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

Diagnostic Performance of 10 Mathematical Formulae for Identifying Blood Donors with Thalassemia Trait

OBJECTIVE

To compare the diagnostic performance of 10 mathematical formulae for identifying thalassemia trait in blood donors.

METHODS

Compete blood counts were conducted on peripheral blood specimens using the UniCel DxH 800 hematology analyzer. Receiver operating characteristic curves were used to evaluate the diagnostic performance of each mathematical formula.

RESULTS

In the 66 donors with thalassemia and 288 subjects with no thalassemia analyzed, donors with thalassemia trait had lower values for mean corpuscular volume and mean corpuscular hemoglobin than subjects without thalassemia donors (77 fL vs 86 fL [P < .001]; 25 pg vs 28 pg [P < .001]). The formula developed by Shine and Lal in 1977 showed the highest area under the curve value, namely, 0.9. At the cutoff value of <1812, this formula had maximum specificity of 82.35% and sensitivity of 89.58%.

CONCLUSIONS

Our data indicate that the Shine and Lal formula has remarkable diagnostic performance in identifying donors with underlying thalassemia trait.

Disrupting the adult globin promoter alleviates promoter competition and reactivates fetal globin gene expression

The benign condition hereditary persistence of fetal hemoglobin (HPFH) is known to ameliorate symptoms of co-inherited β-hemoglobinopathies, such as sickle cell disease and β-thalassemia. The condition is sometimes associated with point mutations in the fetal globin promoters that disrupt the binding of the repressors BCL11A or ZBTB7A/LRF, which have been extensively studied. HPFH is also associated with a range of deletions within the β-globin locus that all reside downstream of the fetal HBG2 gene. These deletional forms of HPFH are poorly understood and are the focus of this study. Numerous different mechanisms have been proposed to explain how downstream deletions can boost the expression of the fetal globin genes, including the deletion of silencer elements, of genes encoding noncoding RNA, and bringing downstream enhancer elements into proximity with the fetal globin gene promoters. Here we systematically analyze the deletions associated with both HPFH and a related condition known as δβ-thalassemia and propose a unifying mechanism. In all cases where fetal globin is upregulated, the proximal adult β-globin (HBB) promoter is deleted. We use clustered regularly interspaced short palindromic repeats-mediated gene editing to delete or disrupt elements within the promoter and find that virtually all mutations that reduce ΗΒΒ promoter activity result in elevated fetal globin expression. These results fit with previous models where the fetal and adult globin genes compete for the distal locus control region and suggest that targeting the ΗΒΒ promoter might be explored to elevate fetal globin and reduce sickle globin expression as a treatment of β-hemoglobinopathies.

Computational Analysis of Protein Structure Changes as a Result of Nondeletion Insertion Mutations in Human β-Globin Gene Suggests Possible Cause of β-Thalassemia

Beta-thalassemia is described as a group of hereditary blood disorders characterized by abnormalities in the synthesis of beta chains of hemoglobin. These anomalies result in different phenotypes ranging from moderate to severe clinical symptoms to no symptoms at all. Most of the defects in hemoglobin arise directly from the mutations in the structural β-globin gene (HBB). Recent advances in computational tools have allowed the study of the relationship between the genotype and phenotype in many diseases including β-thalassemia. Due to high prevalence of β-thalassemia, these analyses have helped to understand the molecular basis of the disease in a better way. In this direction, a relational database, named HbVar, was developed in 2001 by a collective academic effort to provide quality and up-to-date information on the genomic variations leading to hemoglobinopathies and thalassemia. The database recorded details about each variant including the altered sequence, hematological defects, its pathology, and its occurrence along with references. In the present study, an attempt was made to investigate nondeletion mutations in the HBB picked up from HbVar and their effects using the in silico approach. Our study investigated 12 nucleotides insertion mutations in six different altered sequences. These 12 extra nucleotides led to the formation of a loop in the protein structure and did not alter its function. It appears that these mutations act as ‘silent' mutations. However, further in vitro studies are required to reach definitive conclusions.

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.

Phenotype of mutations in the promoter region of the β-globin gene

BACKGROUND

β⁺-Thalassaemia is characterised by reduced production of β chains, which decrease can be caused by mutations in the promoter region (CACCC or TATA box), and is classified as mild or silent depending on the extent of β-globin chain reduction. In both cases, homozygotes or compound heterozygotes for these mutations usually have thalassaemia intermedia. Frequently the diagnosis is made in adulthood or even in old age. A total of 37 alterations in the promoter region have been described so far.

AIMS

In this report we describe the mutations found in the promoter region of the β-globin gene in a single hospital in Madrid.

METHODS

Between 1998 and 2015, more than 9000 blood samples were analysed for full blood count and underwent haemoglobin electrophoresis and high performance liquid chromatography. Genetic analysis of the β and Gγ-globin genes was carried out by automatic sequencing and, in the case of α genes, by multiplex PCR.

RESULTS

35 samples showed mutation in the promoter region of the β-globin gene, with a total of six different mutations identified: one in the distal CACCC box, two in the proximal CACCC box, three in the ATA box.

CONCLUSIONS

Any alterations in the proximal CACCC and TATA boxes lead to a moderate decrease in synthesis of the β-globin chain, which has been demonstrated in cases of thalassaemia intermedia that have presented in the second decade of life with a moderate clinical course.

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 Problem of Borderline Hemoglobin A2 Levels in the Screening for β-Thalassemia Carriers in Sardinia

BACKGROUND

The increase in HbA2 is the most important parameter for the identification of thalassemia carriers. However, in routine screening for hemoglobinopathies, some cases are difficult to classify because the level of HbA2 is not typically elevated. In this work, we report the results of a molecular investigation on a cohort of subjects with borderline HbA2.

METHODS

All subjects with a β-thalassemia carrier partner and a borderline percentage level of HbA2 were investigated for the presence of a pathological mutation in the β-globin gene. All negative subjects were screened for both the KLF1 mutation and the presence of ααα/ or αααα/ alleles. The subjects with reduced MCV and/or MCH were also screened for deletional and nondeletional α-globin gene defects.

RESULTS

Various β-globin mutations and KLF1 gene defects are the most common genetic determinants responsible for this phenotype in our population.

CONCLUSION

KLF1 mutations are important in a screening program for hemoglobinopathies. An increase in HbF in association with borderline HbA2 levels is a useful but not exclusive marker that suggests the investigation of this gene. On the basis of our findings, we are able to suggest the molecular procedure to use in a population characterized by a high prevalence of thalassemia carriers.

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.

Genetic Modifiers in β-Thalassemia Intermedia: A Study on 102 Iraqi Arab Patients

To determine the molecular basis of β-thalassemia intermedia (TI) and the contribution of the three hemoglobin F (HbF) quantitative trait loci (QTLs) on chromosomes 11, 2, and 6 to the milder phenotype, a total of 102 Iraqi Arab patients with TI were studied. The β and α genotypes as well as HBG2 g. 158 C>T (rs7482144), BCL11A (rs1427407 and rs10189857), and HBS1L-MYB (rs28384513 and rs9399137) by multiplex polymerase chain reaction and reverse hybridization were studied. A total of 21 different β-thalassemia mutations arranged in 35 different genotypes were identified. The genotypes encompassed β(+)/β(+) mutations in 33 cases, β(+)/β(0) in 17 cases, β(0)/β(0) in 47 cases, β(0)/wild type in 3 and β(0)/Hb E in 2 cases. The most common was IVS-II-1 (G>A)/IVS-II-1 (G>A), followed by IVS-I-6 (T>C)/IVS-I-6 (T>C) and IVS-I-110 (G>A)/IVS-I-110 (G>A), in 31.4%, 17.6%, and 6.9%, respectively. Alpha-thalassemia mutations were found in 15.2% of those homozygous for the β-mutations, while α gene triplication was identified in all three heterozygotes. Of the five QTLs tested, only rs7482144 and rs10189857 were significantly associated with β(0)/β(0) when compared to β(+)/β(+), with odds ratios of 6.4 (95% confidence interval [CI] 2.9-14.0) and 3.2 (95% CI 1.2-8.6), respectively. In conclusion, this study has demonstrated that among Iraqi patients with thal intermedia, the main contributors to the milder phenotype were β(+) alleles, XmnI polymorphism, and BCL11A (rs10189857), while other QTLs on chromosomes 2 and 6, as well as alpha-thalassemia, were not significantly relevant.

Heterozygosity for deletion of hypersensitive site 3 in the human locus control region has an unexpected minor effect on red cell phenotype

The locus control region (LCR) is a genetic region that regulates the expression of the β-globin locus (HBB locus). This region is composed of several DNase I hypersensitive sites (HSs) in which the regulatory functions of the LCR may reside. To date, some individuals bearing deletions of several HSs or even the complete LCR have been described. Although the globin genes of the HBB locus are intact, most of these patients suffer thalassemia due to the reduced expression of such genes. The LCR and the HSs forming it have been thoroughly studied in different genetic models. However, seemingly contradictory results are often obtained. Here, we describe the first deletion found in humans exclusively affecting the HS3 element of the LCR. The adult carrying this deletion shows very mild hematological modifications, indicating that HS3 deletion does not severely impair the β-gene expression. Our results also reveal limitations of the murine models when studying the native mouse genes for understanding human diseases like thalassemias.

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.

Molecular heterogeneity of beta-thalassemia in Algeria: how to face up to a major health problem

This study concerns the molecular characterization of beta-thalassemia (beta-thal) alleles in 210 chromosomes. In the studied population, mutations were detected in 98% of the beta-thalassemic chromosomes. Twenty-one molecular defects have been found, where the five dominant mutations, IVS-I-110 (G>A), nonsense mutation at codon 39 (C>T), the frameshift codon (FSC) 6 (-A), IVS-I-1 (G>A), and IVS-I-6 (T>C), account for 80% of the independent chromosomes. Among the remaining alleles, 16 different mutations were identified, half of them being described for the first time in Algeria. These include the -101 (C>T) and the -90 (C>T) mutations in the distal and proximal promoter elements, respectively, the FSC 8 (-AA), IVS-I-5 (G>T), IVS-I-128 (T>G), FSC 47 (+A), IVS-II-1 (G>A), and the substitution in the polyadenylation signal (poly A) site AATAAA>AATGAA. Haplotype analyses on rare variants were performed. The possible origin of these mutations either by founder effect or by migrations is discussed, and raises the question of an adequate strategy to be used adapted to socio-economical status.

A novel mutation of the beta-globin gene promoter (-102 C>A) and pitfalls in family screening

We describe a family with beta-thalassemia in which several pitfalls of genetic diagnoses were present. These include coherent family phenotypes with discrepancies in molecular findings because of nonpaternity, and a false beta-globin gene homozygous genotype due to a large deletion in the second locus. These findings underline the difficulties of family genetic studies and the need for tight relationship between professionals involved in laboratory studies and those in-charge of the clinical follow-up and genetic counselling. In this family, we also report a new silent beta-thalassemia mutation, -102 (C>A), in the distal CACCC box of the beta-globin gene promoter.

Large-scale population genetic analysis for hemoglobinopathies reveals different mutation spectra in central Greece compared to the rest of the country

We have undertaken a large population screening study to identify the molecular basis of hemoglobinopathies in the central Greece region. A total of 845 unrelated beta-thalassemia patients and alpha-, beta-, and deltabeta-thalassemia carriers have been recruited and screened for mutations in the alpha- and beta-globin gene clusters. The alpha(-MED) deletion and the Turkish inversion/deletion are the most frequent genetic rearrangements leading to alpha- and deltabeta-thalassemia respectively, contrary to the situation in the rest of the country, while the beta -101 (C>T) promoter mutation is surprisingly frequent in the central part of Greece. Our data indicate that determination of mutation frequencies in different regions is vital for accurate provision of genetic services and counseling and for precise estimation of genetic diversity.

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.

Pathophysiology of beta thalassemia--a guide to molecular therapies

The central mechanism underlying the pathophysiology of the beta thalassemias can be related to the deleterious effects of imbalanced globin chain synthesis on erythroid maturation and survival. An imbalance of the alpha/non-alpha globin chains leads to an excess of unmatched alpha globin which precipitates out, damaging membrane structures leading to accelerated apoptosis and premature destruction of the erythroid precursors in the bone marrow (ineffective erythropoiesis). Close observation of the genotype/phenotype relationships confirms the pathophysiological mechanism and provides clues to molecular therapies, all of which aim to reduce the alpha/non-alpha chain imbalance. They include inheritance of the milder forms of beta thalassemia, co-inheritance of alpha thalassemia, or genetic factors (quantitative trait loci, QTLs) for increasing gamma globin expression. Currently, the most promising molecular therapeutic approaches include increasing beta globin gene expression by stem cell gene therapy and increasing gamma globin expression using pharmacological agents or by transduction of the gamma globin genes.

Mutations associated with beta-thalassemia intermedia in Kuwait

OBJECTIVE

To identify the beta-globin gene mutations associated with beta-thalassemia (beta-thal) intermedia in Kuwait.

SUBJECTS AND METHODS

Eighteen patients from 13 unrelated families, mean age 12.7 +/- 8.1 years, range 4-31 years, were involved in the study. They did not require regular blood transfusion. Complete blood count and cation exchange high-performance liquid chromatography hemoglobin quantitation were carried out using standard techniques. Beta-thal mutations were identified with a combination of PCR amplification, allele- specific oligonucleotide hybridization or direct DNA sequencing. The patients were also screened for the alpha2-globin gene (-3.7 kb) deletion.

RESULTS

Of the 13 families, 4 were homozygous for the IVS-I-II (G-->A) and 4 for the IVS-I-6 (T-->C) mutations, while 1 each was a compound heterozygote for the following mutation combinations: CD 8 (-AA) and -101 (C-->T); IVS-I-6 (T-->C) and CD 19 (A-->G); IVS-II-1 (G-->A) and -28 (A-->C); IVS-I-110 (G-->A) and deltabeta0 deletion. Therefore, homozygosity for two typically mild mutations (IVS-II-1 and IVS-I-6) accounted for 61% of the genotypes in our patients.

CONCLUSION

Our results indicate that screening should commence with these two common alleles in Kuwaiti patients presenting with beta-thal syndrome. Early identification of intermedia patients will avoid the complications following an unnecessary hypertransfusion program.

Modifier Genes and Oligogenic Disease

It is now increasingly apparent that modifier genes have a considerable role to play in phenotypic variations of single-gene disorders. Intrafamilial variations, altered penetrance, and altered severity are now common features of single gene disorders because of the involvement of several genes in the expression of the disease phenotype. Oligogenic disorders occur because of a second gene modifying the action of a dominant gene. It is now certain that cancer occurs due to the action of the environment acting in combination with several genes. Although modifier genes make it impossible to predict phenotype from the genotype and cause considerable difficulties in genetic counseling, they have their uses. In the future, it is hoped that modifier genes will allow us to understand cell and protein interactions and thus allow us to understand the pathogenesis of disease.

Spectrum of beta thalassemia mutations and HbF levels in the heterozygous Moroccan population

A comprehensive hematological and molecular analysis of 57 beta thalassemic heterozygotes, 28 homozygotes, 18 double heterozygotes, 3 compound heterozygotes beta thal/beta S and one compound heterozygote beta thal/Hb Newcastle, in 46 Moroccan families with at least one beta thalassemia patient is reported. Six major mutations: beta(0)39 (C-->T), beta(0)FsCD8(-AA), beta(+)IVS1,nt6 (T-->C) and beta(0)IVS1,nt1 (G-->A), beta(0)FsCD6 (-A) and beta(+)-29 (A-->G) cap site account for 75% of the 86 independent beta thal chromosomes studied. For the first time, an extensive mutation/haplotype study has been performed on the Moroccan population, and data are consistent with the geographical location of the country and historical links with both the Mediterranean and the Sub-Saharan Africa communities. Despite the heterogeneous spectrum of mutations, good genetic counseling can be offered to the carrier population. This study focuses on the analysis of fetal hemoglobin levels in beta thalassemic heterozygotes and its correlation with beta globin cluster polymorphic markers in this population. Fetal hemoglobin levels in heterozygotes vary from trace quantities to 17.9% (2.38 g/dl) of total hemoglobin in the adult. No statistically significant correlation was found, either between genders and HbF levels, or between the mutation and the HbF level, with the exception of mutation beta(0)FSCD6(-A). We have examined the alpha globin genotype and the beta globin genotype of heterozygotes, namely, the extended haplotype, which includes the XmnI site at -158 bp of the Ggamma gene and the microsatellite (AT)(x)T(y) at -540 bp of the beta globin gene. In this sample, we confirm the existence of linkage disequilibrium between the C-->T variation at -158 bp of Ggamma globin gene (XmnI(+)) and Orkin's haplotypes III, IV, or IX (the 5' subhaplotype class A). At 5' beta globin gene, we observe exclusively the allele (AT)(7)T(7). In the beta thalassemic heterozygotes studied, no correlation of those genetic markers with HbF levels is observed.

Beta-thalassaemia prototype of a single gene disorder with multiple phenotypes

As the defective genes for more and more genetic disorders become unravelled, it is clear that patients with the same genotype can have many different clinical conditions even in monogenic disorders. The remarkable phenotypic diversity of the beta thalassaemias is prototypical of how the wide spectrum in disease severity can be generated. The most reliable and predictive factor of disease phenotype is the nature of the mutation at the beta-globin locus itself. However, relating phenotype to genotype is complicated by the complex interaction of the environment and other genetic factors at the secondary and tertiary levels, some implicated, and others, as yet unidentified. This article reviews the clinical and haematological diversity encountered in beta thalassaemia and their relationship with the underlying genotypes.

Evaluation of a single-tube multiplex polymerase chain reaction screen for detection of common alpha-thalassemia genotypes in a clinical laboratory

We prospectively compared a single-tube multiplex polymerase chain reaction (PCR) for detecting alpha-thalassemia with our current approach using 452 blood samples. Initial evaluation of 89 specimens revealed sensitivity and specificity, respectively, for the hemoglobin H inclusion body test (HbH prep) vs PCR for detecting alpha0-thalassemia carriers of 0.79 and 0.96 and for a mean corpuscular volume (MCV) of 82 microm3 (82 fL) or less, 1.0 and 0.45. Detection of all alpha-thalassemia genotypes was significantly lower for HbH prep and MCV (sensitivity and specificity, respectively: HbH prep, 0.48 and 0.96; MCV, 0.87 and 0.47). In a follow-up evaluation of patients with positive HbH prep results or suspected alpha-thalassemia prescreened by low MCV, the sensitivity and specificity, respectively, of HbH prep vs PCR increased to 0.97 and 0.93 for alpha0-thalassemia and 0.83 and 0.92 for any alpha-thalassemia. PCR detected alpha-thalassemia in 37.2% of 298 suspected alpha-thalassemia cases with suggestive indices but negative HbH prep results and no detectable hemoglobinopathy. This multiplex approach was more sensitive than the HbH prep for detecting all alpha-thalassemia genotypes, particularly alpha+-thalassemia; was particularly valuable for identifying carriers of alpha0-thalassemia at risk for offspring with hemoglobin Bart hydropsfetalis, regardless of other diagnosed hemoglobinopathies; and is an ideal adjunct to standard clinical screening protocols for detecting alpha-globin deletions.