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Bishop CR, Yan K, Nguyen W, Rawle DJ, Tang B, Larcher T, Suhrbier A. Microplastics dysregulate innate immunity in the SARS-CoV-2 infected lung. Front Immunol 2024; 15:1382655. [PMID: 38803494 PMCID: PMC11128561 DOI: 10.3389/fimmu.2024.1382655] [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: 02/06/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Global microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis, with a growing body of concern surrounding the potential impacts on human health. Methods Using a mouse model of mild COVID-19, we describe herein the effects of azide-free 1 μm polystyrene MP beads, co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum. The effect of MPs on the host response to SARS-CoV-2 infection was analysed using histopathology and RNA-Seq at 2 and 6 days post-infection (dpi). Results Although infection reduced clearance of MPs from the lung, virus titres and viral RNA levels were not significantly affected by MPs, and overt MP-associated clinical or histopathological changes were not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 dpi and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the 'cytokine release syndrome' signature observed in some COVID-19 patients. Discussion The findings are consistent with the recent finding that MPs can inhibit phagocytosis of apoptotic cells via binding of Tim4. They also add to a growing body of literature suggesting that MPs can dysregulate inflammatory processes in specific disease settings.
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Affiliation(s)
- Cameron R. Bishop
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kexin Yan
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Wilson Nguyen
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daniel J. Rawle
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Bing Tang
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thibaut Larcher
- Institut National de Recherche Agronomique, Unité Mixte de Recherche, Oniris, Nantes, France
| | - Andreas Suhrbier
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Infectious Disease Research Centre, Global Virus Network (GVN) Center of Excellence, Brisbane, QLD, Australia
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2
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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.
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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
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3
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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.
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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
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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.
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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.
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5
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Sun Z, Zhang Z, Banu K, Azzi YA, Reghuvaran A, Fredericks S, Planoutene M, Hartzell S, Kim Y, Pell J, Tietjen G, Asch W, Kulkarni S, Formica R, Rana M, Maltzman JS, Zhang W, Akalin E, Heeger PS, Cravedi P, Menon MC. Blood Transcriptomes of SARS-CoV-2-Infected Kidney Transplant Recipients Associated with Immune Insufficiency Proportionate to Severity. J Am Soc Nephrol 2022; 33:2108-2122. [PMID: 36041788 PMCID: PMC9678030 DOI: 10.1681/asn.2022010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/10/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Among patients with COVID-19, kidney transplant recipients (KTRs) have poor outcomes compared with non-KTRs. To provide insight into management of immunosuppression during acute illness, we studied immune signatures from the peripheral blood during and after COVID-19 infection from a multicenter KTR cohort. METHODS We ascertained clinical data by chart review. A single sample of blood was collected for transcriptome analysis. Total RNA was poly-A selected and RNA was sequenced to evaluate transcriptome changes. We also measured cytokines and chemokines of serum samples collected during acute infection. RESULTS A total of 64 patients with COVID-19 in KTRs were enrolled, including 31 with acute COVID-19 (<4 weeks from diagnosis) and 33 with post-acute COVID-19 (>4 weeks postdiagnosis). In the blood transcriptome of acute cases, we identified genes in positive or negative association with COVID-19 severity scores. Functional enrichment analyses showed upregulation of neutrophil and innate immune pathways but downregulation of T cell and adaptive immune activation pathways. This finding was independent of lymphocyte count, despite reduced immunosuppressant use in most KTRs. Compared with acute cases, post-acute cases showed "normalization" of these enriched pathways after 4 weeks, suggesting recovery of adaptive immune system activation despite reinstitution of immunosuppression. Analysis of the non-KTR cohort with COVID-19 showed significant overlap with KTRs in these functions. Serum inflammatory cytokines followed an opposite trend (i.e., increased with disease severity), indicating that blood lymphocytes are not the primary source. CONCLUSIONS The blood transcriptome of KTRs affected by COVID-19 shows decreases in T cell and adaptive immune activation pathways during acute disease that, despite reduced immunosuppressant use, associate with severity. These pathways show recovery after acute illness.
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Affiliation(s)
- Zeguo Sun
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Khadija Banu
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Yorg Al Azzi
- Montefiore Einstein Center for Transplantation, Albert Einstein College of Medicine, Bronx, New York
| | - Anand Reghuvaran
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Samuel Fredericks
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marina Planoutene
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Susan Hartzell
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yesl Kim
- Geriatric Research Education and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - John Pell
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Gregory Tietjen
- Department of Surgery, Yale University school of Medicine, New Haven, Connecticut
| | - William Asch
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Sanjay Kulkarni
- Department of Surgery, Yale University school of Medicine, New Haven, Connecticut
| | - Richard Formica
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Meenakshi Rana
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jonathan S. Maltzman
- Geriatric Research Education and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California
- Division of Nephrology, Department of Medicine, Stanford University, Palo Alto, California
| | - Weijia Zhang
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Enver Akalin
- Montefiore Einstein Center for Transplantation, Albert Einstein College of Medicine, Bronx, New York
| | - Peter S. Heeger
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paolo Cravedi
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Madhav C. Menon
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Division of Nephrology, Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
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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.
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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.
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