Background
Methods
SCA3 mice and tissue sampling
Analysis | Tissue | Wild-type mice | SCA3 mice |
---|---|---|---|
RNA-seq | brainstem | 8 | 6 |
RNA-seq | cerebellum | 7 | 6 |
RNA-seq | cortex | 7 | 6 |
RNA-seq | striatum | 8 | 5 |
RNA-seq | blood (9 and 17.5 months) | 6 | 5 |
Metabolomics | plasma (4 and 16 months) | 4 | 4 |
Lipidomics | plasma (4 and 16 months) | 4 | 4 (4 months), 3 (16 months) |
Behavioural testing
Metabolite profiling in plasma
Lipid profiling in plasma
RNA isolation
RNA sequencing
Sequencing data processing
Differential gene expression and statistical analysis
Functional annotation of gene sets and pathway analysis
Validation with RT-qPCR
Western blotting
Results
SCA3 mice do not present with overt motor symptoms at 17 months of age
Individual brain regions are differently affected by mutant ataxin-3
Gene symbol | Name | FDR | Brainstem log2 fold change | Cerebellum log2 fold change | Striatum log2 fold change | Cortex log2 fold change | Protein function (GO term mol function or biological process) |
---|---|---|---|---|---|---|---|
Tmc3
| transmembrane channel-like gene family 3 | 1.30E-61 | 1.16a | 0.42 | 1.47a | 1.16a | ion transport |
Zfp488
| zinc finger protein 488 | 1.05E-56 | 1.79a | 1.25a | 1.29a | 1.45a | transcription, oligodendrocyte specific |
Car2
| carbonic anhydrase 2 | 3.63E-44 | −1.26a | −0.64a | − 1.26a | −0.72a | carbonate dehydratase activity |
Chdh
| choline dehydrogenase | 3.26E-40 | 1.04a | 0.66a | 0.85a | 0.87a | choline dehydrogenase activity |
Prob1
| proline rich basic protein 1 | 9.30E-38 | 1a | 0.62a | 0.68a | 0.59a | unknown |
Il33
| interleukin 33 | 9.98E-35 | −1.3a | −0.98a | −1.2a | −0.87a | cytokine activity |
Fbxw15
| F-box and WD-40 domain protein 15 | 5.97E-27 | −1.8a | −0.84 | −1.44a | −0.79 | unknown |
Rnf43
| ring finger protein 43 | 5.64E-21 | 1.06a | 0.74a | 0.65a | 0.88a | ubiquitin-protein transferase activity |
Polr2a
| RNA polymerase II subunit A | 2.00E-20 | 0.74a | 0.16 | 0.47a | 0.35 | DNA-directed RNA polymerase activity |
Ppl
| periplakin | 1.50E-19 | 2.14a | 0.73 | 0.9a | 0.62 | cadherin binding involved in cell-cell adhesion |
Arsb
| arylsulfatase B | 2.48E-16 | 0.53a | 0.2 | 0.32a | 0.18 | sulphate hydrolysis |
Kcnk13
| potassium two pore domain channel subfamily k member 13 | 3.04E-16 | −0.97a | −0.73a | −0.81a | −0.44 | voltage-gated ion channel |
Chil1
| chitinase-3-like protein 1 | 7.24E-16 | −0.75a | −0.28 | − 0.69a | −0.56a | carbohydrate metabolic process |
Serpinb1a
| serpin Family B Member 1 | 1.16E-15 | −1.34a | −0.86 | −1.21a | −0.81 | negative regulation of endopeptidase activity |
Tspan2
| tetraspanin 2 | 5.27E-15 | −0.87a | −0.3 | − 0.99a | −0.41 | astrocyte and microglia development |
Hist1h2be
| Histone H2B type 1-C/E/G | 2.39E-14 | 0.78a | 0.18 | 0.77a | 0.66a | antibacterial humoral response |
Acot1
| Acyl-coenzyme A thioesterase 1 | 1.90E-13 | 0.74a | 0.35 | 0.28 | 0.29 | acyl-CoA metabolic process |
Erbb2ip
| erbin | 1.86E-12 | −0.89a | −0.44 | −0.54a | − 0.30 | cellular response to tumor necrosis factor |
Glul
| Glutamine synthetase | 1.12E-11 | −0.63a | −0.25 | − 0.45a | −0.21 | glutamine biosynthetic process |
Cbs
| Cystathionine beta-synthase | 1.68E-11 | −0.41a | −0.06 | − 0.40a | −0.14 | catalyzes first step of the transsulfuration pathway |
Qdpr
| Dihydropteridine reductase | 2.10E-11 | −0.64a | −0.39 | − 0.70a | −0.36 | 6,7-dihydropteridine reductase activity |
Sox8
| Transcription factor SOX-8 | 6.57E-11 | 0.58a | 0.37 | 0.42a | 0.38 | enteric nervous system development |
Psat1
| Phosphoserine aminotransferase | 6.63E-11 | 0.48a | 0.39 | 0.40a | 0.46a | L-serine biosynthetic process |
Enpp6
| Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | 2.01E-10 | 0.20a | 0.58 | 0.76a | 1.25a | choline metabolic process |
Ttyh1
| Protein tweety homolog 1 | 1.37E-09 | −0.44a | −0.12 | −0.04 | −0.14 | chloride transport |
Cellular signalling pathways are altered in SCA3 mouse brain
Pathway | Number of genes | p-value | Pathway database |
---|---|---|---|
Brain regions combined analysis (585 genes) | |||
α-adrenergic signalling | 11 | 1.23E-05 | IPA |
CREB signalling in neurons | 25 | 1.95E-05 | IPA |
Protein kinase A signalling | 25 | 2.57E-05 | IPA |
Axon guidance | 24 | 3.63E-05 | IPA + Euretos |
Transmission across chemical synapses | 13 | 5.50E-05 | IPA + Euretos |
Superpathway of cholesterol biosynthesis (srebp) | 6 | 6.03E-05 | IPA + Euretos |
Myelination (cellular process) | 24 | 8.02E-06 | IPA + Euretos |
Brainstem (195 genes) | |||
pi-3 k cascade | 6 | 1.20E-04 | IPA + Euretos |
amino acid metabolism | 9 | 1.31E-04 | Euretos |
Superpathway of Cholesterol Biosynthesis | 5 | 1.74E-04 | IPA + Euretos |
Striatum (824 genes) | |||
axon guidance | 38 | 2.19E-07 | IPA + Euretos |
neurotransmitter receptor binding and downstream transmission in the postsynaptic cell | 19 | 9.72E-06 | Euretos |
synaptic transmission/long term potentiation | 23 | 3.02E-05 | IPA + Euretos |
Differential gene expression in blood
Gene symbol | Name | FDR | Log fold change | Protein function (GO term mol. function or biological process) |
---|---|---|---|---|
Pdia6
| protein disulfide isomerase associated 6 | 0.002 | −0.6 | apoptotic cell clearance |
Hs3st3b1
| heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 | 0.002 | 0.9 | glycosaminoglycan biosynthetic process |
Klk8
| kallikrein related-peptidase 8 | 0.004 | 1.0 | endopeptidase activity |
Il18r1
| interleukin 18 receptor 1 | 0.007 | 0.7 | interleukin-18-mediated signaling pathway |
Runx2
| runt related transcription factor 2 | 0.007 | 0.8 | ATP binding |
Reck
| reversion-inducing-cysteine-rich protein with kazal motifs | 0.007 | 1.1 | endopeptidase inhibitor activity |
Tob1
| transducer of ErbB-2.1 | 0.007 | 0.8 | receptor tyrosine kinase binding |
Phf13
| PHD finger protein 13 | 0.007 | 0.6 | chromatin binding |
Rhoh
| ras homolog family member H | 0.007 | −0.5 | mast cell activation |
Smad7
| Mothers Against Decapentaplegic Homolog 7 | 0.010 | 0.7 | activin binding |
Metabolic and lipid changes in blood of SCA3 mice
Compound | ChEBI ID | Fold change | p-value | Altered at Time points | Associated pathway |
---|---|---|---|---|---|
4 months | |||||
DL-Dihydroorotic-acid | 17025 | 1.61 ± 0.19 | 0.002 | 4 months | Pyrimidine Metabolism |
N-a-acetyl-L-arginine | 40521 | 1.95 ± 0.39 | 0.003 | 4 months | NA |
3-hydroxydecanoic-acid / 10-hydroxydecanoic-acid | 17409 | 1.51 ± 0.21 | 0.005 | 4 months | Fatty Acid |
12 months | |||||
L-Threonic-acid | 15908 | 0.55 ± 0.08 | 0.001 | 12 months | Ascorbate and aldarate metabolism |
2-Aminoisobutyric-acid / Aminobutyric-acid | 27971 | 2.58 ± 0.69 | 0.002 | 12 months | NA |
Asparagine | 17196 | 0.68 ± 0.08 | 0.003 | 12 months | Ammonia Recycling / Aspartate Metabolism / Transcription/Translation |
16 months | |||||
Methylhistamine | 29009 | 0.87 ± 0.06 | 0.019 | 16 months | Histidine Metabolism |
DL-Tryptophan | 27897 | 0.74 ± 0.11 | 0.020 | 12 and 16 months | NA |
Threonine / D-allo-Threonine | 16857 | 0.77 ± 0.09 | 0.038 | 16 months | Glycine and Serine Metabolism / Threonine and 2-Oxobutanoate Degradation / Transcription/Translation |