Novel large deletions in the human alpha-globin gene cluster: Clarifying the HS-40 long-range regulatory role in the native chromosome environment

Globin genes, which encode the protein subunits of hemoglobin (Hb), are organized in two different gene clusters and present a coordinated and differential pattern of expression during development. Concerning the human α-globin gene cluster (located at chromosome region 16p13.3), four upstream highly conserved elements known as multispecies conserved sequences (MCS-R1-4) or DNase I hypersensitive sites (HSs) are implicated in the long-range regulation of downstream gene expression. However, only the absence of the MCS-R2 site (HS-40) has proven to drastically downregulate the expression of those genes, and consequently, it has been regarded as the major and crucial distal regulatory element. In this study, Multiplex Ligation-dependent Probe Amplification was used to screen for deletions in the telomeric region of the short arm of chromosome 16, in an attempt to explain the α-thalassemia or the HbH disease present in a group of Portuguese patients. We report four novel and five uncommon deletions that remove the α-globin distal regulatory elements and/or the complete α-globin gene cluster. Interestingly, one of them occurred de novo and removes all HSs except HS-10, while other eliminates only the HS-40 site, the latter being replaced by the insertion of a 39 nucleotide orphan sequence. Our results demonstrate that HS-10 alone does not significantly enhance the α-globin gene expression. The absence of HS-40 in homozygosity, found in a patient with Hb H disease, strongly downregulates the expression of α-globin genes but it is not associated with a complete absence of α-globin chain production. The study of naturally occurring deletions in this region is of great interest to understand the role of each upstream regulatory element in the native human erythroid environment

Controlo da qualidade interno e avaliação externa da qualidade para a quantificação da HbA2

As hemoglobinopatias são doenças monogénicas de transmissão autossómica recessiva, causadas por mutações nos genes que codificam para as cadeias globínicas, ou nas suas regiões regulatórias. Podem conduzir à síntese reduzida da hemoglobina (Hb) (talassemias) ou à formação de hemoglobinas estruturalmente anómalas (variantes). Em Portugal, a percentagem de portadores de hemoglobinopatias na população em geral varia entre 0,5 e 2,0%1. A quantificação da Hb A2 é essencial na deteção de portadores de β-talassemia, sendo muito importante na prevenção do aparecimento de formas graves de hemoglobinopatias. A deteção de portadores de β-talassemia é facilmente realizada nos fenótipos clássicos caracterizados por aumento da Hb A2 (4-6%) e diminuição dos índices eritrocitários (VGM e HGM). No entanto, devido à proximidade entre os valores de Hb A2 normais e patológicos, e aos fenótipos atípicos, com índices eritrocitários próximos do normal e valores de Hb A2 borderline (3,3-3,8%), é muito importante determinações com alto grau de reprodutibilidade e exatidão 2,3. O Controlo da Qualidade Laboratorial através do Controlo da Qualidade Interno (CQI) e da participação em programas de Avaliação Externa da Qualidade (AEQ), permite avaliar e melhorar os níveis de precisão e exatidão analítica, possibilitando a longo termo, uma avaliação retrospetiva do desempenho do laboratório, demonstrando a sua competência relativamente aos seus pares

Hemoglobin variants with electrophoretic mobility similar to hemoglobin S

9ª Reunião Científica da Sociedade Portuguesa de Medicina Laboratorial, 7-8 abril 2017Hemoglobinopathies are among the most common inherited diseases around the world and are one of the world’s major health problems. They are monogenic diseases of autosomal recessive transmission resulting from mutations affecting the genes responsible for the synthesis of globin chains. Abnormal hemoglobins (Hb), named Hb variants, are caused by structural defects resulting from an altered amino acid sequence in globin chains, being Hb S the more frequent and pathogenic/disease associated. The aim of this work was to identify and characterize Hb variants with mobility similar to Hb S when using common laboratorial methodologies, such as isoelectric focusing and high pressure ion exchange chromatography (HPLC). Hemoglobin analysis was performed by isoelectric focusing and HPLC. Globin chain variants were classified in alpha or beta type by reversed phase high performance chromatography. Hb S was confirmed by the solubility test. In order to identify the rare Hb variants, molecular analyses were performed in patient’s DNA. From 2010 to 2016, in the routine practice of our laboratory, 601 cases of variants of Hb were detected with mobility Hb S-like. Amongst them, 433 were confirmed as being Hb S (72.0%). Others hemoglobins also with clinical relevance, Hb D and Hb Lepore, were prevalent, 90 (15.0%) and 61 (10.2%), respectively. The remaining 17 cases were classified as rare (2.8%) and 10 of them were identified by molecular studies as: Hb Maputo (1), Hb G-Coushata (1), Hb Summer Hill (1), Hb Setif (1), Hb G Waimanalo (1), Hb D Iran (1) Hb Oleander (1), Hb Ottawa (1), Hb Etobicoque (1) and Hb Matsue-Oki (1). Hb Matsue-Oki was found in compound heterozygosity with the –α3.7kb-thalassemia deletion. We can conclude that combining the results obtained by the different biochemical methodologies allow the presumptive identification of the more prevalent variants, namely Hb S, Hb D and Hb Lepore, and direct the molecular study for the definitive identification. This study also revealed that several rare variants have similar mobility as Hb S and, consequently, some safety measures should be applied in order to achieve their accurate identification. A correct laboratorial diagnosis is essential for proper patient’s clinical management and genetic counselling.info:eu-repo/semantics/publishedVersio

Hemoglobinas variantes com mobilidade eletroforética semelhante à da Hemoglobina S

Introdução: As hemoglobinopatias são doenças monogénicas hereditárias, de transmissão autossómica recessiva, resultantes de mutações nos genes codificantes para as cadeias de globina da hemoglobina (Hb), ou nas suas regiões regulatórias. Encontram-se entre as doenças hereditárias mais comuns e constituem um dos principais problemas de saúde a nível mundial. As variantes das hemoglobinas são causadas por defeitos estruturais resultantes de alterações na sequência de aminoácidos nas cadeias de globina, sendo a Hb S a mais frequente e associada a patologia. As hemoglobinopatias são as únicas, entre todas as doenças genéticas, em que a deteção de portadores é possível por testes hematológicos e bioquímicos. No entanto, a análise molecular do respetivo gene, deve ser realizada para a identificação definitiva de casos complexos ou quando os resultados hematológicos/bioquímicos não são conclusivos. A identificação de hemoglobinopatias é frequentemente presuntiva, com base em tempos de retenção e padrões de migração, e deve ser baseada preferencialmente no mínimo em duas metodologias com princípios de separação diferentes. A identificação definitiva requer a análise do respetivo gene, espectrometria de massa ou sequenciação de proteínas 1, 2 .Os procedimentos analíticos mais comumente utilizados devem ter capacidade de detetar as variantes de hemoglobina clinicamente mais significativas: Hb S, Hb C, Hb D Punjab, Hb Lepore , Hb E e Hb OArab. .Objetivo: Caraterizar e identificar as variantes de Hb com mobilidade eletroforética semelhante à Hb S..N/

Hemoglobin variants with electrophoretic behavior similar to hemoglobin S

As hemoglobinopatias são doenças genéticas relacionadas com défice da hemoglobina, a proteína vital para o transporte de oxigénio no organismo. De entre elas salienta-se a Drepanocitose causada pela variante S da hemoglobina (HbS) em homozigotia. Neste estudo pretendeu-se identificar as variantes de hemoglobina cujo padrão de migração eletroforética é semelhante ao da HbS. Foram investigados 660 casos de variantes com as características acima referidas detetadas por focagem isoelétrica. Para a identificação presuntiva foi efetuado o teste de solubilidade e a caracterização por HPLC de troca iónica e de fase reversa. A identificação das variantes raras foi efetuada através de sequenciação de Sanger do respetivo gene globínico. De entre os casos estudados, 467 foram confirmados como sendo HbS (70,8%), 101 HbD (15,3%) e 74 HbLepore (11,2%). Os restantes 18 casos (2,7%) foram classificados como variantes raras tendo sido 11 identificadas por sequenciação de DNA. Concluímos que a combinação metodológica utilizada é adequada pois permitiu o correto diagnóstico das variantes mais frequentes e com relevância clínica (HbS, HbD e HbLepore) e, nos casos raros, direcionou o estudo molecular para a análise do gene globínico alterado. A correta identificação de cada variante é essencial para um adequado acompanhamento clínico e aconselhamento genético do doente e seus familiares.Hemoglobinopathies are genetic diseases related to hemoglobin deficiency, the vital protein for the transpor t of ox ygen in the body. Among them, the most significant is Sickle Cell Anemia caused by homoz ygosity for the hemoglobin variant S (HbS). The aim of this work was to identif y hemoglobin variants with electrophoretic mobility similar to HbS. In this study we analysed 660 cases of variants with HbS-like mobility in isoelectric focusing. For the presumptive identification the solubility test was per formed followed by ion-exchange HPLC and reversed phase-HPLC. The rare variants identification was per formed by Sanger sequencing of the corresponding globin gene. Among the evaluated cases, 467 were confirmed as HbS (70.8%), 101 HbD (15.3%) and 74 HbLepore (11.2%). The remaining 18 cases (2.7%) were classified as rare variants and 11 of them were identified by DNA sequencing. We can conclude that the methodological combination used allows the correct diagnosis of the more frequent and clinical relevant variants (HbS, HbD and HbLepore) and, in the other cases, helps to direct the molecular study for the analysis of the affected globin gene. The correct laboratorial diagnosis of each variant is essential for the adequate clinical follow-up and genetic counselling of the patients and their relatives.info:eu-repo/semantics/publishedVersio

Delta Beta (δβ) thalassemia: Learning from External Quality Assessment

Introduction: External Quality Assessment Programs (EQA) evaluate retrospectively the laboratory results, assessing their performance and competence. They play a key role in the continuous training process of the professionals, contributing not only for precise and accurate results, but also to a correct interpretation. δβ thalassemia results from a deletion in genes delta and beta of chromosome 11. Although its definitive identification demands genetic analysis, the hematologic evaluation allows the presumptive identification. The hematologic phenotype of heterozygotes for δβ-thalassemia is identic to β-thalassemia carrier, with microcytosis and hypochromia where the percentage of HbA2 is not increased and Hb F is usually high, varying from 5 to 20%. In 2018, the National External Quality Assessment Program (PNAEQ), sent a sample that simulated a carrier of delta beta (δβ) thalassemia, in order to evaluate the performance of the participants registered in the Hemoglobinopathies Program. Objective: Evaluate the performance of PNAEQ’s participants in the quantification of HbA2 and HbF, and interpretation of results of a sample that simulated an δβ-thalassemia carrier.info:eu-repo/semantics/publishedVersio

Deletional alpha-thalassemia and hematological phenotype: indicative parameters of the different deletions in the series from 2015 to 2019

As talassémias são caracterizadas por um desequilíbrio quantitativo nas cadeias globinicas devido à redução ou supressão da síntese de uma das cadeias. Foram avaliados retrospetivamente os resultados de 496 casos suspeitos de α-talassémia delecional e correlacionados com os dados hematológicos. A pesquisa de deleções causadoras de α-talassémia foi efetuada por Gap e Multiplex Gap-PCR. A maioria dos casos (n=190) apresentou um genótipo normal (αα /αα), seguido de heterozigotia (-α 3 ,7 /αα) (n=148) e homozigotia (-α 3 ,7 /α 3 ,7 ) (n=141) para a deleção de 3,7kb. Detetaram-se ainda 5 casos de heterozigotia para a deleção de 4,2Kb (-α 4,2 /αα), 4 de dupla heterozigotia ( α 3 ,7 /α 4,2 ), 7 de heterozigotia α 0 (-- S E A /αα ), e 1 de Hb H (-- S E A /-α 3 ,7 ). Os resultados evidenciaram que o VGM e o HGM são excelentes índices hematológicos de rastreio e seleção dos testes moleculares, sendo o seu valor tanto mais baixo quanto maior o número de genes delecionados. Os resultados obtidos são ainda concordantes com o descrito na literatura e reforçam que o valor de cut-off de 25 pg (HGM), tem sensibilidade adequada para inferir da presença de uma deleção α 0 -talassémia. A deteção da deleção α 0 assume particular importância na prevenção da ocorrência de Hb Bart’s na descendência de um casal de portadores. O diagnóstico de α-talassémia é efetuado por métodos moleculares, no entanto os índices hematológicos são importantes marcadores preditivos do número de genes alfa delecionados e da relação fenótipo / genótipo.Thalassemias are characterized by a quantitative imbalance of the globin chains due to the reduction or suppression of the synthesis of one of the globin chains. In the present study, we evaluated retrospectively 496 cases suspected of deletional α-thalassemia and we correlated them with the hematological data available. We searched for α-thalassemia deletions by performing Gap and Multiplex Gap-PCR. Most patients (n=190) had a normal genotype (αα /αα), followed by heterozygosity (-α 3 .7 /αα) (n=148) and homozygosity (-α 3 .7 /α 3 .7 ) (n=141) for the 3.7kb deletion. We also detected 5 cases of heterozygosity for the 4.2Kb deletion (-α 4 .2 /αα), 4 of double heterozygosity ( α 3 .7 /α 4 .2 ),7 heterozygosity α0 (-- SEA /αα ) and 1 of HbH (-- SEA /-α 3.7 ). The results showed that the MCV and the MCH are excellent hematological indices for screening and selection of patients for molecular testing (their value being the lower the greater the number of deleted genes ). Our results are in line with those described in the literature and reinforce that the cut-off value of 25 pg (HGM) is sensitive enough to infer the presence of an α0 -thalassemia deletion. The detection of the α0 deletion is very important in preventing the occurrence of Hb Bart's in the offspring of a carrier couple. Genetic testing makes the diagnosis of α-thalassemia, however hematological indices are relevant predictive markers of the number of deleted alpha genes and the phenotype /genotype correlation.info:eu-repo/semantics/publishedVersio

Novel deletions and unusual genetic mechanisms underlying alpha-thalassemia

Hemoglobin (Hb) is a protein responsible for oxygen transportation from lungs to the entire body. It is composed by four globular subunits - the globins - each with a central core containing a heme molecule. Globins are encoded by the α- and β-globin gene clusters located at 16p13.3 and 11p15.5, respectively. The pattern of globin genes expression during development is precisely controlled by the interaction of cis-regulatory genomic regions (located in close proximity to and far from genes) with trans-activating/silencing factors within permissive chromatin domains. In fact, approximately 25-65 kb upstream of the α-globin genes there are four multispecies conserved sequences (MCS-R1 to R4) which are critical for the expression regulation of the downstream globin genes. The main objectives of this work were to characterize the molecular lesions underlying eight unusual cases of α-thalassemia or Hb H disease, and to understand their origin and functional consequences. Deletions were detected by Multiplex Ligation-dependent Probe Amplification (MLPA) using the SALSA MLPA P140B HBA kit (MCR-Holland). Additionally, specifically designed synthetic MLPA probes, as well as Gap-PCR and Sanger sequencing were performed for fine deletion breakpoint mapping. We have found seven different deletions (ranging from 3.3 to ≈323 kb), four of them not previously described. The four largest deletions removed all the α-globin genes, whereas the other three deletions removed one or more of the distal regulatory elements keeping the globin genes structurally intact. In one case, only the MCS-R2 (also known as HS-40) was removed and replaced by a 39 nt DNA fragment possibly resulting from a complex rearrangement that introduces new pieces of DNA (probably from Chrs. 3 and 7) bridging the two deletion breakpoints. In the remaining case, no deletion was found and the patient revealed to be a very unusual case of acquired alpha-thalassemia-myelodysplastic syndrome. It is important to detect individuals with this type of uncommon deletions as there is a 25% risk of having a child with Hb Bart’s hydrops fetalis or Hb H disease if their partner is a carrier of an α0-thal or α+-thal allele, respectively. Moreover, further investigation is currently being developed on one of these natural mutants which is bringing new insights into the long-range regulation mechanism of the globin gene expression and to the pathophysiology of the α-thalassemia.N/

Alpha-thalassemia due to novel deletions and complex rearrangements in the subtelomeric region of chromosome 16p

2º Dia do Jovem Investigador do Instituto Nacional de Saúde Doutor Ricardo Jorge, INSA, 8 maio 2017Introduction: Inherited deletions removing the α-globin genes and/or their upstream regulatory elements (MCSs) give rise to alpha-thalassemia, one of the most common genetic recessive disorders worldwide. The pathology is characterized by microcytic hypochromic anemia due to reduction of the α-globin chain synthesis, which are essential for hemoglobin tetramerization. Material and Methods: In order to clarify the suggestive α-thalassemia phenotype in eleven patients, we performed Multiplex Ligation-dependent Probe Amplification with commercial and synthetic engineered probes, gap-PCR, and Sanger sequencing to search for deletions in the subtelomeric region of chromosome 16p. Results: We have identified five distinct large deletions, two of them novel, and one indel. The deletions range from approximately 3.3 to 323 kb, and i) remove the whole α-globin cluster; or ii) remove exclusively the upstream regulatory elements leaving the α-globin genes structurally intact. The indel consists in the loss of MCS-R2 (HS-40), which is the most important distal regulatory element for the α-globin gene expression, and the insertion of 39 bp, seemingly resulting from a complex rearrangement involving two DNA segments (probably from chromosome 3q) bridging the deletion breakpoints with a CC-bp orphan sequence in between. Finally, in one patient no α-globin deletion or point mutation were found. This patient revealed to be a very unusual case of acquired alpha-thalassemia associated with a myelodysplastic syndrome. Conclusions: Our study widens the spectrum of molecular lesions by which α-thalassemia may occur and emphasizes the importance of diagnosing large α-zero-deletions to provide patients with appropriate genetic counseling.info:eu-repo/semantics/publishedVersio

Hemoglobinopatias nas células do cordão umbilical

Segundo dados da Organização Mundial de Saúde, de janeiro de 2011, estima-se que cerca de 5% da população mundial seja portadora dos genes responsáveis pelo desenvolvimento de hemoglobinopatias e que, anualmente, nasçam cerca de 300.000 crianças com variantes graves destas patologias. O rastreio neonatal é uma forma eficaz de combate a este problema grave de saúde pública. Está bem estabelecido que a identificação neonatal da anemia das células falciformes pode diminuir substancialmente a mortalidade e morbilidade durante os primeiros 5 anos de vida. Esta informação fornece aos profissionais de saúde uma oportunidade de organizar uma supervisão médica imediata. O rastreio de hemoglobinopatias em amostras de sangue do cordão umbilical tem como principal objetivo identificar variantes de hemoglobinas em recém-nascidos. Por outro lado, este rastreio é obrigatório como controlo de qualidade de unidades de sangue de cordão umbilical (SCU) para criopreservação, pelo que todas as amostras de SCU devem ser sujeitas a este rastreio para eventual utilização terapêutica e/ou de transplante. O rastreio de hemoglobinopatias em amostras de sangue de recém-nascidos ou de SCU é realizado no nosso laboratório por duas metodologias alternativas - cromatografia líquida de alta pressão de troca iónica (HPLC) e focagem isoelétrica (FIE) em gel de agarose.N/