Predicting the Impact of PHEX, FGF23 and DMP1 Gene Variants Found in Malaysian Malay Patients with Hypophosphataemic Rickets Through In Silico Analysis of Protein Function and mRNA Secondary Structure

Authors

  • Nurul Nadirah Razali Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
  • Hwu Ting Tzer epartment of Paediatrics, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
  • Hwa Ling King Genetics and Regenerative Medicine Research Center, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
  • Marina L. Kennerson Northcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney Concord NSW 2139, Australia.
  • Karuppiah Thilakavathy Department of Biomedical Science, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.

DOI:

https://doi.org/10.54987/jobimb.v7i2.477

Keywords:

Hypophosphataemic Rickets; PHEX; FGF23; DMP1; in silico analysis

Abstract

Hypophosphataemic Rickets (HR) is a rare bone disorder characterised by chronic hypophosphataemia caused by defective phosphate reabsorption in the renal tubules. Variants in phosphate-regulating endopeptidase homolog, X-linked (PHEX), fibroblast growth factor-23 (FGF23) and dentin matrix protein-1 (DMP1) genes contribute to X-linked dominant, autosomal dominant and autosomal recessive forms of HR, respectively. In this study, four Malaysian patients’ DNA samples were subjected to polymerase chain reaction and Sanger sequencing to identify the types and locations of the variants. Then, in silico study was conducted based on the variants found to predict the effects of amino acid substitution on protein functions using SIFT and PolyPhen-2 software and RNAfold was used to construct the mRNA secondary structure. Mutational analyses had revealed two variants in PHEX; c.10G>C (E4Q), c.1970A>G (Y657C), one mutation in FGF23; c.716C>T (T239M) and three variants on DMP1; c.309A>T (S69C), c.1322C>T (S406S), c.1334G>A (E410E). The variants in these Malay patients were previously reported in different ethnic HR patients. Protein prediction programs suggested that the PHEX Y657C and DMP1 S69C variants may affect protein function. All variants were predicted to alter the secondary mRNA structure. These findings suggest that these missense and silent variants may lead to changes in protein function and mRNA secondary structure that are associated with the manifestation of HR phenotype.

References

Pettifor JM. What’s new in hypophosphataemic rickets? Eur J Pediatr 2008; 167: 493–9.

Jagtap VS, Sarathi V, Lila AR, Bandgar T, Menon P, Shah NS. Hypophosphataemic rickets. Indian J Endocrinol Metab 2012; 16: 177–82.

Bergwitz C, Jüppner H. Regulation of phosphate homeostasis by PTH, vitamin D, and FGF23. Annu Rev Med 2010; 61: 91–104.

Penido MGMG, Alon US. Phosphate homeostasis and its role in bone health. Pediatr Nephrol 2012; 27: 2039–48.

Douyere D, Joseph C, Gaucher C, Chaussain C, Courson F. Familial Hypophosphataemic vitamin D-resistant rickets--prevention of spontaneous dental abscesses on primary teeth: a case report. Oral Surg Oral Med Oral Pathol Oral Radiol Endod 2009; 107: 525–30.

Yong SM, Aik S. X-linked Hypophosphataemic Rickets - a report of 2 cases and review of literature. Med J Malaysia. 2000 Sep; 55 Suppl C: 101-4.

Bhadada SK, Bhansali A, Upreti V, Dutta P, Santosh R, Das S, et al. Hypophosphataemic rickets/osteomalacia: a descriptive analysis. Indian J Med Res 2010; 131: 399–404.

Ruppe MD, Brosnan PG, Au KS, Tran PX, Barbara W. Mutation Analysis of PHEX, FGF23 and DMP1 in a cohort of patients with Hypophosphataemic rickets. Clin Endocrinol (Oxf) 2012; 74: 312–318.

Medscape. Hypophosphataemic Rickets. Available at emedicine.medscape.com/article/922305-overview#showall. Accessed: 22 Sept 2014.

Sabbagh Y, Jones AO, Tenenhouse HS. PHEXdb, a locus-specific database for mutations causing X-linked hypophosphataemia. Hum Mutat 2000;16:1-6.

Sabbagh Y, Boileau G, DesGroseillers L, Tenenhouse HS. Disease-causing missense mutations in the PHEX gene interfere with membrane targeting of the recombinant protein. Hum Mol Genet 2001; 10: 1539–46.

Durmaz E, Zou M, Al-Rijjal RA, Baitei EY, Hammami S, Bircan I, et al. Novel and de novo PHEX mutations in patients with Hypophosphataemic rickets. Bone 2013; 52: 286–91.

Farrow EG, Davis SI, Ward LM, Summers LJ, Bubbear JS, Keen R, et al. Molecular analysis of DMP1 mutants causing autosomal recessive Hypophosphataemic rickets. Bone 2009; 44: 287–94.

Fukumoto S, Yamashita T. FGF23 is a hormone-regulating phosphate metabolism-unique biological characteristic of FGF23. Bone 2007; 40:1190–5.

Razali NN, Ting TH, Thilakavathy K. Phosphate homeostasis and genetic mutations of familial Hypophosphataemic rickets. J Pediatr Endocrinol Metab 2015; 28:1009-17.

Nelson AE, Mason RS, Robinson BG. The PEX gene: not a simple answer for X-linked hypophosphataemic rickets and oncogenic osteomalacia. Mol Cell Endocrinol 1997; 132: 1–5.

Baroncelli GI, Toschi B, Bertelloni S. Hypophosphataemic Rickets. Curr Opin Endocrinol Diabetes Obes 2012; 19:460–467.

Goji K, Ozaki K, Sadewa AH, Nishio H, Matsuo M. Somatic and Germline Mosaicism for a Mutation of the PHEX Gene Can Lead to

Genetic Transmission of X-Linked Hypophosphataemic Rickets That Mimics an Autosomal Dominant Trait. J Clin Endocrinol Metab 2006; 91: 365–370.

Koshida R, Yamaguchi H, Yamasaki K, Tsuchimochi W, Yonekawa T, Nakazato M. A novel nonsense mutation in the DMP1 gene in a Japanese family with autosomal recessive Hypophosphataemic rickets. J Bone Miner Metab 2010; 28: 585–90.

Pauline CN, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003; 31:3812-4.

Adzhubei I, Jordan DM, Sunyaev SR. Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2. Curr Protoc Hum Genet 2013; 7.

Ng PC, Henikoff S. Predicting Deleterious Amino Acid Substitutions. Genome Res 2001; 11: 863–874.

Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A Method and Server for Predicting Damaging Missense Mutations. Nat Methods 2010; 7:248-9.

Tavtigian SV, Greenbelt MS, Lesueur F. Byrnes GB. In silico analysis of missense substitutions using sequence- alignment based methods. Hum Mutat 2012; 29: 1327–1336.

Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. The Vienna RNA websuite. Nucleic Acids Res 2008; 36: W70–4.

Sato K, Tajima T, Nakae J, Adachi M, Asakura Y, Tachibana K, et al. Three novel PHEX gene mutations in Japanese patients with X-linked Hypophosphataemic rickets. Pediatr Res 2000; 48: 536–40.

Li, SS, Gu JM, Yu WJ, He JW, Fu WZ, Zhang ZL. Seven novel and six de novo PHEX gene mutations in patients with Hypophosphataemic rickets. Int J Mol Med 2016; 38: 1703-1714.

Farrow EG, Yu X, Summers LJ, Davis SI, Fleet JC, Allen MR, et al. Iron deficiency drives an autosomal dominant Hypophosphataemic rickets (ADHR) phenotype in fibroblast growth factor-23 (Fgf23) knock-in mice. Proc Natl Acad Sci U S A 2011; 108:E1146-55.

Brame LA, White KE, Econs MJ. Renal phosphate wasting disorders: clinical features and pathogenesis. Semin Nephrol 2004; 24: 39–47.

Kim J, Yang KH, Nam JS, Choi JR, Song J, Chang M, et al. A novel PHEX mutation in a Korean patient with sporadic Hypophosphataemic rickets. Ann Clin Lab Sci 2009; 39: 182–7.

Sun Y, Xia W, Li M, Jiang Y, Wang O, Nie M, et al. Genetic analysis of 128 Chinese patients with Hypophosphataemic rickets. Bone Abstract. 2010; 47; S385-458.

St-louis M. Contrôle de l ’ expression de la protéine PHEX et rôle de PHEX et FGF23 dans la minéralisation par les cellules. PhD thesis, Université de Montréal, 2009. Available from: https://papyrus.bib.umontreal.ca/xmlui/handle/1866/5136.

Gaucher C, Walrant-Debray O, Nguyen TM, Esterle L, Garabedian M, et al. PHEX analysis in 118 pedigrees reveals new genetic clues in Hypophosphataemic rickets. Hum Genet 2009; 125:401-11.

Rowe PSN. Regulation of Bone–Renal Mineral and Energy Metabolism: The PHEX, FGF23, DMP1, MEPE ASARM Pathway. Crit Rev Eukaryot Gene Expr. 2012; 22(1):61-86.

Rendina D, Esposito T, Mossetti G, De Filippo G, Gianfrancesco F, Perfetti A, et al. A functional allelic variant of the FGF23 gene is associated with renal phosphate leak in calcium nephrolithiasis. J Clin Endocrinol Metab 2012; 97:E840-4.

Merlotti D, Rendina D, Gennari L, Esposito T, Magliocca S, De Filippo G, et al. Interaction between FGF23 R176W mutation and C716T nonsynonymous change (T239M, rs7955866) in FGF23 on the clinical phenotype in a family with autosomal dominant Hypophosphataemic rickets. Bone Abstract 2013; 1: PP120.

Turan S, Aydin C, Bereket A, Akcay T, Güran T, Yaralioglu BA, et al. Identification of a novel dentin matrix protein-1 (DMP-1) mutation and dental anomalies in a kindred with autosomal recessive hypophosphataemia. Bone. 2010; 46: 402–9.

De Smit MH, Van Duin J. Secondary structure of the ribosome binding site determines translational efficiency : A quantitative analysis. Proc Natl Acad Sci U S A. 1990; 87:7668-72.

Gaspar P, Moura G, Santos MAS, Oliveira JL. mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res 2013; 41:e73

Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger, A. et al. Deciphering the rules by which 5′-UTR sequences affect protein expression yeast. Proc Natl Acad Sci U S A 2013; 110:E2792-801.

Komar AA. SNPs, Silent But Not Invisible. Science 2007; 315, 466–467.

Hrzenjak A, Artl A, Knipping G, Kostner G, Sattler W, Malle E. Silent mutations in secondary Shine – Dalgarno sequences in the cDNA of human serum amyloid A4 promotes expression of recombinant protein in Escherichia coli. Protein Eng Des Sel 2001; 14:949-52.

Paek KY, Hong KY, Ryu I, Park SM, Keum SJ, Kwon OS, et al. Translation initiation mediated by RNA looping. Proc Natl Acad Sci U S A 2015; 112:1041-1046.

Paulus M, Haslbeck M, Watzele M. RNA stem–loop enhanced expression of previously non-expressible genes. Nucleic Acids Res 2004; 32:e78.

Supek F, Miñana B, Valcárcel J, Gabaldón T, Lehner B. Synonymous mutations frequently act as driver mutations in human cancers. Cell 2014; 156:1324–35.

Mao Y, Liu H, Liu Y, Tao S. Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae. Nucleic Acids Res 2014; 42:4813-22.

Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, et al. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Mol Syst Biol 2014; 10:770

Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, et al. A new and updated resource for codon usage tables. BMC Bioinformatics 2017; 18: 391.

Huang T, Wan S, Xu Z, Zheng Y, Feng K-Y, Li H-P, et al. Analysis and Prediction of Translation Rate Based on Sequence and Functional Features of the mRNA. PLoS ONE 2011; 6(1): e16036.

Frumkin I, Lajoie MJ, Gregg CJ, Hornung G, Church GM, Pilpel Y. Codon usage of highly expressed genes affects proteome-wide translation efficiency. Proc Natl Acad Sci U S A 2018; 115:E4940-E4949.

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Published

26.12.2019

How to Cite

Razali, N. N., Tzer, H. T., King, H. L., Kennerson, M. L., & Thilakavathy, K. (2019). Predicting the Impact of PHEX, FGF23 and DMP1 Gene Variants Found in Malaysian Malay Patients with Hypophosphataemic Rickets Through In Silico Analysis of Protein Function and mRNA Secondary Structure. Journal of Biochemistry, Microbiology and Biotechnology, 7(2), 14–23. https://doi.org/10.54987/jobimb.v7i2.477

Issue

Vol. 7 No. 2 (2019)

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Articles

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