Background
Methods
Animals
RNA and protein isolation
RNA sequencing
RNA-Seq bioinformatics analysis
Proteomics
In-gel tryptic digest
Data-independent acquisition LC-MS/MS
Proteomics data analysis
Western blotting
Pathway analysis
Results
Global gene expression in symptomatic Mecp2 Jae/y whole cortex
Gene targets: this study | UniProt: function keywords | Fold change | RTT gene hits: direction of expression (with references) |
---|---|---|---|
Aacs* | • Molecular function: ligase • Biological process: fatty acid metabolism; lipid metabolism • Ligand: ATP-binding; nucleotide-binding | − 0.79 | Decrease4
|
Aldh1a1* | • Molecular function: oxidoreductase • Ligand: NAD | − 0.67 | Decrease4
|
Arhgdig
| • Molecular function: GTPase activation
|
− 0.69
|
Decrease
2
|
Auts2
| N/A | 1.40 | Increase7
|
C1qa
| • Biological process: complement pathways; immunity; innate immunity | − 0.76 | Decrease7
|
Cacnb3
| • Molecular function: calcium channel; ion channel; voltage-gated channel
• Biological process: calcium transport; ion transport; transport
• Ligand: calcium
|
− 0.79
|
Increase
2
|
Calb1
| • Ligand: calcium; metal-binding; vitamin D
|
− 0.79
|
Decrease
5
|
Calr* | • Molecular function: chaperone • Ligand: calcium; lectin; metal-binding | − 0.80 | Decrease8
|
Dgkg* | • Molecular function: kinase; transferase • Ligand: ATP-binding; calcium; metal-binding; nucleotide-binding; zinc | 1.42 | Increase4, 8
|
Ephx2* | • Molecular function: hydrolase • Biological process: aromatic hydrocarbons catabolism; detoxification; lipid metabolism • Ligand: magnesium; metal-binding | − 0.71 | Decrease4
|
Fabp7
| • Biological process: transport
• Ligand: lipid-binding
|
− 0.39
|
Decrease
2,5
|
Fkbp5
| • Molecular function: chaperone; isomerase; rotamase
|
1.81
|
Increase
3,4,5,7,8
|
Gabra3
| • Molecular function: chloride channel; ion channel; ligand-gated ion channel; receptor • Biological process: ion transport; transport • Ligand: chloride | − 0.81 | Decrease6
|
Gfra1* | • Molecular function: receptor | 1.26 | Increase4, 8
|
Grm3* | • Molecular function: G-protein coupled receptor; receptor; transducer | − 0.63 | Decrease4
|
Hpcal4* | • Ligand: calcium; metal-binding | − 0.69 | Decrease4, 8
|
Hsph1
| • Biological process: stress response • Ligand: ATP-binding; nucleotide-binding | − 0.80 | Decrease3
|
Itm2a
|
N/A
|
− 0.73
|
Decrease
5
|
Mecp2
| • Molecular function: DNA-binding; repressor • Biological process: transcription; transcription regulation | − 0.66 | Decrease1, 4
|
Msmo1
/
Sc4mol
| • Molecular function: oxidoreductase
• Biological process: lipid biosynthesis; lipid metabolism; steroid biosynthesis; steroid metabolism; steroid biosynthesis; sterol metabolism
• Ligand: iron; NAD
|
− 0.77
|
Decrease
5
|
Myo1b* | • Molecular function: actin-binding; calmodulin-binding; motor protein; myosin • Ligand: ATP-binding; nucleotide-binding | 1.32 | Increase4, 8
|
Pcsk1
| • Molecular function: hydrolase; protease; serine protease • Ligand: calcium | − 0.74 | Decrease6
|
Pdia4* | • Molecular function: isomerase | − 0.71 | Decrease4, 8
|
Plagl1
| • Ligand: metal-binding; zinc
|
1.37
|
Increase
5
|
Prkcg* | • Molecular function: kinase; serine/threonine-protein kinase; transferase • Biological process: biological rhythms • Ligand: ATP-binding; calcium; metal-binding; nucleotide-binding; zinc | − 0.82 | Decrease8
|
Pvalb
| • Molecular function: muscle protein
• Ligand: calcium; metal-binding
|
1.27
|
Increase
2
|
Pygm
| • Molecular function: glycosyltransferase; transferase • Biological process: carbohydrate metabolism; glycogen metabolism • Ligand: nucleotide-binding; pyridoxal phosphate | 1.29 | Increase6
|
Qdpr* | • Molecular function: oxidoreductase • Biological process: tetrahydrobiopterin biosynthesis • Ligand: NADP | − 0.74 | Decrease4
|
Rnpep* | • Molecular function: aminopeptidase; hydrolase; metalloprotease; protease • Ligand: metal-binding; zinc | − 0.78 | Decrease4
|
Sgk1
| • Molecular function: kinase; serine/threonine-protein kinase; transferase
• Biological process: apoptosis; stress response
• Ligand: ATP-binding; nucleotide-binding
|
1.37
|
Increase
2,3
|
Slc24a4* | • Biological process: antiport; calcium transport; ion transport; olfaction; potassium transport; sensory transduction; sodium transport; symport; transport • Ligand: calcium; potassium; sodium | 1.58 | Increase4
|
Slc9a3r1* | • Biological process: Wnt signaling pathway | − 0.74 | Decrease8
|
Sun2* | • Biological process: meiosis | 1.42 | Increase8
|
Ugp2* | • Molecular function: nucleotidyltransferase; transferase • Ligand: magnesium; metal-binding | − 0.73 | Decrease4
|
Zmat4* | • Molecular function: DNA-binding • Ligand: metal-binding; zinc | 1.5 | Increase8
|
Protein expression in symptomatic Mecp2 Jae/y whole cortex
Gene name | Protein description | FC |
p-value | General putative function |
---|---|---|---|---|
RNA metabolism
| ||||
H2afy2
|
Core histone macro-H2A.2 (mH2A2)
|
1.8
|
0.050
|
Gene repression
|
Cdc5l
| Cell division cycle 5-like protein | 2.2 | 0.013 | mRNA splicing |
Cd2bp2
| CD2 antigen cytoplasmic tail-binding protein 2 | 1.8 | 0.072 | mRNA splicing |
Hnrnpa0
| Heterogeneous nuclear ribonucleoprotein (hnRNP) A0 | 2.0 | 0.076 | RNA-binding protein |
Hnrnpd
| Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 | 1.4 | 0.029 | RNA-binding protein |
Hnrnpdl
| Heterogeneous nuclear ribonucleoprotein (hnRNP) D-like | 2.1 | 0.024 | RNA-binding protein |
Hnrnph2
| Heterogeneous nuclear ribonucleoprotein (hnRNP) H2 | 1.5 | 0.034 | RNA-binding protein |
Hnrnpl
| Heterogeneous nuclear ribonucleoprotein (hnRNP) L | 1.8 | 0.077 | RNA-binding protein |
Cirbp
|
Cold-inducible RNA-binding protein
|
4.3
|
0.047
|
RNA-binding protein
|
Ddx21
| Nucleolar RNA helicase 2 | 2.9 | 0.009 | rRNA transcription, processing, and modification |
Hp1bp3
| Heterochromatin protein 1-binding protein 3 | 2.1 | 0.057 | Transcription regulation |
Proteostasis
| ||||
Impact
| Protein IMPACT | 1.8 | 0.002 | Translational activation |
Uchl5
| Ubiquitin carboxyl-terminal hydrolase isozyme L5 | 1.6 | 0.037 | Deubiquitylation |
Adrm1
| Proteasomal ubiquitin receptor ADRM1 | 3.0 | 0.007 | Enhances Uchl5 |
Ublcp1
| Ubiquitin-like domain-containing CTD phosphatase 1 | 3.5 | 0.068 | Nuclear proteasome activity |
Cryab
| Alpha-crystallin B chain | −2.1 | 0.003 | Chaperone-like activity |
Hspb1
| Heat shock protein beta-1 (HspB1) | −1.7 | 0.020 | Chaperone for protein folding maintenance |
Hsph1*
|
Heat shock protein 105 kDa
|
−2.1
|
0.004
|
Chaperone activity regulation
|
Hsp90aa1
| Heat shock protein HSP 90-alpha (HSP90α) | −1.5 | 0.058 | ATP-dependent chaperone |
Hsp90ab1
| Heat shock protein HSP 90-beta (HSP90β) | −1.4 | 0.056 | ATP-dependent chaperone |
Hspa4
| Heat shock 70 kDa protein 4 | −1.5 | 0.067 | Molecular chaperone |
Ahsa1
| Activator of 90 kDa heat shock protein ATPase homolog 1 | −1.3 | 0.059 | Chaperone binding |
Gene name | Protein description | FC |
p-value | General putative function |
---|---|---|---|---|
Metabolism
| ||||
Lss
| Lanosterol synthase | 8.1 | 0.016 | Cholesterol synthesis |
Aacs*
|
Acetoacetyl-CoA synthetase
|
− 1.4
|
0.059
|
Ketone body utilization
|
Acadvl
| Very long-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.6 | 0.045 | Fatty acid oxidation |
Ugp2
#
|
UTP-glucose-1-phosphate uridylyltransferase
|
− 1.7
|
0.011
|
Glycogen metabolism
|
Acot7
| Cytosolic acyl coenzyme A thioester hydrolase | − 1.3 | 0.087 | Fatty Acyl-CoA biosynthesis |
Monoamine metabolism
| ||||
Qdpr
#
|
Dihydropteridine reductase
|
− 1.7
|
0.029
|
Tetrahydrobiopterin synthesis
|
Spr*
| Sepiapterin reductase | − 1.5 | 0.083 | Tetrahydrobiopterin synthesis |
Maoa
| Amine oxidase [flavin-containing] A | 1.4 | 0.096 | Degradation of monoamines |
S-adenosylmethionine-dependent methylation
| ||||
Gamt
|
Guanidinoacetate
N
-methyltransferase
|
− 1.7
|
0.089
|
Creatine synthesis
|
Srm
| Spermidine synthase (SPDSY) | − 1.5 | 0.024 | Polyamine synthesis |
Mthfd1l
| Monofunctional C1-tetrahydrofolate synthase, mitochondrial | 1.7 | 0.054 | Folate synthesis |
Significant proteins in symptomatic Mecp2 Jae/y whole cortex are expressed in multiple CNS cell types
Transcriptome-proteome expression comparison identifies novel hits
Gene/protein | UniProt accession | Gene fold change | Protein fold change | RTT hit? | Putative function |
---|---|---|---|---|---|
Mecp2/MeCP2 | Q9Z2D6 | − 0.66 | − 10.6 | Yes1, 2
| DNA binding protein; transcriptional regulator |
Rnpep/RNPEP* | Q8VCT3 | − 0.78 | − 3.47 | Yes2
| Peptide catabolic process |
Pdia4/ERp72* | P08003 | − 0.71 | − 2.22 | Yes2,3
| ER protein processing |
Hsph1/HSPH1 | Q61699 | − 0.80 | − 2.13 | Yes4
| Protein chaperone |
Rnpep/RNPEP(Ac)* | Q8VCT3 | − 0.78 | − 2.02 | Yes2
| Peptide catabolic process |
Aldh1a1/ALDH1A1* | P24549 | − 0.67 | − 1.95 | Yes2
| Retinal dehydrogenase |
Slc9a3r1/NHERF1(P)* | P70441 | − 0.74 | − 1.79 | Yes3
| Scaffold protein |
Ugt8a/UGT8 | Q64676 | − 0.79 | − 1.76 | --- | Sphingolipid metabolism |
Qdpr/QDPR (or DHPR)* | Q8BVI4 | − 0.74 | − 1.68 | Yes2
| Monoamine metabolism (tetrahydrobiopterin biosynthesis) |
Ugp2/UGP2* | Q91ZJ5 | − 0.73 | − 1.67 | Yes2
| Glycogen synthesis |
Car2/Ca2 | P00920 | − 0.72 | − 1.61 | --- | Reversible hydration of carbon dioxide |
Grm3/mGluR3* | Q9QYS2 | − 0.63 | − 1.6 | Yes2
| Protein coupled glutamate receptor |
Ephx2/EPHX2* | P34914 | − 0.71 | − 1.59 | Yes2
| Cholesterol synthesis |
Hpcal4/HPCAL4* | Q8BGZ1 | − 0.69 | − 1.51 | Yes2,3
| Calcium binding |
Spr/SPR | Q64105 | − 0.77 | − 1.47 | --- | Monoamine metabolism (tetrahydrobiopterin metabolic process) |
Sash1/SASH1 | P59808 | − 0.82 | − 1.44 | --- | p38 MAPK and NIK/NF-kappaB signaling |
Calr/CRT* | P14211 | − 0.80 | − 1.43 | Yes3
| ER calcium-binding protein |
Aacs/AACS* | Q9D2R0 | − 0.79 | − 1.37 | Yes2
| Fatty acid and lipid metabolism |
S1pr1/S1P1 | O08530 | − 0.78 | − 1.28 | --- | Cell-cell adhesion |
Slc9a3r1/NHERF1(Ac)* | P70441 | − 0.74 | − 1.24 | Yes3
| Scaffold protein |
Nova1/NOVA1 | Q9JKN6 | 1.26 | 1.28 | --- | RNA/mRNA-binding protein |
Slc24a4/Nckx4* | Q8CGQ8 | 1.58 | 1.3 | Yes3
| K+-dependent Na+/Ca2+ exchanger |
Kcnab3/Kvβ3.1 | P97382 | 1.27 | 1.43 | --- | Voltage gated K+ channel |
Me3/NADP-ME3 | Q8BMF3 | 1.28 | 1.46 | --- | Mitochondrial NADP(+)-dependent malic enzyme |
Tfrc/TfR | Q62351 | 1.32 | 1.48 | --- | Cell surface receptor required for iron uptake |
Dgkg/DGKγ* | Q91WG7 | 1.42 | 1.51 | Yes2,3
| Lipid metabolism |
Prkcg/PKCγ(P)* | P63318 | − 0.82 | 1.66 | Yes3
| Protein kinase; LTP |
Rasgrf1/RasGRF1 | P27671 | 1.32 | 1.68 | --- | Stimulates the dissociation of GDP from RAS protein |
Zmat4/ZMAT4* | Q8BZ94 | 1.50 | 1.88 | Yes3
| DNA/RNA and p53 binding |
Myo1b/Myo1b* | P46735 | 1.32 | 2.02 | Yes2,3
| Actin binding; calmodulin binding |
Fkbp5/FKBP5 | Q64378 | 1.81 | 2.02 | Yes2–6
| Immunoregulation; protein trafficking |
Wipf3/WIPF3 | P0C7L0 | 1.23 | 2.26 | --- | Cytoskeleton organization |
Itih3/ITI-HC3 | Q61704 | 1.52 | 2.37 | --- | Anchor protein between hyaluronan and matrix proteins |
Gfra1/GDNFRα1* | P97785 | 1.26 | 2.64 | Yes2,3
| RET and RAF/MAP kinase signaling cascade |
Sun2/SUN2* | Q8BJS4 | 1.42 | 2.86 | Yes3
| Nuclear envelope protein |