Skeletal muscle transcriptome response to a bout of endurance exercise in physically active and sedentary older adults

Abstract

Age-related declines in cardiorespiratory fitness and physical function are mitigated by regular endurance exercise in older adults. This may be due, in part, to changes in the transcriptional program of skeletal muscle following repeated bouts of exercise. However, the impact of chronic exercise training on the transcriptional response to an acute bout of endurance exercise has not been clearly determined. Here, we characterized baseline differences in muscle transcriptome and exercise-induced response in older adults who were active/endurance trained or sedentary. RNA-sequencing was performed on vastus lateralis biopsy specimens obtained before, immediately after, and 3 h following a bout of endurance exercise (40 min of cycling at 60%-70% of heart rate reserve). Using a recently developed bioinformatics approach, we found that transcript signatures related to type I myofibers, mitochondria, and endothelial cells were higher in active/endurance-trained adults and were associated with key phenotypic features including V̇o_2peak, ATP_max, and muscle fiber proportion. Immune cell signatures were elevated in the sedentary group and linked to visceral and intermuscular adipose tissue mass. Following acute exercise, we observed distinct temporal transcriptional signatures that were largely similar among groups. Enrichment analysis revealed catabolic processes were uniquely enriched in the sedentary group at the 3-h postexercise timepoint. In summary, this study revealed key transcriptional signatures that distinguished active and sedentary adults, which were associated with difference in oxidative capacity and depot-specific adiposity. The acute response signatures were consistent with beneficial effects of endurance exercise to improve muscle health in older adults irrespective of exercise history and adiposity.NEW & NOTEWORTHY Muscle transcript signatures associated with oxidative capacity and immune cells underlie important phenotypic and clinical characteristics of older adults who are endurance trained or sedentary. Despite divergent phenotypes, the temporal transcriptional signatures in response to an acute bout of endurance exercise were largely similar among groups. These data provide new insight into the transcriptional programs of aging muscle and the beneficial effects of endurance exercise to promote healthy aging in older adults.

Keywords: RNA-seq; cardiorespiratory fitness; endothelial cell; mitochondria.

Graphical abstract

Figure 1.

Study design outline. Baseline and exercise-induced clinical phenotyping was performed across four separate visits. Following written informed consent, medical history, assessment of self-reported physical activity [physical activity survey for the elderly (PASE)], and assessment of body composition [dual X-ray absorptiometry (DXA)] were assessed on the screening visit for each participant. Following the screening visit, assessments of cardiorespiratory fitness (V̇o₂ peak test), muscle volume, and mitochondrial function [magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS)] on visits 2 and 3. Objective physical activity was assessed for at least 7 days between visits 3 and 4 via the SenseWear Pro Armband. During the exercise visit (visit 4), muscle biopsy specimens were obtained before (Pre), immediately (0 h) following an acute bout of endurance (cycling) exercise [40 min at 60%–70% heart rate reserve (HRR)] and 3 h into recovery postexercise (3-h post). Biopsies were used for immunohistology and transcriptome profiling by RNA-seq followed by informatics. Exercise intensity was evaluated throughout the exercise bout by examining heart rate, power output, ventilatory gas exchange volume of oxygen consumed (V̇o₂) and volume of carbon dioxide produced (V̇co₂) by indirect calorimetry and rating of perceived exertion (RPE).

Figure 2.

Cell type and pathways associated with PLIER latent variables (LVs). Heatmap of selected latent variable (LV) pathway associations (colored entries) that showed differences between active/endurance trained and sedentary groups, distinct temporal responses to acute exercise, or both group and time differences, as well as cell signatures that have been implicated in skeletal muscle adaptations with aging (i.e., FAP cells, ribosome, lysosome). Prior knowledge inputs provided to PLIER included canonical pathways (KEGG, Reactome), muscle fiber type-specific pathways, and immune cell-specific pathways. Darker colors indicate greater (LV) pathway associations. LVs were selected based on the presence of significant differences between groups, timepoints, or both. Star indicates gene signatures that were derived from single cell (gold star) or individual muscle fiber (blue star) RNA-seq analysis described by Rubenstein et al. (35). PLIER, pathway-level information ExtractoR.

Figure 3.

Muscle fiber transcriptome signatures are associated with histological analysis of muscle fiber type proportion in older active/endurance trained and sedentary adults. Heatmaps represent transcripts for the top thirty transcripts that are associated with LV10 (slow fiber type) (A) and LV17 (fast fiber type) (B). Each column represents one sample; columns are ordered by timepoint (Pre, light purple; Post, orange; 3-h post, maroon) and group [active/trained, green (n = 10); sedentary, blue (n = 9)]. Black squares indicate transcripts that mapped to specific prior knowledge pathway. Data are presented as z-scored regularized log-transformed gene expression data. Transcript signatures for slow fiber type (LV10) (C) and fast fiber type (LV17) (D) were evaluated in older active/endurance trained (green circles and lines, n = 10) and sedentary adults (blue circles and lines, n = 9) adults at before (Pre), immediately following (Post), and 3 h after (3-h Post) an acute bout of endurance exercise. Data are presented as means ± SD. ^Significant difference (P < 0.05) between groups; †P < 0.05 vs. Pre; §P < 0.05 vs. Post using a repeated-measures ANOVA with group, timepoint, and their interactions as factors in the model, followed by Tukey’s post hoc test. Pearson partial correlations were then used to examine the relationship between LV signatures and type I myofiber proportion (E) and type II proportion (F) in older active/endurance trained [green circles, n = 9 (7 male/2 female)] and older sedentary [blue circles, n = 8 (6 male/2 female)].

Figure 4.

Mitochondrial transcriptome signatures are associated with whole body and muscle-specific oxidative capacity in older active/endurance trained and sedentary adults. A: heatmaps represent transcripts for the top 30 transcripts that are associated with LV11. Each column represents one sample; columns are ordered by timepoint (Pre, light purple; Post, orange; 3-h Post, maroon) and group [active/trained, green (n = 10); sedentary, blue (n = 9)]. Black squares indicate transcripts that mapped to specific prior knowledge pathway. Data are presented as z-scored regularized log-transformed gene expression data. B: transcript signatures for mitochondria (LV11) were evaluated in older active/endurance trained (green circles and lines, n = 10) and sedentary adults (blue circles and lines, n = 9) adults at before (Pre), immediately following (Post), and 3 h after (3-h Post) an acute bout of endurance exercise. Data are presented as means ± SD. ^Significant difference (P < 0.05) between groups. Pearson partial correlations were then used to examine the relationship between LV signatures and cardiorespiratory fitness (Relative V̇o_2peak) (C) and in vivo mitochondrial energetics (ATP_max) (D) in older active/endurance trained (green circles, n = 10) and older sedentary (blue circles, n = 9).

Figure 5.

Endothelial cell transcriptome signatures are associated with oxidative capacity and skeletal muscle mass in older active/endurance trained and sedentary adults. A: heatmaps represent transcripts for the top 30 transcripts that are associated with LV33. Each column represents one sample; columns are ordered by timepoint (Pre, light purple; Post, orange; 3-h Post, maroon) and group [active/trained, green (n = 10); sedentary, blue (n = 9)]. Black squares indicate transcripts that mapped to specific prior knowledge pathway. Data are presented as z-scored regularized log-transformed gene expression data. B: transcript signatures for endothelial cells (LV33) were evaluated in older active/endurance trained (green circles and lines, n = 10) and sedentary adults (blue circles and lines, n = 9) adults at before (Pre), immediately following (Post), and 3 h after (3-h Post) an acute bout of endurance exercise. Data are presented as means ± SD. ^Significant difference (P < 0.05) between groups; †P < 0.05 vs. Pre; §P < 0.05 vs. Post using a repeated-measures ANOVA with group, timepoint, and their interactions as factors in the model, followed by Tukey’s post hoc test. Pearson partial correlations were then used to examine the relationship between LV signatures and cardiorespiratory fitness (Relative V̇o_2peak) (C) and in vivo mitochondrial energetics (ATPmax) (D) in older active/endurance trained (green circles, n = 10) and older sedentary (blue circles, n = 9).

Figure 6.

Immune cell signatures are elevated in older sedentary adults and are related to visceral and intermuscular adipose tissue accumulation. A: heatmaps represent transcripts for the top 30 transcripts that are associated with LV42 (immune cells). Each column represents one sample; columns are ordered by timepoint (Pre, light purple; Post, orange; 3-h Post, maroon) and group [active/trained, green (n = 10); sedentary, blue (n = 9)]. Black squares indicate transcripts that mapped to specific prior knowledge pathway. Data are presented as z-scored regularized log-transformed gene expression data. B: transcript signatures for immune cells (LV42) were evaluated in older active/endurance trained (green circles and lines, n = 10) and sedentary adults (blue circles and lines, n = 9) adults at before (Pre), immediately following (Post), and 3 h after (3-h Post) an acute bout of endurance exercise. Data are presented as means ± SD. ^Significant difference (P < 0.05) between groups using a repeated-measures ANOVA with group, timepoint, and their interactions as factors in the model, followed by Tukey’s post hoc test. Pearson partial correlations were then used to examine the relationship between LV signatures and visceral adipose tissue mass (C) and intermuscular adipose tissue (IMAT) volume (D) in older active/endurance trained (green circles, n = 10) and older sedentary (blue circles, n = 9).

Figure 7.

Latent variables (LVs) that define time-dependent transcriptional responses to exercise are similar between active/endurance trained and sedentary older adults. LVs associated with the early (LV2; A), late (LV5; B and LV28; C), and gradual (LV39; D) transcriptional response to an acute bout of endurance exercise were evaluated in older active/endurance trained (green circles and lines, n = 10) and sedentary adults (blue circles and lines, n = 9). Data are presented as means ± SD. †P < 0.05 vs. Pre; §P < 0.05 vs. Post; ‡P < 0.05 vs. 3-h Post using a repeated-measures ANOVA with group, timepoint, and their interactions as factors in the model, followed by Tukey’s post hoc test. Heatmaps were generated using transcripts that are differentially expressed in LV2 (E), LV5 (F), LV28 (G), and LV39 (H). Data are presented as z-scored regularized log-transformed gene expression data. Each column represents an individual participant and are separated by timepoint (Pre, purple; Post, orange; 3-h Post, red) and group (active/trained, green; sedentary, blue).

Figure 8.

Pathway analysis of transcriptome pathways that are similarly provoked in skeletal muscle by endurance exercise in older active/endurance trained and sedentary adults. Venn diagrams represent DE transcripts for each cohort (green, active/endurance trained-specific transcripts; blue, sedentary (Sed)-specific transcripts; gray, transcripts with similar response between active/endurance trained and sedentary adults) in every comparison [Pre vs. Post (A), Pre vs. 3-h Post (B), Post vs. 3 h Post (C)]. Pathway analysis of transcripts that showed similar response between groups in each comparison [Pre vs. Post (D), Pre vs. 3-h Post (E and F), Post vs. 3 h Post (G)]. Color of dot indicates level of significance (P-adjusted value) and size of dot indicates number of transcripts found in each pathway.