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Swint-Kruse L, Dougherty LL, Page B, Wu T, O’Neil PT, Prasannan CB, Timmons C, Tang Q, Parente DJ, Sreenivasan S, Holyoak T, Fenton AW. PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Database (Oxford) 2023; 2023:baad030. [PMID: 37171062 PMCID: PMC10176505 DOI: 10.1093/database/baad030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family-pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization-including quantitative evaluation of allosteric regulation-of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms. Database URL https://github.com/djparente/PYK-DB.
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Affiliation(s)
- Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Larissa L Dougherty
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Braelyn Page
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Tiffany Wu
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Pierce T O’Neil
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Charulata B Prasannan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Cody Timmons
- Chemistry Department, Southwestern Oklahoma State University, 100 Campus Dr., Weatherford, OK 73096, USA
| | - Qingling Tang
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Daniel J Parente
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Family Medicine and Community Health, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Shwetha Sreenivasan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
| | - Todd Holyoak
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
- Department of Biology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Aron W Fenton
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
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Jamwal M, Sharma P, Das R. Laboratory Approach to Hemolytic Anemia. Indian J Pediatr 2020; 87:66-74. [PMID: 31823208 DOI: 10.1007/s12098-019-03119-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/04/2019] [Indexed: 12/12/2022]
Abstract
Hemolytic anemias are a group of disorders with varied clinical and molecular heterogeneity. They are characterized by decreased levels of circulating erythrocytes in blood. The pathognomic finding is a reduced red cell life span with severe anemia or, compensated hemolysis accompanied by reticulocytosis. The diagnostic workup or laboratory approach for hemolytic anemias is based on methodical step-wise testing which includes red blood cell morphology, hematological indices with increased reticulocyte count along with clinical features of hemolytic anemias. If conventional laboratory tests are unable to detect the underlying cause of hemolysis, genetic testing is recommended. Sanger sequencing along with conventional testing is the most efficient way to diagnose the underlying genetic causes, especially in thalassemias/hemoglobinopathies, if required. However, hemolytic anemias being highly heterogeneous disorders, next-generation sequencing-based screening is rapidly becoming an efficient way to decipher the etiologies where common causes have been excluded.
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Affiliation(s)
- Manu Jamwal
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Prashant Sharma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Reena Das
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India.
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3
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Canu G, De Bonis M, Minucci A, Capoluongo E. Red blood cell PK deficiency: An update of PK-LR gene mutation database. Blood Cells Mol Dis 2016; 57:100-9. [PMID: 26832193 DOI: 10.1016/j.bcmd.2015.12.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 11/16/2022]
Abstract
Pyruvate kinase (PK) deficiency is known as being the most common cause of chronic nonspherocytic hemolytic anemia (CNSHA). Clinical PK deficiency is transmitted as an autosomal recessive trait, that can segregate neither in homozygous or in a compound heterozygous modality, respectively. Two PK genes are present in mammals: the pyruvate kinase liver and red blood cells (PK-LR) and the pyruvate kinase muscle (PK-M), of which only the first encodes for the isoenzymes normally expressed in the red blood cells (R-type) and in the liver (L-type). Several reports have been published describing a large variety of genetic defects in PK-LR gene associated to CNSHA. Herein, we present a review of about 250 published mutations and six polymorphisms in PK-LR gene with the corresponding clinical and molecular data. We consulted the PubMed website for searching mutations and papers, along with two main databases: the Leiden Open Variation Database (LOVD, https://grenada.lumc.nl/LOVD2/mendelian_genes/home.php?select_db=PKLR) and Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/gene.php?gene=PKLR) for selecting, reviewing and listing the annotated PK-LR gene mutations present in literature. This paper is aimed to provide useful information to clinicians and laboratory professionals regarding overall reported PK-LR gene mutations, also giving the opportunity to harmonize data regarding PK-deficient individuals.
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Affiliation(s)
- Giulia Canu
- Laboratory of Clinical Molecular and Personalized Diagnostics, Department of Laboratory Medicine, "A Gemelli" Hospital, Catholic University, Largo Agostino Gemelli 8, Roma, Italy.
| | - Maria De Bonis
- Laboratory of Clinical Molecular and Personalized Diagnostics, Department of Laboratory Medicine, "A Gemelli" Hospital, Catholic University, Largo Agostino Gemelli 8, Roma, Italy
| | - Angelo Minucci
- Laboratory of Clinical Molecular and Personalized Diagnostics, Department of Laboratory Medicine, "A Gemelli" Hospital, Catholic University, Largo Agostino Gemelli 8, Roma, Italy.
| | - Ettore Capoluongo
- Laboratory of Clinical Molecular and Personalized Diagnostics, Department of Laboratory Medicine, "A Gemelli" Hospital, Catholic University, Largo Agostino Gemelli 8, Roma, Italy
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Warang P, Kedar P, Ghosh K, Colah R. Molecular and clinical heterogeneity in pyruvate kinase deficiency in India. Blood Cells Mol Dis 2013; 51:133-7. [PMID: 23770304 DOI: 10.1016/j.bcmd.2013.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/12/2013] [Accepted: 05/13/2013] [Indexed: 01/30/2023]
Abstract
We studied the PK-LR gene in 10 unrelated Indian patients with congenital haemolytic anemia associated with erythrocyte pyruvate kinase deficiency. The patients had a variable presentation ranging from a very mild compensated hemolysis to severe anemia. Nine different mutations were detected among the 20 mutated alleles identified: one deletion (c.1042-1044del) p.Lys348del and eight single-nucleotide (nt) substitutions resulting in amino acid exchanges c.397A>G (p.Asn133Asp), c.992A>G (p.Asp331Gly), c.1072G>A (p.Gly358Arg), c.1076G>A (p.Arg359His), c.1219G>A (p.Glu407Lys), c.1241C>T (p.Pro414Leu), c.1436G>A (p.Arg479His) and c.1529G>A (p.Arg510Gln) were identified. Although all the exons, the flanking regions and the promoter region were sequenced in all cases, we failed to detect the second expected mutation in two subjects. Two mutations [c.397A>G; c.1241C>T] were novel. These novel missense mutations involved highly conserved amino acids. Two mutations were identified for the first time in the homozygous state globally (c1042-1044del; c.1072G>A) and two other mutations were identified for the first time in our population (c.1076G>A; c.1529G>A). This study along with our earlier report suggests that the most frequent mutations in India would appear to be c.1436G>A (18.33%), followed by c.992A>G (11.66%) and c.1456C>T (11.66%). Structural implications of amino acid substitutions were correlated with the clinical phenotypes seen.
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Affiliation(s)
- Prashant Warang
- National Institute of Immunohaematology (Indian Council of Medical Research), K.E.M. Hospital Campus, Parel, Mumbai, India
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5
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Machado P, Manco L, Gomes C, Mendes C, Fernandes N, Salomé G, Sitoe L, Chibute S, Langa J, Ribeiro L, Miranda J, Cano J, Pinto J, Amorim A, do Rosário VE, Arez AP. Pyruvate kinase deficiency in sub-Saharan Africa: identification of a highly frequent missense mutation (G829A;Glu277Lys) and association with malaria. PLoS One 2012; 7:e47071. [PMID: 23082140 PMCID: PMC3474807 DOI: 10.1371/journal.pone.0047071] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 09/07/2012] [Indexed: 01/05/2023] Open
Abstract
Background Pyruvate kinase (PK) deficiency, causing hemolytic anemia, has been associated to malaria protection and its prevalence in sub-Saharan Africa is not known so far. This work shows the results of a study undertaken to determine PK deficiency occurrence in some sub-Saharan African countries, as well as finding a prevalent PK variant underlying this deficiency. Materials and Methods Blood samples of individuals from four malaria endemic countries (Mozambique, Angola, Equatorial Guinea and Sao Tome and Principe) were analyzed in order to determine PK deficiency occurrence and detect any possible high frequent PK variant mutation. The association between this mutation and malaria was ascertained through association studies involving sample groups from individuals showing different malaria infection and outcome status. Results The percentage of individuals showing a reduced PK activity in Maputo was 4.1% and the missense mutation G829A (Glu277Lys) in the PKLR gene (only identified in three individuals worldwide to date) was identified in a high frequency. Heterozygous carrier frequency was between 6.7% and 2.6%. A significant association was not detected between either PK reduced activity or allele 829A frequency and malaria infection and outcome, although the variant was more frequent among individuals with uncomplicated malaria. Conclusions This was the first study on the occurrence of PK deficiency in several areas of Africa. A common PKLR mutation G829A (Glu277Lys) was identified. A global geographical co-distribution between malaria and high frequency of PK deficiency seems to occur suggesting that malaria may be a selective force raising the frequency of this 277Lys variant.
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Affiliation(s)
- Patrícia Machado
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Licínio Manco
- Centro de Investigação em Antropologia e Saúde (CIAS), Universidade de Coimbra, Coimbra, Portugal
| | - Cláudia Gomes
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Cristina Mendes
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Natércia Fernandes
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Graça Salomé
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Luis Sitoe
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Sérgio Chibute
- Faculdade de Medicina da Universidade Eduardo Mondlane, Maputo, Mozambique
| | - José Langa
- Banco de Sangue do Hospital Central de Maputo, Maputo, Mozambique
| | - Letícia Ribeiro
- Departmento de Hematologia, Centro Hospitalar de Coimbra, Coimbra, Portugal
| | | | - Jorge Cano
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III, Madrid, Spain
| | - João Pinto
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - António Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Virgílio E. do Rosário
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Ana Paula Arez
- Centro de Malária e outras Doenças Tropicais, Unidade de Parasitologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal
- * E-mail:
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Machado P, Pereira R, Rocha AM, Manco L, Fernandes N, Miranda J, Ribeiro L, do Rosário VE, Amorim A, Gusmão L, Arez AP. Malaria: looking for selection signatures in the human PKLR gene region. Br J Haematol 2010; 149:775-84. [PMID: 20377593 DOI: 10.1111/j.1365-2141.2010.08165.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The genetic component of susceptibility to malaria is both complex and multigenic and the better-known protective polymorphisms are those involving erythrocyte-specific structural proteins and enzymes. In vivo and in vitro data have suggested that pyruvate kinase deficiency, which causes a nonspherocytic haemolytic anaemia, could be protective against malaria severity in humans, but this hypothesis remains to be tested. In the present study, we conducted a combined analysis of Short Tandem Repeats (STRs) and Single Nucleotide Polymorphisms (SNPs) in the pyruvate kinase-encoding gene (PKLR) and adjacent regions (chromosome 1q21) to look for malaria selective signatures in two sub-Saharan African populations from Angola and Mozambique, in several groups with different malaria infection outcome. A European population from Portugal, including a control and a pyruvate kinase-deficient group, was used for comparison. Data from STR and SNP loci spread along the PKLR gene region showed a considerably higher differentiation between African and Portuguese populations than that usually found for neutral markers. In addition, a wider region showing strong linkage disequilibrium was found in an uncomplicated malaria group, and a haplotype was found to be associated with this clinical group. Altogether, this data suggests that malaria selective pressure is acting in this genomic region.
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Affiliation(s)
- Patrícia Machado
- Centre for Malaria and Tropical Diseases, Malaria Unit, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal.
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7
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Alves J, Machado P, Silva J, Gonçalves N, Ribeiro L, Faustino P, do Rosário VE, Manco L, Gusmão L, Amorim A, Arez AP. Analysis of malaria associated genetic traits in Cabo Verde, a melting pot of European and sub Saharan settlers. Blood Cells Mol Dis 2009; 44:62-8. [PMID: 19837619 DOI: 10.1016/j.bcmd.2009.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 09/17/2009] [Indexed: 11/16/2022]
Abstract
Malaria has occurred in the Cabo Verde archipelago with epidemic characteristics since its colonization. Nowadays, it occurs in Santiago Island alone and though prophylaxis is not recommended by the World Health Organization, studies have highlight the prospect of malaria becoming a serious public health problem as a result of the presence of antimalarial drug resistance associated with mutations in the parasite populations and underscore the need for tighter surveillance. Despite the presumptive weak immune status of the population, severe symptoms of malaria are not observed and many people present a subclinical course of the disease. No data on the prevalence of sickle-cell trait and red cell glucose-6-phosphate dehydrogenase deficiency (two classical genetic factors associated with resistance to severe malaria) were available for the Cabo Verde archipelago and, therefore, we studied the low morbidity from malaria in relation to the particular genetic characteristics of the human host population. We also included the analysis of the pyruvate kinase deficiency associated gene, reported as putatively associated with resistance to the disease. Allelic frequencies of the polymorphisms examined are closer to European than to African populations and no malaria selection signatures were found. No association was found between the analyzed human factors and infection but one result is of high interest: a linkage disequilibrium test revealed an association of distant loci in the PKLR gene and adjacent regions, only in non-infected individuals. This could mean a more conserved gene region selected in association to protection against the infection and/or the disease.
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Affiliation(s)
- Joana Alves
- Centre for Malaria and Tropical Diseases, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
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Coutinho R, Bento C, Almeida H, Cunha E, Manco L, Ferreira F, Ribeiro ML. Complex inheritance of chronic haemolytic anaemia. Br J Haematol 2008; 144:615-6. [PMID: 19036089 DOI: 10.1111/j.1365-2141.2008.07479.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Kedar P, Hamada T, Warang P, Nadkarni A, Shimizu K, Fujji H, Ghosh K, Kanno H, Colah R. Spectrum of novel mutations in the human PKLR gene in pyruvate kinase-deficient Indian patients with heterogeneous clinical phenotypes. Clin Genet 2008; 75:157-62. [PMID: 18759866 DOI: 10.1111/j.1399-0004.2008.01079.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eighteen unrelated pyruvate kinase (PK)-deficient Indian patients were identified in the past 4 years with varied clinical phenotypes ranging from a mild chronic haemolytic anaemia to a severe transfusion-dependent disorder. We identified 17 different mutations in the PKLR gene among the 36 mutated alleles. Ten novel mutations were identified: 427G>A, 499C>A, 1072G>A, 1180G>T, 1216G>A, 1220A>G, 644delG, IVS5 (+20) C>A, IVS9 (+44) C>T, and IVS9 (+93) A>C. A severe syndrome was commonly associated with some mutations, 992A>G, 1436G>A, 1220A>G, 644delG and IVS9 (+93) A>C, in the PKLR gene. Molecular graphics analysis of human red blood cell PK (RPK), based on the crystal structure of human PK, shows that mutations located near the substrate or fructose 1,6-diphosphate binding site may change the conformation of the active site, resulting in very low PK activity and severe clinical symptoms. The mutations target distinct regions of RPK structure, including domain interfaces and catalytic and allosteric sites. In particular, the 1216G>A and 1219G>A mutations significantly affect the interdomain interaction because they are located near the catalytic site in the A/B interface domains. The most frequent mutations in the Indian population appear to be 1436G>A (19.44%), followed by 1456C>T (16.66%) and 992A>G (16.66%). This is the first study to correlate the clinical profile with the molecular defects causing PK deficiency from India where 10 novel mutations that produce non-spherocytic haemolytic anaemia were identified.
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Affiliation(s)
- P Kedar
- National Institute of Immunohaematology, Indian Council of Medical Research, K.E.M. Hospital Campus, Parel, Mumbai, India
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10
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Raphaël MF, Van Wijk R, Schweizer JJ, Schouten-van Meeteren NAY, Kindermann A, van Solinge WW, Smiers FJ. Pyruvate kinase deficiency associated with severe liver dysfunction in the newborn. Am J Hematol 2007; 82:1025-8. [PMID: 17654506 DOI: 10.1002/ajh.20942] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Significant hyperbilirubinaemia, anemia, and splenomegaly are common features in patients with severe haemolysis due to pyruvate kinase (PK) deficiency. Until now, severe neonatal PK deficiency has not been associated with fatal liver disease at this age. We present two neonatal cases of severe PK deficiency complicated with progressive fatal liver disease. The patients presented with severe haemolysis, progressive cholestasis, and hepatosplenomegaly, and both patients ultimately developed liver failure at a very young age. Despite extensive investigations, no specific explanation for liver disease and failure was found. We suggest that the PK deficiency itself directly led to liver dysfunction.
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Affiliation(s)
- Martine F Raphaël
- Department of Paediatric Haematology and Oncology, Wilhelmina Children's Hospital, University Medical Center of Utrecht, The Netherlands.
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Zanella A, Fermo E, Bianchi P, Chiarelli LR, Valentini G. Pyruvate kinase deficiency: the genotype-phenotype association. Blood Rev 2007; 21:217-31. [PMID: 17360088 DOI: 10.1016/j.blre.2007.01.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Red cell pyruvate kinase (PK) deficiency is the most frequent enzyme abnormality of glycolysis causing chronic non-spherocytic haemolytic anaemia. The disease is transmitted as an autosomal recessive trait, clinical symptoms usually occurring in compound heterozygotes for two mutant alleles and in homozygotes. The severity of haemolysis is highly variable, ranging from very mild or fully compensated forms to life-threatening neonatal anaemia necessitating exchange transfusions. Erythrocyte PK is synthesised under the control of the PK-LR gene located on chromosome 1. One hundred eighty different mutations in PK-LR gene, mostly missense, have been so far reported associated to PK deficiency. First attempts to delineate the genotype-phenotype association were mainly based on the analysis of the enzyme's three-dimensional structure and the observation of the few homozygous patients. More recently, the comparison of the recombinant mutants of human red cell PK with the wild-type enzyme has enabled the effects of amino acid replacements on the enzyme molecular properties to be determined. However, the clinical manifestations of red cell enzyme defects are not merely dependent on the molecular properties of the mutant protein but rather reflect the complex interactions of additional factors, including genetic background, concomitant functional polymorphisms of other enzymes, posttranslational or epigenetic modifications, ineffective erythropoiesis and differences in splenic function.
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Affiliation(s)
- Alberto Zanella
- Department of Haematology, Fondazione IRCCS Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy.
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Gupta N, Bianchi P, Fermo E, Kabra M, Warang P, Kedar P, Gupta N, Colah R. Prenatal diagnosis for a novel homozygous mutation inPKLR gene in an Indian family. Prenat Diagn 2007; 27:117-8. [PMID: 17191259 DOI: 10.1002/pd.1616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To provide prenatal diagnosis of pyruvate kinase deficiency by direct DNA analysis in an Indian family. MATERIALS AND METHOD This case report describes diagnosis of a novel homozygous mutation in PKLR gene that subsequently helped the family in the next pregnancy. RESULTS Advancement in molecular genetics has resulted in the prenatal diagnosis of relatively uncommon genetic disorders like pyruvate kinase deficiency. CONCLUSION This case reiterates the importance of application of molecular genetics in clinical practice and prenatal diagnosis especially for rare, incurable genetic disorders.
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Affiliation(s)
- Neerja Gupta
- Genetics Unit, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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13
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Zanella A, Fermo E, Bianchi P, Valentini G. Red cell pyruvate kinase deficiency: molecular and clinical aspects. Br J Haematol 2005; 130:11-25. [PMID: 15982340 DOI: 10.1111/j.1365-2141.2005.05527.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Red cell pyruvate kinase (PK) deficiency is the most frequent enzyme abnormality of the glycolytic pathway causing hereditary non-spherocytic haemolytic anaemia. The degree of haemolysis varies widely, ranging from very mild or fully compensated forms, to life-threatening neonatal anaemia and jaundice necessitating exchange transfusions. Erythrocyte PK is synthesized under the control of the PK-LR gene located on chromosome 1. To date, more than 150 different mutations in the PK-LR gene have been associated with PK deficiency. First attempts to delineate the biochemical and clinical consequences of the molecular defect were mainly based on the observation of the few homozygous patients and on the analysis of the three-dimensional structure of the enzyme. More recently, the comparison of the recombinant mutants of human red cell PK with the wild-type enzyme has enabled the effects of amino acid replacements on the enzyme molecular properties to be determined and help to correlate genotype to clinical phenotype.
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Affiliation(s)
- Alberto Zanella
- Department of Haematology, IRCCS Ospedale Maggiore, Milan, Italy.
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14
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Manco L, Bento C, Ribeiro ML, Tamagnini G. Consequences at mrna level of the pklr gene splicing mutations IVS10(+1)G→C and IVS8(+2)T→G causing pyruvate kinase deficiency. Br J Haematol 2002. [DOI: 10.1046/j.0007-1048.2002.03665.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Manco L, Bento C, Ribeiro ML, Tamagnini G. Consequences at mRNA level of the PKLR gene splicing mutations IVS10(+1)GC and IVS8(+2)TG causing pyruvate kinase deficiency. Br J Haematol 2002. [DOI: 10.1046/j.1365-2141.2002.03631_9.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Manco L, Abade A. Pyruvate kinase deficiency: prevalence of the 1456C-->T mutation in the Portuguese population. Clin Genet 2001; 60:472-3. [PMID: 11846742 DOI: 10.1034/j.1399-0004.2001.600612.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Zanella A, Bianchi P, Fermo E, Iurlo A, Zappa M, Vercellati C, Boschetti C, Baronciani L, Cotton F. Molecular characterization of the PK-LR gene in sixteen pyruvate kinase-deficient patients. Br J Haematol 2001; 113:43-8. [PMID: 11328279 DOI: 10.1046/j.1365-2141.2001.02711.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We studied the PK-LR gene in 16 unrelated patients with congenital haemolytic anaemia associated with erythrocyte pyruvate kinase deficiency. Fifteen different mutations were detected among the 28 mutated alleles identified: two deletions (del 1010G, del 1042--1044); one four nucleotide duplication (nt 1515--1518, GGTC); one splice site [IVS6(-2)t]; nine missense (991A, 1003A, 1151T, 1160G, 1181T, 1181A, 1456T, 1483A, 1529A); and two nonsense (721T, 1675T) mutations. Eight of them [del 1010G, del 1042--1044, dupl 1515--1518, IVS6(-2)t, 1003A, 1160G, 1181T, 1181A] were novel. The deletion 1042-1044 causes the loss of Lys 348. Deletion 1010G and duplication 1515-1518 determine a frameshift and the creation of a stop codon at nucleotides 1019 and 1554 respectively. Mutation IVS6(-2)t leads to an alteration of the 5' and 3' splice site consensus sequence; the cDNA analysis shows a 67-bp deletion in the first part of exon 11 (del 1437--1503). All the four new missense mutations involve highly conserved amino acids. The most frequent mutation in Italy would appear to be 1456T. Correlation was made between mutations, biochemical characteristics of the enzyme and clinical course of the disease.
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Affiliation(s)
- A Zanella
- Divisione di Ematologia, IRCCS Ospedale Maggiore of Milan, Italy.
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18
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Manco L, Ribeiro ML, Máximo V, Almeida H, Costa A, Freitas O, Barbot J, Abade A, Tamagnini G. A new PKLR gene mutation in the R-type promoter region affects the gene transcription causing pyruvate kinase deficiency. Br J Haematol 2000; 110:993-7. [PMID: 11054094 DOI: 10.1046/j.1365-2141.2000.02283.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mutations in the PKLR gene responsible for pyruvate kinase (PK)-deficient anaemia are mainly located in the coding regions: 11 are in the splicing sites and, recently, three mutations have been described in the promoter region. We now report a novel point mutation A-->G on nucleotide 72, upstream from the initiation codon of the PKLR gene, in four Portuguese PK-deficient patients. This new regulatory mutation occurs within the most proximal of the four GATA motifs (GATA-A element) in the R-type promoter region. In two patients who were homozygous for this mutation, a semiquantitative reverse transcription polymerase chain reaction (PCR) procedure was used to evaluate the amount of R-PK mRNA transcript in the reticulocytes. The mRNA level was about five times lower than in normal controls, demonstrating that the PKLR gene transcription is severely affected, most probably because the -72A-->G point mutation disables the binding of the erythroid transcription factor GATA-1 to the GATA-A element. Supporting these data, the two patients homozygous for the -72A-->G mutation had severe haemolytic anaemia and were transfusion dependent until splenectomy. Two other patients who were compound heterozygous for this mutation and the previously described missense mutation 1456C-->T had a mild condition.
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Affiliation(s)
- L Manco
- Unidade de Hematologia Molecular, Centro Hospitalar de Coimbra, Portugal.
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19
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Abstract
Pyruvate kinase (PK) deficiency is the most common cause of hereditary nonspherocytic hemolytic anemia. The prevalence of this deficiency is unknown, though some estimates have been made based on the frequency of low red cell PK activity in the population. An additional 20 patients with hereditary nonspherocytic hemolytic anemia caused by PK deficiency have been genotyped. One previously unreported mutation 1153C→T (R385W) was encountered. The relative frequency of PK mutations in patients with hemolytic anemia caused by PK deficiency was calculated from the 18 white patients reported here and from 102 patients previously reported in the literature. DNA samples from 3785 subjects from different ethnic groups have been screened for the 4 more frequently encountered mutations—c.1456 C→T(1456T), c.1468 C→T(1468T), c.1484 C→T(1484T), and c.1529 G6A (1529A)—by allele-specific oligonucleotide hybridization. Among white patients the frequency of the 1456T mutation was 3.50 × 10−3; that of the 1529A mutation was 2.03 × 10−3. Among African Americans the frequency of the 1456T mutation was 3.90 × 10−3 The only mutation found in the limited number of Asians tested was 1468T at a frequency of 7.94 × 10−3. Based on the gene frequency of the 1529A mutation in the white population and on its relative abundance in patients with hemolytic anemia caused by PK deficiency, the prevalence of PK deficiency is estimated at 51 cases per million white population. This number would be increased by inbreeding and decreased by failure of patients with PK deficiency to survive.
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20
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Estimating the prevalence of pyruvate kinase deficiency from the gene frequency in the general white population. Blood 2000. [DOI: 10.1182/blood.v95.11.3585] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Pyruvate kinase (PK) deficiency is the most common cause of hereditary nonspherocytic hemolytic anemia. The prevalence of this deficiency is unknown, though some estimates have been made based on the frequency of low red cell PK activity in the population. An additional 20 patients with hereditary nonspherocytic hemolytic anemia caused by PK deficiency have been genotyped. One previously unreported mutation 1153C→T (R385W) was encountered. The relative frequency of PK mutations in patients with hemolytic anemia caused by PK deficiency was calculated from the 18 white patients reported here and from 102 patients previously reported in the literature. DNA samples from 3785 subjects from different ethnic groups have been screened for the 4 more frequently encountered mutations—c.1456 C→T(1456T), c.1468 C→T(1468T), c.1484 C→T(1484T), and c.1529 G6A (1529A)—by allele-specific oligonucleotide hybridization. Among white patients the frequency of the 1456T mutation was 3.50 × 10−3; that of the 1529A mutation was 2.03 × 10−3. Among African Americans the frequency of the 1456T mutation was 3.90 × 10−3 The only mutation found in the limited number of Asians tested was 1468T at a frequency of 7.94 × 10−3. Based on the gene frequency of the 1529A mutation in the white population and on its relative abundance in patients with hemolytic anemia caused by PK deficiency, the prevalence of PK deficiency is estimated at 51 cases per million white population. This number would be increased by inbreeding and decreased by failure of patients with PK deficiency to survive.
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21
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Kugler W, Willaschek C, Holtz C, Ohlenbusch A, Laspe P, Krügener R, Muirhead H, Schröter W, Lakomek M. Eight novel mutations and consequences on mRNA and protein level in pyruvate kinase-deficient patients with nonspherocytic hemolytic anemia. Hum Mutat 2000; 15:261-72. [PMID: 10679942 DOI: 10.1002/(sici)1098-1004(200003)15:3<261::aid-humu7>3.0.co;2-t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pyruvate kinase (PK) deficiency (PKD) is an autosomal recessive disorder with the typical manifestation of nonspherocytic hemolytic anemia. We analyzed the mutant enzymes of 10 unrelated patients with PKD, whose symptoms ranged from a mild, chronic hemolytic anemia to a severe anemia, by sequence analysis for the presence of alterations in the PKLR gene. In all cases the patients were shown to be compound heterozygous. Eight novel mutations were identified: 458T-->C (Ile153Thr), 656T-->C (Ile219Thr), 877G-->A (Asp293Asn), 991G-->A (Asp331Asn), 1055C-->A (Ala352Asp), 1483G-->A (Ala495Thr), 1649A-->T (Asp550Val), and 183-184ins16bp. This 16 bp duplication produces a frameshift and subsequent stop codon resulting in a drastically reduced mRNA level, and probably in an unstable gene product. Surprisingly, the existence of M2-type PK could be demonstrated in the patient's red blood cells. The study of different polymorphic sites revealed, with one exception, a strict linkage of the 1705C, 1738T, IVS5(+51)T, T(10) polymorphisms and the presence of 14 ATT repeats in intron 11. Our analyses show the consequences of a distorted structure on enzyme function and we discuss the correlations between the mutations identified and the parameters indicative for enzyme function.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Amino Acid Substitution
- Anemia, Hemolytic, Congenital Nonspherocytic/enzymology
- Anemia, Hemolytic, Congenital Nonspherocytic/genetics
- Anemia, Hemolytic, Congenital Nonspherocytic/pathology
- Base Sequence
- DNA/chemistry
- DNA/genetics
- DNA Mutational Analysis
- Female
- Genotype
- Haplotypes
- Heterozygote
- Humans
- Male
- Molecular Sequence Data
- Mutagenesis, Insertional
- Mutation
- Point Mutation
- Pyruvate Kinase/deficiency
- Pyruvate Kinase/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Homology, Amino Acid
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Affiliation(s)
- W Kugler
- Universitäts-Kinderklinik, Göttingen, Germany
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22
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Abstract
Enzyme deficiencies have been identified in all erythrocyte pathways. Their frequencies differ with respect to the affected enzyme, the severity of the clinical manifestations and the geographical distribution. Most mutations are found within the coding sequences of genes, missense mutations occurring more often than deletions, insertions, splice site defects or premature stop codons. Promoter mutations are rare. The clinical manifestations are chronic or non-chronic haemolytic anaemias. The first of these are characterized by an impairment of cell function at normal values of the external load parameters kATPase and kGSHox. Haemolysis with a non-chronic course is induced only at enhanced values of the load parameters, caused by free radical generation by oxidative drugs, fava beans, infections, fever and physical exercise. The development of secondary haemochromatosis is the most common cause of mortality in patients suffering from severe chronic non-spherocytic haemolytic anaemia. Intracellular iron deposits must be prevented by timely treatment with effective chelating agents.
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Affiliation(s)
- G Jacobasch
- German Institute of Human Nutrition, Potsdam-Rehbrücke, Germany
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23
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Zanella A, Bianchi P. Red cell pyruvate kinase deficiency: from genetics to clinical manifestations. Best Pract Res Clin Haematol 2000; 13:57-81. [PMID: 10916678 DOI: 10.1053/beha.1999.0057] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Pyruvate kinase deficiency is the most frequent enzyme abnormality of the Embden-Meyerhof pathway causing hereditary non-spherocytic haemolytic anaemia. The degree of haemolysis varies widely, ranging from very mild or fully compensated forms, to life-threatening neonatal anaemia and jaundice necessitating exchange transfusions. Splenectomy should be reserved for young patients who require regular blood transfusions. The gene encoding for pyruvate kinase (PK-LR) has been localized to the long arm of chromosome I; the cDNA of R-type is 2060 bp long and codes for 574 amino acids. More than 130 different mutations, mostly missense, have so far been described in association with PK deficiency, 1529A and 1456T being considered to be the most common mutations in Caucasians. Analysis of the three-dimensional structure of the enzyme may help in predicting the severity of the molecular defect. Further data on clinical features of homozygous patients are needed, at least for some mutations, to allow a more precise genotype/phenotype correlation.
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MESH Headings
- Anemia, Hemolytic, Congenital Nonspherocytic/diagnosis
- Anemia, Hemolytic, Congenital Nonspherocytic/enzymology
- Anemia, Hemolytic, Congenital Nonspherocytic/genetics
- Anemia, Hemolytic, Congenital Nonspherocytic/therapy
- Chromosomes, Human, Pair 1
- DNA/chemistry
- Erythrocytes/enzymology
- Humans
- Molecular Structure
- Mutation
- Pyruvate Kinase/chemistry
- Pyruvate Kinase/deficiency
- Pyruvate Kinase/genetics
- Pyruvate Kinase/physiology
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Affiliation(s)
- A Zanella
- Division of Haematology, IRCCS Ospedale Maggiore, Milan, Italy
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24
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Bianchi P, Zanella A. Hematologically important mutations: red cell pyruvate kinase (Third update). Blood Cells Mol Dis 2000; 26:47-53. [PMID: 10772876 DOI: 10.1006/bcmd.2000.0276] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- P Bianchi
- Divisione di Ematologia, IRCCS Ospedale Maggiore, Milano, Italy
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