Sodium valproate rescues expression of TRANK1 in iPSC-derived neural cells that carry a genetic variant associated with serious mental illness

Abstract

Biological characterization of genetic variants identified in genome-wide association studies (GWAS) remains a substantial challenge. Here we used human-induced pluripotent stem cells (iPSC) and their neural derivatives to characterize common variants on chromosome 3p22 that have been associated by GWAS with major mental illnesses. IPSC-derived neural progenitor cells carrying the risk allele of the single nucleotide polymorphism (SNP), rs9834970, displayed lower baseline TRANK1 expression that was rescued by chronic treatment with therapeutic dosages of valproic acid (VPA). VPA had the greatest effects on TRANK1 expression in iPSC, NPC, and astrocytes. Although rs9834970 has no known function, we demonstrated that a nearby SNP, rs906482, strongly affects binding by the transcription factor, CTCF, and that the high-affinity allele usually occurs on haplotypes carrying the rs9834970 risk allele. Decreased expression of TRANK1 perturbed expression of many genes involved in neural development and differentiation. These findings have important implications for the pathophysiology of major mental illnesses and the development of novel therapeutics.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. 1.

    Richards AL, Jones L, Moskvina V, Kirov G, Gejman PV, Levinson DF, et al. Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain. Mol Psychiatry. 2012;17:193–201.

  2. 2.

    Shinozaki G, Potash JB. New developments in the genetics of bipolar disorder. Curr Psychiatry Rep. 2014;16:493.

  3. 3.

    Kirsten H, Al-Hasani H, Holdt L, Gross A, Beutner F, Krohn K, et al. Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci. Hum Mol Genet. 2015;24:4746–63.

  4. 4.

    GTEx Consortium. The genotype-tissue expression (GTEx) project. Nat Genet. 2013;45:580–5.

  5. 5.

    Liu F, Wang X, Hu G, Wang Y, Zhou J. The transcription factor TEAD1 represses smooth muscle-specific gene expression by abolishing myocardin function. J Biol Chem. 2014;289:3308–16.

  6. 6.

    De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, et al. Tissue-specific histone modification and transcription factor binding in alpha globin gene expression. Blood. 2007;110:4503–10.

  7. 7.

    Mele M, Ferreira PG, Reverter F, DeLuca DS, Monlong J, Sammeth M, et al. Human genomics. The human transcriptome across tissues and individuals. Science. 2015;348:660–5.

  8. 8.

    Gay MH, Valenta T, Herr P, Paratore-Hari L, Basler K, Sommer L. Distinct adhesion-independent functions of beta-catenin control stage-specific sensory neurogenesis and proliferation. BMC Biol. 2015;13:24.

  9. 9.

    Latham KE. Stage-specific and cell type-specific aspects of genomic imprinting effects in mammals. Differentiation. 1995;59:269–82.

  10. 10.

    Rueckert EH, Barker D, Ruderfer D, Bergen SE, O’Dushlaine C, Luce CJ, et al. Cis-acting regulation of brain-specific ANK3 gene expression by a genetic variant associated with bipolar disorder. Mol Psychiatry. 2013;18:922–9.

  11. 11.

    Korecka JA, Levy S, Isacson O. In vivo modeling of neuronal function, axonal impairment and connectivity in neurodegenerative and neuropsychiatric disorders using induced pluripotent stem cells. Mol Cell Neurosci. 2016;73:3–12.

  12. 12.

    Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, et al. Molecular and functional variation in iPSC-derived sensory neurons. Nat Genet. 2018;50:54–61.

  13. 13.

    McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, et al. Mosaic copy number variation in human neurons. Science. 2013;342:632–7.

  14. 14.

    Kim DS, Lee JS, Leem JW, Huh YJ, Kim JY, Kim HS, et al. Robust enhancement of neural differentiation from human ES and iPS cells regardless of their innate difference in differentiation propensity. Stem Cell Rev. 2010;6:270–81.

  15. 15.

    Wen Z, Nguyen HN, Guo Z, Lalli MA, Wang X, Su Y, et al. Synaptic dysregulation in a human iPS cell model of mental disorders. Nature. 2014;515:414–8.

  16. 16.

    Brennand K, Savas JN, Kim Y, Tran N, Simone A, Hashimoto-Torii K, et al. Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Mol Psychiatry. 2015;20:361–8.

  17. 17.

    Mertens J, Wang QW, Kim Y, Yu DX, Pham S, Yang B, et al. Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder. Nature. 2015;527:95–99.

  18. 18.

    Bidinosti M, Botta P, Kruttner S, Proenca CC, Stoehr N, Bernhard M, et al. CLK2 inhibition ameliorates autistic features associated with SHANK3 deficiency. Science. 2016;351:1199–203.

  19. 19.

    Forrest MP, Zhang H, Moy W, McGowan H, Leites C, Dionisio LE, et al. Open chromatin profiling in hIPSC-derived neurons prioritizes functional noncoding psychiatric risk variants and highlights neurodevelopmental loci. Cell Stem Cell. 2017;21:305–18 e308.

  20. 20.

    Chen DT, Jiang X, Akula N, Shugart YY, Wendland JR, Steele CJ, et al. Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder. Mol Psychiatry. 2013;18:195–205.

  21. 21.

    Ruderfer DM, Fanous AH, Ripke S, McQuillin A, Amdur RL, Gejman PV, et al. Polygenic dissection of diagnosis and clinical dimensions of bipolar disorder and schizophrenia. Mol Psychiatry. 2013;19:1017–24.

  22. 22.

    Goes FS, Hamshere ML, Seifuddin F, Pirooznia M, Belmonte-Mahon P, Breuer R, et al. Genome-wide association of mood-incongruent psychotic bipolar disorder. Transl Psychiatry. 2012;2:e180.

  23. 23.

    Cross-Disorder Group of the Psychiatric Genomics Consortium. Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis. Lancet. 2013;381:1371–9.

  24. 24.

    Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014;511:421–7.

  25. 25.

    Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007;318:1917–20.

  26. 26.

    Bergen SE, O’Dushlaine CT, Ripke S, Lee PH, Ruderfer DM, Akterin S, et al. Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder. Mol Psychiatry. 2012;17:880–6.

  27. 27.

    Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, et al. RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Mol Psychiatry. 2014;19:1179–85.

  28. 28.

    Kreutzer J, Yla-Outinen L, Maki AJ, Ristola M, Narkilahti S, Kallio P. Cell culture chamber with gas supply for prolonged recording of human neuronal cells on microelectrode array. J Neurosci Methods. 2017;280:27–35.

  29. 29.

    Muhleisen TW, Leber M, Schulze TG, Strohmaier J, Degenhardt F, Treutlein J, et al. Genome-wide association study reveals two new risk loci for bipolar disorder. Nat Commun. 2014;5:3339.

  30. 30.

    Ward LD, Kellis M. HaploRegv4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res. 2016;44:D877–881.

  31. 31.

    Ghirlando R, Felsenfeld G. CTCF: making the right connections. Genes Dev. 2016;30:881–91.

  32. 32.

    Hasan MR, Kim JH, Kim YJ, Kwon KJ, Shin CY, Kim HY, et al. Effect of HDAC inhibitors on neuroprotection and neurite outgrowth in primary rat cortical neurons following ischemic insult. Neurochem Res. 2013;38:1921–34.

  33. 33.

    Kim BW, Yang S, Lee CH, Son H. A critical time window for the survival of neural progenitor cells by HDAC inhibitors in the hippocampus. Mol Cells. 2011;31:159–64.

  34. 34.

    Yu IT, Park JY, Kim SH, Lee JS, Kim YS, Son H. Valproic acid promotes neuronal differentiation by induction of proneural factors in association with H4 acetylation. Neuropharmacology. 2009;56:473–80.

  35. 35.

    Chung WS, Welsh CA, Barres BA, Stevens B. Do glia drive synaptic and cognitive impairment in disease? Nat Neurosci. 2015;18:1539–45.

  36. 36.

    Peng L, Li B, Verkhratsky A. Targeting astrocytes in bipolar disorder. Expert Rev Neurother. 2016;16:649–57.

  37. 37.

    Stevens B, Muthukumar AK. Cellular neuroscience. Differences among astrocytes. Science. 2016;351:813.

  38. 38.

    Gottlicher M, Minucci S, Zhu P, Kramer OH, Schimpf A, Giavara S, et al. Valproic acid defines a novel class of HDAC inhibitors inducing differentiation of transformed cells. EMBO J. 2001;20:6969–78.

  39. 39.

    Ganai SA, Ramadoss M, Mahadevan V. Histone deacetylase (HDAC) inhibitors—emerging roles in neuronal memory, learning, synaptic plasticity and neural regeneration. Curr Neuropharmacol. 2016;14:55–71.

  40. 40.

    Guo Y, Fu X, Jin Y, Sun J, Liu Y, Huo B, et al. Histone demethylase LSD1-mediated repression of GATA-2 is critical for erythroid differentiation. Drug Des Devel Ther. 2015;9:3153–62.

  41. 41.

    Lutz M, Burke LJ, Barreto G, Goeman F, Greb H, Arnold R, et al. Transcriptional repression by the insulator protein CTCF involves histone deacetylases. Nucleic Acids Res. 2000;28:1707–13.

  42. 42.

    Oti M, Falck J, Huynen MA, Zhou H. CTCF-mediated chromatin loops enclose inducible gene regulatory domains. BMC Genom. 2016;17:252.

  43. 43.

    Buonocore F, Hill MJ, Campbell CD, Oladimeji PB, Jeffries AR, Troakes C, et al. Effects of cis-regulatory variation differ across regions of the adult human brain. Human Mol Genet. 2010;19:4490–6.

  44. 44.

    Burkhardt MF, Martinez FJ, Wright S, Ramos C, Volfson D, Mason M, et al. A cellular model for sporadic ALS using patient-derived induced pluripotent stem cells. Mol Cell Neurosci. 2013;56:355–64.

  45. 45.

    Won H, de la Torre-Ubieta L, Stein JL, Parikshak NN, Huang J, Opland CK, et al. Chromosome conformation elucidates regulatory relationships in developing human brain. Nature. 2016;538:523–7.

  46. 46.

    Cooper AR, Patel S, Senadheera S, Plath K, Kohn DB, Hollis RP. Highly efficient large-scale lentiviral vector concentration by tandem tangential flow filtration. J Virol Methods. 2011;177:1–9.

  47. 47.

    Muller FJ, Brandl B, Loring JF. Assessment of human pluripotent stem cells with PluriTest. Cambridge, MA: StemBook; 2008.

  48. 48.

    Jiang X, Tian F, Du Y, Copeland NG, Jenkins NA, Tessarollo L, et al. BHLHB2 controls Bdnf promoter 4 activity and neuronal excitability. J Neurosci. 2008;28:1118–30.

  49. 49.

    Xiao T, Wallace J, Felsenfeld G. Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity. Mol Cell Biol. 2011;31:2174–83.

  50. 50.

    Yusufzai TM, Felsenfeld G. The 5’-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element. Proc Natl Acad Sci USA. 2004;101:8620–4.

  51. 51.

    Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44–57.

  52. 52.

    Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1–13.

Download references

Acknowledgements

This study was supported by the Intramural Research Programs of the National Institute of Mental Health (NIMH; ZIA-MH00284311/NCT00001174), National Institute of Neurological Disease and Stroke (NINDS), and the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health. Dr. Kevin Chen, at the NINDS Stem Cell Unit helped with Flow Cytometry Analysis; Dr. Wei Lu at the Synapse and Neural Circuit Unit (NINDS) helped with electrophysiological recordings; Dr. Mahendra Rao, formerly of the Center for Regenerative medicine (CRM), provided 2 neural progenitor lines; Dr. Manfred Boehm (Laboratory of Cardiovascular Regenerative Medicine, NHLBI) provided 5 iPSC lines; Dr. Kory Johnson (NINDS) Microarray Core helped analyze the microarray gene expression data; Drs. Amalia Dutra and Evgenia Pak of the NHGRI Cytogenetics Core performed spectral karyotyping. GM05990, GM23240, and GM23476 were obtained from Coriell Cell Repositories (Camden, NJ). Line 10593 was obtained from the Rutgers University Cell and DNA Repository (Piscataway, NJ; catalog #10C117904). Special thanks to Ioline Henter (NIMH), who provided invaluable editorial assistance.

Author contributions

XJ and FJM conceived the project, designed the experiments, conducted data analyses, and wrote the manuscript. X.J. performed most of the experimental procedures. SDD-W generated the GM05990 iPSC line, NA carried out SNP genotyping, XG performed and analyzed the electrophysiological experiments, TX and GF helped to design CTCF and EMSA assays and provided reagents and technical assistance; BSM provided technical assistance and advice on culture and differentiation of iPSC lines; LH performed the conditional association analysis; CS assisted with laboratory assays and manuscript preparation. All co-authors reviewed the manuscript before submission.

Author information

Correspondence to Francis J. McMahon.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Jiang, X., Detera-Wadleigh, S.D., Akula, N. et al. Sodium valproate rescues expression of TRANK1 in iPSC-derived neural cells that carry a genetic variant associated with serious mental illness. Mol Psychiatry 24, 613–624 (2019). https://doi.org/10.1038/s41380-018-0207-1

Download citation

Further reading