Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

Toonen, Lodewijk J. A.; Overzier, Maurice; Evers, Melvin M.; Leon, Leticia G.; van der Zeeuw, Sander A. J.; Mei, Hailiang; Kielbasa, Szymon M.; Goeman, Jelle J.; Hettne, Kristina M.; Magnusson, Olafur Th.; Poirel, Marion; Seyer, Alexandre; ‘t Hoen, Peter A. C.; van Roon-Mom, Willeke M. C.

doi:10.1186/s13024-018-0261-9

Molecular Neurodegeneration

Table 2 Top 25 differentially expressed genes in SCA3 mice brains (regions combined)

From: Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model

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	1.16^a	0.42	1.47^a	1.16^a	ion transport
Zfp488	zinc finger protein 488	1.05E-56	1.79^a	1.25^a	1.29^a	1.45^a	transcription, oligodendrocyte specific
Car2	carbonic anhydrase 2	3.63E-44	−1.26^a	−0.64^a	− 1.26^a	−0.72^a	carbonate dehydratase activity
Chdh	choline dehydrogenase	3.26E-40	1.04^a	0.66^a	0.85^a	0.87^a	choline dehydrogenase activity
Prob1	proline rich basic protein 1	9.30E-38	1^a	0.62^a	0.68^a	0.59^a	unknown
Il33	interleukin 33	9.98E-35	−1.3^a	−0.98^a	−1.2^a	−0.87^a	cytokine activity
Fbxw15	F-box and WD-40 domain protein 15	5.97E-27	−1.8^a	−0.84	−1.44^a	−0.79	unknown
Rnf43	ring finger protein 43	5.64E-21	1.06^a	0.74^a	0.65^a	0.88^a	ubiquitin-protein transferase activity
Polr2a	RNA polymerase II subunit A	2.00E-20	0.74^a	0.16	0.47^a	0.35	DNA-directed RNA polymerase activity
Ppl	periplakin	1.50E-19	2.14^a	0.73	0.9^a	0.62	cadherin binding involved in cell-cell adhesion
Arsb	arylsulfatase B	2.48E-16	0.53^a	0.2	0.32^a	0.18	sulphate hydrolysis
Kcnk13	potassium two pore domain channel subfamily k member 13	3.04E-16	−0.97^a	−0.73^a	−0.81^a	−0.44	voltage-gated ion channel
Chil1	chitinase-3-like protein 1	7.24E-16	−0.75^a	−0.28	− 0.69^a	−0.56^a	carbohydrate metabolic process
Serpinb1a	serpin Family B Member 1	1.16E-15	−1.34^a	−0.86	−1.21^a	−0.81	negative regulation of endopeptidase activity
Tspan2	tetraspanin 2	5.27E-15	−0.87^a	−0.3	− 0.99^a	−0.41	astrocyte and microglia development
Hist1h2be	Histone H2B type 1-C/E/G	2.39E-14	0.78^a	0.18	0.77^a	0.66^a	antibacterial humoral response
Acot1	Acyl-coenzyme A thioesterase 1	1.90E-13	0.74^a	0.35	0.28	0.29	acyl-CoA metabolic process
Erbb2ip	erbin	1.86E-12	−0.89^a	−0.44	−0.54^a	− 0.30	cellular response to tumor necrosis factor
Glul	Glutamine synthetase	1.12E-11	−0.63^a	−0.25	− 0.45^a	−0.21	glutamine biosynthetic process
Cbs	Cystathionine beta-synthase	1.68E-11	−0.41^a	−0.06	− 0.40^a	−0.14	catalyzes first step of the transsulfuration pathway
Qdpr	Dihydropteridine reductase	2.10E-11	−0.64^a	−0.39	− 0.70^a	−0.36	6,7-dihydropteridine reductase activity
Sox8	Transcription factor SOX-8	6.57E-11	0.58^a	0.37	0.42^a	0.38	enteric nervous system development
Psat1	Phosphoserine aminotransferase	6.63E-11	0.48^a	0.39	0.40^a	0.46^a	L-serine biosynthetic process
Enpp6	Ectonucleotide pyrophosphatase/phosphodiesterase family member 6	2.01E-10	0.20^a	0.58	0.76^a	1.25^a	choline metabolic process
Ttyh1	Protein tweety homolog 1	1.37E-09	−0.44^a	−0.12	−0.04	−0.14	chloride transport

Noted with ^aare genes that are also differentially expressed in individual brain regions

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ISSN: 1750-1326

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