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Li SY, Hammarlund JA, Wu G, Lian JW, Howell SJ, Clarke RB, Adamson AD, Gonçalves CF, Hogenesch JB, Anafi RC, Meng QJ. Tumor circadian clock strength influences metastatic potential and predicts patient prognosis in luminal A breast cancer. Proc Natl Acad Sci U S A 2024; 121:e2311854121. [PMID: 38319971 PMCID: PMC10873596 DOI: 10.1073/pnas.2311854121] [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: 07/14/2023] [Accepted: 12/18/2023] [Indexed: 02/08/2024] Open
Abstract
Studies in shift workers and model organisms link circadian disruption to breast cancer. However, molecular circadian rhythms in noncancerous and cancerous human breast tissues and their clinical relevance are largely unknown. We reconstructed rhythms informatically, integrating locally collected, time-stamped biopsies with public datasets. For noncancerous breast tissue, inflammatory, epithelial-mesenchymal transition (EMT), and estrogen responsiveness pathways show circadian modulation. Among tumors, clock correlation analysis demonstrates subtype-specific changes in circadian organization. Luminal A organoids and informatic ordering of luminal A samples exhibit continued, albeit dampened and reprogrammed rhythms. However, CYCLOPS magnitude, a measure of global rhythm strength, varied widely among luminal A samples. Cycling of EMT pathway genes was markedly increased in high-magnitude luminal A tumors. Surprisingly, patients with high-magnitude tumors had reduced 5-y survival. Correspondingly, 3D luminal A cultures show reduced invasion following molecular clock disruption. This study links subtype-specific circadian disruption in breast cancer to EMT, metastatic potential, and prognosis.
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Affiliation(s)
- Shi-Yang Li
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM13 9PT, United Kingdom
| | - Jan A. Hammarlund
- School of Biomedical Engineering, Science and Health Systems, Bossone Research Center, Drexel University, Philadelphia, PA19104
| | - Gang Wu
- Division of Human Genetics, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
- Division of Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
| | - Jia-Wen Lian
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM13 9PT, United Kingdom
| | - Sacha J. Howell
- Breast Biology Group, Manchester Breast Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM20 4GJ, United Kingdom
| | - Robert B. Clarke
- Breast Biology Group, Manchester Breast Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM20 4GJ, United Kingdom
| | - Antony D. Adamson
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM13 9PT, United Kingdom
| | - Cátia F. Gonçalves
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM13 9PT, United Kingdom
| | - John B. Hogenesch
- Division of Human Genetics, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
- Division of Immunobiology, Center for Circadian Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH45229
| | - Ron C. Anafi
- Department of Medicine, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Qing-Jun Meng
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, ManchesterM13 9PT, United Kingdom
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2
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Douglas M, O'Loughlin C, Lynch AT, Prialgauskaite R, Adamson AD, Dibb KM, Kimber SJ, Birket MJ. The generation and validation of two NKX2-5 fluorescent reporter human embryonic stem cell lines: UMANe002-A-1 and UMANe002-A-2. Stem Cell Res 2024; 74:103262. [PMID: 38100908 DOI: 10.1016/j.scr.2023.103262] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/31/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
The transcription factor NKX2-5 is a highly conserved master regulator of heart development which is widely expressed in cardiac progenitors and cardiomyocytes. Fluorescent reporters of NKX2-5 that minimally perturb normal protein expression can enable the identification, quantification and isolation of NKX2-5-expressing cells in a normal physiological state. Here we report the generation of two new hESC lines with eGFP inserted upstream (5') or downstream (3') of NKX2-5, linked by a cleavable T2A peptide. These complementary reporters produce a robust fluorescent signal in cardiac cells and have wide utility particularly for research on developmental biology and disease modelling.
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Affiliation(s)
| | | | | | | | | | - K M Dibb
- The University of Manchester, UK
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3
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Downton P, Bagnall JS, England H, Spiller DG, Humphreys NE, Jackson DA, Paszek P, White MRH, Adamson AD. Overexpression of IκB⍺ modulates NF-κB activation of inflammatory target gene expression. Front Mol Biosci 2023; 10:1187187. [PMID: 37228587 PMCID: PMC10203502 DOI: 10.3389/fmolb.2023.1187187] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Cells respond to inflammatory stimuli such as cytokines by activation of the nuclear factor-κB (NF-κB) signalling pathway, resulting in oscillatory translocation of the transcription factor p65 between nucleus and cytoplasm in some cell types. We investigate the relationship between p65 and inhibitor-κB⍺ (IκBα) protein levels and dynamic properties of the system, and how this interaction impacts on the expression of key inflammatory genes. Using bacterial artificial chromosomes, we developed new cell models of IκB⍺-eGFP protein overexpression in a pseudo-native genomic context. We find that cells with high levels of the negative regulator IκBα remain responsive to inflammatory stimuli and maintain dynamics for both p65 and IκBα. In contrast, canonical target gene expression is dramatically reduced by overexpression of IκBα, but can be partially rescued by overexpression of p65. Treatment with leptomycin B to promote nuclear accumulation of IκB⍺ also suppresses canonical target gene expression, suggesting a mechanism in which nuclear IκB⍺ accumulation prevents productive p65 interaction with promoter binding sites. This causes reduced target promoter binding and gene transcription, which we validate by chromatin immunoprecipitation and in primary cells. Overall, we show how inflammatory gene transcription is modulated by the expression levels of both IκB⍺ and p65. This results in an anti-inflammatory effect on transcription, demonstrating a broad mechanism to modulate the strength of inflammatory response.
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Affiliation(s)
- Polly Downton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James S. Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Hazel England
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David G. Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil E. Humphreys
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Dean A. Jackson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Pawel Paszek
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Michael R. H. White
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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4
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Hunter AL, Adamson AD, Poolman TM, Grudzien M, Loudon ASI, Ray DW, Bechtold DA. HaloChIP-seq for Antibody-Independent Mapping of Mouse Transcription Factor Cistromes in vivo. Bio Protoc 2022; 12:e4460. [PMID: 35937930 PMCID: PMC9303821 DOI: 10.21769/bioprotoc.4460] [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: 02/17/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) maps, on a genome-wide scale, transcription factor binding sites, and the distribution of other chromatin-associated proteins and their modifications. As such, it provides valuable insights into mechanisms of gene regulation. However, successful ChIP experiments are dependent on the availability of a high-quality antibody against the target of interest. Using antibodies with poor sensitivity and specificity can yield misleading results. This can be partly circumvented by using epitope-tagged systems ( e.g. , HA, Myc, His), but these approaches are still antibody-dependent. HaloTag ® is a modified dehalogenase enzyme, which covalently binds synthetic ligands. This system can be used for imaging and purification of HaloTag ® fusion proteins, and has been used for ChIP in vitro . Here, we present a protocol for using the HaloTag ® system for ChIP in vivo , to map, with sensitivity and specificity, the cistrome of a dynamic mouse transcription factor expressed at its endogenous locus. Graphical abstract.
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Affiliation(s)
- Ann Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Toryn M. Poolman
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, United Kingdom
| | - Magdalena Grudzien
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Andrew S. I. Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - David W. Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LE, United Kingdom
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - David A. Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, United Kingdom
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5
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Gemperle J, Harrison TS, Flett C, Adamson AD, Caswell PT. On demand expression control of endogenous genes with DExCon, DExogron and LUXon reveals differential dynamics of Rab11 family members. eLife 2022; 11:e76651. [PMID: 35708998 PMCID: PMC9203059 DOI: 10.7554/elife.76651] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/29/2022] [Indexed: 11/28/2022] Open
Abstract
CRISPR technology has made generation of gene knock-outs widely achievable in cells. However, once inactivated, their re-activation remains difficult, especially in diploid cells. Here, we present DExCon (Doxycycline-mediated endogenous gene Expression Control), DExogron (DExCon combined with auxin-mediated targeted protein degradation), and LUXon (light responsive DExCon) approaches which combine one-step CRISPR-Cas9-mediated targeted knockin of fluorescent proteins with an advanced Tet-inducible TRE3GS promoter. These approaches combine blockade of active gene expression with the ability to re-activate expression on demand, including activation of silenced genes. Systematic control can be exerted using doxycycline or spatiotemporally by light, and we demonstrate functional knock-out/rescue in the closely related Rab11 family of vesicle trafficking regulators. Fluorescent protein knock-in results in bright signals compatible with low-light live microscopy from monoallelic modification, the potential to simultaneously image different alleles of the same gene, and bypasses the need to work with clones. Protein levels are easily tunable to correspond with endogenous expression through cell sorting (DExCon), timing of light illumination (LUXon), or by exposing cells to different levels of auxin (DExogron). Furthermore, our approach allowed us to quantify previously unforeseen differences in vesicle dynamics, transferrin receptor recycling, expression kinetics, and protein stability among highly similar endogenous Rab11 family members and their colocalization in triple knock-in ovarian cancer cell lines.
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Affiliation(s)
- Jakub Gemperle
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of ManchesterManchesterUnited Kingdom
| | - Thomas S Harrison
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of ManchesterManchesterUnited Kingdom
| | - Chloe Flett
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of ManchesterManchesterUnited Kingdom
| | - Antony D Adamson
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of ManchesterManchesterUnited Kingdom
| | - Patrick T Caswell
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of ManchesterManchesterUnited Kingdom
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6
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Koch AA, Bagnall JS, Smyllie NJ, Begley N, Adamson AD, Fribourgh JL, Spiller DG, Meng QJ, Partch CL, Strimmer K, House TA, Hastings MH, Loudon ASI. Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock. eLife 2022; 11:73976. [PMID: 35285799 PMCID: PMC8983044 DOI: 10.7554/elife.73976] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 09/16/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The mammalian circadian clock exerts control of daily gene expression through cycles of DNA binding. Here, we develop a quantitative model of how a finite pool of BMAL1 protein can regulate thousands of target sites over daily time scales. We used quantitative imaging to track dynamic changes in endogenous labelled proteins across peripheral tissues and the SCN. We determine the contribution of multiple rhythmic processes coordinating BMAL1 DNA binding, including cycling molecular abundance, binding affinities, and repression. We find nuclear BMAL1 concentration determines corresponding CLOCK through heterodimerisation and define a DNA residence time of this complex. Repression of CLOCK:BMAL1 is achieved through rhythmic changes to BMAL1:CRY1 association and high-affinity interactions between PER2:CRY1 which mediates CLOCK:BMAL1 displacement from DNA. Finally, stochastic modelling reveals a dual role for PER:CRY complexes in which increasing concentrations of PER2:CRY1 promotes removal of BMAL1:CLOCK from genes consequently enhancing ability to move to new target sites.
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Affiliation(s)
- Alex Ashton Koch
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - James S Bagnall
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Nicola J Smyllie
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, United Kingdom
| | - Nicola Begley
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antony D Adamson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - David G Spiller
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Qing-Jun Meng
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - Korbinian Strimmer
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Thomas A House
- Department of Mathematics, University of Manchester, Manchester, United Kingdom
| | - Michael H Hastings
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, United Kingdom
| | - Andrew S I Loudon
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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7
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Marinopoulou E, Biga V, Sabherwal N, Miller A, Desai J, Adamson AD, Papalopulu N. HES1 protein oscillations are necessary for neural stem cells to exit from quiescence. iScience 2021; 24:103198. [PMID: 34703994 PMCID: PMC8524149 DOI: 10.1016/j.isci.2021.103198] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/10/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Quiescence is a dynamic process of reversible cell cycle arrest. High-level persistent expression of the HES1 transcriptional repressor, which oscillates with an ultradian periodicity in proliferative neural stem cells (NSCs), is thought to mediate quiescence. However, it is not known whether this is due to a change in levels or dynamics. Here, we induce quiescence in embryonic NSCs with BMP4, which does not increase HES1 level, and we find that HES1 continues to oscillate. To assess the role of HES1 dynamics, we express persistent HES1 under a moderate strength promoter, which overrides the endogenous oscillations while maintaining the total HES1 level within physiological range. We find that persistent HES1 does not affect proliferation or entry into quiescence; however, exit from quiescence is impeded. Thus, oscillatory expression of HES1 is specifically required for NSCs to exit quiescence, a finding of potential importance for controlling reactivation of stem cells in tissue regeneration and cancer.
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Affiliation(s)
- Elli Marinopoulou
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
| | - Veronica Biga
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
| | - Nitin Sabherwal
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
- Imagen Therapeutics, Unit 2 & 2a, Enterprise House, Lloyd Street North, M15 6SE Manchester, UK
| | - Anzy Miller
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
| | - Jayni Desai
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
| | - Antony D. Adamson
- Genome Editing Unit, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
| | - Nancy Papalopulu
- Division of Developmental Biology and Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, M13 9PT Manchester, UK
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8
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Hunter AL, Pelekanou CE, Barron NJ, Northeast RC, Grudzien M, Adamson AD, Downton P, Cornfield T, Cunningham PS, Billaud JN, Hodson L, Loudon ASI, Unwin RD, Iqbal M, Ray DW, Bechtold DA. Adipocyte NR1D1 dictates adipose tissue expansion during obesity. eLife 2021; 10:e63324. [PMID: 34350828 PMCID: PMC8360653 DOI: 10.7554/elife.63324] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 09/22/2020] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
The circadian clock component NR1D1 (REVERBα) is considered a dominant regulator of lipid metabolism, with global Nr1d1 deletion driving dysregulation of white adipose tissue (WAT) lipogenesis and obesity. However, a similar phenotype is not observed under adipocyte-selective deletion (Nr1d1Flox2-6:AdipoqCre), and transcriptional profiling demonstrates that, under basal conditions, direct targets of NR1D1 regulation are limited, and include the circadian clock and collagen dynamics. Under high-fat diet (HFD) feeding, Nr1d1Flox2-6:AdipoqCre mice do manifest profound obesity, yet without the accompanying WAT inflammation and fibrosis exhibited by controls. Integration of the WAT NR1D1 cistrome with differential gene expression reveals broad control of metabolic processes by NR1D1 which is unmasked in the obese state. Adipocyte NR1D1 does not drive an anticipatory daily rhythm in WAT lipogenesis, but rather modulates WAT activity in response to alterations in metabolic state. Importantly, NR1D1 action in adipocytes is critical to the development of obesity-related WAT pathology and insulin resistance.
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Affiliation(s)
- Ann Louise Hunter
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Charlotte E Pelekanou
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Nichola J Barron
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Rebecca C Northeast
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Magdalena Grudzien
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Antony D Adamson
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Polly Downton
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Thomas Cornfield
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - Peter S Cunningham
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - Andrew SI Loudon
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Richard D Unwin
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Mudassar Iqbal
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - David W Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, and NIHR Oxford Biomedical Research Centre, John Radcliffe HospitalOxfordUnited Kingdom
| | - David A Bechtold
- Centre for Biological Timing, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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9
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Thieme F, Henschel L, Hammond NL, Ishorst N, Hausen J, Adamson AD, Biedermann A, Bowes J, Zieger HK, Maj C, Kruse T, Buness A, Hoischen A, Gilissen C, Kreusch T, Jäger A, Gölz L, Braumann B, Aldhorae K, Rojas-Martinez A, Krawitz PM, Mangold E, Dixon MJ, Ludwig KU. Extending the allelic spectrum at noncoding risk loci of orofacial clefting. Hum Mutat 2021; 42:1066-1078. [PMID: 34004033 DOI: 10.1002/humu.24219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 03/12/2020] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 11/08/2022]
Abstract
Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.
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Affiliation(s)
- Frederic Thieme
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nigel L Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nina Ishorst
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jonas Hausen
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Antony D Adamson
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Angelika Biedermann
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Hanna K Zieger
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Carlo Maj
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Andreas Buness
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany.,Department of Orthodontics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Bert Braumann
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Khalid Aldhorae
- Department of Orthodontics, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey, Mexico
| | - Peter M Krawitz
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Kerstin U Ludwig
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
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10
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Biga V, Hawley J, Soto X, Johns E, Han D, Bennett H, Adamson AD, Kursawe J, Glendinning P, Manning CS, Papalopulu N. A dynamic, spatially periodic, micro-pattern of HES5 underlies neurogenesis in the mouse spinal cord. Mol Syst Biol 2021; 17:e9902. [PMID: 34031978 PMCID: PMC8144840 DOI: 10.15252/msb.20209902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 11/12/2022] Open
Abstract
Ultradian oscillations of HES Transcription Factors (TFs) at the single‐cell level enable cell state transitions. However, the tissue‐level organisation of HES5 dynamics in neurogenesis is unknown. Here, we analyse the expression of HES5 ex vivo in the developing mouse ventral spinal cord and identify microclusters of 4–6 cells with positively correlated HES5 level and ultradian dynamics. These microclusters are spatially periodic along the dorsoventral axis and temporally dynamic, alternating between high and low expression with a supra‐ultradian persistence time. We show that Notch signalling is required for temporal dynamics but not the spatial periodicity of HES5. Few Neurogenin 2 cells are observed per cluster, irrespective of high or low state, suggesting that the microcluster organisation of HES5 enables the stable selection of differentiating cells. Computational modelling predicts that different cell coupling strengths underlie the HES5 spatial patterns and rate of differentiation, which is consistent with comparison between the motoneuron and interneuron progenitor domains. Our work shows a previously unrecognised spatiotemporal organisation of neurogenesis, emergent at the tissue level from the synthesis of single‐cell dynamics.
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Affiliation(s)
- Veronica Biga
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Joshua Hawley
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Ximena Soto
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Emma Johns
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Daniel Han
- Department of Mathematics, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Hayley Bennett
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Antony D Adamson
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Jochen Kursawe
- School of Mathematics and Statistics, University of St Andrews, St Andrews, UK
| | - Paul Glendinning
- Department of Mathematics, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Cerys S Manning
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
| | - Nancy Papalopulu
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
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11
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Gurumurthy CB, O'Brien AR, Quadros RM, Adams J, Alcaide P, Ayabe S, Ballard J, Batra SK, Beauchamp MC, Becker KA, Bernas G, Brough D, Carrillo-Salinas F, Chan W, Chen H, Dawson R, DeMambro V, D'Hont J, Dibb K, Eudy JD, Gan L, Gao J, Gonzales A, Guntur A, Guo H, Harms DW, Harrington A, Hentges KE, Humphreys N, Imai S, Ishii H, Iwama M, Jonasch E, Karolak M, Keavney B, Khin NC, Konno M, Kotani Y, Kunihiro Y, Lakshmanan I, Larochelle C, Lawrence CB, Li L, Lindner V, Liu XD, Lopez-Castejon G, Loudon A, Lowe J, Jerome-Majeweska L, Matsusaka T, Miura H, Miyasaka Y, Morpurgo B, Motyl K, Nabeshima YI, Nakade K, Nakashiba T, Nakashima K, Obata Y, Ogiwara S, Ouellet M, Oxburgh L, Piltz S, Pinz I, Ponnusamy MP, Ray D, Redder RJ, Rosen CJ, Ross N, Ruhe MT, Ryzhova L, Salvador AM, Alam SS, Sedlacek R, Sharma K, Smith C, Staes K, Starrs L, Sugiyama F, Takahashi S, Tanaka T, Trafford A, Uno Y, Vanhoutte L, Vanrockeghem F, Willis BJ, Wright CS, Yamauchi Y, Yi X, Yoshimi K, Zhang X, Zhang Y, Ohtsuka M, Das S, Garry DJ, Hochepied T, Thomas P, Parker-Thornburg J, Adamson AD, Yoshiki A, Schmouth JF, Golovko A, Thompson WR, Lloyd KCK, Wood JA, Cowan M, Mashimo T, Mizuno S, Zhu H, Kasparek P, Liaw L, Miano JM, Burgio G. Response to correspondence on "Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation". Genome Biol 2021; 22:99. [PMID: 33827648 PMCID: PMC8025318 DOI: 10.1186/s13059-021-02320-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA. .,Developmental Neuroscience, Munroe Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Aidan R O'Brien
- Transformational Bioinformatics, Health and Biosecurity Business Unit, CSIRO, Sydney, Australia.,Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - John Adams
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Pilar Alcaide
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Shinya Ayabe
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Johnathan Ballard
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Marie-Claude Beauchamp
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Kathleen A Becker
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Guillaume Bernas
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | | | - Wesley Chan
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Hanying Chen
- School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Ruby Dawson
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Victoria DeMambro
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Jinke D'Hont
- Transgenic mouse core facility, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Katharine Dibb
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - James D Eudy
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Lin Gan
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jing Gao
- Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Amy Gonzales
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Anyonya Guntur
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Huiping Guo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne Harrington
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil Humphreys
- Transgenic Unit core facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shiho Imai
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mizuho Iwama
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Eric Jonasch
- The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Karolak
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester AND Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nay-Chi Khin
- Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yuko Kotani
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yayoi Kunihiro
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Larochelle
- Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Catherine B Lawrence
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Lin Li
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Volkhard Lindner
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Xian-De Liu
- The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Gloria Lopez-Castejon
- Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Andrew Loudon
- Centre for Biological Timing, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jenna Lowe
- Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Loydie Jerome-Majeweska
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Taiji Matsusaka
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hiromi Miura
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan.,Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yoshiki Miyasaka
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Benjamin Morpurgo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Katherine Motyl
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Yo-Ichi Nabeshima
- Laboratory of Molecular Life Science, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Koji Nakade
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - Kenichi Nakashima
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuichi Obata
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sanae Ogiwara
- Department of Laboratory Animal Science, Support Center for Medical Research and Education, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Mariette Ouellet
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Leif Oxburgh
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Sandra Piltz
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Ilka Pinz
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ronald J Redder
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Clifford J Rosen
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Nikki Ross
- Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Mark T Ruhe
- Mouse Biology Program, University of California, Davis, USA
| | - Larisa Ryzhova
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Ane M Salvador
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Sabrina Shameen Alam
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karan Sharma
- College of Osteopathic Medicine, Marian University, Indianapolis, IN, 46222, USA
| | - Chad Smith
- The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Katrien Staes
- Transgenic mouse core facility, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Lora Starrs
- Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Andrew Trafford
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - Yoshihiro Uno
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Leen Vanhoutte
- Transgenic mouse core facility, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frederique Vanrockeghem
- Transgenic mouse core facility, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Christian S Wright
- Department of Physical Therapy, School of Health and Human Sciences, Indiana University, Indianapolis, IN, 46202, USA
| | - Yuko Yamauchi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Xin Yi
- Department of Physical Therapy, School of Health and Human Sciences, Indiana University, Indianapolis, IN, 46202, USA
| | - Kazuto Yoshimi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Xuesong Zhang
- The University of Texas, MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Zhang
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Masato Ohtsuka
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan.,Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Satyabrata Das
- Lillehei Heart Institute Regenerative Medicine and Sciences Program, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Garry
- Lillehei Heart Institute Regenerative Medicine and Sciences Program, University of Minnesota, Minneapolis, MN, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
| | - Tino Hochepied
- Transgenic mouse core facility, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paul Thomas
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | | | - Antony D Adamson
- Transgenic Unit core facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Atsushi Yoshiki
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Jean-Francois Schmouth
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Andrei Golovko
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - William R Thompson
- Department of Physical Therapy, School of Health and Human Sciences, Indiana University, Indianapolis, IN, 46202, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, USA.,Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Joshua A Wood
- Mouse Biology Program, University of California, Davis, USA
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), Montreal, Canada
| | - Tomoji Mashimo
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Hao Zhu
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucy Liaw
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Joseph M Miano
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, the John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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12
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Green JP, Swanton T, Morris LV, El-Sharkawy LY, Cook J, Yu S, Beswick J, Adamson AD, Humphreys NE, Bryce R, Freeman S, Lawrence C, Brough D. LRRC8A is essential for hypotonicity-, but not for DAMP-induced NLRP3 inflammasome activation. eLife 2020; 9:59704. [PMID: 33216713 PMCID: PMC7679132 DOI: 10.7554/elife.59704] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 06/05/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
The NLRP3 inflammasome is a multi-molecular protein complex that converts inactive cytokine precursors into active forms of IL-1β and IL-18. The NLRP3 inflammasome is frequently associated with the damaging inflammation of non-communicable disease states and is considered an attractive therapeutic target. However, there is much regarding the mechanism of NLRP3 activation that remains unknown. Chloride efflux is suggested as an important step in NLRP3 activation, but which chloride channels are involved is still unknown. We used chemical, biochemical, and genetic approaches to establish the importance of chloride channels in the regulation of NLRP3 in murine macrophages. Specifically, we identify LRRC8A, an essential component of volume-regulated anion channels (VRAC), as a vital regulator of hypotonicity-induced, but not DAMP-induced, NLRP3 inflammasome activation. Although LRRC8A was dispensable for canonical DAMP-dependent NLRP3 activation, this was still sensitive to chloride channel inhibitors, suggesting there are additional and specific chloride sensing and regulating mechanisms controlling NLRP3.
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Affiliation(s)
- Jack P Green
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Tessa Swanton
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Lucy V Morris
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Lina Y El-Sharkawy
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - James Cook
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - Shi Yu
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - James Beswick
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Antony D Adamson
- Genome Editing Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Neil E Humphreys
- Genome Editing Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.,EMBL-ROME, Epigenetics and Neurobiology Unit, Adriano Buzzati-Traverso Campus, Monterotondo, Italy
| | - Richard Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Sally Freeman
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Catherine Lawrence
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, United Kingdom
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13
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Baxter M, Voronkov M, Poolman T, Galli G, Pinali C, Goosey L, Knight A, Krakowiak K, Maidstone R, Iqbal M, Zi M, Prehar S, Cartwright EJ, Gibbs J, Matthews LC, Adamson AD, Humphreys NE, Rebelo-Guiomar P, Minczuk M, Bechtold DA, Loudon A, Ray D. Cardiac mitochondrial function depends on BUD23 mediated ribosome programming. eLife 2020; 9:e50705. [PMID: 31939735 PMCID: PMC7002040 DOI: 10.7554/elife.50705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/30/2019] [Accepted: 12/24/2019] [Indexed: 01/21/2023] Open
Abstract
Efficient mitochondrial function is required in tissues with high energy demand such as the heart, and mitochondrial dysfunction is associated with cardiovascular disease. Expression of mitochondrial proteins is tightly regulated in response to internal and external stimuli. Here we identify a novel mechanism regulating mitochondrial content and function, through BUD23-dependent ribosome generation. BUD23 was required for ribosome maturation, normal 18S/28S stoichiometry and modulated the translation of mitochondrial transcripts in human A549 cells. Deletion of Bud23 in murine cardiomyocytes reduced mitochondrial content and function, leading to severe cardiomyopathy and death. We discovered that BUD23 selectively promotes ribosomal interaction with low GC-content 5'UTRs. Taken together we identify a critical role for BUD23 in bioenergetics gene expression, by promoting efficient translation of mRNA transcripts with low 5'UTR GC content. BUD23 emerges as essential to mouse development, and to postnatal cardiac function.
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Affiliation(s)
- Matthew Baxter
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
- NIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Maria Voronkov
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
- NIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Toryn Poolman
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
- NIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Gina Galli
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Christian Pinali
- Division of Cardiovascular SciencesUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Laurence Goosey
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Abigail Knight
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Karolina Krakowiak
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Robert Maidstone
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
- NIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Mudassar Iqbal
- Division of Cardiovascular SciencesUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Min Zi
- Division of Cardiovascular SciencesUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Sukhpal Prehar
- Division of Cardiovascular SciencesUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Elizabeth J Cartwright
- Division of Cardiovascular SciencesUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Julie Gibbs
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Laura C Matthews
- Leeds Institute of Medical ResearchFaculty of Medicine and Health, University of LeedsLeedsUnited Kingdom
| | - Antony D Adamson
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Neil E Humphreys
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Pedro Rebelo-Guiomar
- Graduate Program in Areas of Basic and Applied Biology (GABBA)University of PortoPortoPortugal
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUnited Kingdom
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUnited Kingdom
| | - David A Bechtold
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - Andrew Loudon
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
| | - David Ray
- Faculty of Biology, Medicine and HealthUniversity of Manchester, Manchester Academic Health Science CentreManchesterUnited Kingdom
- Oxford Centre for Diabetes, Endocrinology and MetabolismUniversity of OxfordOxfordUnited Kingdom
- NIHR Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUnited Kingdom
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14
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Gurumurthy CB, O'Brien AR, Quadros RM, Adams J, Alcaide P, Ayabe S, Ballard J, Batra SK, Beauchamp MC, Becker KA, Bernas G, Brough D, Carrillo-Salinas F, Chan W, Chen H, Dawson R, DeMambro V, D'Hont J, Dibb KM, Eudy JD, Gan L, Gao J, Gonzales A, Guntur AR, Guo H, Harms DW, Harrington A, Hentges KE, Humphreys N, Imai S, Ishii H, Iwama M, Jonasch E, Karolak M, Keavney B, Khin NC, Konno M, Kotani Y, Kunihiro Y, Lakshmanan I, Larochelle C, Lawrence CB, Li L, Lindner V, Liu XD, Lopez-Castejon G, Loudon A, Lowe J, Jerome-Majewska LA, Matsusaka T, Miura H, Miyasaka Y, Morpurgo B, Motyl K, Nabeshima YI, Nakade K, Nakashiba T, Nakashima K, Obata Y, Ogiwara S, Ouellet M, Oxburgh L, Piltz S, Pinz I, Ponnusamy MP, Ray D, Redder RJ, Rosen CJ, Ross N, Ruhe MT, Ryzhova L, Salvador AM, Alam SS, Sedlacek R, Sharma K, Smith C, Staes K, Starrs L, Sugiyama F, Takahashi S, Tanaka T, Trafford AW, Uno Y, Vanhoutte L, Vanrockeghem F, Willis BJ, Wright CS, Yamauchi Y, Yi X, Yoshimi K, Zhang X, Zhang Y, Ohtsuka M, Das S, Garry DJ, Hochepied T, Thomas P, Parker-Thornburg J, Adamson AD, Yoshiki A, Schmouth JF, Golovko A, Thompson WR, Lloyd KCK, Wood JA, Cowan M, Mashimo T, Mizuno S, Zhu H, Kasparek P, Liaw L, Miano JM, Burgio G. Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation. Genome Biol 2019; 20:171. [PMID: 31446895 PMCID: PMC6709553 DOI: 10.1186/s13059-019-1776-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [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: 04/01/2019] [Accepted: 07/27/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study reported up to 16% efficiency in generating conditional knockout (cKO or floxed) alleles by microinjection of 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides as donors (referred herein as "two-donor floxing" method). RESULTS We re-evaluate the two-donor method from a consortium of 20 laboratories across the world. The dataset constitutes 56 genetic loci, 17,887 zygotes, and 1718 live-born mice, of which only 15 (0.87%) mice contain cKO alleles. We subject the dataset to statistical analyses and a machine learning algorithm, which reveals that none of the factors analyzed was predictive for the success of this method. We test some of the newer methods that use one-donor DNA on 18 loci for which the two-donor approach failed to produce cKO alleles. We find that the one-donor methods are 10- to 20-fold more efficient than the two-donor approach. CONCLUSION We propose that the two-donor method lacks efficiency because it relies on two simultaneous recombination events in cis, an outcome that is dwarfed by pervasive accompanying undesired editing events. The methods that use one-donor DNA are fairly efficient as they rely on only one recombination event, and the probability of correct insertion of the donor cassette without unanticipated mutational events is much higher. Therefore, one-donor methods offer higher efficiencies for the routine generation of cKO animal models.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Aidan R O'Brien
- Transformational Bioinformatics, Health and Biosecurity Business Unit, CSIRO, North Ryde, Australia
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - John Adams
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Pilar Alcaide
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Shinya Ayabe
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Johnathan Ballard
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Marie-Claude Beauchamp
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Kathleen A Becker
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Guillaume Bernas
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | | | - Wesley Chan
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Hanying Chen
- School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Ruby Dawson
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Victoria DeMambro
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Jinke D'Hont
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Katharine M Dibb
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - James D Eudy
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Lin Gan
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jing Gao
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Amy Gonzales
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Anyonya R Guntur
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Huiping Guo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne Harrington
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil Humphreys
- Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shiho Imai
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mizuho Iwama
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Eric Jonasch
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Karolak
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nay-Chi Khin
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuko Kotani
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yayoi Kunihiro
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Larochelle
- Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Catherine B Lawrence
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Lin Li
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Volkhard Lindner
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Xian-De Liu
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gloria Lopez-Castejon
- Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Andrew Loudon
- Centre for Biological Timing, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jenna Lowe
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Loydie A Jerome-Majewska
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Taiji Matsusaka
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hiromi Miura
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yoshiki Miyasaka
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Benjamin Morpurgo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Katherine Motyl
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Yo-Ichi Nabeshima
- Laboratory of Molecular Life Science, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Koji Nakade
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - Kenichi Nakashima
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuichi Obata
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sanae Ogiwara
- Department of Laboratory Animal Science, Support Center for Medical Research and Education, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Mariette Ouellet
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Leif Oxburgh
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
- Basic and Clinical Research, The Rogosin Institute, New York, USA
| | - Sandra Piltz
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Ilka Pinz
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ronald J Redder
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Clifford J Rosen
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Nikki Ross
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Mark T Ruhe
- Mouse Biology Program, University of California, Davis, USA
| | - Larisa Ryzhova
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Ane M Salvador
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Sabrina Shameen Alam
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karan Sharma
- College of Osteopathic Medicine, Marian University, Indianapolis, IN, 46222, USA
| | - Chad Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katrien Staes
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Lora Starrs
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Andrew W Trafford
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - Yoshihiro Uno
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Leen Vanhoutte
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frederique Vanrockeghem
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Christian S Wright
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - Yuko Yamauchi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Xin Yi
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - Kazuto Yoshimi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Xuesong Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Zhang
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Masato Ohtsuka
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Satyabrata Das
- Lillehei Heart Institute Regenerative Medicine and Sciences Program, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Garry
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Tino Hochepied
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paul Thomas
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | | | - Antony D Adamson
- Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Atsushi Yoshiki
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Jean-Francois Schmouth
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Andrei Golovko
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - William R Thompson
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Joshua A Wood
- Mouse Biology Program, University of California, Davis, USA
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), Montreal, Canada
| | - Tomoji Mashimo
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Hao Zhu
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucy Liaw
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Joseph M Miano
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia.
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15
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Birket MJ, Raibaud S, Lettieri M, Adamson AD, Letang V, Cervello P, Redon N, Ret G, Viale S, Wang B, Biton B, Guillemot JC, Mikol V, Leonard JP, Hanley NA, Orsini C, Itier JM. A Human Stem Cell Model of Fabry Disease Implicates LIMP-2 Accumulation in Cardiomyocyte Pathology. Stem Cell Reports 2019; 13:380-393. [PMID: 31378672 PMCID: PMC6700557 DOI: 10.1016/j.stemcr.2019.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 03/06/2018] [Revised: 07/04/2019] [Accepted: 07/05/2019] [Indexed: 01/19/2023] Open
Abstract
Here, we have used patient-derived induced pluripotent stem cell (iPSC) and gene-editing technology to study the cardiac-related molecular and functional consequences of mutations in GLA causing the lysosomal storage disorder Fabry disease (FD), for which heart dysfunction is a major cause of mortality. Our in vitro model recapitulated clinical data with FD cardiomyocytes accumulating GL-3 and displaying an increased excitability, with altered electrophysiology and calcium handling. Quantitative proteomics enabled the identification of >5,500 proteins in the cardiomyocyte proteome and secretome, and revealed accumulation of the lysosomal protein LIMP-2 and secretion of cathepsin F and HSPA2/HSP70-2 in FD. Genetic correction reversed these changes. Overexpression of LIMP-2 directly induced the secretion of cathepsin F and HSPA2/HSP70-2, implying causative relationship, and led to massive vacuole accumulation. In summary, our study has revealed potential new cardiac biomarkers for FD, and provides valuable mechanistic insight into the earliest pathological events in FD cardiomyocytes.
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Affiliation(s)
- Matthew J Birket
- Sanofi, Translational Sciences Unit, Sanofi, 13 quai Jules Guesdes, 94400 Vitry-sur-Seine, France; Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Sophie Raibaud
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - Miriam Lettieri
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Antony D Adamson
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Valerie Letang
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - Pauline Cervello
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - Nicolas Redon
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - Gwenaelle Ret
- Sanofi, Translational Sciences Unit, Sanofi, 13 quai Jules Guesdes, 94400 Vitry-sur-Seine, France
| | - Sandra Viale
- Sanofi, Translational Sciences Unit, Sanofi, 13 quai Jules Guesdes, 94400 Vitry-sur-Seine, France
| | - Bing Wang
- Sanofi, GBD-Analytical R&D, 211 Second Avenue, Waltham, MA 02451, USA
| | - Bruno Biton
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - Jean-Claude Guillemot
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - Vincent Mikol
- Sanofi, Translational Sciences Unit, Avenue Pierre Brossolette, 91380 Chilly-Mazarin, France
| | - John P Leonard
- Sanofi, Rare Disease Science Unit, 153 Second Avenue, Waltham, MA 02451, USA
| | - Neil A Hanley
- Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, The University of Manchester, Oxford Road, Manchester M13 9PT, UK; Endocrinology Department, Manchester University NHS Foundation Trust, Grafton Street, Manchester M13 9WU, UK
| | - Cecile Orsini
- Sanofi, Translational Sciences Unit, Sanofi, 13 quai Jules Guesdes, 94400 Vitry-sur-Seine, France
| | - Jean-Michel Itier
- Sanofi, Translational Sciences Unit, Sanofi, 13 quai Jules Guesdes, 94400 Vitry-sur-Seine, France.
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16
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Mularczyk EJ, Singh M, Godwin ARF, Galli F, Humphreys N, Adamson AD, Mironov A, Cain SA, Sengle G, Boot-Handford RP, Cossu G, Kielty CM, Baldock C. ADAMTS10-mediated tissue disruption in Weill-Marchesani syndrome. Hum Mol Genet 2018; 27:3675-3687. [PMID: 30060141 PMCID: PMC6196651 DOI: 10.1093/hmg/ddy276] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 06/20/2018] [Revised: 07/19/2018] [Accepted: 07/20/2018] [Indexed: 01/13/2023] Open
Abstract
Fibrillin microfibrils are extracellular matrix assemblies that form the template for elastic fibres, endow blood vessels, skin and other elastic tissues with extensible properties. They also regulate the bioavailability of potent growth factors of the TGF-β superfamily. A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS)10 is an essential factor in fibrillin microfibril function. Mutations in fibrillin-1 or ADAMTS10 cause Weill-Marchesani syndrome (WMS) characterized by short stature, eye defects, hypermuscularity and thickened skin. Despite its importance, there is poor understanding of the role of ADAMTS10 and its function in fibrillin microfibril assembly. We have generated an ADAMTS10 WMS mouse model using Clustered Regularly Spaced Interspaced Short Palindromic Repeats and CRISPR associated protein 9 (CRISPR-Cas9) to introduce a truncation mutation seen in WMS patients. Homozygous WMS mice are smaller and have shorter long bones with perturbation to the zones of the developing growth plate and changes in cell proliferation. Furthermore, there are abnormalities in the ciliary apparatus of the eye with decreased ciliary processes and abundant fibrillin-2 microfibrils suggesting perturbation of a developmental expression switch. WMS mice have increased skeletal muscle mass and more myofibres, which is likely a consequence of an altered skeletal myogenesis. These results correlated with expression data showing down regulation of Growth differentiation factor (GDF8) and Bone Morphogenetic Protein (BMP) growth factor genes. In addition, the mitochondria in skeletal muscle are larger with irregular shape coupled with increased phospho-p38 mitogen-activated protein kinase (MAPK) suggesting muscle remodelling. Our data indicate that decreased SMAD1/5/8 and increased p38/MAPK signalling are associated with ADAMTS10-induced WMS. This model will allow further studies of the disease mechanism to facilitate the development of therapeutic interventions.
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Affiliation(s)
- Ewa J Mularczyk
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Mukti Singh
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Alan R F Godwin
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Francessco Galli
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Neil Humphreys
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Antony D Adamson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Aleksandr Mironov
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Stuart A Cain
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Gerhard Sengle
- Center for Biochemistry, Center for Molecular Medicine (CMMC), Medical Faculty, University of Cologne, Germany
| | - Ray P Boot-Handford
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Giulio Cossu
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Cay M Kielty
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
| | - Clair Baldock
- Wellcome Centre for Cell Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, UK
- Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK
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17
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Ankers JM, Awais R, Jones NA, Boyd J, Ryan S, Adamson AD, Harper CV, Bridge L, Spiller DG, Jackson DA, Paszek P, Sée V, White MR. Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation. eLife 2016; 5. [PMID: 27185527 PMCID: PMC4869934 DOI: 10.7554/elife.10473] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [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: 07/30/2015] [Accepted: 04/13/2016] [Indexed: 01/07/2023] Open
Abstract
Dynamic cellular systems reprogram gene expression to ensure appropriate cellular fate responses to specific extracellular cues. Here we demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling and the cell cycle are prioritised differently depending on the timing of an inflammatory signal. Using iterative experimental and computational analyses, we show physical and functional interactions between NF-κB and the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators. These interactions modulate the NF-κB response. In S-phase, the NF-κB response was delayed or repressed, while cell cycle progression was unimpeded. By contrast, activation of NF-κB at the G1/S boundary resulted in a longer cell cycle and more synchronous initial NF-κB responses between cells. These data identify new mechanisms by which the cellular response to stress is differentially controlled at different stages of the cell cycle. DOI:http://dx.doi.org/10.7554/eLife.10473.001 Investigating how cells adapt to the constantly changing environment inside the body is vitally important for understanding how the body responds to an injury or infection. One of the ways in which human cells adapt is by dividing to produce new cells. This takes place in a repeating pattern of events, known as the cell cycle, through which a cell copies its DNA (in a stage known as S-phase) and then divides to make two daughter cells. Each stage of the cell cycle is tightly controlled; for example, a family of proteins called E2 factors control the entry of the cell into S phase. “Inflammatory” signals produced by a wound or during an infection can activate a protein called Nuclear Factor-kappaB (NF-κB), which controls the activity of genes that allow cells to adapt to the situation. Research shows that the activity of NF-κB is also regulated by the cell cycle, but it has not been clear how this works. Here, Ankers et al. investigated whether the stage of the cell cycle might affect how NF-κB responds to inflammatory signals. The experiments show that the NF-κB response was stronger in cells that were just about to enter S-phase than in cells that were already copying their DNA. An E2 factor called E2F-1 –which accumulates in the run up to S-phase – interacts with NF-κB and can alter the activity of certain genes. However, during S-phase, another E2 factor family member called E2F-4 binds to NF-κB and represses its activation. Next, Ankers et al. used a mathematical model to understand how these protein interactions can affect the response of cells to inflammatory signals. These findings suggest that direct interactions between E2 factor proteins and NF-κB enable cells to decide whether to divide or react in different ways to inflammatory signals. The research tools developed in this study, combined with other new experimental techniques, will allow researchers to accurately predict how cells will respond to inflammatory signals at different points in the cell cycle. DOI:http://dx.doi.org/10.7554/eLife.10473.002
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Affiliation(s)
- John M Ankers
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom
| | - Raheela Awais
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom.,Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Nicholas A Jones
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - James Boyd
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Sheila Ryan
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom.,Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Antony D Adamson
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Claire V Harper
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Lloyd Bridge
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom.,Department of Mathematics, University of Swansea, Swansea, United Kingdom
| | - David G Spiller
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Dean A Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Pawel Paszek
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
| | - Violaine Sée
- Centre for Cell Imaging, Institute of Integrative Biology, Liverpool, United Kingdom
| | - Michael Rh White
- Systems Microscopy Centre, Faculty of Life Sciences, Manchester, United Kingdom
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18
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McNamara AV, Adamson AD, Dunham LSS, Semprini S, Spiller DG, McNeilly AS, Mullins JJ, Davis JRE, White MRH. Role of Estrogen Response Element in the Human Prolactin Gene: Transcriptional Response and Timing. Mol Endocrinol 2015; 30:189-200. [PMID: 26691151 PMCID: PMC4792233 DOI: 10.1210/me.2015-1186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The use of bacterial artificial chromosome (BAC) reporter constructs in molecular physiology enables the inclusion of large sections of flanking DNA, likely to contain regulatory elements and enhancers regions that contribute to the transcriptional output of a gene. Using BAC recombineering, we have manipulated a 160-kb human prolactin luciferase (hPRL-Luc) BAC construct and mutated the previously defined proximal estrogen response element (ERE) located -1189 bp relative to the transcription start site, to assess its involvement in the estrogen responsiveness of the entire hPRL locus. We found that GH3 cell lines stably expressing Luc under control of the ERE-mutated hPRL promoter (ERE-Mut) displayed a dramatically reduced transcriptional response to 17β-estradiol (E2) treatment compared with cells expressing Luc from the wild-type (WT) ERE hPRL-Luc promoter (ERE-WT). The -1189 ERE controls not only the response to E2 treatment but also the acute transcriptional response to TNFα, which was abolished in ERE-Mut cells. ERE-WT cells displayed a biphasic transcriptional response after TNFα treatment, the acute phase of which was blocked after treatment with the estrogen receptor antagonist 4-hydroxy-tamoxifen. Unexpectedly, we show the oscillatory characteristics of hPRL promoter activity in individual living cells were unaffected by disruption of this crucial response element, real-time bioluminescence imaging showed that transcription cycles were maintained, with similar cycle lengths, in ERE-WT and ERE-Mut cells. These data suggest the -1189 ERE is the dominant response element involved in the hPRL transcriptional response to both E2 and TNFα and, crucially, that cycles of hPRL promoter activity are independent of estrogen receptor binding.
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Affiliation(s)
- Anne V McNamara
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Antony D Adamson
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Lee S S Dunham
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Sabrina Semprini
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - David G Spiller
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Alan S McNeilly
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - John J Mullins
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Julian R E Davis
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
| | - Michael R H White
- Systems Microscopy Centre (A.V.M., A.D.A., D.G.S., M.R.H.W.), Faculty of Life Sciences, and Faculty of Medical and Human Sciences (L.S.S.D., J.R.E.D.), Centre for Endocrinology and Diabetes, Institute of Human Development, University of Manchester, Manchester M13 9PT, United Kingdom; and The Molecular Physiology Group (S.S., J.J.M.), Centre for Cardiovascular Science, and Medical Research Council Human Reproductive Sciences Unit (A.S.M.), Centre for Reproductive Biology, Queen's Medical Research Institute, Edinburgh EH16 4TJ, United Kingdom
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19
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Abstract
The study of gene expression is a major focus in biological research and is recognised to be critical for our understanding of physiological and pathophysiological processes. Methods to study gene expression range from in vitro biochemical assays through cultured cells and tissue biopsies to whole organisms. In the early stages of project development, considerations about which model system to use should be addressed and may influence future experimental procedures. The aim of this review is to briefly describe advantages and disadvantages of the existing techniques available to study eukaryote gene expression in vitro, including the mechanism of transgene integration (transient or stable), the different transgenesis systems available, including plasmids, viruses and targeted integration and knockin approaches, and paying particular attention to expression systems such as bacterial artificial chromosomes and episomal vectors that offer a number of advantages and are increasing in popularity. We also discuss novel approaches that combine some of the above techniques, generating increasingly complex but physiologically accurate expression systems.
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Affiliation(s)
- A D Adamson
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, UK.
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20
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Semprini S, Friedrichsen S, Harper CV, McNeilly JR, Adamson AD, Spiller DG, Kotelevtseva N, Brooker G, Brownstein DG, McNeilly AS, White MRH, Davis JRE, Mullins JJ. Real-time visualization of human prolactin alternate promoter usage in vivo using a double-transgenic rat model. Mol Endocrinol 2009; 23:529-38. [PMID: 19147700 DOI: 10.1210/me.2008-0399] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We have generated a humanized double-reporter transgenic rat for whole-body in vivo imaging of endocrine gene expression, using the human prolactin (PRL) gene locus as a physiologically important endocrine model system. The approach combines the advantages of bacterial artificial chromosome recombineering to report appropriate regulation of gene expression by distant elements, with double reporter activity for the study of highly dynamic promoter regulation in vivo and ex vivo. We show first that this rat transgenic model allows quantitative in vivo imaging of gene expression in the pituitary gland, allowing the study of pulsatile dynamic activity of the PRL promoter in normal endocrine cells in different physiological states. Using the dual reporters in combination, dramatic and unexpected changes in PRL expression were observed after inflammatory challenge. Expression of PRL was shown by RT-PCR to be driven by activation of the alternative upstream extrapituitary promoter and flow cytometry analysis pointed at diverse immune cells expressing the reporter gene. These studies demonstrate the effective use of this type of model for molecular physiology and illustrate the potential for providing novel insight into human gene expression using a heterologous system.
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Affiliation(s)
- Sabrina Semprini
- University of Edinburgh, Queen's Medical Research Institute, Edinburgh EH16 4TJ, Scotland, UK
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21
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Adamson AD, Friedrichsen S, Semprini S, Harper CV, Mullins JJ, White MRH, Davis JRE. Human prolactin gene promoter regulation by estrogen: convergence with tumor necrosis factor-alpha signaling. Endocrinology 2008; 149:687-94. [PMID: 18006630 PMCID: PMC2342177 DOI: 10.1210/en.2007-1066] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Estrogens have been implicated in the regulation of prolactin gene expression in man, although previous studies have not defined the molecular mechanism whereby estradiol activates the human prolactin gene promoter (hPrl). We found that estradiol induced a reproducible 1.8-fold activation of the hPrl gene promoter, using pituitary GH3 cells stably transfected with a 5000-bp hPrl promoter fragment linked to luciferase reporter gene. This activation was blocked by treatment with estrogen receptor (ER) antagonists 4-hydroxytamoxifen and ICI-182,780. Promoter deletion and mutagenesis experiments identified a functional estrogen response element (ERE) sequence 1189 bp upstream of the transcription start site that was responsible for estrogen-mediated promoter activation. This site differed from the consensus ERE sequence by two base pairs, one in each half-site. This ERE was identified to be functional through binding ERalpha in EMSAs. Chromatin immunoprecipitation assays confirmed ERalpha binding to this sequence in vivo in the absence of ligand, with increased recruitment when cells were cultured in the presence of estradiol. When cells were treated with both estradiol and TNFalpha, we observed synergistic activation of the hPrl promoter, which was mediated by the -1189-bp ERE. Mutagenesis of this ERE abolished the promoter-activating effect not only of estradiol but also of TNFalpha. These data suggest a novel, promoter-specific signaling interaction between estrogen and TNFalpha signaling, which is likely to be important for prolactin regulation in vivo.
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Affiliation(s)
- A D Adamson
- Endocrine Sciences Research Group, School of Clinical & Laboratory Sciences, University of Manchester, Core Technology Facility 3rd floor, Manchester, UK.
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22
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Friedrichsen S, Harper CV, Semprini S, Wilding M, Adamson AD, Spiller DG, Nelson G, Mullins JJ, White MRH, Davis JRE. Tumor necrosis factor-alpha activates the human prolactin gene promoter via nuclear factor-kappaB signaling. Endocrinology 2006; 147:773-81. [PMID: 16254029 PMCID: PMC1863827 DOI: 10.1210/en.2005-0967] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Pituitary function has been shown to be regulated by an increasing number of intrapituitary factors, including cytokines. Here we show that the important cytokine TNF-alpha activates prolactin gene transcription in pituitary GH3 cells stably expressing luciferase under control of 5 kb of the human prolactin promoter. Similar regulation of the endogenous rat prolactin gene by TNF-alpha in GH3 cells was confirmed using real-time PCR. Luminescence microscopy revealed heterogeneous dynamic response patterns of promoter activity in individual cells. In GH3 cells treated with TNF-alpha, Western blot analysis showed rapid inhibitory protein kappaB (IkappaBalpha) degradation and phosphorylation of p65. Confocal microscopy of cells expressing fluorescence-labeled p65 and IkappaBalpha fusion proteins showed transient cytoplasmic-nuclear translocation and subsequent oscillations in p65 localization and confirmed IkappaBalpha degradation. This was associated with increased nuclear factor kappaB (NF-kappaB)-mediated transcription from an NF-kappaB-responsive luciferase reporter construct. Disruption of NF-kappaB signaling by expression of dominant-negative variants of IkappaB kinases or truncated IkappaBalpha abolished TNF-alpha activation of the prolactin promoter, suggesting that this effect was mediated by NF-kappaB. TNF-alpha signaling was found to interact with other endocrine signals to regulate prolactin gene expression and is likely to be a major paracrine modulator of lactotroph function.
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Affiliation(s)
- Sönke Friedrichsen
- Endocrine Science Research Group School of Biological Sciences, University of Manchester, UK
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