Molecular Analysis of Non-Transfusion Dependent Thalassemia Associated with Hemoglobin E-β-Thalassemia Disease without α-Thalassemia

Genetic polymorphism of novel SNP rs5006884 in OR51B6 and SNP rs4499252 in AHSP among transfusion-dependent and non-transfusion-dependent β-thalassemia/Hb E patients in Thailand: a multivariate analysis of clinical and genetic polymorphism

Compound heterozygous β-thalassemia and Hb E, a prevalent and severe form of thalassemia in Southeast Asia, manifests in two major clinical forms: transfusion-dependent thalassemia (TDT) and non-transfusion-dependent thalassemia (NTDT). This study investigates the association of genetic polymorphisms rs5006884 in OR51B6, rs4499252 in AHSP, rs9399137 in HBS1L-MYB, and rs4671393 in BCL11A with clinical severity and transfusion dependency in β-thalassemia/Hb E patients in Thailand. A total of 189 samples, including 58 TDT, 58 NTDT, 33 homozygous Hb E, and 40 wild-type individuals, were analyzed. Genotyping of the four single nucleotide polymorphisms (SNPs) was conducted using the rhAmp SNP Genotyping assay. Multivariate regression models were developed to evaluate the combined effects of genetic and clinical factors on transfusion dependency. The results showed that OR51B6 SNP rs5006884 TT genotype was significantly more frequent in the NTDT group (P < 0.05), suggesting a strong association with reduced transfusion dependency. Conversely, the AHSP SNP rs4499252 GG genotype was significantly less frequent in the homozygous Hb E group (P < 0.05) compared to other groups. Multivariate analyses highlighted hemoglobin (Hb) levels as a robust predictor of transfusion dependency, with specific HBB mutations including HBB:c.59 A > G, HBB:c.-78 A > G, HBB:c.316-197 C > T, and NC_000011.10:g.5224302_5227791del being significantly associated with NTDT (P < 0.05). Furthermore, rs5006884 in OR51B6 also played a significant role in NTDT in multivariate analyses. In contrast, SNPs in BCL11A (rs4671393), HBS1L-MYB (rs9399137), and AHSP (rs4499252) showed no significant independent associations with transfusion dependency or disease severity in this cohort. This study explores rs5006884 in OR51B6 and rs4499252 in AHSP in TDT and NTDT patients for the first time. These findings elucidate the interplay of genetic and clinical factors influencing β-thalassemia severity, paving the way for personalized management strategies to mitigate transfusion requirements.

Molecular and haematological characterisation of haemolytic anaemia associated with biallelic KLF1 mutations: a case series

AIMS

Krüppel-like factor 1 (KLF1) is an erythroid-specific transcription factor playing an important role in erythropoiesis and haemoglobin (Hb) switching. Biallelic KLF1 mutations can cause haemolytic anaemia with thalassaemia-like syndromes but are rarely reported. We explore the KLF1 mutations in Thai subjects with unexplainable haemolytic anaemia.

METHODS

The study was done on 57 subjects presented with haemolytic anaemia and elevated Hb F without β-thalassaemia diseases. Hb analysis was performed using capillary electrophoresis. Analyses of α-thalassaemia, β-thalassaemia and KLF1 genes were performed using PCR-based methods and DNA sequencing.

RESULTS

Thirteen subjects with compound heterozygous for a known and five new genetic KLF1 interactions were identified, including KLF1:c.519_525dupCGGCGCC/c.892G>C with class 3/2 (n=8), and each subject with new genetic interaction, including KLF1:c.-154C>T;643C>T/c.983G>A with class 3/2, KLF1:c.-154C>T;643C>T/c.809C>G with class 3/2, KLF1:c892G>C/c.983G>A with class 2/2, KLF1:c.892G>C/c.1001C>G with class 2/2 and KLF1:c.1001C>G/c.1003G>A with class 2/2. Most of them had anaemia with Hb levels ranging from 45 to 110 g/L, hypochromic microcytosis, aniso-poikilocytosis, increased Hb F levels (17.9%-47.4%), small amounts of Hb Bart's, regular blood transfusion, hyperbilirubinaemia, increased serum ferritin and nucleated red blood cell.

CONCLUSIONS

Biallelic KLF1 mutations associated with anaemia may not be uncommon in Thailand. Characteristics of haemolytic anaemia, abnormal red cell morphology with nucleated red blood cells and elevated Hb F, and presenting small amounts of Hb Bart's without thalassaemia diseases are useful markers to further investigation of the KLF1 gene.

A Population-Oriented Genetic Scoring System to Predict Phenotype: A Pathway to Personalized Medicine in Iraqis With β-Thalassemia

To assess the roles of genetic modifiers in Iraqi β-thalassemia patients, and determine whether a genotype-based scoring system could be used to predict phenotype, a total of 224 Iraqi patients with molecularly characterized homozygous or compound heterozygous β-thalassemia were further investigated for α-thalassemia deletions as well as five polymorphisms namely: rs7482144 C > T at HBG2, rs1427407 G > T and rs10189857 A > G at BCL11A, and rs28384513 A > C and rs9399137 T > C at HMIP. The enrolled patients had a median age of 14 years, with 96 males and 128 females. They included 144 thalassemia major, and 80 thalassemia intermedia patients. Multivariate logistic regression analysis revealed that a model including sex and four of these genetic modifiers, namely: β+ alleles, HBG2 rs7482144, α-thalassemia deletions, and BCL11A rs1427407 could significantly predict phenotype (major versus intermedia) with an overall accuracy of 83.9%. Furthermore, a log odds genetic score based on these significant predictors had a highly significant area under curve of 0.917 (95% CI 0.882-0.953). This study underscores the notion that genetic scoring systems should be tailored to populations in question, since genetic modifiers (and/or their relative weight) vary between populations. The population-oriented genetic scoring system created by the current study to predict β-thalassemia phenotype among Iraqis may pave the way to personalized medicine in this patient's group.

Whole exome sequencing and rare variant association study to identify genetic modifiers, KLF1 mutations, and a novel double mutation in Thai patients with hemoglobin E/beta-thalassemia

OBJECTIVES

Clinical manifestations of patients with Hemoglobin E/beta-thalassemia vary from mild to severe phenotypes despite exhibiting the same genotype. Studies have partially identified genetic modifiers. We aimed to study the association between rare variants in protein-coding regions and clinical severity in Thai patients.

METHODS

From April to November 2018, a case-control study was conducted based on clinical information and DNA samples collected from Thai patients with hemoglobin E/beta-thalassemia over the age of four years. Cases were patients with severe symptoms, while patients with mild symptoms acted as controls. Whole exome sequencing and rare variant association study were used to analyze the data.

RESULTS

All 338 unrelated patients were classified into 165 severe and 173 mild cases. Genotypes comprised 81.4% of hemoglobin E/beta-thalassemia, 2.7% of homozygous or compound heterozygous beta-thalassemia, and 0.3% of (δβ)⁰ thalassemia Hb E while 15.7% of samples were not classified as beta-thalassemia. A novel cis heterozygotes of IVS I-7 (A > T) and codon 26 (G > A) was identified. Six genes (COL4A3, DLK1, FAM186A, PZP, THPO, and TRIM51) showed the strongest associations with severity (observed p-values of <0.05; significance lost after correction for multiplicity). Among known modifiers, KLF1 variants were found in four mild patients and one severe patient.

CONCLUSION

No rare variants were identified as contributors to the clinical heterogeneity of hemoglobin E/beta-thalassemia. KLF1 mutations are potential genetic modifiers. Studies to identify genetic factors are still important and helpful for predicting severity and developing targeted therapy.

Molecular basis of a high Hb A2/Hb Fβ-thalassemia trait: a retrospective analysis, genotype-phenotype interaction, diagnostic implication, and identification of a novel interaction with α-globin gene triplication

Background

β ⁰-thalassemia deletion removing 5´β-globin promoter usually presents phenotype with high hemoglobin (Hb) A₂ and Hb F levels. We report the molecular characteristics and phenotype-genotype correlation in a large cohort of the β ⁰-thalassemia with 3.4 kb deletion.

Methods

A total of 148 subjects, including 127 heterozygotes, 20 Hb E-β-thalassemia patients, and a double heterozygote with α-globin gene triplication, were recruited. Hb and DNA analysis were performed to identify thalassemia mutations and four high Hb F single nucleotide polymorphisms (SNPs) including four base pair deletion (-AGCA) at ^A γ-globin promoter, rs5006884 on OR51B6 gene, -158 ^G γ-XmnI, BCL11A binding motifs (TGGTCA) between 3´^A γ-globin gene and 5´δ-globin gene.

Results

It was found that heterozygous β ⁰-thalassemia and Hb E-β ⁰-thalassemia with 3.4 kb deletion had significantly higher Hb, hematocrit, mean corpuscular volume, mean corpuscular hemoglobin and Hb F values as compared with those with other mutations. Co-inheritance of heterozygous β ⁰-thalassemia with 3.4 kb deletion and α-thalassemia was associated with even higher MCV and MCH values. The Hb E-β ⁰-thalassemia patients carried a non-transfusion-dependent thalassemia phenotype with an average Hb of around 10 g/dL without blood transfusion. A hitherto undescribed double heterozygous β ⁰-thalassemia with 3.4 kb deletion and α-globin gene triplication presented as a plain β-thalassemia trait. Most of the subjects had wild-type sequences for the four high Hb F SNPs examined. No significant difference in Hb F was observed between those of subjects with and without these SNPs. Removal of the 5´β-globin promoter may likely be responsible for this unusual phenotype.

Conclusions

The results indicate that β ⁰-thalassemia with 3.4 kb deletion is a mild β-thalassemia allele. This information should be provided at genetic counseling and prenatal thalassemia diagnosis.

α0-thalassemia in affected fetuses with hemoglobin E-β0-thalassemia disease in a high-risk population in Thailand

OBJECTIVES

A co-inheritance of α⁰-thalassemia can ameliorate the clinical severity of the hemoglobin (Hb) E-β-thalassemia disease. This information should be provided at prenatal diagnosis. Identification of α⁰-thalassemia in an affected fetus is therefore valuable. We have explored this genetic interaction in a large cohort of affected fetuses with hemoglobin (Hb) E-β-thalassemia in northeast Thailand.

METHODS

A study was done retrospectively on 1,592 couples at risk of having fetuses with Hb E-β⁰-thalassemia, encountered from January 2011 to December 2019. A total of 415 left-over DNA specimens of the affected fetuses with Hb E-β⁰-thalassemia disease were further investigated. Examination of α⁰-thalassemia was done using gap-PCR or a multiplex PCR assay for simultaneous detection of Hb E and α⁰-thalassemia mutations.

RESULTS

Of the 415 affected fetuses, the two most common β⁰-thalassemia genes found were the codons 41/42 (-TTCT) (199/415; 48.0%) and codon 17 (A-T) (115/415; 27.7%). α⁰-thalassemia was found unexpectedly in 21 (5.1%) fetuses. Hematologic phenotypes of the parents indicated that it was impossible to differentiate a pure β⁰-thalassemia carrier from a double β⁰-thalassemia/α⁰-thalassemia heterozygote unless DNA analysis is performed. In contrast, a reduced level of Hb E in the Hb E carrier (<25%) is a valuable marker for predicting double heterozygosity for Hb E/α⁰-thalassemia. This could be further confirmed using a multiplex PCR assay.

CONCLUSIONS

There is a high prevalence of co-inheritance of α⁰-thalassemia in fetuses with Hb E-β⁰-thalassemia disease. In a high-risk population such as Thailand, we recommend screening for α⁰-thalassemia in all affected fetuses with Hb E-β⁰-thalassemia disease and providing complete genetic information to the parents to make appropriate decisions at prenatal diagnosis and genetic counseling.

Direct Amplification of Whole Blood and Amniotic Fluid Specimens for Prenatal and Postnatal Diagnosis of Hb E-β 0-Thalassemia Diseases

OBJECTIVE

Prenatal and postnatal diagnosis of hemoglobin E-β 0-thalassemia can be made using polymerase chain reaction (PCR) analysis mostly on purified DNA. We have establihed a direct amplification method without DNA extraction on whole blood (WB) and amniotic fluid (AF) specimens to diagnose the disease.

METHODS

Three reactions of WB PCR assays and 7 reactions of AF PCR tests were developed for postnatal and prenatal diagnosis, respectively. Assays were validated against routine tests in a blinded trial.

RESULTS

The results showed 100% concordance with routine DNA PCR assays. Among 309 β-thalassemia carriers, 191 patients (61.8%) carried common β-thalassemia mutations. Among 448 AF specimens, 116 (25.9%) fetuses were found to be affected, 247 (55.1%) fetuses were carriers, and 85 (19%) fetuses were unaffected.

CONCLUSION

We found that WB and AF PCR assays are simple, rapid, and reliable. The developed techniques could be applicable in routine settings.

β-Hemoglobinopathies in the Lao People's Democratic Republic: Molecular diagnostics and implication for a prevention and control program

INTRODUCTION

A high frequency of β-thalassemia in Lao People's Democratic Republic necessitates the importance of complete molecular data before a prevention and control program could be established. Limited data are available for Lao PDR. We have now reported an extended information on the molecular basis of β-hemoglobinopathies in this population.

METHODS

The study was done on 519 unrelated Laos subjects requested for thalassemia investigation. Hematological data were recorded. Hb profiles were obtained using a capillary electrophoresis system. α-And β-globin genotyping was performed using PCR and related techniques.

RESULTS

Among the 519 subjects, 287 (55.3%) were found to carry β-hemoglobinopathies based on Hb and DNA analyses. These included Hb E carriers (n = 135), homozygous Hb E (n = 47), β-thalassemia carriers (n = 70), Hb E-β-thalassemia (n = 25), homozygous β-thalassemia (n = 4), heterozygous δβ⁰ -thalassemia (n = 2), and carriers of the β-Hb variant (n = 3). Mutation analysis identified in addition to the Hb E, 8 different β-thalassemia mutations including codon 17 (A-T), codons 41/42 (-TTCT), NT-28 (A-G), codons 71/72 (+A), IVS1-1 (G-T), 3.4 kb deletion, an initiation codon (T-G) and IVS2-654 (C-T). Two δβ⁰ -thalassemia carriers (12.6 kb deletion) and three subjects with Hb Hope (β^136GGT-GAT ) were identified. Hematological features associated with these β-hemoglobinopathies were presented.

CONCLUSION

β-hemoglobinopathies in the Laos population is heterogeneous. This information is relevant for setting up a molecular diagnostics and can provide a basis for genetic counseling and enable prenatal diagnosis.

Association Between Genetic Polymorphisms and Hb F Levels in Heterozygous β-Thalassemia 3.5 kb Deletions

Single nucleotide polymorphisms (SNPs) in several genetic modifying factors have been related to Hb F levels, including ^Gγ XmnI polymorphism, B-cell lymphoma/leukemia 11 A (BCL11A), HBS1L-MYB intergenic polymorphism (HMIP) and a mutation in the Krüppel-like factor 1 (KLF1). This study aimed to determine whether genetic variability of these modifying factors affects Hb F levels in heterozygous β-thalassemia (β-thal) 3.5 kb deletion (NC_000011.10: g.5224302-5227791del13490bp). A total of 111 β-thal 3.5 kb deletion carriers with Hb F levels ranging from 0.9 to 18.4% was recruited for this study. Genotyping of SNPs including HBG2 rs7482144, HMIP rs4895441 and rs9399137, BCL11A rs4671393 and KLF1 rs2072596 was identified. Multiple regression analyses showed that only two SNPs (HMIP rs4895441 and rs9399137) influenced Hb F levels. Interestingly, a combination of these two SNPs was associated with higher Hb F levels. Our study is the first to demonstrate that the rs4895441, rs9399137 of HMIP are associated with elevated Hb F levels in the heterozygous β-thal 3.5 kb deletion.

The Effect of Five Single Nucleotide Polymorphisms on Hb F Variation of β-Thalassemia Traits and Hematologically Normal Individuals in Southeast Turkey

β-Thalassemia (β-thal) is caused by deficiency of β-globin chain synthesis and leads to the accumulation of unstable globin chain production. This results in a higher Hb F level in order to neutralize the excess α chains. In addition, γ-globin gene expression, due to genetic factors after birth, leads to increased Hb F levels in adulthood [hereditary persistence of fetal hemoglobin (Hb) (HPFH)]. In this study, the relationship between β-thal trait and individuals with suspected HPFH and a control group was investigated in Adıyaman, Turkey. Single nucleotide polymorphism (SNP) analyses were performed in five different polymorphic regions using real-time polymerase chain reaction (qPCR) methods [rs4671393 (G>A), rs766432 (A>C), rs9402686 (G>A), rs28384513 (T>G), rs1609812 (A>G)]. No significant difference was found between the control and β-thal group in the codominant inheritance model in the rs1609812 (A>G) polymorphism region only, while all the other polymorphic regions were found to be statistically significant. It was found that different genotype models increased Hb F levels between 1.6- and 3.06-fold in four studied polymorphic regions [rs4671393 (G>A), rs766432 (A>C), rs9402686 (G>A), rs28384513 (T>G)]. All of the polymorphic regions increased the Hb F levels from 1.86- to 24.76-fold, except rs9402686 (G>A) and rs28384513 (T>G) over dominant and rs1609812 (A>G) codominant inheritance models. The AC and AA genotypes increased Hb F levels in the B-cell CLL/lymphoma 11 A haplotype studies. It was determined that both haplotypes 2 and 4 increased Hb F levels. As a result, SNPs strongly affect the Hb F levels in both healthy individuals and β-thal trait.

A novel SNP rs11759328 on Rho GTPase-activating protein 18 gene is associated with the expression of Hb F in hemoglobin E-related disorders

Hemoglobin (Hb) F has a modulatory effect on the clinical phenotype of β-thalassemia disease. High expression of Hb F in Hb E-related disorders has been noted, but the mechanism is not well understood. We have examined the association of a novel SNP rs11759328 on ARHGAP 18 gene and other known modulators with a variability of Hb F in Hb E-related disorders. Genotyping of SNP rs11759328 (G/A) was performed based on high-resolution melting analysis. The rs11759328 (A allele) was shown to be significantly associated with Hb F levels (p < 0.05) in heterozygous and homozygous Hb E. High levels of Hb F in both heterozygous and homozygous Hb E were also found to be associated with SNPs in the study of other modifying genes including KLF 1 mutation, rs7482144 (Gγ-XmnI), rs4895441, rs9399137 of (HBS1L-MYB), and rs4671393 (BCL11A). Multivariate analysis showed that KLF1 mutation and SNP rs11759328 (GA) (ARHGAP18) modulated Hb F expression in heterozygous Hb E. For homozygous Hb E, this was found to be related to five modifying factors, i.e., KLF1 mutation, rs4895441 (GG), rs9399137 (CC), rs4671393 (AA), and rs4671393 (GA). These results indicate that a novel SNP rs11759328 is a genetically modifying factor associated with increased Hb F in Hb E disorder.