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Schimke LF, Marques AHC, Baiocchi GC, de Souza Prado CA, Fonseca DLM, Freire PP, Rodrigues Plaça D, Salerno Filgueiras I, Coelho Salgado R, Jansen-Marques G, Rocha Oliveira AE, Peron JPS, Cabral-Miranda G, Barbuto JAM, Camara NOS, Calich VLG, Ochs HD, Condino-Neto A, Overmyer KA, Coon JJ, Balnis J, Jaitovich A, Schulte-Schrepping J, Ulas T, Schultze JL, Nakaya HI, Jurisica I, Cabral-Marques O. Severe COVID-19 Shares a Common Neutrophil Activation Signature with Other Acute Inflammatory States. Cells 2022; 11:cells11050847. [PMID: 35269470 PMCID: PMC8909161 DOI: 10.3390/cells11050847] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Severe COVID-19 patients present a clinical and laboratory overlap with other hyperinflammatory conditions such as hemophagocytic lymphohistiocytosis (HLH). However, the underlying mechanisms of these conditions remain to be explored. Here, we investigated the transcriptome of 1596 individuals, including patients with COVID-19 in comparison to healthy controls, other acute inflammatory states (HLH, multisystem inflammatory syndrome in children [MIS-C], Kawasaki disease [KD]), and different respiratory infections (seasonal coronavirus, influenza, bacterial pneumonia). We observed that COVID-19 and HLH share immunological pathways (cytokine/chemokine signaling and neutrophil-mediated immune responses), including gene signatures that stratify COVID-19 patients admitted to the intensive care unit (ICU) and COVID-19_nonICU patients. Of note, among the common differentially expressed genes (DEG), there is a cluster of neutrophil-associated genes that reflects a generalized hyperinflammatory state since it is also dysregulated in patients with KD and bacterial pneumonia. These genes are dysregulated at the protein level across several COVID-19 studies and form an interconnected network with differentially expressed plasma proteins that point to neutrophil hyperactivation in COVID-19 patients admitted to the intensive care unit. scRNAseq analysis indicated that these genes are specifically upregulated across different leukocyte populations, including lymphocyte subsets and immature neutrophils. Artificial intelligence modeling confirmed the strong association of these genes with COVID-19 severity. Thus, our work indicates putative therapeutic pathways for intervention.
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Affiliation(s)
- Lena F. Schimke
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Correspondence: (L.F.S.); (O.C.-M.); Tel.: +55-11-943661555 (L.F.S.); +55-11-974642022 (O.C.-M.)
| | - Alexandre H. C. Marques
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gabriela Crispim Baiocchi
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Caroline Aliane de Souza Prado
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Dennyson Leandro M. Fonseca
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Paula Paccielli Freire
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Desirée Rodrigues Plaça
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Igor Salerno Filgueiras
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Ranieri Coelho Salgado
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gabriel Jansen-Marques
- Information Systems, School of Arts, Sciences and Humanities, University of Sao Paulo, São Paulo 03828-000, Brazil;
| | - Antonio Edson Rocha Oliveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
| | - Jean Pierre Schatzmann Peron
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Gustavo Cabral-Miranda
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - José Alexandre Marzagão Barbuto
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Laboratory of Medical Investigation in Pathogenesis, Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo 05403-000, Brazil
| | - Niels Olsen Saraiva Camara
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Vera Lúcia Garcia Calich
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Hans D. Ochs
- Department of Pediatrics, Seattle Children’s Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA;
| | - Antonio Condino-Neto
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
| | - Katherine A. Overmyer
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; (K.A.O.); (J.J.C.)
- Morgridge Institute for Research, Madison, WI 53562, USA
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53562, USA; (K.A.O.); (J.J.C.)
- Morgridge Institute for Research, Madison, WI 53562, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53506, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53506, USA
| | - Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; (J.B.); (A.J.)
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY 12208, USA; (J.B.); (A.J.)
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Jonas Schulte-Schrepping
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; (J.S.-S.); (J.L.S.)
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; (J.S.-S.); (J.L.S.)
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), University of Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, University of Bonn, 53127 Bonn, Germany
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
- Hospital Israelita Albert Einstein, São Paulo 05652-900, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo 05508-020, Brazil
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada;
- Departments of Medical Biophysics and Computer Science, Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1L7, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Otávio Cabral-Marques
- Department of Imunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (A.H.C.M.); (G.C.B.); (P.P.F.); (I.S.F.); (R.C.S.); (J.P.S.P.); (G.C.-M.); (J.A.M.B.); (N.O.S.C.); (V.L.G.C.); (A.C.-N.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, Brazil; (C.A.d.S.P.); (D.L.M.F.); (D.R.P.); (A.E.R.O.); (H.I.N.)
- Network of Immunity in Infection, Malignancy, Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), São Paulo 05508-000, Brazil
- Correspondence: (L.F.S.); (O.C.-M.); Tel.: +55-11-943661555 (L.F.S.); +55-11-974642022 (O.C.-M.)
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Ye Y, Gao L, Zhang S. Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach. Front Genet 2017; 8:140. [PMID: 29033978 PMCID: PMC5625019 DOI: 10.3389/fgene.2017.00140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/15/2017] [Indexed: 11/13/2022] Open
Abstract
Transcription factors play a key role in transcriptional regulation of genes and determination of cellular identity through combinatorial interactions. However, current studies about combinatorial regulation is deficient due to lack of experimental data in the same cellular environment and extensive existence of data noise. Here, we adopt a Bayesian CANDECOMP/PARAFAC (CP) factorization approach (BCPF) to integrate multiple datasets in a network paradigm for determining precise TF interaction landscapes. In our first application, we apply BCPF to integrate three networks built based on diverse datasets of multiple cell lines from ENCODE respectively to predict a global and precise TF interaction network. This network gives 38 novel TF interactions with distinct biological functions. In our second application, we apply BCPF to seven types of cell type TF regulatory networks and predict seven cell lineage TF interaction networks, respectively. By further exploring the dynamics and modularity of them, we find cell lineage-specific hub TFs participate in cell type or lineage-specific regulation by interacting with non-specific TFs. Furthermore, we illustrate the biological function of hub TFs by taking those of cancer lineage and blood lineage as examples. Taken together, our integrative analysis can reveal more precise and extensive description about human TF combinatorial interactions.
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Affiliation(s)
- Yusen Ye
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Shihua Zhang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.,School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China
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