Identification and characterization of 40 novel hydroxymethylbilane synthase mutations that cause acute intermittent porphyria

  • Brenden Chen
  • Constanza Solis-Villa
  • Angelika L. Erwin
  • Manisha Balwani
  • Irina Nazrenko
  • John D. Phillips
  • Robert J. Desnick
  • Makiko Yasuda
Original Article

Abstract

Acute intermittent porphyria (AIP), an autosomal dominant disorder due to the half-normal activity of hydroxymethylbilane synthase (HMBS), is characterized by acute neurovisceral attacks that are precipitated by factors that induce heme biosynthesis. Molecular diagnosis is the most sensitive and specific diagnostic test for AIP, and importantly, it permits the identification of asymptomatic family members for genetic counseling and avoidance of precipitating factors. Here, we report the identification of 40 novel HMBS mutations, including 11 missense, four nonsense, 16 small insertions or deletions, eight consensus splice site mutations, and a complex insertion-deletion mutation in unrelated individuals with AIP. Prokaryotic expression of the missense mutations demonstrated that all mutants had ≤5% of expressed wildtype activity, except for c.1039G>C (p.A347P), which had 51% residual HMBS activity but was markedly thermolabile. Of note, the mutation c.612G>T (p.Q204H) altered the last nucleotide of exon 10, which resulted in an alternative HMBS transcript with an in-frame nine base-pair deletion at the 3'-terminus of exon 10 (encoding protein Q204HΔ3). When expressed, Q204HΔ3 and an in-frame three base-pair deletion (c.639_641delTGC) had no detectable HMBS activity. Western blot analyses and mapping of the missense mutations on the human HMBS crystal structure revealed that mutations near the active site or at the dimerization interface resulted in stably expressed proteins, while most that altered surface residues resulted in unstable proteins, presumably due to improper protein folding. These studies identified novel pathogenic HMBS mutations and expanded the molecular heterogeneity of AIP.

Notes

Acknowledgements

We thank Vendenii Zaikov for his excellent technical assistance.

Compliance with ethical standards

Conflict of interest

Manisha Balwani, Robert Desnick and John Phillips are consultants for Alnylam Pharmaceuticals and Recordati Rare Diseases. Manisha Balwani receives clinical trial grants and Robert Desnick has received research grants from Alnylam Pharmaceuticals and Recordati Rare Diseases. Robert Desnick and Makiko Yasuda are inventors of intellectual property licensed to Alnylam Pharmaceuticals. Brenden Chen, Constanza Solis-Villa, Angelika Erwin, and Irina Nazrenko declare that they have no conflict of interest.

Supplementary material

10545_2018_163_MOESM1_ESM.docx (34 kb)
ESM 1 (DOCX 33 kb)

References

  1. Aarsand AK, Petersen PH, Sandberg S (2006) Estimation and application of biological variation of urinary delta-aminolevulinic acid and porphobilinogen in healthy individuals and in patients with acute intermittent porphyria. Clin Chem 52:650–656CrossRefPubMedGoogle Scholar
  2. Anderson KE, Sassa S, Bishop DF, Desnick RJ (2001) Disorders of heme biosynthesis: X-linked sideroblastic anemia and the porphyrias. In: Valle D, Beaudet AL, Vogelstein B, Kinzler KW, Antonarakis SE, Ballabio A, Gibson K, Mitchell G (eds) The metabolic and molecular bases of inherited disease. 8th edn. McGraw-Hill, New York, pp 2961–3062Google Scholar
  3. Anderson KE, Bloomer JR, Bonkovsky HL et al (2005) Recommendations for the diagnosis and treatment of the acute porphyrias. Ann Intern Med 142:439–450CrossRefPubMedGoogle Scholar
  4. Bonkovsky HL, Maddukuri VC, Yazici C et al (2014) Acute porphyrias in the USA: features of 108 subjects from porphyrias consortium. Am J Med 127:1233–1241CrossRefPubMedPubMedCentralGoogle Scholar
  5. Chang TH, Huang HY, Hsu JB et al (2013) An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs. BMC Bioinf 14 Suppl 2:S4Google Scholar
  6. Chen CH, Astrin KH, Lee G et al (1994) Acute intermittent porphyria: identification and expression of exonic mutations in the hydroxymethylbilane synthase gene. An initiation codon missense mutation in the housekeeping transcript causes “variant acute intermittent porphyria” with normal expression of the erythroid-specific enzyme. J Clin Invest 94:1927–1937CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chen B, Solis-Villa C, Hakenberg J et al (2016) Acute intermittent porphyria: predicted pathogenicity of HMBS variants indicates extremely low penetrance of the autosomal dominant disease. Hum Mutat 37:1215–1222CrossRefPubMedPubMedCentralGoogle Scholar
  8. De Siervi A, Rossetti MV, Parera VE et al (1999) Acute intermittent porphyria: biochemical and clinical analysis in the Argentinean population. Clin Chim Acta 288:63–71CrossRefPubMedGoogle Scholar
  9. Divina P, Kvitkovicova A, Buratti E et al (2009) Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping. Eur J Hum Genet 17:759–765CrossRefPubMedPubMedCentralGoogle Scholar
  10. Floderus Y, Shoolingin-Jordan PM, Harper P (2002) Acute intermittent porphyria in Sweden. Molecular, functional and clinical consequences of some new mutations found in the porphobilinogen deaminase gene. Clin Genet 62:288–297CrossRefPubMedGoogle Scholar
  11. Grandchamp B, De Verneuil H, Beaumont C et al (1987) Tissue-specific expression of porphobilinogen deaminase. Two isoenzymes from a single gene. Eur J Biochem 162:105–110CrossRefPubMedGoogle Scholar
  12. Granick S (1963) Induction of the synthesis of delta-aminolevulinic acid synthetase in liver parenchyma cells in culture by chemical that induce acute porphyria. J Biol Chem 238:2247–2249PubMedGoogle Scholar
  13. Granick S (1966) The induction in vitro of the synthesis of delta-aminolevulinic acid synthetase in chemical porphyria: a response to certain drugs, sex hormones, and foreign chemicals. J Biol Chem 241:1359–1375PubMedGoogle Scholar
  14. Gu XF, de Rooij F, Lee JS et al (1993) High prevalence of a point mutation in the porphobilinogen deaminase gene in Dutch patients with acute intermittent porphyria. Hum Genet 91:128–130CrossRefPubMedGoogle Scholar
  15. Hift RJ, Meissner PN (2005) An analysis of 112 acute porphyric attacks in cape town, South Africa: evidence that acute intermittent porphyria and variegate porphyria differ in susceptibility and severity. Medicine (Baltimore) 84:48–60CrossRefGoogle Scholar
  16. Jordan PM, Warren MJ (1987) Evidence for a dipyrromethane cofactor at the catalytic site of E. Coli porphobilinogen deaminase. FEBS Lett 225:87–92CrossRefPubMedGoogle Scholar
  17. Kauppinen R, von und zu Fraunberg M (2002) Molecular and biochemical studies of acute intermittent porphyria in 196 patients and their families. Clin Chem 48:1891–1900PubMedGoogle Scholar
  18. Mustajoki P, Desnick RJ (1985) Genetic heterogeneity in acute intermittent porphyria: characterisation and frequency of porphobilinogen deaminase mutations in Finland. Br Med J (Clin Res Ed) 291:505–509CrossRefGoogle Scholar
  19. Mykletun M, Aarsand AK, Stole E et al (2014) Porphyrias in Norway. Tidsskr Nor Laegeforen 134:831–836CrossRefPubMedGoogle Scholar
  20. Puy H, Gouya L, Deybach JC (2010) Porphyrias. Lancet 375:924–937CrossRefPubMedGoogle Scholar
  21. Sassa S, Granick S (1970) Induction of -aminolevulinic acid synthetase in chick embryo liver cells in cluture. Proc Natl Acad Sci U S A 67:517–522CrossRefPubMedPubMedCentralGoogle Scholar
  22. Schindelin J, Arganda-Carreras I, Frise E et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682CrossRefPubMedGoogle Scholar
  23. Schuurmans MM, Schneider-Yin X, Rufenacht UB et al (2001) Influence of age and gender on the clinical expression of acute intermittent porphyria based on molecular study of porphobilinogen deaminase gene among Swiss patients. Mol Med 7:535–542PubMedPubMedCentralGoogle Scholar
  24. Song G, Li Y, Cheng C et al (2009) Structural insight into acute intermittent porphyria. FASEB J 23:396–404CrossRefPubMedGoogle Scholar
  25. Stenson PD, Mort M, Ball EV et al (2017) The human gene mutation database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet 136:665–677CrossRefPubMedPubMedCentralGoogle Scholar
  26. van Hoof A, Frischmeyer PA, Dietz HC, Parker R (2002) Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 22:2262–2264CrossRefGoogle Scholar
  27. von und zu Fraunberg M, Pischik E, Udd L et al (2005) Clinical and biochemical characteristics and genotype-phenotype correlation in 143 Finnish and Russian patients with acute intermittent porphyria. Medicine (Baltimore) 84:35–47CrossRefGoogle Scholar
  28. Whatley SD, Badminton MN (2005) Acute intermittent porphyria. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH et al (eds) GeneReviews. University of Washington, SeattleGoogle Scholar
  29. Whatley SD, Badminton MN (2013) Role of genetic testing in the management of patients with inherited porphyria and their families. Ann Clin Biochem 50:204–216CrossRefPubMedGoogle Scholar

Copyright information

© SSIEM 2018

Authors and Affiliations

  1. 1.Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkUSA
  2. 2.Department of Internal MedicineUniversity of UtahSalt Lake CityUSA

Personalised recommendations