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Ojewunmi OO, Adeyemo TA, Oyetunji AI, Inyang B, Akinrindoye A, Mkumbe BS, Gardner K, Rooks H, Brewin J, Patel H, Lee SH, Chung R, Rashkin S, Kang G, Chianumba R, Sangeda R, Mwita L, Isa H, Agumadu UN, Ekong R, Faruk JA, Jamoh BY, Adebiyi NM, Umar IA, Hassan A, Grace C, Goel A, Inusa BPD, Falchi M, Nkya S, Makani J, Ahmad HR, Nnodu O, Strouboulis J, Menzel S. The genetic dissection of fetal haemoglobin persistence in sickle cell disease in Nigeria. Hum Mol Genet 2024:ddae014. [PMID: 38339995 DOI: 10.1093/hmg/ddae014] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024] Open
Abstract
The clinical severity of sickle cell disease (SCD) is strongly influenced by the level of fetal haemoglobin (HbF) persistent in each patient. Three major HbF loci (BCL11A, HBS1L-MYB, and Xmn1-HBG2) have been reported, but a considerable hidden heritability remains. We conducted a genome-wide association study for HbF levels in 1006 Nigerian patients with SCD (HbSS/HbSβ0), followed by a replication and meta-analysis exercise in four independent SCD cohorts (3,582 patients). To dissect association signals at the major loci, we performed stepwise conditional and haplotype association analyses and included public functional annotation datasets. Association signals were detected for BCL11A (lead SNP rs6706648, β = -0.39, P = 4.96 × 10-34) and HBS1L-MYB (lead SNP rs61028892, β = 0.73, P = 1.18 × 10-9), whereas the variant allele for Xmn1-HBG2 was found to be very rare. In addition, we detected three putative new trait-associated regions. Genetically, dissecting the two major loci BCL11A and HBS1L-MYB, we defined trait-increasing haplotypes (P < 0.0001) containing so far unidentified causal variants. At BCL11A, in addition to a haplotype harbouring the putative functional variant rs1427407-'T', we identified a second haplotype, tagged by the rs7565301-'A' allele, where a yet-to-be-discovered causal DNA variant may reside. Similarly, at HBS1L-MYB, one HbF-increasing haplotype contains the likely functional small indel rs66650371, and a second tagged by rs61028892-'C' is likely to harbour a presently unknown functional allele. Together, variants at BCL11A and HBS1L-MYB SNPs explained 24.1% of the trait variance. Our findings provide a path for further investigation of the causes of variable fetal haemoglobin persistence in sickle cell disease.
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Affiliation(s)
- Oyesola O Ojewunmi
- School of Cancer and Pharmaceutical Sciences, King's College London, 123 Coldharbour Lane, London SE5 9NU, United Kingdom
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Titilope A Adeyemo
- Department of Haematology and Blood Transfusion, College of Medicine, University of Lagos, P.M.B 12003, Lagos, Nigeria
| | - Ajoke I Oyetunji
- Sickle Cell Foundation Nigeria, Ishaga Road, Idi-Araba, P.O. Box 3463, Lagos, Nigeria
| | - Bassey Inyang
- Department of Medical Biochemistry, College of Health Sciences, University of Abuja, Mohammed Maccido Road, Airport Road, P.M.B 117, Abuja, Nigeria
| | - Afolashade Akinrindoye
- Sickle Cell Foundation Nigeria, Ishaga Road, Idi-Araba, P.O. Box 3463, Lagos, Nigeria
- School of Science, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, United Kingdom
| | - Baraka S Mkumbe
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, United Nations Rd, Dar es Salaam, Tanzania
- Department of Artificial Intelligence and Innovative Medicine, Tohoku University Graduate School of Medicine, 980-8573, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan
| | - Kate Gardner
- School of Cancer and Pharmaceutical Sciences, King's College London, 123 Coldharbour Lane, London SE5 9NU, United Kingdom
- Clinical Haematology, Haematology and Oncology Directorate, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Helen Rooks
- School of Cancer and Pharmaceutical Sciences, King's College London, 123 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - John Brewin
- School of Cancer and Pharmaceutical Sciences, King's College London, 123 Coldharbour Lane, London SE5 9NU, United Kingdom
- Department of Haematological Medicine, King's College Hospital, London SE5 9RS, United Kingdom
| | - Hamel Patel
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) and Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London SE5 8AB, United Kingdom
| | - Sang Hyuck Lee
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) and Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London SE5 8AB, United Kingdom
| | - Raymond Chung
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) and Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, 16 De Crespigny Park, London SE5 8AB, United Kingdom
| | - Sara Rashkin
- St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Guolian Kang
- St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Reuben Chianumba
- Centre of Excellence for Sickle Cell Disease Research and Training (CESRTA), University of Abuja, Mohammed Maccido Road, Airport Road, P.M.B 117, Abuja, Nigeria
| | - Raphael Sangeda
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Liberata Mwita
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Hezekiah Isa
- Centre of Excellence for Sickle Cell Disease Research and Training (CESRTA), University of Abuja, Mohammed Maccido Road, Airport Road, P.M.B 117, Abuja, Nigeria
- Department of Haematology and Blood Transfusion, University of Abuja Teaching Hospital, Gwagwalada, P.M.B. 228, Gwagwalada, FCT Abuja, Nigeria
| | - Uche-Nnebe Agumadu
- Department of Paediatrics, College of Health Sciences, University of Abuja, Mohammed Maccido Road, Airport Road, P.M.B 117, Abuja, Nigeria
| | - Rosemary Ekong
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Jamilu A Faruk
- Department of Paediatrics, Ahmadu Bello University/Ahmadu Bello University Teaching Hospital, P.M.B 006, Zaria, Nigeria
| | - Bello Y Jamoh
- Department of Internal Medicine, Ahmadu Bello University/Ahmadu Bello University Teaching Hospital, P.M.B 006, Zaria, Nigeria
| | - Niyi M Adebiyi
- Department of Paediatrics, Ahmadu Bello University/Ahmadu Bello University Teaching Hospital, P.M.B 006, Zaria, Nigeria
| | - Ismail A Umar
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Sokoto Road, Samaru, P.M.B 006, Zaria, Nigeria
| | - Abdulaziz Hassan
- Department of Haematology and Blood Transfusion, Ahmadu Bello University, Sokoto Road, Samaru, P.M.B 006, Zaria, Nigeria
| | - Christopher Grace
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Centre for Human Genetics, Roosevelt Drive, Oxford OX37BN, United Kingdom
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Centre for Human Genetics, Roosevelt Drive, Oxford OX37BN, United Kingdom
| | - Baba P D Inusa
- Evelina London Children's Hospital, Guy's and St. Thomas' NHS Foundation Trust, Westminster Bridge Rd, London SE1 7EH, United Kingdom
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, United Kingdom
| | - Siana Nkya
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, United Nations Rd, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Sickle Cell Centre, 1 Kipalapala Street, Dar es Salaam, Tanzania
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, United Nations Rd, Dar es Salaam, Tanzania
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Science, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Julie Makani
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, United Nations Rd, Dar es Salaam, Tanzania
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Science, P.O. Box 65001, Dar es Salaam, Tanzania
- Centre for Haematology, Department of Immunology & Inflammation, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Rd, London W12 0NN, United Kingdom
| | - Hafsat R Ahmad
- Department of Paediatrics, Ahmadu Bello University/Ahmadu Bello University Teaching Hospital, P.M.B 006, Zaria, Nigeria
| | - Obiageli Nnodu
- Centre of Excellence for Sickle Cell Disease Research and Training (CESRTA), University of Abuja, Mohammed Maccido Road, Airport Road, P.M.B 117, Abuja, Nigeria
- Department of Haematology and Blood Transfusion, University of Abuja Teaching Hospital, Gwagwalada, P.M.B. 228, Gwagwalada, FCT Abuja, Nigeria
| | - John Strouboulis
- School of Cancer and Pharmaceutical Sciences, King's College London, 123 Coldharbour Lane, London SE5 9NU, United Kingdom
| | - Stephan Menzel
- School of Cancer and Pharmaceutical Sciences, King's College London, 123 Coldharbour Lane, London SE5 9NU, United Kingdom
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Cato LD, Li R, Lu HY, Yu F, Wissman M, Mkumbe BS, Ekwattanakit S, Deelen P, Mwita L, Sangeda R, Suksangpleng T, Riolueang S, Bronson PG, Paul DS, Kawabata E, Astle WJ, Aguet F, Ardlie K, de Lapuente Portilla AL, Kang G, Zhang Y, Nouraie SM, Gordeuk VR, Gladwin MT, Garrett ME, Ashley-Koch A, Telen MJ, Custer B, Kelly S, Dinardo CL, Sabino EC, Loureiro P, Carneiro-Proietti AB, Maximo C, Méndez A, Hammerer-Lercher A, Sheehan VA, Weiss MJ, Franke L, Nilsson B, Butterworth AS, Viprakasit V, Nkya S, Sankaran VG. Genetic regulation of fetal hemoglobin across global populations. medRxiv 2023:2023.03.24.23287659. [PMID: 36993312 PMCID: PMC10055601 DOI: 10.1101/2023.03.24.23287659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Human genetic variation has enabled the identification of several key regulators of fetal-to-adult hemoglobin switching, including BCL11A, resulting in therapeutic advances. However, despite the progress made, limited further insights have been obtained to provide a fuller accounting of how genetic variation contributes to the global mechanisms of fetal hemoglobin (HbF) gene regulation. Here, we have conducted a multi-ancestry genome-wide association study of 28,279 individuals from several cohorts spanning 5 continents to define the architecture of human genetic variation impacting HbF. We have identified a total of 178 conditionally independent genome-wide significant or suggestive variants across 14 genomic windows. Importantly, these new data enable us to better define the mechanisms by which HbF switching occurs in vivo. We conduct targeted perturbations to define BACH2 as a new genetically-nominated regulator of hemoglobin switching. We define putative causal variants and underlying mechanisms at the well-studied BCL11A and HBS1L-MYB loci, illuminating the complex variant-driven regulation present at these loci. We additionally show how rare large-effect deletions in the HBB locus can interact with polygenic variation to influence HbF levels. Our study paves the way for the next generation of therapies to more effectively induce HbF in sickle cell disease and β-thalassemia.
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Affiliation(s)
- Liam D. Cato
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rick Li
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Henry Y. Lu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Mariel Wissman
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Baraka S. Mkumbe
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Department of Artificial Intelligence and Innovative Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Supachai Ekwattanakit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Liberata Mwita
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Thidarat Suksangpleng
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suchada Riolueang
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Paola G. Bronson
- R&D Translational Biology, Biogen, Cambridge, Massachusetts, USA
| | - Dirk S. Paul
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
| | - Emily Kawabata
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - William J. Astle
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Francois Aguet
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kristin Ardlie
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Guolian Kang
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yingze Zhang
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Seyed Mehdi Nouraie
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Victor R. Gordeuk
- Division of Hematology and Oncology, Department of Medicine, Comprehensive Sickle Cell Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mark T. Gladwin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Melanie E. Garrett
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Marilyn J. Telen
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | - Shannon Kelly
- Vitalant Research Institute, San Francisco, California, USA
- Division of Pediatric Hematology, UCSF Benioff Children's Hospital, Oakland, California, USA
| | - Carla Luana Dinardo
- Fundacao Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Ester C. Sabino
- Institute of Tropical Medicine, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | | | - Adriana Méndez
- Institute of Laboratory Medicine, Cantonal Hospital Aarau, 5000 Aarau, Switzerland
| | | | - Vivien A. Sheehan
- Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta & Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Lude Franke
- Oncode Institute, Amsterdam, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Björn Nilsson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
- Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Vip Viprakasit
- Siriraj Thalassemia Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siana Nkya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry, Muhimbili University of Health and Allied Science, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Tanzania
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
- Department of Biochemistry, Muhimbili University of Health and Allied Science
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Nkya S, Mwita L, Mgaya J, Kumburu H, van Zwetselaar M, Menzel S, Mazandu GK, Sangeda R, Chimusa E, Makani J. Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. BMC Med Genet 2020; 21:125. [PMID: 32503527 PMCID: PMC7275552 DOI: 10.1186/s12881-020-01059-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/24/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common genetic variants which differ across populations and hence do not fully account for HbF variation. METHODS We investigated rare and common genetic variants that influence HbF levels in 14 SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A, MYB, HOXA9, HBB, HBG1, HBG2, CHD4, KLF1, MBD3, ZBTB7A and PGLYRP1. RESULTS Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletions in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. CONCLUSIONS This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD interrogating multiple genomic variants associated with HbF in SCD.
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Affiliation(s)
- Siana Nkya
- Department of Biological Sciences, Dar es Salaam University College of Education, Dar es Salaam, Tanzania. .,Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - Liberata Mwita
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Josephine Mgaya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Happiness Kumburu
- Department of Biotechnology Laboratory, Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Marco van Zwetselaar
- Department of Biotechnology Laboratory, Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Stephan Menzel
- Department of Molecular Hematology, King's College of London, London, UK
| | - Gaston Kuzamunu Mazandu
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa. .,Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Observatory, 7925, South Africa. .,African Institute for Mathematical Sciences, Muizenberg, Cape Town, 7945, South Africa.
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Emile Chimusa
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa
| | - Julie Makani
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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4
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Makani J, Tluway F, Makubi A, Soka D, Nkya S, Sangeda R, Mgaya J, Rwezaula S, Kirkham FJ, Kindole C, Osati E, Meda E, Snow RW, Newton CR, Roberts D, Aboud M, Thein SL, Cox SE, Luzzatto L, Mmbando BP. A ten year review of the sickle cell program in Muhimbili National Hospital, Tanzania. BMC Hematol 2018; 18:33. [PMID: 30459954 PMCID: PMC6236876 DOI: 10.1186/s12878-018-0125-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/16/2018] [Indexed: 11/10/2022]
Abstract
Background Africa has the highest burden of Sickle cell disease (SCD) but there are few large, systematic studies providing reliable descriptions of the disease spectrum. Tanzania, with 11,000 SCD births annually, established the Muhimbili Sickle Cell program aiming to improve understanding of SCD in Africa. We report the profile of SCD seen in the first 10 years at Muhimbili National Hospital (MNH). Methods Individuals seen at MNH known or suspected to have SCD were enrolled at clinic and laboratory testing for SCD, haematological and biochemical analyses done. Ethnicity was self-reported. Clinical and laboratory features of SCD were documented. Comparison was made with non-SCD population as well as within 3 different age groups (< 5, 5–17 and ≥ 18 years) within the SCD population. Results From 2004 to 2013, 6397 individuals, 3751 (58.6%) SCD patients, were enrolled, the majority (47.4%) in age group 5–17 years. There was variation in the geographical distribution of SCD. Individuals with SCD compared to non-SCD, had significantly lower blood pressure and peripheral oxygen saturation (SpO2). SCD patients had higher prevalence of severe anemia, jaundice and desaturation (SpO2 < 95%) as well as higher levels of reticulocytes, white blood cells, platelets and fetal hemoglobin. The main causes of hospitalization for SCD within a 12-month period preceding enrolment were pain (adults), and fever and severe anemia (children). When clinical and laboratory features were compared in SCD within 3 age groups, there was a progressive decrease in the prevalence of splenic enlargement and an increase in prevalence of jaundice. Furthermore, there were significant differences with monotonic trends across age groups in SpO2, hematological and biochemical parameters. Conclusion This report confirms that the wide spectrum of clinical expression of SCD observed elsewhere is also present in Tanzania, with non-uniform geographical distribution across the country. Age-specific analysis is consistent with different disease-patterns across the lifespan.
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Affiliation(s)
- Julie Makani
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,2University of Oxford, Oxford, UK.,3Muhimbili National Hospital, Dar-es-Salaam, Tanzania
| | - Furahini Tluway
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Abel Makubi
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Deogratius Soka
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Siana Nkya
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,4Dar-es-Salaam University College of Education, Dar-es-Salaam, Tanzania
| | - Raphael Sangeda
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Josephine Mgaya
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Stella Rwezaula
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,3Muhimbili National Hospital, Dar-es-Salaam, Tanzania
| | | | - Christina Kindole
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,3Muhimbili National Hospital, Dar-es-Salaam, Tanzania
| | - Elisha Osati
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,3Muhimbili National Hospital, Dar-es-Salaam, Tanzania
| | - Elineema Meda
- 3Muhimbili National Hospital, Dar-es-Salaam, Tanzania
| | - Robert W Snow
- 2University of Oxford, Oxford, UK.,6Centre for Geographic Medicine Research, Kenya Medical Research Institute, Kilifi, Kenya
| | - Charles R Newton
- 2University of Oxford, Oxford, UK.,6Centre for Geographic Medicine Research, Kenya Medical Research Institute, Kilifi, Kenya
| | | | - Muhsin Aboud
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | | | - Sharon E Cox
- 8London School of Hygiene & Tropical Medicine, London, UK
| | - Lucio Luzzatto
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Bruno P Mmbando
- 1Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,National Institute for Medical Research Tanga Centre, Tanga, Tanzania
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5
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Ben Hamda C, Sangeda R, Mwita L, Meintjes A, Nkya S, Panji S, Mulder N, Guizani-Tabbane L, Benkahla A, Makani J, Ghedira K. A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study. PLoS One 2018; 13:e0199461. [PMID: 29979707 PMCID: PMC6034806 DOI: 10.1371/journal.pone.0199461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 01/03/2018] [Accepted: 06/07/2018] [Indexed: 12/16/2022] Open
Abstract
A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysiology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets.
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Affiliation(s)
- Cherif Ben Hamda
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Science of Bizerte, Jarzouna, University of Carthage, Tunisia
- * E-mail: (KG); (CBH)
| | - Raphael Sangeda
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Liberata Mwita
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Siana Nkya
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sumir Panji
- University of Cape Town, Cape Town, South Africa
| | | | - Lamia Guizani-Tabbane
- University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Medical Parasitology, Biotechnology and Biomolecules, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Julie Makani
- Faculty of Science of Bizerte, Jarzouna, University of Carthage, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institute Pasteur of Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- * E-mail: (KG); (CBH)
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6
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Mulder N, Nembaware V, Adekile A, Anie KA, Inusa B, Brown B, Campbell A, Chinenere F, Chunda-Liyoka C, Derebail VK, Geard A, Ghedira K, Hamilton CM, Hanchard NA, Haendel M, Huggins W, Ibrahim M, Jupp S, Kamga KK, Knight-Madden J, Lopez-Sall P, Mbiyavanga M, Munube D, Nirenberg D, Nnodu O, Ofori-Acquah SF, Ohene-Frempong K, Opap KB, Panji S, Park M, Pule G, Royal C, Sangeda R, Tayo B, Treadwell M, Tshilolo L, Wonkam A. Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease. Appl Transl Genom 2016; 9:23-9. [PMID: 27354937 PMCID: PMC4911424 DOI: 10.1016/j.atg.2016.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 03/11/2016] [Accepted: 03/11/2016] [Indexed: 11/20/2022]
Abstract
Sickle cell disease (SCD) is a debilitating single gene disorder caused by a single point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% of SCD in newborns world-wide occurs in sub-Saharan Africa, where neonatal and childhood mortality from sickle cell related complications is high. While SCD research across the globe is tackling the disease on multiple fronts, advances have yet to significantly impact on the health and quality of life of SCD patients, due to lack of coordination of these disparate efforts. Ensuring data across studies is directly comparable through standardization is a necessary step towards realizing this goal. Such a standardization requires the development and implementation of a disease-specific ontology for SCD that is applicable globally. Ontology development is best achieved by bringing together experts in the domain to contribute their knowledge. The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology.
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Affiliation(s)
- Nicola Mulder
- H3ABioNet Consortium, Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Victoria Nembaware
- H3ABioNet Consortium, Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Adekunle Adekile
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Kofi A Anie
- London North West Healthcare NHS Trust & Imperial College London, London, United Kingdom
| | - Baba Inusa
- Evelina Children's Hospital, Guy's and St Thomas NHS Trust, London, United Kingdom
| | - Biobele Brown
- Department of Paediatrics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Andrew Campbell
- Pediatric Hematology/Oncology and Center for Human Growth and Development, University of Michigan, Ann Arbor, MI, United States
| | | | - Catherine Chunda-Liyoka
- University Teaching Hospital (UTH), Lusaka, Zambia; University of Zambia (UNZA) School of medicine, Lusaka, Zambia
| | - Vimal K Derebail
- Division of Nephrology and Hypertension, Department of Medicine, UNC Kidney Center, University of North Carolina at Chapel Hill, NC, United States
| | - Amy Geard
- Division of Human Genetics, Department of Clinical Laboratory Sciences, National Health Laboratory Service and University of Cape Town, 7925, South Africa
| | - Kais Ghedira
- Université de Tunis El Manar, Institut Pasteur de Tunis, LR11IPT06 Laboratory of medical parasitology, biotechnologies and biomolecules, Group of Bioinformatics and mathematical modeling, Tunis, Tunisia
| | - Carol M Hamilton
- Research Computing Division, RTI International, Research Triangle Park, NC, United States
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Melissa Haendel
- Oregon Health and Science University, Portland, OR, United States
| | - Wayne Huggins
- Research Computing Division, RTI International, Research Triangle Park, NC, United States
| | | | - Simon Jupp
- European Bioinformatics Institute, London, United Kingdom
| | | | | | - Philomène Lopez-Sall
- Department of Pharmacy, Biochemistry Unit, , Cheikh Anta Diop University, Dakar, Senegal
| | - Mamana Mbiyavanga
- H3ABioNet Consortium, Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Deogratias Munube
- Department of Paediatrics and Child Health, College of Health Sciences, Makerere University/Mulago Hospital, Kampala, Uganda
| | - Damian Nirenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Obiageli Nnodu
- Centre of Excellence for Sickle Cell Disease Research and Training, University of Abuja, Abuja, Nigeria
| | - Solomon Fiifi Ofori-Acquah
- Center for Translational and International Hematology, Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Kenneth Babu Opap
- H3ABioNet Consortium, Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Sumir Panji
- H3ABioNet Consortium, Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Miriam Park
- Instituto da Criança, Hospital das Clínicas, São Paulo Medical School, University of São Paulo, Brazil
| | - Gift Pule
- Division of Human Genetics, Department of Clinical Laboratory Sciences, National Health Laboratory Service and University of Cape Town, 7925, South Africa
| | | | | | - Bamidele Tayo
- Loyola University Chicago, Chicago, IL, United States
| | - Marsha Treadwell
- UCSF Benioff Children's Hospital Oakland, Oakland, CA, United States
| | | | - Ambroise Wonkam
- Division of Human Genetics, Department of Clinical Laboratory Sciences, National Health Laboratory Service and University of Cape Town, 7925, South Africa
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7
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Assel M, van de Vijver D, Libin P, Theys K, Harezlak D, O Nualláin B, Nowakowski P, Bubak M, Vandamme AM, Imbrechts S, Sangeda R, Jiang T, Frentz D, Sloot P. A collaborative environment allowing clinical investigations on integrated biomedical databases. Stud Health Technol Inform 2009; 147:51-61. [PMID: 19593044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In order to perform clinical investigations on integrated biomedical data sets and to predict virological and epidemiological outcome, medical experts require an IT-based collaborative environment that provides them a user-friendly space for building and executing their complex studies and workflows on largely available and high-quality data repositories. In this paper, the authors introduce such a novel collaborative working environment a so-called virtual laboratory for clinicians and medical researchers, which allows users to interactively access and browse several biomedical research databases and re-use relevant data sets within own designed experiments. Firstly, technical details on the integration of relevant data resources into the virtual laboratory infrastructure and specifically developed user interfaces are briefly explained. The second part describes research possibilities for medical scientists including potential application fields and benefits as using the virtual laboratory functionalities for a particular exemplary study.
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Affiliation(s)
- Matthias Assel
- University of Stuttgart, High Performance Computing Centre, Germany
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