Molecular basis of acute intermittent porphyria: mutations and polymorphisms in the human hydroxymethylbilane synthase gene

Network analysis of hydroxymethylbilane synthase dynamics

Hydroxymethylbilane synthase (HMBS) is one of the key enzymes of the heme biosynthetic pathway that catalyzes porphobilinogen to form the linear tetrapyrrole 1-hydroxymethylbilane through four intermediate steps. Mutations in the human HMBS (hHMBS) can lead to acute intermittent porphyria (AIP), a lethal metabolic disorder. The molecular basis of importance of the amino acid residues at the catalytic site of hHMBS has been well studied. However, the role of non-active site residues toward the activity of the enzyme and hence the association of their mutations with AIP is not known. Network-based analyses of protein structures provide a systems approach to understand the correlations of the residues through a series of inter-residue interactions. We analyzed the dynamic network representation of HMBS protein derived from five molecular dynamics trajectories corresponding to the five steps of pyrrole polymerization. We analyzed the network clusters for each stage and identified the amino acid residues and interactions responsible for the structural stability and catalytic function of the protein. The analysis of high betweenness nodes and interaction paths from the active site help in understanding the molecular basis of the effect of non-active site AIP-causing mutations on the catalytic activity.

Human hereditary hepatic porphyrias

The human hereditary hepatic porphyrias are diseases due to marked deficiencies of enzymes in the heme biosynthetic pathway. Porphyrias can be classified as either hepatic or erythroid, depending on the major production site of porphyrins or their precursors. The pathogenesis of inherited hepatic porphyrias has now been defined at the molecular level. Some gene carriers are vulnerable to a range of exogenous and endogenous factors, which may trigger neuropsychiatric and/or cutaneous symptoms. Early diagnosis is of prime importance since it makes way for counselling. In this article we present an overview of recent advances on hepatic porphyrias: 5-aminolevulinic acid dehydratase deficiency porphyria, acute intermittent porphyria (AIP), porphyria cutanea tarda (PCT), hereditary coproporphyria (HC), and variegate porphyria (VP).

Acute intermittent porphyria: heterogeneity of mutations in the hydroxymethylbilane synthase gene in Italy

Acute intermittent porphyria (AIP) is an autosomal disorder caused by molecular abnormalities in the gene coding for hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthetic pathway. So far, more than 170 different mutations responsible for AIP have been identified worldwide in the HMBS gene. In this study we have performed molecular characterization in 14 patients with suspected diagnosis of AIP and in 29 family members of Italian ancestry. Molecular analysis of the HMBS gene allowed us to identify 13 different mutations among 14 patients with reduced HMBS activity: 5 splicing defects (IVS9+22 G>A, 612 G>T, IVS11-2 delA, IVS12+2 T>C, and IVS13-1 G>A), 1 small insertion (182 insGA), 1 small deletion (730-731 delCT), and 6 missense/nonsense mutations (76 C>T, 295 G>A, 331 G>A, 580 C>T, 673 C>T, and 874 C>T), resulting in single-amino-acid substitutions or protein truncations. Six of these molecular abnormalities had already been described and 7 are new findings. In a previous work on an Italian population we detected 7 different mutations among 8 AIP patients. This study has raised to 18 the number of different mutations so far found among the Italian AIP population, 11 of which are new findings. We can conclude that the mutation screening in the Italian population contributes to improvement of the diagnostic approach of AIP and to establishing possible clustering of mutations in the Mediterranean area.

Acute intermittent porphyria: novel missense mutations in the human hydroxymethylbilane synthase gene

PURPOSE

To identify mutations in families with acute intermittent porphyria, an autosomal dominant inborn error of metabolism that results from the half-normal activity of the third enzyme in the heme biosynthetic pathway, hydroxymethylbilane synthase.

METHODS

Mutations were identified by direct solid phase sequencing.

RESULTS

Two novel missense mutations E80G and T78P and three previously reported mutations, R173W, G111R, and the splice site lesion, IVS1+1, were detected, each in an unrelated proband. The causality of the novel missense mutations was demonstrated by expression studies.

CONCLUSION

These findings provide for the precise diagnosis of carriers in these families and further expand the molecular heterogeneity of AIP.

Hereditary coproporphyria: exon screening by heteroduplex analysis detects three novel mutations in the coproporphyrinogen oxidase gene

Hereditary coproporphyria is a dominantly inherited disorder of porphyrin metabolism caused by a partial deficiency of coproporphyrinogen oxidase, the sixth enzyme in the heme synthetic pathway. We investigated the molecular basis of hereditary coproporphyria in three unrelated patients, amplifying each exon of the coproporphyrinogen oxidase gene and performing heteroduplex analysis to look for mutations. Unique heteroduplex patterns were noted in exons 2, 3, and 6. Sequencing revealed different mutations in each patient: a G-->A point mutation encoding a glutamic acid to lysine substitution at codon 101 (E101K), a C-->T point mutation encoding a proline to serine substitution at codon 149 (P149S), and a one base-pair insertion in exon 6 (968insT). No other mutations were found on sequencing the remaining exons and their intron-exon junctions. The two point mutations affect amino acids that are conserved in all species studied to date. The one base-pair insertion in exon 6 is the first frameshift mutation to be described in the coproporphyrinogen oxidase gene. This study adds three new mutations to those that have been previously reported, and all have been restricted to single families. These results indicate that hereditary coproporphyria is a genetically heterogeneous disease.

Diagnostic strategy, genetic diagnosis and identification of new mutations in intermittent porphyria by denaturing gradient gel electrophoresis

Acute intermittent porphyria (AIP) is an autosomal dominant inherited disease of heme metabolism caused by mutations in the hydroxymethylbilane synthase gene. Diagnosing AIP during an acute attack using traditional biochemical markers is unproblematic, but it can be difficult to obtain a definite diagnosis in asymptomatic carriers. These limitations may, however, be solved through a genetic approach for diagnosing AIP carrier status. A mutation screening assay based on the denaturing gradient gel electrophoresis (DGGE) principle was established in a setup that allows within 24 hr to pinpoint which of the 15 exons of the hydroxymethylbilane synthase gene carries the underlying mutation, and thereby reduces subsequent sequencing, needed to determine the specific mutation, to this particular gene region. To evaluate sensitivity and specificity of the DGGE assay, samples from 22 AIP patients with known mutations and six healthy controls were examined in a blinded design. Following unblinding, it was revealed that in all 22 AIP samples the correct mutation carrying region had been pointed out. In two samples containing a previously undescribed polymorphism, this additional region was also pointed out. All controls were correctly characterized as normal in the DGGE assay. Subsequently, to evaluate the assay in the clinical setting, samples from six previously uncharacterized Danish AIP probands were examined and the underlying mutation detected in all six. In conclusion, a simple and sensitive mutation screening assay based on the DGGE principle allows genetic diagnosis of AIP in a routine setting and may be used as an additional tool in genetic counseling of AIP families.

Acute intermittent porphyria: biochemical and clinical analysis in the Argentinean population

Acute intermittent porphyria (AIP) is the most common type of hepatic acute porphyria. In this work, we have analyzed the biochemical data of all Argentinean AIP families studied in the Porphyrins and Porphyrias Research Centre (CIPYP). We have shown that: (i) the prevalence for this population is about 1:125,000; (ii) the disease is more frequent in women than in men (7:3); (iii) about 60% are latent carriers; (iv) 15% of patients with symptomatic AIP died during an acute attack; (v) the most important precipitating factors of acute attacks in our population were the ingestion of therapeutic drugs (25%), anesthetics in surgical interventions (25%) and infections (20%); (vi) the initial symptom in Argentinean AIP individuals is severe abdominal pain (100%), and it is often accompanied by constipation (37%), anorexia (37%) and tachycardia (30%); and (vii) the percentage of recurrence of the acute attacks is high (81%).

Ionizing radiation and genetic risks IX. Estimates of the frequencies of mendelian diseases and spontaneous mutation rates in human populations: a 1998 perspective

This paper is focused on baseline frequencies of mendelian diseases and the conceptual basis for calculating doubling doses both of which are relevant for the doubling dose method of estimating genetic risks of exposure of human populations to ionizing radiation. With this method, the risk per unit dose is obtained as a product of three quantities, namely, the baseline frequency of the disease class under consideration, the relative mutation risk (which is the reciprocal of the doubling dose, which in turn, is calculated as a ratio of spontaneous and induction rates of mutations) and mutation component, i.e., the responsiveness of the disease class to an increase in mutation rate. The estimates of baseline frequencies of mendelian diseases that are currently used in risk estimation date back to the late 1970s. Advances in human genetics during the past two decades now permit an upward revision of these estimates. The revised estimates are 150 per 10(4) livebirths for autosomal dominants (from the earlier estimate of 95 per 10(4)), 75 per 10(4) livebirths for autosomal recessives (from 25 per 10(4)) and to 15 per 10(4) livebirths for X-linked diseases (from 5 per 10(4)). The revised total frequency of mendelian diseases is thus 240 per 10(4) livebirths and is about twice the earlier figure of 125 per 10(4) livebirths. All these estimates, however, pertain primarily to Western European and Western European-derived populations. The fact that in several population isolates or ethnic groups, some of these diseases (especially the autosomal recessives) are more common as a result of founder effects and/or genetic drift is well known and many more recent examples have come to light. These data are reviewed and illustrated with data from studies of the Ashkenazi Jewish, Finnish, French Canadian, Afrikaner and some other populations to highlight the need for caution in extrapolating radiation risks between populations. The doubling dose of 1 Gy that has been used for the past 20 years for risk estimation is based on mouse data for both spontaneous and induction rates of mutations. In extrapolating the mouse-data-based doubling dose to humans, it is assumed that the spontaneous rates in mice and humans are similar. This assumption is incorrect because of the fact that in humans, for several well-studied mendelian diseases, the mutation rate differs between the two sexes and it increases with paternal age. In estimates of spontaneous mutation rates in humans (which represent averages over both sexes), however, paternal age effects are automatically incorporated. In the mouse, these effects are expected to be much less (if they exist at all), but the problem has not been specifically addressed. The complexities and uncertainties associated with assessing the potential impact of spontaneous mutations which arise as germinal mosaics (and which can result in clusters of mutations in the following generation) on mutation rate estimates (in the mouse) and on mutation rate estimates and disease frequencies (in humans) are discussed. In view of (i) the lack of comparability of spontaneous mutation rates in mice and humans and (ii) the fact that these estimates for human genes already include both paternal age effects and correction for clusters (if they had occurred), it is suggested that a prudent procedure now is to base doubling dose calculations on spontaneous mutation rates of human genes (and induction rates of mouse genes, in the absence of a better alternative). This concept, however, is not new and was used by the US National Academy's Committee on the Biological Effects of Ionizing Radiation in its 1972 report.

Detection of a R173W mutation in the porphobilinogen deaminase gene in the Nova Scotian "foreign Protestant" population with acute intermittent porphyria: a founder effect

OBJECTIVES

Acute intermittent porphyria (AIP) is caused by mutations in the porphobilinogen deaminase (PBGD) gene that disrupt the function of the enzyme. Many mutations that lead to decreased PBGD activity have been described. An Arg to Trp substitution at codon 173 (CGG-->TGG in exon 10) and designated R173W, which leads to a CRIM-negative phenotype, has been reported in Swedish, Finnish, Scottish, and South African kindreds, and in a Nova Scotian proband with fatal AIP. In this work, we investigated the presence of this mutation in a Nova Scotian patient population presenting with AIP.

DESIGN AND METHODS

Single-strand conformation polymorphism analysis and DNA sequencing by TA cloning and Sanger's dideoxy chain termination method, were used to confirm the maternal transmission of this mutation to the proband. The mutation also eliminates an Ncil (also Mspl) endonuclease restriction site, which allows for detection of the mutant allele by polymerase chain reaction amplification and restriction enzyme digestion.

RESULTS

The family of the Nova Scotian proband and four other AIP kindreds showed the presence of the same mutation. These five families are descendants of German, Swiss, and French immigrants historically known as the "Foreign Protestants," who were recruited to Nova Scotia in the 1750s.

CONCLUSION

In all these families, descent from one couple that settled in Nova Scotia in 1751 has been identified by genealogy research, consistent with a founder effect within this population. This is the first identified mutation in PBGD causing AIP that has been linked to a founder effect in descendants of an immigrant population to North America, and which could be traced to such a distant background, similar to the South African variegate porphyria mutation.

Molecular epidemiology and diagnosis of PBG deaminase gene defects in acute intermittent porphyria

Acute intermittent porphyria (AIP) is the major autosomal dominant form of acute hepatic porphyrias. The disease is due to mutations in the gene encoding for porphobilinogen (PBG) deaminase and is characterized by life-threatening neurovisceral attacks, often precipitated by drugs, fasting, cyclical hormonal changes, or infectious diseases. This report describes a prospective study on the molecular epidemiology of PBG deaminase gene defects in AIP. It uses a sensitive, reliable, and easy-to-handle method for routine AIP molecular diagnosis and family study based on an exon-by-exon denaturing gradient gel electrophoresis (DGGE) strategy followed by direct sequencing. Fifteen genomic DNA fragments, including all the coding sequence and covering 3.35 kb of the PBG deaminase gene, were investigated in 405 subjects from 121 unrelated French Caucasian AIP families who had not been screened previously at the DNA level. PBG deaminase gene mutations were identified in 109 families, but only 78 were of different type, and each of them had a prevalence rate < 5%. Among these mutations, 33 had not been published previously. Sixty percent of these 78 mutations were located in only three exons (exons 10, 12, and 14), 44% were missense, 18% were splice defect, 19% were frameshift, and 16% were nonsense. In addition, two de novo mutational events were characterized. The evaluation of the efficiency of the standard PBG deaminase enzymatic screening method for gene-carrier detection indicated 95% of concordancy with the molecular-based diagnosis.

Acute intermittent porphyria: a single-base deletion and a nonsense mutation in the human hydroxymethylbilane synthase gene, predicting truncations of the enzyme polypeptide

Acute intermittent porphyria (AIP) is an autosomal-dominant inborn error of metabolism that results from the half-normal activity of the third enzyme in the heme biosynthetic pathway, hydroxymethylbilane synthase (HMB-synthase). AIP is an ecogenetic condition, since the life-threatening acute attacks are precipitated by various factors, including drugs, alcohol, fasting, and certain hormones. Biochemical diagnosis is problematic, and the identification of mutations in the HMB-synthase gene provides accurate detection of presymptomatic heterozygotes, permitting avoidance of the acute precipitating factors. By direct solid-phase sequencing, two mutations causing AIP were identified, an adenine deletion at position 629 in exon 11(629delA), which alters the reading frame and predicts premature truncation of the enzyme protein after amino acid 255, and a nonsense mutation in exon 12 (R225X). These mutations were confirmed by either restriction enzyme analysis or family studies of symptomatic patients, permitting accurate presymptomatic diagnosis of affected relatives.

Porphobilinogen deaminase gene structure and molecular defects

Porphobilinogen deaminase (PBGD) is the third enzyme of the heme biosynthetic pathway. The half-normal activity of human PBGD causes acute intermittent porphyria (AIP), an autosomal dominant inherited disease. Two PBGD isoforms, one ubiquitous and one erythroid specific, are encoded by a single gene localized to chromosomal region 11q24.1-11q24.2. The 10-kb PBGD gene comprises 15 exons and two distinct promoters initiate the ubiquitous and the erythroid transcripts by alternative splicing. In AIP, diagnosis of asymptomatic heterozygotes is crucial to prevent occurrence of life-threatening acute attacks by avoiding known precipitating factors. Difficulties with the biochemical diagnosis could be overcome by the ability to identify the PBGD gene defects in AIP patients. Mutational analysis of the PBGD gene or the use of intragenic polymorphisms offer accurate identification of the gene carriers. To date, 58 mutations and 10 polymorphisms have been reported at the PBGD locus. The great heterogeneity of the mutations in AIP patients requires appropriate screening and diagnostic strategies to identify gene defects in AIP families.