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Weener ME, Obrubov SA, Barh D, Gubanov AA, Yushina VS. [Features of genetic mutations in children with high myopia combined with peripheral retinal degenerations]. Vestn Oftalmol 2024; 140:19-24. [PMID: 38450462 DOI: 10.17116/oftalma202414001119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Degenerative changes in the peripheral regions of the ocular fundus allow a closer look at both the role of collagen genes and their mutations in children with high myopia. PURPOSE The study investigates the features of genetic mutations in children with high myopia combined with peripheral retinal degenerations. MATERIAL AND METHODS Study group was formed from the database of genetic studies of the Scientific and Clinical Center OOO Oftalmic, which consists of 4362 patients referred for medical genetic counseling and molecular genetic testing from 2016 to 2021. Selection criteria were: male and female patients, aged 5-18 years old, who had the following clinical signs: high myopia (>6.00 D) and the presence of peripheral retinal degenerations (PRD). The study considered both isolated cases of ophthalmic pathology, as well as its syndromic forms. The final selection included 40 children. All patients had consulted with a geneticist. Whole-exome sequencing (WES), next generation sequencing (NGS), and single gene sequencing were conducted by taking 5 mL of peripheral venous blood and extracting deoxyribonucleic acid (DNA). RESULTS In patients with isolated cases of ophthalmic pathology (peripheral retinal degenerations and high myopia) with a confirmed genetic diagnosis, mutations in the COL2A1 gene were detected in 77.4% of cases, and in the COL11A1 gene - in 22.6% of cases. In Stickler syndrome with a confirmed genetic diagnosis, mutations in the COL2A1 gene were detected in 33.3% of cases. In Marshall syndrome, the mutation in the COL11A1 gene was detected in 11.1% of cases. In children with Ehlers-Danlos, Knobloch type 1, Cohen, Marfan, Wagner syndromes mutations in the genes COL5A1, COL18A1, VPS13B, FBN1, VCAN were detected in 55.6% of cases. In 33.3% of cases of Knobloch type 1, Cohen, Wagner syndromes the mutation is found in both copies of the gene (i.e., in both chromosomes), which leads to the development of peripheral retinal degenerations with high myopia. CONCLUSION The results of the conducted molecular genetic testing expand our understanding of the mutation spectrum in the genes of children with both isolated cases of ophthalmic pathology, as well as syndromic pathology.
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Affiliation(s)
| | - S A Obrubov
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D Barh
- OOO Oftalmic, Moscow, Russia
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, India
| | - A A Gubanov
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - V S Yushina
- Pirogov Russian National Research Medical University, Moscow, Russia
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de Bruijn SE, Rodenburg K, Corominas J, Ben-Yosef T, Reurink J, Kremer H, Whelan L, Plomp AS, Berger W, Farrar GJ, Ferenc Kovács Á, Fajardy I, Hitti-Malin RJ, Weisschuh N, Weener ME, Sharon D, Pennings RJE, Haer-Wigman L, Hoyng CB, Nelen MR, Vissers LELM, van den Born LI, Gilissen C, Cremers FPM, Hoischen A, Neveling K, Roosing S. Optical genome mapping and revisiting short-read genome sequencing data reveal previously overlooked structural variants disrupting retinal disease-associated genes. Genet Med 2023; 25:100345. [PMID: 36524988 DOI: 10.1016/j.gim.2022.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Structural variants (SVs) play an important role in inherited retinal diseases (IRD). Although the identification of SVs significantly improved upon the availability of genome sequencing, it is expected that involvement of SVs in IRDs is higher than anticipated. We revisited short-read genome sequencing data to enhance the identification of gene-disruptive SVs. METHODS Optical genome mapping was performed to improve SV detection in short-read genome sequencing-negative cases. In addition, reanalysis of short-read genome sequencing data was performed to improve the interpretation of SVs and to re-establish SV prioritization criteria. RESULTS In a monoallelic USH2A case, optical genome mapping identified a pericentric inversion (173 megabase), with 1 breakpoint disrupting USH2A. Retrospectively, the variant could be observed in genome sequencing data but was previously deemed false positive. Reanalysis of short-read genome sequencing data (427 IRD cases) was performed which yielded 30 pathogenic SVs affecting, among other genes, USH2A (n = 15), PRPF31 (n = 3), and EYS (n = 2). Eight of these (>25%) were overlooked during previous analyses. CONCLUSION Critical evaluation of our findings allowed us to re-establish and improve our SV prioritization and interpretation guidelines, which will prevent missing pathogenic events in future analyses. Our data suggest that more attention should be paid to SV interpretation and the current contribution of SVs in IRDs is still underestimated.
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Affiliation(s)
- Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura Whelan
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland; Neuroscience Center Zurich (ZNZ), University and ETH Zurich, Zurich, Switzerland; Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - G Jane Farrar
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Árpád Ferenc Kovács
- 2nd Department of Paediatrics, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Isabelle Fajardy
- Division of Maternal Malnutrition, Department of Perinatal Environment and Health, Lille University, Lille, France; Division Biochemistry and Molecular Biology, Biology and Pathology Center, Lille, France
| | - Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicole Weisschuh
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | | | - Dror Sharon
- Division of Ophthalmology, Hadassah University Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ronald J E Pennings
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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Markova TG, Lalayants MR, Alekseeva NN, Ryzhkova OP, Shatokhina OL, Galeeva NM, Bliznetz EA, Weener ME, Belov OA, Chibisova SS, Polyakov AV, Tavartkiladze GA. Early audiological phenotype in patients with mutations in the USH2A gene. Int J Pediatr Otorhinolaryngol 2022; 157:111140. [PMID: 35452909 DOI: 10.1016/j.ijporl.2022.111140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Nowadays, due to universal newborn hearing screening (UNHS) the number of children with mild-to-moderate hearing loss diagnosed in the first year of life has increased significantly. Aside from that, identification of the genetic cause improves the genetic counselling of the families and allows to reveal possible comorbidities which may need a special approach. OBJECTIVE To present the characteristics of the early audiologic phenotype in hearing impaired patients with biallelic mutations in the USH2A gene based on systematic analysis of the audiological data. PATIENTS AND METHODS 13 patients with mutations in the USH2A gene underwent audiological examination. Most of them were found among a large group of infants with bilateral nonsyndromic sensorineural hearing loss (SNHL) examined under 12 months. RESULTS Eight out of eleven children failed UNHS and were initially diagnosed as having bilateral nonsyndromic SNHL. Seven children underwent an audiological assessment before the age of 9 months. The earliest audiological examination was carried out at 1 and 3 months. The children with pathogenic variants in the USH2A gene in our examined group were identified in the first year of life via UNHS. The hearing threshold levels (HTL) for the USH2A group are compactly distributed between 51.25 dB and 66.25 dB, quartiles are 54 dB and 63.4 dB, with a median of 60 dB. The audiological profile of patients with biallelic USH2A mutations differs from audiograms of patients who had STRC-related hearing loss. We have not found any significant elevation in hearing thresholds in the first decade of life. We also estimated the prevalence of the USH2A and STRC mutations among GJB2-negative infants with bilateral nonsyndromic SNHL examined under 12 months, and it was 7.5% and 16.1%, respectively. CONCLUSION According to our results, the early hearing phenotype in pediatric patients with biallelic mutations in the USH2A- gene is characterized by nonsyndromic mild-to-moderate SNHL in the first decade of life. Our results indicate that the presence of mutations in the USH2A or STRC genes can be expected in a child with congenital mild-to-moderate nonsyndromic SNHL. This information is of practical importance for parents, as they have to know the prognosis of hearing loss for their child from the very beginning. Post-screening follow-up should include adequate clinical, genetic, and social support for children and their parents.
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Affiliation(s)
- T G Markova
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - M R Lalayants
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - N N Alekseeva
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - O L Shatokhina
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - N M Galeeva
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - E A Bliznetz
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - M E Weener
- CRO LLC «Oftalmic», Moscow, 125167, Russia
| | - O A Belov
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia
| | - S S Chibisova
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - A V Polyakov
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - G A Tavartkiladze
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia.
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Barh D, Tiwari S, Gabriel Rodrigues Gomes L, Weener ME, Alzahrani KJ, Alsharif KF, Aljabali AAA, Tambuwala MM, Lundstrom K, Hassan SS, Serrano-Aroca Á, Takayama K, Ghosh P, Redwan EM, Silva Andrade B, Soares SDC, Azevedo V, Uversky VN. Potential Molecular Mechanisms of Rare Anti-Tumor Immune Response by SARS-CoV-2 in Isolated Cases of Lymphomas. Viruses 2021; 13:v13101927. [PMID: 34696358 PMCID: PMC8539762 DOI: 10.3390/v13101927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, two cases of complete remission of classical Hodgkin lymphoma (cHL) and follicular lymphoma (FL) after SARS-CoV-2 infection were reported. However, the precise molecular mechanism of this rare event is yet to be understood. Here, we hypothesize a potential anti-tumor immune response of SARS-CoV-2 and based on a computational approach show that: (i) SARS-CoV-2 Spike-RBD may bind to the extracellular domains of CD15, CD27, CD45, and CD152 receptors of cHL or FL and may directly inhibit cell proliferation. (ii) Alternately, upon internalization after binding to these CD molecules, the SARS-CoV-2 membrane (M) protein and ORF3a may bind to gamma-tubulin complex component 3 (GCP3) at its tubulin gamma-1 chain (TUBG1) binding site. (iii) The M protein may also interact with TUBG1, blocking its binding to GCP3. (iv) Both the M and ORF3a proteins may render the GCP2-GCP3 lateral binding where the M protein possibly interacts with GCP2 at its GCP3 binding site and the ORF3a protein to GCP3 at its GCP2 interacting residues. (v) Interactions of the M and ORF3a proteins with these gamma-tubulin ring complex components potentially block the initial process of microtubule nucleation, leading to cell-cycle arrest and apoptosis. (vi) The Spike-RBD may also interact with and block PD-1 signaling similar to pembrolizumab and nivolumab- like monoclonal antibodies and may induce B-cell apoptosis and remission. (vii) Finally, the TRADD interacting “PVQLSY” motif of Epstein-Barr virus LMP-1, that is responsible for NF-kB mediated oncogenesis, potentially interacts with SARS-CoV-2 Mpro, NSP7, NSP10, and spike (S) proteins, and may inhibit the LMP-1 mediated cell proliferation. Taken together, our results suggest a possible therapeutic potential of SARS-CoV-2 in lymphoproliferative disorders.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
- Correspondence:
| | - Sandeep Tiwari
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Lucas Gabriel Rodrigues Gomes
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Marianna E. Weener
- Clinical Research Center, Oftalmic, CRO, 119334 Bardina Str. 22/4, 119991 Moscow, Russia;
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (K.J.A.); (K.F.A.)
| | - Khalaf F. Alsharif
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (K.J.A.); (K.F.A.)
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK;
| | | | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India;
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan;
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Elrashdy M. Redwan
- Department of Biological Science, Faculty of Science, King Abdulazizi University, Jeddah 21589, Saudi Arabia;
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié 45206-190, Brazil;
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38025-180, Brazil;
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, 141700 Dolgoprudny, Russia
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Kumavath R, Barh D, Andrade BS, Imchen M, Aburjaile FF, Ch A, Rodrigues DLN, Tiwari S, Alzahrani KJ, Góes-Neto A, Weener ME, Ghosh P, Azevedo V. The Spike of SARS-CoV-2: Uniqueness and Applications. Front Immunol 2021; 12:663912. [PMID: 34305894 PMCID: PMC8297464 DOI: 10.3389/fimmu.2021.663912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point-of-care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.
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Affiliation(s)
- Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Flavia Figueira Aburjaile
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Athira Ch
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Diego Lucas Neres Rodrigues
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Barh D, Tiwari S, Andrade BS, Weener ME, Góes-Neto A, Azevedo V, Ghosh P, Blum K, Ganguly NK. A novel multi-omics-based highly accurate prediction of symptoms, comorbid conditions, and possible long-term complications of COVID-19. Mol Omics 2021; 17:317-337. [PMID: 33683246 DOI: 10.1039/d0mo00189a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Comprehensive clinical pictures, comorbid conditions, and long-term complications of COVID-19 are still unknown. Recently, using a multi-omics-based strategy, we predicted potential drugs for COVID-19 with ∼70% accuracy. Herein, using a novel multi-omics-based bioinformatic approach and three ways of analysis, we identified the symptoms, comorbid conditions, and short-, mid-, and possible long-term complications of COVID-19 with >90% precision including 27 parent, 170 child, and 403 specific conditions. Among the specific conditions, 36 viral, 53 short-term, 62 short-mid-long-term, 194 mid-long-term, and 57 congenital conditions are identified. At a threshold "count of occurrence" of 4, we found that 83-100% (average 92.67%) of enriched conditions are associated with COVID-19. Except for dry cough and loss of taste, all the other COVID-19-associated mild and severe symptoms are enriched. CVDs, and pulmonary, metabolic, musculoskeletal, neuropsychiatric, kidney, liver, and immune system disorders are top comorbid conditions. Specific diseases like myocardial infarction, hypertension, COPD, lung injury, diabetes, cirrhosis, mood disorders, dementia, macular degeneration, chronic kidney disease, lupus, arthritis, etc. along with several other NCDs were found to be top candidates. Interestingly, many cancers and congenital disorders associated with COVID-19 severity are also identified. Arthritis, gliomas, diabetes, psychiatric disorders, and CVDs having a bidirectional relationship with COVID-19 are also identified as top conditions. Based on our accuracy (>90%), the long-term presence of SARS-CoV-2 RNA in human, and our "genetic remittance" assumption, we hypothesize that all the identified top-ranked conditions could be potential long-term consequences in COVID-19 survivors, warranting long-term observational studies.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India.
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Barh D, Tiwari S, Weener ME, Azevedo V, Góes-Neto A, Gromiha MM, Ghosh P. Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19. Comput Biol Med 2020; 126:104051. [PMID: 33131530 PMCID: PMC7547373 DOI: 10.1016/j.compbiomed.2020.104051] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs, including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, plasma components, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management.
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Affiliation(s)
- Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India.
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marianna E Weener
- Clinical Research Center, Oftalmic, CRO, 119334, Bardina Str.22/4, Moscow, Russia
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IIT-M), Chennai, 600036, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
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