Muhammad Ikram ULLAH, Irfan ULLAH, Abdul NASIR, Sarmad MEHMOOD, Sohail AHMED, Asmat ULLAH, Abdul AZIZ2, Khadim SHAH, Saadullah KHAN, Muhammad Jawad HASSAN, Wasim AHMAD, Syed Irfan RAZA

Identification and in silico analysis of GALNS mutations causing Morquio A syndrome in eight consanguineous families

Genetic deficiency of N-acetylgalactosamine-6-sulfate sulfatase (GALNS) due to mutations in the GALNS gene results in the pathogenesis of Morquio A syndrome. To date, more than 200 mutations have been reported in GALNS, resulting in variable clinical features. For this reason, bioinformatics analysis of these mutations is important to determine their effect on the structure and functions of the protein and to establish a correlation between genotype and phenotype. In the present study, eight Pakistani consanguineous families with Morquio A syndrome were clinically and genetically evaluated. Linkage analysis followed by sequence analysis of the gene detected four novel (p.Phe216Ser, p.Met38Arg, p.Ala291Ser, p.Glu121Argfs*37) and two reported (p.Pro420Arg, p.Arg386Cys) mutations in the eight families. In silico structural and functional analysis predicted that these mutations disrupt the function of GALNS protein through fluctuating its three-dimensional structure, stability, and binding affinity and produce severe phenotypes. This is the first comprehensive study on molecular analysis of patients with Morquio A syndrome from Pakistan that reports four novel mutations with their structural and functional consequences.

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Akhavan S, Miteva MA, Villoutreix BO, Venisse L, Peyvandi F, Mannucci PM, Guillin MC, Bezeaud A (2005). A critical role for Gly25 in the B chain of human thrombin. J Thromb Haemost 3: 139-145.
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M et al (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498.
Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA (2007). The protein folding problem: when will it be solved? Curr Opin Struct Biol 17: 342-346.
Dobson CM (2003). Protein folding and misfolding. Nature 426: 884-890.
Dunker AK, Brown CJ, Lawson JD, Iakoucheva LM, Obradović Z (2002). Intrinsic disorder and protein function. Biochemistry 41: 6573-6582.
Gnad F, Baucom A, Mukhyala K, Manning G, Zhang Z (2013). Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC Genomics 14 (Suppl 3): S7.
Harmatz P, Mengel KE, Giugliani R, Valayannopoulos V, Lin SP, Parini R, Guffon N, Burton BK, Hendriksz CJ, Mitchell J et al (2013). The Morquio A Clinical Assessment Program: baseline results illustrating progressive, multisystemic clinical impairments in Morquio A subjects. Mol Genet Metab 109: 54-61.
Hendriksz CJ, Harmatz P, Beck M, Jones S, Wood T, Lachman R, Gravance CG, Orii T, Tomatsu S (2013). Review of clinical presentation and diagnosis of mucopolysaccharidosis IVA. Mol Genet Metab 110: 54-64.
Irfanullah, Umair M, Khan S, Ahmad W (2015). Homozygous sequence variants in the NPR2 gene underlying Acromesomelic dysplasia Maroteaux type (AMDM) in consanguineous families. Ann Hum Genet 79: 238-244.
Jones R, Ruas M, Gregory F, Moulin S, Delia D, Manoukian S, Rowe J, Brookes S, Peters G (2007). A CDKN2A mutation in familial melanoma that abrogates binding of p16INK4a to CDK4 but not CDK6. Cancer Res 67: 9134-9141.
Karplus M, Kuriyan J (2005). Molecular dynamics and protein function. Proc Natl Acad Sci U S A 102: 6679-6685.
Khan S, Vihinen M (2010). Performance of protein stability predictors. Hum Mutat 31: 675-684.
Koukouritaki SB, Poch MT, Henderson MC, Siddens LK, Krueger SK, VanDyke JE, Williams DE, Pajewski NM, Wang T, Hines RN (2007). Identification and functional analysis of common human flavin-containing monooxygenase 3 genetic variants. J Pharmacol Exp Ther 320: 266-273.
Li H, Durbin R (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1754-1760.
Masue M, Sukegawa K, Orii T, Hashimoto T (1991). N-acetylgalactosamine-6-sulfate sulfatase in human placenta: purification and characteristics. J Bioche 110: 965-970.
Masuno M, Tomatsu S, Nakashima Y, Hori T, Fukuda S, Masue M, Sukegawa K, Orii T (1993). Mucopolysaccharidosis IV A: assignment of the human Nacetylgalactosamine-6-sulfate sulfatase (GALNS) gene to chromosome 16q24. Genomics 16: 777-778.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M et al (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303.
Montaño AM, Sukegawa K, Kato Z, Carrozzo R, Di Natale P, Christensen E, Orii KO, Orii T, Kondo N, Tomatsu S (2007b). Effect of attenuated mutations in mucopolysaccharidosis IVA on molecular phenotypes of N-acetylgalactosamine-6-sulfate sulfatase. J Inherit Metab Dis 30: 758-767.
Montaño AM, Tomatsu S, Gottesman GS, Smith M, Orii T (2007a). International Morquio A Registry: clinical manifestation and natural course of Morquio A disease. J Inherit Metab Dis 30: 165-174.
Morrone A, Tylee KL, Al-Sayed M, Brusius-Facchin AC, Caciotti A, Church HJ (2014 a). Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations. Mol Genet Metab 112: 160-170.
Morrone A, Caciotti A, Atwood R, Davidson K, Du C, Francis-Lyon P, Harmatz P, Mealiffe M, Mooney S, Oron TR et al (2014). Morquio A syndrome-associated mutations: a review of alterations in the GALNS gene and a new locus-specific database. Hum Mutat 35: 1271-1279.
Pohl S, Marschner K, Storch S, Braulke T (2009). Glycosylation- and phosphorylation-dependent intracellular transport of lysosomal hydrolases. Biol Chem 390: 521-527.
Rivera-Colón Y, Schutsky EK, Kita AZ, Garman SC (2012). The structure of human GALNS reveals the molecular basis for mucopolysaccharidosis IV A. J Mol Biol 423: 736-751.
Rozen S, Skaletsky H (2000). Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN (2014). The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet 133: 1-9.
Sudhakar SC, Mahalingam K (2011). Structural and functional analysis of N-acetylgalactosamine-6-sulfate sulfatase using bioinformatics tools: insight into Mucopolysaccharidosis IVA. J Pharm Res 4: 3958-3962.
Sukegawa K, Nakamura H, Kato Z, Tomatsu S, Montaño AM, Fukao T, Toietta G, Tortora P, Orii T, Kondo N (2000). Biochemical and structural analysis of missense mutations in Nacetylgalactosamine-6-sulfate sulfatase causing Mucopolysaccharidosis IVA phenotypes. Hum Mol Genet 9: 1283-1290.
Tomatsu S, Montaño AM, Nishioka T, Gutierrez MA, Peña OM, Tranda Firescu GG, Lopez P, Yamaguchi S, Noguchi A, Orii T (2005). Mutation and polymorphism spectrum of the GALNS gene in mucopolysaccharidosis IVA (Morquio A). Hum Mutat 26: 500-512.
Tomatsu S, Montaño AM, Oikawa H, Smith M, Barrera L, Chinen Y, Thacker MM, Mackenzie WG, Suzuki Y, Orii T (2011). Mucopolysaccharidosis type IVA (Morquio A disease): clinical review and current treatment. Curr Pharm Biotechnol 12: 931- 945.
Tomatsu S, Nishioka T, Montaño AM, Gutierrez MA, Pena OS, Orii KO, Sly WS, Yamaguchi S, Orii T, Paschke E et al (2004). Mucopolysaccharidosis IVA: identification of mutations and methylation study in GALNS gene. J Med Genet 41: e98.
Wang Z, Moult J (2001). SNPs, protein structure, and disease. Hum Mutat 17: 263-270.
Wujek P, Kida E, Walus M, Wisniewski KE, Golabek AA (2004). N-glycosylation is crucial for folding, trafficking, and stability of human tripeptidyl-peptidase I. J Biol Chem 279: 12827- 12839.
Yasuda E, Fushimi K, Suzuki Y, Shimizu K, Takami T, Zustin J, Patel P, Ruhnke K, Shimada T, Boyce B et al (2013). Pathogenesis of Morquio A syndrome: an autopsied case reveals systemic storage disorder. Mol Genet Metab 109: 301-311.
Ye Y, Li Z, Godzik A (2006). Modeling and analyzing threedimensional structures of human disease proteins. Pac Symp Biocomput 439-450.
Young MA, Gonfloni S, Superti-Furga G, Roux B, Kuriyan J (2001). Dynamic coupling between the SH2 and SH3 domains of c-Src and Hck underlies their inactivation by C-terminal tyrosine phosphorylation. Cell 105: 115-126.
Zhang Z, Miteva MA, Wang L, Alexov E (2012). Analyzing effects of naturally occurring missense mutations. Comput Math Methods Med 2012: 805827.
Zhang Z, Teng S, Wang L, Schwartz CE, Alexov E (2010). Computational analysis of missense mutations causing SnyderRobinson syndrome. Hum Mutat 31: 1043-1049.