple Reaction Monitoring Tandem Mass Spectrometry. ACS OMEGA 2021; 6:34945-34953. [PMID: 34926968 PMCID: PMC8672425 DOI: 10.1021/acsomega.1c05587] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/02/2021] [Indexed: 05/12/2023]
Abstract
Numerous reverse transcription polymerase chain reaction (RT-PCR) tests have emerged over the past year as the gold standard for detecting millions of cases of SARS-CoV-2 reported daily worldwide. However, problems with critical shortages of key reagents such as PCR primers and RNA extraction kits and unpredictable test reliability related to high viral replication cycles have triggered the need for alternative methodologies to PCR to detect specific COVID-19 proteins. Several authors have developed methods based on liquid chromatography with tandem mass spectrometry (LC-MS/MS) to confirm the potential of the technique to detect two major proteins, the spike and the nucleoprotein, of COVID-19. In the present work, an S-Trap mini spin column digestion protocol was used for sample preparation prodromal to LC-MS/MS analysis in multiple reactions monitoring ion mode (MRM) to obtain a comprehensive method capable of detecting different viral proteins. The developed method was applied to n. 81 oro/nasopharyngeal swabs submitted in parallel to quantitative reverse transcription PCR (RT-qPCR) assays to detect RdRP, the S and N genes specific for COVID-19, and the E gene for all Sarbecoviruses, including SARS-CoV-2 (with cycle negativity threshold set to 40). A total of 23 peptides representative of the six specific viral proteins were detected in the monitoring of 128 transitions found to have good ionic currents extracted in clinical samples that reacted differently to the PCR assay. The best instrumental response came from the FLPFQFGR sequence of spike [558-566] peptide used to test the analytical performance of the method that has good sensitivity with a low false-negative rate. Transition monitoring using a targeted MS approach has the great potential to detect the fragmentation reactions of any peptide molecularly defined by a specific amino acid sequence, offering the extensibility of the approach to any viral sequence including derived variants and thus providing insights into the development of new types of clinical diagnostics.
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Affiliation(s)
- Gabriella Pinto
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Anna Illiano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Veronica Ferrucci
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | | | - Carolina Fontanarosa
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
| | - Roberto Siciliano
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Carmela Di Domenico
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Barbara Izzo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Piero Pucci
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Gennaro Marino
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
| | - Massimo Zollo
- CEINGE
Advanced Biotechnology, Via Gaetano Salvatore 486, 80145 Naples, Italy
- Department
of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80145 Naples, Italy
| | - Angela Amoresano
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cinthia 26, 80126 Naples, Italy
- Istituto
Nazionale Biostrutture e Biosistemi-Consorzio Interuniversitario, Viale delle Medaglie d’Oro,
305, 00136 Rome, Italy
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