Copy number variant risk loci for schizophrenia converge on the BDNF pathway

References

• Abbi S, Ueda H, Zheng C, Cooper LA, Zhao J, Christopher R, Guan JL. 2002. Regulation of focal adhesion kinase by a novel protein inhibitor FIP200. Mol Biol Cell. 13(9):3178–3191. doi: 10.1091/mbc.e02-05-0295.
   PubMed Web of Science ®Google Scholar
• Blizinsky KD, Diaz-Castro B, Forrest MP, Schürmann B, Bach AP, Martin-de-Saavedra MD, Wang L, Csernansky JG, Duan J, Penzes P. 2016. Reversal of dendritic phenotypes in 16p11.2 microduplication mouse model neurons by pharmacological targeting of a network hub. Proc Natl Acad Sci U S A. 113(30):8520–8525. doi: 10.1073/pnas.1607014113.
   PubMed Web of Science ®Google Scholar
• Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen T-MT, Texier Y, van Beersum SEC, Horn N, Willer JR, Mans DA, et al. 2016. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nat Commun. 7(1):11491. doi: 10.1038/ncomms11491.
   PubMedGoogle Scholar
• Cleynen I, Engchuan W, Hestand MS, Heung T, Holleman AM, Johnston HR, Monfeuga T, McDonald-McGinn DM, Gur RE, Morrow BE, et al. 2020. Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion. Mol Psychiatry. 26(8):4496–4510. doi: 10.1038/s41380-020-0654-3.
   PubMed Web of Science ®Google Scholar
• Cox DM, Butler MG. 2015. A clinical case report and literature review of the 3q29 microdeletion syndrome. Clin Dysmorphol. 24(3):89–94. doi: 10.1097/MCD.0000000000000077.
   PubMed Web of Science ®Google Scholar
• De Rubeis S, Pasciuto E, Li KW, Fernández E, Di Marino D, Buzzi A, Ostroff LE, Klann E, Zwartkruis FJT, Komiyama NH, et al. 2013. CYFIP1 coordinates mRNA translation and cytoskeleton remodeling to ensure proper dendritic spine formation. Neuron. 79(6):1169–1182. doi: 10.1016/j.neuron.2013.06.039.
   PubMed Web of Science ®Google Scholar
• Degenhardt F, Priebe L, Meier S, Lennertz L, Streit F, Witt SH, Hofmann A, Becker T, Mössner R, Maier W, et al. 2013. Duplications in RB1CC1 are associated with schizophrenia; identification in large European sample sets. Transl Psychiatry. 3(11):e326–e326. doi: 10.1038/tp.2013.101.
   PubMedGoogle Scholar
• Dell’Edera D, Dilucca C, Allegretti A, Simone F, Lupo MG, Liccese C, Davanzo R. 2018. 16p11.2 microdeletion syndrome: a case report. J Med Case Rep. 12(1):90.
   PubMedGoogle Scholar
• Fisher E, Wood SJ, Elsworthy RJ, Upthegrove R, Aldred S. 2020. Exercise as a protective mechanism against the negative effects of oxidative stress in first-episode psychosis: a biomarker-led study. Transl Psychiatry. 10(1):254. doi: 10.1038/s41398-020-00927-x.
   PubMed Web of Science ®Google Scholar
• Golzio C, Willer J, Talkowski ME, Oh EC, Taniguchi Y, Jacquemont S, Reymond A, Sun M, Sawa A, Gusella JF, et al. 2012. KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Nature. 485(7398):363–367. doi: 10.1038/nature11091.
   PubMed Web of Science ®Google Scholar
• Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. 2019. RCy3: network biology using cytoscape from within R. F1000Res. 8:1774. doi: 10.12688/f1000research.20887.3.
   PubMedGoogle Scholar
• Kendall KM, Rees E, Escott-Price V, Einon M, Thomas R, Hewitt J, O'Donovan MC, Owen MJ, Walters JTR, Kirov G. 2017. Cognitive performance among carriers of pathogenic copy number variants: analysis of 152,000 UK biobank subjects. Biol Psychiatry. 82(2):103–110. doi: 10.1016/j.biopsych.2016.08.014.
   PubMed Web of Science ®Google Scholar
• Kirov G, Rees E, Walters JT, Escott-Price V, Georgieva L, Richards AL, Chambert KD, Davies G, Legge SE, Moran JL, et al. 2014. The penetrance of copy number variations for schizophrenia and developmental delay. Biol Psychiatry. 75(5):378–385. doi: 10.1016/j.biopsych.2013.07.022.
   PubMed Web of Science ®Google Scholar
• Kutmon M, Ehrhart F, Willighagen EL, Evelo CT, Coort SL. 2018. CyTargetLinker app update: a flexible solution for network extension in cytoscape. F1000Res. 7:743. doi: 10.12688/f1000research.14613.1.
   Google Scholar
• Kutmon M, Lotia S, Evelo CT, Pico AR. 2014. WikiPathways app for cytoscape: making biological pathways amenable to network analysis and visualization. F1000Res. 3:152. doi: 10.12688/f1000research.4254.1.
   PubMedGoogle Scholar
• Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT. 2015. PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput Biol. 11(2):e1004085. doi: 10.1371/journal.pcbi.1004085.
   PubMed Web of Science ®Google Scholar
• Le Hellard S, Mühleisen TW, Djurovic S, Fernø J, Ouriaghi Z, Mattheisen M, Vasilescu C, Raeder MB, Hansen T, Strohmaier J, et al. 2010. Polymorphisms in SREBF1 and SREBF2, two antipsychotic-activated transcription factors controlling cellular lipogenesis, are associated with schizophrenia in German and Scandinavian samples. Mol Psychiatry. 15(5):463–472. doi: 10.1038/mp.2008.110.
   PubMed Web of Science ®Google Scholar
• Magrinelli F, Balint B, Bhatia KP. 2021. Challenges in clinicogenetic correlations: one gene - many phenotypes. Mov Disord Clin Pract. 8(3):299–310. doi: 10.1002/mdc3.13165.
   PubMed Web of Science ®Google Scholar
• Marshall CR, Howrigan DP, Merico D, Thiruvahindrapuram B, Wu W, Greer DS, Antaki D, Shetty A, Holmans PA, Pinto D, et al. 2017. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat Genet. 49(1):27–35. doi: 10.1038/ng.3725.
   PubMed Web of Science ®Google Scholar
• Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, R AM, Digles D, Lopes EN, Ehrhart F, et al. 2021. WikiPathways: connecting communities. Nucleic Acids Res. 49(D1):D613–D621. doi: 10.1093/nar/gkaa1024.
   PubMed Web of Science ®Google Scholar
• McDonald-McGinn DM, et al. 1993. 22q11.2. In: Adam MP, Ardinger HH, Pagon RA editors. Seattle (WA): GeneReviews((R)).
   Google Scholar
• Mervis CB, et al. 1993. 7q11.23 duplication syndrome. In: Adam MP, Ardinger HH, Pagon RA editors. Seattle (WA): GeneReviews((R)).
   Google Scholar
• NetPath MK, Hanspers K, Roudbari Z, Evelo C, Chichester C, Willighagen E, Weitz E. 2021. Brain-derived neurotrophic factor (BDNF) signaling pathway (Homo sapiens). www.wikipathways.org/instance/WP2380. [accessed 2021].
   Google Scholar
• Nielsen PA, Baruch A, Shestopalov VI, Giepmans BN, Dunia I, Benedetti EL, Kumar NM. 2003. Lens connexins alpha3Cx46 and alpha8Cx50 interact with zonula occludens protein-1 (ZO-1). Mol Biol Cell. 14(6):2470–2481. doi: 10.1091/mbc.e02-10-0637.
   PubMed Web of Science ®Google Scholar
• Pardiñas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S, Carrera N, Legge SE, Bishop S, Cameron D, Hamshere ML, et al. 2018. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet. 50(3):381–389. doi: 10.1038/s41588-018-0059-2.
   PubMed Web of Science ®Google Scholar
• Piñero J, Bravo À, Queralt-Rosinach N, Gutiérrez-Sacristán A, Deu-Pons J, Centeno E, García-García J, Sanz F, Furlong LI. 2017. DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants. Nucleic Acids Res. 45(D1):D833–D839. doi: 10.1093/nar/gkw943.
   PubMed Web of Science ®Google Scholar
• Prata DP, Costa-Neves B, Cosme G, Vassos E. 2019. Unravelling the genetic basis of schizophrenia and bipolar disorder with GWAS: a systematic review. J Psychiatr Res. 114:178–207. doi: 10.1016/j.jpsychires.2019.04.007.
   PubMed Web of Science ®Google Scholar
• Schizophrenia Working Group of the Psychiatric Genomics C. 2014. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 511(7510):421–427.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11):2498–2504. doi: 10.1101/gr.1239303.
   PubMed Web of Science ®Google Scholar
• Silva AI, Haddon JE, Ahmed Syed Y, Trent S, Lin T-CE, Patel Y, Carter J, Haan N, Honey RC, Humby T, et al. 2019. Cyfip1 haploinsufficient rats show white matter changes, myelin thinning, abnormal oligodendrocytes and behavioural inflexibility. Nat Commun. 10(1):3455. doi: 10.1038/s41467-019-11119-7.
   PubMedGoogle Scholar
• Tripathi A, Nasrallah HA, Pillai A. 2023. Pimavanserin treatment increases plasma brain-derived neurotrophic factor levels in rats. Front Neurosci. 17:1237726. doi: 10.3389/fnins.2023.1237726.
   PubMed Web of Science ®Google Scholar
• Trubetskoy V, Pardiñas AF, Qi T, Panagiotaropoulou G, Awasthi S, Bigdeli TB, Bryois J, Chen C-Y, Dennison CA, Hall LS, et al. 2022. Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature. 604(7906):502–508. doi: 10.1038/s41586-022-04434-5.
   PubMed Web of Science ®Google Scholar
• van Bon BWM, et al. 1993. 15q13.3 microdeletion. In: Adam MP, Ardinger HH, Pagon RA editors. Seattle (WA): GeneReviews((R)).
   Google Scholar
• van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. 2010. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinf. 11(1):5. doi: 10.1186/1471-2105-11-5.
   PubMedGoogle Scholar
• Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, et al. 2008. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 320(5875):539–543. doi: 10.1126/science.1155174.
   PubMed Web of Science ®Google Scholar
• Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, et al. 2016. Ensembl 2016. Nucleic Acids Res. 44(D1):D710–716. doi: 10.1093/nar/gkv1157.
   PubMed Web of Science ®Google Scholar
• Zhuo C, Hou W, Li G, Mao F, Li S, Lin X, Jiang D, Xu Y, Tian H, Wang W, et al. 2019. The genomics of schizophrenia: shortcomings and solutions. Prog Neuropsychopharmacol Biol Psychiatry. 93:71–76. doi: 10.1016/j.pnpbp.2019.03.009.
   PubMed Web of Science ®Google Scholar