(A gamma delta beta)0-Thalassaemia in Blacks is due to a deletion of 34 kbp of DNA

A large cohort of deletional high hemoglobin F determinants in Thailand: A molecular revisited and identification of a novel mutation

BACKGROUND AND AIMS

High hemoglobin F determinants can be classified into hereditary persistence of fetal hemoglobin (HPFH) and δβ-thalassemia with different phenotype. We report the molecular basis and hematological features in a large cohort of deletional high Hb F determinants in Thailand.

MATERIALS AND METHODS

Subjects (n = 28,177) encountered during 2015-2022 were reviewed, and those with phenotypically suspected of having high Hb F determinants were selected. Combined PCR, multiplex ligation-dependent probe amplification, next-generation sequencing, and DNA sequencing were used to identify the mutations.

RESULTS

Among 28,177 subjects investigated, 300 (1.06 %) were found to carry deletional high Hb F determinants in a total of 302 alleles, including heterozygote, compound heterozygote with β-hemoglobinopathies, and homozygote. DNA analysis identified eight different DNA deletions, including δβ0-thalassemia (12.6 kb deletion) (73.8 %), HPFH-6 (14.9 %), Indian deletion-inversion Aγδβ0-thalassemia (3.6 %), Thai deletion-inversion-insertion Aγδβ0-thalassemia (3.0 %), SEA-HPFH (3.0 %), Chinese Aγδβ0-thalassemia (1.0 %), Thai δβ0-thalassemia (11.3 kb deletion) (0.3 %), and a novel δβ0-thalassemia (137.1 kb deletion) (0.3 %). In addition, three novel genetic interactions, including Chinese Aγδβ0-thalassemia/Hb E, δβ0-thalassemia/Indian deletion-inversion Aγδβ0-thalassemia, and homozygous δβ0-thalassemia were found. Hematological features and Hb analysis results of 20 different genotypes were recorded. Multiplex gap-PCR assays for detection of these genetic determinants were described.

CONCLUSIONS

Deletional high Hb F determinants are common and heterogeneous in Thailand. Data on the prevalence, molecular spectrum, phenotypic expression, and complex interactions of these genetic determinants should prove useful in the study and a prevention and control program of hemoglobinopathies in the region.

Clinical variability and molecular characterization of Hbs/Gγ (Aγδβ)0-thal and Hbs/HPFH in Indian sickle cell disease patients: AIIMS experience

INTRODUCTION

In sickle cell disease (SCD) patients, among the predictors of survival, HbF levels play a significant role in lowering the morbidity and mortality. Coinheritance of δβ thalassemia and hereditary persistence of fetal hemoglobin (HPFH) may contribute to variable HbF levels in SCD patients, thus influencing their clinicopathological profile. Such cases are sparsely documented in the literature and thus, we screened the presence of δβ thalassemia and HPFH in 126 cases of SCD with high HbF.

MATERIAL AND METHODS

A total 126 SCD individuals with raised HbF levels were the study subject. Capillary zone electrophoresis (CZE) was done for the quantitative assessment of hemoglobin variants. HbSC, HbSD, HbAS and HbSE cases were excluded. Asian Indian Gγ(Aγδβ)0-thal, δβ0-thal (Sicilian, 13.4 kb), (Chinese, 100 kb), HPFH-1 (Black, 106 kb), HPFH-2 (Ghanaian, 105 kb), HPFH-3 (Indian, 48.5 kb) were done by GAP-PCR.

RESULTS

Out of 126, 78 cases (62%) were homozygous for SCD. The remaining 48 cases suspected to be heterozygous were furthered screened and 6/48 cases (12.5%) were found to be compound heterozygous. Out of these 6 cases,4(66.66%) had HbS/ δβ- Gγ(Aγδβ)0 and 2(33%) had HbS/HPFH compound heterozygous condition. None of the patients had δβ0-thal (Sicilian, 13.4 kb), (Chinese, 100 kb), HPFH-1 (Black, 106 kb), HPFH-2 (Ghanaian, 105 kb).

CONCLUSION

This study highlights the importance of understanding the complex patho-physiology of compound heterozygous cases of HbS/HPFH and HbS/δβ thalassemia, as these infrequent conditions lead to change in phenotype and clinical severity of the disease. Insight into more such cases will open the window to better analyze the disease pathogenesis in these rare compound heterozygous conditions, as this will be beneficial to formulate proper management protocol in these patients.

HbS-Sicilian (δβ)0-Thalassemia: A Rare Variant of Sickle Cell

Sickle cell disease (SCD) is caused by a mutation in the sixth codon of the β-globin gene on chromosome 11, which leads to a single amino acid substitution (glutamine to valine). Sickle-(δβ)⁰-thalassemia is a rare variant of sickle cell disease (delta-beta thalassemia occurring in association with sickle hemoglobin, HbS), sparsely reported in literature, and has been associated with symptomatology necessitating careful monitoring and follow-up. We describe a patient who presented with a newborn screen reported as “FS” and a negative family history for sickle cell disease and sickle cell trait. Subsequent gene sequencing studies demonstrated the presence of Sickle-(δβ)⁰-thalassemia. Clinical course has remained relatively stable for this patient now at 18 months of age without any SCD related symptomatology or complications. As this is a rare variant of SCD with potential complications, it is important to establish diagnosis towards planning comprehensive care.

The clinical severity of hemoglobin S/Black (A γδβ)0 -thalassemia

Hemoglobin S/Black (^A γδβ)⁰ -thalassemia is a rare sickle cell disease (SCD) variant. On the basis of limited descriptions in the literature, the disease is reported as a mild microcytic anemia with an uncomplicated course. We report the clinical and laboratory data of nine patients whose diagnoses were confirmed by DNA-based techniques. Despite having mild anemia and high fetal hemoglobin level postinfancy, these patients developed many of the classic complications of SCD, including vaso-occlusive crisis, acute chest syndrome, avascular necrosis, and cholelithiasis. On the basis of these findings, we recommend that patients with this rare disorder receive specialized hematology care according to SCD guidelines.

Application of multiplex ligation-dependent probe amplification to screen for β-globin cluster deletions: detection of two novel deletions in a multi ethnic population

Hereditary persistence of fetal hemoglobin (HPFH) and δβ-thalassemia (δβ-thal) are heterogeneous disorders caused by deletions within the β-globin gene cluster. When combined with other β-thal mutations or structural hemoglobin (Hb) variants, these deletions give rise to clinical phenotypes ranging from an asymptomatic condition to β-thal major (β-TM). Overlap in hematological parameters and variability in expression of Hbs A2 and F make molecular testing necessary to distinguish clinically relevant deletions. Multiplex ligation-dependent probe amplification (MLPA) was used to screen for β-globin gene cluster deletions in 49 unresolved samples referred for a suspected β-thal anomaly. The 1.39 kb Black β(0), 3.5 kb Thai β(0), 118 kb Filipino β(0), 11.8 kb Black (δβ)(0), 13.4 kb Sicilian (δβ)(0), 35.8 kb Black ((A)γδβ)0, Hb Lepore-Boston-Washington (Hb LBW) and HPFH-2 deletions, and two novel deletions, a 61.7 kb Pakistani β(0) deletion and an ((A)γδβ)(0) deletion, were identified in 15 cases. Detection of both known and unknown deletional Hb disorders provides for appropriate clinical management and genetic counseling.

Clinical and molecular characterization of β(S) and (G)γ((A)γδβ)⁰-thalassemia in eastern India

Fetal hemoglobin (Hb F) is the most studied modifier of sickle cell disease. Coinheritance of high Hb F determinants such as δβ-thalassemia (δβ-thal) and hereditary persistence of fetal hemoglobin (HPFH) can contribute to raised Hb F concentration in these patients. One hundred and seventy-six cases of sickle cell disease with high Hb F were screened for the presence of the Asian Indian deletion-inversion (G)γ((A)γδβ)⁰-thal and HPFH-3 (Indian, 48.5 kb) disorders. Three cases from two unrelated families were found to have sickle cell disease and the ((A)γδβ)⁰-thal genotype. Three other members had heterozygous (G)γ((A)γδβ)⁰-thal. None had HPFH-3. Despite very high Hb F concentrations and linkage of the β(S) gene to Asian haplotypes, the compound heterozygotes had severe clinical presentation, possibly because of heterocellular distribution of Hb F. In conclusion, these high Hb F determinants are not common causes of high Hb F in Indian sickle cell disease patients.

Molecular characterization of a novel 55.1 kb (G)gamma((A)gammadeltabeta)(0)-thalassemia deletion in two Canadian families

We report two Canadian families in which there are four carriers of a novel (G)gamma((A)gammadeltabeta)(0)-thalassemia deletion. The patients all have mild microcytosis and hypochromia, and elevated levels of Hb F ranging from 9.7 to 17.3%. The precise endpoints of the deletion have been identified and are unique relative to other forms of (G)gamma((A)gammadeltabeta)(0)-thal reported in the literature. The deletion encompasses approximately 55.1 kb, beginning approximately 1.6 kb downstream of the (G)gamma-globin gene and extending approximately 29.0 kb downstream of the beta-globin gene.

Fetal hemoglobin levels in adults

The synthesis of fetal hemoglobin (HbF) is normally reduced to very low levels of less than 0.6% of the total hemoglobin in adults. The HbF is restricted to a sub-population of erythrocytes termed 'F-cells'; 85% of the normal adult population have 0.3% to 4.4% F-cells. The levels of HbF and F-cells vary by more than 10-fold in normal adults; family studies show that these levels are genetically controlled but the number and nature of these genetic factors are still poorly understood. HbF levels may be increased in adults in a number of inherited and acquired disorders, accompanied by an increase in both the number of F-cells and the amount of HbF per F-cell. The clinical significance of these conditions with raised HbF relates to their interaction in disorders such as sickle cell disease and beta thalassaemia in which raised levels of HbF can lead to considerable amelioration of disease severity. Study of the 'natural' mutants primarily associated with increased HbF has provided considerable insight into the understanding of the control of globin gene regulation and hemoglobin switching. Currently considerable effort is being channelled into clinical trials and the search for the 'ideal' therapeutic agents which could increase HbF in adult life with minimal drug toxicity.

The in vivo expression of the globin genes of the beta cistron in gamma-, delta-, and delta beta-thalassemia heterozygotes

There is considerable evidence suggesting that the switch from gamma to delta and beta chain production after birth is due, in part, to silencing of the gamma genes by stage-specific factors which bind to their promoters and to the competition from the adult (delta and beta) genes for a common enhancer element located in the locus control region. As a consequence one can expect that the increased Hb F production in adults with hereditary persistence of fetal hemoglobin or delta beta-thalassemia is directed mainly by gamma-globin genes in cis to the deletion(s) responsible for these conditions. Here we review data on heterozygotes with gamma-, delta- or delta beta-thalassemia, who also had an A gamma T mutation, in cis or in trans, which was used as a marker of gamma gene expression. The results show that a deletion affecting adult beta genes favors the expression of gamma genes in cis, while the deletion of a single gamma gene does not affect the expression of the beta gene in cis but leads to a faster gamma-->beta switch postnatally.

Increased HbF in adult life

Considerable advances have been made recently in our understanding of globin gene expression, its developmental regulation and the altered patterns in various inherited and acquired disorders. Each advance has revealed a new layer of complexity and as many questions remain as have been answered. Adult levels of HbF are clearly under genetic control but the number and nature of these genetic factors, either within or outside of the beta-globin gene cluster, remain to be determined. Many of the conditions resulting in increased HbF in adult life appear to involve an increased erythropoietic drive which results in a higher proportion of erythroid progenitor cells activating their inherent ability to synthesise low amounts of HbF. The mechanism by which this is achieved remains unknown but these observations have been confirmed in a number of experimental systems and have led to the use of mildly cytotoxic drugs to increase the HbF levels in sickle cell anaemia. Similarly, the clinical observation that infants of diabetic mothers show delayed fetal to adult haemoglobin switching has led to the development of butyrate derivatives to increase adult HbF levels. Analysis of the HPFH mutations has so far been largely limited to the deletion conditions and the gamma-gene promoter base substitutions. In neither case is there a complete explanation which can account for the raised adult HbF level characteristic of these conditions. Rather, they seem to demonstrate the complexity, and perhaps redundancy, of the mechanisms which control haemoglobin production. Both conditions show features which are consistent with competition between the gamma- and beta-genes in adult life, an interpretation which is apparently at odds with the 'autonomous' regulation of the gamma-genes in adult transgenic mice. Analysis of further transgenic mice, including ones bearing HPFH mutations, may help resolve this apparent contradiction and may provide suitable material to examine the in vivo protein-DNA interactions in this region.

Filipino beta zero thalassaemia: a high Hb A2 beta zero thalassaemia resulting from a large deletion of the 5' beta globin gene region

A large novel deletional beta zero thalassaemia mutation associated with unusually high levels of haemoglobin (Hb) A2 in heterozygotes is described in two unrelated subjects of Filipino background. The deletion was characterised by DNA mapping including pulsed field gel electrophoresis. Filipino beta zero thalassaemia extends for approximately 45 kb beginning approximately 1.5 kb 3' to the delta globin gene. It is the largest deletion to date which gives rise to the beta zero thalassaemia phenotype. This mutation, similar to previously described deletional beta zero thalassaemias associated with high Hb A2, removes sequences 5' to the beta globin gene promoter and emphasises the functional importance of the 5' beta globin region in eliciting the unusually high level of Hb A2. This example also suggests that it is the 3' sequences which are transposed rather than the actual deletion size which are significant in the raised fetal haemoglobin (Hb F) found with some of the thalassaemias.

Molecular analysis of deletions in the human beta-globin gene cluster: deletion junctions and locations of breakpoints

DNA fragments that contain the deletion junction regions of four independent deletions involving the human beta-globin gene cluster have been isolated and cloned. The fragments were isolated from individuals with the conditions referred to as Sicilian (delta beta)zero-thalassemia, Turkish G gamma+(A gamma delta beta)zero-thalassemia, Black G gamma+(A gamma delta beta)zero-thalassemia, and HPFH-2. The sequences of the deletion junctions and of the normal DNA surrounding their 3' breakpoints were determined and compared to the previously determined sequences of normal DNA surrounding their 5' breakpoints. These comparisons show that the deletions were the result of nonhomologous recombinational events. Two of the deletion junctions contain "orphan" nucleotides, while the other two show very limited amounts of "junctional homology." Both types of junctions are common among recombination events in mammalian cells and we discuss a simple joining scheme that could account for the junctions reported here. Unlike other deletions in this cluster and in other gene clusters, none of the eight deletion breakpoints examined here occurred within Alu family repeats. To examine the significance of deletion breakpoints within various sequence categories, we analyzed the data from a well-defined set of deletions within this locus. In contrast to deletions in the alpha-globin gene cluster, the occurrence of breakpoints in Alu family repetitive sequences is not statistically significant within the beta-globin gene cluster. However, breakpoints do occur within transcriptional units of the beta-globin gene cluster more frequently than expected by chance alone. We conclude from our analysis that the mechanisms of DNA joining are not locus or location specific, but at least a portion of the mechanisms of chromosomal breakages do show locus specificity.

The DNA deletion in an Indian delta beta-thalassaemia begins one kilobase from the A gamma globin gene and ends in an L1 repetitive sequence

High fetal haemoglobin levels of 5-15% are present in adult heterozygotes for delta beta-thalassaemia as the result of large deletions of DNA. We have cloned DNA spanning the deletion breakpoint for a new Indian delta beta-thalassaemia associated with mild anaemia. The 5' breakpoint is at 42151 of GenBank file HUMHBB, which is about 1 kb 3' of the A gamma globin gene poly A site at 41003. On the 3' side of the breakpoint, the sequence is homologous to L1 (KpnI) repetitive DNA located 3.6-10 kb 3' of the beta-globin gene: Indian delta beta-thalassaemia DNA is 74% homologous to the inverted complement of HUMHBB from 69849 to 70020, followed by a region 78% homologous to the direct sequence of HUMHBB from 70534 to 71010. The precise location of the 3' endpoint of this deletion has not been determined, but it is within L1 sequences located more than 10 kb 3' of the beta-globin gene.

Severe Hb S-beta zero-thalassaemia with a T----C substitution in the donor splice site of the first intron of the beta-globin gene

Through direct sequencing and dot-blot analyses with synthetic oligonucleotide probes of amplified DNA, a new nucleotide substitution was discovered in a Black teenager with severe Hb S-beta zero-thalassaemia. The substitution involved a T----C replacement at the second position of the donor splice site of the first intervening sequence of the beta-globin gene. The clinical and haematological observations made in Black subjects with Hb S-beta zero-thalassaemia, with different types of thalassaemia, suggest severe disease resembling sickle cell anaemia. Only an occasional patient had a milder clinical course, perhaps because of a greatly increased production of fetal haemoglobin.

Molecular characterization of a novel form of (A gamma delta beta)zero-thalassemia deletion with a 3' breakpoint close to those of HPFH-3 and HPFH-4: insights for a common regulatory mechanism

We have molecularly characterized a novel (A gamma delta beta)zero-thalassemia associated with increased synthesis of HbF in three members of a German family. The levels of HbF in the peripheral blood red cells of the heterozygotes ranged between 9.9% and 12.5% with a heterocellular distribution in the red cells, as detected by immunofluorescence. The mutation resulted from a deletion starting about 1.5 to 1.9 kb from the 3' end of the G gamma-gene and ending 27 +/- 0.5 kb 3' to the beta-globin gene. Thus, the total deletion is 52 +/- 0.5 kb. Its 5' breakpoint is similar to that of the previously described (A gamma delta beta)zero-thalassemias, while the location of the 3' breakpoint is placed very close to the 3' breakpoints of HPFH-4 and HPFH-3 deletions. The proximity of the 3' breakpoint of the German (A gamma delta beta)zero-thalassemia to those of HPFH-3 and HPFH-4 deletions raises the possibility that a common mechanism, such as the juxtaposition of an enhancer, might underlie the activation of the gamma-globin genes in these three mutants.

Homozygosity for a new type of G gamma (A gamma delta beta)zero-thalassemia in a Malaysian male

Hematological and clinical data are presented for a young Malay patient with a homozygous (delta beta)zero-thalassemic condition. His red blood cells contained 100% fetal hemoglobin with alpha and G gamma chains only. Detailed gene mapping defined a large deletion with a 5' end between the Aha III and Apa I sites, some 200-400 bp 5' to the A gamma globin gene and a 3' end beyond sequences 17-18 kb 3' to the beta globin gene. This G gamma (A gamma delta beta)zero-type of thalassemia is different from all the other six types described before. Comparison of the hematological data of this patient with those of homozygotes for either the Sicilian or Spanish types of G gamma A gamma (delta beta)zero-thalassemia showed no differences; all homozygotes have a moderate anemia which is accentuated by the relatively high oxygen affinity of the Hb F containing erythrocytes.

A Chinese G gamma + (A gamma delta beta)zero thalassemia deletion: comparison to other deletions in the human beta-globin gene cluster and sequence analysis of the breakpoints

A clone was isolated that contains the deletion junction region from an individual with a deletion associated with Chinese G gamma + (A gamma delta beta)zero thalassemia. A clone containing the normal DNA corresponding to the 3' breakpoint of this deletion was also isolated. Portions of these two clones were sequenced and compared to the region in the A gamma-globin gene where the 5' breakpoint occurs. This comparison reveals that the breakage and reunion event was nonhomologous and that it probably involved the insertion of 36-41 bases of DNA belonging to the L1 (KpnI) family of repetitive DNA. Genomic mapping revealed that the DNA on the 3' side of this deletion is closely linked in normal DNA to the 3' breakpoints of two different large deletions that are associated with hereditary persistence of fetal hemoglobin (HPFH). We cloned and mapped 35 kbp of normal DNA from this region (greater than 45 kbp downstream of the human beta-globin gene) that contains the 3' breakpoints of the Chinese thalassemia and the two HPFH deletions. An endogenous retrovirus-like element and several other repetitive sequences are located within this region. We show that the Chinese thalassemia deletion is greater than 80 kbp in length and differs in size from the two HPFH deletions by less than 6%. We also show that the Chinese thalassemia deletion is at least 40 kbp larger than several other deletions associated with a very similar phenotype.