A new genetic variant of beta-thalassaemia

Molecular characterization of a novel homozygous deletion in β-globin cluster causing (δβ)0-Thalassemia among Tunisian family

BACKGROUND

Deletions in the β-globin cluster are uncommon and cause thalassemia (thal) with hereditary persistence of fetal hemoglobin. They constitute a heterogenous group of disorders characterized by absent or reduced synthesis of adult hemoglobin (Hb A) and increased synthesis of fetal hemoglobin (Hb F). Although the clinical severity of these disorders are asymptomatic owing to the increased Hb F levels, the molecular basis is very heterogenous due to the large deletions in the β-globin cluster spanning both HBD and HBB genes. Here, we describe a Tunisian family carrying a novel deletion mutation causing (δβ)°-thalassemia.

METHODS

The amounts of hemoglobin fractions were measured by capillary electrophoresis of hemoglobin. Amplification and sequencing of different regions on the β-gene cluster were performed by Sanger method.

RESULTS

Family study and genetic analysis revealed a large deletion mutation in the β-globin cluster of 14.5 kb (NG_000,007.3:g. 58,253 to g.72837del14584) at the homozygous state in the patient and at heterozygous state at the other members of the family. This deletion removes the HBD and HBB genes.

CONCLUSIONS

In our knowledge, this new large deletion is described for the first time in the Tunisian population and in the world, designed Tunisian(δβ)⁰ in Ithanet database (IthaID: 3971). Therefore, it is important to identify the deletion leading to δβ-thalassemia carriers at the molecular level, to highlight the importance of recognizing the clinical features and implementing appropriate testing to clarify the diagnosis and manage the condition.

Whole genome sequence-based haplotypes reveal a single origin of the 1393 bp HBB deletion

BACKGROUND

Mutations of HBB give rise to two prevalent haemoglobin disorders-sickle cell disease (SCD) and β-thalassaemia. While SCD is caused by a single base substitution, nearly 300 mutations that downregulate expression of HBB have been described. The vast majority of β-thalassaemia alleles are point mutations or small insertion/deletions within the HBB gene; deletions causing β-thalassaemia are very rare. We have identified three individuals with haemoglobin Sβ0-thalassaemia in which the β0-thalassaemia mutation is caused by a large deletion.

OBJECTIVE

To use whole genome sequence data to determine whether these deletions arose from a single origin.

METHODS

We used two approaches to confirm unrelatedness: pairwise comparison of SNPs and identity by descent analysis. Eagle, V.2.4, was used to generate phased haplotypes for the 683 individuals. The Neighbor-Net method implemented in SplitsTree V.4.13.1 was used to construct the network of haplotypes.

RESULTS

All three deletions involved 1393 bp, encompassing the β-promoter, exons 1 and 2, and part of intron 2, with identical breakpoints. The cases were confirmed to be unrelated. Haplotypes based on 29 SNPs in the HBB cluster showed that the three individuals harboured different βS haplotypes. In contrast, the haplotype harbouring the 1393 bp deletion was the same in all three individuals.

CONCLUSION

We suggest that all the reported cases of the 1393 bp HBB deletion, including the three cases here, are likely to be of the same ancestral origin.

Molecular basis of β thalassemia and potential therapeutic targets

The remarkable phenotypic diversity of β thalassemia that range from severe anemia and transfusion-dependency, to a clinically asymptomatic state exemplifies how a spectrum of disease severity can be generated in single gene disorders. While the genetic basis for β thalassemia, and how severity of the anemia could be modified at different levels of its pathophysiology have been well documented, therapy remains largely supportive with bone marrow transplant being the only cure. Identification of the genetic variants modifying fetal hemoglobin (HbF) production in combination with α globin genotype provide some prediction of disease severity for β thalassemia but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered. Nonetheless, genetic studies have been successful in characterizing the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation. BCL11A has been established as a quantitative repressor, and progress has been made in manipulating its expression using genomic and gene-editing approaches for therapeutic benefits. Recent discoveries and understanding in the mechanisms associated with ineffective and abnormal erythropoiesis have also provided additional therapeutic targets, a couple of which are currently being tested in clinical trials.

Genetic Basis and Genetic Modifiers of β-Thalassemia and Sickle Cell Disease

β-thalassemia and sickle cell disease (SCD) are prototypical Mendelian single gene disorders, both caused by mutations affecting the adult β-globin gene. Despite the apparent genetic simplicity, both disorders display a remarkable spectrum of phenotypic severity and share two major genetic modifiers-α-globin genotype and innate ability to produce fetal hemoglobin (HbF, α₂γ₂).This article provides an overview of the genetic basis for SCD and β-thalassemia, and genetic modifiers identified through phenotype correlation studies. Identification of the genetic variants modifying HbF production in combination with α-globin genotype provide some prediction of disease severity for β-thalassemia and SCD but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered.Nonetheless, genetic studies have been successful in characterizing some of the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation.

The molecular basis of β-thalassemia

The β-thalassemias are characterized by a quantitative deficiency of β-globin chains underlaid by a striking heterogeneity of molecular defects. Although most of the molecular lesions involve the structural β gene directly, some down-regulate the gene through distal cis effects, and rare trans-acting mutations have also been identified. Most β-thalassemias are inherited in a Mendelian recessive fashion but there is a subgroup of β-thalassemia alleles that behave as dominant negatives. Unraveling the molecular basis of β-thalassemia has provided a paradigm for understanding of much of human genetics.

The importance of β globin deletion analysis in the evaluation of patients with β thalassemia

INTRODUCTION

Beta globin deletion/duplication analysis may serve as a useful adjunct to sequence analysis. Our purpose was to develop a robust assay for beta globin deletion/duplication analysis and determine its role in evaluating patients with beta thalassemia.

METHODS

A single tube semi-quantitative fluorescent PCR assay capable of detecting deletions and duplications in the beta globin cluster and the associated locus control region (LCR) was developed and validated.

RESULTS

Six hundred seventy one de-identified samples submitted for beta globin sequence analysis were tested for deletions and duplications of the beta globin cluster. Twenty-two deletions were detected (3%, 22/671). Seventeen of the 22 (82%) deletion samples were negative for mutations in the whole gene sequencing assay. For 5 of the samples, homozygous point mutations were inferred by beta globin sequencing. Among the deletions detected, 11 (50%) involved only the beta globin gene (5 covering the entire gene, 2 spanning the 5' end of the gene and 4 encompassing the 3' end of the gene). Ten samples (45%) were heterozygous delta-beta deletions spanning both the delta globin and beta globin genes. One patient with a single deletion had Hb Lepore.

CONCLUSION

Beta globin deletion/duplication analysis is necessary to correctly identify the genotype in some patients being evaluated for beta thalassemia.

Gene regulation and deregulation: a beta globin perspective

The study of the beta globin gene has provided great insights into the mechanisms of gene regulation and expression. In this review, we consider the normal regulation and expression of the beta globin gene and illustrate how the various steps may be affected, providing a basis for understanding the molecular pathophysiology of beta thalassemia. Mutations causing beta thalassemia can be classified as beta0 or B+ according to whether they abolish or reduce the production of beta globin chains. The vast majority of beta thalassemia is caused by point mutations, mostly single base substitutions, within the gene or its immediate flanking sequences. Rarely, beta thalassemia is caused by major deletions of the beta globin cluster. All these mutations behave as alleles of the beta locus but in several families the beta thalassemia phenotype segregates independently of the beta globin complex, and are likely to be caused by mutations in trans-acting regulatory factors.

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.

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.

Molecular characterization of a novel 10.3 kb deletion causing beta-thalassaemia with unusually high Hb A2

A family of Asian-Indian descent has a variant form of beta-thalassaemia characterized by unusually high levels of Hb A2 in the heterozygous state. The propositus who is homozygous for the mutation has thalassaemia intermedia. Restriction endonuclease mapping suggested the presence of a 10.3 kilobase (kb) deletion removing the whole of the beta-globin gene. Subsequently, molecular analysis was performed by directly sequencing a specifically amplified region of genomic DNA. A 10329 basepair deletion was precisely defined which results in the loss of the 5' beta promoter region and the entire beta-globin gene. The deletion extends from 3011 bp 5' to the mRNA cap site to an L1 repeat element downstream of the beta-globin gene and is very similar to the 12.6 kb deletion of Dutch beta zero-thalassaemia. In common with four other mutations, both these deletions remove the 5' promoter region of the beta gene and all are associated with unusually elevated levels of Hb A2 in the heterozygous state.

Thalassemia: genotypes and phenotypes

The large degree of phenotypic heterogeneity of thalassemia can now be related to the underlying genomic defects. This information has accumulated rapidly over the last years through the recent advances in molecular technology. The list of main types of thalassemia (alpha or beta) that can be differentiated includes several gene deletions (complete or partial) and point mutations (or very short deletions). These occur within the genes or across the flanking DNA sequences and apparently interfere with the expression of these genes. From a quantitative point of view, the severity of the condition is directly related to the amount of functional globin chain mRNA which is made available to the ribosomes; this may vary from zero (gene deletions, frameshift, non-sense mutations or mutations at the splice-junction nucleotides) to very little (mostly hnRNA processing mutants) or to slightly subnormal (transcriptional mutants, mutations resulting in cryptic site activation or in defective cleavage of the poly-A tail). A few hyper-unstable globin chains also produce a thalassemic phenotype. This pattern is straightforward in the alpha-thalassemias. In the beta-thalassemias, the decreased beta-chain synthesis reflects the available mRNA, but the phenotypic expression depends also on the ability of the patient to reactivate gamma-chain synthesis and complement the red cell content with hemoglobin F.

Clinical and haematological evaluation of beta thalassaemia intermedia with increased Hb F and Hb A2 in heterozygotes: beta thalassaemia intermedia I

Family studies were performed in 10 patients from seven different families with homozygous beta zero thalassaemia intermedia and in three patients with homozygous beta+ or compound heterozygous beta+ and beta zero thalassaemia intermedia. In nine of the 10 families at least one of the parents was found to have raised Hb A2 and Hb F. In the heterozygotes with increased Hb A2 and Hb F, the means of Hb F and MCV were significantly higher than those observed in regular Hb A2 thalassaemia heterozygotes. However, the severity of imbalance in in vitro haemoglobin synthesis was similar in these two groups. The imbalance in the alpha/non-alpha synthetic ratio was heterogeneous in the patients, being 2.1 and 4.0. Segregation of the raised Hb F from the Hb A2 beta thalassaemia determinant was found to be possible in only one of the 36 heterozygotes. This may exclude the possibility of the presence of an additional determinant responsible for the activation of the gamma chain. The G gamma/A gamma ratio of Hb F was that of the fetal type (G gamma was between 50 and 71% of the total gamma chain). The A gamma T variant of gamma chain was not detected in cis of the beta zero thalassaemia determinant characterised by increased Hb F and Hb A2. A retrospective study of 180 patients with beta thalassaemia and their parents indicated that the combined rise in Hb A2 and Hb F was more common in the heterozygous parents (11 out of 30 parents) of the patients with beta zero thalassaemia than it was in the parents of patients with beta+ thalassaemia (three out of 140 parents). The presence of increased Hb A2 and Hb F in the heterozygote may in some cases determine the relative mildness of the disease.

Dutch beta 0-thalassaemia: a 10 kilobase DNA deletion associated with significant gamma-chain production

A unique beta 0-thalassaemia in a Dutch family results in fetal haemoglobin expression comparable to that of delta 0 beta 0-thalassaemia. Haemoglobin analysis and restriction endonuclease mapping studies of DNA suggest that the beta-globin gene is entirely deleted, but that the delta-globin gene is intact. The 5' break point of the deletion is 3-4 kilobases 3' to the delta-globin gene, while the 3' break point is 6-7 kilobases 3' to the beta-globin gene (relative to the normal DNA restriction map). The result is a approximately 10 kilobase deletion of DNA whose 3' end point may lie very close to that for one delta 0 beta 0-thalassaemia, within a cluster of Kpn I-family repetitive sequences. The Dutch beta 0-thalassaemia deletion is thus the shortest one which, in the absence of additional chromosomal rearrangements, results in enhancement of gamma-chain synthesis above that seen for haemoglobin Lepore. These data support the hypothesis that the region of DNA 3' to the beta-globin gene may be important to the developmental regulation of fetal gamma versus adult beta chain production.

Unusual combination of genetic defects in a Sicilian boy: G gamma delta beta thalassemia, G gamma A gamma heterocellular HPFH, beta (0) thalassemia, and albinism

We describe the clinical and hematological findings in a 5-year-old boy with G gamma A gamma delta beta thalassemia, a G gamma A gamma heterocellular form of HPFH, beta(0) thalassemia, and albinism. Clinically he manifested only the characteristics of beta-thalassemia trait and not the typical picture of doubly heterozygous beta thal/delta beta thal. The simultaneous presence of heterocellular HPFH improves gamma chain synthesis, thus reducing the alpha chain excess. It is also possible that gene expression can be modified by the presence of other genetic anomalies.

Spinal cord compression in a new homozygous variant of beta-thalassemia. Case report

✓ A patient is reported with a new genetic variant of beta-thalassemia, who suffered from a progressive partial transverse cord lesion caused by epidural hematopoietic tissue. He recovered after partial surgical removal of this tissue and subsequent radiotherapy.

The clinical phenotype of beta and delta beta thalassemias in Greece

Based on precise evaluation of hematological findings and clinical manifestations, the relationship between genotype and clinical phenotype was studied in 475 Greek patients with beta and delta beta thalassemias. Almost all known genotypes are included in this series, but the most frequent was homozygous beta th high A2 (71.6%), beta th/beta th silent (7.4%), beta th/delta beta oth high F (6.3%) and beta th/beta th Dutch (6.3%). In general, the phenotype was related to the genotype, though clinical heterogeneity was detected among patients with the same genotype. The severe type of thalassemia major was most commonly found in homozygous beta th patients mainly of beta o/beta o and beta o/beta + genotypes while homozygous beta + patients had milder clinical manifestation. Furthermore a small group of patients, characterized as homozygous beta ++ (HbF less than 30%) had mild thalassemia intermedia. In addition mild thalassemia intermedia was principally related with homozygous delta beta oth, and compound heterozygous beta th/beta th silent I, and less frequently with other genotypes such as compound heterozygous with beta th/beta th Dutch, beta th/beta th silent II, beta th/delta beta oth high F or Lepore. It was shown that precise genetic characterization and clinical evaluation is of primary importance in predicting the prognosis and formulating the proper treatment for the individual patient with thalassemia.

Interaction between homozygous beta (0) thalassaemia and the Swiss type of hereditary persistence of fetal haemoglobin

The interaction between beta(0) thalassemia and an heterocellular form of hereditary persistence of fetal haemoglobin (HPFH), presumably of the Swiss type, has been studied in three generations of a family in which both traits occur. The haematological parameters and the segregation of the two characters in the family suggest that the propositus, a 52-year-old male from southern Sardinia, is homozygous for beta(0) thalassemia and carrier of the HPFH. In spite of the complete suppression of adult haemoglobin synthesis, the patient is not anaemic and shows only morphological abnormalities of the red cells associated with a moderate decrease of the erythrocyte life span. Studies of the synthesis of haemoglobin chains in vitro have revealed only a mild degree of unbalance in the propositus, with a gamma/alpha ratio of 0.67, and a very slight unbalance in a 3-year-old child heterozygous for beta thalassaemia and HPFH. Preliminary analysis of the linkage between this kind of heterocellular HPFH and the beta Hb locus has been performed, utilizing all the suitable families reported in the literature. Although positive lod scores (1.535) have been obtained at a recombination fraction of 0.20, the data available are not sufficient to conclude in favour or against the linkage between the beta Hb locus and the heterocellular type of HPFH.

beta Thalassemia associated with increased HB F production. Evidence for the existence of a heterocellular hereditary persistence of fetal hemoglobin (HPFH) determinant linked to beta thalassemia in a southern Italian population

A family has been observed in which a beta thalassemia determinant is inherited over three generations together with high Hb F level (8-12%) and increased number of fetal-hemoglobin-containing-cells (F-cells). The values of red cell indices and globin chain synthesis ratios, yet typical of beta thalassemia, were significantly shifted to the normal values when compared with those of typical beta thalassemia heterozygotes belonging to the same family group. The occurrence in these individuals of a heterocellular hereditary persistence of fetal hemoglobin (HPFH) determinant and its linkage relationship with the beta thalassemia is discussed. In the third generation two adult individuals were beta thalassemia homozygotes having inherited a beta thalassemia determinant from one parent and a beta thalassemia together with the HPFH determinant from the other. They showed an extremely mild clinical condition, and 11-12 g/dl of mainly Hb F without having ever required blood transfusions. Virtually all the red cells were F-cells in both subjects. The importance of the coexistence of HPFH determinants capable of increasing the size of the F-cell population in patients affected by homozygous thalassemia is discussed, considering the sensible benefit which derives from enhanced Hb F production in this syndrome.

Overview: mechanisms of the regulation of hemoglobin synthesis at the cellular level

The concept that has emerged from our experiments and those of others is that erythroid stem cells are committed to undergo a program of erythroid differentiation with respect to the ultimate hemoglobin phenotype of their progeny erythrocytes. A clear distinction can be drawn between the switch from Hb A (or Hb F) to Hb C in sheep and the switch from Hb F to adult hemoglobin in humans. The former appears to be regulated in a relatively late erythroid stem cell with characteristics of CFU-E. In contrast, the CFU-E found in adult sheep bone marrow from animals that lack the beta C gene appear to be preprogrammed to produce only adult hemoglobin. Fetal stem cells may be induced to synthesize Hb C within a time frame that is similar to that seen in cultures of adult bone marrow. Thus, a common mechanism modulating the potential for expression of this gene and commitment of erythroid stem cells with respect to Hb C production in progeny erythroblasts seems quite likely. Again fetal CFU-E and BFU-E in animals lacking the beta C gene appear to be, for the most part, committed toward producing erythroblasts making Hb F. Further analysis will be required to determine at exactly which stage of stem cell differentiation this programming occurs and also the factors that are important in modulating the potential for fetal and adult hemoglobin synthesis.

Beta-thalassaemia of clinical significance in adult Jamaican Negroes

Over a 9-year period, three adult Negro patients with beta-thalassaemia of clinical significance were recognized out of approximately 185 000 new adult patients attending the University Hospital. These patients, aged 15-58 years, have clinical and haematological characteristics within the spectrum of beta-thalassaemia intermedia; which in this paper refers to phenotypes resulting from defects in beta-chain synthesis clinically intermediate between classical Cooley's anaemia and beta-thalassaemia trait, genetic classification being dependent on family study. Family studies established the presence of two beta-thalassaemia genes conclusively in one case (proposita, family A); presumptively in another (propositus, family C); while in the remaining subject (proposita, family B), who has two similarly affected siblings, homozygosity is suspected, but not proven by family study. In simultaneous 59Fe and 51 Cr studies, estimates of effective erythropoiesis are in reasonable agreement with measurements of red cell destruction.

Spinal cord compression due to extramedullary hematopoiesis in homozygous thalassemia. Case report

The authors report a case of homozygous thalassemia in which a mass of hematopoietic tissue in the vertebral canal caused spastic paraparesis. Surgical removal of the tissue plus radiotherapy were successful. The pathological findings indicated direct extension of hematopoietic tissue from the adjacent bone marrow into the epidural space of the vertebral canal.

Chimpanzee foetal haemoglobin: structure and heterogeneity of the gamma chain

The amino acid compositions of soluble tryptic and chymotryptic peptides of the gamma chain of chimpanzee foetal haemoglobin have been determined. The peptides, accounting for all 146 residues of the gamma chain, were found to be identical in composition to the corresponding human gamma chain peptides. As in man, position gamma 136 can be occupied by glycine (G gamma chain) as well as alanine (A gamma chain). The ratio of G gamma to A gamma chains in the infant chimpanzee is approx. 2:1, and in the adult approx. 1:2.