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Research Article

A meta-analysis of differentially expressed and regulatory genes with their functional enrichment analysis for brain transcriptome data in autism spectrum disorder

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Pages 9382-9388 | Received 04 Jul 2022, Accepted 24 Oct 2022, Published online: 14 Nov 2022

References

  • Anderson, G. (2019). Autism spectrum disorder: Pathophysiology and treatment implications. Current Pharmaceutical Design, 25(41), 4319–4320. https://doi.org/10.2174/138161282541191230102715
  • Ayhan, F., & Konopka, G. (2019). Regulatory genes and pathways disrupted in autism spectrum disorders. Progress in Neuro-Psychopharmacology & Biological Psychiatry, 89, 57–64. https://doi.org/10.1016/j.pnpbp.2018.08.017
  • Baizer, J. S. (2021). Functional and neuropathological evidence for a role of the brainstem in autism. Frontiers in Integrative Neuroscience, 15, 748977. Oct 20 PMID: 34744648; PMCID: PMC8565487. https://doi.org/10.3389/fnint.2021.748977
  • Baribeau, D., & Anagnostou, E. (2022). Novel treatments for autism spectrum disorder based on genomics and systems biology. Pharmacology & Therapeutics, 230, 107939. https://doi.org/10.1016/j.pharmthera.2021.107939
  • Baumer, N., & Spence, S. J. (2018). Evaluation and management of the child with autism spectrum disorder. Continuum (Minneapolis, Minn.), 24(1, Child Neurology), 248–275. https://doi.org/10.1212/CON.0000000000000578
  • Björkqvist, M., Wild, E. J., Thiele, J., Silvestroni, A., Andre, R., Lahiri, N., Raibon, E., Lee, R. V., Benn, C. L., Soulet, D., Magnusson, A., Woodman, B., Landles, C., Pouladi, M. A., Hayden, M. R., Khalili-Shirazi, A., Lowdell, M. W., Brundin, P., Bates, G. P., … Tabrizi, S. J. (2008). A novel pathogenic pathway of immune activation detectable before clinical onset in Huntington’s disease. The Journal of Experimental Medicine, 205(8), 1869–1877. https://doi.org/10.1084/jem.20080178
  • Buxbaum, J. D., Daly, M. J., Devlin, B., Lehner, T., Roeder, K., & State, M. W. (2012). The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders. Neuron, 76(6), 1052–1056. https://doi.org/10.1016/j.neuron.2012.12.008
  • Ch’ng, C., Kwok, W., Rogic, S., & Pavlidis, P. (2015). Meta-Analysis of Gene Expression in Autism Spectrum Disorder. Autism Research: Official Journal of the International Society for Autism Research, 8(5), 593–608. https://doi.org/10.1002/aur.1475
  • Chaste, P., & Leboyer, M. (2012). Autism risk factors: genes, environment, and gene-environment interactions. Dialogues in Clinical Neuroscience, 14(3), 281–292. https://doi.org/10.31887/DCNS.2012.14.3/pchaste.
  • Cohly, H. H., & Panja, A. (2005). Immunological findings in autism. International Review of Neurobiology, 71, 317–341. https://doi.org/10.1016/s0074-7742(05)71013-8.
  • Demetriou, E. A., Lampit, A., Quintana, D. S., Naismith, S. L., Song, Y. J. C., Pye, J. E., Hickie, I., & Guastella, A. J. (2018). Autism spectrum disorders: a meta-analysis of executive function. Molecular Psychiatry, 23(5), 1198–1204. https://doi.org/10.1038/mp.2017.75
  • Doncheva, N. T., Morris, J. H., Gorodkin, J., & Jensen, L. J. (2019). Cytoscape StringApp: Network analysis and visualization of proteomics data. Journal of Proteome Research, 18(2), 623–632. https://doi.org/10.1021/acs.jproteome.8b00702
  • Elsabbagh, M., Divan, G., Koh, Y. J., Kim, Y. S., Kauchali, S., Marcín, C., Montiel-Nava, C., Patel, V., Paula, C. S., Wang, C., Yasamy, M. T., & Fombonne, E. (2012). Global prevalence of autism and other pervasive developmental disorders. Autism Research: Official Journal of the International Society for Autism Research, 5(3), 160–179. https://doi.org/10.1002/aur.239
  • Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., Shieh, A. W., Haney, J., Parhami, S., Belmont, J., Kim, M., Losada, M., Khan, P., Mleczko, Z., Xia, J., … Geschwind, D. H. (2018). Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science, 362(6420), eaat8127. PMID: 30545856; PMCID: PMC6443102. https://doi.org/10.1126/science.aat8127
  • Guarente, L., & Hoar, E. (1984). Upstream activation sites of the CYC1 gene of Saccharomyces cerevisiae are active when inverted but not when placed downstream of the "TATA box. Proceedings of the National Academy of Sciences of the United States of America, 81(24), 7860–7864. https://doi.org/10.1073/pnas.81.24.7860
  • Guarente, L., & Mason, T. (1983). Heme regulates transcription of the CYC1 gene of S. cerevisiae via an upstream activation site. Cell, 32(4), 1279–1286. https://doi.org/10.1016/0092-8674(83)90309-4
  • Ha, A. D., & Fung, V. S. (2012). Huntington’s disease. Current Opinion in Neurology, 25(4), 491–498. https://doi.org/10.1097/WCO.0b013e3283550c97
  • Ha, S., Sohn, I. J., Kim, N., Sim, H. J., & Cheon, K. A. (2015). Characteristics of brains in autism spectrum disorder: Structure, function and connectivity across the lifespan. Experimental Neurobiology, 24(4), 273–284. https://doi.org/10.5607/en.2015.24.4.273
  • He, Y., Zhou, Y., Ma, W., & Wang, J. (2019). An integrated transcriptomic analysis of autism spectrum disorder. Scientific Reports, 9(1), 11818. https://doi.org/10.1038/s41598-019-48160-x
  • Horiuchi, F., Yoshino, Y., Kumon, H., Hosokawa, R., Nakachi, K., Kawabe, K., Iga, J. I., & Ueno, S. I. (2021). Identification of aberrant innate and adaptive immunity based on changes in global gene expression in the blood of adults with autism spectrum disorder. Journal of Neuroinflammation, 18(1), 102. https://doi.org/10.1186/s12974-021-02154-7
  • Hossain, M. M., Khan, N., Sultana, A., Ma, P., McKyer, E. L. J., Ahmed, H. U., & Purohit, N. (2020 May). Prevalence of comorbid psychiatric disorders among people with autism spectrum disorder: An umbrella review of systematic reviews and meta-analyses. Psychiatry Research, 287, 112922. https://doi.org/10.1016/j.psychres.2020.112922
  • Huang, K., Wu, Y., Shin, J., Zheng, Y., Siahpirani, A. F., Lin, Y., Ni, Z., Chen, J., You, J., Keles, S., Wang, D., Roy, S., & Lu, Q. (2021). Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLoS Genetics, 17(2), e1009309. https://doi.org/10.1371/journal.pgen.1009309
  • Hyman, S. L., Levy, S. E., Myers, S. M., Kuo, D. Z., Apkon, S., Davidson, L. F., Ellerbeck, K. A., Foster, J. E., Noritz, G. H., Leppert, M. O., Saunders, B. S., Stille, C., Yin, L., Weitzman, C. C., Childers, D. O., Levine, J. M., Peralta-Carcelen, A. M., Poon, J. K., Smith, P. J., … Bridgemohan, C, (2020). Myers sm; council on children with disabilities, section on developmental and behavioral pediatrics. Identification, evaluation, and management of children with autism spectrum disorder. Pediatrics, 145(1), e20193447. https://doi.org/10.1542/peds.2019-3447
  • Kodak, T., & Bergmann, S. (2020). Autism spectrum disorder: Characteristics, associated behaviors, and early intervention. Pediatric Clinics of North America, 67(3), 525–535. https://doi.org/10.1016/j.pcl.2020.02.007
  • Lei, J., & Ventola, P. (2017). Pivotal response treatment for autism spectrum disorder: current perspectives. Neuropsychiatric Disease and Treatment, 13, 1613–1626. https://doi.org/10.2147/NDT.S120710
  • Li, X., Zhang, Y., Wang, L., Lin, Y., Gao, Z., Zhan, X., Huang, Y., Sun, C., Wang, D., Liang, S., & Wu, L. (2019). Integrated analysis of brain transcriptome reveals convergent molecular pathways in autism spectrum disorder. Frontiers in Psychiatry, 10, 706. https://doi.org/10.3389/fpsyt.2019.00706
  • Lord, C., Elsabbagh, M., Baird, G., & Veenstra-Vanderweele, J. (2018). Autism spectrum disorder. Lancet (London, England), 392(10146), 508–520. https://doi.org/10.1016/S0140-6736(18)31129-2
  • Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8
  • Martens, C., Krett, B., & Laybourn, P. J. (2001). RNA polymerase II and TBP occupy the repressed CYC1 promoter. Molecular Microbiology, 40(4), 1009–1019. https://doi.org/10.1046/j.1365-2958.2001.02445.x
  • Mi, H., Huang, X., Muruganujan, A., Tang, H., Mills, C., Kang, D., & Thomas, P. D. (2017). PANTHER version 11: Expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Research, 45(D1), D183–D189. Jan 4 Epub 2016 Nov 29. PMID: 27899595; PMCID: PMC5210595. https://doi.org/10.1093/nar/gkw1138
  • Mi, H., Muruganujan, A., Casagrande, J. T., & Thomas, P. D. (2013). Large-scale gene function analysis with the PANTHER classification system. Nature Protocols, 8(8), 1551–1566. Aug https://doi.org/10.1038/nprot.2013.092
  • Mi, H., Muruganujan, A., Huang, X., Ebert, D., Mills, C., Guo, X., & Thomas, P. D. (2019). Protocol update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nature Protocols, 14(3), 703–721. https://doi.org/10.1038/s41596-019-0128-8
  • Minshew, N. J., & Williams, D. L. (2007). The new neurobiology of autism: Cortex, connectivity, and neuronal organization. Archives of Neurology, 64(7), 945–950. https://doi.org/10.1001/archneur.64.7.945
  • Pirone, A., Alexander, J. M., Koenig, J. B., Cook-Snyder, D. R., Palnati, M., Wickham, R. J., Eden, L., Shrestha, N., Reijmers, L., Biederer, T., Miczek, K. A., Dulla, C. G., & Jacob, M. H. (2018). Social stimulus causes aberrant activation of the medial prefrontal cortex in a mouse model with autism-like behaviors. Frontiers in Synaptic Neuroscience, 10, 35. https://doi.org/10.3389/fnsyn.2018.00035
  • Prigge, M. B., Lange, N., Bigler, E. D., Merkley, T. L., Neeley, E. S., Abildskov, T. J., Froehlich, A. L., Nielsen, J. A., Cooperrider, J. R., Cariello, A. N., Ravichandran, C., Alexander, A. L., & Lainhart, J. E. (2013). Corpus callosum area in children and adults with autism. Research in Autism Spectrum Disorders, 7(2), 221–234. https://doi.org/10.1016/j.rasd.2012.09.007
  • Rahman, M. R., Petralia, M. C., Ciurleo, R., Bramanti, A., Fagone, P., Shahjaman, M., Wu, L., Sun, Y., Turanli, B., Arga, K. Y., Islam, M. R., Islam, T., & Nicoletti, F. (2020). Comprehensive analysis of RNA-Seq gene expression profiling of brain transcriptomes reveals novel genes, regulators, and pathways in autism spectrum disorder. Brain Sciences, 10(10), 747. https://doi.org/10.3390/brainsci10100747
  • Rau, A., Marot, G., & Jaffrézic, F. (2014). Differential meta-analysis of RNA-seq data from multiple studies. BMC Bioinformatics, 15, 91. https://doi.org/10.1186/1471-2105-15-91
  • Reimand, J., Isserlin, R., Voisin, V., Kucera, M., Tannus-Lopes, C., Rostamianfar, A., Wadi, L., Meyer, M., Wong, J., Xu, C., Merico, D., & Bader, G. D. (2019). Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap. Nature Protocols, 14(2), 482–517. Doi: 10.1038/s41596-018-0103-9.
  • Rose, S., Niyazov, D. M., Rossignol, D. A., Goldenthal, M., Kahler, S. G., & Frye, R. E. (2018). Clinical and molecular characteristics of mitochondrial dysfunction in autism spectrum disorder. Molecular Diagnosis & Therapy, 22(5), 571–593. https://doi.org/10.1007/s40291-018-0352-x
  • Rossignol, D. A., & Frye, R. E. (2012). Mitochondrial dysfunction in autism spectrum disorders: a systematic review and meta-analysis. Molecular Psychiatry, 17(3), 290–314. https://doi.org/10.1038/mp.2010.136
  • Takumi, T., Tamada, K., Hatanaka, F., Nakai, N., & Bolton, P. F. (2020). Behavioral neuroscience of autism. Neuroscience and Biobehavioral Reviews, 110, 60–76. https://doi.org/10.1016/j.neubiorev.2019.04.012
  • Wajant, H. (2002). The Fas signaling pathway: more than a paradigm. Science (New York, N.Y.), 296(5573), 1635–1636. https://doi.org/10.1126/science.1071553
  • Wei, L., Xiao, M., Hayward, A., & Fu, D. (2013). Applications and challenges of next-generation sequencing in Brassica species. Planta, 238(6), 1005–1024. https://doi.org/10.1007/s00425-013-1961-6
  • Wolff, J. J., Gerig, G., Lewis, J. D., Soda, T., Styner, M. A., Vachet, C., Botteron, K. N., Elison, J. T., Dager, S. R., Estes, A. M., Hazlett, H. C., Schultz, R. T., Zwaigenbaum, L., & Piven, J. (2015). Altered corpus callosum morphology associated with autism over the first 2 years of life. Brain: A Journal of Neurology, 138(Pt 7), 2046–2058. https://doi.org/10.1093/brain/awv118
  • Xia, J., Fjell, C. D., Mayer, M. L., Pena, O. M., Wishart, D. S., & Hancock, R. E. (2013). INMEX–a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Research, 41(Web Server issue), W63–70. https://doi.org/10.1093/nar/gkt338
  • Xia, J., Benner, M. J., & Hancock, R. E. (2014). NetworkAnalyst–integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Research, 42(Web Server issue), W167–74. https://doi.org/10.1093/nar/gku443
  • Xia, J., Gill, E. E., & Hancock, R. E. (2015). NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data. Nature Protocols, 10(6), 823–844. https://doi.org/10.1038/nprot.2015.052
  • Yang, I. S., & Kim, S. (2015). Analysis of whole transcriptome sequencing data: Workflow and software. Genomics & Informatics, 13(4), 119–125. https://doi.org/10.5808/GI.2015.13.4.119
  • Yu, C., Yin, J., Wang, X., Chen, L., Wei, Y., Lu, C., & You, Y. (2020). Association between SNAP25 and human glioblastoma multiform: A comprehensive bioinformatic analysis. Bioscience Reports. 40(6), BSR20200516. https://doi.org/10.1042/BSR20200516.
  • Zeidan, J., Fombonne, E., Scorah, J., Ibrahim, A., Durkin, M. S., Saxena, S., Yusuf, A., Shih, A., & Elsabbagh, M. (2022). Global prevalence of autism: A systematic review update. Autism Research: Official Journal of the International Society for Autism Research, 15(5), 778–790. https://doi.org/10.1002/aur.2696
  • Zhang, Z. H., Jhaveri, D. J., Marshall, V. M., Bauer, D. C., Edson, J., Narayanan, R. K., Robinson, G. J., Lundberg, A. E., Bartlett, P. F., Wray, N. R., & Zhao, Q. Y. (2014). A comparative study of techniques for differential expression analysis on RNA-Seq data. PloS One, 9(8), e103207. https://doi.org/10.1371/journal.pone.0103207
  • Zhou, G., Soufan, O., Ewald, J., Hancock, R. E. W., Basu, N., & Xia, J. (2019). NetworkAnalyst 3.0: A visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic Acids Research, 47(W1), W234–W241. https://doi.org/10.1093/nar/gkz240.
  • Zikopoulos, B., & Barbas, H. (2010). Changes in prefrontal axons may disrupt the network in autism. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 30(44), 14595–14609. https://doi.org/10.1523/JNEUROSCI.2257-10.2010

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