1
|
Granholm ACE, Englund E, Gilmore A, Head E, Yong WH, Perez SE, Guzman SJ, Hamlett ED, Mufson EJ. Neuropathological findings in Down syndrome, Alzheimer's disease and control patients with and without SARS-COV-2: preliminary findings. Acta Neuropathol 2024; 147:92. [PMID: 38801558 PMCID: PMC11130011 DOI: 10.1007/s00401-024-02743-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024]
Abstract
The SARS-CoV-2 virus that led to COVID-19 is associated with significant and long-lasting neurologic symptoms in many patients, with an increased mortality risk for people with Alzheimer's disease (AD) and/or Down syndrome (DS). However, few studies have evaluated the neuropathological and inflammatory sequelae in postmortem brain tissue obtained from AD and people with DS with severe SARS-CoV-2 infections. We examined tau, beta-amyloid (Aβ), inflammatory markers and SARS-CoV-2 nucleoprotein in DS, AD, and healthy non-demented controls with COVID-19 and compared with non-infected brain tissue from each disease group (total n = 24). A nested ANOVA was used to determine regional effects of the COVID-19 infection on arborization of astrocytes (Sholl analysis) and percent-stained area of Iba-1 and TMEM 119. SARS-CoV-2 antibodies labeled neurons and glial cells in the frontal cortex of all subjects with COVID-19, and in the hippocampus of two of the three DS COVID-19 cases. SARS-CoV-2-related alterations were observed in peri-vascular astrocytes and microglial cells in the gray matter of the frontal cortex, hippocampus, and para-hippocampal gyrus. Bright field microscopy revealed scattered intracellular and diffuse extracellular Aβ deposits in the hippocampus of controls with confirmed SARS-CoV-2 infections. Overall, the present preliminary findings suggest that SARS-CoV-2 infections induce abnormal inflammatory responses in Down syndrome.
Collapse
Affiliation(s)
- Ann-Charlotte E Granholm
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Research Complex II, Aurora, CO, USA.
| | - Elisabet Englund
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Anah Gilmore
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Research Complex II, Aurora, CO, USA
| | - Elizabeth Head
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, USA
- Department of Neurology, University of California Irvine, Irvine, CA, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, USA
| | - Sylvia E Perez
- Department of Translational Neuroscience and Neurology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Samuel J Guzman
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Eric D Hamlett
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Elliott J Mufson
- Department of Translational Neuroscience and Neurology, Barrow Neurological Institute, Phoenix, AZ, USA
| |
Collapse
|
2
|
Chang H, Chen E, Hu Y, Wu L, Deng L, Ye‐Lehmann S, Mao X, Zhu T, Liu J, Chen C. Extracellular Vesicles: The Invisible Heroes and Villains of COVID-19 Central Neuropathology. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305554. [PMID: 38143270 PMCID: PMC10933635 DOI: 10.1002/advs.202305554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/18/2023] [Indexed: 12/26/2023]
Abstract
Acknowledging the neurological symptoms of COVID-19 and the long-lasting neurological damage even after the epidemic ends are common, necessitating ongoing vigilance. Initial investigations suggest that extracellular vesicles (EVs), which assist in the evasion of the host's immune response and achieve immune evasion in SARS-CoV-2 systemic spreading, contribute to the virus's attack on the central nervous system (CNS). The pro-inflammatory, pro-coagulant, and immunomodulatory properties of EVs contents may directly drive neuroinflammation and cerebral thrombosis in COVID-19. Additionally, EVs have attracted attention as potential candidates for targeted therapy in COVID-19 due to their innate homing properties, low immunogenicity, and ability to cross the blood-brain barrier (BBB) freely. Mesenchymal stromal/stem cell (MSCs) secreted EVs are widely applied and evaluated in patients with COVID-19 for their therapeutic effect, considering the limited antiviral treatment. This review summarizes the involvement of EVs in COVID-19 neuropathology as carriers of SARS-CoV-2 or other pathogenic contents, as predictors of COVID-19 neuropathology by transporting brain-derived substances, and as therapeutic agents by delivering biotherapeutic substances or drugs. Understanding the diverse roles of EVs in the neuropathological aspects of COVID-19 provides a comprehensive framework for developing, treating, and preventing central neuropathology and the severe consequences associated with the disease.
Collapse
Affiliation(s)
- Haiqing Chang
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| | - Erya Chen
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| | - Yi Hu
- Department of Cardiology, Honghui hospitalXi'an Jiaotong UniversityXi'an710049China
| | - Lining Wu
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| | - Liyun Deng
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| | - Shixin Ye‐Lehmann
- Diseases and Hormones of the Nervous System University of Paris‐Scalay Bicêtre Hosptial BâtGrégory Pincus 80 Rue du Gal Leclerc, CedexLe Kremlin Bicêtre94276France
| | - Xiaobo Mao
- Department of NeurologyInstitute of Cell EngineeringSchool of MedicineJohns Hopkins UniversityBaltimoreMD21218USA
| | - Tao Zhu
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| | - Jin Liu
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| | - Chan Chen
- Department of AnesthesiologyWest China HospitalSichuan UniversityLaboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Centre of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduSichuan610041China
| |
Collapse
|
3
|
Munawar WASWA, Elias MH, Addnan FH, Hassandarvish P, AbuBakar S, Roslan N. Gene expression profiling of host lipid metabolism in SARS-CoV-2 infected patients: a systematic review and integrated bioinformatics analysis. BMC Infect Dis 2024; 24:124. [PMID: 38263024 PMCID: PMC10807267 DOI: 10.1186/s12879-024-08983-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The Coronavirus disease 2019 (COVID-19) pandemic occurred due to the dispersion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe symptoms can be observed in COVID-19 patients with lipid-related comorbidities such as obesity and diabetes. Yet, the extensive molecular mechanisms of how SARS-CoV-2 causes dysregulation of lipid metabolism remain unknown. METHODS Here, an advanced search of articles was conducted using PubMed, Scopus, EBSCOhost, and Web of Science databases using terms from Medical Subject Heading (MeSH) like SARS-CoV-2, lipid metabolism and transcriptomic as the keywords. From 428 retrieved studies, only clinical studies using next-generation sequencing as a gene expression method in COVID-19 patients were accepted. Study design, study population, sample type, the method for gene expression and differentially expressed genes (DEGs) were extracted from the five included studies. The DEGs obtained from the studies were pooled and analyzed using the bioinformatics software package, DAVID, to determine the enriched pathways. The DEGs involved in lipid metabolic pathways were selected and further analyzed using STRING and Cytoscape through visualization by protein-protein interaction (PPI) network complex. RESULTS The analysis identified nine remarkable clusters from the PPI complex, where cluster 1 showed the highest molecular interaction score. Three potential candidate genes (PPARG, IFITM3 and APOBEC3G) were pointed out from the integrated bioinformatics analysis in this systematic review and were chosen due to their significant role in regulating lipid metabolism. These candidate genes were significantly involved in enriched lipid metabolic pathways, mainly in regulating lipid homeostasis affecting the pathogenicity of SARS-CoV-2, specifically in mechanisms of viral entry and viral replication in COVID-19 patients. CONCLUSIONS Taken together, our findings in this systematic review highlight the affected lipid-metabolic pathways along with the affected genes upon SARS-CoV-2 invasion, which could be a potential target for new therapeutic strategies study in the future.
Collapse
Grants
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- FRGS/1/2021/SKK0/USIM/02/2; USIM/FRGS/FPSK/KPT/50321 Ministry of Higher Education, Malaysia
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
- PPPI/FPSK/0121/USIM/16121 USIM Internal Grant Scheme, USIM
Collapse
Affiliation(s)
| | - Marjanu Hikmah Elias
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Faizul Helmi Addnan
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), Universiti Malaya, Kuala Lumpur, Malaysia
| | - Nuruliza Roslan
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Malaysia.
| |
Collapse
|
4
|
Hirata Y, Katano H, Iida S, Mine S, Nagasawa S, Makino Y, Motomura A, Ozono S, Sato Y, Sekizuka T, Kuroda M, Yamaguchi R, Inokuchi G, Torimitsu S, Akitomi S, Yajima D, Saitoh H, Suzuki T, Iwase H. Genomic analysis of SARS-CoV-2 in forensic autopsy cases of COVID-19. J Med Virol 2023; 95:e28990. [PMID: 37537838 DOI: 10.1002/jmv.28990] [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: 04/24/2023] [Revised: 06/25/2023] [Accepted: 07/14/2023] [Indexed: 08/05/2023]
Abstract
Numerous genomic analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been conducted, highlighting its variations and lineage transitions. Despite the importance of forensic autopsy in investigating deaths due to coronavirus disease 2019 (COVID-19), including out-of-hospital deaths, viral genomic analysis has rarely been reported due in part to postmortem changes. In this study, various specimens were collected from 18 forensic autopsy cases with SARS-CoV-2 infection. Reverse-transcription quantitative polymerase chain reaction revealed the distribution of the virus in the body, primarily in the respiratory organs. Next-generation sequencing determined the complete genome sequences in 15 of the 18 cases, although some cases showed severe postmortem changes or degradation of tissue RNA. Intrahost genomic diversity of the virus was identified in one case of death due to COVID-19. The accumulation of single-nucleotide variations in the lung of the case suggested the intrahost evolution of SARS-CoV-2. Lung of the case showed diffuse alveolar damage histologically and positivity for SARS-CoV-2 by immunohistochemical analysis and in situ hybridization, indicating virus-associated pneumonia. This study provides insights into the feasibility of genomic analysis of SARS-CoV-2 in forensic autopsy cases and the potential for uncovering important information in COVID-19 deaths, including out-of-hospital deaths.
Collapse
Affiliation(s)
- Yuichiro Hirata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sohtaro Mine
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sayaka Nagasawa
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yohsuke Makino
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ayumi Motomura
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Legal Medicine, International University of Health and Welfare, Chiba, Japan
| | - Seiya Ozono
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Sato
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Rutsuko Yamaguchi
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Go Inokuchi
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Suguru Torimitsu
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinji Akitomi
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Japan Medical Association Research Institute, Tokyo, Japan
| | - Daisuke Yajima
- Department of Legal Medicine, International University of Health and Welfare, Chiba, Japan
| | - Hisako Saitoh
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Dentistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirotaro Iwase
- Department of Legal Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
5
|
Olivera E, Sáez A, Carniglia L, Caruso C, Lasaga M, Durand D. Alzheimer's disease risk after COVID-19: a view from the perspective of the infectious hypothesis of neurodegeneration. Neural Regen Res 2023; 18:1404-1410. [PMID: 36571334 PMCID: PMC10075115 DOI: 10.4103/1673-5374.360273] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In light of the rising evidence of the association between viral and bacterial infections and neurodegeneration, we aimed at revisiting the infectious hypothesis of Alzheimer's disease and analyzing the possible implications of COVID-19 neurological sequelae in long-term neurodegeneration. We wondered how SARS-CoV-2 could be related to the amyloid-β cascade and how it could lead to the pathological hallmarks of the disease. We also predict a paradigm change in clinical medicine, which now has a great opportunity to conduct prospective surveillance of cognitive sequelae and progression to dementia in people who suffered severe infections together with other risk factors for Alzheimer's disease.
Collapse
Affiliation(s)
- Eugenia Olivera
- Instituto de Investigaciones Biomédicas INBIOMED UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Albany Sáez
- Instituto de Investigaciones Biomédicas INBIOMED UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Lila Carniglia
- Instituto de Investigaciones Biomédicas INBIOMED UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Carla Caruso
- Instituto de Investigaciones Biomédicas INBIOMED UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Mercedes Lasaga
- Instituto de Investigaciones Biomédicas INBIOMED UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Daniela Durand
- Instituto de Investigaciones Biomédicas INBIOMED UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| |
Collapse
|
6
|
Lebrun L, Absil L, Remmelink M, De Mendonça R, D'Haene N, Gaspard N, Rusu S, Racu ML, Collin A, Allard J, Zindy E, Schiavo AA, De Clercq S, De Witte O, Decaestecker C, Lopes MB, Salmon I. SARS-Cov-2 infection and neuropathological findings: a report of 18 cases and review of the literature. Acta Neuropathol Commun 2023; 11:78. [PMID: 37165453 PMCID: PMC10170054 DOI: 10.1186/s40478-023-01566-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/15/2023] [Indexed: 05/12/2023] Open
Abstract
INTRODUCTION COVID-19-infected patients harbour neurological symptoms such as stroke and anosmia, leading to the hypothesis that there is direct invasion of the central nervous system (CNS) by SARS-CoV-2. Several studies have reported the neuropathological examination of brain samples from patients who died from COVID-19. However, there is still sparse evidence of virus replication in the human brain, suggesting that neurologic symptoms could be related to mechanisms other than CNS infection by the virus. Our objective was to provide an extensive review of the literature on the neuropathological findings of postmortem brain samples from patients who died from COVID-19 and to report our own experience with 18 postmortem brain samples. MATERIAL AND METHODS We used microscopic examination, immunohistochemistry (using two different antibodies) and PCR-based techniques to describe the neuropathological findings and the presence of SARS-CoV-2 virus in postmortem brain samples. For comparison, similar techniques (IHC and PCR) were applied to the lung tissue samples for each patient from our cohort. The systematic literature review was conducted from the beginning of the pandemic in 2019 until June 1st, 2022. RESULTS In our cohort, the most common neuropathological findings were perivascular haemosiderin-laden macrophages and hypoxic-ischaemic changes in neurons, which were found in all cases (n = 18). Only one brain tissue sample harboured SARS-CoV-2 viral spike and nucleocapsid protein expression, while all brain cases harboured SARS-CoV-2 RNA positivity by PCR. A colocalization immunohistochemistry study revealed that SARS-CoV-2 antigens could be located in brain perivascular macrophages. The literature review highlighted that the most frequent neuropathological findings were ischaemic and haemorrhagic lesions, including hypoxic/ischaemic alterations. However, few studies have confirmed the presence of SARS-CoV-2 antigens in brain tissue samples. CONCLUSION This study highlighted the lack of specific neuropathological alterations in COVID-19-infected patients. There is still no evidence of neurotropism for SARS-CoV-2 in our cohort or in the literature.
Collapse
Affiliation(s)
- Laetitia Lebrun
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Lara Absil
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Myriam Remmelink
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Ricardo De Mendonça
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Nicky D'Haene
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Nicolas Gaspard
- Department of Neurology, Université Libre de Bruxelles (ULB), Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, Erasme University Hospital, Brussels, Belgium
| | - Stefan Rusu
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Marie-Lucie Racu
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Amandine Collin
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
| | - Justine Allard
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
| | - Egor Zindy
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
| | - Andrea Alex Schiavo
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Sarah De Clercq
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium
| | - Olivier De Witte
- Department of Neurosurgery, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital ErasmeErasme University Hospital, Brussels, Belgium
| | - Christine Decaestecker
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium
- Laboratory of Image Synthesis and Analysis, Brussels School of Engineering/École Polytechnique de Brussels, ULB, Brussels, Belgium
| | - Maria-Beatriz Lopes
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Isabelle Salmon
- Department of Pathology, Erasme University Hospital, Université Libre de Bruxelles (ULB)Hôpital Universitaire de Bruxelles (HUB), CUB Hôpital Erasme, 808 Route de Lennik, B-1070, Brussels, Belgium.
- DIAPath, Center for Microscopy and Molecular Imaging (CMMI), ULB, Gosselies, Belgium.
| |
Collapse
|
7
|
Xu Y, Ma Q, Ren J, Chen L, Guo W, Feng K, Zeng Z, Huang T, Cai Y. Using Machine Learning Methods in Identifying Genes Associated with COVID-19 in Cardiomyocytes and Cardiac Vascular Endothelial Cells. Life (Basel) 2023; 13:life13041011. [PMID: 37109540 PMCID: PMC10146712 DOI: 10.3390/life13041011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/02/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) not only causes respiratory system damage, but also imposes strain on the cardiovascular system. Vascular endothelial cells and cardiomyocytes play an important role in cardiac function. The aberrant expression of genes in vascular endothelial cells and cardiomyocytes can lead to cardiovascular diseases. In this study, we sought to explain the influence of respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the gene expression levels of vascular endothelial cells and cardiomyocytes. We designed an advanced machine learning-based workflow to analyze the gene expression profile data of vascular endothelial cells and cardiomyocytes from patients with COVID-19 and healthy controls. An incremental feature selection method with a decision tree was used in building efficient classifiers and summarizing quantitative classification genes and rules. Some key genes, such as MALAT1, MT-CO1, and CD36, were extracted, which exert important effects on cardiac function, from the gene expression matrix of 104,182 cardiomyocytes, including 12,007 cells from patients with COVID-19 and 92,175 cells from healthy controls, and 22,438 vascular endothelial cells, including 10,812 cells from patients with COVID-19 and 11,626 cells from healthy controls. The findings reported in this study may provide insights into the effect of COVID-19 on cardiac cells and further explain the pathogenesis of COVID-19, and they may facilitate the identification of potential therapeutic targets.
Collapse
Affiliation(s)
- Yaochen Xu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200030, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yudong Cai
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai 200444, China
| |
Collapse
|
8
|
Solomon IH, Singh A, Folkerth RD, Mukerji SS. What Can We Still Learn from Brain Autopsies in COVID-19? Semin Neurol 2023. [PMID: 37023787 DOI: 10.1055/s-0043-1767716] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Neuropathological findings have been published from ∼900 patients who died with or from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, representing less than 0.01% of the close to 6.4 million deaths reported to the World Health Organization 2 years into the coronavirus disease 2019 (COVID-19) pandemic. In this review, we extend our prior work summarizing COVID-19 neuropathology by including information on published autopsies up to June 2022, and neuropathological studies in children, COVID-19 variants, secondary brain infections, ex vivo brain imaging, and autopsies performed in countries outside of the United States or Europe. We also summarize research studies that investigate mechanisms of neuropathogenesis in nonhuman primates and other models. While a pattern of cerebrovascular pathology and microglial-predominant inflammation remains the primary COVID-19-associated neuropathological finding, there is no singular understanding of the mechanisms that underlie neurological symptoms in acute COVID-19 or the post-acute COVID-19 condition. Thus, it is paramount that we incorporate microscopic and molecular findings from brain tissue into what we know about the clinical disease so that we attain best practice guidance and direct research priorities for the study of the neurological morbidity of COVID-19.
Collapse
Affiliation(s)
- Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Arjun Singh
- Division of Neuroimmunology and Neuro-Infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
- Healing Hospital, Chandigarh, India
| | - Rebecca D Folkerth
- Office of Chief Medical Examiner and Department of Forensic Medicine, New York University School of Medicine, New York, New York
| | - Shibani S Mukerji
- Harvard Medical School, Boston, Massachusetts
- Division of Neuroimmunology and Neuro-Infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
- Division of Infectious Diseases, Vaccine and Immunotherapy Center, Massachusetts General Hospital, Charlestown, Massachusetts
| |
Collapse
|
9
|
Ong'era EM, Mohammed KS, Makori TO, Bejon P, Ocholla-Oyier LI, Nokes DJ, Agoti CN, Githinji G. High-throughput sequencing approaches applied to SARS-CoV-2. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18701.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
High-throughput sequencing is crucial for surveillance and control of viral outbreaks. During the ongoing coronavirus disease 2019 (COVID-19) pandemic, advances in the high-throughput sequencing technology resources have enhanced diagnosis, surveillance, and vaccine discovery. From the onset of the pandemic in December 2019, several genome-sequencing approaches have been developed and supported across the major sequencing platforms such as Illumina, Oxford Nanopore, PacBio, MGI DNBSEQTM and Ion Torrent. Here, we share insights from the sequencing approaches developed for sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between December 2019 and October 2022.
Collapse
|
10
|
Normandin E, Valizadeh N, Rudmann EA, Uddin R, Dobbins ST, MacInnis BL, Padera RF, Siddle KJ, Lemieux JE, Sabeti PC, Mukerji SS, Solomon IH. Neuropathological features of SARS-CoV-2 delta and omicron variants. J Neuropathol Exp Neurol 2023; 82:283-295. [PMID: 36847705 PMCID: PMC10025880 DOI: 10.1093/jnen/nlad015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continually evolving resulting in variants with increased transmissibility, more severe disease, reduced effectiveness of treatments or vaccines, or diagnostic detection failure. The SARS-CoV-2 Delta variant (B.1.617.2 and AY lineages) was the dominant circulating strain in the United States from July to mid-December 2021, followed by the Omicron variant (B.1.1.529 and BA lineages). Coronavirus disease 2019 (COVID-19) has been associated with neurological sequelae including loss of taste/smell, headache, encephalopathy, and stroke, yet little is known about the impact of viral strain on neuropathogenesis. Detailed postmortem brain evaluations were performed for 22 patients from Massachusetts, including 12 who died following infection with Delta variant and 5 with Omicron variant, compared to 5 patients who died earlier in the pandemic. Diffuse hypoxic injury, occasional microinfarcts and hemorrhage, perivascular fibrinogen, and rare lymphocytes were observed across the 3 groups. SARS-CoV-2 protein and RNA were not detected in any brain samples by immunohistochemistry, in situ hybridization, or real-time quantitative PCR. These results, although preliminary, demonstrate that, among a subset of severely ill patients, similar neuropathological features are present in Delta, Omicron, and non-Delta/non-Omicron variant patients, suggesting that SARS-CoV-2 variants are likely to affect the brain by common neuropathogenic mechanisms.
Collapse
Affiliation(s)
- Erica Normandin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Navid Valizadeh
- Division of Neuroimmunology and Neuro-infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Emily A Rudmann
- Division of Neuroimmunology and Neuro-infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rockib Uddin
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | | | - Robert F Padera
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | | | - Jacob E Lemieux
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Shibani S Mukerji
- Division of Neuroimmunology and Neuro-infectious Diseases, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| |
Collapse
|
11
|
Dumenil T, Le TT, Rawle DJ, Yan K, Tang B, Nguyen W, Bishop C, Suhrbier A. Warmer ambient air temperatures reduce nasal turbinate and brain infection, but increase lung inflammation in the K18-hACE2 mouse model of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160163. [PMID: 36395835 PMCID: PMC9659553 DOI: 10.1016/j.scitotenv.2022.160163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Warmer climatic conditions have been associated with fewer COVID-19 cases. Herein we infected K18-hACE2 mice housed at the standard animal house temperature of ∼22 °C, or at ∼31 °C, which is considered to be thermoneutral for mice. On day 2 post infection, RNA-Seq analyses showed no significant differential gene expression lung in lungs of mice housed at the two temperatures, with almost identical viral loads and type I interferon responses. There was also no significant difference in viral loads in lungs on day 5, but RNA-Seq and histology analyses showed clearly elevated inflammatory signatures and infiltrates. Thermoneutrality thus promoted lung inflammation. On day 2 post infection mice housed at 31 °C showed reduced viral loads in nasal turbinates, consistent with increased mucociliary clearance at the warmer ambient temperature. These mice also had reduced virus levels in the brain, and an ensuing amelioration of weight loss and a delay in mortality. Warmer air temperatures may thus reduce infection of the upper respiratory track and the olfactory epithelium, resulting in reduced brain infection. Potential relevance for anosmia and neurological sequelae in COVID-19 patients is discussed.
Collapse
Affiliation(s)
- Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Thuy T Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Daniel J Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Wilson Nguyen
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Cameron Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland 4029, 4072, Australia.
| |
Collapse
|
12
|
Host Response of Syrian Hamster to SARS-CoV-2 Infection including Differences with Humans and between Sexes. Viruses 2023; 15:v15020428. [PMID: 36851642 PMCID: PMC9960357 DOI: 10.3390/v15020428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the importance of having proper tools and models to study the pathophysiology of emerging infectious diseases to test therapeutic protocols, assess changes in viral phenotypes, and evaluate the effects of viral evolution. This study provided a comprehensive characterization of the Syrian hamster (Mesocricetus auratus) as an animal model for SARS-CoV-2 infection using different approaches (description of clinical signs, viral load, receptor profiling, and host immune response) and targeting four different organs (lungs, intestine, brain, and PBMCs). Our data showed that both male and female hamsters were susceptible to the infection and developed a disease similar to the one observed in patients with COVID-19 that included moderate to severe pulmonary lesions, inflammation, and recruitment of the immune system in the lungs and at the systemic level. However, all animals recovered within 14 days without developing the severe pathology seen in humans, and none of them died. We found faint evidence for intestinal and neurological tropism associated with the absence of lesions and a minimal host response in intestines and brains, which highlighted another crucial difference with the multiorgan impairment of severe COVID-19. When comparing male and female hamsters, we observed that males sustained higher viral RNA shedding and replication in the lungs, suffered from more severe symptoms and histopathological lesions, and triggered higher pulmonary inflammation. Overall, these data confirmed the Syrian hamster as a suitable model for mild to moderate COVID-19 and reflected sex-related differences in the response against the virus observed in humans.
Collapse
|
13
|
COVID-19-associated monocytic encephalitis (CAME): histological and proteomic evidence from autopsy. Signal Transduct Target Ther 2023; 8:24. [PMID: 36609561 PMCID: PMC9816522 DOI: 10.1038/s41392-022-01291-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Severe neurological symptoms are associated with Coronavirus disease 2019 (COVID-19). However, the morphologic features, pathological nature and their potential mechanisms in patient brains have not been revealed despite evidence of neurotropic infection. In this study, neuropathological damages and infiltrating inflammatory cells were quantitatively evaluated by immunohistochemical staining, ultrastructural examination under electron microscopy, and an image threshold method, in postmortem brains from nine critically ill COVID-19 patients and nine age-matched cadavers of healthy individuals. Differentially expressed proteins were identified by quantitative proteomic assays. Histopathological findings included neurophagocytosis, microglia nodules, satellite phenomena, extensive edema, focal hemorrhage, and infarction, as well as infiltrating mononuclear cells. Immunostaining of COVID-19 brains revealed extensive activation of both microglia and astrocytes, severe damage of the blood-brain barrier (BBB) and various degrees of perivascular infiltration by predominantly CD14+/CD16+/CD141+/CCR7+/CD11c+ monocytes and occasionally CD4+/CD8+ T lymphocytes. Quantitative proteomic assays combined with bioinformatics analysis identified upregulated proteins predominantly involved in immune responses, autophagy and cellular metabolism in COVID-19 patient brains compared with control brains. Proteins involved in brain development, neuroprotection, and extracellular matrix proteins of the basement membrane were downregulated, potentially caused by the activation of transforming growth factor β receptor and vascular endothelial growth factor signaling pathways. Thus, our results define histopathological and molecular profiles of COVID-19-associated monocytic encephalitis (CAME) and suggest potential therapeutic targets.
Collapse
|
14
|
Mavrikaki M, Lee JD, Solomon IH, Slack FJ. Severe COVID-19 is associated with molecular signatures of aging in the human brain. NATURE AGING 2022; 2:1130-1137. [PMID: 37118539 DOI: 10.1038/s43587-022-00321-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/25/2022] [Indexed: 04/30/2023]
Abstract
As coronavirus disease 2019 (COVID-19) and aging are both accompanied by cognitive decline, we hypothesized that COVID-19 might lead to molecular signatures similar to aging. We performed whole-transcriptome analysis of the frontal cortex, a critical area for cognitive function, in individuals with COVID-19, age-matched and sex-matched uninfected controls, and uninfected individuals with intensive care unit/ventilator treatment. Our findings indicate that COVID-19 is associated with molecular signatures of brain aging and emphasize the value of neurological follow-up in recovered individuals.
Collapse
Affiliation(s)
- Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Jonathan D Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Frank J Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
15
|
Lin X, Nie H, Tang R, Wang P, Jin X, Jiang Q, Han F, Chen N, Li Y. Network analysis between neuron dysfunction and neuroimmune response based on neural single-cell transcriptome of COVID-19 patients. Comput Biol Med 2022; 150:106055. [PMID: 36137317 PMCID: PMC9462930 DOI: 10.1016/j.compbiomed.2022.106055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022]
Abstract
Despite global vaccination efforts, COVID-19 breakthrough infections caused by variant virus continue to occur frequently, long-term sequelae of COVID-19 infection like neuronal dysfunction emerge as a noteworthy issue. Neuroimmune disorder induced by Inflammatory factor storm was considered as a possible reason, however, little was known about the functional factors affecting neuroimmune response to this virus. Here, using medial prefrontal cortex single cell data of COVID-19 patients, expression pattern analysis indicated that some immune-related pathway genes expressed specifically, including genes associated with T cell receptor, TNF signaling in microglia and Cytokine-cytokine receptor interaction and HIF-1 signaling pathway genes in astrocytes. Besides the well-known immune-related cell type microglia, we also observed immune-related factors like IL17D, TNFRSF1A and TLR4 expressed in Astrocytes. Based on the ligand-receptor relationship of immune-related factors, crosstalk landscape among cell clusters were analyzed. The findings indicated that astrocytes collaborated with microglia and affect excitatory neurons, participating in the process of immune response and neuronal dysfunction. Moreover, subset of astrocytes specific immune factors (hinged neuroimmune genes) were proved to correlate with Covid-19 infection and ventilator-associated pneumonia using multi-tissue RNA-seq and scRNA-seq data. Function characterization clarified that hinged neuroimmune genes were involved in activation of inflammation and hypoxia signaling pathways, which could lead to hyper-responses related neurological sequelae. Finally, a risk model was constructed and testified in RNA-seq and scRNA data of peripheral blood.
Collapse
Affiliation(s)
- Xiaoyu Lin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Ran Tang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China
| | - Fang Han
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
| | - Na Chen
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China; Department of Hematology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
| | - Yu Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150000, China.
| |
Collapse
|
16
|
Hazra S, Chaudhuri AG, Tiwary BK, Chakrabarti N. Integrated network-based multiple computational analyses for identification of co-expressed candidate genes associated with neurological manifestations of COVID-19. Sci Rep 2022; 12:17141. [PMID: 36229517 PMCID: PMC9558001 DOI: 10.1038/s41598-022-21109-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/22/2022] [Indexed: 01/04/2023] Open
Abstract
'Tripartite network' (TN) and 'combined gene network' (CGN) were constructed and their hub-bottleneck and driver nodes (44 genes) were evaluated as 'target genes' (TG) to identify 21 'candidate genes' (CG) and their relationship with neurological manifestations of COVID-19. TN was developed using neurological symptoms of COVID-19 found in literature. Under query genes (TG of TN), co-expressed genes were identified using pair-wise mutual information to genes available in RNA-Seq autopsy data of frontal cortex of COVID-19 victims. CGN was constructed with genes selected from TN and co-expressed in COVID-19. TG and their connecting genes of respective networks underwent functional analyses through findings of their enrichment terms and pair-wise 'semantic similarity scores' (SSS). A new integrated 'weighted harmonic mean score' was formulated assimilating values of SSS and STRING-based 'combined score' of the selected TG-pairs, which provided CG-pairs with properties of CGs as co-expressed and 'indispensable nodes' in CGN. Finally, six pairs sharing seven 'prevalent CGs' (ADAM10, ADAM17, AKT1, CTNNB1, ESR1, PIK3CA, FGFR1) showed linkages with the phenotypes (a) directly under neurodegeneration, neurodevelopmental diseases, tumour/cancer and cellular signalling, and (b) indirectly through other CGs under behavioural/cognitive and motor dysfunctions. The pathophysiology of 'prevalent CGs' has been discussed to interpret neurological phenotypes of COVID-19.
Collapse
Affiliation(s)
- Suvojit Hazra
- CPEPA-UGC Centre for "Electro-Physiological and Neuro-Imaging Studies Including Mathematical Modelling", University of Calcutta, Kolkata, West Bengal, India
- Department of Physiology, University of Calcutta, Kolkata, West Bengal, India
| | | | - Basant K Tiwary
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India.
| | - Nilkanta Chakrabarti
- CPEPA-UGC Centre for "Electro-Physiological and Neuro-Imaging Studies Including Mathematical Modelling", University of Calcutta, Kolkata, West Bengal, India.
- Department of Physiology, University of Calcutta, Kolkata, West Bengal, India.
| |
Collapse
|
17
|
Yang J, Song H, Hao X. Whole-transcriptome sequencing data reveals a disparate cognitive and immune signature in COVID-19 patients with and without dementia. J Med Virol 2022; 95:e28177. [PMID: 36168207 PMCID: PMC9538945 DOI: 10.1002/jmv.28177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/24/2022] [Accepted: 09/24/2022] [Indexed: 01/11/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused more than 6.3 million deaths worldwide. Recent evidence has indicated that elderly people with dementia are particularly vulnerable to COVID-19 and severe disease outcomes. However, its molecular mechanism remains largely unknown. Here, we retrieved frontal cortex samples of COVID-19 patients from the Gene Expression Omnibus database and performed a systematic transcriptomic analysis to compare COVID-19 patients and controls with or without dementia. In nondemented patients, SARS-CoV-2 infection obviously activated T helper type 2 (Th2) cell-mediated humoral immunity and reduced the pathogenesis of dementia-related Alzheimer's disease and Parkinson's disease. In demented patients, conversely, SARS-CoV-2 infection significantly increased T helper type 1 (Th1) cell-mediated cellular immunity and exacerbated the progression of dementia-related diseases. We further analyzed the molecular characteristics of COVID-19 patients with and without dementia. Compared with nondemented COVID-19 patients, demented COVID-19 patients showed decreased enrichment scores of Calcium signaling pathway, Neuroactive ligand-receptor interaction, ABC transporters, and Peroxisome, and increased enrichment scores of Olfactory transduction and Regulation of autophagy. The ratio of Th1/Th2 cells was significantly increased from 1.17 in nondemented COVID-19 patients to 33.32 in demented COVID-19 patients. Taken together, our findings provide transcriptomic evidence that COVID-19 has distinct influences on cognitive function and immune response in patients with and without dementia.
Collapse
Affiliation(s)
- Jue Yang
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang & State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, China & Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyangChina
| | - Hui Song
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, China & Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyangChina
| | - Xiaojiang Hao
- The State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang & State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, China & Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou ProvinceGuizhou Medical UniversityGuiyangChina
| |
Collapse
|
18
|
Liu L, Zhang Y, Chen Y, Zhao Y, Shen J, Wu X, Li M, Chen M, Li X, Sun Y, Gu L, Li W, Wang F, Yao L, Zhang Z, Xiao Z, Du F. Therapeutic prospects of ceRNAs in COVID-19. Front Cell Infect Microbiol 2022; 12:998748. [PMID: 36204652 PMCID: PMC9530275 DOI: 10.3389/fcimb.2022.998748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 01/08/2023] Open
Abstract
Since the end of 2019, COVID-19 caused by SARS-CoV-2 has spread worldwide, and the understanding of the new coronavirus is in a preliminary stage. Currently, immunotherapy, cell therapy, antiviral therapy, and Chinese herbal medicine have been applied in the clinical treatment of the new coronavirus; however, more efficient and safe drugs to control the progress of the new coronavirus are needed. Long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) may provide new therapeutic targets for novel coronavirus treatments. The first aim of this paper is to review research progress on COVID-19 in the respiratory, immune, digestive, circulatory, urinary, reproductive, and nervous systems. The second aim is to review the body systems and potential therapeutic targets of lncRNAs, miRNAs, and circRNAs in patients with COVID-19. The current research on competing endogenous RNA (ceRNA) (lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA) in SARS-CoV-2 is summarized. Finally, we predict the possible therapeutic targets of four lncRNAs, MALAT1, NEAT1, TUG1, and GAS5, in COVID-19. Importantly, the role of PTEN gene in the ceRNA network predicted by lncRNA MALAT1 and lncRNA TUG1 may help in the discovery and clinical treatment of effective drugs for COVID-19.
Collapse
Affiliation(s)
- Lin Liu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yao Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Meijuan Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xiaobing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yuhong Sun
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Li Gu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wanping Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Fang Wang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhuo Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Zhuo Zhang, ; Zhangang Xiao, ; Fukuan Du,
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, China
- *Correspondence: Zhuo Zhang, ; Zhangang Xiao, ; Fukuan Du,
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
- Cell Therapy & Cell Drugs of Luzhou Key Laboratory, Luzhou Science and Technology Bureau, Luzhou, China
- South Sichuan Institute of Translational Medicine, Luzhou, China
- *Correspondence: Zhuo Zhang, ; Zhangang Xiao, ; Fukuan Du,
| |
Collapse
|
19
|
Mesmoudi S, Lapina C, Rodic M, Peschanski D. Multi-Data Integration Towards a Global Understanding of the Neurological Impact of Human Brain Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Front Integr Neurosci 2022; 16:756604. [PMID: 35910337 PMCID: PMC9326261 DOI: 10.3389/fnint.2022.756604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
As the COVID-19 pandemic continues to unfold, numerous neurological symptoms emerge. The literature reports more and more manifestations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related to headache, dizziness, impaired consciousness, cognitive impairment, and motor disorders. Moreover, the infection of SARS-CoV-2 may have a durable neurological impact. ACE2/TMPRSS2 is the main entry point into cells for some strains of coronaviruses (CoVs), including SARS-CoV-2, which uses it to target the central nervous system (CNS). The aim of this study was to characterize the scope of the potential complex impact of a SARS-CoV-2 infection in the brain. It concerns different scales: the topographic, cognitive, sensorimotor, and genetic one. We investigated which cognitive and sensorimotor functions are associated with the brain regions where ACE2/TMPRSS2 is overexpressed, hypothesising that they might be particularly affected by the infection. Furthermore, overexpressed genes in these regions are likely to be impacted by COVID-19. This general understanding is crucial to establish the potential neurological manifestations of the infection. Data on mRNA expression levels of genes were provided by the Allen Institute for Brain Science (AIBS), and the localisation of brain functions by the LinkRbrain platform. The latter was also used to analyze the spatial overlap between ACE2/TMPRSS2 overexpression, and either function-specific brain activations or regional overexpression of other genes. The characterisation of these overexpressed genes was based on the GeneCards platform and the gene GSE164332 from the Gene Expression Omnibus database. We analysed the cognitive and sensorimotor functions whose role might be impaired, of which 88 have been categorised into seven groups: memory and recollection, motor function, pain, lucidity, emotion, sensory, and reward. Furthermore, we categorised the genes showing a significant increase in concentration of their mRNAs in the same regions where ACE2/TMPRSS2 mRNA levels are the highest. Eleven groups emerged from a bibliographical research: neurodegenerative disease, immunity, inflammation, olfactory receptor, cancer/apoptosis, executive function, senses, ischemia, motor function, myelination, and dependence. The results of this exploration could be in relation to the neurological symptoms of COVID-19. Furthermore, some genes from peripheral blood are already considered as biomarker of COVID-19. This method could generate new hypotheses to explore the neurological manifestations of COVID-19.
Collapse
Affiliation(s)
- Salma Mesmoudi
- Paris-1-Panthéon-Sorbonne University CESSP-UMR 8209, Paris, France
- French National Centre for Scientific Research (CNRS), Paris, France
- MATRICE Equipex, Seine-Saint-Denis, France
- Complex Systems Institute Paris Île-de-France, Paris, France
| | - Colline Lapina
- French National Centre for Scientific Research (CNRS), Paris, France
- MATRICE Equipex, Seine-Saint-Denis, France
- Complex Systems Institute Paris Île-de-France, Paris, France
- Graduate School of Cognitive Engineering (ENSC), Talence, France
| | | | - Denis Peschanski
- Paris-1-Panthéon-Sorbonne University CESSP-UMR 8209, Paris, France
- French National Centre for Scientific Research (CNRS), Paris, France
- MATRICE Equipex, Seine-Saint-Denis, France
| |
Collapse
|
20
|
Serrano GE, Walker JE, Tremblay C, Piras IS, Huentelman MJ, Belden CM, Goldfarb D, Shprecher D, Atri A, Adler CH, Shill HA, Driver-Dunckley E, Mehta SH, Caselli R, Woodruff BK, Haarer CF, Ruhlen T, Torres M, Nguyen S, Schmitt D, Rapscak SZ, Bime C, Peters JL, Alevritis E, Arce RA, Glass MJ, Vargas D, Sue LI, Intorcia AJ, Nelson CM, Oliver J, Russell A, Suszczewicz KE, Borja CI, Cline MP, Hemmingsen SJ, Qiji S, Hobgood HM, Mizgerd JP, Sahoo MK, Zhang H, Solis D, Montine TJ, Berry GJ, Reiman EM, Röltgen K, Boyd SD, Pinsky BA, Zehnder JL, Talbot P, Desforges M, DeTure M, Dickson DW, Beach TG. SARS-CoV-2 Brain Regional Detection, Histopathology, Gene Expression, and Immunomodulatory Changes in Decedents with COVID-19. J Neuropathol Exp Neurol 2022; 81:666-695. [PMID: 35818336 PMCID: PMC9278252 DOI: 10.1093/jnen/nlac056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Brains of 42 COVID-19 decedents and 107 non-COVID-19 controls were studied. RT-PCR screening of 16 regions from 20 COVID-19 autopsies found SARS-CoV-2 E gene viral sequences in 7 regions (2.5% of 320 samples), concentrated in 4/20 subjects (20%). Additional screening of olfactory bulb (OB), amygdala (AMY) and entorhinal area for E, N1, N2, RNA-dependent RNA polymerase, and S gene sequences detected one or more of these in OB in 8/21 subjects (38%). It is uncertain whether these RNA sequences represent viable virus. Significant histopathology was limited to 2/42 cases (4.8%), one with a large acute cerebral infarct and one with hemorrhagic encephalitis. Case-control RNAseq in OB and AMY found more than 5000 and 700 differentially expressed genes, respectively, unrelated to RT-PCR results; these involved immune response, neuronal constituents, and olfactory/taste receptor genes. Olfactory marker protein-1 reduction indicated COVID-19-related loss of OB olfactory mucosa afferents. Iba-1-immunoreactive microglia had reduced area fractions in cerebellar cortex and AMY, and cytokine arrays showed generalized downregulation in AMY and upregulation in blood serum in COVID-19 cases. Although OB is a major brain portal for SARS-CoV-2, COVID-19 brain changes are more likely due to blood-borne immune mediators and trans-synaptic gene expression changes arising from OB deafferentation.
Collapse
Affiliation(s)
- Geidy E Serrano
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Jessica E Walker
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Cécilia Tremblay
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Ignazio S Piras
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - Danielle Goldfarb
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - David Shprecher
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Alireza Atri
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA.,Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Charles H Adler
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Holly A Shill
- Barrow Neurological Institute, Phoenix, Arizona, USA
| | | | - Shyamal H Mehta
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Richard Caselli
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Bryan K Woodruff
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | | | - Thomas Ruhlen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Maria Torres
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Steve Nguyen
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | - Dasan Schmitt
- Banner Boswell Medical Center, Sun City, Arizona, USA
| | | | | | | | | | - Richard A Arce
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Michael J Glass
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Daisy Vargas
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Lucia I Sue
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Courtney M Nelson
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Javon Oliver
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Aryck Russell
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | | | - Claryssa I Borja
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Madison P Cline
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Sanaria Qiji
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Holly M Hobgood
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | - Joseph P Mizgerd
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Haiyu Zhang
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Daniel Solis
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, California, USA.,From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| | | | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, California, USA.,Division of Infectious Disease & Geographic Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - James L Zehnder
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pierre Talbot
- Laboratory of Neuroimmunology, Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Marc Desforges
- Laboratory of Virology, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada.,Département de microbiologie, infectiologie et Immunologie, Université de Montréal, Montréal, Quebec, Canada
| | - Michael DeTure
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Dennis W Dickson
- Mayo Clinic College of Medicine, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Thomas G Beach
- From the Banner Sun Health Research Institute, Sun City, Arizona, USA
| |
Collapse
|
21
|
Muhammad JS, Siddiqui R, Khan NA. COVID-19 and alcohol use disorder: putative differential gene expression patterns that might be associated with neurological complications. Hosp Pract (1995) 2022; 50:189-195. [PMID: 35686663 DOI: 10.1080/21548331.2022.2088183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Several lines of evidence suggest that SARS-CoV-2 invasion of the central nervous system leads to meningitis and encephalopathy syndromes. Additionally, chronic alcoholics were found to be at a higher risk of developing mental health problems and serious neurological manifestations, if exposed to SARS-CoV-2 infection. METHODS Herein, we studied RNA seq data from alcoholics' brain tissue and COVID-19 patient's brain tissue to identify the common differentially expressed genes. RESULTS Overlap analysis depicted the expression of seven genes (GHRL, SLN, VGF, IL1RL1, NPTX2, PDYN, and RPRML) that were significantly upregulated in both groups. Along with these, protein-protein interaction analysis revealed 10 other key molecules with strong interactions with the aforementioned genes. CONCLUSIONS Taken together with the functional effect of these genes, we suggest a strong molecular link between COVID-19-induced severities and neurological impairment in patients suffering from alcohol abuse disorder. These findings emphasize the importance of identifying chronic alcoholism as a risk factor for developing cognitive and memory impairment in COVID-19 patients.
Collapse
Affiliation(s)
- Jibran Sualeh Muhammad
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
| | - Ruqaiyyah Siddiqui
- College of Arts and Sciences, American University of Sharjah, Sharjah, UAE
| | - Naveed Ahmed Khan
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, UAE
| |
Collapse
|
22
|
Ruz-Caracuel I, Pian-Arias H, Corral Í, Carretero-Barrio I, Bueno-Sacristán D, Pérez-Mies B, García-Cosío M, Caniego-Casas T, Pizarro D, García-Narros MI, Piris-Villaespesa M, Pestaña D, de Pablo R, Galán JC, Masjuan J, Palacios J. Neuropathological findings in fatal COVID-19 and their associated neurological clinical manifestations. Pathology 2022; 54:738-745. [PMID: 35691726 PMCID: PMC9182090 DOI: 10.1016/j.pathol.2022.03.006] [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: 12/02/2021] [Revised: 02/27/2022] [Accepted: 03/07/2022] [Indexed: 12/19/2022]
Abstract
Severe cases of Coronavirus Disease 2019 (COVID-19) can present with multiple neurological symptoms. The available neuropathological studies have described different lesions; the most frequent was the presence of neuroinflammation and vascular-related lesions. The objective of this study was to report the neuropathological studies performed in a medical institution, with abundant long intensive care unit stays, and their associated clinical manifestations. This is a retrospective monocentric case series study based on the neuropathological reports of 13 autopsies with a wide range of illness duration (13–108 days). A neuroinflammatory score was calculated based on the quantification of CD8- and CD68-positive cells in representative areas of the central nervous system. This score was correlated afterwards with illness duration and parameters related to systemic inflammation. Widespread microglial and cytotoxic T-cell activation was found in all patients. There was no correlation between the neuroinflammatory score and the duration of the illness; nor with parameters of systemic inflammation such as the peak of IL-6 or the HScore (a parameter of systemic macrophage activation syndrome). Two patients had global hypoxic ischaemic damage and five patients had subacute infarcts. One patient had many more brain vascular microthrombi compared to the others and multiple subacute pituitary infarcts. SARS-CoV-2 RNA was not detected with qRT-PCR. The proportion of brain lesions in severe COVID-19 patients could be related to illness duration. In our series, with abundant long hospitalisation stays, neuroinflammation was present in all patients and was more prominent between day 34 and day 45 after onset of symptoms. Clinical correlation showed that two patients with the highest neuroinflammatory scores had severe encephalopathies that were not attributable to any other cause. The second most frequent lesions were related to vascular pathology.
Collapse
Affiliation(s)
| | - Héctor Pian-Arias
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Íñigo Corral
- Neurology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; Universidad de Alcalá de Henares, Madrid, Spain
| | - Irene Carretero-Barrio
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; Universidad de Alcalá de Henares, Madrid, Spain
| | | | - Belén Pérez-Mies
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; Universidad de Alcalá de Henares, Madrid, Spain; CIBERONC, Madrid, Spain
| | - Mónica García-Cosío
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; Universidad de Alcalá de Henares, Madrid, Spain; CIBERONC, Madrid, Spain
| | - Tamara Caniego-Casas
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; CIBERONC, Madrid, Spain
| | - David Pizarro
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | | | | | - David Pestaña
- Universidad de Alcalá de Henares, Madrid, Spain; Anesthesiology and Surgical Critical Care Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Raúl de Pablo
- Universidad de Alcalá de Henares, Madrid, Spain; Department of Intensive Care Medicine, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Juan Carlos Galán
- Clinical Microbiology Department, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; CIBERESP, Madrid, Spain
| | - Jaime Masjuan
- Neurology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; Universidad de Alcalá de Henares, Madrid, Spain.
| | - José Palacios
- Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, Madrid, Spain; Universidad de Alcalá de Henares, Madrid, Spain; CIBERONC, Madrid, Spain.
| |
Collapse
|
23
|
Orendáčová M, Kvašňák E. Possible Mechanisms Underlying Neurological Post-COVID Symptoms and Neurofeedback as a Potential Therapy. Front Hum Neurosci 2022; 16:837972. [PMID: 35431842 PMCID: PMC9010738 DOI: 10.3389/fnhum.2022.837972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 12/13/2022] Open
Abstract
Theoretical considerations related to neurological post-COVID complications have become a serious issue in the COVID pandemic. We propose 3 theoretical hypotheses related to neurological post-COVID complications. First, pathophysiological processes responsible for long-term neurological complications caused by COVID-19 might have 2 phases: (1) Phase of acute Sars-CoV-2 infection linked with the pathogenesis responsible for the onset of COVID-19-related neurological complications and (2) the phase of post-acute Sars-CoV-2 infection linked with the pathogenesis responsible for long-lasting persistence of post-COVID neurological problems and/or exacerbation of another neurological pathologies. Second, post-COVID symptoms can be described and investigated from the perspective of dynamical system theory exploiting its fundamental concepts such as system parameters, attractors and criticality. Thirdly, neurofeedback may represent a promising therapy for neurological post-COVID complications. Based on the current knowledge related to neurofeedback and what is already known about neurological complications linked to acute COVID-19 and post-acute COVID-19 conditions, we propose that neurofeedback modalities, such as functional magnetic resonance-based neurofeedback, quantitative EEG-based neurofeedback, Othmer's method of rewarding individual optimal EEG frequency and heart rate variability-based biofeedback, represent a potential therapy for improvement of post-COVID symptoms.
Collapse
Affiliation(s)
- Mária Orendáčová
- Department of Medical Biophysics and Medical Informatics, Third Faculty of Medicine, Charles University in Prague, Prague, Czechia
| | - Eugen Kvašňák
- Department of Medical Biophysics and Medical Informatics, Third Faculty of Medicine, Charles University in Prague, Prague, Czechia
| |
Collapse
|
24
|
Ahmed Z, Renart EG, Zeeshan S. Investigating underlying human immunity genes, implicated diseases and their relationship to COVID-19. Per Med 2022; 19:229-250. [PMID: 35261286 PMCID: PMC8919975 DOI: 10.2217/pme-2021-0132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Aim: A human immunogenetics variation study was conducted in samples collected from diverse COVID-19 populations. Materials & methods: Whole-genome and whole-exome sequencing (WGS/WES), data processing, analysis and visualization pipeline were applied to identify variants associated with genes of interest. Results: A total of 2886 mutations were found across the entire set of 13 genomes. Functional annotation of the gene variants revealed mutation type and protein change. Many variants were found to be biologically implicated in COVID-19. The involvement of these genes was also found in multiple other diseases. Conclusion: The analysis determined that ACE2, TMPRSS4, TMPRSS2, SLC6A20 and FYCOI had functional implications and TMPRSS4 was the gene most altered in virally infected patients. The quest to establish an understanding of the genetics underlying COVID-19 is a central focus of life sciences today. COVID-19 is triggered by SARS-CoV-2, a single-stranded RNA respiratory virus. Several clinical-genomics studies have emerged positing different human gene mutations occurring due to COVID-19. A global analysis of these genes was conducted targeting major components of the immune system to identify possible variations likely to be involved in COVID-19 predisposition. Gene-variant analysis was performed on whole-genome sequencing samples collected from diverse populations. ACE2, TMPRSS4, TMPRSS2, SLC6A20 and FYCOI were found to have functional implications and TMPRSS4 may have a role in the severity of clinical manifestations of COVID-19.
Collapse
Affiliation(s)
- Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy & Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ 08901, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers Biomedical & Health Sciences, 125 Paterson Street, New Brunswick, NJ 08901, USA
| | - Eduard Gibert Renart
- Rutgers Institute for Health, Health Care Policy & Aging Research, Rutgers University, 112 Paterson Street, New Brunswick, NJ 08901, USA
| | - Saman Zeeshan
- Rutgers Cancer Institute of New Jersey, Rutgers University, 195 Little Albany St, New Brunswick, NJ 08901, USA
| |
Collapse
|
25
|
Geerling E, Pinski AN, Stone TE, DiPaolo RJ, Zulu MZ, Maroney KJ, Brien JD, Messaoudi I, Pinto AK. Roles of antiviral sensing and type I interferon signaling in the restriction of SARS-CoV-2 replication. iScience 2022; 25:103553. [PMID: 34877479 PMCID: PMC8639477 DOI: 10.1016/j.isci.2021.103553] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/15/2021] [Accepted: 11/30/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019. Few studies have compared replication dynamics and host responses to SARS-CoV-2 in cell lines from different tissues and species. Therefore, we investigated the role of tissue type and antiviral genes during SARS-CoV-2 infection in nonhuman primate (kidney) and human (liver, respiratory epithelial, gastric) cell lines. We report different viral growth kinetics and release among the cell lines despite comparable ACE2 expression. Transcriptomics revealed that absence of STAT1 in nonhuman primate cells appeared to enhance inflammatory responses without effecting infectious viral titer. Deletion of RL-6 in respiratory epithelial cells increased viral replication. Impaired infectious virus release was detected in Huh7 but not Huh7.5 cells, suggesting a role for RIG1. Gastric cells MKN45 exhibited robust antiviral gene expression and supported viral replication. Data here provide insight into molecular pathogenesis of and alternative cell lines for studying SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO 63103, USA
| | - Amanda N. Pinski
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Taylor E. Stone
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO 63103, USA
| | - Richard J. DiPaolo
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO 63103, USA
| | - Michael Z. Zulu
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Kevin J. Maroney
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - James D. Brien
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO 63103, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Amelia K. Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, MO 63103, USA
| |
Collapse
|
26
|
SARS-CoV-2 Exacerbates Beta-Amyloid Neurotoxicity, Inflammation and Oxidative Stress in Alzheimer's Disease Patients. Int J Mol Sci 2021; 22:ijms222413603. [PMID: 34948400 PMCID: PMC8705864 DOI: 10.3390/ijms222413603] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggered the pandemic Coronavirus Disease 19 (COVID-19), causing millions of deaths. The elderly and those already living with comorbidity are likely to die after SARS-CoV-2 infection. People suffering from Alzheimer’s disease (AD) have a higher risk of becoming infected, because they cannot easily follow health roles. Additionally, those suffering from dementia have a 40% higher risk of dying from COVID-19. Herein, we collected from Gene Expression Omnibus repository the brain samples of AD patients who died of COVID-19 (AD+COVID-19), AD without COVID-19 (AD), COVID-19 without AD (COVID-19) and control individuals. We inspected the transcriptomic and interactomic profiles by comparing the COVID-19 cohort against the control cohort and the AD cohort against the AD+COVID-19 cohort. SARS-CoV-2 in patients without AD mainly activated processes related to immune response and cell cycle. Conversely, 21 key nodes in the interactome are deregulated in AD. Interestingly, some of them are linked to beta-amyloid production and clearance. Thus, we inspected their role, along with their interactors, using the gene ontologies of the biological process that reveals their contribution in brain organization, immune response, oxidative stress and viral replication. We conclude that SARS-CoV-2 worsens the AD condition by increasing neurotoxicity, due to higher levels of beta-amyloid, inflammation and oxidative stress.
Collapse
|
27
|
Mavrikaki M, Lee JD, Solomon IH, Slack FJ. Severe COVID-19 induces molecular signatures of aging in the human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.11.24.21266779. [PMID: 34845457 PMCID: PMC8629201 DOI: 10.1101/2021.11.24.21266779] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is predominantly an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and remains a significant threat to public health. COVID-19 is accompanied by neurological symptoms and cognitive decline, but the molecular mechanisms underlying this effect remain unclear. As aging induces distinct molecular signatures in the brain associated with cognitive decline in healthy populations, we hypothesized that COVID-19 may induce molecular signatures of aging. Here, we performed whole transcriptomic analysis of human frontal cortex, a critical area for cognitive function, in 12 COVID-19 cases and age- and sex-matched uninfected controls. COVID-19 induces profound changes in gene expression, despite the absence of detectable virus in brain tissue. Pathway analysis shows downregulation of genes involved in synaptic function and cognition and upregulation of genes involved in immune processes. Comparison with five independent transcriptomic datasets of aging human frontal cortex reveals striking similarities between aged individuals and severe COVID-19 patients. Critically, individuals below 65 years of age exhibit profound transcriptomic changes not observed among older individuals in our patient cohort. Our data indicate that severe COVID-19 induces molecular signatures of aging in the human brain and emphasize the value of neurological follow-up in recovered individuals.
Collapse
Affiliation(s)
- Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally: Maria Mavrikaki and Jonathan D. Lee
- Correspondence to M.M. and F.J.S.: ;
| | - Jonathan D. Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- These authors contributed equally: Maria Mavrikaki and Jonathan D. Lee
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02215, USA
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02215, USA
- Correspondence to M.M. and F.J.S.: ;
| |
Collapse
|
28
|
Khan M, Yoo SJ, Clijsters M, Backaert W, Vanstapel A, Speleman K, Lietaer C, Choi S, Hether TD, Marcelis L, Nam A, Pan L, Reeves JW, Van Bulck P, Zhou H, Bourgeois M, Debaveye Y, De Munter P, Gunst J, Jorissen M, Lagrou K, Lorent N, Neyrinck A, Peetermans M, Thal DR, Vandenbriele C, Wauters J, Mombaerts P, Van Gerven L. Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb. Cell 2021; 184:5932-5949.e15. [PMID: 34798069 PMCID: PMC8564600 DOI: 10.1016/j.cell.2021.10.027] [Citation(s) in RCA: 224] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/01/2021] [Accepted: 10/25/2021] [Indexed: 12/28/2022]
Abstract
Anosmia, the loss of smell, is a common and often the sole symptom of COVID-19. The onset of the sequence of pathobiological events leading to olfactory dysfunction remains obscure. Here, we have developed a postmortem bedside surgical procedure to harvest endoscopically samples of respiratory and olfactory mucosae and whole olfactory bulbs. Our cohort of 85 cases included COVID-19 patients who died a few days after infection with SARS-CoV-2, enabling us to catch the virus while it was still replicating. We found that sustentacular cells are the major target cell type in the olfactory mucosa. We failed to find evidence for infection of olfactory sensory neurons, and the parenchyma of the olfactory bulb is spared as well. Thus, SARS-CoV-2 does not appear to be a neurotropic virus. We postulate that transient insufficient support from sustentacular cells triggers transient olfactory dysfunction in COVID-19. Olfactory sensory neurons would become affected without getting infected.
Collapse
Affiliation(s)
- Mona Khan
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Seung-Jun Yoo
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Marnick Clijsters
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium
| | - Wout Backaert
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, KU Leuven, Leuven, Belgium
| | - Arno Vanstapel
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Kato Speleman
- Department of Otorhinolaryngology, Head and Neck Surgery, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Charlotte Lietaer
- Department of Otorhinolaryngology, Head and Neck Surgery, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Sumin Choi
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | | | - Lukas Marcelis
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Andrew Nam
- NanoString Technologies Inc., Seattle, WA, USA
| | - Liuliu Pan
- NanoString Technologies Inc., Seattle, WA, USA
| | | | - Pauline Van Bulck
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Hai Zhou
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Marc Bourgeois
- Department of Anesthesiology and Intensive Care Medicine, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium
| | - Yves Debaveye
- Intensive Care Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Cellular and Molecular Medicine, Laboratory of Intensive Care Medicine, KU Leuven, Leuven, Belgium
| | - Paul De Munter
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, Leuven, Belgium
| | - Jan Gunst
- Intensive Care Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Cellular and Molecular Medicine, Laboratory of Intensive Care Medicine, KU Leuven, Leuven, Belgium
| | - Mark Jorissen
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium; Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Katrien Lagrou
- Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, Leuven, Belgium
| | - Natalie Lorent
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Arne Neyrinck
- Department of Anesthesia, University Hospitals Leuven, Leuven, Belgium; Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Marijke Peetermans
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, Leuven, Belgium
| | - Dietmar Rudolf Thal
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium; Department of Imaging and Pathology, Laboratory of Neuropathology and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Christophe Vandenbriele
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium; Department of Cardiovascular Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Joost Wauters
- Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, Leuven, Belgium
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany.
| | - Laura Van Gerven
- Department of Neurosciences, Experimental Otorhinolaryngology, Rhinology Research, KU Leuven, Leuven, Belgium; Department of Otorhinolaryngology, Head and Neck Surgery, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Unit, KU Leuven, Leuven, Belgium.
| |
Collapse
|
29
|
Garofalo M, Gagliardi S, Zucca S, Pandini C, Dragoni F, Sproviero D, Pansarasa O, Poloni TE, Medici V, Davin A, Visonà SD, Moretti M, Guaita A, Ceroni M, Tronconi L, Cereda C. COVID-19 patients and Dementia: Frontal cortex transcriptomic data. Data Brief 2021; 38:107432. [PMID: 34604485 PMCID: PMC8479506 DOI: 10.1016/j.dib.2021.107432] [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: 06/03/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 10/28/2022] Open
Abstract
Since the association of SARS-Cov-2 infection with Nervous System (NS) manifestations, we performed RNA-sequencing analysis in Frontal Cortex of COVID-19 positive or negative individuals and affected or not by Dementia individuals. We examined gene expression differences in individuals with COVID-19 and Dementia compared to Dementia only patients by collecting transcript counts in each sample and performing Differential Expression analysis. We found eleven genes satisfying our significance criteria, all of them being protein coding genes. These data are suitable for integration with supplemental samples and for analysis according to different individuals' classification. Also, differential expression evaluation may be implemented with other scientific purposes, such as research of unannotated genes, mRNA splicing and genes isoforms. The analysis of Differential Expressed genes in COVID-19 positive patients compared to non-COVID-19 patients is published in: S. Gagliardi, E.T. Poloni, C. Pandini, M. Garofalo, F. Dragoni, V. Medici, A. Davin, S.D. Visonà, M. Moretti, D. Sproviero, O. Pansarasa, A. Guaita, M. Ceroni, L. Tronconi, C. Cereda, Detection of SARS-CoV-2 genome and whole transcriptome sequencing in frontal cortex of COVID-19 patients., Brain. Behav. Immun. (2021). https://doi.org/10.1016/j.bbi.2021.05.012.
Collapse
Affiliation(s)
- Maria Garofalo
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy.,Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Stella Gagliardi
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy
| | | | - Cecilia Pandini
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy
| | - Francesca Dragoni
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy.,Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Daisy Sproviero
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy
| | - Orietta Pansarasa
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy
| | - Tino Emanuele Poloni
- Department of Neurology and Neuropathology, Golgi-Cenci Foundation & ASP Golgi-Redaelli Abbiategrasso, Milano, Italy
| | - Valentina Medici
- Department of Neurology and Neuropathology, Golgi-Cenci Foundation & ASP Golgi-Redaelli Abbiategrasso, Milano, Italy
| | - Annalisa Davin
- Department of Neurology and Neuropathology, Golgi-Cenci Foundation & ASP Golgi-Redaelli Abbiategrasso, Milano, Italy
| | - Silvia Damiana Visonà
- Department of Public Health, Experimental and Forensic Medicine, Unit of Legal Medicine and Forensic Sciences "A. Fornari", University of Pavia, Pavia, Italy
| | - Matteo Moretti
- Department of Public Health, Experimental and Forensic Medicine, Unit of Legal Medicine and Forensic Sciences "A. Fornari", University of Pavia, Pavia, Italy
| | - Antonio Guaita
- Department of Neurology and Neuropathology, Golgi-Cenci Foundation & ASP Golgi-Redaelli Abbiategrasso, Milano, Italy
| | - Mauro Ceroni
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Department of General Neurology, IRCCS Mondino Foundation, Pavia, Italy
| | - Livio Tronconi
- Department of Public Health, Experimental and Forensic Medicine, Unit of Legal Medicine and Forensic Sciences "A. Fornari", University of Pavia, Pavia, Italy.,U.O. Medicina Legale, IRCCS Mondino Foundation, Pavia, Italy
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Via Mondino, 2, Pavia 27100, Italy
| |
Collapse
|
30
|
Yang J, Yan Y, Zhong W. Application of omics technology to combat the COVID-19 pandemic. MedComm (Beijing) 2021; 2:381-401. [PMID: 34766152 PMCID: PMC8554664 DOI: 10.1002/mco2.90] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/22/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
As of August 27, 2021, the ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread to over 220 countries, areas, and territories. Thus far, 214,468,601 confirmed cases, including 4,470,969 deaths, have been reported to the World Health Organization. To combat the COVID-19 pandemic, multiomics-based strategies, including genomics, transcriptomics, proteomics, and metabolomics, have been used to study the diagnosis methods, pathogenesis, prognosis, and potential drug targets of COVID-19. In order to help researchers and clinicians to keep up with the knowledge of COVID-19, we summarized the most recent progresses reported in omics-based research papers. This review discusses omics-based approaches for studying COVID-19, summarizing newly emerged SARS-CoV-2 variants as well as potential diagnostic methods, risk factors, and pathological features of COVID-19. This review can help researchers and clinicians gain insight into COVID-19 features, providing direction for future drug development and guidance for clinical treatment, so that patients can receive appropriate treatment as soon as possible to reduce the risk of disease progression.
Collapse
Affiliation(s)
- Jingjing Yang
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
- School of Pharmaceutical SciencesHainan UniversityHaikouHainanChina
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| | - Wu Zhong
- National Engineering Research Center for the Emergency DrugBeijing Institute of Pharmacology and ToxicologyBeijingChina
| |
Collapse
|