Quantitative proteomic analysis of skeletal muscles from wild-type and transgenic mice carrying recessive Ryr1 mutations linked to congenital myopathies

  1. Jan Eckhardt
  2. Alexis Ruiz
  3. Stéphane Koenig
  4. Maud Frieden
  5. Hervé Meier
  6. Alexander Schmidt
  7. Susan Treves  Is a corresponding author
  8. Francesco Zorzato  Is a corresponding author
  1. Departments of Biomedicine and Neurology, Basel University Hospital, Switzerland
  2. Department of Cell Physiology and Metabolism, University of Geneva, Switzerland
  3. Proteomics Core Facility, Biozentrum, Basel University, Switzerland
  4. Department of Life Science and Biotechnology, University of Ferrara, Italy
9 figures, 5 tables and 2 additional files

Figures

Schematic overview of the workflow.

(A) Skeletal muscles from 12 weeks old WT (5 mice) and dHT littermates (5 mice) were isolated and flash frozen. Three different types of muscles were isolated per mouse, namely EDL, soleus and EOMs. On the day of the experiment, muscles were solubilized and processed for LC-MS. (B) For absolute protein quantification, synthetic peptides of RyR1, Cav1.1, Stim1 and Orai1 were used. (C) Protein content in different muscle types and in the different mouse genotypes were analyzed and compared.

Proteomic analysis of EDL, soleus and EOM muscles from WT mice confirms the significant difference in content if proteins involved in the TCA cycle and electron transport chain, fatty acid metabolism and muscle contraction.

(A) Hierarchically clustered heatmaps of the relative abundance of proteins in EDL (columns 1–5) and soleus muscles (columns 6–10) from five mice. Blue blocks represent proteins which are increased in content, yellow blocks proteins which are decreased in content in EDL versus soleus muscles. Right pie chart shows overall number of increased (blue) and decreased (yellow) proteins. Areas are relative to their numbers. (B) Volcano plot of a total of 1866 quantified proteins which showed significant increased (blue) and decreased (yellow) content. The horizontal coordinate is the difference multiple (logarithmic transformation at the base of 2), and the vertical coordinate is the significant difference p value (logarithmic transformation at the base of 10). The proteins showing major change in content are abbreviated. Soleus: condition 2; EDL: condition 1(C) Reactome pathway analysis showing major pathways which differ between EDL and soleus muscles. (D) Hierarchically clustered heatmaps of the relative abundance of proteins in EDL (columns 1–5) and EOM muscles (columns 6–10) from five mice. Blue blocks represent proteins which are increased in content, yellow blocks proteins which are decreased in content in EDL versus EOM muscles. Right pie chart shows overall number of increased (blue) and decreased (yellow) proteins. Areas are relative to their numbers. (E) Volcano plot of a total of 1866 quantified proteins which showed significant increased (blue) and decreased (yellow) content. The horizontal coordinate is the difference multiple (logarithmic transformation at the base of 2), and the vertical coordinate is the significant difference p value (logarithmic transformation at the base of 10). The proteins showing major change in content are abbreviated. EOM: condition 2; EDL: condition 1 (F) Reactome pathway analysis showing major pathways which differ between EDL and EOM muscles. (G) Hierarchically clustered heatmaps of the relative abundance of proteins in soleus muscles (columns 1–5) and EOM (columns 6–10) from five mice. Blue blocks represent proteins which are increased in content, yellow blocks proteins which are decreased in content in soleus muscles versus EOM. Right pie chart shows overall number of increased (blue) and decreased (yellow) proteins. Areas are relative to their numbers. (H) Volcano plot of a total of 1866 quantified proteins which showed significant increased (blue) and decreased (yellow) content. The horizontal coordinate is the difference multiple (logarithmic transformation at the base of 2), and the vertical coordinate is the significant difference p value (logarithmic transformation at the base of 10). The proteins showing major change in content are abbreviated. EOM: condition 2; soleus: condition 1 (I) Reactome pathway analysis showing major pathways which differ between soleus and EOM muscles. A q-value of equal or less than 0.05 was used to filter significant changes prior to the pathway analyses. An additional filter was applied to the Heatmaps and Piecharts and only proteins showing a significant change ≥0.2 fold are included.

Figure 3 with 1 supplement
Proteomic analysis comparison of muscles from dHT and WT mice.

(A, C and E) Hierarchically clustered heatmaps of the relative abundance of proteins in EDL (A), soleus muscles (C) and EOMs (E) from three to five mice. Blue blocks represent proteins which are increased in content, yellow blocks proteins which are decreased in content in WT (columns 1–5 in A and E; 1–3 in C) versus dHT (5–10 in A and E; 4–8 in C). Right pie chart shows overall number of increased (purple) and decreased (yellow) proteins. Areas are relative to their numbers. (B, D and F) Volcano plots of total quantified proteins showing significant increased (blue) and decreased (yellow) content in dHT (condition 2) versus WT (condition 1) EDL (B), soleus (D) and EOMs (F). The horizontal coordinate is the difference multiple (logarithmic transformation at the base of 2), and the vertical coordinate is the significant difference p value (logarithmic transformation at the base of 10). The proteins showing major change in content are abbreviated. A q-value of equal or less than 0.05 was used to filter significant changes prior to the pathway analyses. An additional filter was applied to the Heatmaps and Piecharts and only proteins showing a significant change ≥0.2-fold are included.

Figure 3—figure supplement 1
Reactome pathway analysis showing major pathways which differ between EDL muscles (A) and EOM muscles (B) in dHT versus WT mice.

A q-value of equal or less than 0.05 and showing a significant change ≥0.2 fold was used to filter significant changes prior to the pathway analyses.

Figure 4 with 1 supplement
Changes in protein content in EDL, soleus and EOM between dHT vs WT mice.

(A) Venn diagram showing significantly decreased proteins (left) and increased proteins (right) in the three muscle types. (B) GO biological process analysis of common proteins that are downregulated and (C) upregulated in muscle from dHT mice. Left panels, common proteins showing significant changes in content in both EDL and soleus muscles. Central panels, common proteins showing significant changes in content in EDL and EOMs; right panels, common proteins showing significant changes in content in EOM and soleus muscles. (D) List of the 39 proteins whose content is increased in EDL, soleus and EOMs in dHT mice. (E) GO analysis annotated to Biological processes of the 39 proteins that are increased in muscles from dHT mice.

Figure 4—figure supplement 1
Gene Ontology annotated to Biological process genes showing significant differences in content between muscles from dHT and WT mice.

(A, B) and (C) Downregulated genes and (D, E) and (F) upregulated genes in EDL (A and C), soleus (B and E) and EOM (C and F) muscles. The N° of genes annotated to each category is indicated on the Y-axis. Only proteins showing a q-value equal to or less than 0.05 and showing a significant change ≥0.2 fold were included in the pathway analyses.

Correlation of the actual cellular abundances of four selected proteins (in µmol/kg wet weight) determined by PRM/SID (n=2) and the iBAQ values (n=5) determined by label-free/TMT quantification (both in logarithmic scale, base 2) from the global proteomics discovery dataset for EDL samples.

Error bars are indicated for the y-axis, but for the x-axis, due to their low scale (range from 0.058 to 0.086), they are not shown by the software PRISM, GraphPad Software, (v9). The simple linear regression results obtained by PRISM GraphPad Software, (v9) are shown on the right.

EOMs are enriched in Stim 1.

(A) Representative western blots showing Stim1 and Stim1L immunopositive bands. Forty and eighty micrograms of total homogenates from EOM, soleus, and EDL muscles isolated from WT mice were loaded onto a 7.5% SDS PAGE. Proteins were blotted onto nitrocellulose, probed with an antibody recognizing Stim1 and Stim1L, followed by incubation with an anti-rabbit IgG HRP-linked antibody. Bands were visualized by chemiluminescence. Blots were subsequently stripped and probed with anti-MyHC (all) for loading normalization (bottom panel). (B) Relative content of Stim1 in the three muscle types examined. Each symbol represents the value of a single mouse. *** p<0.001.

Figure 6—source data 1

Bots refer to data shown in Figure 6A.

TOP: Original uncropped western blots showing immunoreactivity of STIM1L and STIM1 in EDL, Soleus and EOM muscles from WT mouse N° 5. BOTTOM: same blot re-probed with anti-MyHC recognizing all isoforms (loading normalization).

https://cdn.elifesciences.org/articles/83618/elife-83618-fig6-data1-v2.zip
Figure 6—source data 2

Bots refer to data used for statistical analysis depicted in Figure 6B.

Original uncropped western blots showing immunoreactivity of STIM1L, STIM1 and MyHC in EDL, Soleus and EOM muscles from WT mouse N° 1, 2, 3 (TOP) and WT mouse N° 4 (BOTTOM).

https://cdn.elifesciences.org/articles/83618/elife-83618-fig6-data2-v2.zip
Author response image 1
Western blot analysis of muscle homogenates from WT mice probed with anti- junctophilin-1 and anti-Collagen Ia1 antibodies.

Proteins in total muscle homogenates of EDL, soleus and EOM were separated on a 7.5% PAGE-SDS gel, transferred overnight onto nitrocellulose and probed with the following Ab: rabbit anti-Junctophilin-1 (1:2000, a generous gift of Takeshima, Kyoto University, Kyoto, Japan); mouse anti-collagen I alpha1 (1:2000 Novus Biological Catalog N° NBP2-92858); anti-MyHC all isoforms (1:5000; Millipore Catalog N° 41025). Western blots were incubated with the primary antibodies followed by peroxidase conjugated Protein G (Σ-Aldrich, 1:130000) or peroxidase-conjugated anti-mouse IgG (Fab Specific) Ab (Σ-Aldrich; 1:200 000). The immuno-positive bands were visualized by chemiluminescence using the WesternBright ECL HRP Substrate. For junctophilin-1 and Collagen Ia1 blots, 30 µg protein per lane were loaded; for MyHC, 5 µg protein per lane were loaded.

Author response image 2
qPCR of Cacna1s and Stac3 in muscles from WT mice.

The expression levels of the transcripts encoding Cacna1s and Stac3 are the highest in EDL muscles and the lowest in soleus muscles (top panels). There are no significant changes in their relative expression levels in dHT vs WT. Each symbol represents the value from of a single mouse. * p=0.028 Mann Whitney test qPCR was performed as described in Elbaz et al., 2019 (Hum Mol Genet 28, 2987-2999).

Author response image 3
Histological staining of EDL and soleus muscles from EDL and soleus.

Cross sectional area of HandE stained muscle sections from WT and dHT mice. No evidence of inflammation or necrosis is present in muscles from dHT mice. Bar = 100 µm. Muscles were isolated and embedded in OCT and deep-frozen in 2-methylbutane. Transver 10 µm thick muscle sections were made with a Leica Cryostat (CM1950).

Tables

Table 1
Relative change in the content of selected proteins in EDL muscles isolated from WT (baseline) and dHT mice.
Gene nameProtein*Relative contentq value
ECCRyr1Ryanodine receptor 1 (RyR1)0.403.97x10–5
Jph1Junctophillin-10.640.025
Cacna1sVoltage dependent L type calcium channel subunit a1s (DHPR α1s)0.730.018
Dhrs7cDehydrogenase/reductase SDR family member 7 C (SRP-35)1.340.0045
AsphAspartyl/asparaginyl ß-hydroxylase (junctin/junctate/asp-ß-hydroxylase)1.840.00095
Contractile proteinsMyh13MyHC-EO0.350.0063
Myh1Myosin-1 (MyHC-2x)0.610.043
Myh4Myosin-4 (MyHC 2b)0.710.018
Actn3α-actinin 30.740.012
Collagen and ECM proteinsCol2a1Collagen (II)α–1 chain0.180.0043
Col1a2Collagen (I) α –2 chain0.250.027
Col11a1Collagen (XI) α –1 chain0.350.0047
Col5a2Collagen (V)α –2 chain0.370.00059
Col5a1Collagen (V) aα –1 chain0.500.00156
Col16a1Collagen (XVI) α –1 chain0.530.00154
Col4a2Collagen (IV) α –2 chain0.70.040
ItgavIntegrin α -V0.770.044
Itgb1bp2Integrin ß–1- binding protein 21.30.045
Heat shock proteinsHspb3Hsp ß–30.730.00376
Hspb8Hsp ß–8 (a-crystallin C chain)0.750.0160
Hspa2Heat shock related 70 kDa protein (Hsp70-2)0.770.026
Hspd160 kDa Hsp, mitochondrial (Chaperonin 60)1.300.011
Hspa5Heat Shock Protein Family A (Hsp70) Member 5 (BiP)1.410.00928
Hsph1Hsp 105 kDa (Hsp105, Hsp110)1.470.0155
Hspb6Hsp ß–6 (HspB6)1.50.0259
Hspbp1Hsp 70-binding protein1.80.022
Ribosomal proteinsRpl2360 S Ribosomal protein L230.4330.023
Mrpl139 S ribosomal protein L1, mitochondrial0.5260.004
Mrpl4639 S ribosomal protein L46, mitochondrial0.5920.011
Rpl3460 S ribosomal protein L340.6590.0042
Rps15a40 S ribosomal protein S15a0.6590.0056
Mrpl4339 S ribosomal protein L43, mitochondrial0.6840.029
Mrps528 S ribosomal protein S5, mitochondrial0.740.0021
Rpl1160 S ribosomal protein L111.2650.013
Rpl660 S ribosomal protein L61.2730.012
Rpl3560 S ribosomal protein L351.2900.034
Mrpl1939 S ribosomal protein L19, mitochondrial1.3460.028
Rps2540 S ribosomal protein S251.350.0076
Rpl27a60 S ribosomal protein L27a1.3650.02
Rpl2760 S ribosomal protein L271.3740.016
Rpl960 S ribosomal protein L91.3740.015
Rps240 S ribosomal protein S21.390.0065
Rps840 S ribosomal protein S81.390.013
Rplp260 S acidic ribosomal protein P21.4030.0087
Rps1040 S ribosomal protein S101.410.033
Rpl3860 S ribosomal protein L381.4310.025
Rpl23a60 S ribosomal protein L23a1.4590.005
Rps1240 S ribosomal protein S121.4730.0128
Rps940 S ribosomal protein S91.500.0278
Rpl1860 S ribosomal protein L181.4910.017
Mrps728 S ribosomal protein S7, mitochondrial1.5670.010
Rpl10a60 S ribosomal protein L10a1.5910.017
Rpl2260 S ribosomal protein L221.6510.017
Rps1740 S ribosomal protein S171.6610.0016
Rps1640 S ribosomal protein S161.820.0020
FK506 binding proteinsFkbp1aPeptidyl-prolyl cis-trans isomerase FKBP1A (FKBP12; calstabin-1)0.640.0025
Fkbp8Peptidyl-prolyl cis-trans isomerase FKBP8 (38 kDa FKBP)1.300.024
Fkbp9Peptidyl-prolyl cis-trans isomerase FKBP9 (63 kDa FK506-binding protein)1.600.0057
Calcium-dependent protein kinasesCamk1Calcium/Calmodulin-dependent protein kinase type 1 (CaM kinase I)1.320.022
Camk2aCalcium/calmodulin-dependent protein kinase type II subunit α1.400.0189
Camk2bCalcium/calmodulin-dependent protein kinase type II subunit ß1.460.010
Camk2dCalcium/calmodulin-dependent protein kinase type II subunit δ2.240.00025
VariaPsmd726 S proteasome non-ATPase regulatory subunit 70.580.0016
Psmg2Proteasome assembly chaperone 21.660.038
Fth1Ferritin1.690.0033
  1. *

    The nomenclature of Proteins is based on that of the UniProtKB database.

Table 2
Relative change in the content of selected proteins in soleus muscles isolated from WT (baseline) and dHT mice.
Gene nameProtein*Relative contentq value
ECCRyr1Ryanodine receptor 1 (RyR1)0.660.0080
Jph1Junctophillin 10.730.026
Cacna1sVoltage-dependent L type calcium channel subunit α1s (DHPR α1s)0.670.017
TrdnTriadin0.690.0352
AsphAspartyl/asparaginyl ß-hydroxylase (junctin/junctate/aspß-hydroxylase)1.310.045
ATP2a2Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2)1.650.0256
Contractile proteinsTnnt3Troponin 3 (fast skeletal muscle type)0.690.017
Calcium binding proteinsS100a1Protein S100 A11.690.033
Camk2dCalcium/calmodulin-dependent protein kinase type II subunit δ1.230.033
Camk2gCalcium/calmodulin-dependent protein kinase type II subunitγ1.430.039
Ion PumpsAtp1b1Na+/K+ATPase ß10.770.047
Atp1a1Na+/K+ATPase α 11.410.017
Collagen and ECM proteinsCol11a1Collagen (XI) α –1 chain1.630.031
Itgb5Integrin a V/ß–511.950.044
Ribosomal proteinsRpl36a60 S ribosomal protein L36a0.2630.0021
Mrpl1039 S ribosomal protein L10, mitochondrial0.5770.040
Rpl860 S ribosomal protein L80.6610.022
Rpl2660 S ribosomal protein L260.6950.022
Mrpl4239 S ribosomal protein L42, mitochondrial0.7880.026
Rpl3060 S ribosomal protein L301.2590.020
Rpl1960 S ribosomal protein L191.2600.050
Mrpl4139 S ribosomal protein L41, mitochondrial1.2890.033
Rpl1160 S ribosomal protein L111.3250.026
Rpl1060 S ribosomal protein L101.4320.013
Rpl2260 S ribosomal protein L221.4360.017
Rplp260 S acidic ribosomal protein P21.4730.022
Rpl3560 S ribosomal protein L351.5330.040
Rpl23a60 S ribosomal protein L23a1.6120.014
Rpl2360 S ribosomal protein L231.6380.022
VariaPsmg1Proteasome Assembly Chaperone 10.4880.024
Dnajb6DnaJ homolog subfamily B member 6 (Hsp J-2)1.450.033
Psma2Proteasome 20 S Subunit α 21.510.011
  1. *

    The nomenclature of Proteins is based on that of the UniProtKB database.

Table 3
Relative change in the content of selected proteins in EOM isolated from WT and dHT mice.
Gene nameProtein*Relative contentq value
ECCRyr1Ryanodine receptor 1 (RyR1)0.421.73x10–6
AsphAspartyl/asparaginyl ß-hydroxylase (junctin/junctate/aspß-hydroxylase)1.350.00028
Casq2Calsequestrin-21.450.00031
Casq1Calsequestrin-11.550.0063
ATP2a2Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2)1.550.00052
Contractile proteinsMyh13MyHC-EO0.271.01x10–5
Actn2α -actinin 21.360.0047
Myh7bMyosin-7B (MyH7B, cardiac musle ß isoform, MyHC14)1.440.0038
Actn1α -actinin 11.450.015
Tnnt2Troponin T, cardiac isoform1.450.0037
MyotMyotilin1.610.0018
Tnnt1Troponin T slow, skeletal muscle (TnTs)1.850.022
Myoz3Myozenin 32.031.29x10–5
Myh6Myosin 6 (MyHC cardiac muscle α-isoform)2.221.01x10–5
Tnnc1Troponin C, slow skeletal and cardiac (TN-C)2.618.1x10–5
Collagen and ECM proteinsItga7Integrin α 71.290.000191
Col6a5Collagen (VI) α –5 chain1.320.0033
Col6a6Collagen (VI) α –6 chain1.320.0087
Col12a1Collagen (XII) α –1 chain1.340.012
Col14a1Collagen (XIV) α –1 chain1.610.00072
Col11a2Collagen (XI) α –2 chain4.461.27x10–5
Heat shock proteinsHspa9Mitochondrial, stress-70 protein0.780.013
Hsp90b1Hsp 90b1 (GRP-94; 90 kDa glucose regulated protein)1.260.0052
Hspb3Hsp ß- 31.270.0056
Dnaja1Dnaj homolog subfamily A member 1 (Hsp 40 kDa protein 4)1.280.0067
Hspb1Hsp ß–1 (Hsp25)1.290.00029
Hspa5Heat Shock Protein Family A (Hsp70) Member 5 (BiP)1.320.00033
Hspa1aHeat shock 70 kDa protein 1 A1.330.0069
Hsp90aa1Hsp 90 a1.400.00094
Dnajb1Dnaj homolog subfamily B member 1 (Hsp40)1.460.00021
Dnajb4DnaJ homolog subfamily B member 4 (Hsp40)1.540.011
Hspb6Hsp ß- 61.614.05x10–5
Ribosomal ProteinsRps240 S ribosomal protein S21.2600.004
Rpsa40 S ribosomal protein SA1.2760.0035
Rps1140 S ribosomal protein S111.3210.0016
Rps2040 S ribosomal protein S201.3240.0007
Rpl1060 S ribosomal protein L101.3320.0035
Rplp260 S acidic ribosomal protein P21.3320.00048
Rpl1160 S ribosomal protein L111.3350.0077
Rps2840 S ribosomal protein S281.3460.0041
Rpl360 S ribosomal protein L131.3851.42x10–5
Rps740 S ribosomal protein S71.3960.0125
Rpl27a60 S ribosomal protein L27a1.4610.00034
Rps27a40 S ribosomal protein S27a1.5700.038
FK506 binding proteinsFkbp1aPeptidyl-prolyl cis-trans isomerase FKBP1A (FKBP12; calstabin-1)0.790.015
Calcium-dependent protein kinasesCamk2bCalcium/Calmodulin-Dependent Protein Kinase IIß1.300.0018
Camk2dCalcium/Calmodulin-Dependent Protein Kinase IIδ2.328.35x10–6
Calcium binding proteinsS100a16S100 A161.290.014
S100a1S100 A11.300.029
  1. *

    The nomenclature of Proteins is based on that of the UniProtKB database.

Table 4
Concentration µmol/Kg (mean ± SD) of proteins involved in ECC in EDL, soleus and EOM muscles from WT (n=5 mice) and dHT (n=5 mice) using the peptide 4 point calibration curve.
Gene nameEDLsoleusEOM
WTdHTWTdHTWTdHT
Ryr1 monomers
(terameric channel)
1.29±0.07
(0.32)
0.86±0.01
(0.21)
0.49±0.02
(0.12)
0.40±0.002
(0.10)
0.59±0.02
(0.15)
0.35±0.01
(0.09)
Cacna1s0.56±0.030.49±0.010.18±0.010.16±0.0020.21±0.010.19±0.004
Stac30.62±0.070.53±0.060.22±0.020.20±0.010.17±0.010.15±0.01
Jsrp10.42±0.030.40±0.010.32±0.010.29±0.030.35±0.010.35±0.02
Asph0.21±0.010.26±0.010.30±0.020.35±0.030.82±0.031.00±0.03
Trdn0.96±0.180.79±0.060.16±0.030.13±0.010.23±0.010.22±0.01
Jph10.71±0.090.58±0.040.29±0.020.25±0.010.24±0.010.23±0.01
Stim10.46±0.020.48±0.030.55±0.030.56±0.031.35±0.031.42±0.09
Orai1 monomers
(6-subunt complex)
0.11±0.01
(0.02)
0.13±0.02
(0.02)
Not detectedNot detected0.16±0.03
(0.03)
0.17±0.01
(0.03)
Table 5
Calculated ratio values.
Gene nameEDLsoleusEOM
WTdHTWTdHTWTdHT
Ryr1 complex/Cacna1s0.5710.4290.6670.6250.7140.474
Stac3/Cacna1s1.111.081.221.251.671.84
Jsrp1/Cacna1s0.750.821.781.810.951.00
Stim1/Orai1 complex23.024.0--45.047.3

Additional files

Supplementary file 1

Tables of relative changes in protein content between soleus and EDL, EDL and EOM and soleus and EOM muscles iin WT mice.

(a) Table showing relative change in protein content between soleus and EDL muscles isolated from WT mice. (b) Table showing relative change in protein content between EOM and EDL muscles isolated from WT mice. (c) Table showing relative change in protein content between EOM and soleus muscles isolated from WT mice.

https://cdn.elifesciences.org/articles/83618/elife-83618-supp1-v2.docx
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https://cdn.elifesciences.org/articles/83618/elife-83618-mdarchecklist1-v2.pdf

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  1. Jan Eckhardt
  2. Alexis Ruiz
  3. Stéphane Koenig
  4. Maud Frieden
  5. Hervé Meier
  6. Alexander Schmidt
  7. Susan Treves
  8. Francesco Zorzato
(2023)
Quantitative proteomic analysis of skeletal muscles from wild-type and transgenic mice carrying recessive Ryr1 mutations linked to congenital myopathies
eLife 12:e83618.
https://doi.org/10.7554/eLife.83618