1
|
Alda-Catalinas C, Ibarra-Soria X, Flouri C, Gordillo JE, Cousminer D, Hutchinson A, Sun B, Pembroke W, Ullrich S, Krejci A, Cortes A, Acevedo A, Malla S, Fishwick C, Drewes G, Rapiteanu R. Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens. Genome Biol 2024; 25:42. [PMID: 38308274 PMCID: PMC10835965 DOI: 10.1186/s13059-024-03176-z] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/18/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Drug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease-associated genetic variants into functional knowledge remains a fundamental challenge of drug discovery. A key issue is that the vast majority of complex disease associations cannot be cleanly mapped to a gene. Immune disease-associated variants are enriched within regulatory elements found in T-cell-specific open chromatin regions. RESULTS To identify genes and molecular programs modulated by these regulatory elements, we develop a CRISPRi-based single-cell functional screening approach in primary human T cells. Our pipeline enables the interrogation of transcriptomic changes induced by the perturbation of regulatory elements at scale. We first optimize an efficient CRISPRi protocol in primary CD4+ T cells via CROPseq vectors. Subsequently, we perform a screen targeting 45 non-coding regulatory elements and 35 transcription start sites and profile approximately 250,000 T -cell single-cell transcriptomes. We develop a bespoke analytical pipeline for element-to-gene (E2G) mapping and demonstrate that our method can identify both previously annotated and novel E2G links. Lastly, we integrate genetic association data for immune-related traits and demonstrate how our platform can aid in the identification of effector genes for GWAS loci. CONCLUSIONS We describe "primary T cell crisprQTL" - a scalable, single-cell functional genomics approach for mapping regulatory elements to genes in primary human T cells. We show how this framework can facilitate the interrogation of immune disease GWAS hits and propose that the combination of experimental and QTL-based techniques is likely to address the variant-to-function problem.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Bin Sun
- Genomic Sciences, GSK, Stevenage, UK
| | | | | | | | | | | | | | | | - Gerard Drewes
- Genomic Sciences, GSK, Stevenage, UK
- Genomic Sciences, GSK, Collegeville, PA, USA
| | | |
Collapse
|
2
|
Koniali L, Flouri C, Kostopoulou MI, Papaioannou NY, Papasavva PL, Naiisseh B, Stephanou C, Demetriadou A, Sitarou M, Christou S, Antoniou MN, Kleanthous M, Patsali P, Lederer CW. Evaluation of Mono- and Bi-Functional GLOBE-Based Vectors for Therapy of β-Thalassemia by HBBAS3 Gene Addition and Mutation-Specific RNA Interference. Cells 2023; 12:2848. [PMID: 38132168 PMCID: PMC10741507 DOI: 10.3390/cells12242848] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Therapy via the gene addition of the anti-sickling βAS3-globin transgene is potentially curative for all β-hemoglobinopathies and therefore of particular clinical and commercial interest. This study investigates GLOBE-based lentiviral vectors (LVs) for βAS3-globin addition and evaluates strategies for an increased β-like globin expression without vector dose escalation. First, we report the development of a GLOBE-derived LV, GLV2-βAS3, which, compared to its parental vector, adds anti-sickling action and a transcription-enhancing 848-bp transcription terminator element, retains high vector titers and allows for superior β-like globin expression in primary patient-derived hematopoietic stem and progenitor cells (HSPCs). Second, prompted by our previous correction of HBBIVSI-110(G>A) thalassemia based on RNApol(III)-driven shRNAs in mono- and combination therapy, we analyzed a series of novel LVs for the RNApol(II)-driven constitutive or late-erythroid expression of HBBIVSI-110(G>A)-specific miRNA30-embedded shRNAs (shRNAmiR). This included bifunctional LVs, allowing for concurrent βAS3-globin expression. LVs were initially compared for their ability to achieve high β-like globin expression in HBBIVSI-110(G>A)-transgenic cells, before the evaluation of shortlisted candidate LVs in HBBIVSI-110(G>A)-homozygous HSPCs. The latter revealed that β-globin promoter-driven designs for monotherapy with HBBIVSI-110(G>A)-specific shRNAmiRs only marginally increased β-globin levels compared to untransduced cells, whereas bifunctional LVs combining miR30-shRNA with βAS3-globin expression showed disease correction similar to that achieved by the parental GLV2-βAS3 vector. Our results establish the feasibility of high titers for LVs containing the full HBB transcription terminator, emphasize the importance of the HBB terminator for the high-level expression of HBB-like transgenes, qualify the therapeutic utility of late-erythroid HBBIVSI-110(G>A)-specific miR30-shRNA expression and highlight the exceptional potential of GLV2-βAS3 for the treatment of severe β-hemoglobinopathies.
Collapse
Affiliation(s)
- Lola Koniali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Christina Flouri
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London SE1 9RT, UK; (C.F.); (M.N.A.)
| | - Markela I. Kostopoulou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Nikoletta Y. Papaioannou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Panayiota L. Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Basma Naiisseh
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Anthi Demetriadou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, 6301 Larnaca, Cyprus;
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, 1474 Nicosia, Cyprus;
| | - Michael N. Antoniou
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London SE1 9RT, UK; (C.F.); (M.N.A.)
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Nicosia, Cyprus; (L.K.); (M.I.K.); (N.Y.P.); (P.L.P.); (B.N.); (C.S.); (A.D.); (M.K.)
| |
Collapse
|
3
|
Shangaris P, Loukogeorgakis SP, Subramaniam S, Flouri C, Jackson LH, Wang W, Blundell MP, Liu S, Eaton S, Bakhamis N, Ramachandra DL, Maghsoudlou P, Urbani L, Waddington SN, Eddaoudi A, Archer J, Antoniou MN, Stuckey DJ, Schmidt M, Thrasher AJ, Ryan TM, De Coppi P, David AL. Publisher Correction: In Utero Gene Therapy (IUGT) Using GLOBE Lentiviral Vector Phenotypically Corrects the Heterozygous Humanised Mouse Model and Its Progress Can Be Monitored Using MRI Techniques. Sci Rep 2019; 9:20214. [PMID: 31874968 PMCID: PMC6930216 DOI: 10.1038/s41598-019-55754-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- Panicos Shangaris
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK.
- UCL Institute of Child Health, UCL, London, United Kingdom.
| | | | | | - Christina Flouri
- Department of Medical and Molecular Genetics, KCL, London, United Kingdom
| | | | - Wei Wang
- Department of Translational Oncology, National Centre for Tumour Diseases, Heidelberg, Germany
| | | | - Shanrun Liu
- Biochemistry and Molecular Genetics, UAB, Birmingham, Alabama, United States
| | - Simon Eaton
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Nahla Bakhamis
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| | | | | | - Luca Urbani
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Simon N Waddington
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ayad Eddaoudi
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Joy Archer
- Central Diagnostic Services, Queen's Vet School Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Michael N Antoniou
- Department of Medical and Molecular Genetics, KCL, London, United Kingdom
| | - Daniel J Stuckey
- Centre for Advanced Biomedical Imaging, UCL, London, United Kingdom
| | - Manfred Schmidt
- Department of Translational Oncology, National Centre for Tumour Diseases, Heidelberg, Germany
| | | | - Thomas M Ryan
- Biochemistry and Molecular Genetics, UAB, Birmingham, Alabama, United States
| | - Paolo De Coppi
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Anna L David
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| |
Collapse
|
4
|
Shangaris P, Loukogeorgakis SP, Subramaniam S, Flouri C, Jackson LH, Wang W, Blundell MP, Liu S, Eaton S, Bakhamis N, Ramachandra DL, Maghsoudlou P, Urbani L, Waddington SN, Eddaoudi A, Archer J, Antoniou MN, Stuckey DJ, Schmidt M, Thrasher AJ, Ryan TM, De Coppi P, David AL. In Utero Gene Therapy (IUGT) Using GLOBE Lentiviral Vector Phenotypically Corrects the Heterozygous Humanised Mouse Model and Its Progress Can Be Monitored Using MRI Techniques. Sci Rep 2019; 9:11592. [PMID: 31406195 PMCID: PMC6690943 DOI: 10.1038/s41598-019-48078-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 07/29/2019] [Indexed: 02/06/2023] Open
Abstract
In utero gene therapy (IUGT) to the fetal hematopoietic compartment could be used to treat congenital blood disorders such as β-thalassemia. A humanised mouse model of β-thalassemia was used, in which heterozygous animals are anaemic with splenomegaly and extramedullary hematopoiesis. Intrahepatic in utero injections of a β globin-expressing lentiviral vector (GLOBE), were performed in fetuses at E13.5 of gestation. We analysed animals at 12 and 32 weeks of age, for vector copy number in bone marrow, peripheral blood liver and spleen and we performed integration site analysis. Compared to noninjected heterozygous animals IUGT normalised blood haemoglobin levels and spleen weight. Integration site analysis showed polyclonality. The left ventricular ejection fraction measured using magnetic resonance imaging (MRI) in treated heterozygous animals was similar to that of normal non-β-thalassemic mice but significantly higher than untreated heterozygous thalassemia mice suggesting that IUGT ameliorated poor cardiac function. GLOBE LV-mediated IUGT normalised the haematological and anatomical phenotype in a heterozygous humanised model of β-thalassemia.
Collapse
Affiliation(s)
- Panicos Shangaris
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK.
- UCL Institute of Child Health, UCL, London, United Kingdom.
| | | | | | - Christina Flouri
- Department of Medical and Molecular Genetics, KCL, London, United Kingdom
| | | | - Wei Wang
- Department of Translational Oncology, National Centre for Tumour Diseases, Heidelberg, Germany
| | | | - Shanrun Liu
- Biochemistry and Molecular Genetics, UAB, Birmingham, Alabama, United States
| | - Simon Eaton
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Nahla Bakhamis
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| | | | | | - Luca Urbani
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Simon N Waddington
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ayad Eddaoudi
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Joy Archer
- Central Diagnostic Services, Queen's Vet School Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Michael N Antoniou
- Department of Medical and Molecular Genetics, KCL, London, United Kingdom
| | - Daniel J Stuckey
- Centre for Advanced Biomedical Imaging, UCL, London, United Kingdom
| | - Manfred Schmidt
- Department of Translational Oncology, National Centre for Tumour Diseases, Heidelberg, Germany
| | | | - Thomas M Ryan
- Biochemistry and Molecular Genetics, UAB, Birmingham, Alabama, United States
| | - Paolo De Coppi
- UCL Institute of Child Health, UCL, London, United Kingdom
| | - Anna L David
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
| |
Collapse
|
5
|
Christou CM, Hadjisavvas A, Kyratzi M, Flouri C, Neophytou I, Anastasiadou V, Loizidou MA, Kyriacou K. The BRCA1 variant p.Ser36Tyr abrogates BRCA1 protein function and potentially confers a moderate risk of breast cancer. PLoS One 2014; 9:e93400. [PMID: 24695549 PMCID: PMC3973689 DOI: 10.1371/journal.pone.0093400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
The identification of variants of unknown clinical significance (VUS) in the BRCA1 gene complicates genetic counselling and causes additional anxiety to carriers. In silico approaches currently used for VUS pathogenicity assessment are predictive and often produce conflicting data. Furthermore, functional assays are either domain or function specific, thus they do not examine the entire spectrum of BRCA1 functions and interpretation of individual assay results can be misleading. PolyPhen algorithm predicted that the BRCA1 p.Ser36Tyr VUS identified in the Cypriot population was damaging, whereas Align-GVGD predicted that it was possibly of no significance. In addition the BRCA1 p.Ser36Tyr variant was found to be associated with increased risk (OR = 3.47, 95% CI 1.13-10.67, P = 0.02) in a single case-control series of 1174 cases and 1109 controls. We describe a cellular system for examining the function of exogenous full-length BRCA1 and for classifying VUS. We achieved strong protein expression of full-length BRCA1 in transiently transfected HEK293T cells. The p.Ser36Tyr VUS exhibited low protein expression similar to the known pathogenic variant p.Cys61Gly. Co-precipitation analysis further demonstrated that it has a reduced ability to interact with BARD1. Further, co-precipitation analysis of nuclear and cytosolic extracts as well as immunofluorescence studies showed that a high proportion of the p.Ser36Tyr variant is withheld in the cytoplasm contrary to wild type protein. In addition the ability of p.Ser36Tyr to co-localize with conjugated ubiquitin foci in the nuclei of S-phase synchronized cells following genotoxic stress with hydroxyurea is impaired at more pronounced levels than that of the p.Cys61Gly pathogenic variant. The p.Ser36Tyr variant demonstrates abrogated function, and based on epidemiological, genetic, and clinical data we conclude that the p.Ser36Tyr variant is probably associated with a moderate breast cancer risk.
Collapse
Affiliation(s)
- Charita M. Christou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Maria Kyratzi
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- The University of Cyprus, Department of Biological Sciences, Nicosia, Cyprus
| | - Christina Flouri
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Ioanna Neophytou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Violetta Anastasiadou
- The Cyprus Institute of Neurology and Genetics, Department of Clinical Genetics, Nicosia, Cyprus
| | - Maria A. Loizidou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- * E-mail:
| |
Collapse
|