A novel deletion causing alpha thalassemia clarifies the importance of the major human alpha globin regulatory element

Identification of a novel 91.5 kb-deletion (αα)FJ in the α-globin gene cluster using single-molecule real-time (SMRT) sequencing

OBJECTIVES

To present a novel 91.5-kb deletion of the α-globin gene cluster (αα)FJ identified by genetic assay and prenatal diagnosis in a Chinese family.

SUBJECTS AND METHODS

The proband was a 34-year-old G3P1 (Gravida 3, Para 1) female at the gestational age of 21+ weeks with a history of an edematous fetus. A routine genetic assay (reverse dot blot hybridization, RDB) was performed to detect common thalassemia mutations. Multiplex ligation-dependent probe amplification (MLPA) and single-molecule real-time technology (SMRT) were used to detect rare thalassemia mutations.

RESULTS

The hematological phenotypes of the proband, her mother, elder sister, husband, daughter, and nephew were consistent with the phenotype of α-thalassemia trait. No mutations were found in these family members by RDB, except for the proband's husband who carried an α-globin gene deletion --SEA/αα. MLPA results showed that the proband and other α-thalassemia-suspected relatives had heterozygous deletions around the POLR3K-3-463nt, HS40-178nt, and HBA-HS40-382nt probes. The 5'-breakpoint was out of probe scope and could not be determined. SMRT was performed and a 91.5-kb deletion (NC_000016.10: g.39268_130758del) in the α-globin gene cluster (αα)FJ was identified in the proband and other suspected relatives, which could explain their phenotypes. At the proband's gestational age of 22+ weeks, an amniotic fluid sample was collected and analyzed. As only the 91.5-kb deletion (αα)FJ was identified in the fetus with RDB, MLPA, and SMRT. The proband was suggested to continue the pregnancy.

CONCLUSION

We first reported a 91.5-kb deletion (NC_000016.10: g.hg38-chr16:39268-_130758del) of the HS-40 region in the α-globin gene cluster (αα)FJ identified in a Chinese family. Since the HS-40 loss of heterozygosity in combination with the heterozygous deletion --SEA might result in Hb Bart's hydrops fetalis, routine genetic assay, and SMRT were recommended to individuals at risk for prenatal diagnosis.

Molecular characterization of a novel 83.9-kb deletion of the α-globin upstream regulatory elements by long-read sequencing

Inherited deletions of upstream regulatory elements of α-globin genes give rise to α-thalassemia, which is an autosomal recessive monogenic disease. However, conventional thalassemia target diagnosis often fails to identify these rare deletions. Here we reported a family with two previous pregnancies of Hb Bart's hydrops fetalis and was seeking for prenatal diagnosis during the third pregnancy. Both parents had low level of Hemoglobin A2 indicating α-thalassemia. Conventional Gap-PCR and PCR-reverse dot blot showed the father carried -SEA deletion but did not identify any variants in the mother. Multiplex ligation-dependent probe amplification identified a deletion containing two HS-40 probes but could not determine the exact region. Finally, a long-read sequencing (LRS)-based approach directly identified that the exact deletion region was chr16: 48,642-132,584, which was located in the α-globin upstream regulatory elements and named (αα)JM after the Jiangmen city. Gap-PCR and Sanger sequencing confirmed the breakpoint. Both the mother and fetus from the third pregnancy carried heterozygous (αα)JM, and the fetus was normally delivered at gestational age of 39 weeks. This study demonstrated that LRS technology had great advantages over conventional target diagnosis methods for identifying rare thalassemia variants and assisted better carrier screening and prenatal diagnosis of thalassemia.

Functional analysis of three new alpha-thalassemia deletions involving MCS-R2 reveals the presence of an additional enhancer element in the 5' boundary region

We report three novel deletions involving the Multispecies Conserved Sequences (MCS) R2, also known as the Major Regulative Element (MRE), in patients showing the α-thalassemia phenotype. The three new rearrangements showed peculiar positions of the breakpoints. 1) The (αα)ES is a telomeric 110 kb deletion ending inside the MCS-R3 element. 2) The (αα)FG, 984 bp-long, ends 51 bp upstream to MCS-R2; both are associated with a severe α-thalassemia phenotype. 3) The (αα)CT, 5058 bp-long starts at position +93 of MCS-R2 and is the only one associated to a mild α-thalassemia phenotype. To understand the specific role of different segments of the MCS-R2 element and of its boundary regions we carried out transcriptional and expression analysis. Transcriptional analysis of patients' reticulocytes showed that (αα)ES was unable to produce α2-globin mRNA, while a high level of expression of the α2-globin genes (56%) was detected in (αα)CT deletion, characterized by the presence of the first 93 bp of MCS-R2. Expression analysis of constructs containing breakpoints and boundary regions of the deletions (αα)CT and (αα)FG, showed comparable activity both for MCS-R2 and the boundary region (-682/-8). Considering that the (αα)CT deletion, almost entirely removing MCS-R2, has a less severe phenotype than the (αα)FG α0thalassemia deletion, removing both MCS-R2 almost entirely and an upstream 679 bp, we infer for the first time that an enhancer element must exist in this region that helps to increase the expression of the α-globin genes. The genotype-phenotype relationship of other previously published MCS-R2 deletions strengthened our hypothesis.

Non-immune Hemolysis: Diagnostic Considerations

Non-immune hemolytic anemia (NIHA) is characterized by positive routine hemolytic tests but negative anti-human immunoglobulin (Coombs) test. Hereditary non-immune hemolysis includes disorders of erythrocytic enzymes, membrane, hemoglobin (qualitative and quantitative disorders), as well as the rare hereditary forms of thrombotic microangiopathies. Acquired NIHA includes paroxysmal nocturnal hemolysis (PNH), infections, drug and metal intoxications with as a target red blood cells or endothelium of capillaries, the rare acquired forms of thalassemia or erythrocytic membrane disorders, and hemolysis secondary to a dysfunctioning artificial (prosthetic) cardiac valve. Identification of the specific cause of NIHA is sometimes difficult and requires not only a good knowledge of this entity but mainly a qualified specialized hematologic laboratory. An algorithm to be used in every new patient consulting for NIHA is proposed in the last part of this article.

Two complex associations of an HBD mutation and a rare α hemoglobinopathy

We present two case reports in which an HBD mutation is present with a rare α hemoglobinopathy that substantially complicates the associated phenotype. In the first case, a new δ-globin variant, Hb A2-Pierre-Bénite [δ83(EF7)Gly→Arg; HBD: c.250G>C] is associated with Hb Groene Hart [α119(H2)Pro→Ser (α1); HBA1: c.358C>T], an α-thalassemic variant. In the second case, a δ(+)-thalassemic variant, δ4(A1)Thr→Ile; HBD: c.14C>T, is associated with a newly described deletion of the hypersensitive site 40 (HS-40) region on the α-globin gene cluster. In both patients, a δ-globin mutation was suspected because of an abnormally low Hb A2 level, whereas the α hemoglobinopathy was sought to explain the slight microcytosis and hypochromia presented by the probands.

Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network

Laboratory red blood cell (RBC) measurements are clinically important, heritable and differ among ethnic groups. To identify genetic variants that contribute to RBC phenotypes in African Americans (AAs), we conducted a genome-wide association study in up to ~16 500 AAs. The alpha-globin locus on chromosome 16pter [lead SNP rs13335629 in ITFG3 gene; P < 1E-13 for hemoglobin (Hgb), RBC count, mean corpuscular volume (MCV), MCH and MCHC] and the G6PD locus on Xq28 [lead SNP rs1050828; P < 1E - 13 for Hgb, hematocrit (Hct), MCV, RBC count and red cell distribution width (RDW)] were each associated with multiple RBC traits. At the alpha-globin region, both the common African 3.7 kb deletion and common single nucleotide polymorphisms (SNPs) appear to contribute independently to RBC phenotypes among AAs. In the 2p21 region, we identified a novel variant of PRKCE distinctly associated with Hct in AAs. In a genome-wide admixture mapping scan, local European ancestry at the 6p22 region containing HFE and LRRC16A was associated with higher Hgb. LRRC16A has been previously associated with the platelet count and mean platelet volume in AAs, but not with Hgb. Finally, we extended to AAs the findings of association of erythrocyte traits with several loci previously reported in Europeans and/or Asians, including CD164 and HBS1L-MYB. In summary, this large-scale genome-wide analysis in AAs has extended the importance of several RBC-associated genetic loci to AAs and identified allelic heterogeneity and pleiotropy at several previously known genetic loci associated with blood cell traits in AAs.

BRG1 directly regulates nucleosome structure and chromatin looping of the alpha globin locus to activate transcription

α globin expression must be regulated properly to prevent the occurrence of α-thalassemias, yet many questions remain unanswered regarding the mechanism of transcriptional activation. Identifying factors that regulate chromatin structure of the endogenous α globin locus in developing erythroblasts will provide important mechanistic insight. Here, we demonstrate that the BRG1 catalytic subunit of SWI/SNF-related complexes co-immunoprecipitates with GATA-1 and EKLF in murine fetal liver cells in vivo and is recruited to the far-upstream major-regulatory element (MRE) and α2 promoter. Furthermore, based on our analysis of Brg1^null/ENU1 mutant mice, BRG1 regulates DNase I sensitivity, H3ac, and H3K4me2 but not CpG methylation at both sites. Most importantly, BRG1 is required for chromatin loop formation between the MRE and α2 promoter and for maximal RNA Polymerase II occupancy at the α2 promoter. Consequently, Brg1 mutants express α globin mRNA at only 5–10% of wild-type levels and die at mid-gestation. These data identify BRG1 as a chromatin-modifying factor required for nucleosome remodeling and transcriptional activation of the α globin locus. These data also demonstrate that chromatin looping between the MRE and α2 promoter is required as part of the transcriptional activation mechanism.

Dynamics of alpha-globin locus chromatin structure and gene expression during erythroid differentiation of human CD34(+) cells in culture

OBJECTIVE

The aim of the present study has been to establish serum-free culture conditions for ex vivo expansion and differentiation of human CD34(+) cells into erythroid lineage and to study the chromatin structure, gene expression, and transcription factor recruitment at the alpha-globin locus in the developing erythron.

MATERIALS AND METHODS

A basal Iscove's modified Dulbecco's medium cell culture medium with 1% bovine serum albumin as a serum replacement and a combination of cytokines and growth factors was used for expansion and differentiation of the CD34(+) cells. Expression patterns of the alpha- and beta-like genes at various stages of erythropoiesis was studied by reverse transcriptase quantitative polymerase chain reaction analysis, profile of key erythroid transcription factors was investigated by Western blotting, and the chromatin structure and transcription factor recruitment at the alpha-globin locus was investigated by chromatin immunoprecipitation quantitative polymerase chain reaction analysis.

RESULTS

Human CD34(+) cells in the serum-free medium undergo near synchronous erythroid differentiation to yield large amount of cells at different differentiation stages. We observe distinct patterns of the histone modifications and transcription factor binding at the alpha-globin locus during erythroid differentiation of CD34(+) cells. Nuclear factor erythroid-derived 2 (NF-E2) was present at upstream activator sites even before addition of erythropoietin (EPO), while bound GATA-1 was only detectable after EPO treatment. After 7 days of EPO treatment, H3K4Me2 modification uniformly increases throughout the alpha-globin locus. Acetylation at H3K9 and binding of Pol II, NF-E2, and GATA-1 were restricted to certain hypersensitive sites of the enhancer and theta gene, and were conspicuously low at the alpha-like globin promoters. Rearrangement of the insulator binding factor CTCF took place at and around the alpha-globin locus as CD34(+) cells differentiated into erythroid pathway.

CONCLUSION

Our results indicate that remodeling of the upstream elements may be the primary event in activation of alpha-globin gene expression. Activation of alpha-globin genes upon EPO treatment involves initial binding of Pol II, downregulation of pre-existing factors like NF-E2, removal of CTCF from the locus, then rebinding of CTCF in an altered pattern, and concurrent or subsequent binding of transcription factors like GATA-1.

Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease

The spatiotemporally and quantitatively correct activity of a gene requires the presence of intact coding sequence as well as properly functioning regulatory control. One of the great challenges of the post-genome era is to gain a better understanding of the mechanisms of gene control. Proper gene regulation depends not only on the required transcription factors and associated complexes being present (in the correct dosage), but also on the integrity, chromatin conformation and nuclear positioning of the gene's chromosomal segment. Thus, when either the cis-trans regulatory system of a gene or the normal context of its chromatin structure are disrupted, gene expression may be adversely affected, potentially leading to disease. As transcriptional regulation is a highly complex process depending on many factors, there are many different mechanisms that can cause aberrant gene expression. Traditionally, the term 'position effect' was used to refer to situations where the level of expression of a gene is deleteriously affected by an alteration in its chromosomal environment, while maintaining an intact transcription unit. Over the past years, an ever increasing number of such disease-related position effect cases have come to light, and detailed studies have revealed insight into the variety of causes, which can be categorized into a number of different mechanistic groups. We suggest replacing the outdated term of 'position effect disease' with the new generic name of 'cis-ruption disorder' to describe genetic disease cases that are caused by disruption of the normal cis-regulatory architecture of the disease gene locus. Here, we review these various cis-ruption mechanisms and discuss how their studies have contributed to our understanding of long- range gene regulation.

Hb H disease: clinical course and disease modifiers

Hemoglobin H (Hb H) disease is the most common form of thalassemia intermedia and has many features that require careful consideration in management. In the majority of cases, Hb H disease results from double heterozygosity for α0-thalassemia due to deletions that remove both linked α-globin genes on chromosome 16, and deletional α+-thalassemia from single α-globin gene deletions (--/−α). However, Hb H disease may occur from interactions between α0-thalassemia with non-deletional mutations (αTα or αT) or with abnormal hemoglobins such as Hb Constant Spring, Hb Paksé, Hb Quong Sze, and Hb Pak Num Po. In a steady state, patients with Hb H diseases have hemoglobin levels around 9 to 10 g/dL; however, during hemolytic crisis, which frequently develops in or after acute infections with high fever, the hemoglobin level may drop significantly and patients can develop shock or renal shutdown. Even though splenectomy leads to significant elevation of hemoglobin levels, it is not recommended because the majority of patients do well with said steady-state hemoglobin levels. Patients with non-deletional Hb H disease are usually more anemic with significant splenomegaly, and some may require regular blood transfusions and be even as severe as “Hb H hydrops fetalis.” However, there is no clear genotype-phenotype correlation associated with this severe clinical syndrome since patients with identical genotypes do not necessary show the same severity. This suggests that other genetic and environmental factors play a role in modifying the degree of clinical severity in patients with non-deletional Hb H disease.

A large deletion in the human alpha-globin cluster caused by a replication error is associated with an unexpectedly mild phenotype

We have characterized a newly identified 16.6 kb deletion which removes a significant proportion of the human alpha-globin cluster including the psizeta1, alpha(D), psialpha1 and alpha2-globin genes but leaves the duplicated alpha1 gene intact. This complicated rearrangement results from a combination of slippage and strand switching at sites of microhomology during replication. Functional analysis shows that expression of the remaining alpha1 gene is increased, rather than down-regulated by this deletion. This could be related to its proximity to the remote upstream alpha-globin regulatory elements or reduced competition for these elements in the absence of the dominant alpha2-globin gene. The finding of a very mild phenotype associated with such an extensive deletion in the alpha-globin cluster implies that much of the DNA removed by the deletion is likely to be functionally unimportant. These findings suggest that other than the upstream regulatory elements and promoter proximal elements there are unlikely to be additional positive cis-acting sequences in the alpha-globin cluster.

Long-range gene control and genetic disease

The past two decades have seen great progress in the elucidation of the genetic basis of human genetic disease. Many clinical phenotypes have been linked with mutations or deletions in specific causative genes. However, it is often less recognized that in addition to the integrity of the protein-coding sequences, human health critically also depends on the spatially, temporally, and quantitatively correct expression of those genes. Genetic disease can therefore equally be caused by disruption of the regulatory mechanisms that ensure proper gene expression. The term "position effect" is used in those situations where the expression level of a gene is deleteriously affected by an alteration in its chromosomal environment, while maintaining an intact transcription unit. Here, we review recent advances in our understanding of the possible mechanisms of a number of "position effect" disease cases and discuss the findings with respect to current models for genome organization and long-range control of gene expression.

Long-range regulation of alpha-globin gene expression

Over the past 20 years, there has been an increasing awareness that gene expression can be regulated by multiple cis-acting sequences located at considerable distances (10-1000 kb) from the genes they control. Detailed investigation of a few specialized mammalian genes, including the genes controlling the synthesis of hemoglobin, provide important models to understand how such long-range regulatory elements act. In general, these elements contain a high density of evolutionarily conserved, transcription factor-binding sites and in many ways resemble the upstream regulatory elements found adjacent to the promoters of genes in simpler organisms, differing only in the distance over which they act. We have investigated in detail how the remote regulatory elements of the alpha-globin cluster become activated as hematopoietic stem cells (HSCs) undergo commitment, lineage specification, and differentiation to form red blood cells. In turn, we have addressed how, during this process, the upstream elements control the correct spatial and temporal expression from the alpha-gene promoter which lies approximately 60 kb downstream of these elements. At present too few loci have been studied to determine whether there are general principles underlying long-range regulation but some common themes are emerging.

Tissue-specific histone modification and transcription factor binding in α globin gene expression

To address the mechanism by which the human globin genes are activated during erythropoiesis, we have used a tiled microarray to analyze the pattern of transcription factor binding and associated histone modifications across the telomeric region of human chromosome 16 in primary erythroid and nonerythroid cells. This 220-kb region includes the α globin genes and 9 widely expressed genes flanking the α globin locus. This un-biased, comprehensive analysis of transcription factor binding and histone modifications (acetylation and methylation) described here not only identified all known cis-acting regulatory elements in the human α globin cluster but also demonstrated that there are no additional erythroid-specific regulatory elements in the 220-kb region tested. In addition, the pattern of histone modification distinguished promoter elements from potential enhancer elements across this region. Finally, comparison of the human and mouse orthologous regions in a unique mouse model, with both regions coexpressed in the same animal, showed significant differences that may explain how these 2 clusters are regulated differently in vivo.

HS-48 alone has no enhancement role on the expression of human α-globin gene cluster

To investigate the in vivo function of the newly defined DNase I hypersensitive site HS-48 on the whole human alpha-globin gene cluster, the region containing all the other known 5 hypersensitive sites HS-4 to HS-40 was deleted from a 117 kb bacterial artificial chromosome clone bearing the whole human alpha-globin gene cluster. Transgenic mice were generated from this construct. The RNase protection assays showed that with HS-48 left and all the other 5 hypersensitive sites deleted, the expression of human alpha-like globin genes was completely silenced in embryonic, fetal and adult stages in all tissues. This finding indicates that HS-48 alone has no enhancer activity on the expression of human alpha-like globin genes, and that the region of HS-4 to HS-40 already contains all the upstream cis-elements needed for regulating human alpha-like globin genes.