1
|
Fujimura K, Guise AJ, Nakayama T, Schlaffner CN, Meziani A, Kumar M, Cheng L, Vaughan DJ, Kodani A, Van Haren S, Parker K, Levy O, Durbin AF, Bosch I, Gehrke L, Steen H, Mochida GH, Steen JA. Integrative systems biology characterizes immune-mediated neurodevelopmental changes in murine Zika virus microcephaly. iScience 2023; 26:106909. [PMID: 37332674 PMCID: PMC10275723 DOI: 10.1016/j.isci.2023.106909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/12/2023] [Accepted: 05/12/2023] [Indexed: 06/20/2023] Open
Abstract
Characterizing perturbation of molecular pathways in congenital Zika virus (ZIKV) infection is critical for improved therapeutic approaches. Leveraging integrative systems biology, proteomics, and RNA-seq, we analyzed embryonic brain tissues from an immunocompetent, wild-type congenital ZIKV infection mouse model. ZIKV induced a robust immune response accompanied by the downregulation of critical neurodevelopmental gene programs. We identified a negative correlation between ZIKV polyprotein abundance and host cell cycle-inducing proteins. We further captured the downregulation of genes/proteins, many of which are known to be causative for human microcephaly, including Eomesodermin/T-box Brain Protein 2 (EOMES/TBR2) and Neuronal Differentiation 2 (NEUROD2). Disturbances of distinct molecular pathways in neural progenitors and post-mitotic neurons may contribute to complex brain phenotype of congenital ZIKV infection. Overall, this report on protein- and transcript-level dynamics enhances understanding of the ZIKV immunopathological landscape through characterization of fetal immune response in the developing brain.
Collapse
Affiliation(s)
- Kimino Fujimura
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and The Manton Center for Orphan Disease, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Department of Pediatrics, Shin-Yurigaoka General Hospital, Kanagawa, Japan
| | - Amanda J. Guise
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Tojo Nakayama
- Division of Genetics and Genomics and The Manton Center for Orphan Disease, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christoph N. Schlaffner
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Anais Meziani
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Mukesh Kumar
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Long Cheng
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dylan J. Vaughan
- Division of Genetics and Genomics and The Manton Center for Orphan Disease, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Andrew Kodani
- Center for Pediatric Neurological Disease Research and Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Simon Van Haren
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | | | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Ann F. Durbin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Irene Bosch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lee Gehrke
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hanno Steen
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Ganeshwaran H. Mochida
- Division of Genetics and Genomics and The Manton Center for Orphan Disease, Boston Children’s Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Judith A. Steen
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
2
|
Fatoki TH. Human adenovirus DNA polymerase is evolutionarily and functionally associated with human telomerase reverse transcriptase based on in silico molecular characterization that implicate abacavir and zidovudine. FRONTIERS IN BIOINFORMATICS 2023; 3:1123307. [PMID: 37351013 PMCID: PMC10282644 DOI: 10.3389/fbinf.2023.1123307] [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: 12/13/2022] [Accepted: 05/29/2023] [Indexed: 06/24/2023] Open
Abstract
Human adenoviruses (HAdVs) are non-enveloped, small double stranded DNA (dsDNA) viruses that cause asymptomatic infections, clinical syndromes and significant susceptibility to infections in immunocompromised people. The aim of the present study was to identify critical host proteins and HAdV hypothetical proteins that could be developed as potential host-viral targets for antiHAdV therapy. Here, the function of selected hypothetical proteins of HAdV based on phylogenetic relationship with the therapeutic targets of antiretroviral drugs of human immunodeficiency virus (HIV) was predicted computationally, and characterized the molecular dynamics and binding affinity of DNA polymerase of HAdV. Thirty-eight hypothetical proteins (HPs) of human adenovirus (HAdV) were used in this study. The results showed that HAdV DNA polymerase (P03261) is related to Human TERT (O14746) and HLA-B (P01889) genes. The protein-protein interaction of human five molecular targets (PNP, TERT, CCR5, HLA-B, and NR1I2) of ARVDs are well-coordinated/networked with CD4, AHR, FKBP4, NR3C1, HSP90AA1, and STUB1 proteins in the anti-HIV infection mechanism. The results showed that the free energy score of abacavir and zidovudine binding to HAdV DNA polymerase are -5.8 and -5.4 kcal mol-1 respectively. Also, the control drug, cidofovir and ganciclovir have less binding affinity for DNA polymerase of HAdV when compare to that of abacavir and zidovudine. Similarity was observed in the binding of abacavir and zidovudine to HAdV DNA polymerase (ASP742, ALA743, LEU772, ARG773 and VAL776). In conclusion, combination of abacavir and zidovudine was predicted to be potential therapy for controlling HAdV infection targeting HAdV DNA polymerase.
Collapse
|
3
|
Guo Y, Liu K, Yang X, Lv Z, Zhao K, Wang X, Chu Y, Li J, Huang T. Multi-omics-based characterization of the influences of Mycobacterium tuberculosis virulence factors EsxB and PPE68 on host cells. Arch Microbiol 2023; 205:230. [PMID: 37162591 PMCID: PMC10170423 DOI: 10.1007/s00203-023-03576-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023]
Abstract
Mycobacterium tuberculosis, the ancient master of causing tuberculosis, is one of the most successful pathogens capable of persistently colonizing host lungs. The EsxB (CFP-10) of ESX-1 system and PPE68 of the PPE family contribute to the virulence of M. tuberculosis. However, the virulence potential and pathogenetic characteristics of these two proteins during M. tuberculosis infection remain unclear. In this study, two prokaryotic expression plasmids for EsxB or PPE68 of M. tuberculosis were constructed and the recombinant proteins His-EsxB or His-PPE68 were purified. The proteome and transcriptome of MH-S cells treated with His-EsxB or His-PPE68 were explored, followed by validating the expression of the identified differentially expressed genes (DEGs) using quantitative PCR. A total of 159/439 specific proteins or 633/1117 DEGs were obtained between control and His-EsxB or His-PPE68 treated groups in the MH-S proteomes and transcriptomes. Additionally, 37/60 signal pathways were predicted in the His-EsxB or His-PPE68 treated groups and "Cytokine-cytokine receptor interaction" was the most represented pathway. Furthermore, the expression of the DEGs (IL-1β, IL-6, and TNF-α) was significantly upregulated, suggesting that these DEGs contributed to the host response during EsxB or PPE68 treatment. These findings provide detailed information on developing an effective intervention strategy to control M. tuberculosis infection.
Collapse
Affiliation(s)
- Yidong Guo
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Kanghua Liu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, 610064, Chengdu, People's Republic of China
| | - Xiting Yang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Zheng Lv
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Kelei Zhao
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Xinrong Wang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Yiwen Chu
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, 610064, Chengdu, People's Republic of China.
| | - Ting Huang
- Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, No. 2025 Chengluo Avenue, 610106, Chengdu, People's Republic of China.
| |
Collapse
|
4
|
Price AM, Steinbock RT, Lauman R, Charman M, Hayer KE, Kumar N, Halko E, Lum KK, Wei M, Wilson AC, Garcia BA, Depledge DP, Weitzman MD. Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts. PLoS Pathog 2022; 18:e1010797. [PMID: 36095031 PMCID: PMC9499273 DOI: 10.1371/journal.ppat.1010797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/22/2022] [Accepted: 08/05/2022] [Indexed: 01/07/2023] Open
Abstract
Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.
Collapse
Affiliation(s)
- Alexander M. Price
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Robert T. Steinbock
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard Lauman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Matthew Charman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Katharina E. Hayer
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Namrata Kumar
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Edwin Halko
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Krystal K. Lum
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Monica Wei
- Cell & Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York city, New York, United States of America
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Matthew D. Weitzman
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
5
|
Saha B, Parks RJ. Recent Advances in Novel Antiviral Therapies against Human Adenovirus. Microorganisms 2020; 8:E1284. [PMID: 32842697 PMCID: PMC7563841 DOI: 10.3390/microorganisms8091284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 12/27/2022] Open
Abstract
Human adenovirus (HAdV) is a very common pathogen that typically causes minor disease in most patients. However, the virus can cause significant morbidity and mortality in certain populations, including young children, the elderly, and those with compromised immune systems. Currently, there are no approved therapeutics to treat HAdV infections, and the standard treatment relies on drugs approved to combat other viral infections. Such treatments often show inconsistent efficacy, and therefore, more effective antiviral therapies are necessary. In this review, we discuss recent developments in the search for new chemical and biological anti-HAdV therapeutics, including drugs that are currently undergoing preclinical/clinical testing, and small molecule screens for the identification of novel compounds that abrogate HAdV replication and disease.
Collapse
Affiliation(s)
- Bratati Saha
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Robin J. Parks
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada;
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Centre for Neuromuscular Disease, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Medicine, The Ottawa Hospital, Ottawa, ON K1H 8L6, Canada
| |
Collapse
|
6
|
Valdés A, Zhao H, Pettersson U, Lind SB. Phosphorylation Time-Course Study of the Response during Adenovirus Type 2 Infection. Proteomics 2020; 20:e1900327. [PMID: 32032466 DOI: 10.1002/pmic.201900327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/22/2020] [Indexed: 12/31/2022]
Abstract
PTMs such as phosphorylations are usually involved in signal transduction pathways. To investigate the temporal dynamics of phosphoproteome changes upon viral infection, a model system of IMR-90 cells infected with human adenovirus type 2 (Ad2) is used in a time-course quantitative analysis combining titanium dioxide (TiO2 ) particle enrichment and SILAC-MS. Quantitative data from 1552 phosphorylated sites clustered the highly altered phosphorylated sites to the signaling by rho family GTPases, the actin cytoskeleton signaling, and the cAMP-dependent protein kinase A signaling pathways. Their activation is especially pronounced at early time post-infection. Changes of several phosphorylated sites involved in the glycolysis pathway, related to the activation of the Warburg effect, point at virus-induced energy production. For Ad2 proteins, 32 novel phosphorylation sites are identified and as many as 52 phosphorylated sites on 17 different Ad2 proteins are quantified, most of them at late time post-infection. Kinase predictions highlighted activation of PKA, CDK1/2, MAPK, and CKII. Overlaps of kinase motif sequences for viral and human proteins are observed, stressing the importance of phosphorylation during Ad2 infection.
Collapse
Affiliation(s)
- Alberto Valdés
- Section of Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, 751 24, Sweden.,Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Hongxing Zhao
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, 75185, Uppsala, Sweden
| | - Ulf Pettersson
- The Beijer Laboratory, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Rudbeck Laboratory, 75185, Uppsala, Sweden
| | - Sara Bergström Lind
- Section of Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Uppsala, 751 24, Sweden
| |
Collapse
|
7
|
Zhao H, Punga T, Pettersson U. Adenovirus in the omics era - a multipronged strategy. FEBS Lett 2020; 594:1879-1890. [PMID: 31811727 DOI: 10.1002/1873-3468.13710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/15/2023]
Abstract
Human adenoviruses (HAdVs) are common pathogens associated with a wide variety of respiratory, ocular, and gastrointestinal diseases. To achieve its effective lytic mode of replication, HAdVs have to reprogram host-cell gene expression and fine-tune viral gene expression in a temporal manner. In two decades, omics revolution has advanced our knowledge about the HAdV and host-cell interplay at the RNA and protein levels. This review summarizes the current knowledge from large-scale datasets on how HAdV infections adjust coding and noncoding RNA expression, as well as how they reprogram host-cell proteome during the lytic course of infection.
Collapse
Affiliation(s)
- Hongxing Zhao
- Beijer Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
| | - Ulf Pettersson
- Beijer Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| |
Collapse
|
8
|
Abstract
In this paper I describe aspects of work on the human adenoviruses in which my laboratory has participated. It consists of two sections-one historic dealing with work performed in the previous century, and one dealing with the application of 'omics' technologies to understand how adenovirus-infected cells become reprogrammed to benefit virus multiplication.
Collapse
Affiliation(s)
- Ulf Pettersson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| |
Collapse
|