Cloning and direct examination of a structurally abnormal human beta 0-thalassemia globin gene

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.

Comprehensive and efficient HBB mutation analysis for detection of beta-hemoglobinopathies in a pan-ethnic population

Current methods that assay hemoglobin beta-globin chain variants can have limited clinical sensitivity when applied techniques identify only a predefined panel of mutations. Even sequence-based assays may be limited depending on which gene regions are investigated. We sought to develop a clinically practical yet inclusive molecular assay to identify beta-globin mutations in multicultural populations. We highlight the beta-globin mutation detection assay (beta-GMDA), an extensive gene sequencing assay. The polymerase chain reaction (PCR) primers are located to encompass virtually all hemoglobin beta locus (HBB) mutations. In addition, this assay is able to detect, by gap PCR, a common large deletion (Delta619 base pair), which would be missed by sequencing alone. We describe our 5-year experience with the beta-GMDA and indicate its capability for detecting homozygous, heterozygous, and compound heterozygous sequence changes, including previously unknown HBB variants. The beta-GMDA offers superior sensitivity and ease of use with comprehensive detection of HBB mutations that result in beta-globin chain variants.

Sickle cell disease due to compound heterozygosity for Hb S and a novel 7.7-kb beta-globin gene deletion

A young woman originally from Cape Verde islands presented with mild sickle cell disease. Her blood counts and hemoglobin analysis results initially suggested that she might be either homozygous for the sickle cell hemoglobin (Hb S) with concomitant alpha-thalassemia, or compound heterozygous for Hb S and beta0-thalassemia, deletional deltabeta-thalassemia or hereditary persistence of fetal hemoglobin (HPFH). We utilized a novel polymerase chain reaction (PCR)-based screening technique and found a hitherto unrecognized 7.7-kb deletion, starting from the HBB IVSII to 3' downstream of the beta-globin gene. This diagnostic approach can be applied to decipher other similar deletional mutations. This is the second known deletion that removes the 3'-end but preserves the integrity of the 5'-end of the beta-globin gene. Furthermore, the identification of the deletion allows proper genetic counseling for affected families.

Double heterozygosity for the codon beta 39 C-to-T nonsense mutation and a triplicate alpha-globin gene locus can cause "dominantly" inherited beta-thalassemia intermedia

BACKGROUND

A beta-thalassemia intermedia phenotype can be caused by multiple genotypes.

METHODS

We studied a family where the mother was hematologically normal and both father and daughter had beta-thalassemia intermedia.

RESULTS

Both affected individuals were heterozygous for a codon 39 CAG-to-TAG mutation. They also were heterozygous for a triplicate alpha-globin gene locus (alphaalphaalpha(anti 3.7)).

CONCLUSIONS

This compound heterozygous condition of a beta39 C-to-T mutation and triplicate alpha-globin gene increases alpha:beta-globin chain imbalance and accounts for the presence of beta-thalassemia intermedia. The proband received both an abnormal beta-globin gene and a triplicate alpha-globin locus from her father. Although the phenotype seems to be dominantly inherited, because of independent segregation of the alpha- and beta-globin genes, it is more accurately an example of polygenic inheritance.

Beta-thalassemias: expression, molecular mechanisms and mutations in Indians

The beta-thalassemias are a heterogenous group of inherited disorders of hemoglobin (Hb) synthesis characterized by a reduction (beta+) or absence (beta zero) of synthesis of the beta globin chains of Hb, resulting in an imbalanced chain synthesis. To understand their expression and molecular basis in Indians, it is essential to review briefly the genetic control of normal Hb production and the structure, organization and regulation of different globin genes. The Indian beta-thalassemia mutations and strategies for prevention are described.

A significant beta-thalassemia heterogeneity in the United Arab Emirates

The Dubai Thalassemia Center has identified 35 different beta-thalassemia mutations in 570 chromosomes from the United Arab Emirates population using gene amplification, hybridization with specific labeled oligonucleotide probes, sequencing of amplified DNA, restriction enzymes, and amplification refractory mutation system techniques. This large number of mutations which represent 21% of the total beta-mutations discovered worldwide reflects the heterogenous nature of the population living in the United Arab Emirates (1). We found that 50% of our beta-thalassemia patients have a concomitant alpha-thalassemia; namely the -alpha 3.7 kb deletion. Co-inheritance of alpha-thalassemia especially in the form of two alpha-globin gene deletions have an ameliorating effect on the phenotype presentation of our beta-thalassemia. Nine patients (one homozygote and eight compound heterozygotes) were identified with Hb Monroe (IVS-I,-1 (G-->C)), a thalassemic hemoglobin characterized by an Arg-->Thr substitution in codon 30 of the beta-globin gene. In addition, one of the patients was a compound heterozygote for Hb Tacoma [IVS-I, +1 (G-->C)]; a point mutation affecting the third nucleotide of codon 30 (G-->C) causing an Arg-->Ser replacement.

A comprehensive scanning method for rapid detection of beta-globin gene mutations and polymorphisms

We describe a scanning procedure for the detection of beta-globin gene mutations and the prenatal diagnosis of beta-thalassemias. The method is based on the combined use of PCR and denaturing gradient gel electrophoresis (DGGE) of six amplified fragments encompassing the whole beta-globin coding region and splice junctions, as well as the promoter and 3' untranslated regions. The whole beta-globin gene can be rapidly scanned for the presence of deleterious mutations. The proposed diagnostic strategy provides a major improvement over current approaches to beta-globin gene analysis in both research and clinical laboratories, especially those which analyse DNA samples from individuals belonging to various ethnic or population groups. The use of this procedure has enabled us to detect six novel sequence changes in the beta-globin gene, including two deleterious mutations and four polymorphisms.

A greater than 200 kb deletion removing the entire beta-like globin gene cluster in a family of Irish descent

We describe a new deletional form of gamma delta beta-thalassemia segregating in two generations of a family of Irish descent. Affected family members present with a beta-thalassemia minor phenotype, normal Hb A2 and Hb F levels. Genomic blotting analyses on DNA from affected family members show heterozygosity for a large deletion beginning at least 15 kb upstream of the 5' endpoint of the gamma delta beta-thalassemia-1 deletion, extending through the entire beta-like globin gene cluster, and continuing for at least 10 kb beyond the 3' endpoint of the deletion associated with the Spanish form of delta beta 0-thalassemia. This deletion is among the largest described so far, and removes at least 205 kb encompassing the entire beta-like globin gene cluster on chromosome 11.

Prenatal diagnosis of inherited hemoglobinopathies

This paper reviews the methodology available to make prenatal diagnosis of inherited hemoglobinopathies by DNA analysis and the strategy to be used for the large scale application of this procedure to high-risk populations. The most straightforward approach for prenatal diagnosis is nowadays based on the analysis of DNA enzymatically amplified by the polymerase chain reaction (PCR). The mutations, produced by gross structural rearrangement of the DNA and those affecting a restriction recognition site, are directly detected by visualization following ethidium bromide staining of the electrophoretic pattern resulting from enzymatic digestion of amplified DNA. The remaining ones are detected by dot blot analysis with allelic specific oligonucleotide probes. Because in each population a limited number of specific beta-thalassemia mutations are prevalent, prenatal diagnosis by DNA analysis may be carried out by a population-specific strategy based on the amplification of those regions of the beta-globin genes containing the mutations most frequently occurring in each population followed by dot blot analysis with allelic specific oligonucleotide probes. This approach has the great advantage of being very simple, because radioactive probes are not necessary, very rapid, the results being obtained within 24 hours from sampling and very sensitive, only a limited amount of DNA in the order of 50 ng being necessary.

Type I C1 inhibitor deficiency with a small messenger RNA resulting from deletion of one exon

The molecular genetic basis of C1 inhibitor (C1 INH) deficiency in a patient with type I hereditary angioneurotic edema was studied. This patient was found to have an abnormally short C1 INH mRNA together with a normal message. Restriction fragment length polymorphism of the C1 INH gene was detected by Southern blot analysis of the patient's DNA after digestion with Pst I or Sac I, and hybridization with a full-length C1 INH cDNA. Hybridization of the same blot with three different fragments of the full-length cDNA suggested that exon VII and portions of both flanking introns were deleted in the C1 INH gene. Northern blot analysis of RNA from cultured monocytes, using a probe corresponding to exon VII, also indicated that the abnormal C1 INH mRNA had a deletion of these nucleotides. To confirm the hypothesis that the short C1 INH mRNA contained a deletion, the involved segment of the patient's C1 INH mRNA was amplified using the polymerase chain reaction (PCR). PCR amplification yielded two C1 INH DNA fragments of different lengths (380 and 160 bp). Southern blot and sequence analysis of both DNA fragments clearly revealed that the smaller 160-bp DNA was derived from the abnormal message and had a deletion of nucleotides corresponding to exon VII.

A beta-thalassemia mutant caused by a 300-bp deletion in the human beta-globin gene

Larger deletions are a rare cause of beta-thalassemia. We report a further instance of a deletion comprising about 300 bp in a female heterozygote. Exon 1, part of IVS-1 and the 5' beta-globin gene promotor region are lost.

The beta zero-thalassemia in an American black family is due to a single nucleotide substitution in the acceptor splice junction of the second intervening sequence

An AG dinucleotide is an invariant feature of all acceptor splice sites, and deletion or substitution of (one of) these nucleotides will result in abnormal processing of the beta-globin mRNA. Restriction endonuclease mapping of DNA from an American black patient with Hb S-beta zero-thalassemia failed to detect any deletion in the beta 0-globin gene region, but cloning and sequencing of the beta 0-globin gene showed a point mutation (A----C) in the highly conserved dinucleotide AG of the acceptor splice junction of the IVS-2. Blot hybridization analysis of RNA prepared from the erythroid cells of the patient showed only RNA of normal size. The patient and her daughter, who has the same condition, have high levels of Hb F (27%-35%); the mechanism responsible for the greatly increased gamma chain production remains unclear.

A distant gene deletion affects beta-globin gene function in an atypical gamma delta beta-thalassemia

We describe an English family with an atypical gamma delta beta-thalassemia syndrome. Heterozygosity results in a beta-thalassemia phenotype with normal hemoglobin A2. However, unlike previously described cases, no history of neonatal hemolytic anemia requiring blood transfusion was obtained. Gene mapping showed a deletion that extended from the third exon of the G gamma-globin gene upstream for approximately 100 kilobases (kb). The A gamma-globin, psi beta-, delta-, and beta-globin genes in cis remained intact. The malfunction of the beta-globin gene on a chromosome in which the deletion is located 25 kb away suggests that chromatin structure and conformation are important for globin gene expression.

Abnormal globin gene structure and expression in beta-thalassemia

Over the past five years, several new defects in the beta-thalassemias have been described from this laboratory using both restriction enzyme and sequencing analyses of cloned beta-thalassemia genes. The enzyme HphI has been shown to recognize a single nucleotide change at the 5' end of beta-IVS 2, and, using restriction enzyme analysis, demonstrated for the first time a specific defect associated with beta(0)-thalassemia. Cloning and sequencing of a beta-thalassemia gene have identified a single base change within IVS 2 at a position 705 nucleotides from the 5' end of IVS 2 that results in a beta(0)-thalassemia phenotype; no normal splicing occurs in this gene despite the fact that both the 5' and 3' ends of IVS 2 are unchanged. A unique and strong cryptic 3' acceptor splice site present in the normal gene at a position 580 nucleotides from the 5' end is used extensively in the mutant gene. Studies of this gene have indicated that there are sequences within IVS that are responsible for optimal expression of this gene; changes in these sequences can lead to markedly abnormal patterns of splicing. In addition, beta-globin gene expression has been evaluated in human erythroleukemia cells, K562 cells, and, although stable transformants with integrated beta-globin genes have been obtained, none of these transformants expressed the added beta-globin genes. This is presumably due to trans-acting factors or distal cis-acting effects that suppress the expression of these added beta-globin genes. In addition, a low epsilon-producing cell line, Bos cells, was used as a recipient for an exogenous epsilon-globin gene. A neomycin resistance gene was cotransfected into these cells, and a neomycin analogue (G418) was used to select cells containing both the neomycin resistance and epsilon-globin genes. Using Southern blotting, 10 of 11 stably transformed G418-resistant lines, which contain intact epsilon-globin genes, express epsilon-globin mRNA at much higher levels than the Bos cells into which they were transfected. Two of these lines express the epsilon-globin genes at a level comparable to that of wild-type K562 cells. These results indicate that the transfer and expression of human globin genes in human erythroid cells is feasible, and can occur at a high level.(ABSTRACT TRUNCATED AT 400 WORDS)

Beta-thalassemia resulting from a single nucleotide substitution in an acceptor splice site

Beta-globin gene mutations which alter normal globin RNA splicing have confirmed the necessity of invariant nucleotides GT at donor splice sites. Functional consequences of point mutations in the invariant AG acceptor splice site have not been determined. We have isolated and characterized a beta-globin gene from a Black patient with beta-thalassemia intermedia which has an A-G transition at the usual intervening sequence 2 (IVS2) acceptor splice site. Functional analysis of transcripts produced by this mutant gene in a transient expression vector indicates that the mutation inactivates the normal acceptor splice site and results in some utilization of a cryptic splice site near position 580 of IVS2. This mutation would be expected to produce a beta-globin gene which results in no normal beta-globin mRNA.

Molecular evidence for new mutation at the hprt locus in Lesch-Nyhan patients

Hypoxanthine-guanine phosphoribosyltransferase (HPRT; EC2.4.2.8), which functions in the metabolic salvage of purines, is encoded by an X-linked gene in man. Partial HPRT deficiencies are associated with gouty arthritis, while absence of activity results in Lesch-Nyhan syndrome (L-N). L-N patients fail to reproduce and the heterozygous state appears to confer no selective advantage. Thus, Haldane's principle predicts that new mutations at the hprt locus must occur frequently in order for L-N syndrome to be maintained in the population. This constant introduction of new mutations would be expected to result in a heterogeneous collection of genetic lesions, some of which may be novel. As we report here, the mutations in the hprt gene of seven L-N patients, selected from an initial survey of 28 patients, have been characterized and all were found to be distinctly different, as predicted. The origin of one unusual mutation has been identified by analysis of DNA from four generations of family members. Further molecular analysis of the origin of new mutations at the hprt locus should aid in resolving the issue of an apparent difference in the frequency of hprt mutations in males and females.

Hemolytic disease of the newborn caused by a new deletion of the entire beta-globin cluster

We describe a new type of gamma delta beta-thalassemia in four generations of a family of Scotch-Irish descent. The proposita presented with hemolytic disease of the newborn, which was characterized by a microcytic anemia. Initial restriction endonuclease analysis of the DNA showed no grossly abnormal patterns, but studies of polymorphic restriction sites and gene dosage revealed an extensive deletion that removed all the beta- and beta-like globin genes from the affected chromosome. In situ hybridization of chromosome preparations with radioactive beta-globin gene probes showed that only one 11p homolog contained the beta-globin gene cluster in the affected family members.

Abnormal splice in a mutant human beta-globin gene not at the site of a mutation

We have studied the expression of a cloned mutant human beta-globin gene in tissue culture cells. The gene, which was previously isolated from the chromosomal DNA of an individual with a low level of normal beta-globin expression (beta+-thalassemia), contains five mutations inside the large intervening sequence (IVS2), as well as a silent change in codon 2. This beta-thalassemia gene (thal) was inserted into a plasmid that is replicated and transcribed in a line of monkey kidney cells in culture. S1 nuclease mapping of the beta-globin RNA transcribed from this gene indicates that some of the beta-globin RNA is spliced abnormally by using a cryptic 3' splice sequence normally present in IVS2 but not used in processing the normal beta-globin transcript. The cryptic 3' splice site is not the site of a mutation in the thal gene. Because neither the 5' or 3' splice junction nor the cryptic site is mutated in this gene, it is most likely that the mutation at position 705 of IVS2, the only nonpolymorphic change in the gene, interferes indirectly with normal processing. These results suggest that certain sequences within IVS must be conserved to prevent abnormal splicing and loss of gene function.

Duplication followed by deletion accounts for the structure of an Indian deletion beta (0)-thalassemia gene

Nucleotide sequence analysis of a cloned deletion beta-globin gene from a patient with beta(0)-thalassemia demonstrates a 619 nucleotide deletion extending from the 3' third of the second intervening sequence through 209 bases of 3' flanking DNA. However, an additional novel heptanucleotide was identified between the deletion endpoints, suggesting a complex etiology for this rearrangement.

Genetic diseases: diagnosis by restriction endonuclease analysis

We have summarized a number of different genetic disorders which can be diagnosed at the DNA level using restriction endonuclease fragment analysis. A whole spectrum of defects can be recognized: point mutations, deletions, additions, and crossing-over products or hybrid genes. These same restriction endonuclease techniques can enable different genes to be marked by polymorphism patterns. Thus, abnormal genes can be identified even if their exact DNA lesion is unknown or cannot be directly detected. The progress that has been made with the hemoglobinopathies and the experience from this group of single gene disorders should find application to other diseases as soon as specific probes become available.

Five nucleotide changes in the large intervening sequence of a beta globin gene in a beta+ thalassemia patient

A beta globin gene from a patient with homozygous beta+ thalassemia has been cloned and completely sequenced. No changes from normal are found in the 200 nucleotides 5' to the cap site, in the 3' untranslated region up to the poly A addition site, in the small intervening sequence (IVS 1), or in the coding sequence except for a third base change in codon 2. The only other differences are in the large intervening sequence (IVS 2). One of these, at a position 16 nucleotides from the 5' end of IVS 2, has been reported previously in normal individuals, and is probably a polymorphism. Four other changes, at positions 74, 81, 666, and 705 are also seen in IVS 2. Abnormal beta globin mRNA precursors detected in the bone marrow cells of this patient, and abnormal beta globin RNA splicing observed when this gene is transcribed in a tissue culture system taken together with these IVS 2 changes, suggest that the beta+ thalassemia phenotype is produced by a decrease in normal beta globin mRNA processing.

Two cloned beta thalassemia genes are associated with amber mutations at codon 39

Two beta globin genes from patients with the beta(+) thalassemia phenotype have been cloned and sequenced. A single nucleotide change from CAG to TAG (an amber mutation) at codon 39 is the only difference from normal in both genes analyzed. The results are consistent with the assumption that both patients are doubly heterozygous for beta(+) and beta degrees thalassemia, and that we have isolated and analyzed the beta degrees thalassemia gene.

beta zero thalassemia in Sardinia is caused by a nonsense mutation

We report the characterization of a molecular lesion of beta thalassemia in Sardinia. Beta thalassemia in this area is predominantly the beta zero type with low levels of beta-globin mRNA. Translation assay of this messenger RNA in a cell-free system showed beta-globin chain synthesis only with the addition of an amber (UAG) suppressor transfer RNA. Double-stranded complementary DNA prepared from reticulocyte mRNA from a Sardinian patient was cloned in a bacterial plasmid and a beta-globin complementary DNA containing clone was isolated and sequenced. At the position corresponding to amino acid number 39, a single nucleotide mutation converted a glutamine codon (CAG) to an amber termination codon (UAG). We previously reported an amber nonsense mutation at amino acid 17 as a cause of Chinese beta zero thalassemia. Thus, beta zero thalassemia in Sardinia represents the second example of a nonsense mutation, and we predict that other beta zero thalassemias with mutations at various points along the beta-globin chain will be found to form a discrete subgroup of beta zero thalassemia. These experiments further illustrate the heterogeneity of lesions that lead to defective globin chain synthesis in beta thalassemia.