A novel mutation in TTC8 is associated with progressive retinal atrophy in the golden retriever

Canine Genetics and Epidemiology - Tập 1 - Trang 1-12 - 2014
Louise M Downs1, Berit Wallin-Håkansson1,2, Tomas Bergström3, Cathryn S Mellersh1
1Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, UK
2The Swedish Kennel Club (SKK), Stockholm, Sweden
3Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden

Tóm tắt

Generalized progressive retinal atrophy (PRA) is a group of inherited eye diseases characterised by progressive retinal degeneration that ultimately leads to blindness in dogs. To date, more than 20 different mutations causing canine-PRA have been described and several breeds including the Golden Retriever are affected by more than one form of PRA. Genetically distinct forms of PRA may have different clinical characteristics such as rate of progression and age of onset. However, in many instances the phenotype of different forms of PRA cannot be distinguished at the basic clinical level achieved during routine ophthalmoscopic examination. Mutations in two distinct genes have been reported to cause PRA in Golden Retrievers (prcd-PRA and GR_PRA1), but for approximately 39% of cases in this breed the causal mutation remains unknown. A genome-wide association study of 10 PRA cases and 16 controls identified an association on chromosome 8 not previously associated with PRA (praw = 1.30×10-6 and corrected with 100,000 permutations, pgenome = 0.148). Using haplotype analysis we defined a 737 kb critical region containing 6 genes. Two of the genes (TTC8 and SPATA7) have been associated with Retinitis Pigmentosa (RP) in humans. Using targeted next generation sequencing a single nucleotide deletion was identified in exon 8 of the TTC8 gene of affected Golden Retrievers. The frame shift mutation was predicted to cause a premature termination codon. In a larger cohort, this mutation, TTC8 c.669delA, segregates correctly in 22 out of 29 cases tested (75.9%). Of the PRA controls none are homozygous for the mutation, only 3.5% carry the mutation and 96.5% are homozygous wildtype. Our results show that PRA is genetically heterogeneous in one of the world’s numerically largest breeds, the Golden Retriever, and is caused by multiple, distinct mutations. Here we discuss the mutation that causes a form of PRA, that we have termed PRA2, that accounts for approximately 30% of PRA cases in the breed. The genetic explanation for approximately 9% of cases remains to be identified. PRA2 is a naturally occurring animal model for Retinitis Pigmentosa, and potentially Bardet-Biedl Syndrome.

Tài liệu tham khảo

Parry HB: Degenerations of the dog retina. II. Generalized progressive atrophy of hereditary origin. Br J Ophthalmol 1953, 37: 487–502. 10.1136/bjo.37.8.487 Petersen-Jones S: Advances in the molecular understanding of canine retinal diseases. J Small Anim Pract 2005, 46: 371–380. 10.1111/j.1748-5827.2005.tb00333.x André C, Chaudieu G, Thomas A, Jongh O, Jegou JP, Chahory S, Clerc B, Pilorge P, Brenac O: Hereditary retinopathies in the dog: genetic fundamentals and genetic tests. Pratique Médicale et Chirurgicale de l’Animal de Compagnie 2008, 43: 75–84. 10.1016/j.anicom.2008.06.002 Grondahl J: Estimation of prognosis and prevalence of retinitis pigmentosa and Usher syndrome in Norway. Clin Genet 1987, 31: 255–264. Haim M, Holm NV, Rosenberg T: Prevalence of retinitis pigmentosa and allied disorders in Denmark. I Main results. Acta Ophthalmol (Copenh) 1992, 70: 178–186. Pagon RA: Retinitis pigmentosa. Surv Ophthalmol 1988, 33: 137–177. 10.1016/0039-6257(88)90085-9 RetNet™ Retinal Informatio Network https://sph.uth.edu/retnet/ Daiger SP, Sullivan LS, Bowne SJ: Genes and mutations causing retinitis pigmentosa. Clin Genet 2013, 84: 132–141. 10.1111/cge.12203 Patterson DF, Pexieder T, Schnarr WR, Navratil T, Alaili R: A single major-gene defect underlying cardiac conotruncal malformations interferes with myocardial growth during embryonic development: studies in the CTD line of keeshond dogs. Am J Hum Genet 1993, 52: 388–397. Beggs AH, Bohm J, Snead E, Kozlowski M, Maurer M, Minor K, Childers MK, Taylor SM, Hitte C, Mickelson JR, Guo LT, Mizisin AP, Buj-Bello A, Tiret L, Laporte J, Shelton GD: MTM1 mutation associated with X-linked myotubular myopathy in Labrador Retrievers. Proc Natl Acad Sci U S A 2010, 107: 14697–14702. 10.1073/pnas.1003677107 Sidjanin DJ, Lowe JK, McElwee JL, Milne BS, Phippen TM, Sargan DR, Aguirre GD, Acland GM, Ostrander EA: Canine CNGB3 mutations establish cone degeneration as orthologous to the human achromatopsia locus ACHM3. Hum Mol Genet 2002, 11: 1823–1833. 10.1093/hmg/11.16.1823 Mellersh CS, Boursnell ME, Pettitt L, Ryder EJ, Holmes NG, Grafham D, Forman OP, Sampson J, Barnett KC, Blanton S, Binns MM, Vaudin M: Canine RPGRIP1 mutation establishes cone-rod dystrophy in miniature longhaired dachshunds as a homologue of human Leber congenital amaurosis. Genomics 2006, 88: 293–301. 10.1016/j.ygeno.2006.05.004 Howell JM, Fletcher S, Kakulas BA, O’Hara M, Lochmuller H, Karpati G: Use of the dog model for Duchenne muscular dystrophy in gene therapy trials. Neuromuscul Disord 1997, 7: 325–328. 10.1016/S0960-8966(97)00057-6 Acland GM, Aguirre GD, Ray J, Zhang Q, Aleman TS, Cideciyan AV, Pearce-Kelling SE, Anand V, Zeng Y, Maguire AM, Jacobson SG, Hauswirth WW, Bennett J: Gene therapy restores vision in a canine model of childhood blindness. Nat Genet 2001, 28: 92–95. Mount JD, Herzog RW, Tillson DM, Goodman SA, Robinson N, McCleland ML, Bellinger D, Nichols TC, Arruda VR, Lothrop CD Jr, High KA: Sustained phenotypic correction of hemophilia B dogs with a factor IX null mutation by liver-directed gene therapy. Blood 2002, 99: 2670–2676. 10.1182/blood.V99.8.2670 Ponder KP, Melniczek JR, Xu L, Weil MA, O’Malley TM, O’Donnell PA, Knox VW, Aguirre GD, Mazrier H, Ellinwood NM, Sleeper M, Maguire AM, Volk SW, Mango RL, Zweigle J, Wolfe JH, Haskins ME: Therapeutic neonatal hepatic gene therapy in mucopolysaccharidosis VII dogs. Proc Natl Acad Sci U S A 2002, 99: 13102–13107. 10.1073/pnas.192353499 Bainbridge JW, Smith AJ, Barker SS, Robbie S, Henderson R, Balaggan K, Viswanathan A, Holder GE, Stockman A, Tyler N, Petersen-Jones S, Bhattacharya SS, Thrasher AJ, Fitzke FW, Carter BJ, Rubin GS, Moore AT, Ali RR: Effect of gene therapy on visual function in Leber’s congenital amaurosis. N Engl J Med 2008, 358: 2231–2239. 10.1056/NEJMoa0802268 Downs LM, Wallin-Hakansson B, Boursnell M, Marklund S, Hedhammar A, Truve K, Hubinette L, Lindblad-Toh K, Bergstrom T, Mellersh CS: A frameshift mutation in golden retriever dogs with progressive retinal atrophy endorses SLC4A3 as a candidate gene for human retinal degenerations. PLoS ONE 2011, 6: e21452. 10.1371/journal.pone.0021452 Zangerl B, Goldstein O, Philp AR, Lindauer SJ, Pearce-Kelling SE, Mullins RF, Graphodatsky AS, Ripoll D, Felix JS, Stone EM, Acland GM, Aguirre GD: Identical mutation in a novel retinal gene causes progressive rod-cone degeneration in dogs and retinitis pigmentosa in humans. Genomics 2006, 88: 551–563. 10.1016/j.ygeno.2006.07.007 Nachury MV, Loktev AV, Zhang Q, Westlake CJ, Peranen J, Merdes A, Slusarski DC, Scheller RH, Bazan JF, Sheffield VC, Jackson PK: A core complex of BBS proteins cooperates with the GTPase Rab8 to promote ciliary membrane biogenesis. Cell 2007, 129: 1201–1213. 10.1016/j.cell.2007.03.053 Wang H, den Hollander AI, Moayedi Y, Abulimiti A, Li Y, Collin RW, Hoyng CB, Lopez I, Abboud EB, Al-Rajhi AA, Bray M, Lewis RA, Lupski JR, Mardon G, Koenekoop RK, Chen R: Mutations in SPATA7 cause Leber congenital amaurosis and juvenile retinitis pigmentosa. Am J Hum Genet 2009, 84: 380–387. 10.1016/j.ajhg.2009.02.005 Ansley SJ, Badano JL, Blacque OE, Hill J, Hoskins BE, Leitch CC, Kim JC, Ross AJ, Eichers ER, Teslovich TM, Mah AK, Johnsen RC, Cavender JC, Lewis RA, Leroux MR, Beales PL, Katsanis N: Basal body dysfunction is a likely cause of pleiotropic Bardet-Biedl syndrome. Nature 2003, 425: 628–633. 10.1038/nature02030 Riazuddin SA, Iqbal M, Wang Y, Masuda T, Chen Y, Bowne S, Sullivan LS, Waseem NH, Bhattacharya S, Daiger SP, Zhang K, Khan SN, Riazuddin S, Hejtmancik JF, Sieving PA, Zack DJ, Katsanis N: A splice-site mutation in a retina-specific exon of BBS8 causes nonsyndromic retinitis pigmentosa. Am J Hum Genet 2010, 86: 805–812. 10.1016/j.ajhg.2010.04.001 Stoetzel C, Laurier V, Faivre L, Megarbane A, Perrin-Schmitt F, Verloes A, Bonneau D, Mandel JL, Cossee M, Dollfus H: BBS8 is rarely mutated in a cohort of 128 Bardet-Biedl syndrome families. J Hum Genet 2006, 51: 81–84. 10.1007/s10038-005-0320-2 Kumar P, Henikoff S, Ng PC: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009, 4: 1073–1081. 10.1038/nprot.2009.86 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR: A method and server for predicting damaging missense mutations. Nat Methods 2010, 7: 248–249. 10.1038/nmeth0410-248 Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A: ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 2003, 31: 3784–3788. 10.1093/nar/gkg563 PRA in Golden Retrievers http://www.optigen.com/opt9_pra_goldenrtvr.html Katsanis N, Ansley SJ, Badano JL, Eichers ER, Lewis RA, Hoskins BE, Scambler PJ, Davidson WS, Beales PL, Lupski JR: Triallelic inheritance in Bardet-Biedl syndrome, a Mendelian recessive disorder. Science 2001, 293: 2256–2259. 10.1126/science.1063525 Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132: 365–386. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81: 559–575. 10.1086/519795 Astle W, Balding DJ: Population structure and cryptic relatedness in genetic association studies. Statist Sci 2009, 24: 451–471. 10.1214/09-STS307 Stephens M, Donnelly P: A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 2003, 73: 1162–1169. 10.1086/379378 Agilent Technologies eArray tool https://earray.chem.agilent.com/earray/ Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25: 1754–1760. 10.1093/bioinformatics/btp324 McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20: 1297–1303. 10.1101/gr.107524.110 Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP: Integrative genomics viewer. Nat Biotechnol 2011, 29: 24–26. 10.1038/nbt.1754 Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22: 4673–4680. 10.1093/nar/22.22.4673 Bonfield JK, Smith K, Staden R: A new DNA sequence assembly program. Nucleic Acids Res 1995, 23: 4992–4999. 10.1093/nar/23.24.4992