Alpha-globin Gene Research Articles

Surveyor™ Nuclease: A New Rapid and Effective Strategy for Detection of Single Nucleotide Changes in Alpha Globin Genes.

Alpha thalassemia is the most common globin gene disorder in the world and the disease is caused by mutations in either the alpha2 or alpha1 genes. Deletions of one (-α) or both (--) of these genes are the most common cause of alpha-thalassemia, while point mutations and small insertions/deletions are present but at a much lower frequency (5%). The number of point mutations described in these genes has been steadily increasing, with greater than 40 identified to date. Identifying these point mutations acquires importance as patients with non-deletional hemoglobin (Hb) H disease are more severely affected. Comprehensive evaluation of α globin genes is also essential while determining the molecular basis of the thalassemia intermedia phenotype. Mutations in the alpha globin gene can be detected either by direct DNA sequencing or by screening methods. Although small (about 1kb, 3 exons and 2 introns), the alpha-globin genes are duplicate and highly G-C rich, which makes them difficult to denature and therefore reducing sequencing efficiency and causing frequent artifacts. We have developed a simple and robust method based on mismatch-specific DNA endonuclease, SurveyorTM Nuclease. Genomic DNA control samples (n=21) harboring 12 different nucleotide changes characterized by direct DNA sequencing in either the alpha2 or alpha1 samples were used to validate this method. These samples were heterozygous or homozygous for each point mutation, or compound heterozygous for a deletion and the point mutation. Controls were amplified by gene specific primers designed by Primer3 software followed by digestion with SurveyorTM Nuclease. This endonuclease is a member of the CEL nuclease family of mismatch-specific nucleases derived from celery. It recognizes all insertions, deletions and base substitutions, and cleaves the mismatch of any heteroduplex DNA. After digestion, cleavage products are analyzed by agarose gel electrophoresis. The size of the digestion products indicates the location of the mutation, which is then confirmed and characterized by sequencing. All the 12 different nucleotide changes [α1 CD 14 TàC, α2 CD 104 TàG, α2 IVS II-55 TàG, α1 IVS II 141 TàC, α1 IVS I 117 GàT, α2 IVS I 1 GàA, Poly A (-AA), α1 CD 119 CàT, α2 IVS I 116, α2 CD 22 CàT, α2 CD 29 TàC, α2 +15 CàG] in the alpha globin genes were detected by this assay indicating a high sensitivity and specificity of this method. Mutation screening by SurveyorTM Nuclease is rapid (~ 5 hours), cost effective ($8/sample) and sensitive (100%). This assay in combination with the multiplex-PCR for screening the common alpha globin gene deletions will be the most comprehensive and economical approach for genetic diagnosis of alpha thalassaemia. Mismatch specific nucleases may have increasing application as a mutation detection strategy for human genetic diseases.

Influence of Globin Gene Modifiers on Baseline and Hydroxyurea-Induced Fetal Hemoglobin Levels in Children with Sickle Cell Anemia.

Fetal hemoglobin (HbF) is recognized as a major determinant of clinical disease severity in children and adults with sickle cell anemia (SCA). Patients with elevated HbF levels have a milder disease course, and many current therapeutic protocols for SCA include pharmacological induction of HbF. However, baseline and treatment HbF levels vary widely due to presumed genetic and environmental factors. Recognized globin gene modifiers of HbF include the beta globin haplotype and a potential contribution from concomitant alpha thalassemia. To characterize more fully the influence of globin gene modifiers on both baseline and treatment HbF levels, we retrospectively determined the beta globin haplotype (Benin, CAR, Senegal, Cameroon, or Arab-Indian) by selective gamma globin gene nucleotide sequencing and the alpha globin gene number (2, 3, or 4) by PCR for 67 African-American children with SCA receiving hydroxyurea therapy at stable maximal tolerated dose (MTD). The four beta globin haplotypes and frequencies identified in our cohort of children include Benin (0.61), CAR (0.17), Senegal (0.12), and Cameroon (0.10). The number of alpha globin genes and frequencies identified were 4 genes (0.72), 3 genes (0.25) and 2 genes (0.03). Baseline and MTD HbF levels were analyzed according to each variable. The average baseline HbF value for the entire cohort of children was 7.7 ± 4.4% (median 7.6%, range 1.3 – 19.3%), while the average treatment HbF value was 23.9 ± 7.2 % (median 22.9%, range 10.2 – 40.7%). All 67 children increased their HbF in response to hydroxyurea therapy (median 16.7%, range 5.0 – 28.8%). There was a modest but statistically significant correlation between the baseline and treatment HbF (r=0.66, p<.0001). The estimated effect of one unit change in baseline HbF on treatment HbF was 1.11 (95% CI of 0.78, 1.43). When baseline %HbF was analyzed according to the beta globin haplotype, the overall ANOVA had a p-value of 0.02, indicating a statistically significant influence. Further analysis confirmed associations previously identified in adults with SCA, i.e. children with at least one copy of the CAR haplotype had a lower baseline HbF (5.9% vs 8.4%, p=.05), while those with at least one copy of the Senegal haplotype had a higher baseline HbF (11.1% vs 6.7%, p<.001). When hydroxyurea MTD (treatment) HbF values were analyzed according to beta globin haplotype while adjusting for baseline HbF, however, the effect of beta globin haplotype was not statistically significant (p=.13). Analyses of HbF according to alpha globin gene number revealed no statistically significant effects on either baseline or treatment HbF values. Taken together, these data support the hypothesis that beta globin haplotype significant influences baseline HbF values for children with SCA, but has no significant effects on hydroxyurea MTD HbF values. Accordingly, children with SCA should be offered hydroxyurea based solely on clinical indications, without consideration of baseline HbF or beta globin haplotype. Even children with low baseline HbF values or the CAR beta globin haplotype can respond to hydroxyurea therapy with an elevated %HbF. Future studies designed to identify genetic modifiers of treatment HbF values should focus on sequence polymorphisms in non-globin genes that have trans-acting effects on gamma globin gene expression.

Application of the Luminex Platform for Multiplexed Genotyping of Non-Deletional Alpha Thalassemia Mutations.

Objectives: Certain point mutations in the alpha globin gene may lead to unstable hemoglobins such as Hb Constant-Spring and Hb Quong-Sze. These alpha chain variants, when inherited with deletional α-thalassemia mutations cause more severe forms of HbH disease. To evaluate the utility of the Luminex xMAP platform for rapid screening of non-deletional α-thalassemia mutations, we developed a multiplexed genotyping assay to detect six mutations in the α2-globin gene. that are clinically significant or, when coinherited with α-thalassemia-1, result in HbH disease.Methods: A panel of positive controls with known heterozygosity for Hb Constant-Spring, Hb Quong-Sze, Hb J-Toronto, Hb Hasharon, Hb G-Philadelphia and Hb G-Norfolk, was obtained from anonymized whole blood or newborn dried blood spots. The α2 gene was amplified using nested PCR and single base chain extension (SBCE) was carried out using the PCR products, capture-tagged primers, thermosequenase, and one of four biotinylated ddNTPs. Biotinylated amplicons were hybridized to fluorescent microspheres containing allele-specific capture probes and analyzed by flow cytometry on the Luminex100.Results: Median flourescent intensity (MFI) values uniformly discriminated between wild type and mutant alleles in three independent experiments. Mean background-subtracted MFIs ranged from 255 to 1000 for all positive alleles and genotypes were correctly identified in all of the samples tested.Conclusions: As HbH disease is becoming more prevalent in the U.S., early detection of this disorder using accurate, affordable diagnostic methods will permit timely delivery of health care and prevention of severe clinical manifestations of disease. As the severity of many of these disorders has not been well-characterized, an understanding the phenotypic expression of these hemoglobin disorders is essential to providing adequate counseling and treatment options.

Identification of Switching-Related Transcription Factors from a Comparison of Cord and Adult Human Blood Reticulocytes Transcriptomes.

Hemoglobin switching patterns during human ontogeny are highly correlated with transcription of the alpha and beta globin genes on chromosomes 16 and 11, but the molecular and genetic mechanisms responsible for the switching phenomenon are not yet defined. For a better understanding of post-natal globin gene switching and silencing, the expression profiles from purified reticulocyte mRNA (28 separate clinical samples; 14 cord, 14 adult) were studied using Affymetrix HG-U133 arrays (44,229 probe sets). To validate the transcriptome expression levels derived from the microarrays and to discriminate the differences between cord blood and adult blood reticulocytes, we performed quatitative real-time PCR. Among 21 tested control genes, the ratios of adult-to-cord blood (AB/CB) array hybridization intensities versus PCR copy numbers demonstrated a correlation coefficient of 0.978. Hence, the AB/CB array hybridization intensities provide a reliable description of erythroid transcriptome patterns associated with post-natal hemoglobin switching. Stringent screening criteria were then used to identify genes that may be involved in fetal-to-adult hemoglobin switching. All 44,229 probe sets were filtered to identify genes that demonstrated greater than a five fold difference in AB and CB mean signal intensities as well as consistent differences among the 14 samples from each group. In addition, the screening criteria required high-level signals in either AB or CB (>1000 FU), and t-test p-values between AB and CB <0.0001. 107 switching-related probe sets from 94 genes met these criteria, and over 90% of them were detected at higher levels in CB. When this inventory of probe sets was categorized using Gene Ontology, less than half were assigned a known molecular function. Among those, five transcription factors were identified including LIM domain only 2 (LMO2) and Kruppel like factor 3 (KLF3). Those two transcription factors play known roles in hematopoiesis, and LMO2 is required for embryonic erythropoiesis. Two other genes encode zinc finger proteins, but no description of their expression in hematopoietic tissues has been reported. Finally, a novel gene encoding chromatin remodeling and PHD-finger domains was discovered. Postnatal hemoglobin switching is associated with significant changes in the reticulocyte transcriptome. Among the transcripts demonstrating highly significant shifts in their levels, known and novel transcription factors were identified.

High Throughput Screen To Identify Small Molecules That Differentially Regulate Expression of the Globin Genes.

Several lines of evidence indicate that the pharmacological activation of fetal hemoglobin is an effective therapy for sickle cell anemia and beta thalassemia, but novel treatments for these diseases are needed. We developed and validated a high throughput assay to detect differential regulation of the globin genes and utilized this assay in a small molecule screen to identify novel compounds that increase the relative expression of gamma globin. In our assay, transcripts for the alpha, beta, delta, epsilon, gamma, theta, and zeta globin genes are amplified by multiplexed ligation-mediated PCR. Labeled amplicons are captured on different fluorescent microspheres using molecular barcodes, and the relative abundance of labeled amplicons is detected by high speed flow cytometry. To recapitulate the activity of compounds in the bone marrow of patients as accurately as possible, the screen was performed using primary human erythroid progenitor cells cultured in vitro. The assay was adapted to 384-well format with robotic liquid handling. In validation studies, the assay detected the expected increases in globin gene expression during erythroid differentiation, increased gamma globin expression in umbilical cord blood progenitor cells, and increased gamma globin expression in cells treated with known inducers of fetal hemoglobin including hydroxyurea and sodium butyrate. We screened a library of 1040 known bioactive compounds, 75% of which are FDA approved drugs, and a library of 600 compounds produced by diversity oriented synthesis that have been shown to inhibit histone deacetylase (HDAC) activity. In the screen, we rediscovered previously identified globin gene regulators, further validating our globin assay. For example, corticosteroids, known activators of fetal hemoglobin, increased the relative expression of gamma globin. Thyroid hormone specifically increased expression of delta globin, consistent with clinical observations that hemoglobin A2 levels are increased in hyperthyroidism and decreased in hypothyroidism. We identified ten novel compounds from the diversity oriented synthesis library that powerfully induce expression of the gamma globin gene relative to beta globin. Moreover, HDAC inhibition reversed the ontogeny of globin gene expression, coordinately increasing expression of fetal and embryonic relative to the adult globin genes. Relative to beta globin gene expression, gamma and epsilon globin were induced while delta globin was unaffected by HDAC inhibitors; relative to alpha globin expression, zeta globin was increased and theta globin was unaffected. The identification of compounds that differentially regulate globin gene expression may provide lead compounds for the development of novel therapies for sickle cell disease and beta thalassemia and may help elucidate the molecular events underlying switching of the globin genes during normal development.

Characterisation of SCL DNA-Binding Functions In Vivo in Haematopoiesis.

The basic Helix-Loop-Helix (bHLH) transcription factor SCL is required for specification of haematopoietic stem cells (HSCs) and for differentiation of the megakaryocytic and erythroid lineages. bHLH proteins bind DNA as dimers and this has been thought to be a prerequisite for their function. We challenged this concept by showing that SCL DNA-binding activity was dispensable for some of its functions using SCL−/− ES cells rescued with a DNA-binding defective SCL mutant (SCL-RER) (Porcher et al. Development,1999). We have now studied the in vivo requirements for SCL DNA-binding activity in mice with a germ line SCL-RER mutation. In contrast to SCL knock-out embryos that die at E9.5 from absence of haematopoietic development, specification of primitive erythroid progenitors was observed in SCL RER/RER mutant yolk sacs. At day E12.5 and E13.5, homozygote mutant SCL RER/RER embryos were smaller and paler than wild-type (wt) and heterozygote littermates but presented at the expected mendelian frequency. Lethality was first observed at day E14.5. However, 7% of homozygote mice were born from heterozygous crosses. Surviving adult mice presented with mild microcytic hypochromic anemia. Assessment of progenitor replating potential showed qualitative defects with poor haemoglobinisation of homozygote-derived fetal and adult CFU-Es compared to controls. To understand the cause of the phenotype, expression levels of candidate target genes were assessed in fetal liver cells enriched for either early progenitors or late normoblasts. We observed decreased or increased mRNA expression of most genes tested in mutant-derived erythroid populations when compared to controls matched for differentiation stage, thereby showing that SCL DNA-binding activities are required for both activation and repression of target genes. As examples, mRNA for red cell membrane protein Band 4.2 was dramatically decreased; in contrast, alpha-globin expression was up-regulated in early progenitors, indicating that SCL DNA-binding activity might be required for repression of alpha-globin levels in this setting. We then pursued the analysis of SCL-mediated alpha-globin gene regulation by chromatin immunoprecipitation (ChIP) analysis and tested 4 DNase I hypersensitive sites (DHS) previously shown to bind SCL. From material derived from mutant fetal liver cells, we observed slight variations of SCL binding on 3 out of the 4 cis-acting elements when compared to controls. Importantly, there was a dramatic decrease in SCL binding on the fourth DHS site (HS-12). We concluded that SCL DNA-binding activity was likely to be directly required for repression of alpha-globin levels in erythroid progenitors. Interestingly, we have recently characterised the interaction of SCL with a co-repressor complex comprising the oncoprotein ETO-2 in erythroid cells. We have now shown by ChIP that ETO-2 occupies the alpha-globin locus on HS-12 in wt erythroid progenitors, but not in more mature cells, therefore suggesting a role for the SCL/ETO-2 complex in repression of erythroid-specific genes in the early stages of erythroid maturation. In conclusion, this in vivo model confirms the dispensability of SCL DNA-binding activity for specification of HSCs and allows characterisation of DNA-binding requirements throughout development. Combined with studies of the dynamic of SCL-containing multiprotein complexes during erythroid maturation, this model will help define the molecular pathways involved in erythropoiesis.

Prevalence of Frequent α-Globin Gene Deletions in Neonates with HbH in Cord Blood.

Introduction: Increasing multiethnicity is likely to make α-thalassemia minor more prevalent in Western metropolitan areas. It also increases the probability of finding newborns with Hemoglobin H disease or hydrops foetalis. Therefore, there is a need to implement screening methods to detect α-thalassemia at birth. Screening should also identify patients and families with specific requirements in genetic counselling. The goal of the present study is to evaluate the value of HbH measurement in cord blood to identify patients with α-globin deletions and patients with genotypes at risk that should be directed towards genetic counselling.Methods: A universal neonatal screening for hemoglobinopathies and thalassemia has been performed at our institution since 2002. Between October 2002 and July 2005, hemoglobin HPLC (High Performance Liquid Chromatography, Bio-Rad Variant II)) analysis performed on ombilical cord blood identified 123 newborns with hemoglobin H (HbH). Subsequently, DNA samples were analysed by m-PCR to detect the most common alpha-globin gene deletions:-α 3.7, -α 4.2, -α 20.5, -- SEA,-- FIL, -- THAI, -- MED. Groups were formed based on the genotype (1 deletion, 2 deletions, 2 deletions in cis, 2 deletions in trans) The mean level of HbH was calculated for each genotype and group. Student t-test was used to compare the level of HbH between the different groups. Due to the heterogeneity of the group populations, a Mann-Whitney test was also used to corroborate results obtained with t-test.Results: At least one α-globin gene deletion was observed in 90.2% of cases.(95%I.C: 83.5%-95.0%). Comparison between the groups based on the number of α-globin gene deletion and their allelic distribution allowed identification of significant differences in the HbH levels. Results were similar with Mann-Whitney (data not shown).Comparisons are presented in Table 1. HbH levels for the specific genotypes are presented in Figure 1.Conclusion: Hemoglobin HPLC analysis performed on umbilical cord blood allows rapid and efficient detection of HbH and highly predicts the presence of common α-globin gene deletions. Moreover a significant correlation is demonstrated between the levels of HbH and the presence of an α-thalassemic genotype. HbH level seems to correlate positively with the clinical severity of the genotype. However, a discriminate level of HbH could not be established to identify patients specifically requiring genotyping and genetic counselling. Further testing is necessary to evaluate the causes of HbH expression when there is no α-globin gene deletion. [Display omitted] Mean HbH level (% of total hemoglobin)deletions/allelic distributionHbH level (means)HbH level (range)level of significance1 deletion2.101.4–5.92 deletions6.964.0–12.6p<0.0011 deletion2.101.4–5.92 deletions trans6.504.0–9.2p<0.0011 deletion2.101.4–5.92 deletions cis10.67.3–12.6p<0.012 deletions trans6.504.0–9.22 deletions cis10.67.3–12.6p<0.001

Acquired haemoglobin H disease

Acquired haemoglobin H disease has been described in various premalignant haematological conditions and is most commonly associated with myelodysplastic and myeloproliferative syndromes. The condition is not restricted to any specific population group or geography. Affected individuals have no family or past history of alpha thalassaemia and these subjects usually suffer from severe uncompensated haemolysis. Extensive mapping and sequence analysis of the alpha globin gene cluster have demonstrated intact alpha globin genes, leading workers to conclude that an acquired in trans mechanism is responsible for the disorder. ATRX gene mutations on the X chromosome have been shown to be instrumental in the suppression of α globin gene expression. Despite recent advances in the understanding of its pathogenesis, the precise mechanism of acquired haemoglobin H disease remains a mystery.

Investigation of persistent hypochromic microcytosis unmasks hemoglobin Evanston [α 14 (A12) Try → Arg] in a patient of cyclic thrombocytopenia preceding Takayasu's disease

We report an unusual north Indian patient with Hemoglobin Evanston [α 14 (A12) Try → Arg] who had acquired cyclic thrombocytopenia (10–1230 × 109/l periodic oscillation of four week duration) which recovered without any specific therapy. She later developed Takayasu's disease and underwent three corrective stents. She is presently in clinical remission and is on regular follow up. To the best of our knowledge our patient is the first report of Hb Evanston from the indigenous population of India and highlights the need to look for point mutations in the alpha globin gene, which may interact with thalassemia or other hemoglobinopathies, in atypical cases. The association of these three disorders in our patient is possibly unrelated though an immune basis for the cyclic thrombocytopenia and Takayasu's disease is likely as seen in this report.

Upregulation of alpha globin promotes apoptotic cell death in the hematopoietic cell line FL5.12

The function of alpha globin in the context of oxygen transport in erythroid cells is well described. Recently the expression of alpha globin was shown to be upregulated upon specific apoptotic stimuli like cytokine deprivation or cisplatin treatment in the hematopoietic pro-B cell line, FL5.12. In contrast to alpha globin, beta globin or globin-like genes were expressed at a very low level or were not expressed at all. Further, we found that alpha globin was not associated with heme. Apoptotic cells neither produced hemoglobin nor displayed a phenotype of cells differentiating down the erythroid lineage. Also other cell lines of variable differentiation status (NIH3T3, HeLa, K562) upregulated alpha globin during treatment with apoptosis-inducing agents. Under IL-3-deprived conditions GFP-alpha globin accelerated the progression of apoptosis comparable to GFP-Bax. GFP-alpha globin was expressed at a low level and enrichment of FL5.12 cells expressing GFP-alpha globin was difficult even in the presence of IL-3. Caspase-8, -9 and -3 as well as the proapoptotic factor Bax and cytochrome c were activated. Antisense alpha globin downregulated the expression of endogenous alpha globin und reduced caspase activity. Taken together these data indicate that alpha globin is a new and crucial factor in apoptosis especially supporting the mitochondrial pathway.

The phylogenetic and evolutionary history of a novel alpha-globin-type gene in orangutans ( Pongo pygmaeus)

The alpha-globin genes are implicated in human resistance to malaria, a disease caused by Plasmodium parasites. This study is the first to analyze DNA sequences from a novel alpha-globin-type gene in orangutans, a species affected by Plasmodium. Phylogenetic methods show that the gene is a duplication of an alpha-globin gene and is located 5′ of alpha-2 globin. The alpha-globin-type gene is notable for having four amino acid replacements relative to the orangutan's alpha-1 and alpha-2 globin genes, with no synonymous differences. Pairwise K a/ K s methods and likelihood ratio tests (LRTs) revealed that the evolutionary history of the alpha-globin-type gene has been marked by either neutral or positive evolution, but not purifying selection. A comparative analysis of the amino acid replacements of the alpha-globin-type gene with human hemoglobinopathies and hemoglobin structure showed that two of the four replaced sites are members of the same molecular bond, one that is crucial to the proper functioning of the hemoglobin molecule. This suggested an adaptive evolutionary change. Functionally, this locus may result in a thalassemia-like phenotype in orangutans, possibly as an adaptation to combat Plasmodium.

A novel 33·3 kb deletion (‐ ‐KOL) in the alpha‐globin gene cluster: a brief report on deletional alpha‐thalassaemia in the heterogeneous eastern Indian population

We have detected, in three unrelated eastern Indian individuals, a hitherto unreported alpha zero deletion, - -KOL, in the heterozygous state, encompassing the embryonic zeta2-globin and the duplicated alpha-globin genes extending from c. 1150 bp upstream of the zeta2 globin gene to c. 960 bp downstream of the theta1 gene. Other deletions present in 120 unrelated, eastern Indian, putative alpha-thalassaemia patients are -3.7 kb (16.25%), -4.2 kb (5%) and - -SEA (3.33%).

Noninvasive Prenatal Diagnosis for Hemoglobin Bart's Hydrops Fetalis

Hemoglobin (Hb) Bart's hydrops fetalis, the most severe thalassemic disease, occurs from homozygosity of alpha-thalassemia 1. Deletion of all 4 alpha-globin genes (- -/- -) in this condition results in the absence of alpha-globin chains, and the physiologic dysfunction of Hb Bart's (gamma4) leads to lethality, either in utero or soon after birth. The best strategy for prevention and control of the disease is prenatal diagnosis in the mothers at risk. However, conventional prenatal diagnosis involves invasive procedures that may result in infection or abortion. In this study, a simple technique was developed to identify the presence or absence of alpha-globin chains in fetal nucleated red blood cells (NRBCs) enriched from maternal blood. Mononuclear cells including fetal NRBCs were isolated from maternal blood at 10 to 26 weeks of pregnancy by density-gradient centrifugation. Immunomagnetic separation with anti-CD71 antibody was employed to enrich fetal NRBCs, whose numbers increase with increasing gestational age. For the unaffected fetus, fetal NRBCs were detected by immunofluorescence microscopy after staining with rabbit antihuman alpha-globin antibody. In contrast, fetal red blood cells homozygous for alpha-thalassemia 1, which were identified from their size and morphology, did not stain for alpha-globin antibody. In this study, 3 affected fetuses were detected from 10 pregnancies at risk of Hb Bart's hydrops fetalis, and the results were confirmed by DNA analysis. In the remaining cases, all fetal NRBCs were positive for immunofluorescence staining. DNA analysis revealed that 2 cases were normal, 1 was heterozygous for alpha-thalassemia 2, and the other 4 cases were heterozygous for alpha-thalassemia 1.

The α-Globin Gene Family of an Australian Marsupial, Macropus eugenii: The Long Evolutionary History of the θ-Globin Gene and Its Functional Status in Mammals

Comparative evolutionary analyses of gene families among divergent lineages can provide information on the order and timing of major gene duplication events and evolution of gene function. Here we investigate the evolutionary history of the alpha-globin gene family in mammals by isolating and characterizing alpha-like globin genes from an Australian marsupial, the tammar wallaby, Macropus eugenii. Sequence and phylogenetic analyses indicate that the tammar alpha-globin family consists of at least four genes including a single adult-expressed gene (alpha), two embryonic/neonatally expressed genes (zeta and zeta'), and theta-globin, each orthologous to the respective alpha-, zeta-, and theta-globin genes of eutherian mammals. The results suggest that the theta-globin lineage arose by duplication of an ancestral adult alpha-globin gene and had already evolved an unusual promoter region, atypical of all known alpha-globin gene promoters, prior to the divergence of the marsupial and eutherian lineages. Evolutionary analyses, using a maximum likelihood approach, indicate that theta-globin, has evolved under strong selective constraints in both marsupials and the lineage leading to human theta-globin, suggesting a long-term functional status. Overall, our results indicate that at least a four-gene cluster consisting of three alpha-like and one beta-like globin genes linked in the order 5'-zeta-alpha-theta-omega-3' existed in the common ancestor of marsupials and eutherians. However, results are inconclusive as to whether the two tammar zeta-globin genes arose by duplication prior to the radiation of the marsupial and eutherian lineages, with maintenance of exon sequences by gene conversion, or more recently within marsupials.

The Population Genetics of the α-2 Globin Locus of Orangutans (Pongo pygmaeus)

In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were consistent with neutrality, the observed heterogeneous distribution of polymorphisms was inconsistent with neutral expectations. Furthermore, a single amino acid variant, found in both the Bornean and the Sumatran orangutan subspecies, was associated with different alternative synonymous variants in each subspecies, suggesting that the allele may have spread separately through the two subspecies after two distinct origination events. This variant is not in Hardy-Weinberg equilibrium (HWE). These observations are consistent with neutral models that incorporate population structure and models that invoke selection. The orangutan Plasmodium parasite is a plausible selective agent that may underlie the variation at alpha-2 globin in orangutans.

Association of Hb Q‐Thailand with homozygous Hb E and heterozygous Hb Constant Spring in pregnancy

Hemoglobin (Hb) Q-Thailand [alpha74(EF3): Asp-->His] is an abnormal Hb found mainly in China and South-east Asian countries. Association of the alpha(Q-Thailand) allele with alpha-thalassemia has important implications in diagnosis. We report the hitherto undescribed conditions of this variant in two unrelated pregnant Thai women. Routine Hb analyses using high-performance liquid chromatography identified abnormal Hb migrating after Hb A(2) in addition to a homozygous Hb E in the proband 1 and to a heterozygous Hb Constant Spring (Hb CS) in the proband 2. Further alpha-globin gene analysis identified that the variant was caused by the GAC to CAC mutation at codon 74 of the alpha1-globin gene corresponding to the Hb Q-Thailand, detected in cis to the 4.2 kb deletional alpha-thalassemia 2 in both cases. Interaction of the alpha(Q-Thailand) with the beta(E) globin chains in the proband 1 leads to a Hb variant, namely the Hb QE. Family study of the proband 1 showed that her non-pregnant sister had the same genotype but her father was a double heterozygote for Hb E and Hb Q-Thailand in whom both Hb Q-Thailand and Hb QE were detected. Genotype-phenotype relationships observed in these families with complex hemoglobinopathies are presented and compared with those of simple homozygote for Hb E, heterozygote for Hb CS and heterozygote for Hb Q-Thailand found in other unrelated subjects. A simple DNA assay based on allele-specific polymerase chain reaction for simultaneous detection of the Hb Q-Thailand mutation and the 4.2 kb deletional alpha-thalassemia 2 determinant was developed and validated.

A woman with 46,XX,dup(16)(p13.11 p13.3) and the ATR-X phenotype

We report a Japanese woman with 46,XX,dup(16)(p13.11p13.3), who closely resembled the phenotype of X-linked alpha-thalassemia/mental retardation syndrome (ATR-X, MIM # 301040). Although she never had alpha-thalassemia, she showed characteristic clinical features including severe mental retardation, characteristic facies and behavior. ATR-X is caused by mutations of the ATRX gene. Although the function of ATRX protein has remained unclarified, it is thought to be involved in the regulation of several genes. The only target gene identified so far is the alpha-globin gene at 16p13.3. Clinical similarity among patients with ATR-X and dup(16)(p13.11p13) may indicate that some target genes regulated by ATRX reside in the duplicated region between 16p13.11 and 16p13.3, and that these genes are abnormally upregulated in ATR-X differently from the alpha-globin gene.

Prevalence of α-Globin Gene Deletions Among Patients with Unexplained Microcytosis in a North-American Population

Increasing multi-ethnicity is likely to make alpha-thalassemia (alpha-thal) more prevalent in Western metropolitan areas. Multiplex polymerase chain reaction (m-PCR) allows rapid and precise identification of most of alpha-thal carriers. With this method, we sought to determine the prevalence of alpha-thal and the corresponding genotype, among all non repetitive consecutive blood samples that had an unexplained microcytosis. These specimens had been sent to the hematology laboratory for a blood count analysis, found to be microcytic, and secondarily tested for ferritin level and hemoglobin (Hb) high performance liquid chromatography (HPLC) profile. Five hundred and sixteen microcytic blood samples were evaluated and 197 samples with normal ferritin and Hb HPLC were studied by m-PCR. Among 196 interpretable PCRs, 48 alpha-thal cases (24.5%) were identified: 28 with a single alpha-globin gene deletion and 20 with two alpha-globin gene deletions. Of these 20 cases, six showed two deletions in cis. None of the erythrocytic parameters studied predicted the presence of alpha-thal deletions. We conclude that a significant proportion (24.5%) of blood counts with microcytosis not explained by an iron deficiency, an inflammatory state or an abnormal Hb on HPLC, are caused by an alpha-globin gene deletion. The pertinence of genetic counseling for alpha-thal based on molecular diagnosis should be evaluated more formally in urban centers where this genetic condition is likely to have an increasing prevalence and clinical relevance.

A General Method to Modify BACs to Generate Large Recombinant DNA Fragments

Bacterial artificial chromosome (BAC) has the capacity to clone DNA fragments in excess of 300 kb. It also has the considerable advantages of stable propagation and ease of purification. These features make BAC suitable in genetic research, such as library construction, transgenic mice production, and gene targeting constructs. Homologous recombination in Escherichia coli, a process named recombineering, has made the modification of BACs easy and reliable. We report here a modified recombineering method that can efficiently mediate the fusion of large DNA fragments from two or more different BACs. With the introduction of kanamycin-resistant gene and proposed rare-cutting restriction endonuclease (RCRE) sites into two BACs, a 82.6-kb DNA fragment containing the inverted human alpha-globin genes (theta, alpha1, alpha2, and zeta) from BAC191K2 and the locus control region (LCR) of human beta-globin gene locus (from the BAC186D7) was reconstructed. This approach for combining different BAC DNA fragments should facilitate many kinds of genomic experiments.

Antioxidant deficit and enhanced susceptibility to oxidative damage in individuals with different forms of α‐thalassaemia

alpha-Thalassaemia is a common red cell disorder in Taiwan, affecting 6-8% of Taiwanese. Previous studies have shown that reactive oxygen species are generated in increased amounts in thalassaemic red cells. This implies the possible alteration of redox status in thalassaemic patients, which may adversely affect their health. In the present study, the redox status of patients with alpha-thalassaemia trait and haemoglobin H (Hb H) disease was investigated. Lipid peroxidation, as measured by the level of plasma thiobarbituric acid reactive substances (TBARS), was increased in alpha-thalassaemic patients, with the highest level of TBARS in Hb H disease patient. The plasma levels of vitamin A, C, and E were significantly lower in alpha-thalassaemic patients than in controls. The overall antioxidant capacity in plasma was inversely correlated with the severity of alpha-globin gene defect: the more severe the form of alpha-thalassaemia, the lower the overall antioxidant capacity in plasma. Erythrocytes isolated from alpha-thalassaemia patients had lower levels of vitamin E, glutathione, catalase and superoxide dismutase. In addition, these alpha-thalassaemic red cells were more susceptible to hydrogen peroxide-induced lipid peroxidation and decrease in deformability. All these data suggest that the alpha-thalassaemic patients suffer from increased oxidative stress and antioxidant deficit, which may complicate the pathophysiology of alpha-thalassaemia.