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An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease

European Journal of Human Genetics 26, 1810–1818 (2018) | Download Citation

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Abstract

Approximately 2% of the human genome accounts for protein-coding genes, yet most known Mendelian disease-causing variants lie in exons or splice sites. Individuals who symptomatically present with monogenic disorders but do not possess function-altering variants in the protein-coding regions of causative genes may harbor variants in the surrounding gene regulatory domains. We present such a case: a male of Afghani descent was clinically diagnosed with Wilson Disease—a disorder of systemic copper buildup—but was found to have no function-altering coding variants in ATP7B (ENST00000242839.4), the typically causative gene. Our analysis revealed the homozygous variant chr13:g.52,586,149T>C (NC_000013.10, hg19) 676 bp into the ATP7B promoter, which disrupts a metal regulatory transcription factor 1 (MTF1) binding site and diminishes expression of ATP7B in response to copper intake, likely resulting in Wilson Disease. Our approach to identify the causative variant can be generalized to systematically discover function-altering non-coding variants underlying disease and motivates evaluation of gene regulatory variants.

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References

  1. 1.

    Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NST, et al. Human Gene Mutation Database (HGMD): 2003 update. Hum Mutat. 2003;21:577–81.

  2. 2.

    Zhang F, Lupski JR. Non-coding genetic variants in human disease. Hum Mol Genet. 2015;24:R102–10.

  3. 3.

    Petit F, Sears KE, Ahituv N. Limb development: a paradigm of gene regulation. Nat Rev Genet. 2017;18:245–58.

  4. 4.

    Spitz F. Gene regulation at a distance: from remote enhancers to 3D regulatory ensembles. Semin Cell Dev Biol. 2016;57:57–67.

  5. 5.

    Auton A, Abecasis GR, Altshuler DM, Durbin RM, Bentley DR, Chakravarti A, et al. A global reference for human genetic variation. Nature. 2015;526:68–74.

  6. 6.

    Ala A, Walker AP, Ashkan K, Dooley JS, Schilsky ML. Wilson’s disease. Lancet. 2007;369:397–408.

  7. 7.

    Petrukhin K, Lutsenko S, Chernov I, Ross BM, Kaplan JH, Gilliam TC. Characterization of the Wilson disease gene encoding a P-type copper transporting ATPase: genomic organization, alternative splicing, and structure/function predictions. Hum Mol Genet. 1994;3:1647–56.

  8. 8.

    de Bie P, Muller P, Wijmenga C, Klomp LWJ. Molecular pathogenesis of Wilson and Menkes disease: correlation of mutations with molecular defects and disease phenotypes. J Med Genet. 2007;44:673–88.

  9. 9.

    Bandmann O, Weiss KH, Kaler SG. Wilson’s disease and other neurological copper disorders. Lancet Neurol. 2015;14:103–13.

  10. 10.

    Todorov T, Balakrishnan P, Savov A, Socha P, Schmidt HHJ. Intragenic deletions in ATP7B as an unusual molecular genetics mechanism of Wilson’s disease pathogenesis. PLoS ONE. 2016;11:1–11.

  11. 11.

    Coffey AJ, Durkie M, Hague S, McLay K, Emmerson J, Lo C, et al. A genetic study of Wilson’s disease in the United Kingdom. Brain. 2013;136:1476–87.

  12. 12.

    Vanacore RM, Eskew JD, Morales PJ, Sung L, Smith A. Role for copper in transient oxidation and nuclear translocation of MTF-1, but not of NF-κB, by the heme–hemopexin transport system. Antioxid Redox Signal. 2000;2:739–52.

  13. 13.

    Saydam N, Georgiev O, Nakano MY, Greber UF, Schaffner W. Nucleo-cytoplasmic trafficking of metal-regulatory transcription factor 1 is regulated by diverse stress signals. J Biol Chem. 2001;276:25487–95.

  14. 14.

    Labbé S1, Prévost J, Remondelli P, Leone A, Séguin C. A nuclear factor binds to the metal regulatory elements of the mouse gene encoding metallothionein-l. Nucleic Acids Res. 1991;19:4225–31.

  15. 15.

    Larochelle O, Stewart G, Moffatt P, Tremblay V, Séguin C. Characterization of the mouse metal-regulatory-element-binding proteins, metal element protein-1 and metal regulatory transcription factor-1. Biochem J. 2001;353:591–601.

  16. 16.

    Burke R, Commons E, Camakaris J. Expression and localisation of the essential copper transporter DmATP7 in Drosophila neuronal and intestinal tissues. Int J Biochem Cell Biol. 2008;40:1850–60.

  17. 17.

    Wang M, Yang F, Zhang X, Zhao H, Wang Q, Pan Y. Comparative analysis of MTF-1 binding sites between human and mouse. Mamm Genome. 2010;21:287–98.

  18. 18.

    Grzywacz A, Gdula-Argasińska J, Muszyńska B, Tyszka-Czochara M, Librowski T, Opoka W. Metal responsive transcription factor 1 (MTF-1) regulates zinc dependent cellular processes at the molecular level. Acta Biochim Pol. 2015;62:491–8.

  19. 19.

    Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013. http://arxiv.org/abs/1303.3997.

    • 20.

      Broad Institute. Picard Tools.

      • 21.

        DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.

      • 22.

        Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016;536:285–91.

      • 23.

        Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.

      • 24.

        Yates A, Akanni W, Ridwan MR, Barrell D, Billis K, Carvalho-Silva D, et al. Ensembl 2016. Nucleic Acids Res. 2016;44:D710–6.

      • 25.

        Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, et al. PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res. 2013;23:889–904.

      • 26.

        Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310–5.

      • 27.

        Browning BL, Browning SR. Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics. 2013;194:459–71.

      • 28.

        Lu C-X, Lin Q, Huang W-Q, Tzeng C-M. New mutations and polymorphisms of the ATP7B gene in sporadic Wilson disease. Eur J Med Genet. 2014;57:498–502.

      • 29.

        Mukherjee S, Dutta S, Majumdar S, Biswas T, Jaiswal P, Sengupta M, et al. Genetic defects in Indian Wilson disease patients and genotype–phenotype correlation. Parkinsonism Relat Disord. 2014;20:75–81.

      • 30.

        Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005;15:1034–50.

      • 31.

        ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.

      • 32.

        Stoytcheva ZR, Vladimirov V, Douet V, Stoychev I, Berry MJ. Metal transcription factor-1 regulation via MREs in the transcribed regions of selenoprotein H and other metal-responsive genes. Biochim Biophys Acta. 2010;1800:416–24.

      • 33.

        Günther V, Lindert U, Schaffner W. The taste of heavy metals: gene regulation by MTF-1. Biochim Biophys Acta. 2012;1823:1416–25.

      • 34.

        Hardyman JE, Tyson J, Jackson KA, Aldridge C, Cockell SJ, Wakeling LA, et al. Zinc sensing by metalresponsive transcription factor 1 (MTF1) controls metallothionein and ZnT1 expression to buffer the sensitivity of the transcriptome response to zinc. Metallomics. 2016;8:337–43.

      • 35.

        Loudianos G, Dessi V, Lovicu M, Angius A, Figus A, Lilliu F, et al. Molecular characterization of wilson disease in the Sardinian population—evidence of a founder effect. Hum Mutat. 1999;14:294–303.

      • 36.

        Wan L, Tsai CH, Hsu CM, Huang CC, Yang CC, Liao CC, et al. Mutation analysis and characterization of alternative splice variants of the Wilson disease gene ATP7B. Hepatology. 2010;52:1662–70.

      • 37.

        Cullen LM, Prat L, Cox DW. Genetic variation in the promoter and 5′ UTR of the copper transporter, ATP7B, in patients with Wilson disease. Clin Genet. 2003;64:429–32.

      • 38.

        Shah AB, Chernov I, Zhang HT, Ross BM, Das K, Lutsenko S, et al. Identification and analysis of mutations in the Wilson disease gene (ATP7B): population frequencies, genotype–phenotype correlation, and functional analyses. Am J Hum Genet. 1997;61:317–28.

      • 39.

        de Vooght KMK, van Wijk R, van Solinge WW. Management of gene promoter mutations in molecular diagnostics. Clin Chem. 2009;55:698–708.

      • 40.

        Corradin O, Scacheri PC. Enhancer variants: evaluating functions in common disease. Genome Med. 2014;6:85.

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      Acknowledgements

      We thank the subject family for consenting to this study; Eric Rulifson for key technical guidance on the luciferase reporter assays; Ashby Morrison, Kristy Red-Horse, and Roel Nusse for lending experimental equipment; Alan Boyle, Lingyun Song, and Greg Crawford from Duke University’s Institute for Genome Sciences & Policy (IGSP) for generating the publicly available HepG2 DNase-seq data; and members of the Bejerano Lab for helpful discussions, suggestions, and support.

      Funding

      This study was funded in part by the National Science Foundation Graduate Research Fellowship to HIC, the Stanford Graduate Fellowship and the Computational, Evolutionary and Human Genetics Fellowship to KAJ, the Bio-X Stanford Interdisciplinary Graduate Fellowship to JB, the Stanford Pediatrics Department, DARPA, a Packard Foundation Fellowship and a Microsoft Faculty Fellowship to GB.

      Author contributions

      SS recruited and consented the study subjects. KAJ, JB, AMW, HG, and GB designed the computational approach. HIC designed and performed the experimental evaluation. JB assisted with experiments. KAJ performed the computational analysis. HIC wrote the manuscript with input from all authors. JAB and GB supervised the project.

      Author information

      1. These authors contributed equally: Heidi I. Chen, Karthik A. Jagadeesh

      Affiliations

      1. Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA

        • Heidi I. Chen
        •  & Gill Bejerano

      2. Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA

        • Karthik A. Jagadeesh
        • , Johannes Birgmeier
        •  & Gill Bejerano

      3. Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA

        • Aaron M. Wenger
        • , Harendra Guturu
        • , Susan Schelley
        • , Jonathan A. Bernstein
        •  & Gill Bejerano

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      Conflict of interest

      The authors declare that they have no conflict of interest.

      Corresponding authors

      Correspondence to Jonathan A. Bernstein or Gill Bejerano.

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      DOI

      https://doi.org/10.1038/s41431-018-0221-4