1
|
Bramwell LR, Harries LW. Senescence, regulators of alternative splicing and effects of trametinib treatment in progeroid syndromes. GeroScience 2024; 46:1861-1879. [PMID: 37751047 PMCID: PMC10828446 DOI: 10.1007/s11357-023-00933-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
Progeroid syndromes such as Hutchinson Gilford Progeroid syndrome (HGPS), Werner syndrome (WS) and Cockayne syndrome (CS), result in severely reduced lifespans and premature ageing. Normal senescent cells show splicing factor dysregulation, which has not yet been investigated in syndromic senescent cells. We sought to investigate the senescence characteristics and splicing factor expression profiles of progeroid dermal fibroblasts. Natural cellular senescence can be reversed by application of the senomorphic drug, trametinib, so we also investigated its ability to reverse senescence characteristics in syndromic cells. We found that progeroid cultures had a higher senescence burden, but did not always have differences in levels of proliferation, DNA damage repair and apoptosis. Splicing factor gene expression appeared dysregulated across the three syndromes. 10 µM trametinib reduced senescent cell load and affected other aspects of the senescence phenotype (including splicing factor expression) in HGPS and Cockayne syndromes. Werner syndrome cells did not demonstrate changes in in senescence following treatment. Splicing factor dysregulation in progeroid cells provides further evidence to support this mechanism as a hallmark of cellular ageing and highlights the use of progeroid syndrome cells in the research of ageing and age-related disease. This study suggests that senomorphic drugs such as trametinib could be a useful adjunct to therapy for progeroid diseases.
Collapse
Affiliation(s)
- Laura R Bramwell
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
| |
Collapse
|
2
|
Bramwell LR, Frankum R, Harries LW. Repurposing Drugs for Senotherapeutic Effect: Potential Senomorphic Effects of Female Synthetic Hormones. Cells 2024; 13:517. [PMID: 38534362 DOI: 10.3390/cells13060517] [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: 01/26/2024] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
Repurposing previously approved drugs may fast track the route to the clinic for potential senotherapeutics and improves the inefficiency of the clinical drug development pipeline. We performed a repurposing screen of 240 clinically approved molecules in human primary dermal fibroblasts for their effects on CDKN2A expression. Molecules demonstrating effects on CDKN2A expression underwent secondary screening for senescence-associated beta galactosidase (SAB) activity, based on effect size, direction, and/or molecule identity. Selected molecules then underwent a more detailed assessment of senescence phenotypes including proliferation, apoptosis, DNA damage, senescence-associated secretory phenotype (SASP) expression, and regulators of alternative splicing. A selection of the molecules demonstrating effects on senescence were then used in a new bioinformatic structure-function screen to identify common structural motifs. In total, 90 molecules displayed altered CDKN2A expression at one or other dose, of which 15 also displayed effects on SAB positivity in primary human dermal fibroblasts. Of these, 3 were associated with increased SAB activity, and 11 with reduced activity. The female synthetic sex hormones-diethylstilboestrol, ethynyl estradiol and levonorgestrel-were all associated with a reduction in aspects of the senescence phenotype in male cells, with no effects visible in female cells. Finally, we identified that the 30 compounds that decreased CDKN2A activity the most had a common substructure linked to this function. Our results suggest that several drugs licensed for other indications may warrant exploration as future senotherapies, but that different donors and potentially different sexes may respond differently to senotherapeutic compounds. This underlines the importance of considering donor-related characteristics when designing drug screening platforms.
Collapse
Affiliation(s)
- Laura R Bramwell
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| | - Ryan Frankum
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Department of Clinical and Biomedical Sciences (Medical School), Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| |
Collapse
|
3
|
Mou Z, Spencer J, McGrath JS, Harries LW. Comprehensive analysis of alternative splicing across multiple transcriptomic cohorts reveals prognostic signatures in prostate cancer. Hum Genomics 2023; 17:97. [PMID: 37924098 PMCID: PMC10623736 DOI: 10.1186/s40246-023-00545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) plays a crucial role in transcriptomic diversity and is a hallmark of cancer that profoundly influences the development and progression of prostate cancer (PCa), a prevalent and potentially life-limiting cancer among men. Accumulating evidence has highlighted the association between AS dysregulation and the onset and progression of PCa. However, a comprehensive and integrative analysis of AS profiles at the event level, utilising data from multiple high-throughput cohorts and evaluating the prognosis of PCa progression, remains lacking and calls for thorough exploration. RESULTS We identified a differentially expressed retained intron event in ZWINT across three distinct cohorts, encompassing an original array-based dataset profiled by us previously and two RNA sequencing (RNA-seq) datasets. Subsequent in-depth analyses of these RNA-seq datasets revealed 141 altered events, of which 21 demonstrated a significant association with patients' biochemical recurrence-free survival (BCRFS). We formulated an AS event-based prognostic signature, capturing six pivotal events in genes CYP4F12, NFATC4, PIGO, CYP3A5, ALS2CL, and FXYD3. This signature effectively differentiated high-risk patients diagnosed with PCa, who experienced shorter BCRFS, from their low-risk counterparts. Notably, the signature's predictive power surpassed traditional clinicopathological markers in forecasting 5-year BCRFS, demonstrating robust performance in both internal and external validation sets. Lastly, we constructed a novel nomogram that integrates patients' Gleason scores with pathological tumour stages, demonstrating improved prognostication of BCRFS. CONCLUSIONS Prediction of clinical progression remains elusive in PCa. This research uncovers novel splicing events associated with BCRFS, augmenting existing prognostic tools, thus potentially refining clinical decision-making.
Collapse
Affiliation(s)
- Zhuofan Mou
- Clinical and Biomedical Sciences, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Barrack Road, Exeter, EX2 5DW, UK
| | - Jack Spencer
- Translational Research Exchange at Exeter, Living Systems Institute, University of Exeter, Exeter, UK
| | - John S McGrath
- Clinical and Biomedical Sciences, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Barrack Road, Exeter, EX2 5DW, UK
- Royal Devon University Healthcare NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- Clinical and Biomedical Sciences, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
4
|
Manni E, Jeffery N, Chambers D, Slade L, Etheridge T, Harries LW. An evaluation of the role of miR-361-5p in senescence and systemic ageing. Exp Gerontol 2023; 174:112127. [PMID: 36804517 DOI: 10.1016/j.exger.2023.112127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Senescent cells are key regulators of ageing and age-associated disease. MicroRNAs (miRs) are a key component of the molecular machinery governing cellular senescence, with several known to regulate important genes associated with this process. We sought to identify miRs associated with both senescence and reversal by pinpointing those showing opposing directionality of effect in senescence and in response to senotherapy. Cellular senescence phenotypes were assessed in primary human endothelial cells following targeted manipulation of emergent miRNAs. Finally, the effect of conserved target gene knockdown on lifespan and healthspan was assessed in a C. elegans system in vivo. Three miRNAs (miR-5787, miR-3665 and miR-361-5p) demonstrated associations with both senescence and rejuvenation, but miR-361-5p alone demonstrated opposing effects in senescence and rescue. Treatment of late passage human endothelial cells with a miR-361-5p mimic caused a 14 % decrease in the senescent load of the culture. RNAi gene knockdown of conserved miR-361-5p target genes in a C. elegans model however resulted in adverse effects on healthspan and/or lifespan. Although miR-361-5p may attenuate aspects of the senescence phenotype in human primary endothelial cells, many of its validated target genes also play essential roles in the regulation or formation of the cytoskeletal network, or its interaction with the extracellular matrix. These processes are essential for cell survival and cell function. Targeting miR-361-5p alone may not represent a promising target for future senotherapy; more sophisticated approaches to attenuate its interaction with specific targets without roles in essential cell processes would be required.
Collapse
Affiliation(s)
- Emad Manni
- University of Exeter Medical School, Faculty of Health and Life Sciences, Barrack Road, Exeter EX2 5DW, UK
| | - Nicola Jeffery
- University of Exeter Medical School, Faculty of Health and Life Sciences, Barrack Road, Exeter EX2 5DW, UK
| | - David Chambers
- Wolfson Centre for Age-Related Diseases, King's College London, London WC2R 2LS, UK
| | - Luke Slade
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK
| | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK
| | - Lorna W Harries
- University of Exeter Medical School, Faculty of Health and Life Sciences, Barrack Road, Exeter EX2 5DW, UK.
| |
Collapse
|
5
|
Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
Collapse
|
6
|
Kennedy NA, Janjua M, Chanchlani N, Lin S, Bewshea C, Nice R, McDonald TJ, Auckland C, Harries LW, Davies M, Michell S, Kok KB, Lamb CA, Smith PJ, Hart AL, Pollok RC, Lees CW, Boyton RJ, Altmann DM, Sebastian S, Powell N, Goodhand JR, Ahmad T. Vaccine escape, increased breakthrough and reinfection in infliximab-treated patients with IBD during the Omicron wave of the SARS-CoV-2 pandemic. Gut 2023; 72:295-305. [PMID: 35902214 DOI: 10.1136/gutjnl-2022-327570] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [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: 04/08/2022] [Accepted: 07/16/2022] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Antitumour necrosis factor (TNF) drugs impair serological responses following SARS-CoV-2 vaccination. We sought to assess if a third dose of a messenger RNA (mRNA)-based vaccine substantially boosted anti-SARS-CoV-2 antibody responses and protective immunity in infliximab-treated patients with IBD. DESIGN Third dose vaccine induced anti-SARS-CoV-2 spike (anti-S) receptor-binding domain (RBD) antibody responses, breakthrough SARS-CoV-2 infection, reinfection and persistent oropharyngeal carriage in patients with IBD treated with infliximab were compared with a reference cohort treated with vedolizumab from the impaCt of bioLogic therApy on saRs-cov-2 Infection and immuniTY (CLARITY) IBD study. RESULTS Geometric mean (SD) anti-S RBD antibody concentrations increased in both groups following a third dose of an mRNA-based vaccine. However, concentrations were lower in patients treated with infliximab than vedolizumab, irrespective of whether their first two primary vaccine doses were ChAdOx1 nCoV-19 (1856 U/mL (5.2) vs 10 728 U/mL (3.1), p<0.0001) or BNT162b2 vaccines (2164 U/mL (4.1) vs 15 116 U/mL (3.4), p<0.0001). However, no differences in anti-S RBD antibody concentrations were seen following third and fourth doses of an mRNA-based vaccine, irrespective of the combination of primary vaccinations received. Post-third dose, anti-S RBD antibody half-life estimates were shorter in infliximab-treated than vedolizumab-treated patients (37.0 days (95% CI 35.6 to 38.6) vs 52.0 days (95% CI 49.0 to 55.4), p<0.0001).Compared with vedolizumab-treated, infliximab-treated patients were more likely to experience SARS-CoV-2 breakthrough infection (HR 2.23 (95% CI 1.46 to 3.38), p=0.00018) and reinfection (HR 2.10 (95% CI 1.31 to 3.35), p=0.0019), but this effect was uncoupled from third vaccine dose anti-S RBD antibody concentrations. Reinfection occurred predominantly during the Omicron wave and was predicted by SARS-CoV-2 antinucleocapsid concentrations after the initial infection. We did not observe persistent oropharyngeal carriage of SARS-CoV-2. Hospitalisations and deaths were uncommon in both groups. CONCLUSIONS Following a third dose of an mRNA-based vaccine, infliximab was associated with attenuated serological responses and more SARS-CoV-2 breakthrough infection and reinfection which were not predicted by the magnitude of anti-S RBD responses, indicative of vaccine escape by the Omicron variant. TRIAL REGISTRATION NUMBER ISRCTN45176516.
Collapse
Affiliation(s)
- Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Malik Janjua
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Neil Chanchlani
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Simeng Lin
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Claire Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Rachel Nice
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
- Department of Biochemistry, Exeter Clinical Laboratory International, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Timothy J McDonald
- Department of Biochemistry, Exeter Clinical Laboratory International, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Cressida Auckland
- Department of Microbiology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter, Exeter, UK
| | - Merlin Davies
- Institute of Biomedical and Clinical Sciences, University of Exeter, Exeter, UK
| | - Stephen Michell
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Klaartje B Kok
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
- Department of Gastroenterology, Royal London Hospital, Barts Health NHS Trust, The Royal London Hospital, London, UK
| | - Christopher A Lamb
- Department of Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Translational & Clinical Research Institute, Newcastle University Faculty of Medical Sciences, Newcastle upon Tyne, UK
| | - Philip J Smith
- Department of Gastroenterology, Royal Liverpool Hospital, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Ailsa L Hart
- Department of Gastroenterology, St Mark's Hospital and Academic Institute, London, UK
| | - Richard Cg Pollok
- Department of Gastroenterology, St George's University Hospitals NHS Foundation Trust, London, UK
- Institute for Infection & Immunity, St George's University of London, London, UK
| | - Charlie W Lees
- Department of Gastroenterology, Western General Hospital, Edinburgh, UK
- Institute of Genetic and Molecular Medicine, University of Edinburgh Western General Hospital, Edinburgh, UK
| | - Rosemary J Boyton
- Department of Infectious Disease, Imperial College London, London, UK
- Lung Division, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Daniel M Altmann
- Department of Immunology and Inflammation, Imperial College London, London, UK
| | - Shaji Sebastian
- IBD Unit, Department of Gastroenterology, Hull University Teaching Hospitals NHS Trust, Hull, UK
- Hull York Medical School, University of Hull, Hull, UK
| | - Nicholas Powell
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Gastroenterology, Imperial College Healthcare NHS Trust, London, UK
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| |
Collapse
|
7
|
Turner J, Pound P, Owen C, Hutchinson I, Hop M, Chau DYS, Barrios Silva LV, Coleman M, Dubourg A, Harries LW, Hutter V, Kenna JG, Lauschke VM, Neuhaus W, Roper C, Watkins PB, Welch J, Alvarez LR, Taylor K. Incorporating new approach methodologies into regulatory nonclinical pharmaceutical safety assessment. ALTEX 2023. [PMID: 36692187 DOI: 10.14573/altex.2212081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 01/25/2023]
Abstract
New approach methodologies (NAMs) based on human biology enable the assessment of adverse biological effects of pharmaceuticals and other chemicals. Currently, however, it is unclear how NAMs should be used during drug development to improve human safety evaluation. A series of 5 workshops with 13 international experts (regulators, preclinical scientists and NAMs developers) were conducted to identify feasible NAMs and to discuss how to exploit them in specific safety assessment contexts. Participants generated four 'maps' of how NAMs can be exploited in the safety assessment of the liver, respiratory, cardiovascular and central nervous systems. Each map shows relevant end points measured, tools used (e.g., cells, assays, platforms), and highlights gaps where further development and validation of NAMs remains necessary. Each map addresses the fundamental scientific requirements for the safety assessment of that organ system, providing users with guidance on the selection of appropriate NAMs. In addition to generating the maps, participants offered suggestions for encouraging greater NAM adoption within drug development and their inclusion in regulatory guidelines. A specific recommendation was that pharmaceutical companies should be more transparent about how they use NAMs in-house. As well as giving guidance for the four organ systems, the maps provide a template that could be used for additional organ safety testing contexts. Moreover, their conversion to an interactive format would enable users to drill down to the detail necessary to answer specific scientific and regulatory questions.
Collapse
Affiliation(s)
| | | | | | | | | | - David Y S Chau
- Division of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, London, UK
| | - Lady V Barrios Silva
- Division of Biomaterials and Tissue Engineering, UCL Eastman Dental Institute, London, UK
| | - Mike Coleman
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | | | | | - Victoria Hutter
- ImmuONE Limited, Hatfield, UK; Centre for Topical Drug Delivery and Toxicology, University of Hertfordshire, Hatfield, UK
| | | | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany; University of Tuebingen, Tuebingen, Germany
| | - Winfried Neuhaus
- Austrian Institute of Technology GmbH, Competence Unit Molecular Diagnostics, Vienna, Austria; Department of Medicine, Danube Private University, Krems, Austria
| | - Clive Roper
- Roper Toxicology Consulting Limited, Edinburgh, UK
| | - Paul B Watkins
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School Of Pharmacy, Chapel Hill NC, USA
| | | | | | | |
Collapse
|
8
|
Mou Z, Spencer J, Knight B, John J, McCullagh P, McGrath JS, Harries LW. Gene expression analysis reveals a 5-gene signature for progression-free survival in prostate cancer. Front Oncol 2022; 12:914078. [PMID: 36033512 PMCID: PMC9413154 DOI: 10.3389/fonc.2022.914078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Prostate cancer (PCa) is the second most common male cancer worldwide, but effective biomarkers for the presence or progression risk of disease are currently elusive. In a series of nine matched histologically confirmed PCa and benign samples, we carried out an integrated transcriptome-wide gene expression analysis, including differential gene expression analysis and weighted gene co-expression network analysis (WGCNA), which identified a set of potential gene markers highly associated with tumour status (malignant vs. benign). We then used these genes to establish a minimal progression-free survival (PFS)-associated gene signature (GS) (PCBP1, PABPN1, PTPRF, DANCR, and MYC) using least absolute shrinkage and selection operator (LASSO) and stepwise multivariate Cox regression analyses from The Cancer Genome Atlas prostate adenocarcinoma (TCGA-PRAD) dataset. Our signature was able to predict PFS over 1, 3, and 5 years in TCGA-PRAD dataset, with area under the curve (AUC) of 0.64–0.78, and our signature remained as a prognostic factor independent of age, Gleason score, and pathological T and N stages. A nomogram combining the signature and Gleason score demonstrated improved predictive capability for PFS (AUC: 0.71–0.85) and was superior to the Cambridge Prognostic Group (CPG) model alone and some conventionally used clinicopathological factors in predicting PFS. In conclusion, we have identified and validated a novel five-gene signature and established a nomogram that effectively predicted PFS in patients with PCa. Findings may improve current prognosis tools for PFS and contribute to clinical decision-making in PCa treatment.
Collapse
Affiliation(s)
- Zhuofan Mou
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Devon, United Kingdom
| | - Jack Spencer
- Translational Research Exchange at Exeter, Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Bridget Knight
- National Institute for Health and Care Research (NIHR) Exeter Clinical Research Facility, Royal Devon and Exeter National Health Service (NHS) Foundation Trust, Royal Devon and Exeter Hospital, Exeter, United Kingdom
| | - Joseph John
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Devon, United Kingdom
- Exeter Surgical Health Services Research Unit, Royal Devon and Exeter National Health Service (NHS) Foundation Trust, Exeter, United Kingdom
| | - Paul McCullagh
- Department of Pathology, Royal Devon and Exeter National Health Service (NHS) Foundation Trust, Exeter, United Kingdom
| | - John S. McGrath
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Devon, United Kingdom
- Exeter Surgical Health Services Research Unit, Royal Devon and Exeter National Health Service (NHS) Foundation Trust, Exeter, United Kingdom
| | - Lorna W. Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Devon, United Kingdom
- *Correspondence: Lorna W. Harries,
| |
Collapse
|
9
|
Davies M, Bramwell LR, Jeffery N, Bunce B, Lee BP, Knight B, Auckland C, Masoli JA, Harries LW. Persistence of clinically-relevant levels of SARS-CoV2 envelope gene subgenomic RNAs in non-immunocompromised individuals. Int J Infect Dis 2021; 116:418-425. [PMID: 34890790 PMCID: PMC8757659 DOI: 10.1016/j.ijid.2021.12.312] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 11/19/2022] Open
Abstract
Objectives This study aimed to evaluate the associations between COVID-19 severity and active viral load, and to characterize the dynamics of active SARS-CoV-2 clearance in a series of archival samples taken from patients in the first wave of COVID-19 infection in the South West of the UK. Methods Subgenomic RNA (sgRNA) and E-gene genomic sequences were measured in a retrospective collection of PCR-confirmed SARS-CoV-2-positive samples from 176 individuals, and related to disease severity. Viral clearance dynamics were then assessed in relation to symptom onset and last positive test. Results Whilst E-gene sgRNAs declined before E-gene genomic sequences, some individuals retained sgRNA positivity for up to 68 days. 13% of sgRNA-positive cases still exhibited clinically relevant levels of virus after 10 days, with no clinical features previously associated with prolonged viral clearance times. Conclusions Our results suggest that potentially active virus can sometimes persist beyond a 10-day period, and could pose a potential risk of onward transmission. Where this would pose a serious public health threat, additional mitigation strategies may be necessary to reduce the risk of secondary cases in vulnerable settings.
Collapse
Affiliation(s)
- Merlin Davies
- Institute of Clinical and Biomedical Sciences, University of Exeter, RILD building, Royal Devon and Exeter Hospital (Wonford), Barrack Road, Exeter, UK
| | - Laura R Bramwell
- Institute of Clinical and Biomedical Sciences, University of Exeter, RILD building, Royal Devon and Exeter Hospital (Wonford), Barrack Road, Exeter, UK
| | - Nicola Jeffery
- Institute of Clinical and Biomedical Sciences, University of Exeter, RILD building, Royal Devon and Exeter Hospital (Wonford), Barrack Road, Exeter, UK
| | - Ben Bunce
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital, Barrack Road, Exeter, UK
| | - Ben P Lee
- Institute of Clinical and Biomedical Sciences, University of Exeter, RILD building, Royal Devon and Exeter Hospital (Wonford), Barrack Road, Exeter, UK
| | - Bridget Knight
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital, Barrack Road, Exeter, UK
| | - Cressida Auckland
- Microbiology Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Jane Ah Masoli
- Institute of Clinical and Biomedical Sciences, University of Exeter, RILD building, Royal Devon and Exeter Hospital (Wonford), Barrack Road, Exeter, UK; Healthcare for Older People, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Lorna W Harries
- Institute of Clinical and Biomedical Sciences, University of Exeter, RILD building, Royal Devon and Exeter Hospital (Wonford), Barrack Road, Exeter, UK.
| |
Collapse
|
10
|
Frankum R, Jameson TSO, Knight BA, Stephens FB, Wall BT, Donlon TA, Torigoe T, Willcox BJ, Willcox DC, Allsopp RC, Harries LW. Correction to: Extreme longevity variants at the FOXO3 locus may moderate FOXO3 isoform levels. GeroScience 2021; 44:1169-1170. [PMID: 34637109 PMCID: PMC9135910 DOI: 10.1007/s11357-021-00465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ryan Frankum
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Tom S O Jameson
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Bridget A Knight
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Francis B Stephens
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Benjamin T Wall
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Timothy A Donlon
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI, 96817, USA.,Departments of Cell & Molecular Biology and Pathology, University of Hawaii, Honolulu, HI, 96813, USA
| | - Trevor Torigoe
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Bradley J Willcox
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96817, USA.,Department of Research, Kuakini Medical Center, Honolulu, HI, 96817, USA
| | - D Craig Willcox
- Department of Research, Kuakini Medical Center, Honolulu, HI, 96817, USA.,Okinawa International University, Okinawa, Japan
| | - Richard C Allsopp
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Lorna W Harries
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
11
|
Frankum R, Jameson TSO, Knight BA, Stephens FB, Wall BT, Donlon TA, Torigoe T, Willcox BJ, Willcox DC, Allsopp RC, Harries LW. Extreme longevity variants at the FOXO3 locus may moderate FOXO3 isoform levels. GeroScience 2021; 44:1129-1140. [PMID: 34436732 PMCID: PMC9135902 DOI: 10.1007/s11357-021-00431-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
The rs2802292, rs2764264 and rs13217795 variants of FOXO3 have been associated with extreme longevity in multiple human populations, but the mechanisms underpinning this remain unclear. We aimed to characterise potential effects of longevity-associated variation on the expression and mRNA processing of the FOXO3 gene. We performed a comprehensive assessment of FOXO3 isoform usage across a wide variety of human tissues and carried out a bioinformatic analysis of the potential for longevity-associated variants to disrupt regulatory regions involved in isoform choice. We then related the expression of full length and 5′ truncated FOXO3 isoforms to rs13217795 genotype in peripheral blood and skeletal muscle from individuals of different rs13217795 genotypes. FOXO3 isoforms displayed considerable tissue specificity. We determined that rs13231195 and its tightly aligned proxy variant rs9400239 may lie in regulatory regions involved in isoform choice. The longevity allele at rs13217795 was associated with increased levels of full length FOXO3 isoforms in peripheral blood and a decrease in truncated FOXO3 isoforms in skeletal muscle RNA. We suggest that the longevity effect of FOXO3 SNPs may in part derive from a shift in isoform usage in skeletal muscle away from the production of 5′ truncated FOXO3 isoforms lacking a complete forkhead DNA binding domain, which may have compromised functionality.
Collapse
Affiliation(s)
- Ryan Frankum
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Tom S O Jameson
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Bridget A Knight
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Francis B Stephens
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Benjamin T Wall
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Timothy A Donlon
- Honolulu Heart Program (HHP)/Honolulu-Asia Aging Study (HAAS), Department of Research, Kuakini Medical Center, Honolulu, HI, 96817, USA.,Departments of Cell & Molecular Biology and Pathology, University of Hawaii, Honolulu, HI, 96813, USA
| | - Trevor Torigoe
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Bradley J Willcox
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96817, USA.,Department of Research, Kuakini Medical Center, Honolulu, HI, 96817, USA
| | - D Craig Willcox
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA.,Okinawa International University, Okinawa, Japan
| | - Richard C Allsopp
- Institute for Biogenesis Research, Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Lorna W Harries
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
12
|
Jeffery N, Chambers D, Invergo BM, Ames RM, Harries LW. Changes to the identity of EndoC-βH1 beta cells may be mediated by stress-induced depletion of HNRNPD. Cell Biosci 2021; 11:144. [PMID: 34301309 PMCID: PMC8305497 DOI: 10.1186/s13578-021-00658-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2021] [Indexed: 12/02/2022] Open
Abstract
Background Beta cell identity changes occur in the islets of donors with diabetes, but the molecular basis of this remains unclear. Protecting residual functional beta cells from cell identity changes may be beneficial for patients with diabetes. Results A somatostatin-positive cell population was induced in stressed clonal human EndoC-βH1 beta cells and was isolated using FACS. A transcriptomic characterisation of somatostatin-positive cells was then carried out. Gain of somatostatin-positivity was associated with marked dysregulation of the non-coding genome. Very few coding genes were differentially expressed. Potential candidate effector genes were assessed by targeted gene knockdown. Targeted knockdown of the HNRNPD gene induced the emergence of a somatostatin-positive cell population in clonal EndoC-βH1 beta cells comparable with that we have previously reported in stressed cells. Conclusions We report here a role for the HNRNPD gene in determination of beta cell identity in response to cellular stress. These findings widen our understanding of the role of RNA binding proteins and RNA biology in determining cell identity and may be important for protecting remaining beta cell reserve in diabetes. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00658-6.
Collapse
Affiliation(s)
- Nicola Jeffery
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | | | | | - Ryan M Ames
- University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
13
|
Deane CS, Willis CRG, Phillips BE, Atherton PJ, Harries LW, Ames RM, Szewczyk NJ, Etheridge T. Transcriptomic meta-analysis of disuse muscle atrophy vs. resistance exercise-induced hypertrophy in young and older humans. J Cachexia Sarcopenia Muscle 2021; 12:629-645. [PMID: 33951310 PMCID: PMC8200445 DOI: 10.1002/jcsm.12706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/26/2021] [Accepted: 03/29/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Skeletal muscle atrophy manifests across numerous diseases; however, the extent of similarities/differences in causal mechanisms between atrophying conditions in unclear. Ageing and disuse represent two of the most prevalent and costly atrophic conditions, with resistance exercise training (RET) being the most effective lifestyle countermeasure. We employed gene-level and network-level meta-analyses to contrast transcriptomic signatures of disuse and RET, plus young and older RET to establish a consensus on the molecular features of, and therapeutic targets against, muscle atrophy in conditions of high socio-economic relevance. METHODS Integrated gene-level and network-level meta-analysis was performed on publicly available microarray data sets generated from young (18-35 years) m. vastus lateralis muscle subjected to disuse (unilateral limb immobilization or bed rest) lasting ≥7 days or RET lasting ≥3 weeks, and resistance-trained older (≥60 years) muscle. RESULTS Disuse and RET displayed predominantly separate transcriptional responses, and transcripts altered across conditions were mostly unidirectional. However, disuse and RET induced directly inverted expression profiles for mitochondrial function and translation regulation genes, with COX4I1, ENDOG, GOT2, MRPL12, and NDUFV2, the central hub components of altered mitochondrial networks, and ZMYND11, a hub gene of altered translation regulation. A substantial number of genes (n = 140) up-regulated post-RET in younger muscle were not similarly up-regulated in older muscle, with young muscle displaying a more pronounced extracellular matrix (ECM) and immune/inflammatory gene expression response. Both young and older muscle exhibited similar RET-induced ubiquitination/RNA processing gene signatures with associated PWP1, PSMB1, and RAF1 hub genes. CONCLUSIONS Despite limited opposing gene profiles, transcriptional signatures of disuse are not simply the converse of RET. Thus, the mechanisms of unloading cannot be derived from studying muscle loading alone and provides a molecular basis for understanding why RET fails to target all transcriptional features of disuse. Loss of RET-induced ECM mechanotransduction and inflammatory profiles might also contribute to suboptimal ageing muscle adaptations to RET. Disuse and age-dependent molecular candidates further establish a framework for understanding and treating disuse/ageing atrophy.
Collapse
Affiliation(s)
- Colleen S Deane
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, St. Luke's Campus, Exeter, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Craig R G Willis
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, St. Luke's Campus, Exeter, UK
| | - Bethan E Phillips
- MRC-ARUK Centre for Musculoskeletal Ageing Research and National Institute of Health Research, Biomedical Research Centre, Division of Medical Sciences and Graduate Entry Medicine, Royal Derby Hospital Centre, School of Medicine, University of Nottingham, Derby, UK
| | - Philip J Atherton
- MRC-ARUK Centre for Musculoskeletal Ageing Research and National Institute of Health Research, Biomedical Research Centre, Division of Medical Sciences and Graduate Entry Medicine, Royal Derby Hospital Centre, School of Medicine, University of Nottingham, Derby, UK
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ryan M Ames
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Nathaniel J Szewczyk
- MRC-ARUK Centre for Musculoskeletal Ageing Research and National Institute of Health Research, Biomedical Research Centre, Division of Medical Sciences and Graduate Entry Medicine, Royal Derby Hospital Centre, School of Medicine, University of Nottingham, Derby, UK.,Ohio Musculoskeletal and Neurological Institute & Department of Biomedical Sciences, Ohio University, Athens, OH, USA
| | - Timothy Etheridge
- Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, St. Luke's Campus, Exeter, UK
| |
Collapse
|
14
|
Kuo CL, Joaquim M, Kuchel GA, Ferrucci L, Harries LW, Pilling LC, Melzer D. The Longevity-Associated SH2B3 (LNK) Genetic Variant: Selected Aging Phenotypes in 379,758 Subjects. J Gerontol A Biol Sci Med Sci 2021; 75:1656-1662. [PMID: 31428775 DOI: 10.1093/gerona/glz191] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
Human SH2B3 is involved in growth factor and inflammation signaling. A SH2B3 missense variant (rs3184504) is associated with cardiovascular diseases plus breast, colorectal, and lung cancers, with highly correlated variants across the ATXN2/SH2B3/BRAP locus linked to parental age at death, suggesting a geroscience common mechanism of aging and disease. To better understand the SH2B3-related aging pathway and its potential as an intervention target, we undertook a phenotype-wide association study (PheWAS) of 52 aging traits. Data were obtained from 379,758 European-descent UK Biobank participants, aged 40-70 at baseline: 27% of participants were CC homozygotes and 23% TT at rs3184504. Parental extreme longevity (mothers aged ≥98 years, fathers aged ≥96 years) was more common in CC versus TT (odds ratio [OR] = 1.18, 95% confidence interval [CI]: 1.07 to 1.29) with an additive per allele effect. The C allele associated with better cognitive function and white blood cell counts were more likely to be normal. The C allele reduced risks of coronary heart disease (OR = 0.95, 95% CI: 0.93 to 0.96) but was also associated with a modestly higher cancer rate (OR = 1.03, 95% CI: 1.02 to 1.04), suggesting a trade-off across aging outcomes and limiting its potential as an anti-aging target.
Collapse
Affiliation(s)
- Chia-Ling Kuo
- Connecticut Convergence Institute for Translation in Regenerative Engineering, University of Connecticut Health, Farmington
| | | | - George A Kuchel
- Center on Aging, University of Connecticut Health School of Medicine, Farmington
| | | | | | - Luke C Pilling
- College of Medicine and Health, University of Exeter, UK.,Center on Aging, University of Connecticut Health School of Medicine, Farmington
| | - David Melzer
- College of Medicine and Health, University of Exeter, UK.,Center on Aging, University of Connecticut Health School of Medicine, Farmington
| |
Collapse
|
15
|
Kuo CL, Joaquim M, Kuchel GA, Ferrucci L, Harries LW, Pilling LC, Melzer D. Corrigendum to: The Longevity-Associated SH2B3 (LNK) Genetic Variant: Selected Aging Phenotypes in 379,758 Subjects. J Gerontol A Biol Sci Med Sci 2020; 75:1686. [PMID: 31783406 PMCID: PMC8177806 DOI: 10.1093/gerona/glz268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
|
16
|
Calimport SRG, Bentley BL, Stewart CE, Pawelec G, Scuteri A, Vinciguerra M, Slack C, Chen D, Harries LW, Marchant G, Fleming GA, Conboy M, Antebi A, Small GW, Gil J, Lakatta EG, Richardson A, Rosen C, Nikolich K, Wyss-Coray T, Steinman L, Montine T, de Magalhães JP, Campisi J, Church G. The inherent challenges of classifying senescence-Response. Science 2020; 368:595-596. [PMID: 32381713 PMCID: PMC10569072 DOI: 10.1126/science.abb4073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
17
|
Haque S, Ames RM, Moore K, Lee BP, Jeffery N, Harries LW. Islet-expressed circular RNAs are associated with type 2 diabetes status in human primary islets and in peripheral blood. BMC Med Genomics 2020; 13:64. [PMID: 32312268 PMCID: PMC7171860 DOI: 10.1186/s12920-020-0713-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 11/23/2019] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Circular RNAs are non-coding RNA molecules with gene regulatory potential that have been associated with several human diseases. They are stable and present in the circulation, making them excellent candidates for biomarkers of disease. Despite their promise as biomarkers or future therapeutic targets, information on their expression and functionality in human pancreatic islets is a relatively unexplored subject. METHODS Here we aimed to produce an enriched circRNAome profile for human pancreatic islets by CircleSeq, and to explore the relationship between circRNA expression, diabetes status, genotype at T2D risk loci and measures of glycaemia (insulin secretory index; SI and HbA1c) in human islet preparations from healthy control donors and donors with type 2 diabetes using ANOVA or linear regression as appropriate. We also assessed the effect of elevated glucose, cytokine and lipid and hypoxia on circRNA expression in the human beta cell line EndoC-βH1. RESULTS We identified over 2600 circRNAs present in human islets. Of the five most abundant circRNAs in human islets, four (circCIRBP, circZKSCAN, circRPH3AL and circCAMSAP1) demonstrated marked associations with diabetes status. CircCIRBP demonstrated an association with insulin secretory index in isolated human islets and circCIRBP and circRPH3AL displayed altered expression with elevated fatty acid in treated EndoC-βH1 cells. CircCAMSAP1 was also noted to be associated with T2D status in human peripheral blood. No associations between circRNA expression and genotype at T2D risk loci were identified in our samples. CONCLUSIONS Our data suggest that circRNAs are abundantly expressed in human islets, and that some are differentially regulated in the islets of donors with type 2 diabetes. Some islet circRNAs are also expressed in peripheral blood and the expression of one, circCAMSAP1, correlates with diabetes status. These findings highlight the potential of circRNAs as biomarkers for T2D.
Collapse
Affiliation(s)
- Shahnaz Haque
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK
| | - Ryan M Ames
- Biosciences, University of Exeter, Exeter, UK
| | - Karen Moore
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Benjamin P Lee
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK
| | - Nicola Jeffery
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
18
|
Lee BP, Smith M, Buffenstein R, Harries LW. Negligible senescence in naked mole rats may be a consequence of well-maintained splicing regulation. GeroScience 2020; 42:633-651. [PMID: 31927681 PMCID: PMC7205774 DOI: 10.1007/s11357-019-00150-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 11/22/2019] [Accepted: 12/27/2019] [Indexed: 02/07/2023] Open
Abstract
Naked mole-rats (NMRs) have amongst the longest lifespans relative to body size of any known, non-volant mammalian species. They also display an enhanced stress resistance phenotype, negligible senescence and very rarely are they burdened with chronic age-related diseases. Alternative splicing (AS) dysregulation is emerging as a potential driver of senescence and ageing. We hypothesised that the expression of splicing factors, important regulators of patterns of AS, may differ in NMRs when compared to other species with relatively shorter lifespans. We designed assays specific to NMR splicing regulatory factors and also to a panel of pre-selected brain-expressed genes known to demonstrate senescence-related alterations in AS in other species, and measured age-related changes in the transcript expression levels of these using embryonic and neonatal developmental stages through to extreme old age in NMR brain samples. We also compared splicing factor expression in both young mouse and NMR spleen and brain samples. Both NMR tissues showed approximately double the expression levels observed in tissues from similarly sized mice. Furthermore, contrary to observations in other species, following a brief period of labile expression in early life stages, adult NMR splicing factors and patterns of AS for functionally relevant brain genes remained remarkably stable for at least two decades. These findings are consistent with a model whereby the conservation of splicing regulation and stable patterns of AS may contribute to better molecular stress responses and the avoidance of senescence in NMRs, contributing to their exceptional lifespan and prolonged healthspan.
Collapse
Affiliation(s)
- B P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - M Smith
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA
| | - R Buffenstein
- Calico Life Sciences LLC, 1170 Veterans Blvd., South San Francisco, CA, 94080, USA.
| | - L W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
19
|
Jeffery N, Richardson S, Chambers D, Morgan NG, Harries LW. Cellular stressors may alter islet hormone cell proportions by moderation of alternative splicing patterns. Hum Mol Genet 2020; 28:2763-2774. [PMID: 31098640 PMCID: PMC6687954 DOI: 10.1093/hmg/ddz094] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 01/12/2023] Open
Abstract
Changes to islet cell identity in response to type 2 diabetes (T2D) have been reported in rodent models, but are less well characterized in humans. We assessed the effects of aspects of the diabetic microenvironment on hormone staining, total gene expression, splicing regulation and the alternative splicing patterns of key genes in EndoC-βH1 human beta cells. Genes encoding islet hormones [somatostatin (SST), insulin (INS), Glucagon (GCG)], differentiation markers [Forkhead box O1 (FOXO1), Paired box 6, SRY box 9, NK6 Homeobox 1, NK6 Homeobox 2] and cell stress markers (DNA damage inducible transcript 3, FOXO1) were dysregulated in stressed EndoC-βH1 cells, as were some serine arginine rich splicing factor splicing activator and heterogeneous ribonucleoprotein particle inhibitor genes. Whole transcriptome analysis of primary T2D islets and matched controls demonstrated dysregulated splicing for ~25% of splicing events, of which genes themselves involved in messenger ribonucleic acid processing and regulation of gene expression comprised the largest group. Approximately 5% of EndoC-βH1 cells exposed to these factors gained SST positivity in vitro. An increased area of SST staining was also observed ex vivo in pancreas sections recovered at autopsy from donors with type 1 diabetes (T1D) or T2D (9.3% for T1D and 3% for T2D, respectively compared with 1% in controls). Removal of the stressful stimulus or treatment with the AKT Serine/Threonine kinase inhibitor SH-6 restored splicing factor expression and reversed both hormone staining effects and patterns of gene expression. This suggests that reversible changes in hormone expression may occur during exposure to diabetomimetic cellular stressors, which may be mediated by changes in splicing regulation.
Collapse
Affiliation(s)
- Nicola Jeffery
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK
| | - Sarah Richardson
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK
| | - David Chambers
- Wolfson Centre for Age-Related Diseases, King's College London, London WC2R 2LS, UK
| | - Noel G Morgan
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK
| |
Collapse
|
20
|
Haque S, Ames RM, Moore K, Pilling LC, Peters LL, Bandinelli S, Ferrucci L, Harries LW. circRNAs expressed in human peripheral blood are associated with human aging phenotypes, cellular senescence and mouse lifespan. GeroScience 2019; 42:183-199. [PMID: 31811527 PMCID: PMC7031184 DOI: 10.1007/s11357-019-00120-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022] Open
Abstract
Circular RNAs (circRNAs) are an emerging class of non-coding RNA molecules that are thought to regulate gene expression and human disease. Despite the observation that circRNAs are known to accumulate in older organisms and have been reported in cellular senescence, their role in aging remains relatively unexplored. Here, we have assessed circRNA expression in aging human blood and followed up age-associated circRNA in relation to human aging phenotypes, mammalian longevity as measured by mouse median strain lifespan and cellular senescence in four different primary human cell types. We found that circRNAs circDEF6, circEP300, circFOXO3 and circFNDC3B demonstrate associations with parental longevity or hand grip strength in 306 subjects from the InCHIANTI study of aging, and furthermore, circFOXO3 and circEP300 also demonstrate differential expression in one or more human senescent cell types. Finally, four circRNAs tested showed evidence of conservation in mouse. Expression levels of one of these, circPlekhm1, was nominally associated with lifespan. These data suggest that circRNA may represent a novel class of regulatory RNA involved in the determination of aging phenotypes, which may show future promise as both biomarkers and future therapeutic targets for age-related disease.
Collapse
Affiliation(s)
- Shahnaz Haque
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK
| | - Ryan M Ames
- Biosciences, University of Exeter, Exeter, UK
| | - Karen Moore
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Luanne L Peters
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging, Bar Harbor, ME, USA
| | | | - Luigi Ferrucci
- National Institute on Aging, Clinical Research Branch, Harbor Hospital, Baltimore, MD, 21225, USA
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
21
|
Jeffery N, Harries LW. Corrigendum to "miRNAs responsive to the diabetic microenvironment in the human beta cell line EndoC βH1 may target genes in the FOXO, HIPPO and Lysine degradation pathways" [Exp. Cell Res. 29 (2019) 111559]. Exp Cell Res 2019; 385:111654. [PMID: 31590970 DOI: 10.1016/j.yexcr.2019.111654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Nicola Jeffery
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, United Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, United Kingdom.
| |
Collapse
|
22
|
Lee BP, Mulvey L, Barr G, Garratt J, Goodman E, Selman C, Harries LW. Dietary restriction in ILSXISS mice is associated with widespread changes in splicing regulatory factor expression levels. Exp Gerontol 2019; 128:110736. [DOI: 10.1016/j.exger.2019.110736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/04/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022]
|
23
|
Abstract
BACKGROUND The serotonergic system is a key component of physiological brain function and is essential for proper neurological activity. Numerous neuropsychiatric disorders are associated with deregulation of the serotonergic system. Accordingly, many pharmacological treatments are focused on modulation of this system. While providing a promising line of therapeutic moderation, these approaches may be complicated due to the presence of alternative splicing events for key genes in this pathway. Alternative splicing is a co-transcriptional process by which different mRNA transcripts can be produced from the same gene. These different isoforms may have diverse activities and functions, and their relative balance is often critical for the maintenance of homeostasis. Alternative splicing greatly increases the production of proteins, augmenting cell plasticity, and provides an important control point for regulation of gene expression. AIM The objective of this narrative review is to discuss the potential impact of alternative splicing of different components of the serotonergic system and speculate on their involvement in several neuropsychiatric disorders. CONCLUSIONS The specific role of each isoform in disease and their relative activities in the signalling pathways involved are yet to be determined. We need to gain a better understanding of the basis of alternative isoforms of the serotonergic system in order to fully understand their impact and be able to develop new effective pharmacological isoform-specific targets.
Collapse
Affiliation(s)
- Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
- Instituto Agroalimentario de Aragón - IA2 (Universidad de Zaragoza - CITA), Zaragoza, Spain
| | - Jose Emilio Mesonero
- Instituto Agroalimentario de Aragón - IA2 (Universidad de Zaragoza - CITA), Zaragoza, Spain
- Departamento Farmacología y Fisiología, Facultad de Veterinaria, Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| |
Collapse
|
24
|
Jeffery N, Harries LW. miRNAs responsive to the diabetic microenvironment in the human beta cell line EndoC-βH1 may target genes in the FOXO, HIPPO and Lysine degradation pathways. Exp Cell Res 2019; 384:111559. [PMID: 31425691 DOI: 10.1016/j.yexcr.2019.111559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/20/2019] [Revised: 07/13/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022]
Abstract
Altered expression of miRNAs is evident in the islets of diabetic human donors, but the effects of specific aspects of the diabetic microenvironment and identity of gene ontology pathways demonstrating target gene enrichment in response to each is understudied. We assessed changes in the miRNA milieu in response to high/low glucose, hypoxia, dyslipidaemia and inflammatory factors in a humanised EndoC-βH1 beta cell culture system and performed miRPath analysis for each treatment individually. The 10 miRNAs demonstrating the greatest dysregulation across treatments were then independently validated and Gene Set Enrichment Analysis to confirm targeted pathways undertaken. 171 of 392 miRNAs displayed altered expression in response to one or more cellular stressors. miRNA changes were treatment specific, but their target genes were enriched in conserved pathways. 5 miRNAs (miR-136-5p, miR299-5p, miR-454-5p, miR-152 and miR-185) were dysregulated in response to multiple stressors and survived validation in independent samples (p = 0.008, 0.002, 0.012, 0.005 and 0.024 respectively). Target genes of dysregulated miRNAs were clustered into FOXO1, HIPPO and Lysine degradation pathways (p = 0.02, p = 5.84 × 10-5 and p = 3.00 × 10-3 respectively). We provide evidence that the diabetic microenvironment may induce changes to the expression of miRNAs targeting genes enriched in pathways involved in cell stress response and cell survival.
Collapse
Affiliation(s)
- Nicola Jeffery
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK.
| |
Collapse
|
25
|
Calimport SRG, Bentley BL, Stewart CE, Pawelec G, Scuteri A, Vinciguerra M, Slack C, Chen D, Harries LW, Marchant G, Fleming GA, Conboy M, Antebi A, Small GW, Gil J, Lakatta EG, Richardson A, Rosen C, Nikolich K, Wyss-Coray T, Steinman L, Montine T, de Magalhães JP, Campisi J, Church G. To help aging populations, classify organismal senescence. Science 2019; 366:576-578. [PMID: 31672885 PMCID: PMC7193988 DOI: 10.1126/science.aay7319] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Comprehensive disease classification and staging is required to address unmet needs of aging populations
Collapse
Affiliation(s)
| | - Barry L Bentley
- The list of author affiliations is available in the supplementary materials
| | - Claire E Stewart
- The list of author affiliations is available in the supplementary materials
| | - Graham Pawelec
- The list of author affiliations is available in the supplementary materials
| | - Angelo Scuteri
- The list of author affiliations is available in the supplementary materials
| | - Manlio Vinciguerra
- The list of author affiliations is available in the supplementary materials
| | - Cathy Slack
- The list of author affiliations is available in the supplementary materials
| | - Danica Chen
- The list of author affiliations is available in the supplementary materials
| | - Lorna W Harries
- The list of author affiliations is available in the supplementary materials
| | - Gary Marchant
- The list of author affiliations is available in the supplementary materials
| | | | - Michael Conboy
- The list of author affiliations is available in the supplementary materials
| | - Adam Antebi
- The list of author affiliations is available in the supplementary materials
| | - Gary W Small
- The list of author affiliations is available in the supplementary materials
| | - Jesus Gil
- The list of author affiliations is available in the supplementary materials
| | - Edward G Lakatta
- The list of author affiliations is available in the supplementary materials
| | - Arlan Richardson
- The list of author affiliations is available in the supplementary materials
| | - Clifford Rosen
- The list of author affiliations is available in the supplementary materials
| | - Karoly Nikolich
- The list of author affiliations is available in the supplementary materials
| | - Tony Wyss-Coray
- The list of author affiliations is available in the supplementary materials
| | - Lawrence Steinman
- The list of author affiliations is available in the supplementary materials
| | - Thomas Montine
- The list of author affiliations is available in the supplementary materials
| | | | - Judith Campisi
- The list of author affiliations is available in the supplementary materials
| | - George Church
- The list of author affiliations is available in the supplementary materials
| |
Collapse
|
26
|
Lye JJ, Latorre E, Lee BP, Bandinelli S, Holley JE, Gutowski NJ, Ferrucci L, Harries LW. Astrocyte senescence may drive alterations in GFAPα, CDKN2A p14 ARF, and TAU3 transcript expression and contribute to cognitive decline. GeroScience 2019; 41:561-573. [PMID: 31654269 PMCID: PMC6885035 DOI: 10.1007/s11357-019-00100-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 07/22/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Abstract
The accumulation of senescent cells in tissues is causally linked to the development of several age-related diseases; the removal of senescent glial cells in animal models prevents Tau accumulation and cognitive decline. Senescent cells can arise through several distinct mechanisms; one such mechanism is dysregulation of alternative splicing. In this study, we characterised the senescent cell phenotype in primary human astrocytes in terms of SA-β-Gal staining and SASP secretion, and then assessed splicing factor expression and candidate gene splicing patterns. Finally, we assessed associations between expression of dysregulated isoforms and premature cognitive decline in 197 samples from the InCHIANTI study of ageing, where expression was present in both blood and brain. We demonstrate here that senescent astrocytes secrete a modified SASP characterised by increased IL8, MMP3, MMP10, and TIMP2 but decreased IL10 levels. We identified significant changes in splicing factor expression for 10/20 splicing factors tested in senescent astrocytes compared with early passage cells, as well as dysregulation of isoform levels for 8/13 brain or senescence genes tested. Finally, associations were identified between peripheral blood GFAPα, TAU3, and CDKN2A (P14ARF) isoform levels and mild or severe cognitive decline over a 3–7-year period. Our data are suggestive that some of the features of cognitive decline may arise from dysregulated splicing of important genes in senescent brain support cells, and that defects in alternative splicing or splicing regulator expression deserve exploration as points of therapeutic intervention in the future.
Collapse
Affiliation(s)
- Jed J Lye
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Ben P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | | | - Janet E Holley
- University of Exeter Medical School & Neurology Department, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, UK
| | - Nicholas J Gutowski
- University of Exeter Medical School & Neurology Department, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, UK
| | - Luigi Ferrucci
- National Institute on Aging, Clinical Research Branch, Harbor Hospital, Baltimore, MD, 21225, USA
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.
| |
Collapse
|
27
|
Abstract
Senescent cells provide a good in vitro model to study ageing. However, cultures of ‘senescent’ cells consist of a mix of cell subtypes (proliferative, senescent, growth-arrested and apoptotic). Determining the proportion of senescent cells is crucial for studying ageing and developing new anti-degenerative therapies. Commonly used markers such as doubling population, senescence-associated β-galactosidase, Ki-67, γH2AX and TUNEL assays capture diverse and overlapping cellular populations and are not purely specific to senescence. A newly developed dynamical systems model follows the transition of an initial culture to senescence tracking population doubling, and the proportion of cells in proliferating, growth-arrested, apoptotic and senescent states. Our model provides a parsimonious description of transitions between these states accruing towards a predominantly senescent population. Using a genetic algorithm, these model parameters are well constrained by an in vitro human primary fibroblast dataset recording five markers at 16 time points. The computational model accurately fits to the data and translates these joint markers into the first complete description of the proportion of cells in different states over the lifetime. The high temporal resolution of the dataset demonstrates the efficacy of strategies for reconstructing the trajectory towards replicative senescence with a minimal number of experimental recordings.
Collapse
Affiliation(s)
- Daniel Galvis
- Living Systems Institute, University of Exeter, Exeter, UK.,Translational Research Exchange at Exeter, University of Exeter, Exeter, UK
| | - Darren Walsh
- Institute of Biomedical and Clinical Science, University of Exeter, Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Science, University of Exeter, Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, UK
| | - Eva Latorre
- Institute of Biomedical and Clinical Science, University of Exeter, Medical School, RILD Building, Barrack Road, Exeter EX2 5DW, UK.,Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain
| | - James Rankin
- Department of Mathematics, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Harrison Building, North Park Road, Exeter EX4 4QF, UK.,EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter EX4 4QJ, UK
| |
Collapse
|
28
|
Lee BP, Pilling LC, Bandinelli S, Ferrucci L, Melzer D, Harries LW. The transcript expression levels of HNRNPM, HNRNPA0 and AKAP17A splicing factors may be predictively associated with ageing phenotypes in human peripheral blood. Biogerontology 2019; 20:649-663. [PMID: 31292793 PMCID: PMC6733819 DOI: 10.1007/s10522-019-09819-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/24/2019] [Indexed: 12/18/2022]
Abstract
Dysregulation of splicing factor expression is emerging as a driver of human ageing; levels of transcripts encoding splicing regulators have previously been implicated in ageing and cellular senescence both in vitro and in vivo. We measured the expression levels of an a priori panel of 20 age- or senescence-associated splicing factors by qRT-PCR in peripheral blood samples from the InCHIANTI Study of Aging, and assessed longitudinal relationships with human ageing phenotypes (cognitive decline and physical ability) using multivariate linear regression. AKAP17A, HNRNPA0 and HNRNPM transcript levels were all predictively associated with severe decline in MMSE score (p = 0.007, 0.001 and 0.008 respectively). Further analyses also found expression of these genes was associated with a performance decline in two other cognitive measures; the Trail Making Test and the Purdue Pegboard Test. AKAP17A was nominally associated with a decline in mean hand-grip strength (p = 0.023), and further analyses found nominal associations with two other physical ability measures; the Epidemiologic Studies of the Elderly-Short Physical Performance Battery and calculated speed (m/s) during a timed 400 m fast walking test. These data add weight to the hypothesis that splicing dyregulation may contribute to the development of some ageing phenotypes in the human population.
Collapse
Affiliation(s)
- Benjamin P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK
| | | | - Luigi Ferrucci
- National Institute on Aging, Clinical Research Branch, Harbor Hospital, Baltimore, MD, 21225, USA
| | - David Melzer
- Epidemiology and Public Health, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter College of Medicine and Health, RILD Building, RD&E NHSFT Campus, Barrack Rd, Exeter, EX2 5DW, UK.
| |
Collapse
|
29
|
Abstract
RNA is the messenger molecule that conveys information from the genome and allows the production of biomolecules required for life in a responsive and regulated way. Most genes are able to produce multiple mRNA products in response to different internal or external environmental signals, in different tissues and organs, and at specific times in development or later life. This fine tuning of gene expression is dependent on the coordinated effects of a large and intricate set of regulatory machinery, which together orchestrate the genomic output at each locus and ensure that each gene is expressed at the right amount, at the right time and in the correct location. This complexity of control, and the requirement for both sequence elements and the entities that bind them, results in multiple points at which errors may occur. Errors of RNA biology are common and found in association with both rare, single gene disorders, but also more common, chronic diseases. Fortunately, complexity also brings opportunity. The existence of many regulatory steps also offers multiple levels of potential therapeutic intervention which can be exploited. In this review, I will outline the specific points at which coding RNAs may be regulated, indicate potential means of intervention at each stage, and outline with examples some of the progress that has been made in this area. Finally, I will outline some of the remaining challenges with the delivery of RNA-based therapeutics but indicate why there are reasons for optimism.
Collapse
Affiliation(s)
- Lorna W. Harries
- RNA-Mediated Mechanisms of Disease, College of Medicine and Health, The Institute of Biomedical and Clinical Science, Medical School, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
30
|
Meerson A, Eliraz Y, Yehuda H, Knight B, Crundwell M, Ferguson D, Lee BP, Harries LW. Obesity impacts the regulation of miR-10b and its targets in primary breast tumors. BMC Cancer 2019; 19:86. [PMID: 30658617 PMCID: PMC6339293 DOI: 10.1186/s12885-019-5300-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/11/2018] [Accepted: 01/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Obesity increases breast cancer (BC) risk in post-menopausal women by mostly unknown molecular mechanisms which may partly be regulated by microRNAs (miRNAs). METHODS We isolated RNA from paired benign and malignant biopsies from 83 BC patients and determined miRNA profiles in samples from 12 women at the extremes of the BMI distribution by RNA-seq. Candidates were validated in all samples. Associations between miR-10b expression and validated target transcript levels, and effects of targeted manipulation of miR-10b levels in a primary BC cell line on proliferation and invasion potential, were explored. RESULTS Of the 148 miRNAs robustly expressed in breast tissues, the levels of miR-21, miR-10b, miR-451a, miR-30c, and miR-378d were significantly associated with presence of cancer. Of these, miR-10b showed a stronger down-regulation in the tumors of the obese subjects, as opposed to the lean. In ductal but not lobular tumors, significant inverse correlations were observed between the tumor levels of miR-10b and miR-30c and the mRNA levels of cancer-relevant target genes SRSF1, PIEZO1, MAPRE1, CDKN2A, TP-53 and TRA2B, as well as tumor grade. Suppression of miR-10b levels in BT-549 primary BC-derived cells increased cell proliferation and invasive capacity, while exogenous miR-10b mimic decreased invasion. Manipulation of miR-10b levels also inversely affected the mRNA levels of miR-10b targets BCL2L11, PIEZO1 and NCOR2. CONCLUSIONS Our findings suggest that miR-10b may be a mediator between obesity and cancer in post-menopausal women, regulating several known cancer-relevant genes. MiR-10b expression may have diagnostic and therapeutic implications for the incidence and prognosis of BC in obese women.
Collapse
Affiliation(s)
- Ari Meerson
- MIGAL - Galilee Research Institute, PO Box 831, 11016 Kiryat Shmona, Israel
- Tel Hai Academic College, Tel Hai, Israel
| | - Yaniv Eliraz
- MIGAL - Galilee Research Institute, PO Box 831, 11016 Kiryat Shmona, Israel
- Tel Hai Academic College, Tel Hai, Israel
| | - Hila Yehuda
- MIGAL - Galilee Research Institute, PO Box 831, 11016 Kiryat Shmona, Israel
- Tel Hai Academic College, Tel Hai, Israel
| | - Bridget Knight
- Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital, Barrack Road, Exeter, UK
| | - Malcolm Crundwell
- Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital, Barrack Road, Exeter, UK
- University of Exeter Medical School, Barrack Road, Exeter, UK
| | - Douglas Ferguson
- Royal Devon and Exeter NHS Foundation Trust, Royal Devon and Exeter Hospital, Barrack Road, Exeter, UK
- University of Exeter Medical School, Barrack Road, Exeter, UK
| | - Benjamin P. Lee
- University of Exeter Medical School, Barrack Road, Exeter, UK
| | | |
Collapse
|
31
|
Abstract
Cellular plasticity is a key facet of cellular homeostasis requiring correct temporal and spatial patterns of alternative splicing. Splicing factors, which orchestrate this process, demonstrate age-related dysregulation of expression; they are emerging as potential influences on aging and longevity. The upstream drivers of these alterations are still unclear but may involve aberrant cellular signaling. We compared the phosphorylation status of proteins in multiple signaling pathways in early and late passage human primary fibroblasts. We then assessed the impact of chemical inhibition or targeted knockdown of direct downstream targets of the ERK and AKT pathways on splicing factor expression, cellular senescence, and proliferation kinetics in senescent primary human fibroblasts. Components of the ERK and AKT signaling pathways demonstrated altered activation during cellular aging. Inhibition of AKT and ERK pathways led to up-regulation of splicing factor expression, reduction in senescent cell load, and partial reversal of multiple cellular senescence phenotypes in a dose-dependent manner. Furthermore, targeted knockdown of the genes encoding the downstream targets FOXO1 or ETV6 was sufficient to mimic these observations. Our results suggest that age-associated dysregulation of splicing factor expression and cellular senescence may derive in part from altered activity of ERK and AKT signaling and may act in part through the ETV6 and FOXO1 transcription factors. Targeting the activity of downstream effectors of ERK and AKT may therefore represent promising targets for future therapeutic intervention.-Latorre, E., Ostler, E. L., Faragher, R. G. A., Harries, L. W. FOXO1 and ETV6 genes may represent novel regulators of splicing factor expression in cellular senescence.
Collapse
Affiliation(s)
- Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon, United Kingdom; and
| | - Elizabeth L Ostler
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Richard G A Faragher
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon, United Kingdom; and
| |
Collapse
|
32
|
Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. eLife 2019; 8:47678. [PMID: 31478829 PMCID: PMC6788855 DOI: 10.7554/elife.47678] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/02/2019] [Indexed: 12/14/2022] Open
Abstract
Prostate is the most frequent cancer in men. Prostate cancer progression is driven by androgen steroid hormones, and delayed by androgen deprivation therapy (ADT). Androgens control transcription by stimulating androgen receptor (AR) activity, yet also control pre-mRNA splicing through less clear mechanisms. Here we find androgens regulate splicing through AR-mediated transcriptional control of the epithelial-specific splicing regulator ESRP2. Both ESRP2 and its close paralog ESRP1 are highly expressed in primary prostate cancer. Androgen stimulation induces splicing switches in many endogenous ESRP2-controlled mRNA isoforms, including splicing switches correlating with disease progression. ESRP2 expression in clinical prostate cancer is repressed by ADT, which may thus inadvertently dampen epithelial splice programmes. Supporting this, treatment with the AR antagonist bicalutamide (Casodex) induced mesenchymal splicing patterns of genes including FLNB and CTNND1. Our data reveals a new mechanism of splicing control in prostate cancer with important implications for disease progression.
Collapse
Affiliation(s)
- Jennifer Munkley
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Ling Li
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - S R Gokul Krishnan
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Gerald Hysenaj
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Emma Scott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Caroline Dalgliesh
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Htoo Zarni Oo
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Teresa Mendes Maia
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal,VIB Center for Medical BiotechnologyVIBGhentBelgium,VIB Proteomics CoreVIBGhentBelgium,Department for Biomolecular MedicineGhent UniversityGhentBelgium
| | - Kathleen Cheung
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Ingrid Ehrmann
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Karen E Livermore
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| | - Hanna Zielinska
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Oliver Thompson
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Bridget Knight
- NIHR Exeter Clinical Research FacilityRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Paul McCullagh
- Department of PathologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - John McGrath
- Exeter Surgical Health Services Research UnitRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Malcolm Crundwell
- Department of UrologyRoyal Devon and Exeter NHS Foundation TrustExeterUnited Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - Mads Daugaard
- Department of Urologic SciencesUniversity of British ColumbiaVancouverCanada,Vancouver Prostate CentreVancouverCanada
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical SciencesNewcastle UniversityNewcastleUnited Kingdom
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de MedicinaUniversidade de LisboaLisboaPortugal
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and HealthUniversity of ExeterExeterUnited Kingdom
| | - David J Elliott
- Institute of Genetic MedicineUniversity of NewcastleNewcastleUnited Kingdom
| |
Collapse
|
33
|
Ferguson DCJ, Smerdon GR, Harries LW, Dodd NJF, Murphy MP, Curnow A, Winyard PG. Altered cellular redox homeostasis and redox responses under standard oxygen cell culture conditions versus physioxia. Free Radic Biol Med 2018; 126:322-333. [PMID: 30142453 DOI: 10.1016/j.freeradbiomed.2018.08.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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] [Received: 07/22/2018] [Accepted: 08/20/2018] [Indexed: 01/16/2023]
Abstract
In vivo, mammalian cells reside in an environment of 0.5-10% O2 (depending on the tissue location within the body), whilst standard in vitro cell culture is carried out under room air. Little is known about the effects of this hyperoxic environment on treatment-induced oxidative stress, relative to a physiological oxygen environment. In the present study we investigated the effects of long-term culture under hyperoxia (air) on photodynamic treatment. Upon photodynamic irradiation, cells which had been cultured long-term under hyperoxia generated higher concentrations of mitochondrial reactive oxygen species, compared with cells in a physioxic (2% O2) environment. However, there was no significant difference in viability between hyperoxic and physioxic cells. The expression of genes encoding key redox homeostasis proteins and the activity of key antioxidant enzymes was significantly higher after the long-term culture of hyperoxic cells compared with physioxic cells. The induction of antioxidant genes and increased antioxidant enzyme activity appear to contribute to the development of a phenotype that is resistant to oxidative stress-induced cellular damage and death when using standard cell culture conditions. The results from experiments using selective inhibitors suggested that the thioredoxin antioxidant system contributes to this phenotype. To avoid artefactual results, in vitro cellular responses should be studied in mammalian cells that have been cultured under physioxia. This investigation provides new insights into the effects of physioxic cell culture on a model of a clinically relevant photodynamic treatment and the associated cellular pathways.
Collapse
Affiliation(s)
| | - Gary R Smerdon
- University of Exeter Medical School, Exeter, Devon EX1 2LU, UK; DDRC Healthcare, Plymouth Science Park, Research Way, Plymouth, Devon PL6 8BU, UK
| | - Lorna W Harries
- University of Exeter Medical School, Exeter, Devon EX1 2LU, UK
| | | | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Alison Curnow
- University of Exeter Medical School, Truro, Cornwall TR1 3HD, UK
| | - Paul G Winyard
- University of Exeter Medical School, Exeter, Devon EX1 2LU, UK.
| |
Collapse
|
34
|
Locke JM, Saint-Martin C, Laver TW, Patel KA, Wood AR, Sharp SA, Ellard S, Bellanné-Chantelot C, Hattersley AT, Harries LW, Weedon MN. The Common HNF1A Variant I27L Is a Modifier of Age at Diabetes Diagnosis in Individuals With HNF1A-MODY. Diabetes 2018; 67:1903-1907. [PMID: 29895593 PMCID: PMC6109380 DOI: 10.2337/db18-0133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Received: 01/29/2018] [Accepted: 06/05/2018] [Indexed: 01/03/2023]
Abstract
There is wide variation in the age at diagnosis of diabetes in individuals with maturity-onset diabetes of the young (MODY) due to a mutation in the HNF1A gene. We hypothesized that common variants at the HNF1A locus (rs1169288 [I27L], rs1800574 [A98V]), which are associated with type 2 diabetes susceptibility, may modify age at diabetes diagnosis in individuals with HNF1A-MODY. Meta-analysis of two independent cohorts, comprising 781 individuals with HNF1A-MODY, found no significant associations between genotype and age at diagnosis. However after stratifying according to type of mutation (protein-truncating variant [PTV] or missense), we found each 27L allele to be associated with a 1.6-year decrease (95% CI -2.6, -0.7) in age at diagnosis, specifically in the subset (n = 444) of individuals with a PTV. The effect size was similar and significant across the two independent cohorts of individuals with HNF1A-MODY. We report a robust genetic modifier of HNF1A-MODY age at diagnosis that further illustrates the strong effect of genetic variation within HNF1A upon diabetes phenotype.
Collapse
Affiliation(s)
- Jonathan M Locke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K.
| | - Cécile Saint-Martin
- Department of Genetics, Pitié-Salpétrière Hospital, Assistance Publique-Hôpitaux de Paris, and Pierre et Marie Curie University, Paris, France
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Seth A Sharp
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Christine Bellanné-Chantelot
- Department of Genetics, Pitié-Salpétrière Hospital, Assistance Publique-Hôpitaux de Paris, and Pierre et Marie Curie University, Paris, France
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Lorna W Harries
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, University of Exeter, Exeter, U.K
| |
Collapse
|
35
|
Atkins JL, Pilling LC, Ble A, Dutta A, Harries LW, Murray A, Brayne C, Robine JM, Kuchel GA, Ferrucci L, Melzer D. Longer-Lived Parents and Cardiovascular Outcomes: 8-Year Follow-Up In 186,000 U.K. Biobank Participants. J Am Coll Cardiol 2018; 68:874-5. [PMID: 27539182 DOI: 10.1016/j.jacc.2016.05.072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/22/2016] [Accepted: 05/24/2016] [Indexed: 11/18/2022]
|
36
|
Galloway TS, Baglin N, Lee BP, Kocur AL, Shepherd MH, Steele AM, Harries LW. An engaged research study to assess the effect of a 'real-world' dietary intervention on urinary bisphenol A (BPA) levels in teenagers. BMJ Open 2018; 8:e018742. [PMID: 29431133 PMCID: PMC5829847 DOI: 10.1136/bmjopen-2017-018742] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Bisphenol A (BPA) has been associated with adverse human health outcomes and exposure to this compound is near-ubiquitous in the Western world. We aimed to examine whether self-moderation of BPA exposure is possible by altering diet in a real-world setting. DESIGN An Engaged Research dietary intervention study designed, implemented and analysed by healthy teenagers from six schools and undertaken in their own homes. PARTICIPANTS A total of 94 students aged between 17 and 19 years from schools in the South West of the UK provided diet diaries and urine samples for analysis. INTERVENTION Researcher participants designed a set of literature-informed guidelines for the reduction of dietary BPA to be followed for 7 days. MAIN OUTCOME MEASURES Creatinine-adjusted urinary BPA levels were taken before and after the intervention. Information on packaging and food/drink ingested was used to calculate a BPA risk score for anticipated exposure. A qualitative analysis was carried out to identify themes addressing long-term sustainability of the diet. RESULTS BPA was detected in urine of 86% of participants at baseline at a median value of 1.22 ng/mL (IQR 1.99). No effect of the intervention diet on BPA levels was identified overall (P=0.25), but there was a positive association in those participants who showed a drop in urinary BPA concentration postintervention and their initial BPA level (P=0.003). Qualitative analysis identified themes around feelings of lifestyle restriction and the inadequacy of current labelling practices. CONCLUSIONS We found no evidence in this self-administered intervention study that it was possible to moderate BPA exposure by diet in a real-world setting. Furthermore, our study participants indicated that they would be unlikely to sustain such a diet long term, due to the difficulty in identifying BPA-free foods.
Collapse
Affiliation(s)
- Tamara S Galloway
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Nigel Baglin
- Research Projects, St Lukes campus, University of Exeter, Exeter, UK
| | - Benjamin P Lee
- RNA-Mediated Disease Mechanisms Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - Anna L Kocur
- RNA-Mediated Disease Mechanisms Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| | - Maggie H Shepherd
- National Institute for Health Research Exeter Clinical Research Facility, Royal Devon and Exeter National Health Service Foundation Trust, Exeter, UK
- Medical School Building 03.11, University of Exeter Medical School, Exeter, UK
| | - Anna M Steele
- National Institute for Health Research Exeter Clinical Research Facility, Royal Devon and Exeter National Health Service Foundation Trust, Exeter, UK
- Medical School Building 03.11, University of Exeter Medical School, Exeter, UK
| | - Lorna W Harries
- RNA-Mediated Disease Mechanisms Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, UK
| |
Collapse
|
37
|
Clissold RL, Harries LW, Ellard S, Bingham C, Hattersley AT. Comment on Dubois-Laforgue et al. Diabetes, Associated Clinical Spectrum, Long-term Prognosis, and Genotype/Phenotype Correlations in 201 Adult Patients With Hepatocyte Nuclear Factor 1B ( HNF1B) Molecular Defects. Diabetes Care 2017;40:1436-1443. Diabetes Care 2018; 41:e7. [PMID: 29263197 DOI: 10.2337/dc17-1672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | - Sian Ellard
- University of Exeter Medical School, Exeter, U.K
| | - Coralie Bingham
- University of Exeter Medical School, Exeter, U.K.,Exeter Kidney Unit, Royal Devon and Exeter National Health Service Foundation Trust, Exeter, U.K
| | | |
Collapse
|
38
|
Pilling LC, Kuo CL, Sicinski K, Tamosauskaite J, Kuchel GA, Harries LW, Herd P, Wallace R, Ferrucci L, Melzer D. Human longevity: 25 genetic loci associated in 389,166 UK biobank participants. Aging (Albany NY) 2017; 9:2504-2520. [PMID: 29227965 PMCID: PMC5764389 DOI: 10.18632/aging.101334] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [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: 09/26/2017] [Accepted: 11/26/2017] [Indexed: 12/22/2022]
Abstract
We undertook a genome-wide association study (GWAS) of parental longevity in European descent UK Biobank participants. For combined mothers' and fathers' attained age, 10 loci were associated (p<5*10-8), including 8 previously identified for traits including survival, Alzheimer's and cardiovascular disease. Of these, 4 were also associated with longest 10% survival (mothers age ≥90 years, fathers ≥87 years), with 2 additional associations including MC2R intronic variants (coding for the adrenocorticotropic hormone receptor). Mother's age at death was associated with 3 additional loci (2 linked to autoimmune conditions), and 8 for fathers only. An attained age genetic risk score associated with parental survival in the US Health and Retirement Study and the Wisconsin Longitudinal Study and with having a centenarian parent (n=1,181) in UK Biobank. The results suggest that human longevity is highly polygenic with prominent roles for loci likely involved in cellular senescence and inflammation, plus lipid metabolism and cardiovascular conditions. There may also be gender specific routes to longevity.
Collapse
Affiliation(s)
- Luke C. Pilling
- Epidemiology and Public Health Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, UK
| | - Chia-Ling Kuo
- Department of Community Medicine and Health Care, Connecticut Institute for Clinical and Translational Science, Institute for Systems Genomics, University of Connecticut Health Center, CT 06269 USA
| | - Kamil Sicinski
- Center for Demography of Health and Aging, University of Wisconsin, Madison, WI 53706, USA
| | - Jone Tamosauskaite
- Epidemiology and Public Health Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, UK
| | - George A. Kuchel
- UConn Center on Aging, University of Connecticut, Farmington, CT 06030, USA
| | - Lorna W. Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, UK
| | - Pamela Herd
- La Follette School of Public Affairs and the Department of Sociology, University of Wisconsin, Madison, WI 53706, USA
| | - Robert Wallace
- College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | | | - David Melzer
- Epidemiology and Public Health Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, UK
- UConn Center on Aging, University of Connecticut, Farmington, CT 06030, USA
| |
Collapse
|
39
|
Haque S, Harries LW. Circular RNAs (circRNAs) in Health and Disease. Genes (Basel) 2017; 8:genes8120353. [PMID: 29182528 PMCID: PMC5748671 DOI: 10.3390/genes8120353] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [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: 10/19/2017] [Revised: 11/22/2017] [Accepted: 11/22/2017] [Indexed: 01/17/2023] Open
Abstract
Splicing events do not always produce a linear transcript. Circular RNAs (circRNAs) are a class of RNA that are emerging as key new members of the gene regulatory milieu, which are produced by back-splicing events within genes. In circRNA formation, rather than being spliced in a linear fashion, exons can be circularised by use of the 3′ acceptor splice site of an upstream exon, leading to the formation of a circular RNA species. circRNAs have been demonstrated across species and have the potential to present genetic information in new orientations distinct from their parent transcript. The importance of these RNA players in gene regulation and normal cellular homeostasis is now beginning to be recognised. They have several potential modes of action, from serving as sponges for micro RNAs and RNA binding proteins, to acting as transcriptional regulators. In accordance with an important role in the normal biology of the cell, perturbations of circRNA expression are now being reported in association with disease. Furthermore, the inherent stability of circRNAs conferred by their circular structure and exonuclease resistance, and their expression in blood and other peripheral tissues in association with endosomes and microvesicles, renders them excellent candidates as disease biomarkers. In this review, we explore the state of knowledge on this exciting class of transcripts in regulating gene expression and discuss their emerging role in health and disease.
Collapse
Affiliation(s)
- Shahnaz Haque
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK.
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW, UK.
| |
Collapse
|
40
|
Jeffery N, Richardson S, Beall C, Harries LW. The species origin of the cellular microenvironment influences markers of beta cell fate and function in EndoC-βH1 cells. Exp Cell Res 2017; 361:284-291. [PMID: 29107069 DOI: 10.1016/j.yexcr.2017.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 09/28/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022]
Abstract
Interaction between islet cell subtypes and the extracellular matrix influences beta-cell function in mammals. The tissue architecture of rodent islets is very different to that of human islets; cell-to-cell communication and interaction with the extracellular matrix may vary between species. In this work, we have compared the responses of the human EndoC-βH1 cell line to non-human and human-derived growth matrices in terms of growth morphology, gene expression and glucose-stimulated insulin secretion (GSIS). EndoC-βH1 cells demonstrated a greater tendency to form cell clusters when cultured in a human microenvironment and exhibited reduced alpha cell markers at the mRNA level; mean expression difference - 0.23 and - 0.51; p = 0.009 and 0.002 for the Aristaless-related homeobox (ARX) and Glucagon (GCG) genes respectively. No differences were noted in the protein expression of mature beta cell markers such as Pdx1 and NeuroD1 were noted in EndoC-βH1 cells grown in a human microenvironment but cells were however more sensitive to glucose (4.3-fold increase in insulin secretion following glucose challenge compared with a 1.9-fold increase in cells grown in a non-human microenvironment; p = 0.0003). Our data suggests that the tissue origin of the cellular microenvironment has effects on the function of EndoC-βH1 cells in vitro, and the use of a more human-like culture microenvironment may bring benefits in terms of increased physiological relevance.
Collapse
Affiliation(s)
- N Jeffery
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon EX2 5DW, UK
| | - S Richardson
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon EX2 5DW, UK
| | - C Beall
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon EX2 5DW, UK
| | - L W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon EX2 5DW, UK.
| |
Collapse
|
41
|
Latorre E, Birar VC, Sheerin AN, Jeynes JCC, Hooper A, Dawe HR, Melzer D, Cox LS, Faragher RGA, Ostler EL, Harries LW. Small molecule modulation of splicing factor expression is associated with rescue from cellular senescence. BMC Cell Biol 2017; 18:31. [PMID: 29041897 PMCID: PMC5645932 DOI: 10.1186/s12860-017-0147-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [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: 07/10/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Altered expression of mRNA splicing factors occurs with ageing in vivo and is thought to be an ageing mechanism. The accumulation of senescent cells also occurs in vivo with advancing age and causes much degenerative age-related pathology. However, the relationship between these two processes is opaque. Accordingly we developed a novel panel of small molecules based on resveratrol, previously suggested to alter mRNA splicing, to determine whether altered splicing factor expression had potential to influence features of replicative senescence. Results Treatment with resveralogues was associated with altered splicing factor expression and rescue of multiple features of senescence. This rescue was independent of cell cycle traverse and also independent of SIRT1, SASP modulation or senolysis. Under growth permissive conditions, cells demonstrating restored splicing factor expression also demonstrated increased telomere length, re-entered cell cycle and resumed proliferation. These phenomena were also influenced by ERK antagonists and agonists. Conclusions This is the first demonstration that moderation of splicing factor levels is associated with reversal of cellular senescence in human primary fibroblasts. Small molecule modulators of such targets may therefore represent promising novel anti-degenerative therapies. Electronic supplementary material The online version of this article (10.1186/s12860-017-0147-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Vishal C Birar
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - Angela N Sheerin
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - J Charles C Jeynes
- Centre for Biomedical Modelling and Analysis, University of Exeter, Exeter, Devon, EX2 5DW, UK
| | - Amy Hooper
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Helen R Dawe
- College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | - David Melzer
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Lynne S Cox
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Richard G A Faragher
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - Elizabeth L Ostler
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK.
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK.
| |
Collapse
|
42
|
Pilling LC, Atkins JL, Duff MO, Beaumont RN, Jones SE, Tyrrell J, Kuo CL, Ruth KS, Tuke MA, Yaghootkar H, Wood AR, Murray A, Weedon MN, Harries LW, Kuchel GA, Ferrucci L, Frayling TM, Melzer D. Red blood cell distribution width: Genetic evidence for aging pathways in 116,666 volunteers. PLoS One 2017; 12:e0185083. [PMID: 28957414 PMCID: PMC5619771 DOI: 10.1371/journal.pone.0185083] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 05/22/2017] [Accepted: 09/06/2017] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Variability in red blood cell volumes (distribution width, RDW) increases with age and is strongly predictive of mortality, incident coronary heart disease and cancer. We investigated inherited genetic variation associated with RDW in 116,666 UK Biobank human volunteers. RESULTS A large proportion RDW is explained by genetic variants (29%), especially in the older group (60+ year olds, 33.8%, <50 year olds, 28.4%). RDW was associated with 194 independent genetic signals; 71 are known for conditions including autoimmune disease, certain cancers, BMI, Alzheimer's disease, longevity, age at menopause, bone density, myositis, Parkinson's disease, and age-related macular degeneration. Exclusion of anemic participants did not affect the overall findings. Pathways analysis showed enrichment for telomere maintenance, ribosomal RNA, and apoptosis. The majority of RDW-associated signals were intronic (119 of 194), including SNP rs6602909 located in an intron of oncogene GAS6, an eQTL in whole blood. CONCLUSIONS Although increased RDW is predictive of cardiovascular outcomes, this was not explained by known CVD or related lipid genetic risks, and a RDW genetic score was not predictive of incident disease. The predictive value of RDW for a range of negative health outcomes may in part be due to variants influencing fundamental pathways of aging.
Collapse
Affiliation(s)
- Luke C. Pilling
- Epidemiology and Public Health Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
- * E-mail:
| | - Janice L. Atkins
- Epidemiology and Public Health Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Michael O. Duff
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Robin N. Beaumont
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Samuel E. Jones
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Jessica Tyrrell
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Chia-Ling Kuo
- Department of Community Medicine and Health Care, Connecticut Institute for Clinical and Translational Science, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Katherine S. Ruth
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Marcus A. Tuke
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Hanieh Yaghootkar
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Andrew R. Wood
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Anna Murray
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Michael N. Weedon
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - Lorna W. Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - George A. Kuchel
- Center on Aging, University of Connecticut, Farmington, CT, United States of America
| | - Luigi Ferrucci
- National Institute on Aging, Baltimore, MD, United States
| | - Timothy M. Frayling
- Genetics of Complex Traits Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
| | - David Melzer
- Epidemiology and Public Health Group, University of Exeter Medical School, RILD Level 3, Royal Devon & Exeter Hospital, Exeter, EX2 5DW, United Kingdom
- Center on Aging, University of Connecticut, Farmington, CT, United States of America
| |
Collapse
|
43
|
Flanagan SE, Dũng VC, Houghton JAL, De Franco E, Ngoc CTB, Damhuis A, Ashcroft FM, Harries LW, Ellard S. An ABCC8 Nonsense Mutation Causing Neonatal Diabetes Through Altered Transcript Expression. J Clin Res Pediatr Endocrinol 2017; 9:260-264. [PMID: 28663158 PMCID: PMC5596808 DOI: 10.4274/jcrpe.4624] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The pancreatic ATP-sensitive K+ (K-ATP) channel is a key regulator of insulin secretion. Gain-of-function mutations in the genes encoding the Kir6.2 (KCNJ11) and SUR1 (ABCC8) subunits of the channel cause neonatal diabetes, whilst loss-of-function mutations in these genes result in congenital hyperinsulinism. We report two patients with neonatal diabetes in whom we unexpectedly identified recessively inherited loss-of-function mutations. The aim of this study was to investigate how a homozygous nonsense mutation in ABCC8 could result in neonatal diabetes. The ABCC8 p.Glu747* was identified in two unrelated Vietnamese patients. This mutation is located within the in-frame exon 17 and RNA studies confirmed (a) the absence of full length SUR1 mRNA and (b) the presence of the alternatively spliced transcript lacking exon 17. Successful transfer of both patients to sulphonylurea treatment suggests that the altered transcript expression enhances the sensitivity of the K-ATP channel to Mg-ADP/ATP. This is the first report of an ABCC8 nonsense mutation causing a gain-of-channel function and these findings extend the spectrum of K-ATP channel mutations observed in patients with neonatal diabetes.
Collapse
Affiliation(s)
- Sarah E. Flanagan
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom
,* Address for Correspondence: University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom E-mail:
| | - Vũ Chí Dũng
- National Children’s Hospital, Department of Endocrinology, Metabolism and Genetics, Hanoi, Vietnam
| | - Jayne A. L. Houghton
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom
| | - Elisa De Franco
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom
| | - Can Thi Bich Ngoc
- National Children’s Hospital, Department of Endocrinology, Metabolism and Genetics, Hanoi, Vietnam
| | - Annet Damhuis
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom
| | - Frances M. Ashcroft
- University of Oxford, Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Lorna W. Harries
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom
| | - Sian Ellard
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Department of Molecular Genetics, Exeter, United Kingdom
| |
Collapse
|
44
|
Munkley J, McClurg UL, Livermore KE, Ehrmann I, Knight B, Mccullagh P, Mcgrath J, Crundwell M, Harries LW, Leung HY, Mills IG, Robson CN, Rajan P, Elliott DJ. The cancer-associated cell migration protein TSPAN1 is under control of androgens and its upregulation increases prostate cancer cell migration. Sci Rep 2017; 7:5249. [PMID: 28701765 PMCID: PMC5507901 DOI: 10.1038/s41598-017-05489-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/30/2017] [Indexed: 02/06/2023] Open
Abstract
Cell migration drives cell invasion and metastatic progression in prostate cancer and is a major cause of mortality and morbidity. However the mechanisms driving cell migration in prostate cancer patients are not fully understood. We previously identified the cancer-associated cell migration protein Tetraspanin 1 (TSPAN1) as a clinically relevant androgen regulated target in prostate cancer. Here we find that TSPAN1 is acutely induced by androgens, and is significantly upregulated in prostate cancer relative to both normal prostate tissue and benign prostate hyperplasia (BPH). We also show for the first time, that TSPAN1 expression in prostate cancer cells controls the expression of key proteins involved in cell migration. Stable upregulation of TSPAN1 in both DU145 and PC3 cells significantly increased cell migration and induced the expression of the mesenchymal markers SLUG and ARF6. Our data suggest TSPAN1 is an androgen-driven contributor to cell survival and motility in prostate cancer.
Collapse
Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK.
| | - Urszula L McClurg
- Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Karen E Livermore
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Ingrid Ehrmann
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Bridget Knight
- NIHR Exeter Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Paul Mccullagh
- Department of Pathology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - John Mcgrath
- Exeter Surgical Health Services Research Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Malcolm Crundwell
- Department of Urology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter, Devon, UK
| | - Hing Y Leung
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospitals, Forskningsparken, Gaustadalléen 21, N-0349, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital HE - Norwegian Radium Hospital, Montebello, Ian G. Mills, NO-0424, Oslo, Norway
- Movember/Prostate Cancer UK Centre of Excellence for Prostate Cancer Research, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Craig N Robson
- Northern Institute for Cancer Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Prabhakar Rajan
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - David J Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| |
Collapse
|
45
|
Chen BH, Hivert MF, Peters MJ, Pilling LC, Hogan JD, Pham LM, Harries LW, Fox CS, Bandinelli S, Dehghan A, Hernandez DG, Hofman A, Hong J, Joehanes R, Johnson AD, Munson PJ, Rybin DV, Singleton AB, Uitterlinden AG, Ying S, Melzer D, Levy D, van Meurs JBJ, Ferrucci L, Florez JC, Dupuis J, Meigs JB, Kolaczyk ED. Peripheral Blood Transcriptomic Signatures of Fasting Glucose and Insulin Concentrations. Diabetes 2016; 65:3794-3804. [PMID: 27625022 PMCID: PMC5127245 DOI: 10.2337/db16-0470] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/04/2016] [Indexed: 01/09/2023]
Abstract
Genome-wide association studies (GWAS) have successfully identified genetic loci associated with glycemic traits. However, characterizing the functional significance of these loci has proven challenging. We sought to gain insights into the regulation of fasting insulin and fasting glucose through the use of gene expression microarray data from peripheral blood samples of participants without diabetes in the Framingham Heart Study (FHS) (n = 5,056), the Rotterdam Study (RS) (n = 723), and the InCHIANTI Study (Invecchiare in Chianti) (n = 595). Using a false discovery rate q <0.05, we identified three transcripts associated with fasting glucose and 433 transcripts associated with fasting insulin levels after adjusting for age, sex, technical covariates, and complete blood cell counts. Among the findings, circulating IGF2BP2 transcript levels were positively associated with fasting insulin in both the FHS and RS. Using 1000 Genomes-imputed genotype data, we identified 47,587 cis-expression quantitative trait loci (eQTL) and 6,695 trans-eQTL associated with the 433 significant insulin-associated transcripts. Of note, we identified a trans-eQTL (rs592423), where the A allele was associated with higher IGF2BP2 levels and with fasting insulin in an independent genetic meta-analysis comprised of 50,823 individuals. We conclude that integration of genomic and transcriptomic data implicate circulating IGF2BP2 mRNA levels associated with glucose and insulin homeostasis.
Collapse
Affiliation(s)
- Brian H Chen
- Longitudinal Studies Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA
- Diabetes Research Center, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
- Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, the Netherlands
| | - Luke C Pilling
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, U.K
| | - John D Hogan
- Program in Bioinformatics, Boston University, Boston, MA
| | - Lisa M Pham
- Program in Bioinformatics, Boston University, Boston, MA
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, U.K
| | - Caroline S Fox
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Stefania Bandinelli
- Geriatric Rehabilitation Unit, Azienda Sanitaria di Firenze, Florence, Italy
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dena G Hernandez
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jaeyoung Hong
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Roby Joehanes
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
- Hebrew SeniorLife, Harvard Medical School, Boston, MA
| | - Andrew D Johnson
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Peter J Munson
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD
| | - Denis V Rybin
- Data Coordinating Center, Boston University, Boston, MA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
- Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Saixia Ying
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, MD
| | | | - David Melzer
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, U.K
| | - Daniel Levy
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam, Rotterdam, the Netherlands
- Netherlands Genomics Initiative-sponsored Netherlands Consortium for Healthy Aging, Leiden and Rotterdam, the Netherlands
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - Jose C Florez
- Diabetes Research Center, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA
- Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Josée Dupuis
- Framingham Heart Study, National Heart, Lung, and Blood Institute, Framingham, MA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - James B Meigs
- Metabolism Program and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Eric D Kolaczyk
- Program in Bioinformatics, Boston University, Boston, MA
- Department of Mathematics and Statistics, Boston University, MA
| |
Collapse
|
46
|
Abstract
Type 2 diabetes (T2D) affects 415 million people worldwide and is characterized by chronic hyperglycaemia and insulin resistance, progressing to insufficient insulin production, as a result of β-cell failure. Over time, chronic hyperglycaemia can ultimately lead to loss of β-cell function, leaving patients insulin-dependent. Until recently the loss of β-cell mass seen in T2D was considered to be the result of increased rates of apoptosis; however, it has been proposed that apoptosis alone cannot account for the extent of β-cell mass loss seen in the disease, and that a loss of function may also occur as a result of changes in β-cell differentiation status. In the present review, we consider current knowledge of determinants of β-cell fate in the context of understanding its relevance to disease process in T2D, and also the impact of a diabetogenic environment (hyperglycaemia, hypoxia, inflammation and dyslipidaemia) on the expression of genes involved in maintenance of β-cell identity. We describe current knowledge of the impact of the diabetic microenvironment on gene regulatory processes such alternative splicing, the expression of disallowed genes and epigenetic modifications. Elucidating the molecular mechanisms that underpin changes to β-cell differentiation status and the concomitant β-cell failure offers potential treatment targets for the future management of patients with T2D.
Collapse
Affiliation(s)
- Nicola Jeffery
- Department of Molecular Genetics, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Lorna W Harries
- Department of Molecular Genetics, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon, UK
| |
Collapse
|
47
|
Lee BP, Pilling LC, Emond F, Flurkey K, Harrison DE, Yuan R, Peters LL, Kuchel GA, Ferrucci L, Melzer D, Harries LW. Changes in the expression of splicing factor transcripts and variations in alternative splicing are associated with lifespan in mice and humans. Aging Cell 2016; 15:903-13. [PMID: 27363602 PMCID: PMC5013025 DOI: 10.1111/acel.12499] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2016] [Indexed: 12/31/2022] Open
Abstract
Dysregulation of splicing factor expression and altered alternative splicing are associated with aging in humans and other species, and also with replicative senescence in cultured cells. Here, we assess whether expression changes of key splicing regulator genes and consequent effects on alternative splicing are also associated with strain longevity in old and young mice, across 6 different mouse strains with varying lifespan (A/J, NOD.B10Sn-H2(b) /J, PWD.Phj, 129S1/SvlmJ, C57BL/6J and WSB/EiJ). Splicing factor expression and changes to alternative splicing were associated with strain lifespan in spleen and to a lesser extent in muscle. These changes mainly involved hnRNP splicing inhibitor transcripts with most changes more marked in spleens of young animals from long-lived strains. Changes in spleen isoform expression were suggestive of reduced cellular senescence and retained cellular proliferative capacity in long-lived strains. Changes in muscle isoform expression were consistent with reduced pro-inflammatory signalling in longer-lived strains. Two splicing regulators, HNRNPA1 and HNRNPA2B1, were also associated with parental longevity in humans, in the InCHIANTI aging study. Splicing factors may represent a driver, mediator or early marker of lifespan in mouse, as expression differences were present in the young animals of long-lived strains. Changes to alternative splicing patterns of key senescence genes in spleen and key remodelling genes in muscle suggest that correct regulation of alternative splicing may enhance lifespan in mice. Expression of some splicing factors in humans was also associated with parental longevity, suggesting that splicing regulation may also influence lifespan in humans.
Collapse
Affiliation(s)
| | - Luke C. Pilling
- Epidemiology and Public Health; Institute of Biomedical and Clinical Sciences; University of Exeter Medical School; University of Exeter; Devon UK
| | | | - Kevin Flurkey
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - David E. Harrison
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - Rong Yuan
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - Luanne L. Peters
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging; Bar Harbor ME USA
| | - George A. Kuchel
- UConn Centre on Aging; University of Connecticut Health Centre; Farmington CT USA
| | | | - David Melzer
- Epidemiology and Public Health; Institute of Biomedical and Clinical Sciences; University of Exeter Medical School; University of Exeter; Devon UK
- UConn Centre on Aging; University of Connecticut Health Centre; Farmington CT USA
| | | |
Collapse
|
48
|
Atkins JL, Pilling LC, Ble A, Dutta A, Harries LW, Murray A, Brayne C, Robine JM, Kuchel GA, Ferrucci L, Melzer D. OP82 Long-lived parents and cardiovascular outcomes: 8 year follow-up in 189,000 UK Biobank participants. Br J Soc Med 2016. [DOI: 10.1136/jech-2016-208064.82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
49
|
Kamenska A, Simpson C, Vindry C, Broomhead H, Bénard M, Ernoult-Lange M, Lee BP, Harries LW, Weil D, Standart N. The DDX6-4E-T interaction mediates translational repression and P-body assembly. Nucleic Acids Res 2016; 44:6318-34. [PMID: 27342281 PMCID: PMC5291280 DOI: 10.1093/nar/gkw565] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/14/2016] [Indexed: 12/13/2022] Open
Abstract
4E-Transporter binds eIF4E via its consensus sequence YXXXXLΦ, shared with eIF4G, and is a nucleocytoplasmic shuttling protein found enriched in P-(rocessing) bodies. 4E-T inhibits general protein synthesis by reducing available eIF4E levels. Recently, we showed that 4E-T bound to mRNA however represses its translation in an eIF4E-independent manner, and contributes to silencing of mRNAs targeted by miRNAs. Here, we address further the mechanism of translational repression by 4E-T by first identifying and delineating the interacting sites of its major partners by mass spectrometry and western blotting, including DDX6, UNR, unrip, PAT1B, LSM14A and CNOT4. Furthermore, we document novel binding between 4E-T partners including UNR-CNOT4 and unrip-LSM14A, altogether suggesting 4E-T nucleates a complex network of RNA-binding protein interactions. In functional assays, we demonstrate that joint deletion of two short conserved motifs that bind UNR and DDX6 relieves repression of 4E-T-bound mRNA, in part reliant on the 4E-T-DDX6-CNOT1 axis. We also show that the DDX6-4E-T interaction mediates miRNA-dependent translational repression and de novo P-body assembly, implying that translational repression and formation of new P-bodies are coupled processes. Altogether these findings considerably extend our understanding of the role of 4E-T in gene regulation, important in development and neurogenesis.
Collapse
Affiliation(s)
- Anastasiia Kamenska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Clare Simpson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Caroline Vindry
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Helen Broomhead
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| | - Marianne Bénard
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Michèle Ernoult-Lange
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Benjamin P Lee
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Barrack Road, Exeter EX2 5DW
| | - Dominique Weil
- Sorbonne Universités, UPMC, CNRS, IBPS, Developmental Biology Laboratory, 75005 Paris, France
| | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB21QW, UK
| |
Collapse
|
50
|
Lee BP, Lloyd-Laney HO, Locke JM, McCulloch LJ, Knight B, Yaghootkar H, Cory G, Kos K, Frayling TM, Harries LW. Functional characterisation of ADIPOQ variants using individuals recruited by genotype. Mol Cell Endocrinol 2016; 428:49-57. [PMID: 26996131 DOI: 10.1016/j.mce.2016.03.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 01/20/2016] [Revised: 02/18/2016] [Accepted: 03/15/2016] [Indexed: 12/30/2022]
Abstract
Four non-coding GWAS variants in or near the ADIPOQ gene (rs17300539, rs17366653, rs3821799 and rs56354395) together explain 4% of the variation in circulating adiponectin. The functional basis for this is unknown. We tested the effect of these variants on ADIPOQ transcription, splicing and stability respectively in adipose tissue samples from participants recruited by rs17366653 genotype. Transcripts carrying rs17300539 demonstrated a 17% increase in expression (p = 0.001). Variant rs17366653 was associated with disruption of ADIPOQ splicing leading to a 7 fold increase in levels of a non-functional transcript (p = 0.002). Transcripts carrying rs56354395 demonstrated a 59% decrease in expression (p = <0.0001). No effects of rs3821799 genotype on expression was observed. Association between variation in the ADIPOQ gene and serum adiponectin may arise from effects on mRNA transcription, splicing or stability. These studies illustrate the utility of recruit-by-genotype studies in relevant human tissues in functional interpretation of GWAS signals.
Collapse
Affiliation(s)
- Benjamin P Lee
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Henry O Lloyd-Laney
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Jonathan M Locke
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Laura J McCulloch
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Bridget Knight
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Hanieh Yaghootkar
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Giles Cory
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Katarina Kos
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK
| | - Lorna W Harries
- Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.
| |
Collapse
|