COMBINED ANALYSIS OF LINKAGE AND WHOLE EXOME SEQUENCING REVEALS CIC AS A CANDIDATE GENE FOR ISOLATED DYSTONIA

Year 2021, , 457 - 463, 01.10.2021

Barış Salman , Emrah Yücesan , Bedia Samancı Başar Bilgiç Haşmet Hanağası , Hakan Gürvit , Uğur Özbek , Sibel Uğur İşeri

https://doi.org/10.26650/IUITFD.2021.913346

Abstract

Objective: To explore the underlying genetic variations and mechanisms in a family affected by isolated dystonia. Material and Method: We employed whole genome Single Nucleotide Polymorphism (SNP) based linkage analysis along with whole exome sequencing (WES) in a consanguineous family presenting with isolated dystonia. An in-house pipeline compiled for WES analysis along with in-depth in silico prediction algorithms were used to assess the associated data produced in this study. Sanger sequencing was used for variant confirmation and segregation. Results: Data analysis included locus oriented WES variant prioritization and cryptic splicing predictions. We detected a homozygous and synonymous variation rs748449895 (NM_015125.4: c.4143C>T; p.(Thr1381=)) in the capicua transcriptional repressor, CIC. This variation disrupts the YB-1 RNA recognition motif and creates an alternative SRp20 RNA recognition motif. Conclusion: The resulting variant might cause the dystonia phenotype by affecting the alternative splicing of CIC transcript and altering the exon inclusion motif which may disrupt the ATXN1– CIC complex.

Keywords

Autosomal recessive dystonia, whole genome genotyping, linkage analysis, whole exome sequencing, alternative splicing

Supporting Institution

Scientific Research Projects Coordination Unit of Istanbul University, TUBITAK

Project Number

TYL-2018-30315, ONAP-11021, TUBITAK-113S331, TUBITAK-214S222

Thanks

The authors are grateful to the family for participating in this study. We also thank to Turkish Academy of Sciences for the 2019 Distinguished Young Scientist Award to SAUI.

BAĞLANTI VE TÜM EKZOM DİZİLEME ANALİZLERİNİN BİRLİKTE DEĞERLENDİRİLMESİYLE CIC GENİNİN İZOLE DİSTONİ ADAYI OLARAK BELİRLENMESİ

Abstract

Amaç: İzole distoni hastalığından etkilenmiş bir ailede hastalığa neden olan genetik varyasyonları ve mekanizmaları keşfetmek. Gereç ve Yöntem: İzole distoni hastalığı tanısı konmuş ve akraba evliliği bulunan bir ailede, tüm genom Single Nucleotide Polymorphism (SNP) temelli bağlantı analizi ile beraber tüm ekzom dizileme (TED) gerçekleştirildi. TED analizleri için laboratuvarımızda geliştirilen akış hattı ve in siliko tahmin algoritmaları bu çalışmada üretilen verinin ilişkilendirilmesinde kullanıldı. Sanger dizileme varyantların doğrulanması ve ayrımı için kullanıldı. Bulgular: SNP dizimi ile genotipleme, bağlantı analizi ve ekzom dizileme analizleri sonucu rs748449895 (NM_015125.4: c. 4143C>T;p.(Thr1381=)) homozigot sinonim varyantı tespit edildi. Devamındaki biyoinformatik analizler varyantın YB-1 RNA tanıma motifi olduğunu gösterdi. Bu varyant YB-1 RNA tanıma motifini bozarak, SRp20 RNA tanıma motifi oluşturmaktadır. Sonuç: Bulunan varyant, ekzon katılma motifini değiştirerek CIC transkriptinin alternatif kırpılmasını etkileyip ATXN1-CIC kompleksini bozarak distoni fenotipine yol açabilir.

Keywords

Otozomal resesif distoni, tüm genom genotipleme, bağlantı analizi, tüm ekzom dizileme, alternatif kırpılma

Project Number

TYL-2018-30315, ONAP-11021, TUBITAK-113S331, TUBITAK-214S222

References

• 1. Jinnah HA. Diagnosis & Treatment of Dystonia. Neurol Clin 2015;33(1):77-100. [CrossRef]
• 2. Balint B, Mencacci NE, Valente EM, Pisani A, Rothwell J, Jankovic J, et al. Dystonia. Nature Reviews Disease Primers. 2018;4(1):1-23. [CrossRef]
• 3. Domingo A, Yadav R, Ozelius LJ. Isolated dystonia: clinical and genetic updates. J Neural Transm (Vienna) 2021;128(4):405-16. [CrossRef]
• 4. Charlesworth G, Bhatia KP, Wood NW. The genetics of dystonia: new twists in an old tale. Brain 2013;136(Pt 7):2017-37. [CrossRef]
• 5. Pulst SM. Genetic linkage analysis. Arch Neurol 1999;56(6):667. [CrossRef] 6. Yucesan E, Ugur Iseri SA, Bilgic B, Gormez Z, Bakir Gungor B, Sarac A, et al. SYNE1 related cerebellar ataxia presents with variable phenotypes in a consanguineous family from Turkey. Neurol Sci 2017;38(12):2203-7. [CrossRef]
• 7. Ugur Iseri SA, Yucesan E, Tuncer FN, Calik M, Kesim Y, Altiokka Uzun G, et al. Biallelic loss of EEF1D function links heat shock response pathway to autosomal recessive intellectual disability. Journal of Human Genetics 2019;64(5):421-6. [CrossRef]
• 8. Zech M, Jech R, Boesch S, Škorvánek M, Weber S, Wagner M, et al. Monogenic variants in dystonia: an exome-wide sequencing study. The Lancet Neurology 2020;19(11):908- 18. [CrossRef]
• 9. Mulder R, Lisman T, Meijers JCM, Huntington JA, Mulder AB, Meijer K. Linkage analysis combined with whole-exome sequencing identifies a novel prothrombin (F2) gene mutation in a Dutch Caucasian family with unexplained thrombosis. 1. 2020;105(7):e370-2. [CrossRef]
• 10. Mescheriakova JY, Verkerk AJ, Amin N, Uitterlinden AG, van Duijn CM, Hintzen RQ. Linkage analysis and whole exome sequencing identify a novel candidate gene in a Dutch multiple sclerosis family. Mult Scler 2019;25(7):909- 17. [CrossRef]
• 11. Choi YJ, Ohn JH, Kim N, Kim W, Park K, Won S, et al. Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer. PLOS ONE 2020;15(7):e0236197. [CrossRef]
• 12. Markianos K, Daly MJ, Kruglyak L. Efficient multipoint linkage analysis through reduction of inheritance space. The American Journal of Human Genetics 2001;68(4):963- 77. [CrossRef]
• 13. Hoffmann K, Lindner TH. easyLINKAGE-Plus-automated linkage analyses using large-scale SNP data. Bioinformatics 2005;21(17):3565-7. [CrossRef]
• 14. Thiele H, Nürnberg P. HaploPainter: a tool for drawing pedigrees with complex haplotypes. Bioinformatics 2005;21(8):1730-2. [CrossRef]
• 15. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25(14):1754-60. [CrossRef]
• 16. A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.: broadinstitute/picard [Internet]. Broad Institute; 2019 [cited 2019 May 7]. Available from: https://github.com/broadinstitute/picard
• 17. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20(9):1297-303. [CrossRef]
• 18. McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, et al. The ensembl variant effect predictor. Genome Biology 2016;17(1):122. [CrossRef]
• 19. Piva F, Giulietti M, Burini AB, Principato G. SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum Mutat 2012;33(1):81-5. [CrossRef]
• 20. Jaganathan K, Panagiotopoulou SK, McRae JF, Darbandi SF, Knowles D, Li YI, et al. Predicting splicing from primary sequence with deep learning. Cell 2019;176(3):535-548.e24. [CrossRef]
• 21. Inah Hwang, Heng Pan, Yao J, Olivier Elemento, Hongwu Zheng, Paik J. CIC is a critical regulator of neuronal differentiation. JCI Insight [Internet]. 2020 [cited 2021 Feb 22];5(9). Available from: https://insight.jci.org/articles/ view/135826 [CrossRef]
• 22. Lee C-J, Chan W-I, Cheung M, Cheng Y-C, Appleby VJ, Orme AT, et al. CIC, a member of a novel subfamily of the HMG-box superfamily, is transiently expressed in developing granule neurons. Brain Res Mol Brain Res 2002;106(1-2):151-6. [CrossRef]
• 23. Lu H-C, Tan Q, Rousseaux MWC, Wang W, Kim J-Y, Richman R, et al. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nature Genetics 2017;49(4):527-36. [CrossRef]
• 24. Klein C, Lohmann K, Marras C, Münchau A. Hereditary Dystonia Overview. In: Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJ, Mirzaa G, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993 [cited 2021 Feb 14]. Available from: http://www.ncbi. nlm.nih.gov/books/NBK1155/
• 25. Albanese A, Asmus F, Bhatia KP, Elia AE, Elibol B, Filippini G, et al. EFNS guidelines on diagnosis and treatment of primary dystonias. Eur J Neurol 2011;18(1):5-18. [CrossRef]
• 26. Charlesworth G, Bhatia KP, Wood NW. The genetics of dystonia: new twists in an old tale. Brain 2013;136(Pt 7):2017-37. [CrossRef] 27. Németh AH. The genetics of primary dystonias and related disorders. Brain 2002;125(Pt 4):695-721. [CrossRef]
• 28. Almasy L, Bressman SB, Raymond D, Kramer PL, Greene PE, Heiman GA, et al. Idiopathic torsion dystonia linked to chromosome 8 in two Mennonite families. Ann Neurol 1997;42(4):670-3. [CrossRef]
• 29. Ozelius LJ, Bressman SB. Genetic and clinical features of primary torsion dystonia. Neurobiol Dis 2011;42(2):127-35. [CrossRef]
• 30. Vissers LELM, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, et al. A de novo paradigm for mental retardation. Nat Genet 2010;42(12):1109-12. [CrossRef]
• 31. Bettegowda C, Agrawal N, Jiao Y, Sausen M, Wood LD, Hruban RH, et al. Mutations in CIC and FUBP1 contribute to human oligodendroglioma. Science 2011;333(6048):1453-5. [CrossRef]
• 32. Wei WJ, Mu SR, Heiner M, Fu X, Cao LJ, Gong XF, et al. YB-1 binds to CAUC motifs and stimulates exon inclusion by enhancing the recruitment of U2AF to weak polypyrimidine tracts. Nucleic Acids Res 2012;40(17):8622-36. [CrossRef]
• 33. Hargous Y, Hautbergue GM, Tintaru AM, Skrisovska L, Golovanov AP, Stevenin J, et al. Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8. EMBO J 2006;25(21):5126-37. [CrossRef]
• 34. Änkö ML, Morales L, Henry I, Beyer A, Neugebauer KM. Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nature Structural & Molecular Biology. 2010;17(8):962-70. [CrossRef]
• 35. Tazi J, Bakkour N, Stamm S. Alternative splicing and disease. Biochim Biophys Acta. 2009;1792(1):14-26. [CrossRef]
• 36. Webster NJG. Alternative RNA splicing in the pathogenesis of liver disease. Front Endocrinol (Lausanne).;8:133. [CrossRef]
• 37. Kremer LS, Bader DM, Mertes C, Kopajtich R, Pichler G, Iuso A, et al. Genetic diagnosis of Mendelian disorders via RNA sequencing. Nature Communications 2017;8(1):15824. [CrossRef]
• 38. Poulos MG, Batra R, Charizanis K, Swanson MS. Developments in RNA splicing and disease. Cold Spring Harb Perspect Biol 2011;3(1):a000778. [CrossRef]
• 39. Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nature Reviews Genetics 2002;3(4):285-98. [CrossRef]
• 40. Dredge BK, Polydorides AD, Darnell RB. The splice of life: alternative splicing and neurological disease. Nat Rev Neurosci 2001;2(1):43-50. [CrossRef]
• 41. Licatalosi DD, Darnell RB. Splicing regulation in neurologic disease. Neuron 2006;52(1):93-101. [CrossRef]
• 42. Feng D, Xie J. Aberrant splicing in neurological diseases. Wiley Interdiscip Rev RNA 2013;4(6):631-49. [CrossRef]
• 43. Shohet A, Cohen L, Haguel D, Mozer Y, Shomron N, Tzur S, et al. Variant in SCYL1 gene causes aberrant splicing in a family with cerebellar ataxia, recurrent episodes of liver failure, and growth retardation. European Journal of Human Genetics 2019;27(2):263-8. [CrossRef]
• 44. Xiao J, Zhao Y, Bastian RW, Perlmutter JS, Racette BA, Tabbal SD, et al. Novel THAP1 sequence variants in primary dystonia. Neurology 2010;74(3):229-38. [CrossRef]