An examination of peripheral blood to reflect transcriptomic adaptation to physical exercise training in sedentary men compared with sex-matched athletic phenotypes
- Authors: Marin, Sergio
- Date: 2021
- Type: Text , Thesis , PhD
- Full Text:
- Description: There is renewed interest in exercise genomics that peripheral blood RNA expression may be important to understand exercise mediated adaptations to exercise. However, there is little direct supporting evidence. Therefore, this thesis involved two studies to examine the relationship between RNA expression and exercise, and two experimental studies to examine relationships and adaptive response of peripheral blood RNA in sedentary compared with athletic phenotypes. In the first two studies, we conducted both meta-analysis and network meta-analysis to examine current randomised controlled trial (RCT) evidence to determine current best evidence on the link between RNA expression and athletic phenotype in addition to head-to-head comparison of different exercise types to induce differential expression of RNA transcripts in sedentary compared with athletic phenotypes. We observed that current available body of RCTs in peripheral blood exercise genomics presents too large heterogeneity in study design, methodological and data reporting aspects. Thus, we concluded that peripheral blood cannot be established as a valid source for identifying, neither the effect of physical exercise training on transcriptomic markers nor the distinction of divergent transcriptomic profiles in response to different exercise modalities. In the third and fourth studies, we aimed to determine whether peripheral blood RNA and circular RNA (circRNA) expression was different between sedentary and athletic phenotypes, and whether these transcripts were consistent in response to exercise training in exercise-naïve men. To achieve this, we conducted two STROBE compliant observational experiments of n=71 participants with distinct athletic phenotypes. We concluded that peripheral blood transcriptome expression might allow for identification of divergent athletic phenotypes, although this is not supported by further examination of peripheral blood RNA expression levels in response to an exercise training intervention. The sum of works presented in this thesis does not agree with many propositions relating to the strength of evidence in peripheral blood transcriptomics literature. This is principally due to the heterogeneity and lack of consistency of research in this field which is currently insufficient to provide any strong conclusions. In conclusion, peripheral blood RNA and circRNA do not yet offer useful avenues to predict the adaptive response to different exercise types in athletic and non-athletic men.
- Description: Doctor of Philosophy
- Authors: Marin, Sergio
- Date: 2021
- Type: Text , Thesis , PhD
- Full Text:
- Description: There is renewed interest in exercise genomics that peripheral blood RNA expression may be important to understand exercise mediated adaptations to exercise. However, there is little direct supporting evidence. Therefore, this thesis involved two studies to examine the relationship between RNA expression and exercise, and two experimental studies to examine relationships and adaptive response of peripheral blood RNA in sedentary compared with athletic phenotypes. In the first two studies, we conducted both meta-analysis and network meta-analysis to examine current randomised controlled trial (RCT) evidence to determine current best evidence on the link between RNA expression and athletic phenotype in addition to head-to-head comparison of different exercise types to induce differential expression of RNA transcripts in sedentary compared with athletic phenotypes. We observed that current available body of RCTs in peripheral blood exercise genomics presents too large heterogeneity in study design, methodological and data reporting aspects. Thus, we concluded that peripheral blood cannot be established as a valid source for identifying, neither the effect of physical exercise training on transcriptomic markers nor the distinction of divergent transcriptomic profiles in response to different exercise modalities. In the third and fourth studies, we aimed to determine whether peripheral blood RNA and circular RNA (circRNA) expression was different between sedentary and athletic phenotypes, and whether these transcripts were consistent in response to exercise training in exercise-naïve men. To achieve this, we conducted two STROBE compliant observational experiments of n=71 participants with distinct athletic phenotypes. We concluded that peripheral blood transcriptome expression might allow for identification of divergent athletic phenotypes, although this is not supported by further examination of peripheral blood RNA expression levels in response to an exercise training intervention. The sum of works presented in this thesis does not agree with many propositions relating to the strength of evidence in peripheral blood transcriptomics literature. This is principally due to the heterogeneity and lack of consistency of research in this field which is currently insufficient to provide any strong conclusions. In conclusion, peripheral blood RNA and circRNA do not yet offer useful avenues to predict the adaptive response to different exercise types in athletic and non-athletic men.
- Description: Doctor of Philosophy
Epigenetic modifications in essential hypertension
- Authors: Wise, Ingrid
- Date: 2018
- Type: Text , Thesis , PhD
- Full Text:
- Description: Background: Hypertension (HTN) is a complex, multifactorial, quantitative trait under polygenic control that affects more than one billion people globally. Despite advances in our understanding of the pathophysiology of HTN and the implementation of more effective treatment and prevention strategies, HTN remains one of the world’s great public health problems. The accepted inference from genome-wide association studies (GWAS) is that the genetic code lays the foundation for transcriptomic changes and in turn physiological change. On the other side of the coin, environmental factors (smoking, diet, chemical exposure) can in turn affect DNA itself in genes relevant to blood pressure (BP). Variation in epigenetic forms of modification may thus explain additional phenotypic variation in BP and provide new clues to the physiological processes influencing its regulation. DNA methylation is one of these epigenetic mechanisms responsible for changes to gene expression, activated by interaction with environmental triggers. DNA methylation is a reversible epigenetic modifier of specific dinucleotide sites called CpGs, which consists of a transfer of a methyl group derived from S-adenosyl-L-methionine to position five of a cytosine ring, forming 5mC. Pathophysiologically, the kidney is known as the key organ of BP regulation and one of the most important contributors to HTN. According to the hypothesis put forward by Guyton, over 40 years ago, the control of BP in the steady-state and longer-term is critically dependent on renal mechanisms. In fact, almost all monogenic forms of HTN are driven by rare mutations in genes involved in salt handling in the distal nephron. It is therefore crucial to understand kidney DNA methylation changes that may drive gene expression in kidney and lead to HTN. Hypothesis: The central hypothesis underpinning this PhD thesis is that alterations in kidney specific DNA methylation plays a fundamental role in modulating gene expression changes involved in the regulation of BP and pathophysiology of EH. Aims: This PhD thesis focuses on characterising the role of DNA methylation in the hypertensive kidney using array and RNA-sequencing methods. Three major aims are addressed: • Aim 1: To characterise blood and kidney global DNA methylation dynamics and its functional role in the hypertensive population (Chapter 3). • Aim 2: To determine the role of genome-wide, loci specific DNA methylation in the hypertensive human kidney (Chapter 4). • Aim 3: To understand the relationship between DNA methylation and differential expression of genes associated with BP and HTN in the human kidney (Chapter 5). Results: In Aim 1 global DNA methylation changes were characterised in peripheral blood leukocyte and kidney DNA of the hypertensive (HT) population using he ELISA method. We found no association between HTN diagnosis and global methylation percentage in either peripheral blood leukocytes or kidney DNA. However, a negative correlation was found between global methylation and diastolic blood pressure (DBP), yet this relationship was not evident after adjustment for the effect of antihypertensive medication. Furthermore, we investigated the sensitivity of ELISA-based global methylation detection by calculating the percentage of global methylation in kidney using array based methods; the results were similar, demonstrating no association between HTN diagnosis and median kidney methylation
- Description: Doctor of Philosophy
- Authors: Wise, Ingrid
- Date: 2018
- Type: Text , Thesis , PhD
- Full Text:
- Description: Background: Hypertension (HTN) is a complex, multifactorial, quantitative trait under polygenic control that affects more than one billion people globally. Despite advances in our understanding of the pathophysiology of HTN and the implementation of more effective treatment and prevention strategies, HTN remains one of the world’s great public health problems. The accepted inference from genome-wide association studies (GWAS) is that the genetic code lays the foundation for transcriptomic changes and in turn physiological change. On the other side of the coin, environmental factors (smoking, diet, chemical exposure) can in turn affect DNA itself in genes relevant to blood pressure (BP). Variation in epigenetic forms of modification may thus explain additional phenotypic variation in BP and provide new clues to the physiological processes influencing its regulation. DNA methylation is one of these epigenetic mechanisms responsible for changes to gene expression, activated by interaction with environmental triggers. DNA methylation is a reversible epigenetic modifier of specific dinucleotide sites called CpGs, which consists of a transfer of a methyl group derived from S-adenosyl-L-methionine to position five of a cytosine ring, forming 5mC. Pathophysiologically, the kidney is known as the key organ of BP regulation and one of the most important contributors to HTN. According to the hypothesis put forward by Guyton, over 40 years ago, the control of BP in the steady-state and longer-term is critically dependent on renal mechanisms. In fact, almost all monogenic forms of HTN are driven by rare mutations in genes involved in salt handling in the distal nephron. It is therefore crucial to understand kidney DNA methylation changes that may drive gene expression in kidney and lead to HTN. Hypothesis: The central hypothesis underpinning this PhD thesis is that alterations in kidney specific DNA methylation plays a fundamental role in modulating gene expression changes involved in the regulation of BP and pathophysiology of EH. Aims: This PhD thesis focuses on characterising the role of DNA methylation in the hypertensive kidney using array and RNA-sequencing methods. Three major aims are addressed: • Aim 1: To characterise blood and kidney global DNA methylation dynamics and its functional role in the hypertensive population (Chapter 3). • Aim 2: To determine the role of genome-wide, loci specific DNA methylation in the hypertensive human kidney (Chapter 4). • Aim 3: To understand the relationship between DNA methylation and differential expression of genes associated with BP and HTN in the human kidney (Chapter 5). Results: In Aim 1 global DNA methylation changes were characterised in peripheral blood leukocyte and kidney DNA of the hypertensive (HT) population using he ELISA method. We found no association between HTN diagnosis and global methylation percentage in either peripheral blood leukocytes or kidney DNA. However, a negative correlation was found between global methylation and diastolic blood pressure (DBP), yet this relationship was not evident after adjustment for the effect of antihypertensive medication. Furthermore, we investigated the sensitivity of ELISA-based global methylation detection by calculating the percentage of global methylation in kidney using array based methods; the results were similar, demonstrating no association between HTN diagnosis and median kidney methylation
- Description: Doctor of Philosophy
Telomere, DNA Methylation and Gene Expression changes caused by exercise training
- Authors: Denham, Joshua
- Date: 2016
- Type: Text , Thesis , PhD
- Full Text:
- Description: Exercise training is one of the few therapeutic interventions that improves health span by delaying the onset of age-related diseases and preventing early death. Despite the clear benefits to health conferred by exercise training, our understanding of the underlying molecular mechanisms remain crude. The primary purpose of this thesis is to determine and analyse the molecular biology changes that occur with strenuous aerobic exercise. Specifically, the main objectives were to investigate the impact of strenuous aerobic exercise training on structural DNA modifications, measured in context with cardiovascular health and fitness adaptations. In the first part of this thesis I investigated the influence of endurance exercise training on leukocyte telomere length and cardiovascular health. Leukocyte telomere length reflects biological age. Indeed, excessively short leukocyte telomeres are associated with age-related chronic diseases. Epidemiological studies indicate endurance athletes live longer than people from the general public who do not engage in extensive aerobic exercise training. In Chapter 2, my literature review on the subject of exercise and telomere biology suggested that, at the time of this study, the impact of exercise training on leukocyte telomere length was equivocal. Therefore, to determine whether strenuous aerobic exercise training influences biological ageing (assessed by leukocyte telomere length), I conducted two cross-sectional studies on leukocyte telomere length differences between endurance athletes and healthy controls. The first study (Chapter 3) was a cross-sectional analysis of leukocyte telomere length between athletes and controls, determined by quantitative polymerase chain reaction (qPCR). This is a relative measurement of telomere length expressed as a telomere (T) to single copy gene (S) ratio. Relative to the healthy controls (n = 56), the ultra-marathon runners (n = 67) possessed 11% longer leukocyte telomeres in age-adjusted analysis (ultra-marathon runners vs controls; average T/S ratio: 3.56 vs 3.16, p = 1.4 × 10-4) and the difference was not explained by the favourable cardiovascular health profile exhibited by the athletes (p = 2.2 × 10-4). The difference in leukocyte telomere length indicated the athletes had reduced their biological age by 16.2 years. To elucidate the potential mechanism for the longer leukocyte telomeres observed in endurance athletes, I recruited another cohort of athletes and controls and measured leukocyte telomere length and gene expression of genes involved in telomere length regulation. In the second study (Chapter 4), I describe data replicating the finding that endurance athletes possess longer leukocyte telomeres compared to healthy controls (athletes v controls mean T/S ratio ± SE: 3.64 ± 0.06 vs 3.38 ± 0.06, p = 0.002). This difference was associated with a concomitant increased activity of two important telomere regulating genes, telomerase reverse transcriptase (TERT) and adrenocortical dysplasia homolog (TPP1) (2- fold and 1.3-fold, respectively, both p < 0.05). The difference in leukocyte telomere length and leukocyte telomere-regulating gene (TERT and TPP1 mRNA) expression was ameliorated after adjusting for maximal oxygen uptake and resting heart rate (all p > 0.05). This finding indicates that cardiorespiratory fitness is an important determinant of telomere biology. Together, these two cross-sectional studies suggest that regular endurance exercise training is associated with longer leukocytes telomeres and that this is likely achieved through higher TPP1 and TERT mRNA expression gained through improved cardiorespiratory fitness. The findings in Chapters 3 and 4 provide evidence for extensive endurance exercise training as an effective lifestyle strategy to attenuate biological ageing. In parallel to telomere length changes, epigenetic modifications (e.g. DNA methylation) caused by environmental factors alter the transcriptomic milieu of cells. My thorough literature review (Chapter 5) revealed that exercise training seems to rearrange chromatin by modifying the DNA methylome in a variety of cells and that the extent is dictated by exercise duration and intensity. Therefore, in the second part of my thesis, I investigated the DNA methylation changes in leukocytes (which are somatic cells) and sperm (male germ cells) from healthy men before and after sprint interval training (SIT). Unlike traditional, long duration training at moderate intensity training, SIT involves short, intense (>85% VO2max to supra-maximal) efforts followed by periods of rest (3–4 min), typically repeated 3–8 times. It is an effective type of training that improves cardiorespiratory fitness quicker than traditional long slow distance training. Thus, to establish the DNA methylome changes associated with SIT, I conducted two training studies and analysed the leukocyte and sperm methylomes using the Infinium HumanMethylation450 BeadChip (Illumina). My third study (Chapter 6) provides the first evidence showing an association between DNA methylation changes paralleled with improvements to lipid profile and cardiorespiratory fitness in humans. Twelve young men (18–24 years) undertook SIT (thrice weekly) for four weeks. Resting blood samples were obtained and whole-blood leukocytes were isolated by red blood cell lysis. Genome-wide DNA methylation was assessed using the 450K BeadChip (Illumina). Cardiorespiratory fitness, determined by maximal oxygen uptake, was improved by 2.1 ml.kg-1.min-1 and low-density lipo-protein cholesterol was decreased by 3.9% after SIT (p < 0.05). Notably, the leukocyte methylome was significantly affected by SIT, in regions throughout the genome in relation to CpG islands – CpG islands, North shores, N shelves, South shores and South shelve – and the nearest genes – 3’ untranslated region (UTR), 5’ UTR, exonic, intergenic, intronic, non-coding and promoter regions (all p < 0.001). Genes with differentially methylated CpG sites (q < 0.005) after SIT were enriched for cardiovascular gene ontology (GO) terms that included metabolic activity, biological adhesion and antioxidant activity. Similarly, pathway analysis revealed genes involved in focal adhesion, calcium signaling and mitogen activated protein kinase were modulated by SIT-induced DNA methylation changes. Amongst the 205,987 probes relating 32,445 transcripts differentially methylated after SIT (q < 0.05), with methylation changes between 0.1 – 62.8%, the largest and most statistically significant demethylated site was in the epidermal growth factor (EGF) gene, causing decreased mRNA expression. As with EGF, the microRNA-21 and microRNA-210 genes (MIR21 and MIR210, respectively), known for their roles in cardiovascular disease (ischemic heart disease and coronary atherosclerosis), had modest but consistently statistically significant DNA methylation changes at numerous CpG sites, which altered mature microRNA abundance. Together, these data suggest that genome-wide DNA methylation changes occur after short-term intense exercise training concurrently with improvements to blood cholesterol profile and cardiorespiratory fitness. The data presented in this thesis provided evidence that the epigenome of somatic cells is malleable to exercise. There is mounting evidence supporting the premise that environmental perturbations cause DNA methylation changes and these are subsequently transgenerationally inherited, altering phenotypes of future generations. In the current study I also asked the question; can exercise training reconfigure the DNA methylome of male germ cells (sperm)? Therefore, my next study (Chapter 7) entails an analysis of the impact that three months of SIT has on genome-wide DNA methylation of sperm in healthy men. Thirteen subjects undertook twice-weekly SIT for three months, while the controls were asked not to change their current physical activity habits (if any). Sperm samples were donated before and after the three-month intervention. Mature sperm were isolated using density gradient centrifugation and DNA was extracted using the Purelink Genomic DNA Mini Kit (Life Technologies). Global and genome-wide DNA methylation was assessed using an enzyme-linked immunosorbent assay-based kit and the 450K BeadChip (Illumina), respectively. Relative to controls, the cases decreased their resting heart rate and had a higher maximal treadmill speed during exercise testing (both p < 0.05). Cases had decreased global DNA methylation after SIT compared to controls (p < 0.05). Genome-wide DNA methylation analysis revealed numerous modest (0.3 – 6%) methylation changes to 7509 CpG sites, relating to 4602 transcripts (q ≤ 0.1). Differentially methylated CpG sites were in genes associated with developmental biology, which included GO terms, such as developmental process, anatomical structure, embryonic morphogenesis and organ development, together with known pathways regulated by exercise training (MAPK, ErbB and PI3K-Akt signalling). Genes with increased methylation were associated with numerous human diseases, with most overrepresented being psychiatric disorders (schizophrenia, Parkinson’s disease and autism). Notably, paternally imprinted genes associated with other diseases were also differentially methylated after SIT. Therefore, exercise training is associated with the modifications to genome-wide DNA methylation of both somatic and germ cells. In conclusion, the studies presented as a series of peer-reviewed publications, outlines investigations that describe an influence of strenuous exercise training on leukocyte telomere length regulation and the DNA methylome of both leukocytes and germ cells. Both of these molecular changes in leukocytes and sperm provide evidence for novel molecular mechanisms by which exercise improves cardiovascular health and fitness. Future investigations should focus on longitudinal studies determining whether these changes are required for improved health and fitness, and should establish whether exercise-induced DNA methylation changes are transgenerationally inherited, and if so, what impact this has to future generations. Such discoveries could change national physical activity guidelines and policies, by emphasising the benefit of regular exercise both in the present and to future offspring.
- Description: Doctor of Philosophy
- Authors: Denham, Joshua
- Date: 2016
- Type: Text , Thesis , PhD
- Full Text:
- Description: Exercise training is one of the few therapeutic interventions that improves health span by delaying the onset of age-related diseases and preventing early death. Despite the clear benefits to health conferred by exercise training, our understanding of the underlying molecular mechanisms remain crude. The primary purpose of this thesis is to determine and analyse the molecular biology changes that occur with strenuous aerobic exercise. Specifically, the main objectives were to investigate the impact of strenuous aerobic exercise training on structural DNA modifications, measured in context with cardiovascular health and fitness adaptations. In the first part of this thesis I investigated the influence of endurance exercise training on leukocyte telomere length and cardiovascular health. Leukocyte telomere length reflects biological age. Indeed, excessively short leukocyte telomeres are associated with age-related chronic diseases. Epidemiological studies indicate endurance athletes live longer than people from the general public who do not engage in extensive aerobic exercise training. In Chapter 2, my literature review on the subject of exercise and telomere biology suggested that, at the time of this study, the impact of exercise training on leukocyte telomere length was equivocal. Therefore, to determine whether strenuous aerobic exercise training influences biological ageing (assessed by leukocyte telomere length), I conducted two cross-sectional studies on leukocyte telomere length differences between endurance athletes and healthy controls. The first study (Chapter 3) was a cross-sectional analysis of leukocyte telomere length between athletes and controls, determined by quantitative polymerase chain reaction (qPCR). This is a relative measurement of telomere length expressed as a telomere (T) to single copy gene (S) ratio. Relative to the healthy controls (n = 56), the ultra-marathon runners (n = 67) possessed 11% longer leukocyte telomeres in age-adjusted analysis (ultra-marathon runners vs controls; average T/S ratio: 3.56 vs 3.16, p = 1.4 × 10-4) and the difference was not explained by the favourable cardiovascular health profile exhibited by the athletes (p = 2.2 × 10-4). The difference in leukocyte telomere length indicated the athletes had reduced their biological age by 16.2 years. To elucidate the potential mechanism for the longer leukocyte telomeres observed in endurance athletes, I recruited another cohort of athletes and controls and measured leukocyte telomere length and gene expression of genes involved in telomere length regulation. In the second study (Chapter 4), I describe data replicating the finding that endurance athletes possess longer leukocyte telomeres compared to healthy controls (athletes v controls mean T/S ratio ± SE: 3.64 ± 0.06 vs 3.38 ± 0.06, p = 0.002). This difference was associated with a concomitant increased activity of two important telomere regulating genes, telomerase reverse transcriptase (TERT) and adrenocortical dysplasia homolog (TPP1) (2- fold and 1.3-fold, respectively, both p < 0.05). The difference in leukocyte telomere length and leukocyte telomere-regulating gene (TERT and TPP1 mRNA) expression was ameliorated after adjusting for maximal oxygen uptake and resting heart rate (all p > 0.05). This finding indicates that cardiorespiratory fitness is an important determinant of telomere biology. Together, these two cross-sectional studies suggest that regular endurance exercise training is associated with longer leukocytes telomeres and that this is likely achieved through higher TPP1 and TERT mRNA expression gained through improved cardiorespiratory fitness. The findings in Chapters 3 and 4 provide evidence for extensive endurance exercise training as an effective lifestyle strategy to attenuate biological ageing. In parallel to telomere length changes, epigenetic modifications (e.g. DNA methylation) caused by environmental factors alter the transcriptomic milieu of cells. My thorough literature review (Chapter 5) revealed that exercise training seems to rearrange chromatin by modifying the DNA methylome in a variety of cells and that the extent is dictated by exercise duration and intensity. Therefore, in the second part of my thesis, I investigated the DNA methylation changes in leukocytes (which are somatic cells) and sperm (male germ cells) from healthy men before and after sprint interval training (SIT). Unlike traditional, long duration training at moderate intensity training, SIT involves short, intense (>85% VO2max to supra-maximal) efforts followed by periods of rest (3–4 min), typically repeated 3–8 times. It is an effective type of training that improves cardiorespiratory fitness quicker than traditional long slow distance training. Thus, to establish the DNA methylome changes associated with SIT, I conducted two training studies and analysed the leukocyte and sperm methylomes using the Infinium HumanMethylation450 BeadChip (Illumina). My third study (Chapter 6) provides the first evidence showing an association between DNA methylation changes paralleled with improvements to lipid profile and cardiorespiratory fitness in humans. Twelve young men (18–24 years) undertook SIT (thrice weekly) for four weeks. Resting blood samples were obtained and whole-blood leukocytes were isolated by red blood cell lysis. Genome-wide DNA methylation was assessed using the 450K BeadChip (Illumina). Cardiorespiratory fitness, determined by maximal oxygen uptake, was improved by 2.1 ml.kg-1.min-1 and low-density lipo-protein cholesterol was decreased by 3.9% after SIT (p < 0.05). Notably, the leukocyte methylome was significantly affected by SIT, in regions throughout the genome in relation to CpG islands – CpG islands, North shores, N shelves, South shores and South shelve – and the nearest genes – 3’ untranslated region (UTR), 5’ UTR, exonic, intergenic, intronic, non-coding and promoter regions (all p < 0.001). Genes with differentially methylated CpG sites (q < 0.005) after SIT were enriched for cardiovascular gene ontology (GO) terms that included metabolic activity, biological adhesion and antioxidant activity. Similarly, pathway analysis revealed genes involved in focal adhesion, calcium signaling and mitogen activated protein kinase were modulated by SIT-induced DNA methylation changes. Amongst the 205,987 probes relating 32,445 transcripts differentially methylated after SIT (q < 0.05), with methylation changes between 0.1 – 62.8%, the largest and most statistically significant demethylated site was in the epidermal growth factor (EGF) gene, causing decreased mRNA expression. As with EGF, the microRNA-21 and microRNA-210 genes (MIR21 and MIR210, respectively), known for their roles in cardiovascular disease (ischemic heart disease and coronary atherosclerosis), had modest but consistently statistically significant DNA methylation changes at numerous CpG sites, which altered mature microRNA abundance. Together, these data suggest that genome-wide DNA methylation changes occur after short-term intense exercise training concurrently with improvements to blood cholesterol profile and cardiorespiratory fitness. The data presented in this thesis provided evidence that the epigenome of somatic cells is malleable to exercise. There is mounting evidence supporting the premise that environmental perturbations cause DNA methylation changes and these are subsequently transgenerationally inherited, altering phenotypes of future generations. In the current study I also asked the question; can exercise training reconfigure the DNA methylome of male germ cells (sperm)? Therefore, my next study (Chapter 7) entails an analysis of the impact that three months of SIT has on genome-wide DNA methylation of sperm in healthy men. Thirteen subjects undertook twice-weekly SIT for three months, while the controls were asked not to change their current physical activity habits (if any). Sperm samples were donated before and after the three-month intervention. Mature sperm were isolated using density gradient centrifugation and DNA was extracted using the Purelink Genomic DNA Mini Kit (Life Technologies). Global and genome-wide DNA methylation was assessed using an enzyme-linked immunosorbent assay-based kit and the 450K BeadChip (Illumina), respectively. Relative to controls, the cases decreased their resting heart rate and had a higher maximal treadmill speed during exercise testing (both p < 0.05). Cases had decreased global DNA methylation after SIT compared to controls (p < 0.05). Genome-wide DNA methylation analysis revealed numerous modest (0.3 – 6%) methylation changes to 7509 CpG sites, relating to 4602 transcripts (q ≤ 0.1). Differentially methylated CpG sites were in genes associated with developmental biology, which included GO terms, such as developmental process, anatomical structure, embryonic morphogenesis and organ development, together with known pathways regulated by exercise training (MAPK, ErbB and PI3K-Akt signalling). Genes with increased methylation were associated with numerous human diseases, with most overrepresented being psychiatric disorders (schizophrenia, Parkinson’s disease and autism). Notably, paternally imprinted genes associated with other diseases were also differentially methylated after SIT. Therefore, exercise training is associated with the modifications to genome-wide DNA methylation of both somatic and germ cells. In conclusion, the studies presented as a series of peer-reviewed publications, outlines investigations that describe an influence of strenuous exercise training on leukocyte telomere length regulation and the DNA methylome of both leukocytes and germ cells. Both of these molecular changes in leukocytes and sperm provide evidence for novel molecular mechanisms by which exercise improves cardiovascular health and fitness. Future investigations should focus on longitudinal studies determining whether these changes are required for improved health and fitness, and should establish whether exercise-induced DNA methylation changes are transgenerationally inherited, and if so, what impact this has to future generations. Such discoveries could change national physical activity guidelines and policies, by emphasising the benefit of regular exercise both in the present and to future offspring.
- Description: Doctor of Philosophy
Optimization based clustering and classification algorithms in analysis of microarray gene expression data sets
- Authors: Mardaneh, Karim
- Date: 2007
- Type: Text , Thesis , PhD
- Full Text:
- Description: Doctor of Philosophy
- Description: Bioinformatics and computational biology are relatively new areas that involve the use of different techniques including computer science, informatics, biochemistry, applied math and etc., to solve biological problems. In recent years the development of new molecular genetics technologies, such as DNA microarrays led to the simultaneous measurement of expression levels of thousands and even tens of thousands of genes. Microarray gene expression technology has facilitated the study of genomic structure and investigation of biological systems. Numerical output of this technology is shown as microarray gene expression data sets. These data sets contain a very large number of genes and a relatively small number of samples and their precise analysis requires a robust and suitable computer software. Due to this, only a few existing algorithms are applicable to them, so more efficient methods for solving clustering, gene selection and classification problems of gene expression data sets are required and those methods need to be computationally applicable and less expensive. The aim of this thesis is to develop new algorithms for solving clustering, gene selection and data classification problems on gene expression data sets. Clustering in gene expression data sets is a challenging problem. The increasing use of DNA microarray-based tumour gene expression profiles for cancer diagnosis requires more efficient methods to solve clustering problems of these profiles. Different algorithms for clustering of genes have been proposed, however few algorithms can be applied to the clustering of samples. k-means algorithm, among very few clustering algorithms is applicable to microarray gene expression data sets, however these are not efficient for solving clustering problems when the number of genes is thousands and this algorithm is very sensitive to the choice of a starting point. Additionally, when the number of clusters is relatively large, this algorithm gives local minima which can differ significantly from the global solution. Over the last several years different approaches have been proposed to improve global ii Abstract Abstract search properties of k-means algorithm. One of them is the global k-means algorithm, however this algorithm is not efficient when data are sparse. In this thesis we developed a new version of the global k-means algorithm, the modified global k-means algorithm which is effective for solving clustering problems in gene expression data sets. In a microarray gene expression data set, in many cases only a small fraction of genes are informative whereas most of them are non-informative and make noise. Therefore the development of gene selection algorithms that allow us to remove as many non-informative genes as possible is very important. In this thesis we developed a new overlapping gene selection algorithm. This algorithm is based on calculating overlaps of different genes. It considerably reduces the number of genes and is efficient in finding a subset of informative genes. Over the last decade different approaches have been proposed to solve supervised data classification problems in gene expression data sets. In this thesis we developed a new approach which is based on the so-called max-min separability and is compared with the other approaches. The max-min separability algorithm is an equivalent of piecewise linear separability. An incremental algorithm is presented to compute piecewise linear functions separating two sets. This algorithm is applied along with a special gene selection algorithm. In this thesis, all new algorithms have been tested on 10 publicly available gene expression data sets and our numerical results demonstrate the efficiency of the new algorithms that were developed in the framework of this research
- Authors: Mardaneh, Karim
- Date: 2007
- Type: Text , Thesis , PhD
- Full Text:
- Description: Doctor of Philosophy
- Description: Bioinformatics and computational biology are relatively new areas that involve the use of different techniques including computer science, informatics, biochemistry, applied math and etc., to solve biological problems. In recent years the development of new molecular genetics technologies, such as DNA microarrays led to the simultaneous measurement of expression levels of thousands and even tens of thousands of genes. Microarray gene expression technology has facilitated the study of genomic structure and investigation of biological systems. Numerical output of this technology is shown as microarray gene expression data sets. These data sets contain a very large number of genes and a relatively small number of samples and their precise analysis requires a robust and suitable computer software. Due to this, only a few existing algorithms are applicable to them, so more efficient methods for solving clustering, gene selection and classification problems of gene expression data sets are required and those methods need to be computationally applicable and less expensive. The aim of this thesis is to develop new algorithms for solving clustering, gene selection and data classification problems on gene expression data sets. Clustering in gene expression data sets is a challenging problem. The increasing use of DNA microarray-based tumour gene expression profiles for cancer diagnosis requires more efficient methods to solve clustering problems of these profiles. Different algorithms for clustering of genes have been proposed, however few algorithms can be applied to the clustering of samples. k-means algorithm, among very few clustering algorithms is applicable to microarray gene expression data sets, however these are not efficient for solving clustering problems when the number of genes is thousands and this algorithm is very sensitive to the choice of a starting point. Additionally, when the number of clusters is relatively large, this algorithm gives local minima which can differ significantly from the global solution. Over the last several years different approaches have been proposed to improve global ii Abstract Abstract search properties of k-means algorithm. One of them is the global k-means algorithm, however this algorithm is not efficient when data are sparse. In this thesis we developed a new version of the global k-means algorithm, the modified global k-means algorithm which is effective for solving clustering problems in gene expression data sets. In a microarray gene expression data set, in many cases only a small fraction of genes are informative whereas most of them are non-informative and make noise. Therefore the development of gene selection algorithms that allow us to remove as many non-informative genes as possible is very important. In this thesis we developed a new overlapping gene selection algorithm. This algorithm is based on calculating overlaps of different genes. It considerably reduces the number of genes and is efficient in finding a subset of informative genes. Over the last decade different approaches have been proposed to solve supervised data classification problems in gene expression data sets. In this thesis we developed a new approach which is based on the so-called max-min separability and is compared with the other approaches. The max-min separability algorithm is an equivalent of piecewise linear separability. An incremental algorithm is presented to compute piecewise linear functions separating two sets. This algorithm is applied along with a special gene selection algorithm. In this thesis, all new algorithms have been tested on 10 publicly available gene expression data sets and our numerical results demonstrate the efficiency of the new algorithms that were developed in the framework of this research
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