Expression landscapes of myoblasts and myotubes from T2D individuals are distinct from controls, and identify VPS39 as a previously unrecognized candidate regulating myogenesis

To dissect transcriptional and epigenetic differences between T2D and control muscle cells, we isolated human muscle stem cells (satellite cells) from vastus lateralis from 14 controls with normal glucose tolerance (NGT) and 14 individuals with T2D. Their clinical characteristics are described in Table 11a).

Table 1 Clinical characteristics of human donors of muscle cells.
Fig. 1: Differential gene expression in myoblasts and myotubes from 13 individuals with type 2 diabetes versus 13 controls, and identification of VPS39 as a regulator of human myogenesis.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

a Representative light microscope images of human proliferating myoblasts and differentiated myotubes. Images were taken for 14 individuals with type 2 diabetes and 14 controls. Scale bar 100 µm. b Schematic overview of analyses performed in human myoblasts and myotubes from individuals with type 2 diabetes (T2D) vs. controls (NGT, normal glucose tolerance). cd mRNA expression (microarray) of genes previously not described in relation to myogenesis (VPS39, TDP1, and MAEA) (c), and genes known to be involved in muscle regeneration (d) that exhibit differential expression in myoblasts from individuals with T2D (blue bars) vs. NGT (green bars). n = 13 individuals per group. *qq-values see Supplementary Data 1, Sheet A. e Frequency distribution (%) of CpG sites (n = 832) in relation to gene regions (left panel) and CpG islands (right panel). CpG sites for which a negative correlation between DNA methylation and expression of annotated genes was established are included. TSS, transcription start site; TSS200 and TSS1500, proximal promoter, defined as 1–200 bp (base pairs) or 201–1500 bp upstream of the TSS, respectively; UTR, untranslated region; CpG island, 200 bp (or more) stretch of DNA with a C + G content of > 50% and an observed/expected CpG ratio of > 0.6; Shore, regions flanking CpG islands, 0–2000 bp; Shelf, regions flanking island shores, 0–2000 bp. f Reporter gene transcription measured by luciferase activity (firefly/renilla-ratio) after in vitro methylation with M.SssI (dark gray bars) or mock-methylation (Control, light gray bars) of the VPS39 and FBN2 promoters cloned into a CpG-free vector and transfected into C2C12 myoblasts. n = 5 (VPS39) and n = 6 (FBN2) independent experiments. Numbers in blue above the bars represent the number of target CpG sites in the respective promoter sequence. The Control for each promoter is set to 1. **pp = 0.0501 (VPS39), p = 0.0068 (FBN2). g mRNA expression (microarray) of VPS39 in myoblasts and myotubes from individuals with T2D (blue bars) and NGT (green bars). n = 13 individuals per group. *qq-values see Supplementary Data 1, Sheets A and B. h Knockdown efficiency of VPS39 mRNA (left panel, n = 6 [Day 3] and n = 4 [Day 7] independent experiments) and VPS39 protein (right panel, n = 4 [Day 3] and n = 3 [Day 7] independent experiments) after siRNA silencing of VPS39 (siVPS39, purple bars) throughout cell differentiation. Negative control (NC, gray bars) at each time point is set to 1. Representative blots are shown. *ppVPS39 vs. NC. p = 0.0302 (VPS39 mRNA Day 3), p = 0.0379 (VPS39 mRNA Day 7), and p = 0.004 (VPS39 protein Day 3), p = 0.0389 (VPS39 protein Day 7). ij Assessment of myotube formation (fusion index) at day 7 of differentiation in siVPS39 and NC (i). n = 4 independent experiments, *pVPS39 vs. NC, p = 0.0266. j Representative images from the assay, showing reduced myotube formation after VPS39-silencing. Scale bar 200 µm. Bars represent mean values and error bars display SEM (cd, fi). Statistical significance determined by linear regression adjusted for age, BMI and sex for T2D vs. NGT (cd, g). P-values were adjusted for multiple comparisons with false discovery rate (FDR) analysis (cd, g). Statistical significance determined by paired two-tailed t-test (f, hi).

We then tested whether T2D is associated with altered expression of previously unrecognized and known regulators of muscle regeneration in human myoblasts. We performed genome-wide expression analysis of myoblasts obtained from 13 controls and 13 individuals with T2D (Fig. 1b). Based on a false discovery rate (FDR) below 5% (q1, Sheet A). These included several genes that had not previously been studied in human myoblasts but with identified functions in other cell types or species that suggest that they may also have a role in human muscle cells, e.g., VPS39, TDP1, and MAEA19,20,21,22,23,24,25, as well as genes previously implicated in muscle regeneration, e.g., FBN2, TEAD4, and STAT326,27 (Fig. 1c–d). This highlights differences in expression in myoblasts from individuals with T2D and healthy individuals.

DNA methylation controls cell-specific expression and myogenesis18. Therefore, we proceeded to relate DNA methylation to expression in human myoblasts. Using Infinium 450K BeadChips, we analyzed DNA methylation in myoblasts from 14 controls and 14 individuals with T2D, and filtered 10,992 CpG sites annotated to the 577 unique genes that exhibited differential expression in myoblasts from individuals with T2D versus controls. We then studied the correlations between methylation and expression of these 577 genes since methylation may regulate gene expression. We identified 331 differentially expressed genes that displayed nominal correlations between expression and methylation of one or more CpG site (p2). These included VPS39, TDP1, MAEA, and FBN2. A large proportion of the sites with negative correlations between methylation and expression are located close to transcription start sites (TSS) (TSS200 and 5’UTR) (p-chi2 = 0.001 compared to all analyzed sites, Fig. 1e). These data suggest that DNA methylation may control expression in human myoblasts. To directly confirm that DNA methylation regulates the transcriptional activity, we used luciferase reporter assays to study two of the identified genes, VPS39 and FBN2, presented in Fig. 1c–d and Supplementary Data 2. Indeed, higher methylation of the VPS39 and FBN2 promoters directly led to reduced transcriptional activity of the reporter genes, supporting an epigenetic regulation of expression in myoblasts from individuals with T2D (Fig. 1f).

We next asked whether genes that showed differential expression in myoblasts from individuals with T2D versus control individuals, also showed altered expression after differentiation into multinucleated myotubes (Fig. 1a). We performed genome-wide expression analysis of myotubes from the same 13 individuals with T2D and 13 control individuals, also included for analysis of expression in myoblasts. The analysis revealed 42 unique genes that were differentially expressed in myotubes from individuals with T2D versus controls at FDR below 5% (q1b and Supplementary Data 1, Sheet B). Notably, 20 of these genes, including VPS39, TDP1, MAEA, and FBN2, were among those also differentially expressed in the myoblasts (Fig. 1b, g, Supplementary Fig. 1a–c and Supplementary Data 1, Sheet A).

To identify new regulators of muscle regeneration and function, we asked whether any of the genes with reduced expression in both myoblasts and myotubes from individuals with T2D versus controls, and with an inverse correlation between their expression and DNA methylation, also have a functional role in human myogenesis. We mainly focused on genes that had not been previously studied in human muscle cells, but with known functions in other cell types or species that would suggest an impact also on myogenesis19,20,21,22,23,24,25,26. Based on these criteria, we selected four genes (VPS39, TDP1, MAEA, and FBN2) for functional follow-up experiments (Fig. 1b, g, Supplementary Fig. 1a–c and Supplementary Data 2). To model the situation seen in myoblasts and myotubes from individuals with T2D, we silenced these four genes by using siRNA in human myoblasts from healthy individuals throughout cell differentiation. Knockdown was confirmed at both an early stage of differentiation and after differentiation into myotubes (Fig. 1h and Supplementary Fig. 1d–f). Next, we analyzed the fusion index to examine whether gene silencing affected human myotube formation. Silencing of VPS39 resulted in an almost complete lack of human myotube formation (Fig. 1i–j). Silencing of MAEA or FBN2 did not affect the fusion index, while silencing of TDP1 resulted in a modest reduction in fusion index (Supplementary Fig. 1g–i). These observations suggest that VPS39 is a putative regulator of human myogenesis.

VPS39 controls human myoblast function and differentiation via autophagy and epigenetic mechanisms

VPS39 encodes a protein called Vam6/Vps39-like protein and is a previously unrecognized regulator of human myogenesis. In other tissues, VPS39 is part of the complex that mediates fusion of autophagosomes with lysosomes (HOPS complex) and it has been found in mouse models of myotonic dystrophy type 120,21,25. Because of severe effects of VPS39-silencing on myotube formation (Fig. 1i–j), we decided to dissect its role in the differentiation and function of human muscle cells.

To investigate the role of VPS39 in human myogenesis, we silenced VPS39 in myoblasts and monitored the effects of silencing on protein levels, gene expression, DNA methylome, and cell physiology as the cells differentiated (see Fig. 2a for experimental set up). VPS39-silencing resulted in reduced VPS39 protein levels at both an early stage of differentiation (day 3) and after differentiation into myotubes (day 7) (Fig. 1h). To understand the mechanisms underlying the profound effect of VPS39 knockdown on myotube formation, we compared gene expression in siVPS39 versus control myoblasts at day 3 of differentiation. The analysis revealed that 2635 unique genes were differentially expressed in VPS39-silenced versus control cells (qVPS39 itself (Supplementary Data 3, Sheet A). The expression data clearly indicated that VPS39-silenced cells did not exit the cell cycle and start to differentiate (Fig. 2b–d, and Supplementary Data 3, Sheet B). For example, gene sets related to muscle structure and function, as well as key myogenic transcription factors (TFs) and muscle-specific genes had significantly lower expression (Fig. 2b–c). On the other hand, DNA replication and cell cycle gene sets had higher expression (Fig. 2d). Interestingly, several gene sets known to play a role in autophagy were upregulated in VPS39-silenced cells, e.g., mTOR-signaling pathway, p53-signaling pathway, and lysosome (Fig. 2d). In addition, the expression of numerous epigenetic enzymes was altered in VPS39-silenced cells (Fig. 2e). These are more than expected by chance based on the search terms epigenetics and histone, and a chi2-test (p-chi2

Fig. 2: VPS39 knockdown results in reduced expression of key myogenic genes in human myoblasts.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

a Study design for VPS39-silencing and analyses performed in human myoblasts and myotubes. HAT histone acetyltransferase, HDAC histone deacetylase. be Microarray expression analysis in VPS39-silenced myoblasts (siVPS39b) or upregulated (d) (see also Supplementary Data 3, Sheet B). Bars represent the number of differentially expressed genes contributing to each gene set (white bars), and the total number of genes in each gene set (black bars). mRNA expression (microarray) of myogenic regulatory factors and muscle-specific genes (c), and genes encoding epigenetic enzymes (e) in siVPS39 (purple bars) and NC (gray bars). n = 6 independent experiments. *qVPS39 vs. NC. For exact q-values see Supplementary Data 3, Sheet A. RV right ventricular. f Using PSCAN analysis, the binding motif for myogenin (Myog), presented here, was found to be significantly enriched in the promoter region of genes downregulated after VPS39-silencing. For full PSCAN analysis, see Supplementary Data 3, Sheet C. g The number of down- or upregulated genes with the myogenin binding motif in their promoter region (gray bars) in relation to all differentially expressed genes (black bars) for siVPS39 vs. NC. h Relative expression (qPCR) of VPS39, MYOD1, and MYOG at day 1 (24 h), day 2 (48 h), and day 3 (72 h) after the start of siVPS39 transfection and differentiation. n = 4 independent experiments. NC at day 1 for each gene is set to 1. *p**p***pVPS39 vs. NC. p = 0.0114 (VPS39 Day 1), p = 0.0033 (VPS39 Day 2), p = 0.0022 (VPS39 Day 3), and p = 0.0819 (MYOD1 Day 2), p = 0.0211 (MYOD1 Day 3), and p = 0.0009 (MYOG Day 3). Bars represent mean values and error bars display SEM (c, e, h). Statistical significance was determined by paired two-tailed t-test (c, e, h). P-values were adjusted for multiple comparisons with false discovery rate (FDR) analysis (b, c, d, e, f).

Considering the importance of specific TFs for the regulation of myogenesis8, we used the bioinformatics prediction tools PSCAN28 and JASPAR 201629 to search for TF binding motifs that were enriched in promoter regions of downregulated and upregulated genes, after VPS39 knockdown in human myoblasts (Supplementary Data 3, Sheets C and D). One motif enriched for downregulated genes was that of myogenin (MYOG), whose expression was also lower in VPS39-silenced cells (Fig. 2c, f). Remarkably, 97% of the downregulated genes contained binding motif(s) for myogenin in their promoter region, whereas only 5.7% of the upregulated genes had this motif (Fig. 2g and Supplementary Data 3, Sheets C–F). Myogenin is a key regulator of myogenesis8, and the expression of several genes encoding TFs that activate MYOG transcription30 was reduced in VPS39-silenced cells. These TFs include MYOD1, MEF2s (MEF2A, MEF2C, and MEF2D), and E-box proteins (TCF3, TCF4, and TCF12) (Fig. 2c and Supplementary Data 3, Sheets E and F). Hence, VPS39, directly or indirectly, regulates myogenesis by disrupting MYOG expression.

To delineate the primary and secondary effects of VPS39-deficiency on myogenesis, we examined the expression of VPS39, MYOD1, and MYOG on day 1, 2, and 3 of the differentiation in VPS39-silenced human myoblasts (Fig. 2h). VPS39 expression was downregulated already after 1 day, while MYOD1 was reduced after 2 days and MYOG after 3 days (Fig. 2h). These data suggest that the typically high and/or upregulated expression of MYOD1 and MYOG at an early stage of differentiation is partially repressed or delayed in VPS39-silenced myoblasts. Moreover, MEF2C and myosin protein levels were markedly reduced in VPS39-silenced cells at day 7 of differentiation (Supplementary Fig. 1j–k), further demonstrating the key role of VPS39 in human myogenesis.

In view of our microarray results (Fig. 2b–e), we hypothesized that reduced VPS39 levels in myoblasts might alter autophagy and thereby cell metabolism. This may result in altered activity of epigenetic enzymes followed by changes in epigenetic marks and the expression of myogenic TFs. Subsequently, myogenesis would be impaired. We proceeded to explore this hypothesis.

Rodent data support that proper autophagy is important for myogenesis31, but this has not been verified in human muscle cells. Moreover, VPS39 is part of the complex mediating fusion of autophagosomes with lysosomes, but the role of VPS39 for the regulation of autophagy in human muscle cells remain to be elucidated20,21. To investigate the importance of autophagy also during human myogenesis, human myoblasts were treated with Bafilomycin A1 (Baf-A1) for 3 h per day during the first 3 days of differentiation, and key autophagy markers (LC3B, p62, LAMP1, and LAMP2)32 were studied using both automated high-content screening (HCS) and Western blot analyses (see Supplementary Fig. 2a for experimental setup). Baf-A1 inhibits the fusion of autophagosomes with lysosomes32. Indeed, Baf-A1 altered autophagy (Supplementary Fig. 2b–d) and reduced the expression of myogenic markers (Supplementary Fig. 2e), similar to what we observed in VPS39-silenced cells (Fig. 2c, h). In addition, MYOD1 protein levels were significantly decreased (Supplementary Fig. 2f). These observations further demonstrate the importance of autophagy during human myogenesis.

Next, we investigated the effects of VPS39 on basal autophagy in human myoblasts using both HCS and Western blot analyses for key markers of autophagy — LC3B, p62, LAMP1, and LAMP2. As shown in Fig. 3a–c, VPS39-silenced cells displayed increased amount and size of autophagosomes, determined by quantification of LC3B spot number and area, and increased p62, a marker of selective autophagy32. p62 protein levels are inversely correlated with autophagic activity32, indicating impaired autophagic activity in VPS39-silenced cells. Moreover, the spot number and area of lysosomal markers LAMP1 and LAMP2 were also increased in the HCS analysis (Fig. 3a–c). In addition, the protein levels of LC3B-II and p62 (detected by Western blot) were increased in VPS39-silenced cells, whereas LAMP1 and LAMP2 were not altered (Fig. 3d). The discrepancies in LAMP1/2 levels between the HCS and Western blot assays may depend on that these two separate methods detect different aspects of the protein dynamics, and that HCS is able to detect more subtle changes in LAMP1/2 levels by measuring spot number and spot area per cell compared to Western blot. Together, these results support that knockdown of VPS39 alters basal autophagy in human myoblasts, similar to what was observed after inhibition of autolysosome formation (Supplementary Fig. 2b–d).

Fig. 3: VPS39-silencing impairs autophagic flux in human myoblasts.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

ac High-content screening (HCS) analysis using spot detection application to identify autophagy markers LC3B, p62, LAMP1, and LAMP2 in VPS39-silenced myoblasts (siVPS39, purple bars) and negative control (NC, gray bars) at day 3 of differentiation. n = 4 (LC3B) and n = 8 (p62, LAMP1/2) independent experiments. Graphs show a relative number of detected spots per cell (a) and area per spot (b) for each marker. NC is set to 1. *p**pVPS39 vs. NC. p = 0.0274 (a, LC3B), p = 0.0034 (a, p62), p = 0.0606 (a, LAMP1), p = 0.0112 (a, LAMP2), and p = 0.035 (b, LC3B), p = 0.0059 (b, p62), p = 0.0399 (b, LAMP1), p = 0.0317 (b, LAMP2). c Representative images from the analyses in (ab), showing immunostaining of LC3B (left panel, red) and LAMP1 (left panel, green), and p62 (right panel, red) and LAMP2 (right panel, green). Scale bar 20 µm. d Protein levels of LC3B-II, p62, LAMP1, and LAMP2 in siVPS39 (purple bars) and NC (gray bars) myoblasts at day 3 of differentiation. n = 5 (LC3B-II, p62, LAMP1) and n = 4 (LAMP2) independent experiments. NC is set to 1. Representative blots are shown. *p**pVPS39 vs. NC. p = 0.0062 (LC3B-II), p = 0.0137 (p62). ep Autophagic flux measurements in siVPS39 (purple bars) and NC (gray bars) myoblasts at day 3 of differentiation in both the basal state and after starvation (3 h) to induce autophagy, and in the absence or presence of the lysosomal inhibitor Bafilomycin A1 (Baf-A1, 100 nM). NC in the basal, vehicle-treated state is set to 1. eg Protein levels (Western blot) of LC3B-II (e) and p62 (f). n = 5 independent experiments. Representative blots are shown. #qq*q**qVPS39 vs. NC for each treatment. For exact q-values see Supplementary Table 1. g Autophagic flux calculated as LC3B-II protein levels in Baf-A1-treated vs. vehicle-treated cells under basal and starvation conditions for each genotype (see also Supplementary Fig. 2g). **p****pp = 0.000078 (Basal; siVPS39 vs. NC), p = 0.000022 (Starvation: siVPS39 vs. NC), p = 0.0016 (NC: Basal vs. Starvation). Starv., starvation (hp) HCS analysis using spot detection application to identify p62 (hj), LAMP1 (km), and LAMP2 (np). n = 4 independent experiments. Graphs show the relative number (h, k, n) and area (i, l, o) of detected spots per cell for each marker. #qq*q**q***qVPS39 vs. NC for each treatment. j, m, p Representative images from the analyses, showing immunostaining of p62 (j), LAMP1 (m), and LAMP2 (p). Scale bar 20 µm. Bars represent mean values and error bars display SEM (ab, di, kl, no). Statistical significance determined by paired two-tailed t-test (ab, d). The effects of genotype, starvation, and Baf-A1-treatment stated above the graphs were calculated with repeated measures three-way ANOVA (ef, hi, kl, no) or two-way ANOVA (g). P-values were adjusted for multiple comparisons with false discovery rate (FDR) analysis (ef, hi, kl, no).

To further characterize the role of VPS39 for the regulation of the autophagic process, we performed comprehensive autophagy flux analyses33. Human myoblasts were treated with Baf-A1 under both basal and starvation (serum- and amino acid-free) conditions to induce autophagy, and key markers of autophagy were monitored using the two methods described above. As determined by Western blot, both LC3B-II and p62 protein levels were increased in VPS39-silenced cells compared to control (Fig. 3e–f). As expected, LC3B-II was increased upon starvation and was further increased in response to Baf-A1-treatment due to an accumulation of autophagosomes (Fig. 3e). p62 was increased in response to Baf-A1-treatment in both control and VPS39-silenced cells, but only control cells displayed a significant decrease in p62 upon starvation (Fig. 3f). The autophagic flux (calculated as LC3B-II levels in Baf-A1-treated compared to control cells) was decreased in VPS39-silenced cells, and only control cells displayed an increased autophagic flux upon starvation (Fig. 3g and Supplementary Fig. 2g). LAMP1/2 protein levels were not different between the genotypes, and not altered in response to any of the treatments (Supplementary Fig. 2h–i). In line with the results on protein level, p62 spot number and area were increased overall in VPS39-silenced cells, and only control cells displayed significantly decreased p62 upon activation of autophagy (Fig. 3h–j). The reduction in p62 in response to starvation, determined by both Western blot and HCS, was significantly larger in control cells indicating an impaired autophagic activity in the VPS39-silenced cells (Supplementary Fig. 2j–l). Moreover, both LAMP1 (Fig. 3k–m) and LAMP2 (Fig. 3n–p) spot number and area were significantly increased in VPS39-silenced cells. These results support that VPS39 is required for functional autophagy in human myoblasts and that VPS39-silencing is associated with a reduced autophagic flux, likely due to defects in the late stages of the autophagy process. Furthermore, VPS39 knockdown alone mimicked effects on altered basal autophagy and impaired myogenesis observed in Baf-A1-treated myoblasts.

The autophagic process has been linked to metabolic remodeling and myoblast differentiation in rodents31,34. We proceeded to examine whether VPS39-silenced human muscle cells have altered activation of key proteins involved in metabolic pathways i.e. glucose uptake and glycogen synthesis. VPS39-silenced cells exhibited decreased insulin-induced Akt phosphorylation, at both serine 473 (Ser473) and threonine 308 (Thr308) compared to control cells (Fig. 4a). The phosphorylation of downstream Akt substrates TBC1D4 that controls GLUT4 translocation35, and glycogen synthase kinase 3 (GSK3) that regulates glycogen synthase activity36, was significantly and nominally decreased, respectively, in insulin-stimulated VPS39-silenced cells versus control (Fig. 4b–c). Phosphorylation of TBC1D4 is associated with increased glucose uptake and phosphorylation of GSK3 is associated with activation of glycogen synthesis. These results suggest that the overall activity of the insulin signaling pathway is perturbed in VPS39-silenced myoblasts, and that some metabolic pathways may be altered.

Fig. 4: Reduction of VPS39 levels alters the epigenome and insulin signaling in human myoblasts.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

ac Specific phosphorylation (intensity of phosphorylation divided by total levels for each corresponding protein) for Akt at Ser473 (a, left panel) and Thr308 (a, right panel), TBC1D4 at Thr642 (b), GSK3-α at Ser21 (c, left panel) and GSK3-β at Ser9 (c, right panel) in the basal state and after insulin stimulation (100 nM, 30 min) in VPS39-silenced myoblasts (siVPS39, purple bars) and negative control (NC, gray bars) at day 3 of differentiation. n = 4 independent experiments. NC in the basal state is set to 1. Representative blots are shown. #ppVPS39 vs. NC for each treatment, and *p**p***pp-values see Supplementary Table 1. d Kinetics of histone acetyltransferase (HAT) activity measurement (left panel). HAT (area under the curve) and histone deacetylase (HDAC) (fixed point) activity in nuclear extracts from siVPS39 (purple) and NC (gray) myoblasts at day 3 of differentiation (right panel). n = 4 independent experiments. NC is set to 1. *pVPS39 vs. NC. p = 0.0126 (HAT). e Protein levels (Western blot) of epigenetic enzymes from siVPS39 (purple bars) and NC (gray bars) myoblasts at day 3 of differentiation. Protein levels were measured in whole-cell lysates, or in nuclear and cytosolic fractions as indicated. n = 6 (DNMT1, DNMT3A, HDAC5 [nucleus and cytoplasm]), n = 3 (DNMT3B), n = 5 (EZH2, HAT1 [nucleus], p300 [nucleus and cytoplasm], HDAC4 [nucleus]), n = 4 (HAT1 [cytoplasm]), n = 8 (HDAC4 [cytoplasm]). NC is set to 1. Representative blots are shown. Statistical analysis was performed on log2-transformed values. *p**pVPS39 vs. NC. p = 0.0259 (DNMT1), p = 0.0374 (DNMT3B), p = 0.0081 (EZH2), p = 0.0697 (HAT1 [nucleus]), p = 0.0309 (p300 [nucleus]), p = 0.0493 (HDAC4 [nucleus]), p = 0.001 (HDAC5 [nucleus]), p = 0.0463 (HDAC5 [cytoplasm]). DNMT, DNA methyltransferase, HAT histone acetyltransferase, HDAC histone deacetylase. f The number of genes with altered DNA methylation at one or more CpG site (dark gray) or no change (light gray) among the 2635 genes with differential expression in siVPS39 vs. NC myoblasts. g The number of observed (black bars) and expected (white bars) genes for a selection of GO cellular processes enriched among genes with differential DNA methylation and gene expression in siVPS39 vs. NC myoblasts. Bars sorted by ratio (observed/expected). GO gene ontology. hi Western blot analysis of acetylated histone 3 (ac-H3) levels related to the total amount of H3 in siVPS39 (purple bars) and NC (gray bars) myoblasts at day 3 of differentiation (h), and at days 0, 3, and 7 of differentiation (i). n = 5 independent experiments. NC/WT is set to 1. Representative blots are shown. *pVPS39 vs. NC in (h). p = 0.012. #qq*q***qVPS39 vs. NC at each time point in (i). For exact q-values see Supplementary Table 1. Diff. differentiation. jk Apoptosis measured as Caspase 3/7 activity (j, n = 3 independent experiments) and nucleus size (area of the DAPI-stain measured in the HCS assay) (k, n = 8 independent experiments) in siVPS39 (purple bars) and NC (gray bars) at day 3 of differentiation. NC is set to 1. *p****pVPS39 vs. NC. p = 0.0259 (j), p = 0.000051 (k). Bars (in (ac, d), right panel, and (e, hk)) or points (in (d), left panel) represent mean values and error bars display SEM (ae, hk). The effects of genotype, and insulin-treatment or differentiation stated above the graphs were calculated with repeated measures two-way ANOVA (ac, i). P-values were adjusted for multiple comparisons with false discovery rate (FDR) analysis (g, i). Statistical significance determined by paired two-tailed t-test (de, h, jk).

Metabolic changes can affect the activity of epigenetic enzymes in muscle stem cells37,38. We observed that the expression of genes encoding epigenetic enzymes was altered in VPS39-silenced myoblasts (Fig. 2e), and we therefore postulated that the activity of these enzymes was also altered. To test this, we analyzed the activity and protein levels of epigenetic enzymes in VPS39-silenced cells. The overall activity of histone acetyl transferases (HAT) was reduced, while the overall histone deacetylase (HDAC) activity in nuclear extracts was not significantly affected after VPS39 knockdown (Fig. 4d). In line with the expression analysis, the DNA and histone methyltransferases DNMT1, DNMT3B, and EZH2 protein levels were significantly higher in VPS39-silenced cells (Fig. 4e), which may reflect key mechanisms contributing to impaired differentiation in myoblasts with reduced VPS39 levels39,40,41,42. In addition, the nuclear protein levels of HAT1 were nominally reduced and p300 were increased, while no differences were found in the cytoplasm (Fig. 4e). HDAC4 and HDAC5 levels were also divergently regulated (Fig. 4e), as is often the case with class II HDACs43,44.

We next asked whether the changes seen in epigenetic enzymes were associated with epigenetic alterations in VPS39-silenced human muscle cells. We observed nominally altered DNA methylation at 5045 CpG sites annotated to 72% (1889) of the genes that exhibited differential expression after VPS39 knockdown (Fig. 4f and Supplementary Data 4, pp-chi24g). Specific genes of importance during myogenesis whose DNA methylation was altered in VPS39-silenced cells included MEF2s, myosin heavy and light chains (MHC and MLC), and genes encoding proteins important for myocyte function45,46 (Supplementary Data 4). In addition, we observed that acetylation of histone 3 (ac-H3) was elevated in VPS39-silenced myoblasts at day 3 of differentiation (Fig. 4h), which may be due to increased p300 and reduced HDAC5 levels (Fig. 4e). Global ac-H3 levels are expected to decrease during myoblast differentiation47, which we clearly see in our control cells (Fig. 4i). Specific acetylation of H3 was significantly decreased during differentiation in control cells whereas this response was altered in VPS39-silenced cells that displayed increased levels of H3 acetylation compared to control at both day 3 and 7 of differentiation (Fig. 4i). Together, these data strengthen our hypothesis that reduced VPS39 levels affect epigenetic enzymes and result in an altered epigenome.

To further dissect the mechanisms underlying the impaired differentiation of VPS39-silenced myoblasts, and since the connection between autophagy and apoptosis has been documented48, we measured Caspase 3/7 activity as an estimate of cellular apoptosis. Caspase 3/7 activity was increased in VPS39-silenced cells (Fig. 4j). This is in line with both our microarray and HCS data for VPS39-silenced cells showing that the expression of pro-apoptotic genes, e.g., CASP3 and BAX was higher (Supplementary Data 3, Sheet A), and cell nuclei size was smaller in these cells (Fig. 4k).

Collectively, the data presented above support a model whereby low VPS39 levels in myoblasts impair autophagy, which may result in disturbed homeostasis and alterations of epigenetic enzymes and the epigenome (Supplementary Fig. 3). Consequently, the expression of key myogenic regulatory factors (MRFs and MEFs) and muscle-specific genes is reduced, and a reduced proportion of myoblasts differentiate into myotubes. Instead, apoptosis is increased.

VPS39-deficiency in mice leads to reduced glucose uptake and altered gene expression in muscle

To further elucidate the mechanisms whereby reduced VPS39 expression may contribute to impaired muscle function and T2D, we studied mice heterozygous for a germ-line deletion of Vps39 (Vps39+/− mice)49. Heterozygous mice were used because total VPS39-deficiency is embryonically lethal49. Further, we reasoned that the reduction of Vps39 expression in Vps39+/− mice would mimic the situation in humans with T2D. Skeletal muscle from Vps39+/− mice contained lower Vps39 levels compared to wild-type (WT) littermates (Fig. 5a), confirming that they would be a suitable model to study the role of VPS39 in muscle dysregulation. We observed no differences in body weight or body composition between WT and Vps39+/− mice (Supplementary Fig. 4a–c). We then examined glucose homeostasis in Vps39+/− mice. First, an OGTT was used to examine glucose tolerance in vivo (Fig. 5b). We observed that the fold change in plasma glucose levels was significantly higher in Vps39+/− than in WT mice during the first 15 min of glucose challenge (Fig. 5c), with no difference in insulin levels in Vps39+/− males but a compensatory increased fold change in insulin secretion in Vps39+/− females (Supplementary Fig. 4d–e). Next, we measured tissue-specific glucose uptake using a tracer, i.e., by oral administration of 3H-deoxy-glucose together with D-glucose sufficient to induce an insulin response in the mice (Fig. 5d and Supplementary Fig. 4f). Glucose uptake was significantly reduced in extensor digitorum longus (EDL) muscle of Vps39+/− versus WT mice (Fig. 5d), demonstrating that VPS39-deficiency is associated with glucose intolerance and impaired muscle function in mice, which is in line with what is seen in patients with T2D. To dissect the cause of this in vivo perturbation, we analyzed gene expression in skeletal muscle of Vps39+/− mice. Microarray analysis revealed 1641 nominally differentially expressed genes in the muscle of Vps39+/− versus WT mice (p5, Sheet A). To better understand the biological relevance of these expression differences, and relate them to our human data, we searched the gene ontology (GO) terms for these 1641 genes using four search terms: autophagy, epigenetics and histones, muscle (excluding cardiac and smooth muscle), as well as oxidative phosphorylation and respiratory chain. We then used chi2-tests to examine an overrepresentation of differentially expressed genes belonging to these search terms versus all analyzed genes. The analysis revealed an overrepresentation of genes associated with epigenetics and histones, and a nominal significant enrichment of genes associated with muscle (Fig. 5e and Supplementary Data 5, Sheets A and B). Some differentially expressed genes annotated to these search terms/biological processes are presented in Fig. 5f. Moreover, the mRNA and protein levels of autophagy protein 5 (ATG5) and DNMT3B correlated positively in the muscle of the mice (Supplementary Fig. 4g). We proceeded to perform a gene set enrichment analysis (GSEA) on the complete expression data set in Vps39+/− versus WT mice50. This analysis revealed three significant pathways, including the proteasome, ribosome and spliceosome (Supplementary Data 5, Sheet C).

Fig. 5: Vps39-deficiency alters glucose metabolism and gene expression related to epigenetics, autophagy, and muscle function in mouse skeletal muscle.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

a mRNA expression (qPCR) of Vps39 in skeletal muscle (tibialis anterior) from heterozygous (Vps39+/−, n = 14, including six males and eight females, blue bars) and wild type (WT, n = 14, including seven males and seven females, gray bars) mice. *pVps39+/− vs. WT. p = 0.0247. bc Oral glucose tolerance test (OGTT) in Vps39+/− mice (n = 18, including ten males and eight females, blue points/bars) and WT mice (n = 16, including ten males and six females, gray points/bars). b Blood glucose levels (mmol/L) at 0–90 min during the OGTT. c Fold change in blood glucose levels during the first 15 min of the OGTT (glucose levels at 15 min relative 0 min). *pVps39+/− vs. WT. p = 0.0451. d Relative glucose uptake in the extensor digitorum longus (EDL) muscle from Vps39+/− and WT mice during 45 min after an oral glucose load. Glucose uptake in muscle was measured using 2-[1,2-3H(N)]-Deoxy-D-glucose tracer and normalized to tissue weight. Males: n = 5 WT and n = 5 Vps39+/−, females: n = 6 WT and n = 5 Vps39+/−. WT mice are set to 1. *pVps39+/− vs. WT. p = 0.0474 (males), p = 0.0307 (females). ef mRNA expression analysis (microarray) in skeletal muscle (tibialis anterior) from Vps39+/− vs. WT mice (n = 12 per genotype, including six males and six females per genotype). e Frequency of selected GO terms (“Epigenetics and Histones” [orange], “Autophagy” [blue], “Muscle” [red] and “Oxidative phosphorylation and Respiratory chain” [green]) among the differentially expressed genes (pVps39+/− vs. WT). Chi2-tests were used to analyze overrepresentation of differentially expressed genes belonging to a GO term compared with all analyzed genes. *p-chi2f Heatmap showing the fold change in expression for some selected differentially expressed genes (pVps39+/− vs. WT) related to the GO terms in (e) (“Epigenetics”, “Autophagy” or “Muscle”), based on GO annotation or previously published research. Genes with upregulated expression in Vps39+/− mice displayed in green and downregulated expression displayed in purple. For exact p-values see Supplementary Data 5, Sheet A. GO gene ontology. Bars (in (a, cd)) or points (in (b)) represent mean values and error bars display SEM (ad). Statistical significance determined by unpaired two-tailed t-test (a, cd). Differential gene expression between Vps39+/− and WT mice was analyzed by unpaired two-tailed t-tests (ef).

We conclude that mimicking the VPS39-deficiency observed in muscle cells from individuals with T2D using a mouse model (Vps39+/−) results in impaired glucose uptake in muscle and altered expression of genes affecting autophagy, epigenetic programming, muscle development, and metabolism, highlighting the possible role for VPS39 in muscle pathology.

Markers for autophagy and epigenetic enzymes are altered in myoblasts and myotubes from individuals with T2D

We next asked whether the observations in VPS39-silenced human myoblasts and Vps39+/− mice are also reflected in individuals with T2D. Higher HOMA-IR (Table 1) supported the notion of insulin resistance and an impaired muscle function in individuals with T2D. First, we tested if LAMP2 protein levels were altered during differentiation in muscle cells from individuals with T2D versus controls. Based on the overall two-way ANOVA (*p6a), which agreed with observations in VPS39-silenced cells (Fig. 3a–c) and are generally in line with previous findings51.

Fig. 6: Impact of T2D on LAMP2 and DNMTs during myogenesis in human muscle cells.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

ab Protein levels (Western blot) of LAMP2 (a), and DNMT3A, DNMT3B, SUMOylated DNMT3B, and DNMT1 (b) in muscle cells from individuals with type 2 diabetes (T2D) and controls (NGT normal glucose tolerance) at day 0 (white bars), 3 (light gray bars), and 7 (dark gray bars) of differentiation. n = 5 individuals per group (except for DNMT3B, T2D: Day 0 where n = 4). NGT at day 0 is set to 1. Representative blots are shown. #qqqq*qq = 0.0305 (T2D: Day 0 vs. 3), and DNMT3B: q = 0.0323 (T2D: Day 3 vs. 7), and SUMO-DNMT3B: q = 0.0073 (T2D: Day 0 vs. 3), q = 0.0157 (T2D: Day 0 vs. 7), q = 0.0237 (Day 7: T2D vs. NGT), and DNMT1: q = 0.0003 (NGT: Day 0 vs. 3), q = 0.0009 (NGT: Day 3 vs. 7), q = 0.0000005 (NGT: Day 0 vs. 7), q = 0.0457 (T2D: Day 0 vs. 3), q = 0.0003 (T2D: Day 3 vs. 7), q = 0.0000097 (T2D: Day 0 vs. 7). Bars represent mean values and error bars display SEM (ab). The effects of T2D and differentiation stated above the graphs were calculated with two-way ANOVA, or mixed-effects model (DNMT3B), with repeated measures in the factor “Differentiation” (Day 0, 3, and 7). DNMT3B, SUMOylated DNMT3B, and DNMT1 protein values were log2-transformed before statistical analysis. Non-logarithmic values are presented in the graphs. P-values were adjusted for multiple comparisons with false discovery rate (FDR) analysis (ab).

Next, we studied epigenetic enzymes in muscle cells from individuals with T2D and control individuals. We analyzed the protein levels of all three DNMTs during differentiation (Fig. 6b). Protein levels of the DNMTs responsible for de novo methylation, DNMT3A and an alternative isoform of DNMT3B, were increased during differentiation only in muscle cells from individuals with T2D. The alternative isoform of DNMT3B was also higher in myotubes (day 7) from individuals with T2D versus control individuals (Fig. 6b). siRNA-mediated DNMT3B-silencing confirmed that the alternative and larger-mass (~120 kDa) isoform was DNMT3B (Supplementary Fig. 5a), potentially SUMOylated DNMT3B52. DNMT1 levels were reduced as differentiation progressed in both groups (Fig. 6b), which is expected when cells exit the cell cycle39. In agreement with cells from individuals with T2D, both DNMT3B and DNMT1 levels were decreased at day 7 versus day 3 in VPS39-silenced cells (Fig. 6b and Supplementary Fig. 5b).

In general, although different methods have been used, several of the data for cells from individuals with T2D were similar to our results for VPS39-silenced human myoblasts and Vps39+/− mice, suggesting a model whereby reduced VPS39 levels alter autophagy and epigenetic enzymes, thereby negatively affecting myogenesis and muscle function (Supplementary Fig. 3).

Individuals with T2D show abnormal DNA methylation changes during myogenesis

Having established that epigenetic enzymes responsible for de novo DNA methylation are upregulated during myogenesis only in cells from individuals with T2D but not in controls, we asked whether diabetes is associated with abnormal epigenetic changes during myoblast differentiation. To study if epigenetic changes during myogenesis are different in individuals with T2D versus controls, we separately compared DNA methylation levels at 458,475 CpG sites in myoblasts versus myotubes from 14 individuals with T2D and 14 control individuals (Fig. 7a and Table 1). We first used an unsupervised principal component analysis (PCA) to correlate the top principal components of the methylation data in myoblasts and myotubes with T2D. T2D correlated significantly with the fourth principal component in both myoblasts and myotubes (p = 0.0001 and p = 0.001, respectively), suggesting that T2D influence the DNA methylome.

Fig. 7: Differential changes in DNA methylation and gene expression during differentiation of human muscle cells from individuals with T2D versus controls.
VPS39-deficiency observed in type 2 diabetes impairs muscle
stem cell differentiation via altered autophagy and
epigenetics

a Schematic representation of the analyses performed to compare the myogenic process in cells from individuals with type 2 diabetes (T2D) and controls (NGT, normal glucose tolerance). b Number of CpG sites with significantly (qn = 14 individuals per group. c Overlap of the CpG sites with significantly (qb). ded) or downregulated (e) before vs. after muscle cell differentiation. Bars represent the number of differentially expressed genes contributing to each gene set (white bars), and the total number of genes in each gene set (black bars). Red arrows indicate gene sets regulated only in individuals with NGT. n = 13 individuals per group. Val valine, Leu leucine, Ile isoleucine, USFA unsaturated fatty acid.

We next calculated the average methylation level for all analyzed CpG sites in different gene regions, and regions based on their location in relation to CpG islands53. Myoblasts from individuals with T2D showed higher levels of methylation in regions distant from CpG islands (in shelves and open sea) compared to controls (Supplementary Data 6, Sheet A). Moreover, the average methylation increased significantly in the shelves and open sea during differentiation of myoblasts only in controls, while it was already high and did not increase further in myoblasts from individuals with T2D (Supplementary Data 6, Sheet A).

We then studied methylation changes of individual CpG sites during differentiation. Interestingly, DNA methylation in myoblasts versus myotubes changed significantly at twice as many individual sites in cells from individuals with T2D compared to controls (113,947 versus 49,973 CpG sites, q7b and Supplementary Data 6, Sheets B and C). This was in line with our recent study demonstrating that subjects with obesity had abnormal methylation changes during myogenesis compared with non-obese18. Many sites changed methylation only in cells from either individuals with T2D or control individuals (Fig. 7c and Supplementary Data 6, Sheets D and E), and methylation changes at 39 sites showed opposing patterns before versus after differentiation in individuals with T2D and controls (Table 2).

Table 2 CpG sites with differential DNA methylation in opposite directions before versus after differentiation of myoblasts from 14 controls (normal glucose tolerance (NGT)) and 14 individuals with type 2 diabetes (T2D).

Together, these detected abnormal epigenetic changes during myogenesis in cells from individuals with T2D may partly be due to the impaired regulation of DNMT3A and DNMT3B, reduced VPS39 levels, and alterations in autophagy (Supplementary Fig. 3).

Expression changes during differentiation of myoblasts into myotubes are altered in individuals with T2D

Next, we tested whether T2D also affects the expression changes that take place during myogenesis. We found that the expression of 7086 and 6681 genes changed in “before versus after differentiation” comparisons of muscle cells from individuals with T2D and controls, respectively (Supplementary Data 1, Sheets C and D). Most of these genes overlapped between the two groups, yet a large number changed expression in only one of the groups (Supplementary Fig. 5c). These included several genes related to AMPK/mTOR-signaling and lipid metabolism (Supplementary Fig. 5d). Interestingly, the expression of MLST8 was regulated in the opposite direction in cells from individuals with T2D versus control individuals (Supplementary Fig. 5e). MLST8 encodes a component of the mTOR complex 1 (mTORC1) and mTORC2, which are major regulators of autophagy54. We then performed a GSEA to gain biological understanding of the transcriptional differences that occur in cells from individuals with T2D and controls during myogenesis. Many gene sets were regulated during differentiation in both groups. However, some gene sets related to amino acid and fatty acid metabolism were upregulated only in the controls (Fig. 7d and Supplementary Fig. 5f). Furthermore, gene sets related to glycolysis and one carbon pool by folate were downregulated only in controls (Fig. 7e and Supplementary Fig. 5g). A noteworthy finding is that only controls, but not individuals with T2D, showed the expected changes with increased expression of gene sets related to amino acid and fatty acid metabolism, as well as decreased expression of genes linked to glycolysis during myogenesis (Fig. 7d–e and Supplementary Fig. 5f–g). It is well established that “normal” myoblasts shift from glycolytic metabolism towards a use of amino acids and fatty acids in myotubes37 and our expression data strongly support the existence of metabolic differences during differentiation of myoblasts from individuals with T2D versus controls.

Finally, we tested if VPS39 expression in human skeletal muscle biopsies correlates with measures of insulin sensitivity analyzed in vivo with a euglycemic hyperinsulinemic clamp, and whether the expression is reduced in biopsies from individuals with T2D versus control individuals in a cohort previously described4. Interestingly, VPS39 expression in muscle biopsies correlated positively with glucose uptake (M-value, r = 0.7015, p = 0.0052) in individuals with T2D (Supplementary Fig. 6a), and there was a non-significant trend to reduced VPS39 expression in muscle from individuals with T2D versus controls (Supplementary Fig. 6b).

Altogether, the human and rodent data demonstrate that VPS39 plays a key role in myogenesis and muscle glucose metabolism. We show that T2D is associated with reduced VPS39 levels, which contribute to impaired autophagy, higher DNMT levels, and abnormal epigenetic and expression changes during myogenesis.

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