Abstract
Zika virus (ZIKV) is a neurotropic teratogen that causes congenital Zika syndrome (CZS), characterized by brain and eye anomalies. Impaired gene expression in neural cells after ZIKV infection has been demonstrated; however, there is a gap in the literature of studies comparing whether the differentially expressed genes in such cells are similar and how it can cause CZS. Therefore, the aim of this study was to compare the differential gene expression (DGE) after ZIKV infection in neural cells through a meta-analysis approach. Through the GEO database, studies that evaluated DGE in cells exposed to the Asian lineage of ZIKV versus cells, of the same type, not exposed were searched. From the 119 studies found, five meet our inclusion criteria. Raw data of them were retrieved, pre-processed, and evaluated. The meta-analysis was carried out by comparing seven datasets, from these five studies. We found 125 upregulated genes in neural cells, mainly interferon-stimulated genes, such as IFI6, ISG15, and OAS2, involved in the antiviral response. Furthermore, 167 downregulated, involved with cellular division. Among these downregulated genes, classic microcephaly-causing genes stood out, such as CENPJ, ASPM, CENPE, and CEP152, demonstrating a possible mechanism by which ZIKV impairs brain development and causes CZS.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data Availability
The data presented in this study are openly available in GEO database under ID numbers GSE87750, GSE93385, GSE113636, GSE80434, and GSE129180.
References
Afgan E, Baker D, Batut B et al (2018) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 46:W537–W544. https://doi.org/10.1093/NAR/GKY379
Aguiar RS, Pohl F, Morais GL, et al (2020) Molecular alterations in the extracellular matrix in the brains of newborns with congenital Zika syndrome. Sci Signal 13. https://doi.org/10.1126/SCISIGNAL.AAY6736/SUPPL_FILE/AAY6736_TABLE_S5.XLSX
Amaral MS, Goulart E, Caires-Júnior LC, et al (2020) Differential gene expression elicited by ZIKV infection in trophoblasts from congenital Zika syndrome discordant twins. PLoS Negl Trop Dis 14:e0008424. https://doi.org/10.1371/JOURNAL.PNTD.0008424
Anders S, Pyl PT, Huber W (2015) HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169. https://doi.org/10.1093/BIOINFORMATICS/BTU638
Anderson D, Neri JICF, Souza CRM et al (2021) Zika virus changes methylation of genes involved in immune response and neural development in Brazilian babies born with congenital microcephaly. J Infect Dis 223:435–440. https://doi.org/10.1093/INFDIS/JIAA383
Andrews S (2010) FastQC a quality control tool for high throughput sequence data
Anfasa F, Siegers JY, van Der Kroeg M, et al (2017) Phenotypic differences between Asian and African lineage Zika viruses in human neural progenitor cells. MSphere 2. https://doi.org/10.1128/MSPHERE.00292-17/ASSET/2F718E7D-1EEF-4B05-8A80-53CBF524719F/ASSETS/GRAPHIC/SPH0041723250004.JPEG
Berthoux L (2020) The restrictome of flaviviruses. Virol Sin 354(35):363–377. https://doi.org/10.1007/S12250-020-00208-3
Bhagat R, Kaur G, Seth P (2021) Molecular mechanisms of zika virus pathogenesis: an update. Indian J Med Res 154:433–445. https://doi.org/10.4103/ijmr.IJMR_169_20
Brault JB, Khou C, Basset J et al (2016) Comparative analysis between flaviviruses reveals specific neural stem cell tropism for Zika virus in the mouse developing neocortex. EBioMedicine 10:71–76. https://doi.org/10.1016/J.EBIOM.2016.07.018
Buchwalter RA, Ogden SC, York SB, Sun L, Zheng C, Hammack C, Cheng Y, Chen JV, Cone AS, Meckes DG Jr, Tang H, Megraw TL (2021) Coordination of Zika virus infection and viroplasm organization by microtubules and microtubule-organizing centers. Cells 10:3335. https://doi.org/10.3390/cells10123335
Cassina M, Cagnoli GA, Zuccarello D et al (2017) Human teratogens and genetic phenocopies. Understanding pathogenesis through human genes mutation. Eur J Med Genet 60:22–31. https://doi.org/10.1016/J.EJMG.2016.09.011
Crosse KM, Monson EA, Beard MR, Helbig KJ (2018) Interferon-stimulated genes as enhancers of antiviral innate immune signaling. J Innate Immun 10:85–93. https://doi.org/10.1159/000484258
Dang JW, Tiwari SK, Qin Y, Rana TM (2019) Genome-wide integrative analysis of Zika-virus-infected neuronal stem cells reveals roles for microRNAs in cell cycle and stemness. Cell Rep 27:3618–3628. https://doi.org/10.1016/j.celrep.2019.05.059
del Campo M, Feitosa IML, Ribeiro EM et al (2017) The phenotypic spectrum of congenital Zika syndrome. Am J Med Genet Part A 173:841–857. https://doi.org/10.1002/ajmg.a.38170
Devhare P, Meyer K, Steele R et al (2017) Zika virus infection dysregulates human neural stem cell growth and inhibits differentiation into neuroprogenitor cells. Cell Death Dis 810(8):e3106–e3106. https://doi.org/10.1038/cddis.2017.517
Dukhovny A, Lamkiewicz K, Chen Q, et al (2019) A CRISPR activation screen identifies genes that protect against Zika virus infection. J Virol 93. https://doi.org/10.1128/JVI.00211-19/SUPPL_FILE/JVI.00211-19-SD004.CSV
Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210. https://doi.org/10.1093/NAR/30.1.207
Faheem M, Naseer MI, Rasool M et al (2015) Molecular genetics of human primary microcephaly: an overview. BMC Med Genomics 8:1–11. https://doi.org/10.1186/1755-8794-8-S1-S4/TABLES/3
Falker-Gieske C, Mott A, Franzenburg S, Tetens J (2021) Multi-species transcriptome meta-analysis of the response to retinoic acid in vertebrates and comparative analysis of the effects of retinol and retinoic acid on gene expression in LMH cells. BMC Genomics 22:1–16. https://doi.org/10.1186/S12864-021-07451-2/TABLES/4
Ferraris P, Cochet M, Hamel R, Gladwyn-Ng I, Alfano C, Diop F, Garcia D, Talignani L, Montero-Menei CN, Nougairède A, Yssel H, Nguyen L, Coulpier M, Missé D (2019) Zika virus differentially infects human neural progenitor cells according to their state of differentiation and dysregulates neurogenesis through the Notch pathway. Emerg Microbes Infect 8:1003–1016. https://doi.org/10.1080/22221751.2019.1637283
Finnell RH, Gelineau-van Waes J, Eudy JD, Rosenquist TH (2002) Molecular basis of environmentally induced birth defects 42:181–208 https://doi.org/10.1146/ANNUREV.PHARMTOX.42.083001.110955
Freitas BT, Scholte FEM, Bergeron É, Pegan SD (2020) How ISG15 combats viral infection. Virus Res 286:198036. https://doi.org/10.1016/J.VIRUSRES.2020.198036
Gabriel E, Ramani A, Karow U et al (2017) Recent Zika virus isolates induce premature differentiation of neural progenitors in human brain organoids. Cell Stem Cell 20:397–406. https://doi.org/10.1016/j.stem.2016.12.005
Gomes JA, Wachholz GE, Boquett JA, Vianna FSL, Schuler-Faccini L, Fraga LR (2023) Molecular mechanisms of ZIKV-induced teratogenesis: a systematic review of studies in animal models. Mol Neurobiol 60:68–83. https://doi.org/10.1007/s12035-022-03046-4
Gratton R, Tricarico PM, Agrelli A (2020) In vitro Zika virus infection of human neural progenitor cells: meta-analysis of RNA-Seq assays. Microorg 8:270–8270. https://doi.org/10.3390/MICROORGANISMS8020270
Greco T, Zangrillo A, Biondi-Zoccai G, Landoni G (2013) Meta-analysis: pitfalls and hints. Hear Lung Vessel 5:219
Gurok U, Steinhoff C, Lipkowitz B et al (2004) Gene expression changes in the course of neural progenitor cell differentiation. J Neurosci 24:5982–6002. https://doi.org/10.1523/JNEUROSCI.0809-04.2004
Islam MS, Khan MAAK, Murad MW et al (2019) In silico analysis revealed Zika virus miRNAs associated with viral pathogenesis through alteration of host genes involved in immune response and neurological functions. J Med Virol 91:1584–1594. https://doi.org/10.1002/JMV.25505
Langmead B (2010) Aligning short sequencing reads with bowtie. Curr Protoc Bioinforma 32(1):11–7. https://doi.org/10.1002/0471250953.BI1107S32
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 94(9):357–359. https://doi.org/10.1038/nmeth.1923
Lee SY, Park YK, Yoon CH et al (2019) Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1. BMC Med Genomics 12:1–10. https://doi.org/10.1186/S12920-018-0443-X/FIGURES/6
Leinonen R, Akhtar R, Birney E et al (2011) The European Nucleotide Archive. Nucleic Acids Res 39:D28–D31. https://doi.org/10.1093/NAR/GKQ967
Li C, Wang Q, Jiang YS et al (2018) Disruption of glial cell development by Zika virus contributes to severe microcephalic newborn mice. Cell Discov 4:43. https://doi.org/10.1038/s41421-018-0042-1
Li C, Xu D, Ye Q et al (2016) Zika virus disrupts neural progenitor development and leads to microcephaly in mice. Cell Stem Cell 19:120–126. https://doi.org/10.1016/J.STEM.2016.04.017/ATTACHMENT/610C8246-3C13-4888-B950-394B424EDE3F/MMC2.XLSX
Liao X, Xie H, Li S (2020) 2′, 5′-Oligoadenylate synthetase 2 (OAS2) Inhibits Zika Virus Replication through Activation of Type Ι IFN Signaling Pathway. Viruses 12:418. https://doi.org/10.3390/V12040418
Liu L, Chen Z, Zhang X, Li S, Hui Y, Feng H, Du Y, Jin G, Zhou X, Zhang X (2019) Protection of ZIKV infectioninduced neuropathy by abrogation of acute antiviral response in human neural progenitors. Cell Death Differ 26:2607–2621. https://doi.org/10.1038/s41418-019-0324-7
Martines RB, Bhatnagar J, Keating MK, et al (2019) Notes from the field: evidence of Zika virus infection in brain and placental tissues from two congenitally infected newborns and two fetal losses — Brazil, 2015. MMWR Morb Mortal Wkly Rep 65:1–2. https://doi.org/10.15585/MMWR.MM6506E1ER
McCarthy DJ, Chen Y, Smyth GK (2012) Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40:4288–4297. https://doi.org/10.1093/NAR/GKS042
McGrath EL, Rossi SL, Gao J, Widen SG, Grant AC, Dunn TJ, Azar SR, Roundy CM, Xiong Y, Prusak DJ, Loucas BD, Wood TG, Yu Y, Fernández-Salas I, Weaver SC, Vasilakis N, Wu P (2017) Differential responses of human fetal brain neural stem cells to zika virus infection. Stem Cell Rep 8:715–727. https://doi.org/10.1016/j.stemcr.2017.01.008
McKenzie AT, Wang M, Hauberg ME et al (2018) Brain cell type specific gene expression and co-expression network architectures. Sci Reports 81(8):1–19. https://doi.org/10.1038/s41598-018-27293-5
McLean E, Bhattarai R, Hughes BW, Mahalingam K, Bagasra O (2017) Computational identification of mutually homologous Zika virus miRNAs that target microcephaly genes. Libyan J Med 12:1304505. https://doi.org/10.1080/19932820.2017.1304505
Merfeld E, Ben-Avi L, Kennon M, Cerveny KL (2017) Potential mechanisms of Zika-linked microcephaly. Wiley Interdiscip Rev Dev Biol 6:e273. https://doi.org/10.1002/wdev.273
Mladinich MC, Schwedes J, Mackow ER (2017) Zika virus persistently infects and is basolaterally released from primary human brain microvascular endothelial cells. MBio 8:e00952–17. https://doi.org/10.1128/mBio.00952-17
Naveed M, Kazmi SK, Amin M, et al (2018) Comprehensive review on the molecular genetics of autosomal recessive primary microcephaly (MCPH). Genet Res (Camb) 100. https://doi.org/10.1017/S0016672318000046
Oh Y, Zhang F, Wang Y, Lee EM, Choi IY, Lim H, Mirakhori F, Li R, Huang L, Xu T, Wu H, Li C, Qin CF, Wen Z, Wu QF, Tang H, Xu Z, Jin P, Song H, Ming GL, Lee G (2017) Zika virus directly infects peripheral neurons and induces cell death. Nat Neurosci 20:1209–1212. https://doi.org/10.1038/nn.4612
Parrini E, Conti V, Dobyns WB, Guerrini R (2016) Genetic basis of brain malformations. Mol Syndromol 7:220–233. https://doi.org/10.1159/000448639
Prada C, Lima D (2022) MetaVolcanoR: gene expression meta-analysis visualization tool. R Packag. version 1.10.0
Richardson RB, Ohlson MB, Eitson JL et al (2018) A CRISPR screen identifies IFI6 as an ER-resident interferon effector that blocks Flavivirus replication. Nat Microbiol 311(3):1214–1223. https://doi.org/10.1038/s41564-018-0244-1
Rombi F, Bayliss R, Tuplin A, Yeoh S (2020) The journey of Zika to the developing brain. Mol Biol Rep 47:3097–3115. https://doi.org/10.1007/s11033-020-05349-y
Schneider WM, Chevillotte MD, Rice CM (2014) Interferon-stimulated genes: a complex web of host defenses. 32:513–545 https://doi.org/10.1146/ANNUREV-IMMUNOL-032713-120231
Schwartz DA, Hyg M (2017) Autopsy and postmortem studies are concordant: pathology of Zika virus infection is neurotropic in fetuses and infants with microcephaly following transplacental transmission. Arch Pathol Lab Med 141:68–72. https://doi.org/10.5858/ARPA.2016-0343-OA
Sudmant PH, Alexis MS, Burge CB (2015) Meta-analysis of RNA-seq expression data across species, tissues and studies. Genome Biol 16:1–11. https://doi.org/10.1186/S13059-015-0853-4/FIGURES/5
Wang W, Xu L, Su J, Peppelenbosch MP, Pan Q (2017) Transcriptional regulation of antiviral interferon-stimulated genes. Trends Microbiol 25:573–584. https://doi.org/10.1016/j.tim.2017.01.001
Wang Y, Ren K, Li S, et al (2020) Interferon stimulated gene 15 promotes Zika virus replication through regulating Jak/STAT and ISGylation pathways. Virus Res 287:198087. https://doi.org/10.1016/J.VIRUSRES.2020.198087
Wheeler AC, Toth D, Ridenour T et al (2020) Developmental outcomes among young children with congenital Zika syndrome in Brazil. JAMA Netw Open 3:e204096–e204096. https://doi.org/10.1001/JAMANETWORKOPEN.2020.4096
Wu KY, Zuo GL, Li XF et al (2016) Vertical transmission of Zika virus targeting the radial glial cells affects cortex development of offspring mice. Cell Res 26:645–654. https://doi.org/10.1038/cr.2016.58
Yi L, Pimentel H, Pachter L (2017) Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLoS One 12:e0175744. https://doi.org/10.1371/JOURNAL.PONE.0175744
Zhang F, Hammack C, Ogden SC, Cheng Y, Lee EM, Wen Z, Qian X, Nguyen HN, Li Y, Yao B, Xu M, Xu T, Chen L, Wang Z, Feng H, Huang WK, Yoon KJ, Shan C, Huang L, Qin Z, Christian KM, Shi PY, Xu M, Xia M, Zheng W, Wu H, Song H, Tang H, Ming GL, Jin P (2016) Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic Acids Res. 44:8610-8620. https://doi.org/10.1093/nar/gkw765
Funding
This research was supported by Hospital de Clínicas de Porto Alegre (HCPA) - Fundo de Incentivo a Pesquisa e Eventos (FIPE) (grant numbers 2017-0619 and 2019-0295) and Instituto Nacional de Genética Médica Populacional (INAGEMP), grant numbers CNPq 573993/2008-4 and FAPERGS 17/2551.0000521-0. FSLV is the recipient of a CNPq scholarship, grant number 312960/2021-2.
Author information
Authors and Affiliations
Contributions
JAG, TWK, MRM, and FSLV contributed to the study conception and design. Material preparation, data collection, and analysis were performed by JAG, ES, TWK, and GCG. The first draft of the manuscript was written by JAG, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Ethics Approval
This study was performed with publicly available data, and therefore, no ethical approval was required.
Consent to Participate
This study was performed with publicly available data. No personal or confidential information was evaluated or presented. Therefore, no ethical approval was required.
Competing Interests
The authors declare no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Gomes, J.A., Sgarioni, E., Kowalski, T.W. et al. Downregulation of Microcephaly-Causing Genes as a Mechanism for ZIKV Teratogenesis: A Meta-analysis of RNA-Seq Studies. J Mol Neurosci 73, 566–577 (2023). https://doi.org/10.1007/s12031-023-02126-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12031-023-02126-x