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Heydarzadeh S, Kia SK, Boroomand S, Hedayati M. Recent Developments in Cell Shipping Methods. Biotechnol Bioeng 2022; 119:2985-3006. [PMID: 35898166 DOI: 10.1002/bit.28197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/09/2022] [Accepted: 07/17/2022] [Indexed: 11/11/2022]
Abstract
As opposed to remarkable advances in the cell therapy industry, researches reveal inexplicable difficulties associated with preserving and post-thawing cell death. Post cryopreservation apoptosis is a common occurrence that has attracted the attention of scientists to use apoptosis inhibitors. Transporting cells without compromising their survival and function is crucial for any experimental cell-based therapy. Preservation of cells allows the safe transportation of cells between distances and improves quality control testing in clinical and research applications. The vitality of transported cells is used to evaluate the efficacy of transportation strategies. For many decades, the conventional global methods of cell transfer were not only expensive but also challenging and had adverse effects. The first determination of some projects is optimizing cell survival after cryopreservation. The new generation of cryopreservation science wishes to find appropriate and alternative methods for cell transportation to ship viable cells at an ambient temperature without dry ice or in media-filled flasks. The diversity of cell therapies demands new cell shipping methodologies and cryoprotectants. In this review, we tried to summarize novel improved cryopreservation methods and alternatives to cryopreservation with safe and viable cell shipping at ambient temperature, including dry preservation, hypothermic preservation, gel-based methods, encapsulation methods, fibrin microbeads, and osmolyte solution compositions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shabnam Heydarzadeh
- Department of Biochemistry, School of Biological Sciences, Falavarjan Branch Islamic Azad University, Isfahan, Iran.,Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sima Kheradmand Kia
- Laboratory for Red Blood Cell Diagnostics, Sanquin, Amsterdam, The Netherlands
| | - Seti Boroomand
- Djavad Mowafaghian Centre for Brain Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mehdi Hedayati
- Djavad Mowafaghian Centre for Brain Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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2
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van Dooijeweert B, Kia SK, Dahl N, Fenneteau O, Leguit R, Nieuwenhuis E, van Solinge W, van Wijk R, Da Costa L, Bartels M. GATA-1 Defects in Diamond-Blackfan Anemia: Phenotypic Characterization Points to a Specific Subset of Disease. Genes (Basel) 2022; 13:genes13030447. [PMID: 35328001 PMCID: PMC8949872 DOI: 10.3390/genes13030447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/13/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
Diamond−Blackfan anemia (DBA) is one of the inherited bone marrow failure syndromes marked by erythroid hypoplasia. Underlying variants in ribosomal protein (RP) genes account for 80% of cases, thereby classifying DBA as a ribosomopathy. In addition to RP genes, extremely rare variants in non-RP genes, including GATA1, the master transcription factor in erythropoiesis, have been reported in recent years in patients with a DBA-like phenotype. Subsequently, a pivotal role for GATA-1 in DBA pathophysiology was established by studies showing the impaired translation of GATA1 mRNA downstream of the RP haploinsufficiency. Here, we report on a patient from the Dutch DBA registry, in which we found a novel hemizygous variant in GATA1 (c.220+2T>C), and an Iranian patient with a previously reported variant in the initiation codon of GATA1 (c.2T>C). Although clinical features were concordant with DBA, the bone marrow morphology in both patients was not typical for DBA, showing moderate erythropoietic activity with signs of dyserythropoiesis and dysmegakaryopoiesis. This motivated us to re-evaluate the clinical characteristics of previously reported cases, which resulted in the comprehensive characterization of 18 patients with an inherited GATA-1 defect in exon 2 that is presented in this case-series. In addition, we re-investigated the bone marrow aspirate of one of the previously published cases. Altogether, our observations suggest that DBA caused by GATA1 defects is characterized by distinct phenotypic characteristics, including dyserythropoiesis and dysmegakaryopoiesis, and therefore represents a distinct phenotype within the DBA disease spectrum, which might need specific clinical management.
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Affiliation(s)
- Birgit van Dooijeweert
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
- Department of Pediatric Hematology, van Creveldkliniek, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Sima Kheradmand Kia
- Laboratory for Red Blood Cell Diagnostics, Sanquin, 1006 AD Amsterdam, The Netherlands;
- Peyvand Lab Complex, Shiraz 7363871347, Iran
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Children’s Hospital, 751 85 Uppsala, Sweden;
| | - Odile Fenneteau
- AP-HP, Service d’Hématologie Biologique, Hôpital Robert Debré, University of Paris Cité, Hematim EA 4666, UPJV, F-75019 Paris, France; (O.F.); (L.D.C.)
| | - Roos Leguit
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Edward Nieuwenhuis
- Department of Pediatrics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands;
| | - Wouter van Solinge
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
| | - Richard van Wijk
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
| | - Lydie Da Costa
- AP-HP, Service d’Hématologie Biologique, Hôpital Robert Debré, University of Paris Cité, Hematim EA 4666, UPJV, F-75019 Paris, France; (O.F.); (L.D.C.)
| | - Marije Bartels
- Department of Pediatric Hematology, van Creveldkliniek, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Pediatrics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands;
- Correspondence:
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3
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Sheikholeslami S, Zarif-Yeganeh M, Farashi S, Azizi F, Kia SK, Teimoori-Toolabi L, Hedayati M. Promoter Methylation of Tumor Suppressors in Thyroid Carci-noma: A Systematic Review. ijph 2021; 50:2461-2472. [PMID: 36317025 PMCID: PMC9577160 DOI: 10.18502/ijph.v50i12.7928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/18/2021] [Indexed: 11/24/2022]
Abstract
Background: The tumor suppressor genes play a critical role in cellular and molecular mechanisms such as cell cycle processes, cell differentiation and apoptosis. Aberrant DNA methylation of tumor suppressor genes and subsequent gene expression changes have shown to be involved in the initiation and progression of various malignancies including thyroid malignancies. In this review, we investigated what is known about the impact of promoter hypermethylation on the key tumor suppressor genes known to be involved in cell growth and/or apoptosis of thyroid cancer. Methods: The most important databases were searched for research articles until June 2020 to identify reported tumor suppressor genes that are modulated by methylation modulation changes in thyroid carcinoma. Following the inclusion and exclusion criteria, 26 studies were reviewed using the full text to meet the inclusion and exclusion criteria. Results: The tumor suppressor genes reviewed here are suggestive biomarkers and potential targetable drugs. Inactivation of RASSF1A, DAPK1, SLCFA8, and TSHR through aberrant epigenetic methylation could activate BRAF/MEK/ERK kinase pathways with potential clinical implications in thyroid cancer patients. RARβ2 and RUNX3 could suppress cell cycle and induce apoptosis in malignant cells. TIMP3 and PTEN could prevent angiogenesis and invasion through PIP3 pathway and arrest VEFG activity. Conclusion: The methylation status of key genes in various types of thyroid malignancies could be used in early diagnosis as well as differentiation of malignant and benign thyroid. This is valuable in drug repurposing and discovering alternative treatments or preventions in thyroid cancer.
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Affiliation(s)
- Sara Sheikholeslami
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marjan Zarif-Yeganeh
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samaneh Farashi
- Cancer Program, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, Brisbane, Queensland, 4102, Australia
- Translational Research Institute, Woolloongabba, Queensland, 4102, Australia
| | - Fereidoun Azizi
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Corresponding Authors: Emails: ;
| | - Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Corresponding Authors: Emails: ;
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Hedayati M, Razavi SA, Boroomand S, Kheradmand Kia S. The impact of pre-analytical variations on biochemical analytes stability: A systematic review. J Clin Lab Anal 2020; 34:e23551. [PMID: 32869910 PMCID: PMC7755813 DOI: 10.1002/jcla.23551] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/06/2020] [Accepted: 08/06/2020] [Indexed: 12/24/2022] Open
Abstract
Objective A common problem in clinical laboratories is maintaining the stability of analytes during pre‐analytical processes. The aim of this study was to systematically summarize the results of a set of studies about the biochemical analytes stability. Methods A literature search was performed on the Advanced search field of PubMed using the keywords: “(stability) AND (analytes OR laboratory analytes OR laboratory tests OR biochemical analytes OR biochemical tests OR biochemical laboratory tests).” A total of 56 entries were obtained. After applying the selection criteria, 20 articles were included in the study. Results In the 20 included references, up to 123 different analytes were assessed. The 34 analytes in order of the most frequently studied analytes were evaluated: Alanine aminotransferase, aspartate aminotransferase, potassium, triglyceride, alkaline phosphatase, creatinine, total cholesterol, albumin, lactate dehydrogenase, sodium, calcium, γ‐glutamyltransferase, total bilirubin, urea, creatine kinase, inorganic phosphate, total protein, uric acid, amylase, chloride, high‐density lipoprotein, magnesium, glucose, C‐reactive protein, bicarbonate, ferritin, iron, lipase, transferrin, cobalamin, cortisol, folate, free thyroxine, and thyroid‐stimulating hormone. Stable test results could be varied between 2 hours and 1 week according to the type of samples and/or type of blood collection tubes on a basic classification set as refrigerated or room temperature. Conclusions Biochemical analytes stability could be improved if the best pre‐analytical approaches are used.
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Affiliation(s)
- Mehdi Hedayati
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S Adeleh Razavi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Research and Development (R&D), Saeed Pathobiology & Genetics Laboratory, Tehran, Iran
| | - Seti Boroomand
- Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Sima Kheradmand Kia
- Laboratory for Red Blood Cell Diagnostics, Sanquin, Amsterdam, The Netherlands
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5
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Klei TRL, Kheradmand Kia S, Veldthuis M, Dehbozorgian J, Karimi M, Geissler J, Sellink E, Thiel-Valkhof M, Burger P, van Alphen F, Meijer AB, van Bruggen R, van Zwieten R. A Homozygous Mutation on the HBA1 Gene Coding for Hb Charlieu (HBA1: c.320T>C) Together with β-Thalassemia Trait Results in Severe Hemolytic Anemia. Hemoglobin 2019; 43:77-82. [PMID: 31190578 DOI: 10.1080/03630269.2019.1601107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A 4-year-old boy, a β-thalassemia (β-thal) carrier, with an unexplained severe chronic microcytic anemia was referred to us. Sequencing of the α-globin genes revealed a Hb Charlieu [α106(G13)Leu→Pro, HBA1: c.320T>C, p.Leu107Pro] mutation present on both HBA1 genes. Quantitative polymerase chain reaction (qPCR) confirmed αCharlieu mRNA in the proband and his parents, showing that the mutation does not affect mRNA stability. However, we were unable to detect the Hb Charlieu protein by capillary electrophoresis (CE), reverse phase electrophoresis, cation exchange electrophoresis or isoelectric focusing. Mass spectrometry (MS) allowed us to confirm the presence of the Hb Charlieu peptide in erythrocyte progenitors. These findings suggest that the mutation affects the stability of αCharlieu. As hemoglobin (Hb) heat stability tests showed no abnormalities in erythrocytes, we speculated that αCharlieu is already degraded during red blood cell (RBC) development. The clinical severity in the proband and the presence of new methylene blue-stained aggregates in his reticulocytes indicates that incorporation of αCharlieu destabilizes Hb. This, combined with an excess of unstable free α-globins as the result of β-thal minor, results in severely impaired erythropoiesis and, as a consequence, severe and chronic microcytic anemia in the proband.
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Affiliation(s)
- Thomas R L Klei
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands
| | - Sima Kheradmand Kia
- b Laboratory for Red Blood Cell Diagostics , Sanquin , Amsterdam , The Netherlands.,c Department of Hematology , PeyvandLab Complex , Shiraz , Iran
| | - Martijn Veldthuis
- b Laboratory for Red Blood Cell Diagostics , Sanquin , Amsterdam , The Netherlands
| | | | - Mehran Karimi
- d Hematology Research Center, Shiraz University of Medical Sciences , Shiraz , Iran
| | - Judy Geissler
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands
| | - Erica Sellink
- e Department of Hematopoiesis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , The Netherlands
| | - Marijke Thiel-Valkhof
- e Department of Hematopoiesis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , The Netherlands
| | - Patrick Burger
- e Department of Hematopoiesis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , The Netherlands
| | - Floris van Alphen
- f Department of Molecular and Cellular Hemostasis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , The Netherlands
| | - Alexander B Meijer
- f Department of Molecular and Cellular Hemostasis , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , The Netherlands.,g Department of Biomolecular Mass Spectrometry and Proteomics , Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University , Utrecht 3584 CS , The Netherlands
| | - Robin van Bruggen
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands
| | - Rob van Zwieten
- a Department of Blood Cell Research , Sanquin Research and Landsteiner Laboratory, University of Amsterdam , Amsterdam , the Netherlands.,b Laboratory for Red Blood Cell Diagostics , Sanquin , Amsterdam , The Netherlands
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6
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Vermeulen C, Geeven G, de Wit E, Verstegen MJ, Jansen RP, van Kranenburg M, de Bruijn E, Pulit SL, Kruisselbrink E, Shahsavari Z, Omrani D, Zeinali F, Najmabadi H, Katsila T, Vrettou C, Patrinos GP, Traeger-Synodinos J, Splinter E, Beekman JM, Kheradmand Kia S, te Meerman GJ, Ploos van Amstel HK, de Laat W. Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping. Am J Hum Genet 2017; 101:326-339. [PMID: 28844486 PMCID: PMC5590845 DOI: 10.1016/j.ajhg.2017.07.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022] Open
Abstract
During pregnancy, cell-free DNA (cfDNA) in maternal blood encompasses a small percentage of cell-free fetal DNA (cffDNA), an easily accessible source for determination of fetal disease status in risk families through non-invasive procedures. In case of monogenic heritable disease, background maternal cfDNA prohibits direct observation of the maternally inherited allele. Non-invasive prenatal diagnostics (NIPD) of monogenic diseases therefore relies on parental haplotyping and statistical assessment of inherited alleles from cffDNA, techniques currently unavailable for routine clinical practice. Here, we present monogenic NIPD (MG-NIPD), which requires a blood sample from both parents, for targeted locus amplification (TLA)-based phasing of heterozygous variants selectively at a gene of interest. Capture probes-based targeted sequencing of cfDNA from the pregnant mother and a tailored statistical analysis enables predicting fetal gene inheritance. MG-NIPD was validated for 18 pregnancies, focusing on CFTR, CYP21A2, and HBB. In all cases we could predict the inherited alleles with >98% confidence, even at relatively early stages (8 weeks) of pregnancy. This prediction and the accuracy of parental haplotyping was confirmed by sequencing of fetal material obtained by parallel invasive procedures. MG-NIPD is a robust method that requires standard instrumentation and can be implemented in any clinic to provide families carrying a severe monogenic disease with a prenatal diagnostic test based on a simple blood draw.
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7
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Oegema R, Baillat D, Schot R, van Unen LM, Brooks A, Kia SK, Hoogeboom AJM, Xia Z, Li W, Cesaroni M, Lequin MH, van Slegtenhorst M, Dobyns WB, de Coo IFM, van den Berg D, Verheijen FW, Kremer A, van der Spek PJ, Heijsman D, Wagner EJ, Fornerod M, Mancini GMS. Correction: Human mutations in integrator complex subunits link transcriptome integrity to brain development. PLoS Genet 2017; 13:e1006923. [PMID: 28763441 PMCID: PMC5538630 DOI: 10.1371/journal.pgen.1006923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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8
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Klei TRL, Kheradmand Kia S, Veldthuis M, Beuger BM, Geissler J, Dehbozorgian J, Karimi M, van Bruggen R, van Zwieten R. Residual pyruvate kinase activity in PKLR-deficient erythroid precursors of a patient suffering from severe haemolytic anaemia. Eur J Haematol 2017; 98:584-589. [PMID: 28295642 DOI: 10.1111/ejh.12874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2017] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Here, we present a 7-year-old patient suffering from severe haemolytic anaemia. The most common cause of chronic hereditary non-spherocytic haemolytic anaemia is red blood cell pyruvate kinase (PK-R) deficiency. Because red blood cells rely solely on glycolysis to generate ATP, PK-R deficiency can severely impact energy supply and cause reduction in red blood cell lifespan. We determined the underlying cause of the anaemia and investigated how erythroid precursors in the patient survive. METHODS PK activity assays, Western blot and Sanger sequencing were employed to determine the underlying cause of the anaemia. Patient erythroblasts were cultured and reticulocytes were isolated to determine PK-R and PKM2 contribution to glycolytic activity during erythrocyte development. RESULTS We found a novel homozygous mutation (c.583G>A) in the PK-R coding gene (PKLR). Although this mutation did not influence PKLR mRNA production, no PK-R protein could be detected in the red blood cells nor in its precursors. In spite of the absence of PK-R, the reticulocytes of the patient exhibited 20% PK activity compared with control. Western blotting revealed that patient erythroid precursors, like controls, express residual PKM2. CONCLUSIONS We conclude that PKM2 rescues glycolysis in PK-R-deficient erythroid precursors.
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MESH Headings
- Anemia, Hemolytic, Congenital Nonspherocytic/enzymology
- Anemia, Hemolytic, Congenital Nonspherocytic/genetics
- Anemia, Hemolytic, Congenital Nonspherocytic/pathology
- Base Sequence
- Carrier Proteins/genetics
- Cell Differentiation
- Child
- Consanguinity
- Erythroblasts/enzymology
- Erythroblasts/pathology
- Gene Expression
- Glycolysis/genetics
- Homozygote
- Humans
- Male
- Membrane Proteins/deficiency
- Membrane Proteins/genetics
- Mutation
- Myeloid Cells/cytology
- Myeloid Cells/enzymology
- Primary Cell Culture
- Pyruvate Kinase/deficiency
- Pyruvate Kinase/genetics
- Pyruvate Metabolism, Inborn Errors/enzymology
- Pyruvate Metabolism, Inborn Errors/genetics
- Pyruvate Metabolism, Inborn Errors/pathology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reticulocytes/enzymology
- Reticulocytes/pathology
- Thyroid Hormones/deficiency
- Thyroid Hormones/genetics
- Thyroid Hormone-Binding Proteins
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Affiliation(s)
- Thomas R L Klei
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Sima Kheradmand Kia
- Laboratory for Red Blood Cell Diagnostics, Sanquin, Amsterdam, The Netherlands
- Sara Medical Genetics Centre, Tehran, Iran
| | - Martijn Veldthuis
- Laboratory for Red Blood Cell Diagnostics, Sanquin, Amsterdam, The Netherlands
| | - Boukje M Beuger
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Judy Geissler
- Laboratory for Red Blood Cell Diagnostics, Sanquin, Amsterdam, The Netherlands
| | | | - Mehran Karimi
- Hematology Research Centre, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Robin van Bruggen
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
| | - Rob van Zwieten
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory for Red Blood Cell Diagnostics, Sanquin, Amsterdam, The Netherlands
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9
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Oegema R, Baillat D, Schot R, van Unen LM, Brooks A, Kia SK, Hoogeboom AJM, Xia Z, Li W, Cesaroni M, Lequin MH, van Slegtenhorst M, Dobyns WB, de Coo IFM, Verheijen FW, Kremer A, van der Spek PJ, Heijsman D, Wagner EJ, Fornerod M, Mancini GMS. Human mutations in integrator complex subunits link transcriptome integrity to brain development. PLoS Genet 2017; 13:e1006809. [PMID: 28542170 PMCID: PMC5466333 DOI: 10.1371/journal.pgen.1006809] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 06/09/2017] [Accepted: 05/09/2017] [Indexed: 02/06/2023] Open
Abstract
Integrator is an RNA polymerase II (RNAPII)-associated complex that was recently identified to have a broad role in both RNA processing and transcription regulation. Importantly, its role in human development and disease is so far largely unexplored. Here, we provide evidence that biallelic Integrator Complex Subunit 1 (INTS1) and Subunit 8 (INTS8) gene mutations are associated with rare recessive human neurodevelopmental syndromes. Three unrelated individuals of Dutch ancestry showed the same homozygous truncating INTS1 mutation. Three siblings harboured compound heterozygous INTS8 mutations. Shared features by these six individuals are severe neurodevelopmental delay and a distinctive appearance. The INTS8 family in addition presented with neuronal migration defects (periventricular nodular heterotopia). We show that the first INTS8 mutation, a nine base-pair deletion, leads to a protein that disrupts INT complex stability, while the second missense mutation introduces an alternative splice site leading to an unstable messenger. Cells from patients with INTS8 mutations show increased levels of unprocessed UsnRNA, compatible with the INT function in the 3’-end maturation of UsnRNA, and display significant disruptions in gene expression and RNA processing. Finally, the introduction of the INTS8 deletion mutation in P19 cells using genome editing alters gene expression throughout the course of retinoic acid-induced neural differentiation. Altogether, our results confirm the essential role of Integrator to transcriptome integrity and point to the requirement of the Integrator complex in human brain development. Neurodevelopmental disorders often have a genetic cause, however the genes and the underlying mechanisms that are involved are increasingly diverse, pointing to the complexity of brain development. For normal cell function and in general for normal development, mechanisms that regulate gene transcription into mRNA are of outermost importance as proper spatial and temporal expression of key developmentally regulated transcripts is essential. The Integrator complex was recently identified to have a broad role in both RNA processing and transcription regulation. This complex is assembled from at least 14 different subunits and several animal studies have pointed to an important role in development. Nevertheless, studies directly demonstrating the relevance of this complex in human health and development have been lacking until now. We show here that mutations in the Integrator Complex Subunit 1 gene (INTS1) and Subunit 8 gene (INTS8) cause a severe neurodevelopmental syndrome, characterized by profound intellectual disability, epilepsy, spasticity, facial and limb dysmorphism and subtle structural brain abnormalities. While the role of the Integrator complex in neuronal migration has recently been established, we provide evidence that INTS8 mutations lead in vitro to instability of the complex and impaired function. In patients cultured fibroblasts we found evidence for abnormalities in mRNA transcription and processing. In addition, introduction of INTS8 mutations in an in vitro model of retinoic acid-induced neuronal differentiation results also in transcription alterations. Altogether our results suggest an evolutionary conserved requirement of INTS1 and INTS8 in brain development.
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Affiliation(s)
- Renske Oegema
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - David Baillat
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX, United States of America
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Leontine M. van Unen
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Alice Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Sima Kheradmand Kia
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | | | - Zheng Xia
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Matteo Cesaroni
- The Fels Institute, Temple University School of Medicine, Philadelphia, PA, United States of America
| | - Maarten H. Lequin
- Department of Pediatric Radiology, Erasmus MC- Sophia, University Medical Center Rotterdam, The Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - William B. Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Irenaeus F. M. de Coo
- Department of Neurology, Erasmus MC- Sophia, University Medical Center Rotterdam, The Netherlands
| | - Frans W. Verheijen
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Andreas Kremer
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Daphne Heijsman
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Eric J. Wagner
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX, United States of America
- * E-mail: (GMSM); (EJW)
| | - Maarten Fornerod
- Department of Pediatric Oncology and Biochemistry, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Grazia M. S. Mancini
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
- * E-mail: (GMSM); (EJW)
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Pourfarzad F, von Lindern M, Azarkeivan A, Hou J, Kia SK, Esteghamat F, van Ijcken W, Philipsen S, Najmabadi H, Grosveld F. Hydroxyurea responsiveness in β-thalassemic patients is determined by the stress response adaptation of erythroid progenitors and their differentiation propensity. Haematologica 2012; 98:696-704. [PMID: 23100274 DOI: 10.3324/haematol.2012.074492] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
β-thalassemia is caused by mutations in the β-globin locus resulting in loss of, or reduced, hemoglobin A (adult hemoglobin, HbA, α2β2) production. Hydroxyurea treatment increases fetal γ-globin (fetal hemoglobin, HbF, α2γ2) expression in postnatal life substituting for the missing adult β-globin and is, therefore, an attractive therapeutic approach. Patients treated with hydroxyurea fall into three categories: i) 'responders' who increase hemoglobin to therapeutic levels; (ii) 'moderate-responders' who increase hemoglobin levels but still need transfusions at longer intervals; and (iii) 'non-responders' who do not reach adequate hemoglobin levels and remain transfusion-dependent. The mechanisms underlying these differential responses remain largely unclear. We generated RNA expression profiles from erythroblast progenitors of 8 responder and 8 non-responder β-thalassemia patients. These profiles revealed that hydroxyurea treatment induced differential expression of many genes in cells from non-responders while it had little impact on cells from responders. Part of the gene program up-regulated by hydroxyurea in non-responders was already highly expressed in responders before hydroxyurea treatment. Baseline HbF expression was low in non-responders, and hydroxyurea treatment induced significant cell death. We conclude that cells from responders have adapted well to constitutive stress conditions and display a propensity to proceed to the erythroid differentiation program.
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Kheradmand Kia S, Solaimani Kartalaei P, Farahbakhshian E, Pourfarzad F, von Lindern M, Verrijzer CP. EZH2-dependent chromatin looping controls INK4a and INK4b, but not ARF, during human progenitor cell differentiation and cellular senescence. Epigenetics Chromatin 2009; 2:16. [PMID: 19954516 PMCID: PMC3225837 DOI: 10.1186/1756-8935-2-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 12/02/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The INK4b-ARF-INK4a tumour suppressor locus controls the balance between progenitor cell renewal and cancer. In this study, we investigated how higher-order chromatin structure modulates differential expression of the human INK4b-ARF-INK4a locus during progenitor cell differentiation, cellular ageing and senescence of cancer cells. RESULTS We found that INK4b and INK4a, but not ARF, are upregulated following the differentiation of haematopoietic progenitor cells, in ageing fibroblasts and in senescing malignant rhabdoid tumour cells. To investigate the underlying molecular mechanism we analysed binding of polycomb group (PcG) repressive complexes (PRCs) and the spatial organization of the INK4b-ARF-INK4a locus. In agreement with differential derepression, PcG protein binding across the locus is discontinuous. As we described earlier, PcG repressors bind the INK4a promoter, but not ARF. Here, we identified a second peak of PcG binding that is located approximately 3 kb upstream of the INK4b promoter. During progenitor cell differentiation and ageing, PcG silencer EZH2 attenuates, causing loss of PRC binding and transcriptional activation of INK4b and INK4a. The expression pattern of the locus is reflected by its organization in space. In the repressed state, the PRC-binding regions are in close proximity, while the intervening chromatin harbouring ARF loops out. Down regulation of EZH2 causes release of the approximately 35 kb repressive chromatin loop and induction of both INK4a and INK4b, whereas ARF expression remains unaltered. CONCLUSION PcG silencers bind and coordinately regulate INK4b and INK4a, but not ARF, during a variety of physiological processes. Developmentally regulated EZH2 levels are one of the factors that can determine the higher order chromatin structure and expression pattern of the INK4b-ARF-INK4a locus, coupling human progenitor cell differentiation to proliferation control. Our results revealed a chromatin looping mechanism of long-range control and argue against models involving homogeneous spreading of PcG silencers across the INK4b-ARF-INK4a locus.
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Affiliation(s)
- Sima Kheradmand Kia
- Department of Biochemistry, Center for Biomedical Genetics, Erasmus University Medical Center, PO Box 1738, 3000 DR Rotterdam, The Netherlands.
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Vanmolkot KRJ, Kors EE, Turk U, Turkdogan D, Keyser A, Broos LAM, Kia SK, van den Heuvel JJMW, Black DF, Haan J, Frants RR, Barone V, Ferrari MD, Casari G, Koenderink JB, van den Maagdenberg AMJM. Two de novo mutations in the Na,K-ATPase gene ATP1A2 associated with pure familial hemiplegic migraine. Eur J Hum Genet 2006; 14:555-60. [PMID: 16538223 DOI: 10.1038/sj.ejhg.5201607] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Familial hemiplegic migraine (FHM) is a rare autosomal dominantly inherited subtype of migraine, in which hemiparesis occurs during the aura. The majority of the families carry mutations in the CACNA1A gene on chromosome 19p13 (FHM1). About 20% of FHM families is linked to chromosome 1q23 (FHM2), and has mutations in the ATP1A2 gene, encoding the alpha2-subunit of the Na,K-ATPase. Mutation analysis in a Dutch and a Turkish family with pure FHM revealed two novel de novo missense mutations, R593W and V628M, respectively. Cellular survival assays support the hypothesis that both mutations are disease-causative. The identification of the first de novo mutations underscores beyond any doubt the involvement of the ATP1A2 gene in FHM2.
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Affiliation(s)
- Kaate R J Vanmolkot
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands, and Department of Neurology, Dr Lütfi Kirdar State Hospital, Maltepe, Istanbul, Turkey
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Vries RGJ, Bezrookove V, Zuijderduijn LMP, Kia SK, Houweling A, Oruetxebarria I, Raap AK, Verrijzer CP. Cancer-associated mutations in chromatin remodeler hSNF5 promote chromosomal instability by compromising the mitotic checkpoint. Genes Dev 2005; 19:665-70. [PMID: 15769941 PMCID: PMC1065719 DOI: 10.1101/gad.335805] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The hSNF5 subunit of human SWI/SNF ATP-dependent chromatin remodeling complexes is a tumor suppressor that is inactivated in malignant rhabdoid tumors (MRTs). Here, we report that loss of hSNF5 function in MRT-derived cells leads to polyploidization and chromosomal instability. Re-expression of hSNF5 restored the coupling between cell cycle progression and ploidy checkpoints. In contrast, cancer-associated hSNF5 mutants harboring specific single amino acid substitutions exacerbated poly- and aneuploidization, due to abrogated chromosome segregation. We found that hSNF5 activates the mitotic checkpoint through the p16INK4a-cyclinD/CDK4-pRb-E2F pathway. These results establish that poly- and aneuploidy of tumor cells can result from mutations in a chromatin remodeler.
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Affiliation(s)
- Robert G J Vries
- Department of Molecular and Cell Biology, Leiden University Medical Centre, 2300 RA Leiden, The Netherlands
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