1
|
Ramos-Medina MJ, Echeverría-Garcés G, Kyriakidis NC, León Cáceres Á, Ortiz-Prado E, Bautista J, Pérez-Meza ÁA, Abad-Sojos A, Nieto-Jaramillo K, Espinoza-Ferrao S, Ocaña-Paredes B, López-Cortés A. CardiOmics signatures reveal therapeutically actionable targets and drugs for cardiovascular diseases. Heliyon 2024; 10:e23682. [PMID: 38187312 PMCID: PMC10770621 DOI: 10.1016/j.heliyon.2023.e23682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Cardiovascular diseases are the leading cause of death worldwide, with heart failure being a complex condition that affects millions of individuals. Single-nucleus RNA sequencing has recently emerged as a powerful tool for unraveling the molecular mechanisms behind cardiovascular diseases. This cutting-edge technology enables the identification of molecular signatures, intracellular networks, and spatial relationships among cardiac cells, including cardiomyocytes, mast cells, lymphocytes, macrophages, lymphatic endothelial cells, endocardial cells, endothelial cells, epicardial cells, adipocytes, fibroblasts, neuronal cells, pericytes, and vascular smooth muscle cells. Despite these advancements, the discovery of essential therapeutic targets and drugs for precision cardiology remains a challenge. To bridge this gap, we conducted comprehensive in silico analyses of single-nucleus RNA sequencing data, functional enrichment, protein interactome network, and identification of the shortest pathways to physiological phenotypes. This integrated multi-omics analysis generated CardiOmics signatures, which allowed us to pinpoint three therapeutically actionable targets (ADRA1A1, PPARG, and ROCK2) and 15 effective drugs, including adrenergic receptor agonists, adrenergic receptor antagonists, norepinephrine precursors, PPAR receptor agonists, and Rho-associated kinase inhibitors, involved in late-stage cardiovascular disease clinical trials.
Collapse
Affiliation(s)
- María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | - Nikolaos C. Kyriakidis
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Ángela León Cáceres
- Heidelberg Institute of Global Health, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
- Instituto de Salud Pública, Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Jhommara Bautista
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Álvaro A. Pérez-Meza
- Escuela de Medicina, Colegio de Ciencias de La Salud COCSA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | | | - Karol Nieto-Jaramillo
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuqui, Ecuador
| | | | - Belén Ocaña-Paredes
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| |
Collapse
|
2
|
Zhao H, Li H, Liu Q, Dong G, Hou C, Li Y, Zhao Y. Using TransR to enhance drug repurposing knowledge graph for COVID-19 and its complications. Methods 2024; 221:82-90. [PMID: 38104883 DOI: 10.1016/j.ymeth.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
MOTIVATION The COVID-19 pandemic has been spreading globally for four years, yet specific drugs that effectively suppress the virus remain elusive. Furthermore, the emergence of complications associated with COVID-19 presents significant challenges, making the development of therapeutics for COVID-19 and its complications an urgent task. However, traditional drug development processes are time-consuming. Drug repurposing, which involves identifying new therapeutic applications for existing drugs, presents a viable alternative. RESULT In this study, we construct a knowledge graph by retrieving information on genes, drugs, and diseases from databases such as DRUGBANK and GNBR. Next, we employ the TransR knowledge representation learning approach to embed entities and relationships into the knowledge graph. Subsequently, we train the knowledge graph using a graph neural network model based on TransR scoring. This trained knowledge graph is then utilized to predict drugs for the treatment of COVID-19 and its complications. Based on experimental results, we have identified 15 drugs out of the top 30 with the highest success rates associated with treating COVID-19 and its complications. Notably, out of these 15 drugs, 10 specifically aimed at treating COVID-19, such as Torcetrapib and Tocopherol, has not been previously identified in the knowledge graph. This finding highlights the potential of our model in aiding healthcare professionals in drug development and research related to this disease.
Collapse
Affiliation(s)
- Hongxi Zhao
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Hongfei Li
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Qiaoming Liu
- School of Medicine and Health, Harbin Institute of Technology, 150001, Harbin, HeiLongJiang, China; Zhengzhou Research Institute, Harbin Institute of Technology, 450000, Zhengzhou, Henan, China
| | - Guanghui Dong
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Chang Hou
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China
| | - Yang Li
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.
| | - Yuming Zhao
- College of Computer and Control Engineering, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China; College of Life Science, Northeast Forestry University, 150040, Harbin, HeiLongJiang, China.
| |
Collapse
|
3
|
Sanhueza S, Vidal MA, Hernandez MA, Henriquez-Beltran ME, Cabrera C, Quiroga R, Antilef BE, Aguilar KP, Castillo DA, Llerena FJ, Fraga Figueroa M, Nazal M, Castro E, Lagos P, Moreno A, Lastra JJ, Gajardo J, Garcés P, Riffo B, Buchert J, Sanhueza R, Ormazába V, Saldivia P, Vargas C, Nourdin G, Koch E, Zuñiga FA, Lamperti L, Bustos P, Guzmán-Gutiérrez E, Tapia CA, Ferrada L, Cerda G, Woehlbier U, Riquelme E, Yuseff MI, Muñoz Ramirez BA, Lombardi G, De Gonzalo-Calvo D, Salomon C, Verdugo RA, Quiñones LA, Colombo A, Barría MI, Labarca G, Nova-Lamperti E. Clinical and pulmonary function analysis in long-COVID revealed that long-term pulmonary dysfunction is associated with vascular inflammation pathways and metabolic syndrome. Front Med (Lausanne) 2023; 10:1271863. [PMID: 37869162 PMCID: PMC10590130 DOI: 10.3389/fmed.2023.1271863] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Long-term pulmonary dysfunction (L-TPD) is one of the most critical manifestations of long-COVID. This lung affection has been associated with disease severity during the acute phase and the presence of previous comorbidities, however, the clinical manifestations, the concomitant consequences and the molecular pathways supporting this clinical condition remain unknown. The aim of this study was to identify and characterize L-TPD in patients with long-COVID and elucidate the main pathways and long-term consequences attributed to this condition by analyzing clinical parameters and functional tests supported by machine learning and serum proteome profiling. Methods Patients with L-TPD were classified according to the results of their computer-tomography (CT) scan and diffusing capacity of the lungs for carbon monoxide adjusted for hemoglobin (DLCOc) tests at 4 and 12-months post-infection. Results Regarding the acute phase, our data showed that L-TPD was favored in elderly patients with hypertension or insulin resistance, supported by pathways associated with vascular inflammation and chemotaxis of phagocytes, according to computer proteomics. Then, at 4-months post-infection, clinical and functional tests revealed that L-TPD patients exhibited a restrictive lung condition, impaired aerobic capacity and reduced muscular strength. At this time point, high circulating levels of platelets and CXCL9, and an inhibited FCgamma-receptor-mediated-phagocytosis due to reduced FcγRIII (CD16) expression in CD14+ monocytes was observed in patients with L-TPD. Finally, 1-year post infection, patients with L-TPD worsened metabolic syndrome and augmented body mass index in comparison with other patient groups. Discussion Overall, our data demonstrated that CT scan and DLCOc identified patients with L-TPD after COVID-19. This condition was associated with vascular inflammation and impair phagocytosis of virus-antibody immune complexes by reduced FcγRIII expression. In addition, we conclude that COVID-19 survivors required a personalized follow-up and adequate intervention to reduce long-term sequelae and the appearance of further metabolic diseases.
Collapse
Affiliation(s)
- Sergio Sanhueza
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Mabel A. Vidal
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
- Facultad de Ingeniería, Diseño y Arquitectura, Universidad San Sebastián, Concepción, Chile
| | | | - Mario E. Henriquez-Beltran
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
- Núcleo de Investigación en Ciencias de la Salud, Universidad Adventista de Chile, Chillán, Chile
- Kinesiology School, Escuela de Kinesiología, Facultad de Salud, Universidad Santo Tomás, Los Ángeles, Chile
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Camilo Cabrera
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Romina Quiroga
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Bárbara E. Antilef
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Kevin P. Aguilar
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Daniela A. Castillo
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Faryd J. Llerena
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Marco Fraga Figueroa
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Mauricio Nazal
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Eritson Castro
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Paola Lagos
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Alexa Moreno
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Jaime J. Lastra
- Internal Medicine Department, Hospital Guillermo Grant Benavente and Medicine Faculty, University of Concepción, Concepción, Chile
| | - Jorge Gajardo
- Internal Medicine Department, Hospital Guillermo Grant Benavente and Medicine Faculty, University of Concepción, Concepción, Chile
| | - Pamela Garcés
- Internal Medicine Department, Hospital Guillermo Grant Benavente and Medicine Faculty, University of Concepción, Concepción, Chile
| | | | | | - Rocío Sanhueza
- Kinesiology School, Escuela de Kinesiología, Facultad de Salud, Universidad Santo Tomás, Los Ángeles, Chile
| | - Valeska Ormazába
- Department of Pharmacology, Faculty of Biological Sciences, University of Concepción, Concepción, Chile
| | - Pablo Saldivia
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Chile
| | - Cristian Vargas
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Chile
| | - Guillermo Nourdin
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Chile
| | - Elard Koch
- Division of Biotechnology, MELISA Institute, San Pedro de la Paz, Chile
| | - Felipe A. Zuñiga
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Liliana Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Paula Bustos
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Enrique Guzmán-Gutiérrez
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Claudio A. Tapia
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| | - Luciano Ferrada
- CMA Bío-Bío - Advanced Microscopy Center, University of Concepción, Concepción, Chile
| | - Gustavo Cerda
- CMA Bío-Bío - Advanced Microscopy Center, University of Concepción, Concepción, Chile
| | - Ute Woehlbier
- Center for Integrative Biology, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Erick Riquelme
- Faculty of Medicine, Pontifical Catholic University of Chile, Santiago, Chile
| | - Maria-Isabel Yuseff
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Braulio A. Muñoz Ramirez
- Department of Pharmacology and Toxicology, School of Medicine, Indiana University Bloomington, Bloomington, IN, United States
| | - Giovanna Lombardi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - 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
| | - Carlos Salomon
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, UQ Centre for Clinical Research, Royal Brisbane and Women’s Hospital, Medicine and Biomedical Science Faculty, The University of Queensland, Brisbane, QLD, Australia
| | - Ricardo A. Verdugo
- Instituto de Investigación Interdisciplinaria y Escuela de Medicina, Universidad de Talca, Talca, Chile
| | - Luis A. Quiñones
- Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Pharmaceutical Sciences and Technology, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | - Alicia Colombo
- Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile
- Servicio de Anatomía Patológica, Hospital Clínico, Universidad de Chile, Santiago, Chile
| | - Maria I. Barría
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Puerto Montt, Chile
| | - Gonzalo Labarca
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
- Internal Medicine, Complejo Asistencial Dr. Víctor Ríos Ruiz, Los Ángeles, Chile
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Pharmacy Faculty, University of Concepción, Concepción, Chile
| |
Collapse
|
4
|
Meng R, Yin S, Sun J, Hu H, Zhao Q. scAAGA: Single cell data analysis framework using asymmetric autoencoder with gene attention. Comput Biol Med 2023; 165:107414. [PMID: 37660567 DOI: 10.1016/j.compbiomed.2023.107414] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
In recent years, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique for investigating cellular heterogeneity and structure. However, analyzing scRNA-seq data remains challenging, especially in the context of COVID-19 research. Single-cell clustering is a key step in analyzing scRNA-seq data, and deep learning methods have shown great potential in this area. In this work, we propose a novel scRNA-seq analysis framework called scAAGA. Specifically, we utilize an asymmetric autoencoder with a gene attention module to learn important gene features adaptively from scRNA-seq data, with the aim of improving the clustering effect. We apply scAAGA to COVID-19 peripheral blood mononuclear cell (PBMC) scRNA-seq data and compare its performance with state-of-the-art methods. Our results consistently demonstrate that scAAGA outperforms existing methods in terms of adjusted rand index (ARI), normalized mutual information (NMI), and adjusted mutual information (AMI) scores, achieving improvements ranging from 2.8% to 27.8% in NMI scores. Additionally, we discuss a data augmentation technology to expand the datasets and improve the accuracy of scAAGA. Overall, scAAGA presents a robust tool for scRNA-seq data analysis, enhancing the accuracy and reliability of clustering results in COVID-19 research.
Collapse
Affiliation(s)
- Rui Meng
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Shuaidong Yin
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
| | - Jianqiang Sun
- School of Information Science and Engineering, Linyi University, Linyi, 276000, China
| | - Huan Hu
- Institute of Applied Genomics, Fuzhou University, Fuzhou, 350108, China.
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China.
| |
Collapse
|
5
|
Pérez-Villa A, Echeverría-Garcés G, Ramos-Medina MJ, Prathap L, Martínez-López M, Ramírez-Sánchez D, García-Cárdenas JM, Armendáriz-Castillo I, Guerrero S, Paz C, López-Cortés A. Integrated multi-omics analysis reveals the molecular interplay between circadian clocks and cancer pathogenesis. Sci Rep 2023; 13:14198. [PMID: 37648722 PMCID: PMC10469199 DOI: 10.1038/s41598-023-39401-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023] Open
Abstract
Circadian rhythms (CRs) are fundamental biological processes that significantly impact human well-being. Disruption of these rhythms can trigger insufficient neurocognitive development, insomnia, mental disorders, cardiovascular diseases, metabolic dysfunctions, and cancer. The field of chronobiology has increased our understanding of how rhythm disturbances contribute to cancer pathogenesis, and how circadian timing influences the efficacy of cancer treatments. As the circadian clock steadily gains recognition as an emerging factor in tumorigenesis, a thorough and comprehensive multi-omics analysis of CR genes/proteins has never been performed. To shed light on this, we performed, for the first time, an integrated data analysis encompassing genomic/transcriptomic alterations across 32 cancer types (n = 10,918 tumors) taken from the PanCancer Atlas, unfavorable prognostic protein analysis, protein-protein interactomics, and shortest distance score pathways to cancer hallmark phenotypes. This data mining strategy allowed us to unravel 31 essential CR-related proteins involved in the signaling crossroad between circadian rhythms and cancer. In the context of drugging the clock, we identified pharmacogenomic clinical annotations and drugs currently in late phase clinical trials that could be considered as potential cancer therapeutic strategies. These findings highlight the diverse roles of CR-related genes/proteins in the realm of cancer research and therapy.
Collapse
Affiliation(s)
- Andy Pérez-Villa
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Lavanya Prathap
- Department of Anatomy, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, India
| | - Mayra Martínez-López
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - David Ramírez-Sánchez
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Jennyfer M García-Cárdenas
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain
| | - Isaac Armendáriz-Castillo
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Santiago Guerrero
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Clara Paz
- Grupo de Investigación Bienestar, Salud y Sociedad, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador.
| |
Collapse
|
6
|
López-Cortés A, Prathap L, Ortiz-Prado E, Kyriakidis NC, León Cáceres Á, Armendáriz-Castillo I, Vera-Guapi A, Yumiceba V, Simbaña-Rivera K, Echeverría-Garcés G, García-Cárdenas JM, Pérez-Villa A, Guevara-Ramírez P, Abad-Sojos A, Bautista J, Puig San Andrés L, Varela N, Guerrero S. The close interaction between hypoxia-related proteins and metastasis in pancarcinomas. Sci Rep 2022; 12:11100. [PMID: 35773405 PMCID: PMC9246854 DOI: 10.1038/s41598-022-15246-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
Many primary-tumor subregions exhibit low levels of molecular oxygen and restricted access to nutrients due to poor vascularization in the tissue, phenomenon known as hypoxia. Hypoxic tumors are able to regulate the expression of certain genes and signaling molecules in the microenvironment that shift it towards a more aggressive phenotype. The transcriptional landscape of the tumor favors malignant transformation of neighboring cells and their migration to distant sites. Herein, we focused on identifying key proteins that participate in the signaling crossroads between hypoxic environment and metastasis progression that remain poorly defined. To shed light on these mechanisms, we performed an integrated multi-omics analysis encompassing genomic/transcriptomic alterations of hypoxia-related genes and Buffa hypoxia scores across 17 pancarcinomas taken from the PanCancer Atlas project from The Cancer Genome Atlas consortium, protein-protein interactome network, shortest paths from hypoxia-related proteins to metastatic and angiogenic phenotypes, and drugs involved in current clinical trials to treat the metastatic disease. As results, we identified 30 hypoxia-related proteins highly involved in metastasis and angiogenesis. This set of proteins, validated with the MSK-MET Project, could represent key targets for developing therapies. The upregulation of mRNA was the most prevalent alteration in all cancer types. The highest frequencies of genomic/transcriptomic alterations and hypoxia score belonged to tumor stage 4 and positive metastatic status in all pancarcinomas. The most significantly associated signaling pathways were HIF-1, PI3K-Akt, thyroid hormone, ErbB, FoxO, mTOR, insulin, MAPK, Ras, AMPK, and VEGF. The interactome network revealed high-confidence interactions among hypoxic and metastatic proteins. The analysis of shortest paths revealed several ways to spread metastasis and angiogenesis from hypoxic proteins. Lastly, we identified 23 drugs enrolled in clinical trials focused on metastatic disease treatment. Six of them were involved in advanced-stage clinical trials: aflibercept, bevacizumab, cetuximab, erlotinib, ipatasertib, and panitumumab.
Collapse
Affiliation(s)
- Andrés López-Cortés
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, 170302, Quito, Ecuador.
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas, 170124, Quito, Ecuador.
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain.
| | - Lavanya Prathap
- Department of Anatomy, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, 600077, Chennai, India
| | - Esteban Ortiz-Prado
- One Health Research Group, Universidad de Las Américas, 170124, Quito, Ecuador
| | | | - Ángela León Cáceres
- Heidelberg Institute of Global Health, Faculty of Medicine, University of Heidelberg, 69117, Heidelberg, Germany
| | - Isaac Armendáriz-Castillo
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
- Instituto Nacional de Investigación en Salud Pública, 170136, Quito, Ecuador
- Facultad de Ingenierías y Ciencias Aplicadas, Universidad Internacional SEK, 170302, Quito, Ecuador
| | - Antonella Vera-Guapi
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, 07747, Jena, Germany
| | - Verónica Yumiceba
- Institut Für Humangenetik Lübeck, Universität Zu Lübeck, 23562, Lübeck, Germany
| | - Katherine Simbaña-Rivera
- One Health Research Group, Universidad de Las Américas, 170124, Quito, Ecuador
- Latin American Network for Cancer Research (LAN-CANCER), Lima, Peru
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
| | - Jennyfer M García-Cárdenas
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, 170113, Quito, Ecuador
| | - Andy Pérez-Villa
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
| | - Patricia Guevara-Ramírez
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
| | | | | | | | - Nelson Varela
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, 8320000, Santiago, Chile
| | - Santiago Guerrero
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28015, Madrid, Spain.
- Laboratorio de Ciencia de Datos Biomédicos, Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, 170113, Quito, Ecuador.
| |
Collapse
|
7
|
López-Cortés A, Guerrero S, Ortiz-Prado E, Yumiceba V, Vera-Guapi A, León Cáceres Á, Simbaña-Rivera K, Gómez-Jaramillo AM, Echeverría-Garcés G, García-Cárdenas JM, Guevara-Ramírez P, Cabrera-Andrade A, Puig San Andrés L, Cevallos-Robalino D, Bautista J, Armendáriz-Castillo I, Pérez-Villa A, Abad-Sojos A, Ramos-Medina MJ, León-Sosa A, Abarca E, Pérez-Meza ÁA, Nieto-Jaramillo K, Jácome AV, Morillo A, Arias-Erazo F, Fuenmayor-González L, Quiñones LA, Kyriakidis NC. Pulmonary Inflammatory Response in Lethal COVID-19 Reveals Potential Therapeutic Targets and Drugs in Phases III/IV Clinical Trials. Front Pharmacol 2022; 13:833174. [PMID: 35422702 PMCID: PMC9002106 DOI: 10.3389/fphar.2022.833174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/07/2022] [Indexed: 12/26/2022] Open
Abstract
Background: It is imperative to identify drugs that allow treating symptoms of severe COVID-19. Respiratory failure is the main cause of death in severe COVID-19 patients, and the host inflammatory response at the lungs remains poorly understood. Methods: Therefore, we retrieved data from post-mortem lungs from COVID-19 patients and performed in-depth in silico analyses of single-nucleus RNA sequencing data, inflammatory protein interactome network, and shortest pathways to physiological phenotypes to reveal potential therapeutic targets and drugs in advanced-stage COVID-19 clinical trials. Results: Herein, we analyzed transcriptomics data of 719 inflammatory response genes across 19 cell types (116,313 nuclei) from lung autopsies. The functional enrichment analysis of the 233 significantly expressed genes showed that the most relevant biological annotations were inflammatory response, innate immune response, cytokine production, interferon production, macrophage activation, blood coagulation, NLRP3 inflammasome complex, and the TLR, JAK-STAT, NF-κB, TNF, oncostatin M signaling pathways. Subsequently, we identified 34 essential inflammatory proteins with both high-confidence protein interactions and shortest pathways to inflammation, cell death, glycolysis, and angiogenesis. Conclusion: We propose three small molecules (baricitinib, eritoran, and montelukast) that can be considered for treating severe COVID-19 symptoms after being thoroughly evaluated in COVID-19 clinical trials.
Collapse
Affiliation(s)
- Andrés López-Cortés
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito, Ecuador.,Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Santiago Guerrero
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Verónica Yumiceba
- Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - Antonella Vera-Guapi
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Ángela León Cáceres
- Heidelberg Institute of Global Health, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Katherine Simbaña-Rivera
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador.,Latin American Network for Cancer Research (LAN-CANCER), Lima, Peru
| | - Ana María Gómez-Jaramillo
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Jennyfer M García-Cárdenas
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | | | | | | | | | - Isaac Armendáriz-Castillo
- Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain.,Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Andy Pérez-Villa
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | | | | | | | | | - Álvaro A Pérez-Meza
- Biotechnology Engineering Career, Faculty of Life Sciences, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | | | - Andrea V Jácome
- Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - Luis Abel Quiñones
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain.,Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nikolaos C Kyriakidis
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| |
Collapse
|
8
|
Hasankhani A, Bahrami A, Sheybani N, Aria B, Hemati B, Fatehi F, Ghaem Maghami Farahani H, Javanmard G, Rezaee M, Kastelic JP, Barkema HW. Differential Co-Expression Network Analysis Reveals Key Hub-High Traffic Genes as Potential Therapeutic Targets for COVID-19 Pandemic. Front Immunol 2022; 12:789317. [PMID: 34975885 PMCID: PMC8714803 DOI: 10.3389/fimmu.2021.789317] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/26/2021] [Indexed: 01/08/2023] Open
Abstract
Background The recent emergence of COVID-19, rapid worldwide spread, and incomplete knowledge of molecular mechanisms underlying SARS-CoV-2 infection have limited development of therapeutic strategies. Our objective was to systematically investigate molecular regulatory mechanisms of COVID-19, using a combination of high throughput RNA-sequencing-based transcriptomics and systems biology approaches. Methods RNA-Seq data from peripheral blood mononuclear cells (PBMCs) of healthy persons, mild and severe 17 COVID-19 patients were analyzed to generate a gene expression matrix. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules in healthy samples as a reference set. For differential co-expression network analysis, module preservation and module-trait relationships approaches were used to identify key modules. Then, protein-protein interaction (PPI) networks, based on co-expressed hub genes, were constructed to identify hub genes/TFs with the highest information transfer (hub-high traffic genes) within candidate modules. Results Based on differential co-expression network analysis, connectivity patterns and network density, 72% (15 of 21) of modules identified in healthy samples were altered by SARS-CoV-2 infection. Therefore, SARS-CoV-2 caused systemic perturbations in host biological gene networks. In functional enrichment analysis, among 15 non-preserved modules and two significant highly-correlated modules (identified by MTRs), 9 modules were directly related to the host immune response and COVID-19 immunopathogenesis. Intriguingly, systemic investigation of SARS-CoV-2 infection identified signaling pathways and key genes/proteins associated with COVID-19's main hallmarks, e.g., cytokine storm, respiratory distress syndrome (ARDS), acute lung injury (ALI), lymphopenia, coagulation disorders, thrombosis, and pregnancy complications, as well as comorbidities associated with COVID-19, e.g., asthma, diabetic complications, cardiovascular diseases (CVDs), liver disorders and acute kidney injury (AKI). Topological analysis with betweenness centrality (BC) identified 290 hub-high traffic genes, central in both co-expression and PPI networks. We also identified several transcriptional regulatory factors, including NFKB1, HIF1A, AHR, and TP53, with important immunoregulatory roles in SARS-CoV-2 infection. Moreover, several hub-high traffic genes, including IL6, IL1B, IL10, TNF, SOCS1, SOCS3, ICAM1, PTEN, RHOA, GDI2, SUMO1, CASP1, IRAK3, HSPA5, ADRB2, PRF1, GZMB, OASL, CCL5, HSP90AA1, HSPD1, IFNG, MAPK1, RAB5A, and TNFRSF1A had the highest rates of information transfer in 9 candidate modules and central roles in COVID-19 immunopathogenesis. Conclusion This study provides comprehensive information on molecular mechanisms of SARS-CoV-2-host interactions and identifies several hub-high traffic genes as promising therapeutic targets for the COVID-19 pandemic.
Collapse
Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Negin Sheybani
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Behzad Aria
- Department of Physical Education and Sports Science, School of Psychology and Educational Sciences, Yazd University, Yazd, Iran
| | - Behzad Hemati
- Biotechnology Research Center, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Farhang Fatehi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | | | - Ghazaleh Javanmard
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mahsa Rezaee
- Department of Medical Mycology, School of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - John P Kastelic
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
9
|
Han F, Liu Y, Mo M, Chen J, Wang C, Yang Y, Wu J. Current treatment strategies for COVID‑19 (Review). Mol Med Rep 2021; 24:858. [PMID: 34664677 PMCID: PMC8548951 DOI: 10.3892/mmr.2021.12498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022] Open
Abstract
The spread of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged suddenly at the end of 2019 and the disease came to be known as coronavirus disease 2019 (COVID-19). To date, there is no specific therapy established to treat COVID-19. Identifying effective treatments is urgently required to treat patients and stop the transmission of SARS-CoV-2 in humans. For the present review, >100 publications on therapeutic agents for COVID-19, including in vitro and in vivo animal studies, case reports, retrospective analyses and meta-analyses were retrieved from PubMed and analyzed, and promising therapeutic agents that may be used to combat SARS-CoV-2 infection were highlighted. Since the outbreak of COVID-19, different drugs have been repurposed for its treatment. Existing drugs, including chloroquine (CQ), its derivative hydroxychloroquine (HCQ), remdesivir and nucleoside analogues, monoclonal antibodies, convalescent plasma, Chinese herbal medicine and natural compounds for treating COVID-19 evaluated in experimental and clinical studies were discussed. Although early clinical studies suggested that CQ/HCQ produces antiviral action, later research indicated certain controversy regarding their use for treating COVID-19. The molecular mechanisms of these therapeutic agents against SARS-CoV2 have been investigated, including inhibition of viral interactions with angiotensin-converting enzyme 2 receptors in human cells, viral RNA-dependent RNA polymerase, RNA replication and the packaging of viral particles. Potent therapeutic options were reviewed and future challenges to accelerate the development of novel therapeutic agents to treat and prevent COVID-19 were acknowledged.
Collapse
Affiliation(s)
- Fabin Han
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Yanming Liu
- Laboratory for Stem Cell and Regenerative Medicine, Institute for Tissue Engineering and Regenerative Medicine, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong 252000, P.R. China
| | - Mei Mo
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Juanli Chen
- Laboratory for Stem Cell and Regenerative Medicine, Institute for Tissue Engineering and Regenerative Medicine, Liaocheng People's Hospital/Liaocheng University, Liaocheng, Shandong 252000, P.R. China
| | - Cheng Wang
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Yong Yang
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| | - Jibiao Wu
- The Translational Research Laboratory for Stem Cell and Traditional Chinese Medicine, Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, P.R. China
| |
Collapse
|
10
|
López-Cortés A, Abarca E, Silva L, Velastegui E, León-Sosa A, Karolys G, Cabrera F, Caicedo A. Identification of key proteins in the signaling crossroads between wound healing and cancer hallmark phenotypes. Sci Rep 2021; 11:17245. [PMID: 34446793 PMCID: PMC8390472 DOI: 10.1038/s41598-021-96750-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Wound healing (WH) and cancer seem to share common cellular and molecular processes that could work in a tight balance to maintain tissue homeostasis or, when unregulated, drive tumor progression. The "Cancer Hallmarks" comprise crucial biological properties that mediate the advancement of the disease and affect patient prognosis. These hallmarks have been proposed to overlap with essential features of the WH process. However, common hallmarks and proteins actively participating in both processes have yet to be described. In this work we identify 21 WH proteins strongly linked with solid tumors by integrated TCGA Pan-Cancer and multi-omics analyses. These proteins were associated with eight of the ten described cancer hallmarks, especially avoiding immune destruction. These results show that WH and cancer's common proteins are involved in the microenvironment modification of solid tissues and immune system regulation. This set of proteins, between WH and cancer, could represent key targets for developing therapies.
Collapse
Affiliation(s)
- Andrés López-Cortés
- grid.412257.70000 0004 0485 6316Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito, Ecuador ,Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain ,grid.8073.c0000 0001 2176 8535RNASA-IMEDIR, Computer Science Faculty, Universidad of A Coruna, A Coruña, Spain
| | - Estefanía Abarca
- grid.442129.8Carrera de Biotecnología, Universidad Politécnica Salesiana UPS, Quito, Ecuador
| | - Leonardo Silva
- grid.442129.8Carrera de Biotecnología, Universidad Politécnica Salesiana UPS, Quito, Ecuador
| | - Erick Velastegui
- grid.442129.8Carrera de Biotecnología, Universidad Politécnica Salesiana UPS, Quito, Ecuador
| | - Ariana León-Sosa
- grid.412251.10000 0000 9008 4711Instituto de Investigaciones en Biomedicina iBioMed, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Germania Karolys
- grid.442129.8Carrera de Biotecnología, Universidad Politécnica Salesiana UPS, Quito, Ecuador ,grid.442129.8Grupo de Investigación y Desarrollo en Ciencias Aplicadas a los Recursos Biológicos, Universidad Politécnica Salesiana, Quito, Ecuador
| | - Francisco Cabrera
- grid.412251.10000 0000 9008 4711Instituto de Investigaciones en Biomedicina iBioMed, Universidad San Francisco de Quito USFQ, Quito, Ecuador ,grid.412251.10000 0000 9008 4711Colegio de Ciencias de la Salud, Escuela de Medicina Veterinaria, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Andrés Caicedo
- grid.412251.10000 0000 9008 4711Instituto de Investigaciones en Biomedicina iBioMed, Universidad San Francisco de Quito USFQ, Quito, Ecuador ,grid.412251.10000 0000 9008 4711Colegio de Ciencias de la Salud, Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador ,Mito-Act Research Consortium, Quito, Ecuador ,grid.412251.10000 0000 9008 4711Sistemas Médicos SIME, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| |
Collapse
|
11
|
Manivannan J, Sundaresan L. Systems level insights into the impact of airborne exposure on SARS-CoV-2 pathogenesis and COVID-19 outcome - A multi-omics big data study. GENE REPORTS 2021; 25:101312. [PMID: 34401607 PMCID: PMC8358088 DOI: 10.1016/j.genrep.2021.101312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 07/14/2021] [Accepted: 08/03/2021] [Indexed: 12/24/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a viral pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that led to more than 800,00 deaths and continues to be a major threat worldwide. The scientific community has been studying the risk factors associated with SARS-CoV-2 infection and pathogenesis. Recent studies highlight the possible contribution of atmospheric air pollution, specifically particulate matter (PM) exposure as a co-factor in COVID-19 severity. Hence, meaningful translation of suitable omics datasets of SARS-CoV-2 infection and PM exposure is warranted to understand the possible involvement of airborne exposome on COVID-19 outcome. Publicly available transcriptomic data (microarray and RNA-Seq) related to COVID-19 lung biopsy, SARS-CoV-2 infection in epithelial cells and PM exposure (lung tissue, epithelial and endothelial cells) were obtained in addition with proteome and interactome datasets. System-wide pathway/network analysis was done through appropriate software tools and data resources. The primary findings are; 1. There is no robust difference in the expression of SARS-CoV-2 entry factors upon particulate exposure, 2. The upstream pathways associated with upregulated genes during SARS-CoV-2 infection considerably overlap with that of PM exposure, 3. Similar pathways were differentially expressed during SARS-CoV-2 infection and PM exposure, 4. SARS-CoV-2 interacting host factors were predicted to be associated with the molecular impact of PM exposure and 5. Differentially expressed pathways during PM exposure may increase COVID-19 severity. Based on the observed molecular mechanisms (direct and indirect effects) the current study suggests that airborne PM exposure has to be considered as an additional co-factor in the outcome of COVID-19.
Collapse
Key Words
- ACE2, angiotensin-converting enzyme 2
- COVID-19
- COVID19, coronavirus disease 2019
- CTSB, cathepsin B
- CTSL, cathepsin L
- DEG, differentially expressed genes
- GEO, Gene Expression Omnibus
- GSEA, gene set enrichment analysis
- IL-17, interleukin-17
- Microarray
- Omics
- PM, particulate matter
- PPAR, peroxisome proliferator-activated receptors
- PPI, protein-protein interaction
- PTM, post-translational modification
- Particulate matter
- Pathway analysis
- Proteome
- RNA-seq
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- TLR, Toll-like receptor
- TMPRSS2, transmembrane protease, serine 2
- TNF, tumor necrosis factor
- VEGF, vascular endothelial growth factor
- X2K, eXpression2Kinases
Collapse
Affiliation(s)
- Jeganathan Manivannan
- Environmental Health and Toxicology Lab, Department of Environmental Sciences, School of Life Sciences, Bharathiar University, Coimbatore 641046, Tamil Nadu, India
| | - Lakshmikirupa Sundaresan
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| |
Collapse
|
12
|
Gusev E, Sarapultsev A, Hu D, Chereshnev V. Problems of Pathogenesis and Pathogenetic Therapy of COVID-19 from the Perspective of the General Theory of Pathological Systems (General Pathological Processes). Int J Mol Sci 2021; 22:7582. [PMID: 34299201 PMCID: PMC8304657 DOI: 10.3390/ijms22147582] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic examines not only the state of actual health care but also the state of fundamental medicine in various countries. Pro-inflammatory processes extend far beyond the classical concepts of inflammation. They manifest themselves in a variety of ways, beginning with extreme physiology, then allostasis at low-grade inflammation, and finally the shockogenic phenomenon of "inflammatory systemic microcirculation". The pathogenetic core of critical situations, including COVID-19, is this phenomenon. Microcirculatory abnormalities, on the other hand, lie at the heart of a specific type of general pathological process known as systemic inflammation (SI). Systemic inflammatory response, cytokine release, cytokine storm, and thrombo-inflammatory syndrome are all terms that refer to different aspects of SI. As a result, the metabolic syndrome model does not adequately reflect the pathophysiology of persistent low-grade systemic inflammation (ChSLGI). Diseases associated with ChSLGI, on the other hand, are risk factors for a severe COVID-19 course. The review examines the role of hypoxia, metabolic dysfunction, scavenger receptors, and pattern-recognition receptors, as well as the processes of the hemophagocytic syndrome, in the systemic alteration and development of SI in COVID-19.
Collapse
Affiliation(s)
- Evgenii Gusev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia; (E.G.); (V.C.)
| | - Alexey Sarapultsev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia; (E.G.); (V.C.)
- School of Medical Biology, South Ural State University, 454080 Chelyabinsk, Russia
| | - Desheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 200092, China;
| | - Valeriy Chereshnev
- Institute of Immunology and Physiology, Ural Branch of the Russian Academy of Science, 620049 Ekaterinburg, Russia; (E.G.); (V.C.)
| |
Collapse
|
13
|
Kumar V. Can proteomics-based approaches further help COVID-19 prevention and therapy? Expert Rev Proteomics 2021; 18:241-245. [PMID: 33929923 PMCID: PMC8127169 DOI: 10.1080/14789450.2021.1924684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Vijay Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Tennessee Health Science Center (UTHSC), Memphis, TN, USA
| |
Collapse
|