Introduction
Material and methods
Experimental animals
Scanning electron microscopy with analysis of the elemental spectrum
MALDI-MSI of lipids
UHPLC–HRMS analysis of protein expression
Immunofluorescence
Haematoxylin–eosin staining
Data analyses and statistics
Results
Analysis of elements using energy dispersive X-ray spectroscopy scanning electron microscopy
Analysis of lipids in the cerebrum
Analysis of proteins in the white matter
GO biological process category | Child category | Child category | Child category | Child category | Number of genes process | Number of genes underexpressed | Expected value | Fold enrichment | P-value |
---|---|---|---|---|---|---|---|---|---|
System development (GO:0048731) | 4219 | 50 | 24.98 | 2.00 | 2.61E-03 | ||||
Nervous system development (GO:0007399) | 2264 | 38 | 13.40 | 2.84 | 1.82E-05 | ||||
Neurogenesis (GO:0022008) | 1771 | 31 | 10.48 | 2.96 | 3.26E-04 | ||||
Gliogenesis (GO:0042063) | 235 | 11 | 1.39 | 7.91 | 1.70E-03 | ||||
Glial cell differentiation (GO:0010001) | 185 | 11 | 1.10 | 10.04 | 1.57E-04 | ||||
Anatomical structure development (GO:0048856) | 5208 | 56 | 30.83 | 1.82 | 8.78E-03 | ||||
Glial cell development (GO:0021782) | 113 | 8 | 0.67 | 11.96 | 4.08E-03 | ||||
Oligodendrocyte development (GO:0014003) | 41 | 5 | 0.24 | 20.60 | 4.76E-02 | ||||
Central nervous system development (GO:0007417) | 835 | 20 | 4.94 | 4.05 | 1.07E-03 | ||||
Oligodendrocyte differentiation (GO:0048709) | 68 | 8 | 0.40 | 19.87 | 8.76E-05 |
GO biological process class/child class | Gene name | Sum PEP score | Abundance ratio: (Sample) / (Control) | Abundance ratio P-value: (sample) / (control) |
---|---|---|---|---|
Oligodendrocyte development | ||||
Fatty acid 2-hydroxylase* ** | 4.50 | 0.436 | 0.001 | |
Myelin-associated glycoprotein* ** | 177 | 0.341 | 2.22E-14 | |
Myelin proteolipid protein* ** | 42.4 | 0.324 | 1.33E-15 | |
Oligodendrocyte-myelin glycoprotein* ** | 28.9 | 0.667 | 0.027 | |
Tubulin polymerization-promoting protein * ** | 84 | 0.674 | 0.009 | |
Glial development* | ||||
Calcineurin subunit B type 1 ** | 62.58 | 0.72 | 0.047 | |
Protein NDRG1 ** | 35.04 | 0.666 | 0.043 | |
Tetraspanin-2 ** | 24.51 | 0.283 | 2.36E-11 | |
Glial cell differentiation** | ||||
2',3'-cyclic-nucleotide 3'-phosphodiesterase | 485.39 | 0.401 | 1.16E-10 | |
Dual specificity mitogen-activated protein kinase kinase 1 | 203.85 | 0.661 | 0.006 | |
Receptor-type tyrosine-protein phosphatase zeta | 196.06 | 0.726 | 0.039 |
GO biological process | Child category | Child category | Number of genes process | Number of genes underexpressed | Expected value | Fold enrichment | P-value |
---|---|---|---|---|---|---|---|
Ensheathment of neurons (GO:0007272) | 114 | 12 | 0.67 | 17.78 | 5.62E-08 | ||
Axon ensheathment (GO:0008366) | 114 | 12 | 0.67 | 17.78 | 5.62E-08 | ||
Myelination (GO:0042552) | 112 | 12 | 0.66 | 18.10 | 4.59E-08 | ||
Generation of neurons (GO:0048699) | 1663 | 27 | 9.85 | 2.74 | 1.28E-02 | ||
Neuron projection development (GO:0031175) | 691 | 17 | 4.09 | 4.16 | 7.19E-03 | ||
Axon development (GO:0061564) | 373 | 15 | 2.21 | 6.79 | 6.83E-05 |
Gene name | Sum PEP score | Abundance ratio: (sample) / (control) | Abundance ratio P-value: (sample) / (control) |
---|---|---|---|
Breast carcinoma-amplified sequence 1 homolog | 79.326 | 0.51 | 5.41E-06 |
Calcineurin subunit B type 1 | 62.58 | 0.72 | 0.045 |
CD9 antigen | 6.995 | 0.584 | 0.017 |
Gap junction gamma-3 protein | 18.265 | 0.324 | 9.08E-08 |
Junctional adhesion molecule C | 4.494 | 0.252 | 7.69E-11 |
Myelin-associated glycoprotein* | 177 | 0.341 | 2.22E-14 |
Myelin proteolipid protein* | 42.4 | 0.324 | 1.33E-15 |
Oligodendrocyte-myelin glycoprotein* | 28.9 | 0.667 | 0.026 |
Protein NDRG1e | 35.044 | 0.666 | 0.042 |
Tetraspanin-2 | 24.519 | 0.283 | 2.36E-11 |
Tubulin polymerization-promoting protein | 84.096 | 0.674 | 0.009 |
GO-slim biological process category | Child category | Child category | Number of genes process | Number of genes overexpressed | Expected value | Fold enrichment | P-value |
---|---|---|---|---|---|---|---|
Cellular metabolic process (GO:0044237) | 4357 | 40 | 30.53 | 1.31 | 3.83E-02 | ||
Organonitrogen compound metabolic process (GO:1901564) | 2567 | 28 | 17.71 | 1.58 | 9.64E-03 | ||
Ammonium ion metabolic process (GO:0097164) | 36 | 2 | 0.25 | 7.03 | 2.68E-02 | ||
Biosynthetic process (GO:0009058) | 2006 | 22 | 14.06 | 1.57 | 2.38E-02 | ||
Organic substance biosynthetic process (GO:1901576) | 1986 | 22 | 13.91 | 1.58 | 2.15E-02 | ||
Organonitrogen compound biosynthetic process (GO:1901566) | 589 | 18 | 4.13 | 4.36 | 2.09E-07 | ||
Organophosphate biosynthetic process (GO:0090407) | 167 | 4 | 1.17 | 3.42 | 3.07E-02 | ||
Phospholipid biosynthetic process (GO:0008654) | 50 | 2 | 0.35 | 5.71 | 4.86E-02 |
GO biological process | Child category | Number of genes process | Number of genes underexpressed | Expected value | Fold enrichment | P-value |
---|---|---|---|---|---|---|
Sulfur compound metabolic process (GO:0006790) | 118 | 4 | 0.70 | 5.72 | 5.57E-03 | |
Glutathione metabolic process (GO:0006749) | 35 | 2 | 0.21 | 9.64 | 1.87E-02 |
GO-slim biological process class/child class | Gene name | Sum PEP score | Abundance ratio: (sample) / (control) | Abundance ratio P-value: (sample) / (control) |
---|---|---|---|---|
Glutathione metabolic process | ||||
Glutathione S-transferase Mu 7* | 66.1 | 0.667 | 0.027 | |
Glutathione S-transferase P 1* | 106.96 | 0.727 | 0.039 | |
Sulfur compound metabolic process* | ||||
Carbohydrate sulfotransferase 2 | 7.42 | 0.425 | 2.14E-5 | |
Hydroxymethyl-glutaryl-CoA synthase | 119.39 | 0.688 | 0.014 |
GO-slim biological process Category | Child category | Child category | Child category | Child category | Child category | Child category | Number of genes process | Number of genes overexpressed | Expected value | Fold enrichment | P-value |
---|---|---|---|---|---|---|---|---|---|---|---|
Small molecule metabolic process (GO:0044281) | 587 | 11 | 4.11 | 2.67 | 3.02E-03 | ||||||
Organic acid metabolic process (GO:0006082) | 355 | 7 | 2.49 | 2.81 | 1.31E-02 | ||||||
Oxoacid metabolic process (GO:0043436) | 342 | 7 | 2.40 | 2.92 | 1.08E-02 | ||||||
Carboxylic acid metabolic process (GO:0019752) | 331 | 7 | 2.32 | 3.02 | 9.19E-03 | ||||||
Cellular amino acid metabolic process (GO:0006520) | 123 | 4 | 0.86 | 4.64 | 1.14E-02 | ||||||
Alpha-amino acid metabolic process (GO:1901605) | 77 | 4 | 0.54 | 7.41 | 2.24E-03 | ||||||
Glutamate metabolic process (GO:0006536) | 4 | 2 | 0.3 | 71.36 | 3.83E-04 |
GO-slim biological process class/child class | Gene name | Sum PEP Score | Abundance ratio: (sample) / (control) | Abundance ratio P-value: (sample) / (control) |
---|---|---|---|---|
Glutamate metabolic process | ||||
Proline dehydrogenase 1, mitochondrial* ** *** | 149.81 | 1.479 | 0.004 | |
Glutamate dehydrogenase 1, mitochondrial* ** *** | 376.49 | 1.395 | 0.006 | |
Alpha-amino acid metabolic process*, cellular amino acid metabolic process* | ||||
CAD protein ** *** | 59.22 | 1.389 | 0.008 | |
Thiosulfate sulfurtransferase ** *** | 105.85 | 1.377 | 0.008 | |
Carboxylic acid metabolic process**, oxoacid metabolic process**, organic acid metabolic process** | ||||
Beta-glucuronidase *** | 7.602 | 2.511 | 2.43E-05 | |
Carnitine O-palmitoyltrans-ferase 1, liver isoform*** | 100.58 | 1.354 | 0.024 | |
Pyruvate carboxylase, mitochondrial | 542.37 | 1.458 | 0.002 | |
Small molecule metabolic process*** | ||||
Succinate-CoA ligase [GDP-forming] subunit beta, mitochondrial | 80.578 | 1.851 | 0.005 | |
Hydroxymethyl-glutaryl-CoA synthase, mitochondrial | 34.06 | 1.817 | 0.0010 | |
Triokinase/FMN cyclase | 8.467 | 1.496 | 0.0266 | |
Transthyretin | 48.964 | 2.494 | 1.009E-06 |
Reactome pathways | Number of genes process | Number of genes overexpressed | Expected value | Fold enrich-ment | P-value |
---|---|---|---|---|---|
Formation of the ternary complex, and subsequently, the 43S complex (R-MMU-72695)* | 58 | 17 | 0.41 | 41.89 | 2.79E-19 |
Ribosomal scanning and start codon recognition (R-MMU-72702)* | 59 | 22 | 0.41 | 53.22 | 7.84E-28 |
Translation initiation complex formation (R-MMU-72649)* | 59 | 22 | 0.41 | 53.22 | 7.84E-28 |
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S (R-MMU-72662) | 60 | 22 | 0.42 | 52.33 | 1.13E-27 |
SRP-dependent cotranslational protein targeting to membrane (R-MMU-1799339)* | 90 | 25 | 0.63 | 39.65 | 8.06E-29 |
Formation of a pool of free 40S subunits (R-MMU-72689)* | 99 | 27 | 0.69 | 38.92 | 4.01E-31 |
Nonsense mediated decay (NMD) independent of the Exon Junction Complex (EJC) (R-MMU-975956)** | 92 | 25 | 0.64 | 38.78 | 1.38E-28 |
L13a-mediated translational silencing of Ceruloplasmin expression (R-MMU-156827)* | 109 | 27 | 0.76 | 35.35 | 5.09E-30 |
GTP hydrolysis and joining of the 60S ribosomal subunit (R-MMU-72706)* | 110 | 27 | 0.77 | 35.03 | 6.48E-30 |
Cap-dependent translation initiation (R-MMU-72737) | 117 | 27 | 0.82 | 32.94 | 3.30E-29 |
Nonsense mediated decay (NMD) enhanced by the Exon Junction complex (EJC) (R-MMU-975957)** | 113 | 25 | 0.79 | 31.58 | 2.09E-26 |
Nonsense-mediated decay (NMD) (R-MMU-927802)** | 113 | 25 | 0.79 | 31.58 | 2.09E-26 |
Mitochondrial translation elongation (R-MMU-5389840)* | 86 | 19 | 0.60 | 31.53 | 1.69E-19 |
Mitochondrial translation termination (R-MMU-5419276)* | 88 | 19 | 0.62 | 30.82 | 2.59E-19 |
Mitochondrial translation (R-MMU-5368287)* | 89 | 19 | 0.62 | 30.47 | 3.19E-19 |
Translation (R-MMU-72766) | 225 | 46 | 1.58 | 29.18 | 7.49E-50 |
Nonsense mediated decay (NMD) enhanced by the Exon Junction Complex (EJC) (R-MMU-975957)** | 113 | 25 | 0.79 | 31.58 | 2.09E-26 |
Major pathway of rRNA processing in the nucleolus and cytosol (R-MMU-6791226)** | 175 | 25 | 1.23 | 20.39 | 8.25E-22 |
rRNA processing in the nucleus and cytosol (R-MMU-8868773)** | 175 | 25 | 1.23 | 20.39 | 8.25E-22 |
rRNA processing (R-MMU-72312)** | 175 | 25 | 1.23 | 20.39 | 8.25E-22 |
Metabolism of RNA (R-MMU-8953854)** | 566 | 26 | 3.97 | 6.56 | 6.37E-11 |
Metabolism of proteins (R-MMU-392499)* | 1644 | 59 | 11.52 | 5.12 | 1.03E-23 |
Unclassified (UNCLASSIFIED) | 12,982 | 38 | 90.96 | 0.42 | 0.00E00 |
Gene name | Sum PEP Score | Abundance Ratio: (Sample) / (Control) | Abundance Ratio P-Value: (Sample) / (Control) |
---|---|---|---|
Aldehyde dehydrogenase family 1 member A3 | 9.87 | 3.63 ( >) | 2.42E-07 |
Breast carcinoma-amplified sequence 1 homolog | 79.33 | 0.51 ( <) | 5.41E-06 |
Dynactin subunit 1 | 430.29 | 1.849 ( >) | 1.44E-06 |
Dynactin subunit 4 | 108.84 | 1.58 ( >) | 0.0003 |
Ermin | 56.84 | 0.51 ( <) | 0.0001 |
Galectin 1 | 21.94 | 1.61 ( >) | 0.012 |
Gap junction gamma-3 protein | 18.27 | 0.32 ( <) | 9.09E-08 |
Gap junction alpha-1 protein | 59.62 | 2.52 ( >) | 1.20E-07 |
Gelsolin | 178.38 | 0.72 ( <) | 0.03 |
Neural cell adhesion molecule 1 | 542.26 | 1.62 ( >) | 0.0001 |
Pleiotrophin | 19.36 | 1.47 ( >) | 0.03 |