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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; 33:919-929. [PMID: 38339995 PMCID: PMC11070134 DOI: 10.1093/hmg/ddae014] [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: 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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Day M, Tetik B, Parlak M, Almeida-Hernández Y, Räschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D. TopBP1 utilises a bipartite GINS binding mode to support genome replication. Nat Commun 2024; 15:1797. [PMID: 38413589 PMCID: PMC10899662 DOI: 10.1038/s41467-024-45946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for replication origin firing, and as such for faithful genetic inheritance. Our biochemical and structural studies demonstrate that the helicase activator GINS interacts with TopBP1 through two separate binding surfaces, the first involving a stretch of highly conserved amino acids in the TopBP1-GINI region, the second a surface on TopBP1-BRCT4. The two surfaces bind to opposite ends of the A domain of the GINS subunit Psf1. Mutation analysis reveals that either surface is individually able to support TopBP1-GINS interaction, albeit with reduced affinity. Consistently, either surface is sufficient for replication origin firing in Xenopus egg extracts and becomes essential in the absence of the other. The TopBP1-GINS interaction appears sterically incompatible with simultaneous binding of DNA polymerase epsilon (Polε) to GINS when bound to Mcm2-7-Cdc45, although TopBP1-BRCT4 and the Polε subunit PolE2 show only partial competitivity in binding to Psf1. Our TopBP1-GINS model improves the understanding of the recently characterised metazoan pre-loading complex. It further predicts the coordination of three molecular origin firing processes, DNA polymerase epsilon arrival, TopBP1 ejection and GINS integration into Mcm2-7-Cdc45.
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Affiliation(s)
- Matthew Day
- School of Biological and Behavioural Sciences, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Bilal Tetik
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Milena Parlak
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Räschle
- Molecular Genetics, Technical University Kaiserslautern, Paul-Ehrlich Straße 24, 67663, Kaiserslautern, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Heike Siegert
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Anika Marko
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Kaiser
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Isabel A Barker
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Dominik Boos
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany.
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Noble TD, Sansam CG, Wittig KA, Majchrzycka B, Sansam CL. Cell Cycle-Dependent TICRR/TRESLIN and MTBP Chromatin Binding Mechanisms and Patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578516. [PMID: 38370757 PMCID: PMC10871258 DOI: 10.1101/2024.02.02.578516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The selection of replication origins is a defining characteristic of DNA replication in eukaryotes, yet its mechanism in humans has not been well-defined. In this study, we use Cut&Run to examine genomic binding locations for TICRR/TRESLIN and MTBP, the human orthologs for the yeast DNA replication initiation factors Sld3 and Sld7. We mapped TRESLIN and MTBP binding in HCT116 colorectal cancer cells using asynchronous and G1 synchronized populations. Our data show that TRESLIN and MTBP binding patterns are more defined in a G1 synchronized population compared to asynchronously cycling cells. We also examined whether TRESLIN and MTBP are dependent on one another for binding. Our data suggest MTBP is dependent on TRESLIN for proper association with chromatin during G1 but not S phase. Finally, we asked whether TRESLIN and MTBP binding to chromatin requires licensed origins. Using cell lines with a non-degradable inducible Geminin to inhibit licensing, we show TRESLIN and MTBP binding does not require loaded MCMs. Altogether, our Cut&Run data provides evidence for a chromatin binding mechanism of TRESLIN-MTBP during G1 that is dependent on TRESLIN and does not require interactions with licensed origins.
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Affiliation(s)
- Tyler D Noble
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Courtney G Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Kimberlie A Wittig
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Blanka Majchrzycka
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - Christopher L Sansam
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
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Chen JJ, Zhang LL, Liu Z, Men WQ, Chen F, Shen J. Comprehensive Analysis of TICRR in Hepatocellular Carcinoma Based on Bioinformatics Analysis. Biochem Genet 2024; 62:1-17. [PMID: 37266876 PMCID: PMC10902024 DOI: 10.1007/s10528-023-10378-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/10/2023] [Indexed: 06/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the leading cause of cancer-associated death in the world. However, due to the complexity of HCC, it is urgent for us to find a reliable and accurate biomarker for HCC gene therapy.TopBP1-interacting checkpoint and replication regulator (TICRR), known as Treslin in vertebrate and sld3 in yeast, is involved in the tumorigenesis, progression, matastasis, diagnosis, and predicting prognosis of HCC. Disappointingly, the mechanism of TICRR expression in HCC is still not described in detail and requires further analysis. In this study, TCGA ( www.tcga-data.nci.nih.gov/tcga/ ) datasets and GEO ( www.ncbi.nlm.nih.gov/geo ) datasets were used to analyze the expression of TICRR in HCC, the relevance of TICRR mRNA expression and clinicopathological characteristics in patients with HCC, and the relationship between TICRR expression and immune infiltration level in Patients with HCC. Based on MethSurv database, the impact of TICRR in patients with HCC was investigated. In addition, GO/KEGG enrichment analysis of TICRR co-expression was performed using the R package. TICRR was found drastically highly expressed in a variety of cancer types including HCC.ROC curve analysis showed that TICRR had higher accuracy in predicting HCC compared with AFP. The expression level of TICRR was marked positively correlated with tumor stage and prognosis in Patients with HCC.GO/KEGG enrichment analysis showed that TICRR was associated with cell division and cell cycle as well as p53 signaling pathway. In addition, patients with high TICRR methylation of cg05841809, cg09403165, and cg03312532 CpG sites were significantly correlated with poor prognosis of HCC. This study demonstrated that increased TICRR expression in HCC might play an important role in the tumorigenesis, progression, diagnosis, and predicting prognosis of HCC. Therefore, TICRR might be used as a promising diagnostic and prognostic biomarker for HCC gene therapy.
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Affiliation(s)
- Jing-Jing Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Lu-Lu Zhang
- Public Center of Experimental Technology, The School of Basic Medical, Science and Southwest Medical University, Luzhou, Sichuan, China
| | - Zhen Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Wan Qi Men
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Fang Chen
- UItrasonic Diagnosis Deparment, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- UItrasonic Diagnosis Deparment, Anhui Public Health Clinical Center, Hefei, Anhui, China
| | - Jilu Shen
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
- Department of Clinical Laboratory, Anhui Public Health Clinical Center, Hefei, Anhui, China.
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