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Isik E, Aydinok Y, Albayrak C, Durmus B, Karakas Z, Orhan MF, Sarper N, Aydın S, Unal S, Oymak Y, Karadas N, Turedi A, Albayrak D, Tayfun F, Tugcu D, Karaman S, Tobu M, Unal E, Ozcan A, Unal S, Aksu T, Unuvar A, Bilici M, Azik F, Ay Y, Gelen SA, Zengin E, Albudak E, Eker I, Karakaya T, Cogulu O, Ozkinay F, Atik T. Identification of the molecular etiology in rare congenital hemolytic anemias using next-generation sequencing with exome-based copy number variant analysis. Eur J Haematol 2024; 113:82-89. [PMID: 38556258 DOI: 10.1111/ejh.14194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 04/02/2024]
Abstract
OBJECTIVES In congenital hemolytic anemias (CHA), it is not always possible to determine the specific diagnosis by evaluating clinical findings and conventional laboratory tests. The aim of this study is to evaluate the utility of next-generation sequencing (NGS) and clinical-exome-based copy number variant (CNV) analysis in patients with CHA. METHODS One hundred and forty-three CHA cases from 115 unrelated families referred for molecular analysis were enrolled in the study. Molecular analysis was performed using two different clinical exome panels in 130 patients, and whole-exome sequencing in nine patients. Exome-based CNV calling was incorporated into the traditional single-nucleotide variant and small insertion/deletion analysis pipeline for NGS data in 92 cases. In four patients from the same family, the PK Gypsy variant was investigated using long-range polymerase chain reaction. RESULTS Molecular diagnosis was established in 86% of the study group. The most frequently mutated genes were SPTB (31.7%) and PKLR (28.5%). CNV analysis of 92 cases revealed that three patients had different sizes of large deletions in the SPTB and six patients had a deletion in the PKLR. CONCLUSIONS In this study, NGS provided a high molecular diagnostic rate in cases with rare CHA. Analysis of the CNVs contributed to the diagnostic success.
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Affiliation(s)
- Esra Isik
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Yesim Aydinok
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Canan Albayrak
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Basak Durmus
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Zeynep Karakas
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mehmet Fatih Orhan
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Nazan Sarper
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Sultan Aydın
- Division of Pediatric Hematology and Oncology, Antalya Training and Research Hospital, Antalya, Turkey
| | - Selma Unal
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Yesim Oymak
- Division of Pediatric Hematology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Nihal Karadas
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Aysen Turedi
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Celal Bayar University, Manisa, Turkey
| | - Davut Albayrak
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Medical Park Samsun Hospital, Samsun, Turkey
| | - Funda Tayfun
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Deniz Tugcu
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Serap Karaman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mahmut Tobu
- Department of Hematology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ekrem Unal
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Alper Ozcan
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Sule Unal
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Tekin Aksu
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Aysegul Unuvar
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Mustafa Bilici
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Fatih Azik
- Department of Pediatrics, Division of Pediatric Hematology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Yilmaz Ay
- Division of Pediatric Hematology and Oncology, Kartal Dr Lütfi Kırdar Training and Research Hospital, Istanbul, Turkey
| | - Sema Aylan Gelen
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Emine Zengin
- Division of Pediatric Hematology, Department of Pediatrics, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Esin Albudak
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Ibrahim Eker
- Department of Pediatric Hematology and Oncology and Pediatric Hematopoietic Stem Cell Transplantation Unit, Afyonkarahisar Health Science University Faculty of Medicine, Afyon, Turkey
| | - Taner Karakaya
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun, Turkey
| | - Ozgur Cogulu
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ferda Ozkinay
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Tahir Atik
- Division of Pediatric Genetics, Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey
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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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Concomitant Hereditary Spherocytosis and Pyruvate Kinase Deficiency in a Spanish Family with Chronic Hemolytic Anemia: Contribution of Laser Ektacytometry to Clinical Diagnosis. Cells 2022; 11:cells11071133. [PMID: 35406697 PMCID: PMC8997718 DOI: 10.3390/cells11071133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 01/19/2023] Open
Abstract
Background: Hereditary spherocytosis (HS) and pyruvate kinase deficiency (PKD) are the most common causes of hereditary chronic hemolytic anemia. Here, we describe clinical and genetic characteristics of a Spanish family with concomitant β-spectrin (SPTB) c.647G>A variant and pyruvate kinase (PKLR) c.1706G>A variant. Methods: A family of 11 members was studied. Hematological investigation, hemolysis tests, and specific red cell studies were performed in all family members, according to conventional procedures. An ektacytometric study was performed using the osmoscan module of the Lorca ektacytometer (MaxSis. RR Mechatronics). The presence of the SPTB and PKLR variants was confirmed by t-NGS. Results: The t-NGS genetic characterization of the 11 family members showed the presence of a heterozygous mutation for the β-spectrin (SPTB; c.647G>A) in seven members with HS, three of them co-inherited the PKLR variant c.1706G>A. In the remaining four members, no gene mutation was found. Ektacytometry allowed a clear diagnostic orientation of HS, independently from the PKLR variant. Conclusions: This family study allows concluding that the SPTB mutation, (c.647G>A) previously described as likely pathogenic (LP), should be classified as pathogenic (P), according to the recommendations for pathogenicity of the American College of Medical Genetics and the Association for Molecular Pathology. In addition, after 6 years of clinical follow-up of the patients with HS, it can be inferred that the chronic hemolytic anemia may be attributable to the SPTB mutation only, without influence of the concomitant PKLR. Moreover, only the family members with the SPTB mutation exhibited an ektacytometric profile characteristic of HS.
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Milanesio B, Pepe C, Defelipe LA, Eandi Eberle S, Avalos Gomez V, Chaves A, Albero A, Aguirre F, Fernandez D, Aizpurua L, Paula Dieuzeide M, Turjanski A, Bianchi P, Fermo E, Feliu-Torres A. Six novel variants in the PKLR gene associated with pyruvate kinase deficiency in Argentinian patients. Clin Biochem 2021; 91:26-30. [PMID: 33631127 DOI: 10.1016/j.clinbiochem.2021.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Pyruvate kinase deficiency (PKD) is a rare recessive congenital hemolytic anemia caused by mutations in the PKLR gene. The disease shows a marked variability in clinical expression. We studied the molecular features of nine unrelated Argentinian patients with congenital hemolytic anemia associated with erythrocyte pyruvate kinase deficiency. DESIGN AND METHODS Routine hematologic investigations were performed to rule out other causes of chronic hemolytic anemia. Sanger sequencing and in-sílico analysis were carried out to identify and characterize the genetics variants. RESULTS Six different novel missense variants were detected among the 18 studied alleles: c.661 G > C (Asp221His), c.956 G > T (Gly319Val), c.1595 G > C (Arg532Pro), c.347 G > A (Arg116Gln), c.1232 G > T (Gly411Val), c.1021G > A (Gly341Ser). Structural implications of amino-acid substitutions were correlated with the clinical phenotypes seen in the probands. CONCLUSIONS This is the first comprehensive report on molecular characterization of pyruvate kinase deficiency in Argentina and the second from South America that would contribute to our knowledge on the distribution and frequency of PKLR variants in our population but also offer new insights into the interpretation of the effect of PKLR variants and phenotype.
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Affiliation(s)
- Berenice Milanesio
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Carolina Pepe
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Silvia Eandi Eberle
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Vanesa Avalos Gomez
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Alejandro Chaves
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Agustina Albero
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Fernando Aguirre
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Diego Fernandez
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Luciana Aizpurua
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - María Paula Dieuzeide
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paola Bianchi
- U.O.C. Ematologia, U.O.S. FisiopatologiadelleAnemie, Fondazione IRCCS Ca Granada, OspedaleMaggiore Policlínico, Milan, Italy
| | - Elisa Fermo
- U.O.C. Ematologia, U.O.S. FisiopatologiadelleAnemie, Fondazione IRCCS Ca Granada, OspedaleMaggiore Policlínico, Milan, Italy
| | - Aurora Feliu-Torres
- Servicio de Hematología-Oncología, Hospital de Pediatría "Prof. Dr. Juan P. Garrahan", Combate de los Pozos 1881, (C1245AAM) Buenos Aires, Argentina.
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Bianchi P, Fermo E. Molecular heterogeneity of pyruvate kinase deficiency. Haematologica 2020; 105:2218-2228. [PMID: 33054047 PMCID: PMC7556514 DOI: 10.3324/haematol.2019.241141] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/03/2020] [Indexed: 01/19/2023] Open
Abstract
Red cell pyruvate kinase (PK) deficiency is the most common glycolytic defect associated with congenital non-spherocytic hemolytic anemia. The disease, transmitted as an autosomal recessive trait, is caused by mutations in the PKLR gene and is characterized by molecular and clinical heterogeneity; anemia ranges from mild or fully compensated hemolysis to life-threatening forms necessitating neonatal exchange transfusions and/or subsequent regular transfusion support; complications include gallstones, pulmonary hypertension, extramedullary hematopoiesis and iron overload. Since identification of the first pathogenic variants responsible for PK deficiency in 1991, more than 300 different variants have been reported, and the study of molecular mechanisms and the existence of genotype-phenotype correlations have been investigated in-depth. In recent years, during which progress in genetic analysis, next-generation sequencing technologies and personalized medicine have opened up important landscapes for diagnosis and study of molecular mechanisms of congenital hemolytic anemias, genotyping has become a prerequisite for accessing new treatments and for evaluating disease state and progression. This review examines the extensive molecular heterogeneity of PK deficiency, focusing on the diagnostic impact of genotypes and new acquisitions on pathogenic non-canonical variants. The recent progress and the weakness in understanding the genotype-phenotype correlation, and its practical usefulness in light of new therapeutic opportunities for PK deficiency are also discussed.
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MESH Headings
- Anemia, Hemolytic, Congenital/diagnosis
- Anemia, Hemolytic, Congenital/genetics
- Anemia, Hemolytic, Congenital/therapy
- Anemia, Hemolytic, Congenital Nonspherocytic/diagnosis
- Anemia, Hemolytic, Congenital Nonspherocytic/genetics
- Humans
- Mutation
- Pyruvate Kinase/deficiency
- Pyruvate Kinase/genetics
- Pyruvate Metabolism, Inborn Errors/diagnosis
- Pyruvate Metabolism, Inborn Errors/genetics
- Pyruvate Metabolism, Inborn Errors/therapy
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Affiliation(s)
- Paola Bianchi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, UOC Ematologia, UOS Fisiopatologia delle Anemie, Milan, Italy.
| | - Elisa Fermo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, UOC Ematologia, UOS Fisiopatologia delle Anemie, Milan, Italy
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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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7
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Svidnicki MCCM, Santos A, Fernandez JAA, Yokoyama APH, Magalhães IQ, Pinheiro VRP, Brandalise SR, Silveira PAA, Costa FF, Saad STO. Novel mutations associated with pyruvate kinase deficiency in Brazil. Hematol Transfus Cell Ther 2018; 40:5-11. [PMID: 29519373 PMCID: PMC6003125 DOI: 10.1016/j.bjhh.2017.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/14/2017] [Accepted: 08/02/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Pyruvate kinase deficiency is a hereditary disease that affects the glycolytic pathway of the red blood cell, causing nonspherocytic hemolytic anemia. The disease is transmitted as an autosomal recessive trait and shows a marked variability in clinical expression. This study reports on the molecular characterization of ten Brazilian pyruvate kinase-deficient patients and the genotype-phenotype correlations. METHOD Sanger sequencing and in silico analysis were carried out to identify and characterize the genetic mutations. A non-affected group of Brazilian individuals were also screened for the most commonly reported variants (c.1456C>T and c.1529G>A). RESULTS Ten different variants were identified in the PKLR gene, of which three are reported here for the first time: p.Leu61Gln, p.Ala137Val and p.Ala428Thr. All the three missense variants involve conserved amino acids, providing a rationale for the observed enzyme deficiency. The allelic frequency of c.1456C>T was 0.1% and the 1529G>A variant was not found. CONCLUSION This is the first comprehensive report on molecular characterization of pyruvate kinase deficiency from South America. The results allowed us to correlate the severity of the clinical phenotype with the identified variants.
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Affiliation(s)
| | - Andrey Santos
- Departamento de Medicina Interna da Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Ana Paula Hitomi Yokoyama
- Centro de Hematologia e Hemoterapia da Universidade Estadual de Campinas (HEMOCENTRO/UNICAMP), Campinas, SP, Brazil
| | | | - Vitoria Regia Pereira Pinheiro
- Centro Integrado de Pesquisas Onco-Hematológicas na Infância da Universidade Estadual de Campinas (CIPOI/UNICAMP), Campinas, SP, Brazil
| | | | | | - Fernando Ferreira Costa
- Centro de Hematologia e Hemoterapia da Universidade Estadual de Campinas (HEMOCENTRO/UNICAMP), Campinas, SP, Brazil; Departamento de Medicina Interna da Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Sara Teresinha Olalla Saad
- Centro de Hematologia e Hemoterapia da Universidade Estadual de Campinas (HEMOCENTRO/UNICAMP), Campinas, SP, Brazil; Departamento de Medicina Interna da Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil.
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8
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Phenotypic and molecular genetic analysis of Pyruvate Kinase deficiency in a Tunisian family. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2016. [DOI: 10.1016/j.ejmhg.2015.09.001] [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] Open
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9
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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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10
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van Bruggen R, Gualtieri C, Iliescu A, Louicharoen Cheepsunthorn C, Mungkalasut P, Trape JF, Modiano D, Sodiomon Sirima B, Singhasivanon P, Lathrop M, Sakuntabhai A, Bureau JF, Gros P. Modulation of Malaria Phenotypes by Pyruvate Kinase (PKLR) Variants in a Thai Population. PLoS One 2015; 10:e0144555. [PMID: 26658699 PMCID: PMC4677815 DOI: 10.1371/journal.pone.0144555] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/19/2015] [Indexed: 01/11/2023] Open
Abstract
Pyruvate kinase (PKLR) is a critical erythrocyte enzyme that is required for glycolysis and production of ATP. We have shown that Pklr deficiency in mice reduces the severity (reduced parasitemia, increased survival) of blood stage malaria induced by infection with Plasmodium chabaudi AS. Likewise, studies in human erythrocytes infected ex vivo with P. falciparum show that presence of host PK-deficiency alleles reduces infection phenotypes. We have characterized the genetic diversity of the PKLR gene, including haplotype structure and presence of rare coding variants in two populations from malaria endemic areas of Thailand and Senegal. We investigated the effect of PKLR genotypes on rich longitudinal datasets including haematological and malaria-associated phenotypes. A coding and possibly damaging variant (R41Q) was identified in the Thai population with a minor allele frequency of ~4.7%. Arginine 41 (R41) is highly conserved in the pyruvate kinase family and its substitution to Glutamine (R41Q) affects protein stability. Heterozygosity for R41Q is shown to be associated with a significant reduction in the number of attacks with Plasmodium falciparum, while correlating with an increased number of Plasmodium vivax infections. These results strongly suggest that PKLR protein variants may affect the frequency, and the intensity of malaria episodes induced by different Plasmodium parasites in humans living in areas of endemic malaria.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Base Sequence
- Disease Susceptibility
- Erythrocytes/enzymology
- Erythrocytes/parasitology
- Gene Expression
- Genotype
- Humans
- Malaria/enzymology
- Malaria/genetics
- Malaria/pathology
- Malaria, Falciparum/enzymology
- Malaria, Falciparum/epidemiology
- Malaria, Falciparum/genetics
- Malaria, Falciparum/pathology
- Malaria, Vivax/enzymology
- Malaria, Vivax/epidemiology
- Malaria, Vivax/genetics
- Malaria, Vivax/pathology
- Mice
- Mice, Knockout
- Parasitemia/enzymology
- Parasitemia/epidemiology
- Parasitemia/genetics
- Parasitemia/pathology
- Phenotype
- Plasmodium chabaudi/physiology
- Plasmodium falciparum/physiology
- Plasmodium vivax/physiology
- Polymorphism, Single Nucleotide
- Protein Stability
- Pyruvate Kinase/chemistry
- Pyruvate Kinase/genetics
- Pyruvate Kinase/metabolism
- Senegal/epidemiology
- Sequence Alignment
- Severity of Illness Index
- Thailand/epidemiology
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Affiliation(s)
- Rebekah van Bruggen
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Christian Gualtieri
- Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Alexandra Iliescu
- Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Punchalee Mungkalasut
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand, 10330
| | - Jean-François Trape
- Laboratoire de Paludologie et Zoologie Médicale, Institut de Recherche pour le Développement, Dakar, Sénégal
| | - David Modiano
- Department of Public Health and Infectious Diseases, Instituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Bienvenu Sodiomon Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ministry of Health, Ouagadougou, Burkina Faso
| | - Pratap Singhasivanon
- Department of Tropical Hygiene (Biomedical and Health Informatics), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Mark Lathrop
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Anavaj Sakuntabhai
- Unité de la Génétique Fonctionnelle des Maladies Infectieuses, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, URA3012, F-75015, Paris, France
| | - Jean-François Bureau
- Unité de la Génétique Fonctionnelle des Maladies Infectieuses, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, URA3012, F-75015, Paris, France
| | - Philippe Gros
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail:
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11
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Garate Z, Quintana-Bustamante O, Crane AM, Olivier E, Poirot L, Galetto R, Kosinski P, Hill C, Kung C, Agirre X, Orman I, Cerrato L, Alberquilla O, Rodriguez-Fornes F, Fusaki N, Garcia-Sanchez F, Maia TM, Ribeiro ML, Sevilla J, Prosper F, Jin S, Mountford J, Guenechea G, Gouble A, Bueren JA, Davis BR, Segovia JC. Generation of a High Number of Healthy Erythroid Cells from Gene-Edited Pyruvate Kinase Deficiency Patient-Specific Induced Pluripotent Stem Cells. Stem Cell Reports 2015; 5:1053-1066. [PMID: 26549847 PMCID: PMC4682065 DOI: 10.1016/j.stemcr.2015.10.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 01/30/2023] Open
Abstract
Pyruvate kinase deficiency (PKD) is a rare erythroid metabolic disease caused by mutations in the PKLR gene. Erythrocytes from PKD patients show an energetic imbalance causing chronic non-spherocytic hemolytic anemia, as pyruvate kinase defects impair ATP production in erythrocytes. We generated PKD induced pluripotent stem cells (PKDiPSCs) from peripheral blood mononuclear cells (PB-MNCs) of PKD patients by non-integrative Sendai viral vectors. PKDiPSCs were gene edited to integrate a partial codon-optimized R-type pyruvate kinase cDNA in the second intron of the PKLR gene by TALEN-mediated homologous recombination (HR). Notably, we found allele specificity of HR led by the presence of a single-nucleotide polymorphism. High numbers of erythroid cells derived from gene-edited PKDiPSCs showed correction of the energetic imbalance, providing an approach to correct metabolic erythroid diseases and demonstrating the practicality of this approach to generate the large cell numbers required for comprehensive biochemical and metabolic erythroid analyses. Patient-specific PKDiPSCs are generated from PB-MNCs by a non-integrative system PKDiPSCs are gene edited to insert a partial co-RPK in the PKLR locus mediated by TALEN An SNP in the homology arm leads to allele-specific homologous recombination Gene-edited PKDiPSCs generate a high number of metabolically corrected erythroid cells
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Affiliation(s)
- Zita Garate
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain; Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Oscar Quintana-Bustamante
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain.
| | - Ana M Crane
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Emmanuel Olivier
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | | | - Collin Hill
- Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA
| | - Charles Kung
- Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA
| | - Xabi Agirre
- Hematology and Cell Therapy, Clinica Universidad de Navarra and CIMA, Pamplona 31008, Spain
| | - Israel Orman
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Laura Cerrato
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Omaira Alberquilla
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Fatima Rodriguez-Fornes
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Noemi Fusaki
- JST PRESTO and Ophthalmology, Keio University, Tokyo 108-8345, Japan
| | - Felix Garcia-Sanchez
- Histocompatibility and Molecular Biology Laboratory, Centro de Transfusion de Madrid, Madrid 28032, Spain
| | - Tabita M Maia
- Serviço de Hematologia, Centro Hospitalar e Universitario de Coimbra, Coimbra 3000-075, Portugal
| | - Maria L Ribeiro
- Serviço de Hematologia, Centro Hospitalar e Universitario de Coimbra, Coimbra 3000-075, Portugal
| | | | - Felipe Prosper
- Hematology and Cell Therapy, Clinica Universidad de Navarra and CIMA, Pamplona 31008, Spain
| | - Shengfang Jin
- Agios Pharmaceuticals, Cambridge, MA 02139-4169, USA
| | - Joanne Mountford
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Guillermo Guenechea
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | | | - Juan A Bueren
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain
| | - Brian R Davis
- Center for Stem Cell and Regenerative Medicine, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Jose C Segovia
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid 28040, Spain; Advanced Therapies Mixed Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid 28040, Spain.
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12
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Olivier F, Wieckowska A, Piedboeuf B, Alvarez F. Cholestasis and Hepatic Failure in a Neonate: A Case Report of Severe Pyruvate Kinase Deficiency. Pediatrics 2015; 136:e1366-8. [PMID: 26459649 DOI: 10.1542/peds.2015-0834] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2015] [Indexed: 11/24/2022] Open
Abstract
Unexpected severe cholestasis is part of the presentation in some neonates with hemolytic anemia but is usually self-resolving. Here we report the case of a neonate with pyruvate kinase deficiency (PKD) who presented severe hemolytic anemia at birth, characterized by a rapidly progressive and severe cholestasis with normal γ-glutamyl transpeptidase level associated with hepatic failure. After an extensive investigation to rule out contributing conditions explaining the severity of this patient's clinical presentation, PKD has remained the sole identified etiology. The patient abruptly died of sepsis at 3 months of age before a planned splenectomy and ongoing evaluation for liver transplantation. To the best of our knowledge, only a few similar cases of severe neonatal presentation of PKD complicated with severe hepatic failure and cholestasis have been reported.
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Affiliation(s)
| | - Anna Wieckowska
- Gastroenterology, Department of Pediatrics, CHU de Québec, Université Laval, Québec City, Québec, Canada; and
| | | | - Fernando Alvarez
- Division of Gastroenterology and Hepatology, Department of Pediatrics, Sainte Justine Hospital, Montréal, Québec, Canada
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13
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Liu Y, Wei X, Kong X, Guo X, Sun Y, Man J, Du L, Zhu H, Qu Z, Tian P, Mao B, Yang Y. Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases. PLoS One 2015; 10:e0133636. [PMID: 26274329 PMCID: PMC4537117 DOI: 10.1371/journal.pone.0133636] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/30/2015] [Indexed: 12/04/2022] Open
Abstract
Background Targeted next-generation sequencing (NGS) is a cost-effective approach for rapid and accurate detection of genetic mutations in patients with suspected genetic disorders, which can facilitate effective diagnosis. Methodology/Principal Findings We designed a capture array to mainly capture all the coding sequence (CDS) of 2,181 genes associated with 561 Mendelian diseases and conducted NGS to detect mutations. The accuracy of NGS was 99.95%, which was obtained by comparing the genotypes of selected loci between our method and SNP Array in four samples from normal human adults. We also tested the stability of the method using a sample from normal human adults. The results showed that an average of 97.79% and 96.72% of single-nucleotide variants (SNVs) in the sample could be detected stably in a batch and different batches respectively. In addition, the method could detect various types of mutations. Some disease-causing mutations were detected in 69 clinical cases, including 62 SNVs, 14 insertions and deletions (Indels), 1 copy number variant (CNV), 1 microdeletion and 2 microduplications of chromosomes, of which 35 mutations were novel. Mutations were confirmed by Sanger sequencing or real-time polymerase chain reaction (PCR). Conclusions/Significance Results of the evaluation showed that targeted NGS enabled to detect disease-causing mutations with high accuracy, stability, speed and throughput. Thus, the technology can be used for the clinical diagnosis of 561 Mendelian diseases.
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Affiliation(s)
- Yanqiu Liu
- Department of Genetics, Jiangxi Provincial Women and Children Hospital, Nanchang, 330006, China
| | - Xiaoming Wei
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiangdong Kong
- Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xueqin Guo
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yan Sun
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jianfen Man
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Lique Du
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Hui Zhu
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Zelan Qu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Ping Tian
- Department of Obstetrics and Gynecology, Wuhan Medical and Health Center for Women and Children, Wuhan, 430022, China
| | - Bing Mao
- Department of Neurology, Wuhan Medical and Health Center for Women and Children, Wuhan, 430022, China
| | - Yun Yang
- BGI-Wuhan, Wuhan, 430075, China
- BGI-Shenzhen, Shenzhen, 518083, China
- * E-mail:
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14
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van Oirschot BA, Francois JJJM, van Solinge WW, van Wesel ACW, Rijksen G, van Amstel HKP, van Wijk R. Novel type of red blood cell pyruvate kinase hyperactivity predicts a remote regulatory locus involved in PKLR gene expression. Am J Hematol 2014; 89:380-4. [PMID: 24375447 DOI: 10.1002/ajh.23647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/23/2013] [Accepted: 12/02/2013] [Indexed: 11/09/2022]
Abstract
Red blood cell pyruvate kinase (PK-R) is a key regulatory enzyme of red cell metabolism. Hereditary deficiency of PK-R is caused by mutations in the PKLR gene, leading to chronic nonspherocytic hemolytic anemia. In contrast to PK deficiency, inherited PK hyperactivity has also been described. This very rare abnormality of RBC metabolism has been documented in only two families and appears to be without clinical consequences. Thus far, it has been attributed to either a gain of function mutation in PKLR or to persistent expression of the fetal PK isozyme PK-M2 in mature red blood cells. We here report on a novel type of inherited PK hyperactivity that is characterized by solely increased expression of a kinetically normal PK-R. In line with the latter, no mutations were detected in PKLR. Mutations in regulatory regions as well as variations in PKLR copy number were also absent. In addition, linkage analysis suggested that PK hyperactivity segregated independently from the PKLR locus. We therefore postulate that the causative mutation resides in a novel yet-unidentified locus, and upregulates PKLR gene expression. Other mutations of the same locus may be involved in those cases of PK deficiency that fail to reveal mutations in PKLR.
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Affiliation(s)
| | | | - Wouter Willem van Solinge
- Department of Clinical Chemistry and Hematology; University Medical Center Utrecht; Utrecht The Netherlands
| | | | - Gert Rijksen
- Department of Clinical Chemistry and Hematology; University Medical Center Utrecht; Utrecht The Netherlands
| | | | - Richard van Wijk
- Department of Clinical Chemistry and Hematology; University Medical Center Utrecht; Utrecht The Netherlands
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15
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Gray LR, Tompkins SC, Taylor EB. Regulation of pyruvate metabolism and human disease. Cell Mol Life Sci 2013; 71:2577-604. [PMID: 24363178 PMCID: PMC4059968 DOI: 10.1007/s00018-013-1539-2] [Citation(s) in RCA: 535] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 11/24/2013] [Accepted: 12/02/2013] [Indexed: 12/31/2022]
Abstract
Pyruvate is a keystone molecule critical for numerous aspects of eukaryotic and human metabolism. Pyruvate is the end-product of glycolysis, is derived from additional sources in the cellular cytoplasm, and is ultimately destined for transport into mitochondria as a master fuel input undergirding citric acid cycle carbon flux. In mitochondria, pyruvate drives ATP production by oxidative phosphorylation and multiple biosynthetic pathways intersecting the citric acid cycle. Mitochondrial pyruvate metabolism is regulated by many enzymes, including the recently discovered mitochondria pyruvate carrier, pyruvate dehydrogenase, and pyruvate carboxylase, to modulate overall pyruvate carbon flux. Mutations in any of the genes encoding for proteins regulating pyruvate metabolism may lead to disease. Numerous cases have been described. Aberrant pyruvate metabolism plays an especially prominent role in cancer, heart failure, and neurodegeneration. Because most major diseases involve aberrant metabolism, understanding and exploiting pyruvate carbon flux may yield novel treatments that enhance human health.
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Affiliation(s)
- Lawrence R Gray
- Department of Biochemistry, Fraternal Order of the Eagles Diabetes Research Center, and François M. Abboud Cardiovascular Research Center, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 51 Newton Rd, 4-403 BSB, Iowa City, IA, 52242, USA
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16
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Grahn RA, Grahn JC, Penedo MC, Helps CR, Lyons LA. Erythrocyte pyruvate kinase deficiency mutation identified in multiple breeds of domestic cats. BMC Vet Res 2012; 8:207. [PMID: 23110753 PMCID: PMC3534511 DOI: 10.1186/1746-6148-8-207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 10/22/2012] [Indexed: 11/29/2022] Open
Abstract
Background Erythrocyte pyruvate kinase deficiency (PK deficiency) is an inherited hemolytic anemia that has been documented in the Abyssinian and Somali breeds as well as random bred domestic shorthair cats. The disease results from mutations in PKLR, the gene encoding the regulatory glycolytic enzyme pyruvate kinase (PK). Multiple isozymes are produced by tissue-specific differential processing of PKLR mRNA. Perturbation of PK decreases erythrocyte longevity resulting in anemia. Additional signs include: severe lethargy, weakness, weight loss, jaundice, and abdominal enlargement. In domestic cats, PK deficiency has an autosomal recessive mode of inheritance with high variability in onset and severity of clinical symptoms. Results Sequence analysis of PKLR revealed an intron 5 single nucleotide polymorphism (SNP) at position 304 concordant with the disease phenotype in Abyssinian and Somali cats. Located 53 nucleotides upstream of the exon 6 splice site, cats with this SNP produce liver and blood processed mRNA with a 13 bp deletion at the 3’ end of exon 5. The frame-shift mutation creates a stop codon at amino acid position 248 in exon 6. The frequency of the intronic SNP in 14,179 American and European cats representing 38 breeds, 76 western random bred cats and 111 cats of unknown breed is 6.31% and 9.35% when restricted to the 15 groups carrying the concordant SNP. Conclusions PK testing is recommended for Bengals, Egyptian Maus, La Perms, Maine Coon cats, Norwegian Forest cats, Savannahs, Siberians, and Singapuras, in addition to Abyssinians and Somalis as well an any new breeds using the afore mentioned breeds in out crossing or development programs.
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Affiliation(s)
- Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.
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17
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Gultekin GI, Raj K, Foureman P, Lehman S, Manhart K, Abdulmalik O, Giger U. Erythrocytic pyruvate kinase mutations causing hemolytic anemia, osteosclerosis, and secondary hemochromatosis in dogs. J Vet Intern Med 2012; 26:935-44. [PMID: 22805166 PMCID: PMC3650904 DOI: 10.1111/j.1939-1676.2012.00958.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Erythrocytic pyruvate kinase (PK) deficiency, first documented in Basenjis, is the most common inherited erythroenzymopathy in dogs. OBJECTIVES To report 3 new breed-specific PK-LR gene mutations and a retrospective survey of PK mutations in as mall and selected group of Beagles and West Highland White Terriers (WHWT). ANIMALS Labrador Retrievers (2 siblings, 5 unrelated), Pugs (2 siblings, 1 unrelated), Beagles (39 anemic, 29 other),WHWTs (22 anemic, 226 nonanemic), Cairn Terrier (n = 1). METHODS Exons of the PK-LR gene were sequenced from genomic DNA of young dogs (<2 years) with persistent highly regenerative hemolytic anemia. RESULTS A nonsense mutation (c.799C>T) resulting in a premature stop codon was identified in anemic Labrador Retriever siblings that had osteosclerosis, high serum ferritin concentrations, and severe hepatic secondary hemochromatosis. Anemic Pug and Beagle revealed 2 different missense mutations (c.848T>C, c.994G>A, respectively) resulting in intolerable amino acid changes to protein structure and enzyme function. Breed-specific mutation tests were developed. Among the biased group of 248 WHWTs, 9% and 35% were homozygous (affected) and heterozygous, respectively, for the previously described mutation (mutant allele frequency 0.26). A PK-deficient Cairn Terrier had the same insertion mutation as the affected WHWTs. Of the selected group of 68 Beagles, 35% were PK-deficient and 3% were carriers (0.37). CONCLUSIONS AND CLINICAL IMPORTANCE Erythrocytic PK deficiency is caused by different mutations in different dog breeds and causes chronic severe hemolytic anemia, hemosiderosis, and secondary hemochromatosis because of chronic hemolysis and, an as yet unexplained osteosclerosis. The newly developed breed-specific mutation assays simplify the diagnosis of PK deficiency.
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Affiliation(s)
- G Inal Gultekin
- Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
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18
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So CC, Tang M, Li CH, Ha SY, Pissard S, Chan LC. First reported case of prenatal diagnosis for pyruvate kinase deficiency in a Chinese family. ACTA ACUST UNITED AC 2011; 16:377-9. [PMID: 22183074 DOI: 10.1179/102453311x13127324303317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
We describe the first case of prenatal diagnosis for pyruvate kinase (PK) deficiency in Chinese and emphasize that this disease is an important differential diagnosis in pediatric patients with non-spherocytic hemolytic anemia. A Han Chinese child with a history of severe transfusion-dependent hemolytic anemia was diagnosed to have PK deficiency. Prenatal diagnosis was performed on the second child based on the genetic findings from the family. The index patient was compound heterozygous for a missense mutation (c.1073G > A. p.Gly358Glu) from his father and a large deletion (c.283 + 1914_c.1434del5006) from his mother. The fetus was a simple heterozygote for the paternal mutation. Pregnancy was allowed to continue and a healthy baby was born. Severe PK deficiency warranting prenatal diagnosis is seen in Han Chinese. Genetic characterization and genotype-phenotype correlation studies on PKLR in different populations are indicated to better define the role of prenatal diagnosis in PK deficiency.
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Affiliation(s)
- Chi-Chiu So
- Department of Pathology, University of Hong Kong SAR, China.
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19
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Rider NL, Strauss KA, Brown K, Finkenstedt A, Puffenberger EG, Hendrickson CL, Robinson DL, Muenke N, Tselepis C, Saunders L, Zoller H, Morton DH. Erythrocyte pyruvate kinase deficiency in an old-order Amish cohort: longitudinal risk and disease management. Am J Hematol 2011; 86:827-34. [PMID: 21815188 DOI: 10.1002/ajh.22118] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 06/15/2011] [Accepted: 06/20/2011] [Indexed: 11/06/2022]
Abstract
Pyruvate kinase deficiency is a chronic illness with age specific consequences. Newborns suffer life-threatening hemolytic crisis and hyperbilirubinemia. Adults are at risk for infections because of asplenia, pregnancy-related morbidity, and may suffer organ damage because of systemic iron overload. We describe 27 Old Order Amish patients (ages 8 months-52 years) homozygous for c.1436G>A mutations in PKLR. Each subject had a predictable neonatal course requiring packed red blood cell transfusions (30 ± 5 mL/kg) to control hemolytic disease and intensive phototherapy to prevent kernicterus. Hemochromatosis affected 29% (n = 4) of adult patients, who had inappropriately normal serum hepcidin (34.5 ± 12.7 ng/mL) and GDF-15 (595 ± 335pg/mL) relative to hyperferritinemia (769 ± 595 mg/dL). A high prevalence of HFE gene mutations exists in this population and may contribute to iron-related morbidity. Based on our observations, we present a strategy for long-term management of pyruvate kinase deficiency.
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Affiliation(s)
- Nicholas L Rider
- Clinic for Special Children, Strasburg, Pennsylvania, PA 17579, USA.
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20
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Minucci A, Ricerca BM, Tripodi D, Matarazzo L, De Michele T, Giardina B, Zuppi C, Capoluongo E. Worsening of the clinical-hematological picture in a patient with a rare PK-LR compound heterozygosis after mitral replacement. Clin Biochem 2011; 44:1261-3. [PMID: 21821016 DOI: 10.1016/j.clinbiochem.2011.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/07/2011] [Accepted: 07/10/2011] [Indexed: 11/28/2022]
Abstract
We report a case of a patient affected by compound heterozygosis for two PK-LR gene mutations: p.R486W (c.1456C>T) and p.M403I (c.1209G>A). Our patient suffered from an initial moderate hemolytic anemia which subsequently evolved into a severe form after mitral prosthetic valve replacement for valve regurgitation. Thereafter, the clinical features evolved into a worsening of anemia, heart failure and pulmonary hypertension, in the absence of valve dysfunction. This clinical picture improved only after an intensive transfusion regimen. This case highlights aspects concerning the intricate balance between the risks and benefits of a mechanical prosthetic valve implant in PK-deficient patients.
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Affiliation(s)
- Angelo Minucci
- Laboratory of Clinical Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of the Sacred Heart, Rome, Italy.
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21
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Perseu L, Giagu N, Satta S, Sollaino MC, Congiu R, Galanello R. Red cell pyruvate kinase deficiency in Southern Sardinia. Blood Cells Mol Dis 2010; 45:280-3. [PMID: 20870434 DOI: 10.1016/j.bcmd.2010.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 08/03/2010] [Indexed: 11/24/2022]
Abstract
Pyruvate kinase (PK) deficiency is the most frequent red cell enzymatic defect responsible for hereditary non-spherocytic hemolytic anemia. The clinical picture is quite variable and the reasons of this variability have been only partially clarified. We report the clinical description and the extended molecular analysis in 3 PK deficient patients with clinical phenotype of variable severity. We studied the clinical and hematological aspects of 3 patients and analyzed the following genes: pyruvate kinase-R, glucose-6-phosphate-dehydrogenase, α-globin, uridindiphosphoglucuronil transferase and HFE. One patient (A) with a severe clinical picture resulted homozygote for exon 8 nt994A substitution, the other 2 (brothers) were compound heterozygotes for exon 8 nt994A and exon 11 nt1456T mutation. One of the two brothers with a more severe phenotype coinherited also had G6PD deficiency, while both had microcytosis due to the homozygosity for the non-deletional form of α-thalassemia ATG→ACG substitution at the initiation codon of the alpha2 globin gene. Our results suggest that extended molecular analysis is useful for studying how several interacting gene mutations contribute to the clinical variability of pyruvate kinase deficiency.
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Affiliation(s)
- L Perseu
- Istituto di Neurogenetica e Neurofarmacologia CNR, Cagliari, Italy
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22
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van Wijk R, Huizinga EG, van Wesel AC, van Oirschot BA, A. Hadders M, van Solinge WW. Fifteen novel mutations inPKLRassociated with pyruvate kinase (PK) deficiency: Structural implications of amino acid substitutions in PK. Hum Mutat 2009; 30:446-53. [DOI: 10.1002/humu.20915] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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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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24
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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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25
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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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26
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Pendergrass DC, Williams R, Blair JB, Fenton AW. Mining for allosteric information: Natural mutations and positional sequence conservation in pyruvate kinase. IUBMB Life 2006; 58:31-8. [PMID: 16540430 DOI: 10.1080/15216540500531705] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Although the amino acid sequences and the structures of pyruvate kinase (PYK) isozymes are highly conserved, allosteric regulations differ. This suggests that amino acids with low conservation play important roles in the allosteric mechanism. The current work exploits a 'natural screen'- the 122 point mutations identified in the human gene encoding the erythrocyte PYK isozyme and associated with nonspherocytic hemolytic anemia - to learn what amino acid positions in PYK may be important for allosteric regulations. In addition to the mutations, we consider the conservation of each amino acid position across 241 PYK sequences. Three groups of residue positions have been created, those with: (1) no disease causing mutation identified; (2) a disease causing mutation identified and high conservation across isozymes; and (3) a disease causing mutation identified and low conservation. Mutations at positions not identified in the natural screen are likely to be tolerated with minimal loss of function. Mutations at highly conserved positions are more likely to disrupt properties common to all PYK isozymes (e.g., structure, catalysis). Residues in the third group are likely to be involved in roles that are necessary for function but not common to all isozymes (e.g., allostery). Many of the Group 3 residues are located in the C-domain and to a lesser extent the A domain.
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Affiliation(s)
- David C Pendergrass
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, USA
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Corrigendum. Br J Haematol 2005. [DOI: 10.1111/j.1365-2141.2005.05691.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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