1
|
Santoni D, Ghosh N, Derelitto C, Saha I. Transcription Factor Driven Gene Regulation in COVID-19 Patients. Viruses 2023; 15:v15051188. [PMID: 37243274 DOI: 10.3390/v15051188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
SARS-CoV-2 and its many variants have caused a worldwide emergency. Host cells colonised by SARS-CoV-2 present a significantly different gene expression landscape. As expected, this is particularly true for genes that directly interact with virus proteins. Thus, understanding the role that transcription factors can play in driving differential regulation in patients affected by COVID-19 is a focal point to unveil virus infection. In this regard, we have identified 19 transcription factors which are predicted to target human proteins interacting with Spike glycoprotein of SARS-CoV-2. Transcriptomics RNA-Seq data derived from 13 human organs are used to analyse expression correlation between identified transcription factors and related target genes in both COVID-19 patients and healthy individuals. This resulted in the identification of transcription factors showing the most relevant impact in terms of most evident differential correlation between COVID-19 patients and healthy individuals. This analysis has also identified five organs such as the blood, heart, lung, nasopharynx and respiratory tract in which a major effect of differential regulation mediated by transcription factors is observed. These organs are also known to be affected by COVID-19, thereby providing consistency to our analysis. Furthermore, 31 key human genes differentially regulated by the transcription factors in the five organs are identified and the corresponding KEGG pathways and GO enrichment are also reported. Finally, the drugs targeting those 31 genes are also put forth. This in silico study explores the effects of transcription factors on human genes interacting with Spike glycoprotein of SARS-CoV-2 and intends to provide new insights to inhibit the virus infection.
Collapse
Affiliation(s)
- Daniele Santoni
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, 00185 Rome, Italy
| | - Nimisha Ghosh
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751030, India
| | - Carlo Derelitto
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council of Italy, 00185 Rome, Italy
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata 700106, India
| |
Collapse
|
2
|
Ghosh N, Saha I, Gambin A. Interactome-Based Machine Learning Predicts Potential Therapeutics for COVID-19. ACS OMEGA 2023; 8:13840-13854. [PMID: 37163139 PMCID: PMC10084923 DOI: 10.1021/acsomega.3c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/22/2023] [Indexed: 05/11/2023]
Abstract
COVID-19, the disease caused by SARS-CoV-2, has been disrupting our lives for more than two years now. SARS-CoV-2 interacts with human proteins to pave its way into the human body, thereby wreaking havoc. Moreover, the mutating variants of the virus that take place in the SARS-CoV-2 genome are also a cause of concern among the masses. Thus, it is very important to understand human-spike protein-protein interactions (PPIs) in order to predict new PPIs and consequently propose drugs for the human proteins in order to fight the virus and its different mutated variants, with the mutations occurring in the spike protein. This fact motivated us to develop a complete pipeline where PPIs and drug-protein interactions can be predicted for human-SARS-CoV-2 interactions. In this regard, initially interacting data sets are collected from the literature, and noninteracting data sets are subsequently created for human-SARS-CoV-2 by considering only spike glycoprotein. On the other hand, for drug-protein interactions both interacting and noninteracting data sets are considered from DrugBank and ChEMBL databases. Thereafter, a model based on a sequence-based feature is used to code the protein sequences of human and spike proteins using the well-known Moran autocorrelation technique, while the drugs are coded using another well-known technique, viz., PaDEL descriptors, to predict new human-spike PPIs and eventually new drug-protein interactions for the top 20 predicted human proteins interacting with the original spike protein and its different mutated variants like Alpha, Beta, Delta, Gamma, and Omicron. Such predictions are carried out by random forest as it is found to perform better than other predictors, providing an accuracy of 90.53% for human-spike PPI and 96.15% for drug-protein interactions. Finally, 40 unique drugs like eicosapentaenoic acid, doxercalciferol, ciclesonide, dexamethasone, methylprednisolone, etc. are identified that target 32 human proteins like ACACA, DST, DYNC1H1, etc.
Collapse
Affiliation(s)
- Nimisha Ghosh
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 00-927 Warsaw, Poland
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan, Bhubaneswar, 751030 Odisha, India
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, 700106 West Bengal, India
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 00-927 Warsaw, Poland
| |
Collapse
|
3
|
Duhan N, Kaundal R. HuCoPIA: An Atlas of Human vs. SARS-CoV-2 Interactome and the Comparative Analysis with Other Coronaviridae Family Viruses. Viruses 2023; 15:492. [PMID: 36851706 PMCID: PMC9962590 DOI: 10.3390/v15020492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/01/2023] [Accepted: 02/04/2023] [Indexed: 02/12/2023] Open
Abstract
SARS-CoV-2, a novel betacoronavirus strain, has caused a pandemic that has claimed the lives of nearly 6.7M people worldwide. Vaccines and medicines are being developed around the world to reduce the disease spread, fatality rates, and control the new variants. Understanding the protein-protein interaction mechanism of SARS-CoV-2 in humans, and their comparison with the previous SARS-CoV and MERS strains, is crucial for these efforts. These interactions might be used to assess vaccination effectiveness, diagnose exposure, and produce effective biotherapeutics. Here, we present the HuCoPIA database, which contains approximately 100,000 protein-protein interactions between humans and three strains (SARS-CoV-2, SARS-CoV, and MERS) of betacoronavirus. The interactions in the database are divided into common interactions between all three strains and those unique to each strain. It also contains relevant functional annotation information of human proteins. The HuCoPIA database contains SARS-CoV-2 (41,173), SARS-CoV (31,997), and MERS (26,862) interactions, with functional annotation of human proteins like subcellular localization, tissue-expression, KEGG pathways, and Gene ontology information. We believe HuCoPIA will serve as an invaluable resource to diverse experimental biologists, and will help to advance the research in better understanding the mechanism of betacoronaviruses.
Collapse
Affiliation(s)
- Naveen Duhan
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA
- Department of Computer Science, College of Science, Utah State University, Logan, UT 84322, USA
| |
Collapse
|
4
|
Assone T, Menezes SM, de Toledo Gonçalves F, Folgosi VA, da Silva Prates G, Dierckx T, Braz M, Smid J, Haziot ME, Marcusso RMN, Dahy FE, Vanderlinden E, Claes S, Schols D, Bruhn R, Murphy EL, Penalva de Oliveira AC, Daelemans D, Vercauteren J, Casseb J, Van Weyenbergh J. Systemic cytokines and GlycA discriminate disease status and predict corticosteroid response in HTLV-1-associated neuroinflammation. J Neuroinflammation 2022; 19:293. [PMID: 36482436 PMCID: PMC9733207 DOI: 10.1186/s12974-022-02658-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) is an incapacitating neuroinflammatory disorder for which no disease-modifying therapy is available, but corticosteroids provide some clinical benefit. Although HAM/TSP pathogenesis is not fully elucidated, older age, female sex and higher proviral load are established risk factors. We investigated systemic cytokines and a novel chronic inflammatory marker, GlycA, as possible biomarkers of immunopathogenesis and therapeutic response in HAM/TSP, and examined their interaction with established risk factors. PATIENTS AND METHODS We recruited 110 People living with HTLV-1 (PLHTLV-1, 67 asymptomatic individuals and 43 HAM/TSP patients) with a total of 946 person-years of clinical follow-up. Plasma cytokine levels (IL-2, IL-4, IL-6, IL-10, IL-17A, IFN-γ, TNF) and GlycA were quantified by Cytometric Bead Array and 1NMR, respectively. Cytokine signaling and prednisolone response were validated in an independent cohort by nCounter digital transcriptomics. We used multivariable regression, machine learning algorithms and Bayesian network learning for biomarker identification. RESULTS We found that systemic IL-6 was positively correlated with both age (r = 0.50, p < 0.001) and GlycA (r = 0.45, p = 0.00049) in asymptomatics, revealing an 'inflammaging" signature which was absent in HAM/TSP. GlycA levels were higher in women (p = 0.0069), but cytokine levels did not differ between the sexes. IFN-γ (p = 0.007) and IL-17A (p = 0.0001) levels were increased in untreated HAM/TSP Multivariable logistic regression identified IL-17A and proviral load as independent determinants of clinical status, resulting in modest accuracy of predicting HAM/TSP status (64.1%), while a machine learning-derived decision tree classified HAM/TSP patients with 90.7% accuracy. Pre-treatment GlycA and TNF levels significantly predicted clinical worsening (measured by Osame Motor Disability Scale), independent of proviral load. In addition, a poor prednisolone response was significantly correlated with higher post-treatment IFN-γ levels. Likewise, a transcriptomic IFN signaling score, significantly correlated with previously proposed HAM/TSP biomarkers (CASP5/CXCL10/FCGR1A/STAT1), was efficiently blunted by in vitro prednisolone treatment of PBMC from PLHTLV-1 and incident HAM/TSP. CONCLUSIONS An age-related increase in systemic IL-6/GlycA levels reveals inflammaging in PLHTLV-1, in the absence of neurological disease. IFN-γ and IL-17A are biomarkers of untreated HAM/TSP, while pre-treatment GlycA and TNF predict therapeutic response to prednisolone pulse therapy, paving the way for a precision medicine approach in HAM/TSP.
Collapse
Affiliation(s)
- Tatiane Assone
- Laboratory of Medical Investigation LIM 56, Division of Dermatology and Institute of Tropical Medicine of Sao Paulo, Medical School, University of São Paulo, São Paulo, SP, Brazil
- Laboratory of Immunohematology and Forensic Hematology-LIM40, Department of Forensic Medicine, Medical Ethics, Social Medicine and Work, University of São Paulo Medical School, São Paulo, Brazil
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Soraya Maria Menezes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Fernanda de Toledo Gonçalves
- Laboratory of Medical Investigation LIM 56, Division of Dermatology and Institute of Tropical Medicine of Sao Paulo, Medical School, University of São Paulo, São Paulo, SP, Brazil
- Laboratory of Immunohematology and Forensic Hematology-LIM40, Department of Forensic Medicine, Medical Ethics, Social Medicine and Work, University of São Paulo Medical School, São Paulo, Brazil
| | - Victor Angelo Folgosi
- Laboratory of Medical Investigation LIM 56, Division of Dermatology and Institute of Tropical Medicine of Sao Paulo, Medical School, University of São Paulo, São Paulo, SP, Brazil
- Laboratory of Immunohematology and Forensic Hematology-LIM40, Department of Forensic Medicine, Medical Ethics, Social Medicine and Work, University of São Paulo Medical School, São Paulo, Brazil
| | - Gabriela da Silva Prates
- Laboratory of Medical Investigation LIM 56, Division of Dermatology and Institute of Tropical Medicine of Sao Paulo, Medical School, University of São Paulo, São Paulo, SP, Brazil
- Laboratory of Immunohematology and Forensic Hematology-LIM40, Department of Forensic Medicine, Medical Ethics, Social Medicine and Work, University of São Paulo Medical School, São Paulo, Brazil
| | - Tim Dierckx
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Marcos Braz
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Jerusa Smid
- Institute of Infectious Diseases "Emilio Ribas" (IIER) de São Paulo, São Paulo, SP, Brazil
| | - Michel E Haziot
- Institute of Infectious Diseases "Emilio Ribas" (IIER) de São Paulo, São Paulo, SP, Brazil
| | - Rosa M N Marcusso
- Institute of Infectious Diseases "Emilio Ribas" (IIER) de São Paulo, São Paulo, SP, Brazil
| | - Flávia E Dahy
- Institute of Infectious Diseases "Emilio Ribas" (IIER) de São Paulo, São Paulo, SP, Brazil
| | - Evelien Vanderlinden
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Sandra Claes
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Roberta Bruhn
- Vitalant Research Institute, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | - Edward L Murphy
- Vitalant Research Institute, San Francisco, CA, USA
- University of California San Francisco, San Francisco, CA, USA
| | | | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Jurgen Vercauteren
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Jorge Casseb
- Laboratory of Medical Investigation LIM 56, Division of Dermatology and Institute of Tropical Medicine of Sao Paulo, Medical School, University of São Paulo, São Paulo, SP, Brazil
- Laboratory of Immunohematology and Forensic Hematology-LIM40, Department of Forensic Medicine, Medical Ethics, Social Medicine and Work, University of São Paulo Medical School, São Paulo, Brazil
| | - Johan Van Weyenbergh
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
| |
Collapse
|
5
|
Ghosh N, Saha I, Plewczynski D. Unveiling the Biomarkers of Cancer and COVID-19 and Their Regulations in Different Organs by Integrating RNA-Seq Expression and Protein-Protein Interactions. ACS OMEGA 2022; 7:43589-43602. [PMID: 36506181 PMCID: PMC9730762 DOI: 10.1021/acsomega.2c04389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
Cancer and COVID-19 have killed millions of people worldwide. COVID-19 is even more dangerous to people with comorbidities such as cancer. Thus, it is imperative to identify the key human genes or biomarkers that can be targeted to develop novel prognosis and therapeutic strategies. The transcriptomic data provided by the next-generation sequencing technique makes this identification very convenient. Hence, mRNA (messenger ribonucleic acid) expression data of 2265 cancer and 282 normal patients were considered, while for COVID-19 assessment, 784 and 425 COVID-19 and normal patients were taken, respectively. Initially, volcano plots were used to identify the up- and down-regulated genes for both cancer and COVID-19. Thereafter, protein-protein interaction (PPI) networks were prepared by combining all the up- and down-regulated genes for each of cancer and COVID-19. Subsequently, such networks were analyzed to identify the top 10 genes with the highest degree of connection to provide the biomarkers. Interestingly, these genes were all up-regulated for cancer, while they were down-regulated for COVID-19. This study had also identified common genes between cancer and COVID-19, all of which were up-regulated in both the diseases. This analysis revealed that FN1 was highly up-regulated in different organs for cancer, while EEF2 was dysregulated in most organs affected by COVID-19. Then, functional enrichment analysis was performed to identify significant biological processes. Finally, the drugs for cancer and COVID-19 biomarkers and the common genes between them were identified using the Enrichr online web tool. These drugs include lucanthone, etoposide, and methotrexate, targeting the biomarkers for cancer, while paclitaxel is an important drug for COVID-19.
Collapse
Affiliation(s)
- Nimisha Ghosh
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland
- Department
of Computer Science and Information Technology, Institute of Technical
Education and Research, Siksha ‘O’
Anusandhan (Deemed to Be University), Bhubaneswar 751030 Odisha, India
| | - Indrajit Saha
- Department
of Computer Science and Engineering, National
Institute of Technical Teachers’ Training and Research, Kolkata 700106 West Bengal, India
| | - Dariusz Plewczynski
- Laboratory
of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Warsaw 02-097, Poland
- Laboratory
of Bioinformatics and Computational Genomics, Faculty of Mathematics
and Information Science, Warsaw University
of Technology, Warsaw 00-662, Poland
| |
Collapse
|