ORCID Profile
0000-0003-2035-8475
Current Organisation
King's College London
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Publisher: The Royal Society
Date: 06-2021
DOI: 10.1098/RSOB.200388
Abstract: Three-dimensional (3D) cell culture models that provide a biologically relevant microenvironment are imperative to investigate cell–cell and cell–matrix interactions in vitro . Semi-synthetic star-shaped poly(ethylene glycol) (starPEG)–heparin hydrogels are widely used for 3D cell culture due to their highly tuneable biochemical and biomechanical properties. Changes in gene expression levels are commonly used as a measure of cellular responses. However, the isolation of high-quality RNA presents a challenge as contamination of the RNA with hydrogel residue, such as polymer or glycosaminoglycan fragments, can impact template quality and quantity, limiting effective gene expression analyses. Here, we compare two protocols for the extraction of high-quality RNA from starPEG–heparin hydrogels and assess three subsequent purification techniques. Removal of hydrogel residue by centrifugation was found to be essential for obtaining high-quality RNA in both isolation methods. However, purification of the RNA did not result in further improvements in RNA quality. Furthermore, we show the suitability of the extracted RNA for cDNA synthesis of three endogenous control genes confirmed via quantitative polymerase chain reaction (qPCR). The methods and techniques shown can be tailored for other hydrogel models based on natural or semi-synthetic materials to provide robust templates for all gene expression analyses.
Publisher: Cold Spring Harbor Laboratory
Date: 29-12-2022
DOI: 10.1101/2022.12.27.522062
Abstract: Exercise training prevents age-related decline in muscle function. Targeting epigenetic aging is a promising actionable mechanism and late-life exercise mitigates epigenetic aging in rodent muscle. Whether exercise training can decelerate, or reverse epigenetic aging in humans is unknown. Here, we performed a powerful meta-analysis of the methylome and transcriptome of an unprecedented number of human skeletal muscle s les (n = 3,176). We show that: 1) in iduals with higher baseline aerobic fitness have younger epigenetic and transcriptomic profiles, 2) exercise training leads to significant shifts of epigenetic and transcriptomic patterns towards a younger profile, and 3) muscle disuse “ages” the transcriptome. Higher fitness levels were associated with attenuated differential methylation and transcription during aging. Furthermore, both epigenetic and transcriptomic profiles shifted towards a younger state after exercise training interventions, while the transcriptome shifted towards an older state after forced muscle disuse. We demonstrate that exercise training targets many of the age-related transcripts and DNA methylation loci to maintain younger methylome and transcriptome profiles, specifically in genes related to muscle structure, metabolism and mitochondrial function. Our comprehensive analysis will inform future studies aiming to identify the best combination of therapeutics and exercise regimes to optimize longevity.
Publisher: Wiley
Date: 17-02-2020
DOI: 10.1002/JCSM.12556
Publisher: Public Library of Science (PLoS)
Date: 15-11-2019
Publisher: Springer Science and Business Media LLC
Date: 14-06-2022
DOI: 10.1007/S12035-022-02914-3
Abstract: Monogenic forms of cerebral small vessel disease (CSVD) can be caused by both variants in nuclear DNA and mitochondrial DNA (mtDNA). Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) is known to have a phenotype similar to Cerebral Autosomal Dominant Arteriopathy with Sub-cortical Infarcts and Leukoencephalopathy (CADASIL), and can be caused by variants in the mitochondrial genome and in several nuclear-encoded mitochondrial protein (NEMP) genes. The aim of this study was to screen for variants in the mitochondrial genome and NEMP genes in a NOTCH3 -negative CADASIL cohort, to identify a potential link between mitochondrial dysfunction and CSVD pathology. Whole exome sequencing was performed for 50 patients with CADASIL-like symptomology on the Ion Torrent system. Mitochondrial sequencing was performed using an in-house designed protocol with sequencing run on the Ion GeneStudio S5 Plus (S5 +). NEMP genes and mitochondrial sequencing data were examined for rare (MAF 0.001), non-synonymous variants that were predicted to have a deleterious effect on the protein. We identified 29 candidate NEMP variants that had links to either MELAS-, encephalopathy-, or Alzheimer’s disease–related phenotypes. Based on these changes, variants affecting POLG , MTO1 , LONP1 , NDUFAF6 , NDUFB3 , and TCIRG1 were thought to play a potential role in CSVD pathology in this cohort. Overall, the exploration of the mitochondrial genome identified a potential role for mitochondrial related proteins and mtDNA variants contributing to CSVD pathologies.
Publisher: Cold Spring Harbor Laboratory
Date: 20-02-2020
DOI: 10.1101/2020.02.20.957340
Abstract: Mitochondria supply intracellular energy requirements during exercise. Specific mitochondrial haplogroups and mitochondrial genetic variants have been associated with athletic performance, and exercise responses. However, these associations were discovered using underpowered, candidate gene approaches, and consequently have not been replicated. Here, we used whole-mitochondrial genome sequencing, in conjunction with high-throughput genotyping arrays, to discover novel genetic variants associated with exercise responses in the Gene SMART (Skeletal Muscle Adaptive Response to Training) cohort (n=62 completed). We performed a Principal Component Analysis of cohort aerobic fitness measures to build composite traits and test for variants associated with exercise outcomes. None of the mitochondrial genetic variants but nine nuclear encoded variants in eight separate genes were found to be associated with exercise responses (FDR .05) (rs11061368: DIABLO, rs113400963: FAM185A, rs6062129 and rs6121949: MTG2, rs7231304: AFG3L2, rs2041840: NDUFAF7, rs7085433: TIMM23, rs1063271: SPTLC2, rs2275273: ALDH18A1). Additionally, we outline potential mechanisms by which these variants may be contributing to exercise phenotypes. Our data suggest novel nuclear-encoded SNPs and mitochondrial pathways associated with exercise response phenotypes. Future studies should focus on validating these variants across different cohorts and ethnicities. Previous exercise genetic studies contain many flaws that impede the growth in knowledge surrounding change in exercise outcomes. In particular, exercise studies looking at mtDNA variants have looked at very small portions of the mitochondrial genome. Mitochondria are the ‘power house’ of the cell and therefore understanding the mitochondrial genetics behind adaptations to training can help us fill knowledge gaps in current research. Here, we utilised a new mitochondrial genetic sequencing technique to examine all mitochondrial and mitochondrial related genetic variations. We have shown that there were no mitochondrial specific variants that influenced exercise training however there were 9 related variants that were significantly associated with exercise phenotypes. Additionally, we have shown that building composite traits increased the significance of our association testing and lead to novel findings. We will be able to understand why response to training is so varied and increase the effectiveness of exercise training on a host of metabolic disorders.
Publisher: Cold Spring Harbor Laboratory
Date: 19-03-2023
DOI: 10.1101/2023.03.14.23287211
Abstract: Cognitive impairment has been reported after many types of infection, including SARS-CoV-2. Whether deficits following SARS-CoV-2 improve over time is unclear. Studies to date have focused on hospitalised in iduals with up to a year follow-up. The presence, magnitude, persistence and correlations of effects in community-based cases remain relatively unexplored. Cognitive performance (working memory, attention, reasoning, motor control) was assessed in participants of a voluntary biobank in July, 2021 (Round 1), and April, 2022 (Round 2). Participants, drawn from the COVID Symptom Study smartphone app, comprised in iduals with and without SARS-CoV-2 infection and varying symptom duration. Effects of COVID-19 exposures on cognitive accuracy and reaction time scores were estimated using multivariable ordinary least squares linear regression models weighted for inverse probability of participation, adjusting for potential confounders and mediators. The role of ongoing symptoms after COVID-19 infection was examined stratifying for self-perceived recovery. Longitudinal analysis assessed change in cognitive performance between rounds. 3335 in iduals completed Round 1, of whom 1768 also completed Round 2. At Round 1, in iduals with previous positive SARS-CoV-2 tests had lower cognitive accuracy (N = 1737, β = −0.14 standard deviations, SDs) than negative controls. Deficits were largest for positive in iduals with ≥ 12 weeks of symptoms (N = 495, β = −0.22 SDs). Effects were comparable to hospital presentation during illness (N = 281, β = −0.31 SDs), and 10 years age difference (60-70 years vs. 50-60 years, β = −0.21 SDs) in the whole study population. Stratification by self-reported recovery revealed that deficits were only detectable in SARS-CoV-2 positive in iduals who did not feel recovered from COVID-19, whereas in iduals who reported full recovery showed no deficits. Longitudinal analysis showed no evidence of cognitive change over time, suggesting that cognitive deficits for affected in iduals persisted at almost 2 years since initial infection. Cognitive deficits following SARS-CoV-2 infection were detectable nearly two years post infection, and largest for in iduals with longer symptom durations, ongoing symptoms, and/or more severe infection. However, no such deficits were detected in in iduals who reported full recovery from COVID-19. Further work is needed to monitor and develop understanding of recovery mechanisms for those with ongoing symptoms. Chronic Disease Research Foundation, Wellcome Trust, National Institute for Health and Care Research, Medical Research Council, British Heart Foundation, Alzheimer’s Society, European Union, COVID-19 Driver Relief Fund, French National Research Agency. Abstracts were screened from a PubMed search query (COVID-19) AND (long COVID) AND (cognitive impairment), which returned 409 results between 2020 and January 20, 2023. Multiple systematic reviews and meta-analyses reported consistent observation of cognitive deficits following SARS-CoV-2 infection. Most studies of cognitive impairment have used small s les of less than 200 participants (including any controls), hospitalised cohorts, and measured cognitive impairment through self-report or dichotomised quantitative scales. Only one study was found with a s le size of more than 1,000 in iduals, included cases and controls across both community and hospital settings, and used objective cognitive testing that allowed quantitative estimation of the scale of any cognitive impairment. Previous studies have also been limited insofar as focusing on earlier infections in the first year of the COVID-19 pandemic, prior to introduction of vaccination and emerging variants. Studies focusing on longitudinal follow-up for those hospitalised with COVID-19 or with long COVID have found low rates of full recovery from long-term symptoms at up to one year since infection, including cognitive impairment. We report quantitatively on cognitive impairment following SARS-CoV-2 infection, from a large dataset of 4,000 in iduals with and without test-confirmed SARS-CoV-2 infection and a range of associated symptom durations, with mostly community-based cases. Importantly, we undertook two rounds of cognitive testing allowing longitudinal tracking of cognitive performance. Our longitudinal methods allowed us to report on deficits up to two years since infection, and following infections with SARS-CoV-2 variants that have emerged over 2021 and 2022, not previously studied in the context of COVID-19 and cognition. This study adds to existing evidence of cognitive deficits following SARS-CoV-2 infection, but finds important exceptions. At initial testing in mid-2021, cognitive deficits are not found for in iduals who self-report as feeling recovered from COVID-19, even for those with longest symptom duration. In follow-up testing in mid-2022, we find that deficits appear persistent for those with earlier infections and ongoing symptoms, consistent with previous smaller studies. More research is required to monitor those experiencing persistent cognitive impairment and understand the mechanisms underlying recovery.
Publisher: Springer Science and Business Media LLC
Date: 06-07-2020
DOI: 10.1038/S41598-020-67870-1
Abstract: Mitochondria supply intracellular energy requirements during exercise. Specific mitochondrial haplogroups and mitochondrial genetic variants have been associated with athletic performance, and exercise responses. However, these associations were discovered using underpowered, candidate gene approaches, and consequently have not been replicated. Here, we used whole-mitochondrial genome sequencing, in conjunction with high-throughput genotyping arrays, to discover novel genetic variants associated with exercise responses in the Gene SMART (Skeletal Muscle Adaptive Response to Training) cohort (n = 62 completed). We performed a Principal Component Analysis of cohort aerobic fitness measures to build composite traits and test for variants associated with exercise outcomes. None of the mitochondrial genetic variants but eight nuclear encoded variants in seven separate genes were found to be associated with exercise responses (FDR 0.05) ( rs11061368 : DIABLO , rs113400963 : FAM185A , rs6062129 and rs6121949 : MTG2 , rs7231304 : AFG3L2 , rs2041840 : NDUFAF7 , rs7085433 : TIMM23 , rs1063271 : SPTLC2 ) . Additionally, we outline potential mechanisms by which these variants may be contributing to exercise phenotypes. Our data suggest novel nuclear-encoded SNPs and mitochondrial pathways associated with exercise response phenotypes. Future studies should focus on validating these variants across different cohorts and ethnicities.
Publisher: Frontiers Media SA
Date: 05-02-2019
Publisher: Elsevier BV
Date: 08-2023
Publisher: Cold Spring Harbor Laboratory
Date: 28-09-2020
DOI: 10.1101/2020.09.28.315838
Abstract: Knowledge of age-related DNA methylation changes in skeletal muscle is limited, yet this tissue is severely affected by aging in humans. Using a large-scale epigenome-wide association study (EWAS) meta-analysis of age in human skeletal muscle from 10 studies (total n = 908 human muscle methylomes), we identified 9,986 differentially methylated regions at a stringent false discovery rate 0.005, spanning 8,748 unique genes, many of which related to skeletal muscle structure and development. We then integrated the DNA methylation results with known transcriptomic and proteomic age-related changes in skeletal muscle, and found that even though most differentially methylated genes are not altered at the mRNA or protein level, they are nonetheless strongly enriched for genes showing age-related differential expression. We provide here the most comprehensive picture of DNA methylation aging in human skeletal muscle, and have made our results available as an open-access, user-friendly, web-based tool called MetaMeth ( sarah-voisin.shinyapps.io/MetaMeth/ ).
Publisher: Springer Science and Business Media LLC
Date: 02-01-2020
DOI: 10.1007/S00438-019-01639-8
Abstract: Adaptation to exercise training is a complex trait that may be influenced by genetic variants. We identified 36 single nucleotide polymorphisms (SNPs) that had been previously associated with endurance or strength performance, exercise-related phenotypes or exercise intolerant disorders. A MassARRAY multiplex genotyping assay was designed to identify associations with these SNPs against collected endurance fitness phenotype parameters obtained from two exercise cohorts (Gene SMART study n = 58 and Hawaiian Ironman Triathlon 2008 n = 115). These parameters included peak power output (PP), a time trial (TT), lactate threshold (LT), maximal oxygen uptake (VO
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Nicholas Harvey.