A promoter mutation, C-->T at position -92, leading to silent beta-thalassaemia

Novel Promoter Mutation (HBB:C.-139_-138del) Associated with β-Thalassemia Trait Detected by Next-Generation Sequencing in Southern China

Here we report a novel β-globin gene mutation in the promoter (HBB:c.-139_-138delAC) detected by next-generation sequencing (NGS). The proband was a 28-year-old Chinese male, living in Shenzhen City, Guangdong Province, who originates from Hunan Province. The red cell indices were almost normal, with a slightly decreased Red Cell volume Distribution Width(RDW). Capillary electrophoresis (CE) showed the Hb A (93.1%) value was below normal, while the Hb A₂ (4.2%) and Hb F (2.7%) values were both beyond normal. A set of genetic tests of the α and β-globin genes were then performed to determine whether the subject carried any causative mutations. The results of NGS revealed a two-base pair deletion at position -89 to -88(HBB:c.-139_-138delAC）in the heterozygous state, which was subsequently confirmed by Sanger sequencing.

Borderline HbA2 levels: Dilemma in diagnosis of beta-thalassemia carriers

There is inconsistency in the exact definition of diagnostic levels of HbA₂ for β thalassemia trait. While many laboratories consider HbA₂ ≥4.0 % diagnostic, still others consider HbA₂ ≥3.3 % or HbA₂ ≥3.5 % as the cut-off for establishing β thalassemia carrier diagnosis. This is because, over the years, studies have described β thalassemia carriers showing HbA₂ levels that lie above the normal range of HbA₂ but below the typical carrier range of β thalassemia. These, "borderline HbA₂ levels", though not detrimental to health, are significant in β thalassemia carrier diagnosis because they can lead to misinterpretation of results. In this review, we have evaluated the prevalence of borderline HbA₂ levels and discussed the causes of borderline HbA₂ values. We have also compiled an extensive catalogue of β globin gene defects associated with borderline HbA₂ levels and have discussed strategies to avoid misdiagnosing borderline HbA₂ β thalassemia carriers. Our analysis of studies that have delineated the cause of borderline HbA₂ levels in different populations shows that 35.4 % [626/1766] of all individuals with borderline HbA₂ levels carry a molecular defect. Among the positive samples, 17 % [299/1766] show β globin gene defects, 7.7 % [137/1766] show α thalassemia defects, 2.7 % [49/1766] show KLF1 gene mutations, 2.3 % [41/1766] show the co-inheritance of β and α thalassemia, 2.0 % [37/1766] show the co-inheritance of β and δ thalassemia and 1.8 % [32/1766] show α globin gene triplication. It appears that a comprehensive molecular work up of the β globin gene is the only definite method to detect borderline HbA₂ β thalassemia carriers, especially in populations with a high prevalence of the disease. The presence of associated genetic or acquired determinants may subsequently be assessed to identify the cause of borderline HbA₂.

Incidence of haemoglobinopathies in Sicily: the impact of screening and prenatal diagnosis

BACKGROUND

Haemoglobinopathies are a major public health problem in Sicily: it was estimated a frequency of 1/245 couples are at risk of haemoglobinopathies. This paper reviews legislative actions, prevention activities, carrier screening, genetic counselling, foetal sampling and laboratory methodology analysis evolution reporting the results of 30 years of prevention actions to assess the efficiency of our preventative programme in the control of haemoglobinopathies in Sicily.

METHODS

This programme consisted principally of five phases: legislative actions, public awareness campaign, carrier screening, genetic counselling and prenatal diagnosis.

RESULTS

These programmes have been very effective, which we can see from a greater public awareness of thalassaemia and its prevention in the target population furthermore by a marked decline in the incidence of thalassaemia major and sickle cell anaemia from 1 in 245 live births in the absence of prevention to 1 in 2000, with a reduction in about 85%. The residual cases were because of a conscious choice by expecting parents in relation to improved life expectancy as well as improved quality of life of the affected patients.

CONCLUSION

The study suggests that public health authorities should act and invest in a similar programme for prevention of thalassaemia, as well as in relation to the increased survival of patients and the consequent organ complications.

Two new β+ -thalassemia mutation [β -56 (G → C); HBBc. -106 G → C] and [β -83 (G → A); HBBc. -133 G → A] described among the Tunisian population

OBJECTIVES

Different thalassemia mutations have been reported in various ethnic groups and geographical regions in Tunisia. In the present study, we have investigated two rare β(+) -thalassemia mutations, that have not previously been reported in the Tunisian population [β -56 (G > C); HBBc. -106 G > C] and [β -83 (G > A); HBBc. -133 G > A].

METHODS

The whole β-globin gene was directly sequenced, and haplotype analysis was conducted through a PCR/RFLP method.

RESULTS

Two new mutations were identified for the first time in Tunisia. They are located within the promoter region of β-globin gene at position -56 (G > C) and -83 (G > A). Linkage analysis using β-globin gene cluster haplotypes showed that these two mutations were associated with Mediterranean β-haplotype IX [- + - + + + +] and framework 2 (FW2) [CCTCT].

CONCLUSIONS

The two newly described mutations lead to the β(+) -thalassemia among Tunisian patients. The haplotype analysis and framework assignment have helped to identify the chromosomal background associated with these mutations, and determine their origin and spread.

A novel mutation of −73(A→T) in the CCAAT box of the β-globin gene identified in a patient with the mild β-thalassemia intermedia

The beta-thalassemia is one of the most common autosomal recessive disorders in Southern China. The point mutation of beta-globin gene is the commonest molecular pathogenic mechanism. In Chinese population, over 30 mutations have now been identified. In this paper, we describe a novel beta(++)-thalassemia mutation of -73(A-->T) within the conserved CCAAT box at position -76 to -72 from the cap site of the beta-globin gene. The proband, an 8-year-old Chinese boy, was a compound heterozygote of this promoter mutation and a common beta(0)-thalassemia mutation of codon 41/42(-TCTT). He had a mild thalassemia intermedia phenotype and was transfusion independent with a hemoglobin (Hb) level of 9.4 g/dl, mean corpuscular volume (MCV) of 55.2 fl, and mean corpuscular hemoglobin (MCH) of 17.5 pg. His mother and two maternal uncles were carriers of -73(A-->T) mutation in beta-globin gene with hematological phenotype of silent beta-thalassemia. Real-time quantitative reverse transcript polymerase chain reaction (RT-PCR) analysis showed a slightly reduced beta-globin messenger RNA (mRNA) level (19.35%) in three heterozygotes compared with that in normal subjects. In restriction fragment length polymorphism (RFLP) haplotype analysis, the results indicated that this promoter mutation might be linked to the absence of BamHI-3'beta restriction site.

Thalassaemia-like carriers not linked to the beta-globin gene cluster

This study describes the largest series reported to date, of individuals belonging to unrelated families carrying a beta-thalassaemia-like phenotype in whom the beta-globin gene was found to be structurally intact by sequence analysis. This genetic determinant appears haematologically heterogeneous, displaying either a silent beta-thalassaemia-like phenotype or a typical beta-thalassaemia carrier-like phenotype in different families. Compound heterozygosity for both beta-thalassaemia-like determinant and typical beta-thalassaemia allele resulted either in thalassaemia intermedia or thalassaemia major. By linkage analysis both the silent and the typical beta-like determinants were found not to be linked to the beta-globin cluster. Sequence analysis of the hypersensitive site cores of locus control region and of the genes coding for the transcription factors erythroid Kruppel-like factor and nuclear factor (erythroid-derived 2) were normal. beta-globin mRNA levels determined by real-time polymerase chain reaction were reduced in both types of beta-like carriers. These results indicate the existence of causative genetic determinants not yet molecularly defined, but most likely, resulting from either the reduction or loss of function of a gene coding for unknown transcriptional regulator(s) of the beta-globin gene. The knowledge of these rare beta-thalassaemia-like determinants have implications for clinical and, especially, prenatal diagnosis of beta-thalassaemia.

Genetic modifying factors in beta-thalassemia

The beta-thalassemia is probably the most extensively studied genetic disease. Essentially any molecular defect that has been first described in association with the globin genes has been later implicated as a molecular determinant of newly discovered genes. Accordingly, the thalassemias have always represented a model genetic disease, especially in relation to the development of programs for population screening, genetic counseling and prenatal diagnosis. Here we will review the present knowledge on the genetics of thalassemia and of the relevant modifying factors. Major categories of the carrier state, the genotypes, the clinical phenotypes and the correlation between genotype and phenotype will be discussed.

Molecular, haematological and clinical studies of the -101 C --> T substitution of the beta-globin gene promoter in 25 beta-thalassaemia intermedia patients and 45 heterozygotes

We report the clinical, haematological, biosynthetic and molecular data of 25 double heterozygote beta-thalassaemia intermedia patients and 45 beta-thalassaemia heterozygotes with the C --> T substitution at nucleotide position -101 from the Cap site, in the distal CACCC box of the beta-globin gene promoter. This mutation is considered the most common amongst the silent beta-thalassaemia mutations in Mediterranean populations. Of the 25 compound heterozygotes for the beta -101 C --> T and common severe beta-thalassaemia mutations, all but one had mild thalassaemia intermedia preserving haemoglobin levels around 9.5 g/dl and haemoglobin F levels < 25%. The only transfused patient was characterized to have an additional alpha-globin gene. Strict assessment of haematological and biosynthetic findings in the heterozygotes for the beta -101 C --> T mutation (excluding six cases with an alpha-globin gene defect) demonstrated that less than half of them had completely normal (silent) haematology; the remainder had either high haemoglobin A2 values (in the range of 3.7-5.1%) and/or low red cells indices and/or raised haemoglobin F values. The alpha/non-alpha-globin chain synthesis ratios were generally raised, with mean 1.44 (1.07-2.10). Amongst the parents of the compound heterozygotes, who were not selected for molecular analysis following haematological screening, half of the cases were completely silent. Interaction with severe beta-thalassaemia mutations always resulted in the clinical phenotype of mild non-transfusion-dependent thalassaemia intermedia.

Activation of the delta-globin gene by the beta-globin gene CACCC motif

The promoter region of adult beta globin genes in humans and other mammals contains conserved regions of pivotal importance for their regulated tissue specific expression. These include the CACCC and CAAT motifs. The CACCC motif is duplicated in humans and other mammals. The human delta-globin gene lacks these conserved regions and its expression in normal individuals is about 3% that of the beta globin gene. Previous studies have shown that the introduction of the beta-globin CACCC or CAAT can activate the delta-globin gene promoter, but the effect of the distal CACCC element has not yet been tested. In the present study, using site-specific mutagenesis, we have introduced the consensus sequence for the distal and proximal CACCC motif and the CAAT box alone or in combination in the wild-type delta-globin gene promoter. The resulting mutants, as well as the wild type (wt) delta- and beta-globin gene promoters, have been analyzed in a transient expression assay in Cos7, K562, and MEL cell lines. The results show that the CACCC boxes can increase the transcription efficiency of the delta-globin gene promoter in both erythroid and non-erythroid cell systems. The contribution of the two CACCC elements is almost equal in the non-erythroid (Cos7) and erythroid embryonic-fetal cell lines (K562), while the proximal CACCC element is more active in adult erythroid cells (MEL). Nonetheless, duplication of this element does not appear to affect the efficiency of the promoter synergistically. Furthermore, to assess the competitive ability of the delta globin promoter containing the proximal or distal CACCC consensus sequences over the wt beta globin gene promoter, we have carried out transient expression experiments using DNA constructs in which the delta and beta globin gene promoters are linked in cis and are sharing a single enhancer (competitive transient expression). The results show that both CACCC elements are able to activate the delta globin gene promoter in Cos7 and K562 cells, although to a different extent, whereas only the proximal CACCC element is effective in increasing the transcription efficiency in MEL cells. These findings are in agreement with the more severe clinical phenotype produced by the beta-thalassemia mutations affecting the proximal CACCC box as compared with those within the distal CACCC box. The Erythroid Kruppel Like Factor (EKLF) is a nuclear protein restricted to erythroid cells which specifically bind the CACCC box sequence and activate the beta-globin gene. In the present study we carried out transactivation experiments of the mutagenized delta-globin gene promoter by introducing an EKLF expressing construct in erythroid cells. Constructs containing the proximal but not those bearing the distal CACCC element are transactivated. Our results indicate that the proximal CACCC box and, to a lesser extent, also the distal box have a role in the regulated stage specific expression of a beta-like globin gene, and show that the insertion of a single CACCC motif in the delta-globin gene promoter is sufficient to increase its activity. Nevertheless only the delta globin gene promoter containing the proximal CACCC element is able to compete with the wt beta globin gene promoter in the adult erythroid environment. These findings have potential relevance for the future prospective treatment of inherited hemoglobinopathies based on the conversion of the low functioning delta-globin gene into a high functioning beta-like globin gene.

Molecular, haematological and clinical studies of a silent beta-gene C-->G mutation at 6 bp 3' to the termination codon (+1480 C-->G) in twelve Greek families

We report the clinical, haematological, biosynthetic and molecular data of 12 beta-thalassaemia intermedia patients and their heterozygous parents, all of whom carried a rare C-->G mutation at nucleotide position 6 3' to the termination codon (term. cd +6 C-->G) in the 3' untranslated region (3' UTR) of the beta-globin gene (+1480 C-->G). This mutation has been reported previously in a single beta-thalassaemia intermedia patient of Greek origin. The 12 patients of the present study had the clinical phenotype of mild non-transfusion-dependent thalassaemia intermedia, preserving haemoglobin levels around 9 g/dl and haemoglobin F levels <25%. All were compound heterozygotes for the +1480 C-->G mutation and common severe beta-thalassaemia mutations. The haematological parameters of heterozygotes with this mutation were within the normal range with the exception of a slightly raised alpha/non-alpha-globin chain synthesis (1.2-1.9). mRNA analysis demonstrated a 20-34% reduction in mRNA levels associated with the +1480 C-->G mutation compared to normal beta-globin alleles. These findings confirm that the C-->G mutation at position 6 3' to the termination codon is a mild beta-thalassaemia mutation causing slight reduction in beta-globin mRNA levels and beta-globin chain synthesis. It becomes clinically relevant when co-inherited with a severe beta-thalassaemia mutation in trans.

Beta-thalassaemia

A complete spectrum of genetic lesions affecting the beta-globin gene giving rise to a complete spectrum of phenotypic severity is described. Although most of the molecular lesions involve the structural beta gene directly, some down regulate the gene through in-cis effects at a distance while trans-acting factors are implicated in a few cases. The remarkable phenotypic diversity can be related ultimately to the degree of alpha-globin-beta-globin chain imbalance and arises from variability of mutations affecting the beta gene itself and from interactions with other genetic loci, such as the alpha- and gamma-globin genes. The presence of other interacting loci is implicated by their interactions in increasing gamma gene expression or by an increased proteolytic capacity of the erythroid precursors. It is hoped that observations from the genotype-phenotype relationship might form the basis for a comprehensive diagnostic database that will be useful not only for genetic counselling and prenatal diagnosis but also for providing prognostic information for decision making in bone marrow transplantation and gene therapy programmes in the future. However, it is clear from recent analyses that, apart from the two categories of triplicated alpha genes with heterozygous beta-thalassaemia and inheritance of mild beta(+)-thalassaemia alleles, it is still not possible to predict consistently phenotype from alpha and beta genotypes alone owing to the influence of the other modulating factors, some implicated (such as inheritance of hereditary persistence of fetal haemoglobin) and others as yet unidentified.