Deep proteome profiling reveals signatures of age and sex differences in paw skin and sciatic nerve of naïve mice
- Systems Biology of Pain, Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Austria
Figures
Figure 1 with 1 supplement
Data-independent acquisition paired with parallel accumulation serial fragmentation (DIA-PASEF) acquisition followed by DIA-NN analysis outperforms data-dependent acquisition paired with PASEF (DDA-PASEF) acquisition in deep proteome profiling of paw skin and sciatic nerve (SCN) of naïve mice.
(A, B) Pearson’s correlations of technical controls of paw skin (blue) and SCN (green) acquired over 20 days on a timsTOF Pro. (C, D) Comparisons of identified protein groups (protein IDs) using …
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Figure 1—source data 1
Quantitative proteome and differentially expressed protein (DEP) lists of paw skin.
DEPs from age- and sex-dependent comparisons are listed in separated sheets.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig1-data1-v1.xlsx
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Figure 1—source data 2
Quantitative proteome and differentially expressed protein (DEP) lists of sciatic nerve (SCN).
DEPs from age- and sex-dependent comparisons are listed in separated sheets.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig1-data2-v1.xlsx
Figure 1—figure supplement 1
Experimental workflow of proteome profiling in mouse paw skin and sciatic nerves.
Figure 2 with 1 supplement
Age and sex differences in proteomes of paw skin and sciatic nerve (SCN).
(A) Venn diagram shows unique and shared protein IDs across age and sex groups of paw skin. (B) Comparison of the quantified paw skin proteome with previously reported sub-proteomes of human skin (Dy…
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Figure 2—source data 1
List of myelin proteins (Siems et al., 2020) not quantified in the sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig2-data1-v1.xlsx
Figure 2—figure supplement 1
Fuzzy C-means clustering analysis of the paw skin (A) and sciatic nerve (SCN) (B) proteome.
The R package ‘Mfuzz’ (https://www.bioconductor.org/packages/release/bioc/html/Mfuzz.html) was used for analysis with nine clusters specified for calculation. Y-axis shows the standardized …
Figure 3 with 1 supplement
Differential expression analysis of paw skin samples reveals diverse age-dependent biological pathways in male and female mice.
(A) Venn diagram illustrates unique and shared differentially expressed proteins (DEPs; criteria: q-value ≤ 0.05, absolute log2 fold change [FC] ≥ 0.585, i.e., an absolute FC of 1.5) from …
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Figure 3—source data 1
List of ligands and neuronal receptors found in skin cell types (Wangzhou et al., 2021), which we quantified in the paw skin proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig3-data1-v1.xlsx
Figure 3—figure supplement 1
Gene Ontology Biological Process (GO-BP) analysis of differentially expressed proteins (DEPs) from age-dependent comparisons in female (A) and male (B) paw skin.
Figure 4 with 1 supplement
Age-dependent differential expression analysis in sciatic nerve (SCN) samples.
(A) Venn diagram illustrates unique and shared differentially expressed proteins (DEPs) (criteria: q-value ≤ 0.05, absolute log2 fold change [FC] ≥ 0.585, i.e., an absolute FC of 1.5) from …
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Figure 4—source data 1
Synaptic proteins among differentially expressed proteins (DEPs) from age-dependent comparisons in sciatic nerve (SCN).
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig4-data1-v1.xlsx
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Figure 4—source data 2
Ligand list of neuronal receptors found in immune cells (Wangzhou et al., 2021), which we quantified in the sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig4-data2-v1.xlsx
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Figure 4—source data 3
Neuronal ligands of glial receptors (Wangzhou et al., 2021), which we quantified in the sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig4-data3-v1.xlsx
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Figure 4—source data 4
Glial ligands of neuronal receptors (Wangzhou et al., 2021), which we quantified in the sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig4-data4-v1.xlsx
Figure 4—figure supplement 1
Enriched Gene Ontology Biological Process (GO-BP) terms and their activity scores in age-dependent comparisons using common differentially expressed proteins (DEPs) (A) and DEPs enriched in male sciatic nerve (SCN) (B) and female SCN (C), respectively.
Figure 5 with 1 supplement
Differential expression analysis indicates protein signatures of sexual dimorphism in paw skin and sciatic nerve (SCN).
(A, B) Differentially expressed proteins (DEPs) of sex-dependent comparisons at 4 weeks and 14 weeks in paw skin (A) and SCN (B). Heatmaps show the normalized protein expression (averaged intensity) …
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Figure 5—source data 1
Sex-associated transcripts of human tibial nerves (Ray et al., 2019), which we quantified in the sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig5-data1-v1.xlsx
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Figure 5—source data 2
Sex-associated transcripts of mouse hind paws (Mecklenburg et al., 2020), which we quantified in the paw skin proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig5-data2-v1.xlsx
Figure 5—figure supplement 1
Sexual dimorphism in SCN and paw skin.
(A) Sex-dependent significance in the sciatic nerve (SCN) dataset of proteins previously reported to be sexually dimorphic in the transcriptome of human tibial nerves (Ray et al., 2019). (B) …
Figure 6
Multiple proteins associated with skin diseases and pain exhibit age and sex dependence.
(A) Venn diagram indicates the number of quantified protein IDs in paw skin (white) associated with various human skin diseases (light gray) upon comparison with a skin disease database (dark gray, h…
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Figure 6—source data 1
Gene candidates of various human skin diseases (https://biohub.skinsciencefoundation.org/), which we quantified in the paw skin proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig6-data1-v1.xlsx
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Figure 6—source data 2
Fuzzy C-means clustering membership of 329 and 245 pathology-related proteins quantified in the paw skin and sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig6-data2-v1.xlsx
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Figure 6—source data 3
Differentially expressed genes (DEGs) of hand–foot psoriasis, palmoplantar pustulosis, and vesicular hand eczema quantified in the paw skin proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig6-data3-v1.xlsx
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Figure 6—source data 4
Pain-related genes (https://www.painresearchforum.org/, http://paingeneticslab.ca/4105/06_02_pain_genetics_database.asp, and https://humanpaingeneticsdb.ca/hpgdb/), which we quantified in the sciatic nerve (SCN) proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig6-data4-v1.xlsx
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Figure 6—source data 5
Differentially expressed proteins (DEPs) upon sciatic nerve (SCN) injury (spared nerve injury [SNI] model of neuropathic pain in mice) (Barry et al., 2018) quantified in the SCN proteome.
- https://cdn.elifesciences.org/articles/81431/elife-81431-fig6-data5-v1.xlsx
Author response image 1
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (mouse) | C57BL/6J | In-house bred | Wild type, female and male, 3-4 and 1415 weeks old | |
| Chemical compound, drug | Acetonitrile | Fisher Scientific | 10001334 | |
| Chemical compound, drug | Formic acid | Fisher Scientific | 15658430 | |
| Chemical compound, drug | 10× PBS | Fisher Scientific | 11594516 | |
| Chemical compound, drug | Tris 1 M | Accugene/Avantor | 733-1653 | |
| Chemical compound, drug | Glycerol | Fisher Scientific | 10021083 | |
| Chemical compound, drug | Dithiothreitol 1 M | Sigma-Aldrich | 43816 | |
| Chemical compound, drug | Acetone | Sigma-Aldrich | 1000201000 | |
| Chemical compound, drug | Ethanol | Sigma-Aldrich | 1117272500 | |
| Chemical compound, drug | Iodoacetamide | Sigma-Aldrich | I1149 | |
| Chemical compound, drug | Ammonium bicarbonate | Sigma-Aldrich | 09830-500G | |
| Chemical compound, drug | Water MS grade | Sigma-Aldrich | 1.15333.1000 | |
| Chemical compound, drug | Trypsin/Lys-C | Promega | V5073 | |
| Chemical compound, drug | Trypsin | Serva | 37283.01 | |
| Chemical compound, drug | Sera-Mag SpeedBead beads | Cytiva | 65152105050250, 45152105050250 | 1:1 mix |
| Other | cOmplete Protease Inhibitor Cocktail | Roche/Merck | 58929700001 | Mix of protease inhibitors |
| Other | Protein LoBind tube | Eppendorf | 0030108116 | Reagent tube |
| Other | Aurora Series UHPLC column | IonOpticks | AUR2-25075C18A-CSI | 25 cm × 75 µm column |
| Other | Biopsy punch 4 mm | Kai Medical | 48401 | Skin biopsy punch |
| Software, algorithm | MaxQuant | Max Planck Institute of Biochemistry | Version 1.6.17.0 | |
| Software, algorithm | DIA-NN | https://github.com/vdemichev/DiaNN | RRID:SCR_022865 | Version 1.8.0 |
| Software, algorithm | R | https://www.r-project.org/ | Version 4.1.1 | |
| Software, algorithm | Mouse proteome database | UniProt | UP000000589 | Downloaded on 2021-07-08, 17070 entries |
