Making sense of the ageing methylome.

Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.

Methylome and proteome integration in human skeletal muscle uncover group and individual responses to high-intensity interval training.

Exercise is a major beneficial contributor to muscle metabolism, and health benefits acquired by exercise are a result of molecular shifts occurring across multiple molecular layers (i.e., epigenome, transcriptome, and proteome). Identifying robust, across-molecular level targets associated with exercise response, at both group and individual levels, is paramount to develop health guidelines and targeted health interventions. Sixteen, apparently healthy, moderately trained (VO2 max = 51.0 ± 10.6 mL min-1 kg-1 ) males (age range = 18-45 years) from the Gene SMART (Skeletal Muscle Adaptive Responses to Training) study completed a longitudinal study composed of 12-week high-intensity interval training (HIIT) intervention. Vastus lateralis muscle biopsies were collected at baseline and after 4, 8, and 12 weeks of HIIT. DNA methylation (~850 CpG sites) and proteomic (~3000 proteins) analyses were conducted at all time points. Mixed models were applied to estimate group and individual changes, and methylome and proteome integration was conducted using a holistic multilevel approach with the mixOmics package. A total of 461 proteins significantly changed over time (at 4, 8, and 12 weeks), whilst methylome overall shifted with training only one differentially methylated position (DMP) was significant (adj.p-value < .05). K-means analysis revealed cumulative protein changes by clusters of proteins that presented similar changes over time. Individual responses to training were observed in 101 proteins. Seven proteins had large effect-sizes >0.5, among them are two novel exercise-related proteins, LYRM7 and EPN1. Integration analysis showed bidirectional relationships between the methylome and proteome. We showed a significant influence of HIIT on the epigenome and more so on the proteome in human muscle, and uncovered groups of proteins clustering according to similar patterns across the exercise intervention. Individual responses to exercise were observed in the proteome with novel mitochondrial and metabolic proteins consistently changed across individuals. Future work is required to elucidate the role of these proteins in response to exercise.

Muscle miRNAs are influenced by sex at baseline and in response to exercise.

BACKGROUND: Sex differences in microRNA (miRNA) expression profiles have been found across multiple tissues. Skeletal muscle is one of the most sex-biased tissues of the body. MiRNAs are necessary for development and have regulatory roles in determining skeletal muscle phenotype and have important roles in the response to exercise in muscle. Yet there is limited research into the role and regulation of miRNAs in the skeletal muscle at baseline and in response to exercise, a well-known modulator of miRNA expression. The aim of this study was to investigate the effect of sex on miRNA expression in the skeletal muscle at baseline and after an acute bout of high-intensity interval exercise. A total of 758 miRNAs were measured using Taqman®miRNA arrays in the skeletal muscle of 42 healthy participants from the Gene SMART study (23 males and 19 females of comparable fitness levels and aged 18-45 years), of which 308 were detected. MiRNAs that differed by sex at baseline and whose change in expression following high-intensity interval exercise differed between the sexes were identified using mixed linear models adjusted for BMI and Wpeak. We performed in silico analyses to identify the putative gene targets of the exercise-induced, sex-specific miRNAs and overrepresentation analyses to identify enriched biological pathways. We performed functional assays by overexpressing two sex-biased miRNAs in human primary muscle cells derived from male and female donors to understand their downstream effects on the transcriptome. RESULTS: At baseline, 148 miRNAs were differentially expressed in the skeletal muscle between the sexes. Interaction analysis identified 111 miRNAs whose response to an acute bout of high-intensity interval exercise differed between the sexes. Sex-biased miRNA gene targets were enriched for muscle-related processes including proliferation and differentiation of muscle cells and numerous metabolic pathways, suggesting that miRNAs participate in programming sex differences in skeletal muscle function. Overexpression of sex-biased miRNA-30a and miRNA-30c resulted in profound changes in gene expression profiles that were specific to the sex of the cell donor in human primary skeletal muscle cells. CONCLUSIONS: We uncovered sex differences in the expression levels of muscle miRNAs at baseline and in response to acute high-intensity interval exercise. These miRNAs target regulatory pathways essential to skeletal muscle development and metabolism. Our findings highlight that miRNAs play an important role in programming sex differences in the skeletal muscle phenotype.

Physiological and molecular sex differences in human skeletal muscle in response to exercise training.

Sex differences in exercise physiology, such as substrate metabolism and skeletal muscle fatigability, stem from inherent biological factors, including endogenous hormones and genetics. Studies investigating exercise physiology frequently include only males or do not take sex differences into consideration. Although there is still an underrepresentation of female participants in exercise research, existing studies have identified sex differences in physiological and molecular responses to exercise training. The observed sex differences in exercise physiology are underpinned by the sex chromosome complement, sex hormones and, on a molecular level, the epigenome and transcriptome. Future research in the field should aim to include both sexes, control for menstrual cycle factors, conduct large-scale and ethnically diverse studies, conduct meta-analyses to consolidate findings from various studies, leverage unique cohorts (such as post-menopausal, transgender, and those with sex chromosome abnormalities), as well as integrate tissue and cell-specific -omics data. This knowledge is essential for developing deeper insight into sex-specific physiological responses to exercise training, thus directing future exercise physiology studies and practical application.

Low-Load Resistance Training to Volitional Failure Induces Muscle Hypertrophy Similar to Volume-Matched, Velocity Fatigue.

ABSTRACT: Terada, K, Kikuchi, N, Burt, D, Voisin, S, and Nakazato, K. Full title: Low-load resistance training to volitional failure induces muscle hypertrophy similar to volume-matched, velocity fatigue. J Strength Cond Res 36(6): 1576-1581, 2022-We investigated how resistance training (RT) to failure at low load affects acute responses and chronic muscle adaptations compared with low-load RT to velocity fatigue at equal work volume. Twenty-seven subjects performed 8 weeks of bench press twice weekly. Subjects were randomly assigned to one of 3 groups: low-load volitional failure (LVoF, n = 9), low-load velocity fatigue (LVeF, n = 8), and high-load (HL, n = 10). Resistance training comprised 3 sets to failure at 40% one repetition maximum (1RM) in the LVoF group, 3 sets to velocity fatigue (20% lifting velocity loss) at 40% 1RM in the LVeF group, and 3 sets of 8 repetitions at 80% 1RM in the HL group. We measured muscle strength, hypertrophy, endurance, and power at baseline and after the RT program. We also measured muscle swelling and blood lactate after each RT bout to investigate the acute response. There were no differences in total work volume between the LVoF and LVeF groups. Responses to RT were similar between LVoF and LVeF, whether looking at acute muscle swelling, increase in blood lactate, chronic hypertrophy, and strength gain. However, LVoF and LVeF RT triggered different responses to muscle function in comparison with HL training: LVoF and LVeF showed enhanced acute responses and greater chronic endurance gains, but lower chronic strength gains than HL. In conclusion, low-load RT to volitional failure induces muscle hypertrophy similar to volume-matched velocity fatigue.

Mitochondrial respiration variability and simulations in human skeletal muscle: The Gene SMART study.

Mitochondrial respiration using the oxygraph-2k respirometer (Oroboros) is widely used to estimate mitochondrial capacity in human skeletal muscle. Here, we measured mitochondrial respiration variability, in a relatively large sample, and for the first time, using statistical simulations, we provide the sample size required to detect meaningful respiration changes following lifestyle intervention. Muscle biopsies were taken from healthy, young men from the Gene SMART cohort, at multiple time points. We utilized samples for each measurement with two technical repeats using two respirometer chambers (n = 160 pairs of same muscle after removal of low-quality samples). We measured the Technical Error of measurement (TEM ) and the coefficient of variation (CV) for each mitochondrial complex. There was a high correlation between measurements from the two chambers (R > 0.7 P < .001) for all complexes, but the TEM was large (7.9-27 pmol s-1  mg-1 ; complex dependent), and the CV was >15% for all complexes. We performed statistical simulations of a range of effect sizes at 80% power and found that 75 participants (with duplicate measurements) are required to detect a 6% change in mitochondrial respiration after an intervention, while for interventions with 11% effect size, ~24 participants are sufficient. The high variability in respiration suggests that the typical sample sizes in exercise studies may not be sufficient to capture exercise-induced changes.

Mapping Robust Genetic Variants Associated with Exercise Responses.

This review summarised robust and consistent genetic variants associated with aerobic-related and resistance-related phenotypes. In total we highlight 12 SNPs and 7 SNPs that are robustly associated with variance in aerobic-related and resistance-related phenotypes respectively. To date, there is very little literature ascribed to understanding the interplay between genes and environmental factors and the development of physiological traits. We discuss future directions, including large-scale exercise studies to elucidate the functional relevance of the discovered genomic markers. This approach will allow more rigour and reproducible research in the field of exercise genomics.

Statistical Considerations for Exercise Protocols Aimed at Measuring Trainability.

The individual response to exercise training is of great interest with methods that have been proposed to measure this response reviewed in this paper. However, individual training response estimates may be biased by various sources of variability present in exercise studies, and in particular by within-subject variability. We propose the use of protocols that can separate trainability from within-subject variability.

The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder.

Several reports suggest obesity and bipolar disorder (BD) share some physiological and behavioural similarities. For instance, obese individuals are more impulsive and have heightened reward responsiveness, phenotypes associated with BD, while bipolar patients become obese at a higher rate and earlier age than people without BD; however, the molecular mechanisms of such an association remain obscure. Here we demonstrate, using whole transcriptome analysis, that Drosophila Ets96B, homologue of obesity-linked gene ETV5, regulates cellular systems associated with obesity and BD. Consistent with a role in obesity and BD, loss of nervous system Ets96B during development increases triacylglyceride concentration, while inducing a heightened startle-response, as well as increasing hyperactivity and reducing sleep. Of notable interest, mouse Etv5 and Drosophila Ets96B are expressed in dopaminergic-rich regions, and loss of Ets96B specifically in dopaminergic neurons recapitulates the metabolic and behavioural phenotypes. Moreover, our data indicate Ets96B inhibits dopaminergic-specific neuroprotective systems. Additionally, we reveal that multiple SNPs in human ETV5 link to body mass index (BMI) and BD, providing further evidence for ETV5 as an important and novel molecular intermediate between obesity and BD. We identify a novel molecular link between obesity and bipolar disorder. The Drosophila ETV5 homologue Ets96B regulates the expression of cellular systems with links to obesity and behaviour, including the expression of a conserved endoplasmic reticulum molecular chaperone complex known to be neuroprotective. Finally, a connection between the obesity-linked gene ETV5 and bipolar disorder emphasizes a functional relationship between obesity and BD at the molecular level.

ACTN3 R577X Polymorphism Is Associated With the Incidence and Severity of Injuries in Professional Football Players.

OBJECTIVE: The ACTN3 R577X gene variant results in the absence of the α-actinin-3 protein in ∼18% of humans worldwide and has been associated with athletic performance and increased susceptibility to eccentric muscle damage. The aim of this study was to investigate the association between ACTN3 R577X variant and indirect muscle disorders/injuries in professional football players. DESIGN: A case-control, genotype-phenotype association study. INTERVENTION: Two hundred fifty-seven male professional Italian football players (from Serie A, Primavera, Allievi, and Giovanissimi; age = 21.2 ± 5.3 years) and 265 nonathletic controls were recruited for the study. Genomic DNA was extracted using a buccal swab, and the ACTN3 R577X genotype was performed using a PCR method. Structural-mechanical injuries and functional muscle disorders were collected from a subgroup of 169 football players during the period of 2009 to 2014. MAIN OUTCOME MEASURE: We hypothesized that the 577XX genotype would be associated with higher predisposition to muscle injuries (compared with the other genotypes). RESULTS: ACTN3 XX (α-actinin-3 deficiency) players had 2.66 higher odds for an injury incidence than their ACTN3 RR counterparts (95% confidence interval [CI]: 1.09-6.63, P = 0.02), whereas RX and RR players had similar injury incidence. Furthermore, ACTN3 XX players had 2.13 higher odds for having a severe injury compared with their RR counterparts (95% CI: 1.25-3.74, P = 0.0054), whereas RX individuals had 1.63 higher odds for having a severe injury compared with the RR players (95% CI: 1.10-2.40, P = 0.015). CONCLUSIONS: The ACTN3 R577X polymorphism is associated with the incidence and severity of muscle injuries in professional football players; players with the ACTN3 577XX genotype have higher odds of having muscle injuries than their RR counterparts. CLINICAL RELEVANCE: Discovering the complex relationship between gene variants and muscle injuries may assist coaches, physiologists, and the medical community to development tailored injury prevention program for football players, which could provide a new edge for successful competition.

No association between ACTN3 R577X and ACE I/D polymorphisms and endurance running times in 698 Caucasian athletes.

BACKGROUND: Studies investigating associations between ACTN3 R577X and ACE I/D genotypes and endurance athletic status have been limited by small sample sizes from mixed sport disciplines and lack quantitative measures of performance. AIM: To examine the association between ACTN3 R577X and ACE I/D genotypes and best personal running times in a large homogeneous cohort of endurance runners. METHODS: We collected a total of 1064 personal best 1500, 3000, 5000 m and marathon running times of 698 male and female Caucasian endurance athletes from six countries (Australia, Greece, Italy, Poland, Russia and UK). Athletes were genotyped for ACTN3 R577X and ACE ID variants. RESULTS: There was no association between ACTN3 R577X or ACE I/D genotype and running performance at any distance in men or women. Mean (SD) marathon times (in s) were for men: ACTN3 RR 9149 (593), RX 9221 (582), XX 9129 (582) p = 0.94; ACE DD 9182 (665), ID 9214 (549), II 9155 (492) p = 0.85; for women: ACTN3 RR 10796 (818), RX 10667 (695), XX 10675 (553) p = 0.36; ACE DD 10604 (561), ID 10766 (740), II 10771 (708) p = 0.21. Furthermore, there were no associations between these variants and running time for any distance in a sub-analysis of athletes with personal records within 20% of world records. CONCLUSIONS: Thus, consistent with most case-control studies, this multi-cohort quantitative analysis demonstrates it is unlikely that ACTN3 XX genotype provides an advantage in competitive endurance running performance. For ACE II genotype, some prior studies show an association but others do not. Our data indicate it is also unlikely that ACE II genotype provides an advantage in endurance running.

ACTN3 R577X Gene Variant Is Associated With Muscle-Related Phenotypes in Elite Chinese Sprint/Power Athletes.

Yang, R, Shen, X, Wang, Y, Voisin, S, Cai, G, Fu, Y, Xu, W, Eynon, N, Bishop, DJ, and Yan, X. ACTN3 R577X gene variant is associated with muscle-related phenotypes in elite Chinese sprint/power athletes. J Strength Cond Res 31(4): 1107-1115, 2017-The ACTN3 R577X polymorphism (rs1815739) has been shown to influence athletic performance. The aim of this study was to investigate the prevalence of this polymorphism in elite Chinese track and field athletes, and to explore its effects on athletes' level of competition and lower-extremity power. We compared the ACTN3 R577X genotypes and allele frequencies in 59 elite sprint/power athletes, 44 elite endurance athletes, and 50 healthy controls from Chinese Han origin. We then subcategorized the athletes into international level and national level and investigated the effects of ACTN3 genotype on lower-extremity power. Genotype distribution of the sprint/power athletes was significantly different from endurance athletes (p = 0.001) and controls (p < 0.001). The frequency of the RR genotype was significantly higher in international-level than that in the national-level sprint/power athletes (p = 0.004), with no international-level sprint/power athletes with XX genotype. The best standing long jump and standing vertical jump results of sprint/power athletes were better in the RR than those in the RX + XX genotypes (p = 0.004 and p = 0.001, respectively). In conclusion, the ACTN3 R577X polymorphism influences the level of competition and lower-extremity power of elite Chinese sprint/power athletes. Including relevant phenotypes such as muscle performance in future studies is important to further understand the effects of gene variants on elite athletic performance.

Implication of coronin 7 in body weight regulation in humans, mice and flies.

BACKGROUND: Obesity is a growing global concern with strong associations with cardiovascular disease, cancer and type-2 diabetes. Although various genome-wide association studies have identified more than 40 genes associated with obesity, these genes cannot fully explain the heritability of obesity, suggesting there may be other contributing factors, including epigenetic effects. RESULTS: We performed genome wide DNA methylation profiling comparing normal-weight and obese 9-13 year old children to investigate possible epigenetic changes correlated with obesity. Of note, obese children had significantly lower methylation levels at a CpG site located near coronin 7 (CORO7), which encodes a tryptophan-aspartic acid dipeptide (WD)-repeat containing protein most likely involved in Golgi complex morphology and function. Anatomical profiling of coronin 7 (Coro7) mRNA expression in mice revealed that it is highly expressed in appetite and energy balance regulating regions, including the hypothalamus, striatum and locus coeruleus, the main noradrenergic brain site. Interestingly, we found that food deprivation in mice downregulates hypothalamic Coro7 mRNA levels, and injecting ethanol, an appetite stimulant, increased the number of Coro7 expressing cells in the locus coeruleus. Finally, by employing the genetically-tractable Drosophila melanogaster model we were able to demonstrate an evolutionarily conserved metabolic function for the CORO7 homologue pod1. Knocking down the pod1 in the Drosophila adult nervous system increased their resistance to starvation. Furthermore, feeding flies a high-calorie diet significantly increased pod1 expression. CONCLUSION: We conclude that coronin 7 is involved in the regulation of energy homeostasis and this role stems, to some degree, from the effect on feeding for calories and reward.

EPAS1 gene variants are associated with sprint/power athletic performance in two cohorts of European athletes.

BACKGROUND: The endothelial PAS domain protein 1 (EPAS1) activates genes that are involved in erythropoiesis and angiogenesis, thus favoring a better delivery of oxygen to the tissues and is a plausible candidate to influence athletic performance. Using innovative statistical methods we compared genotype distributions and interactions of EPAS1 SNPs rs1867785, rs11689011, rs895436, rs4035887 and rs1867782 between sprint/power athletes (n=338), endurance athletes (n=254), and controls (603) in Polish and Russian samples. We also examined the association between these SNPs and the athletes' competition level ('elite' and 'sub-elite' level). Genotyping was performed by either Real-Time PCR or by Single-Base Extension (SBE) method. RESULTS: In the pooled cohort of Polish and Russian athletes, 1) rs1867785 was associated with sprint/power athletic status; the AA genotype in rs1867785 was underrepresented in the sprint/power athletes, 2) rs11689011 was also associated with sprint/power athletic status; the TT genotype in rs11689011 was underrepresented sprint/power athletes, and 3) the interaction between rs1867785, rs11689011, and rs4035887 was associated with sprint/power athletic performance; the combinations of the AA genotype in rs4035887 with either the AG or GG genotypes in rs1867785, or with the CT or CC genotypes in rs11689011, were underrepresented in two cohorts of sprint/power athletes. CONCLUSIONS: Based on the unique statistical model rs1867785/rs11689011 are strong predictors of sprint/power athletic status, and the interaction between rs1867785, rs11689011, and rs4035887 might contribute to success in sprint/power athletic performance.

Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle.

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 samples (n = 3176). We show that: (1) individuals with higher baseline aerobic fitness have younger epigenetic and transcriptomic profiles, (2) exercise training leads to significant shifts of epigenetic and transcriptomic patterns toward 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 toward a younger state after exercise training interventions, while the transcriptome shifted toward 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.

Implementation of multiple statistical methods to estimate variability and individual response to training.

Multiple statistical methods have been proposed to estimate individual responses to exercise training; yet, the evaluation of these methods is lacking. We compared five of these methods including the following: the use of a control group, a control period, repeated testing during an intervention, a reliability trial and a repeated intervention. Apparently healthy males from the Gene SMART study completed a 4-week control period, 4 weeks of High-Intensity Interval Training (HIIT), >1 year of washout, and then subsequently repeated the same 4 weeks of HIIT, followed by an additional 8 weeks of HIIT. Aerobic fitness measurements were measured in duplicates at each time point. We found that the control group and control period were not intended to measure the degree to which individuals responded to training, but rather estimated whether individual responses to training can be detected with the current exercise protocol. After a repeated intervention, individual responses to 4 weeks of HIIT were not consistent, whereas repeated testing during the 12-week-long intervention was able to capture individual responses to HIIT. The reliability trial should not be used to study individual responses, rather should be used to classify participants as responders with a certain level of confidence. 12 weeks of HIIT with repeated testing during the intervention is sufficient and cost-effective to measure individual responses to exercise training since it allows for a confident estimate of an individual's true response. Our study has significant implications for how to improve the design of exercise studies to accurately estimate individual responses to exercise training interventions.HighlightsWhat are the findings? We implemented five statistical methods in a single study to estimate the magnitude of within-subject variability and quantify responses to exercise training at the individual level.The various proposed methods used to estimate individual responses to training provide different types of information and rely on different assumptions that are difficult to test.Within-subject variability is often large in magnitude, and as such, should be systematically evaluated and carefully considered in future studies to successfully estimate individual responses to training.How might it impact on clinical practice in the future?Within-subject variability in response to exercise training is a key factor that must be considered in order to obtain a reproducible measurement of individual responses to exercise training. This is akin to ensuring data are reproducible for each subject.Our findings provide guidelines for future exercise training studies to ensure results are reproducible within participants and to minimise wasting precious research resources.By implementing five suggested methods to estimate individual responses to training, we highlight their feasibility, strengths, weaknesses and costs, for researchers to make the best decision on how to accurately measure individual responses to exercise training.

Genetic variants within the COL5A1 gene are associated with ligament injuries in physically active populations from Australia, South Africa, and Japan.

Previous small-scale studies have shown an association between the COL5A1 gene and anterior cruciate ligament (ACL) injury risk. In this larger study, the genotype and allele frequency distributions of the COL5A1 rs12722 C/T and rs10628678 AGGG/deletion (AGGG/-) indel variants were compared between participants: (i) with ACL injury in independent and combined cohorts from South-Africa (SA) and Australia (AUS) vs controls (CON), and (ii) with any ligament (ALL) or only ACL injury in a Japanese (JPN) cohort vs CON. Samples were collected from SA (235 cases; 232 controls), AUS (362 cases; 80 controls) and JPN (500 cases; 1,403 controls). Genomic DNA was extracted and genotyped. Distributions were compared, and inferred haplotype analyses performed. No independent associations were noted for rs12722 or rs10628678 when the combined SA + AUS cohort was analysed. However, the C-deletion (rs12722-rs10628678) inferred haplotype was under-represented (p = 0.040, OR = 0.15, CI = 0.04-0.56), while the T-deletion inferred haplotype was over-represented in the female SA + AUS ACL participants versus controls (p < 0.001, OR = 4.74, CI = 1.66-13.55). Additionally, the rs12722 C/C genotype was under-represented in JPN CON vs ACL (p = 0.039, OR = 0.52, 0.27-1.00), while the rs10628678 -/- genotype was associated with increased risk of any ligament injuries (p = 0.035, OR = 1.31, CI = 1.02-1.68) in the JPN cohort. Collectively, these results highlight that a region within the COL5A1 3'-UTR is associated with ligament injury risk. This must be evaluated in larger cohorts and its functional relevance to the structure and capacity of ligaments and joint biomechanics be explored.Highlights The COL5A1 T-deletion inferred haplotype (rs12722-rs10628678) was associated with an increased risk of ACL rupture in the combined SA and AUS female participants.The COL5A1 C-deletion inferred haplotype (rs12722-rs10628678) was associated with a decreased risk of ACL rupture in the combined SA and AUS female participants.The COL5A1 rs12722 C/C and rs10628678 -/- genotypes were associated with increased risk of ACL rupture and of ligament injuries in JPN, respectively.A region within the COL5A1 3'-UTR is associated with risk of ligament injury, including ACL rupture, and therefore the functional significance of this region on ligament capacity and joint biomechanics requires further exploration.

Sex differences in muscle protein expression and DNA methylation in response to exercise training.

BACKGROUND: Exercise training elicits changes in muscle physiology, epigenomics, transcriptomics, and proteomics, with males and females exhibiting differing physiological responses to exercise training. However, the molecular mechanisms contributing to the differing adaptations between the sexes are poorly understood. METHODS: We performed a meta-analysis for sex differences in skeletal muscle DNA methylation following an endurance training intervention (Gene SMART cohort and E-MTAB-11282 cohort). We investigated for sex differences in the skeletal muscle proteome following an endurance training intervention (Gene SMART cohort). Lastly, we investigated whether the methylome and proteome are associated with baseline cardiorespiratory fitness (maximal oxygen consumption; VO2max) in a sex-specific manner. RESULTS: Here, we investigated for the first time, DNA methylome and proteome sex differences in response to exercise training in human skeletal muscle (n = 78; 50 males, 28 females). We identified 92 DNA methylation sites (CpGs) associated with exercise training; however, no CpGs changed in a sex-dependent manner. In contrast, we identified 189 proteins that are differentially expressed between the sexes following training, with 82 proteins differentially expressed between the sexes at baseline. Proteins showing the most robust sex-specific response to exercise include SIRT3, MRPL41, and MBP. Irrespective of sex, cardiorespiratory fitness was associated with robust methylome changes (19,257 CpGs) and no proteomic changes. We did not observe sex differences in the association between cardiorespiratory fitness and the DNA methylome. Integrative multi-omic analysis identified sex-specific mitochondrial metabolism pathways associated with exercise responses. Lastly, exercise training and cardiorespiratory fitness shifted the DNA methylomes to be more similar between the sexes. CONCLUSIONS: We identified sex differences in protein expression changes, but not DNA methylation changes, following an endurance exercise training intervention; whereas we identified no sex differences in the DNA methylome or proteome response to lifelong training. Given the delicate interaction between sex and training as well as the limitations of the current study, more studies are required to elucidate whether there is a sex-specific training effect on the DNA methylome. We found that genes involved in mitochondrial metabolism pathways are differentially modulated between the sexes following endurance exercise training. These results shed light on sex differences in molecular adaptations to exercise training in skeletal muscle.

A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes.

BACKGROUND: Changes in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect shifts in tissue composition. METHODS: Here we derive a DNA methylation reference matrix for 12 immune-cell types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix, we perform a directional Stouffer and fixed effects meta-analysis comprising 23,053 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes. In a separate cohort of 4386 blood samples, we assess associations between immune-cell fractions and health outcomes. RESULTS: Our meta-analysis reveals many associations of cell-type fractions with age, sex, smoking and obesity, many of which we validate with single-cell RNA sequencing. We discover that naïve and regulatory T-cell subsets are higher in women compared to men, while the reverse is true for monocyte, natural killer, basophil, and eosinophil fractions. Decreased natural killer counts associated with smoking, obesity, and stress levels, while an increased count correlates with exercise and sleep. Analysis of health outcomes revealed that increased naïve CD4 + T-cell and N-cell fractions associated with a reduced risk of all-cause mortality independently of all major epidemiological risk factors and baseline co-morbidity. A machine learning predictor built only with immune-cell fractions achieved a C-index value for all-cause mortality of 0.69 (95%CI 0.67-0.72), which increased to 0.83 (0.80-0.86) upon inclusion of epidemiological risk factors and baseline co-morbidity. CONCLUSIONS: This work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes.