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Archer SN, Möller-Levet C, Bonmatí-Carrión MÁ, Laing EE, Dijk DJ. Extensive dynamic changes in the human transcriptome and its circadian organization during prolonged bed rest. iScience 2024; 27:109331. [PMID: 38487016 PMCID: PMC10937834 DOI: 10.1016/j.isci.2024.109331] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/11/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
Physiological and molecular processes including the transcriptome change across the 24-h day, driven by molecular circadian clocks and behavioral and systemic factors. It is not known how the temporal organization of the human transcriptome responds to a long-lasting challenge. This may, however, provide insights into adaptation, disease, and recovery. We investigated the human 24-h time series transcriptome in 20 individuals during a 90-day constant bed rest protocol. We show that the protocol affected 91% of the transcriptome with 76% of the transcriptome still affected after 10 days of recovery. Dimensionality-reduction approaches revealed that many affected transcripts were associated with mRNA translation and immune function. The number, amplitude, and phase of rhythmic transcripts, including clock genes, varied significantly across the challenge. These findings of long-lasting changes in the temporal organization of the transcriptome have implications for understanding the mechanisms underlying health consequences of conditions such as microgravity and bed rest.
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Affiliation(s)
- Simon N. Archer
- Surrey Sleep Research Centre, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Carla Möller-Levet
- Bioinformatics Core Facility, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - María-Ángeles Bonmatí-Carrión
- Surrey Sleep Research Centre, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
- Chronobiology Laboratory, Department of Physiology, University of Murcia, Murcia, Spain
- Ciber Fragilidad y Envejecimiento Saludable, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Emma E. Laing
- Department of Microbiology, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Derk-Jan Dijk
- Surrey Sleep Research Centre, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
- UK Dementia Research Institute Care Research & Technology Centre, Imperial College London & University of Surrey, Guildford, UK
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Winsky-Sommerer R, King HA, Iadevaia V, Möller-Levet C, Gerber AP. A post-transcriptional regulatory landscape of aging in the female mouse hippocampus. Front Aging Neurosci 2023; 15:1119873. [PMID: 37122377 PMCID: PMC10135431 DOI: 10.3389/fnagi.2023.1119873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/27/2023] [Indexed: 05/02/2023] Open
Abstract
Aging is associated with substantial physiological changes and constitutes a major risk factor for neurological disorders including dementia. Alterations in gene expression upon aging have been extensively studied; however, an in-depth characterization of post-transcriptional regulatory events remains elusive. Here, we profiled the age-related changes of the transcriptome and translatome in the female mouse hippocampus by RNA sequencing of total RNA and polysome preparations at four ages (3-, 6-, 12-, 20-month-old); and we implemented a variety of bioinformatics approaches to unravel alterations in transcript abundance, alternative splicing, and polyadenylation site selection. We observed mostly well-coordinated transcriptome and translatome expression signatures across age including upregulation of transcripts related to immune system processes and neuroinflammation, though transcripts encoding ribonucleoproteins or associated with mitochondrial functions, calcium signaling and the cell-cycle displayed substantial discordant profiles, suggesting translational control associated with age-related deficits in hippocampal-dependent behavior. By contrast, alternative splicing was less preserved, increased with age and was associated with distinct functionally-related transcripts encoding proteins acting at synapses/dendrites, RNA-binding proteins; thereby predicting regulatory roles for RBM3 and CIRBP. Only minor changes in polyadenylation site selection were identified, indicating pivotal 3'-end selection in young adults compared to older groups. Overall, our study provides a comprehensive resource of age-associated post-transcriptional regulatory events in the mouse hippocampus, enabling further examination of the molecular features underlying age-associated neurological diseases.
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Arunachalam E, Rogers W, Simpson GR, Möller-Levet C, Bolton G, Ismael M, Smith C, Keegen K, Bagwan I, Brend T, Short SC, Hong B, Otani Y, Kaur B, Annels N, Morgan R, Pandha H. HOX and PBX gene dysregulation as a therapeutic target in glioblastoma multiforme. BMC Cancer 2022; 22:400. [PMID: 35418059 PMCID: PMC9006463 DOI: 10.1186/s12885-022-09466-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/21/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is the most common high-grade malignant brain tumour in adults and arises from the glial cells in the brain. The prognosis of treated GBM remains very poor with 5-year survival rates of 5%, a figure which has not improved over the last few decades. Currently, there is a modest 14-month overall median survival in patients undergoing maximum safe resection plus adjuvant chemoradiotherapy. HOX gene dysregulation is now a widely recognised feature of many malignancies. METHODS In this study we have focused on HOX gene dysregulation in GBM as a potential therapeutic target in a disease with high unmet need. RESULTS We show significant dysregulation of these developmentally crucial genes and specifically that HOX genes A9, A10, C4 and D9 are strong candidates for biomarkers and treatment targets for GBM and GBM cancer stem cells. We evaluated a next generation therapeutic peptide, HTL-001, capable of targeting HOX gene over-expression in GBM by disrupting the interaction between HOX proteins and their co-factor, PBX. HTL-001 induced both caspase-dependent and -independent apoptosis in GBM cell lines. CONCLUSION In vivo biodistribution studies confirmed that the peptide was able to cross the blood brain barrier. Systemic delivery of HTL-001 resulted in improved control of subcutaneous murine and human xenograft tumours and improved survival in a murine orthotopic model.
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Affiliation(s)
- Einthavy Arunachalam
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
| | - William Rogers
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
| | - Guy R Simpson
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
| | - Carla Möller-Levet
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
| | - Gemma Bolton
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
- Surrey Technology Centre, HOX Therapeutics Ltd, Unit 2440 Occam Rd, Guildford, GU2 7YG, UK
| | - Mohammed Ismael
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
- Surrey Technology Centre, HOX Therapeutics Ltd, Unit 2440 Occam Rd, Guildford, GU2 7YG, UK
| | - Christopher Smith
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
| | - Karl Keegen
- Surrey Technology Centre, HOX Therapeutics Ltd, Unit 2440 Occam Rd, Guildford, GU2 7YG, UK
| | - Izhar Bagwan
- Department of Pathology, Royal Surrey County Hospital, Egerton Road, Guildford, GU2 7XX, Surrey, UK
| | - Tim Brend
- Faculty of Medicine and Health, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, LS9 7TF, UK
| | - Susan C Short
- Faculty of Medicine and Health, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, LS9 7TF, UK
| | - Bangxing Hong
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Centre at Houston, 7000 Fannin Street, Houston, TX, 77030, USA
| | - Yoshihiro Otani
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Centre at Houston, 7000 Fannin Street, Houston, TX, 77030, USA
| | - Balveen Kaur
- Department of Neurosurgery, McGovern Medical School, University of Texas Health Science Centre at Houston, 7000 Fannin Street, Houston, TX, 77030, USA
| | - Nicola Annels
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK
| | - Richard Morgan
- School of Biomedical Sciences, University of West London, St Mary's Road, Ealing, London, W5 5RF, UK
| | - Hardev Pandha
- Targeted Cancer Therapy, Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7WG, UK.
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Durrant LR, Bucca G, Hesketh A, Möller-Levet C, Tripkovic L, Wu H, Hart KH, Mathers JC, Elliott RM, Lanham-New SA, Smith CP. Vitamins D 2 and D 3 Have Overlapping But Different Effects on the Human Immune System Revealed Through Analysis of the Blood Transcriptome. Front Immunol 2022; 13:790444. [PMID: 35281034 PMCID: PMC8908317 DOI: 10.3389/fimmu.2022.790444] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
Vitamin D is best known for its role in maintaining bone health and calcium homeostasis. However, it also exerts a broad range of extra-skeletal effects on cellular physiology and on the immune system. Vitamins D2 and D3 share a high degree of structural similarity. Functional equivalence in their vitamin D-dependent effects on human physiology is usually assumed but has in fact not been well defined experimentally. In this study we seek to redress the gap in knowledge by undertaking an in-depth examination of changes in the human blood transcriptome following supplementation with physiological doses of vitamin D2 and D3. Our work extends a previously published randomized placebo-controlled trial that recruited healthy white European and South Asian women who were given 15 µg of vitamin D2 or D3 daily over 12 weeks in wintertime in the UK (Nov-Mar) by additionally determining changes in the blood transcriptome over the intervention period using microarrays. An integrated comparison of the results defines both the effect of vitamin D3 or D2 on gene expression, and any influence of ethnic background. An important aspect of this analysis was the focus on the changes in expression from baseline to the 12-week endpoint of treatment within each individual, harnessing the longitudinal design of the study. Whilst overlap in the repertoire of differentially expressed genes was present in the D2 or D3-dependent effects identified, most changes were specific to either one vitamin or the other. The data also pointed to the possibility of ethnic differences in the responses. Notably, following vitamin D3 supplementation, the majority of changes in gene expression reflected a down-regulation in the activity of genes, many encoding pathways of the innate and adaptive immune systems, potentially shifting the immune system to a more tolerogenic status. Surprisingly, gene expression associated with type I and type II interferon activity, critical to the innate response to bacterial and viral infections, differed following supplementation with either vitamin D2 or vitamin D3, with only vitamin D3 having a stimulatory effect. This study suggests that further investigation of the respective physiological roles of vitamin D2 and vitamin D3 is warranted.
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Affiliation(s)
- Louise R Durrant
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Giselda Bucca
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Andrew Hesketh
- School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Carla Möller-Levet
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Laura Tripkovic
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Huihai Wu
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Kathryn H Hart
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - John C Mathers
- Human Nutrition Research Centre, Population Health Sciences Institute, Newcastle University, Newcastle, United Kingdom
| | - Ruan M Elliott
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Susan A Lanham-New
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Colin P Smith
- Department of Nutritional Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,School of Applied Sciences, University of Brighton, Brighton, United Kingdom
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Bucca G, Pothi R, Hesketh A, Möller-Levet C, Hodgson DA, Laing EE, Stewart GR, Smith CP. Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor. Nucleic Acids Res 2019; 46:5692-5703. [PMID: 29746664 PMCID: PMC6009599 DOI: 10.1093/nar/gky335] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 12/08/2017] [Accepted: 04/18/2018] [Indexed: 12/29/2022] Open
Abstract
Stress-induced adaptations require multiple levels of regulation in all organisms to repair cellular damage. In the present study we evaluated the genome-wide transcriptional and translational changes following heat stress exposure in the soil-dwelling model actinomycete bacterium, Streptomyces coelicolor. The combined analysis revealed an unprecedented level of translational control of gene expression, deduced through polysome profiling, in addition to transcriptional changes. Our data show little correlation between the transcriptome and ‘translatome’; while an obvious downward trend in genome wide transcription was observed, polysome associated transcripts following heat-shock showed an opposite upward trend. A handful of key protein players, including the major molecular chaperones and proteases were highly induced at both the transcriptional and translational level following heat-shock, a phenomenon known as ‘potentiation’. Many other transcripts encoding cold-shock proteins, ABC-transporter systems, multiple transcription factors were more highly polysome-associated following heat stress; interestingly, these protein families were not induced at the transcriptional level and therefore were not previously identified as part of the stress response. Thus, stress coping mechanisms at the level of gene expression in this bacterium go well beyond the induction of a relatively small number of molecular chaperones and proteases in order to ensure cellular survival at non-physiological temperatures.
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Affiliation(s)
- Giselda Bucca
- School of Pharmacy and Biomolecular Sciences, University of Brighton, UK
| | - Radhika Pothi
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, UK
| | - Andrew Hesketh
- School of Pharmacy and Biomolecular Sciences, University of Brighton, UK
| | - Carla Möller-Levet
- Bioinformatics facility, Faculty of Health and Medical Sciences, University of Surrey, UK
| | | | - Emma E Laing
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, UK
| | - Graham R Stewart
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, UK
| | - Colin P Smith
- School of Pharmacy and Biomolecular Sciences, University of Brighton, UK
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Betts GNJ, Eustace A, Patiar S, Valentine HR, Irlam J, Ramachandran A, Merve A, Homer JJ, Möller-Levet C, Buffa FM, Hall G, Miller CJ, Harris AL, West CML. Prospective technical validation and assessment of intra-tumour heterogeneity of a low density array hypoxia gene profile in head and neck squamous cell carcinoma. Eur J Cancer 2013; 49:156-65. [PMID: 22951015 DOI: 10.1016/j.ejca.2012.07.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [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] [Received: 05/21/2012] [Revised: 07/24/2012] [Accepted: 07/30/2012] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND PURPOSE Tumour hypoxia is associated with a poor prognosis in head and neck squamous cell carcinoma (HNSCC), however there is no accepted method for assessing hypoxia clinically. We aimed to conduct a technical validation of a hypoxia gene expression signature using the TaqMan Low Density Array (TLDA) platform to investigate if this approach reliably identified hypoxic tumours. MATERIALS AND METHODS Tumour samples (n=201) from 80 HNSCC patients were collected prospectively from two centres. Fifty-three patients received pimonidazole prior to surgery. TaqMan Low Density Array-Hypoxia Scores (TLDA-HS) were obtained by quantitative real-time PCR (qPCR) using a 25-gene signature and customised TLDA cards. Assay performance was assessed as coefficient of variation (CoV). RESULTS The assay was sensitive with linear reaction efficiencies across a 4 log(10) range of inputted cDNA (0.001-10 ng/μl). Intra- (CoV=6.9%) and inter- (CoV=2.0%) assay reproducibility were excellent. Intra-tumour heterogeneity was lower for TLDA-HS (23.2%) than for pimonidazole (67.2%) or single gene measurements of CA9 (62.2%), VEGFA (45.0%) or HIG2 (39.4%). TLDA-HS in HNSCC cell lines increased with decreasing pO(2). TLDA-HS correlated with Affymetrix U133 Plus 2.0 microarray HS (p<0.01) and positive pimonidazole scores (p=0.005). CONCLUSIONS Gene expression measurements of hypoxia using a 25-gene signature and TLDA cards are sensitive, reproducible and associated with lower intra-tumour heterogeneity than assaying individual genes or pimonidazole binding. The approach is suitable for further assessment of prognostic and predictive capability in clinical trial material.
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Affiliation(s)
- Guy N J Betts
- Translational Radiobiology Group, Institute of Cancer Sciences, Manchester Academic Health Science Centre, Christie Hospital, Wilmslow Road, Manchester M20 4BX, United Kingdom
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Hall JS, Leong HS, Armenoult LSC, Newton GE, Valentine HR, Irlam JJ, Möller-Levet C, Sikand KA, Pepper SD, Miller CJ, West CML. Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples. Br J Cancer 2011; 104:971-81. [PMID: 21407225 PMCID: PMC3065290 DOI: 10.1038/bjc.2011.66] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [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] [Indexed: 12/25/2022] Open
Abstract
Background: Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples. Methods: Nineteen cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples (10–16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen non-small cell lung cancer (NSCLC) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT–PCR. Results: In all, 1062 genes were higher in SCC vs AC, and 155 genes higher in AC. The 1217-gene signature correctly separated 58 NSCLC into SCC and AC. A gene network centered on hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as SCC or AC. Conclusion: FFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.
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Affiliation(s)
- J S Hall
- Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
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Abstract
Despite its enormous promise to further our understanding of cellular processes involved in the regulation of gene expression, microarray technology generates data
for which statistical pre-processing has become a necessity before any interpretation
of data can begin. The process by which we distinguish (and remove) non-biological
variation from biological variation is called normalization. With a multitude of
experimental designs, techniques and technologies influencing the acquisition of data,
numerous approaches to normalization have been proposed in the literature. The
purpose of this short review is not to add to the many suggestions that have been
made, but to discuss some of the difficulties we encounter when analysing microarray
data.
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Affiliation(s)
- Olaf Wolkenhauer
- Department of Biomolecular Sciences, Control Systems Centre, UMIST, Manchester M60 1QD, UK.
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