New roles for Hoxc8 in the establishment and maintenance of motor neuron identity
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE174709 | GEO | 2021/05/20
REPOSITORIES: GEO
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Project description:Purpose: Conducted expression profiling by RNA-seq as unbiased screen to identify genes that are altered in motor neurons of PbxMNΔ mice at e12.5 at brachial and thoracic levels of the spinal cord. Because loss of Pbx genes affects MN organization at all rostrocaudal levels, we focused on genes whose profiles were altered at both brachial and thoracic levels. Methods: We compared gene expression profiles in MNs isolated from control Hb9::GFP and PbxMNΔ; Hb9::GFP embryos at e12.5. MNs were purified by FACS, and RNA was extracted from 9 PbxMNΔ; Hb9::GFP and 9 control Hb9::GFP embryos at brachial and thoracic levels using the Arcturus Picopure RNA isolation kit. 10ng of RNA was pooled from 3 RNA samples of each genotype, and used to amplify 100ng of cDNA using Nugene's Ovation RNA-Seq System V2 kit, 100ng of cDNA for each sample was used as in input to prepare 12 bar coded libraries using the Ovation Ultralow Library system. We then performed expression profiling by RNA-seq. The samples were mixed into two pools and run on two 50-nucleotide paired end read rapid run flow cell lanes with the Illumina HiSeq 2500 sequencer. Generating on average 74 and 101 million reads passing filter for brachial and thoracic samples respectively. Results: This analysis yielded 64 brachial and 124 thoracic genes that were differentially expressed with a stringent cutoff of padj.<0.05. Of these genes, we found 31 genes in common between the two, brachial and thoracic, levels of the spinal cord that may play a role in motor neuron columnar organization. Furthermore our expression profiling of control brachial and control thoracic MNs identified 61 genes with (padj.<0.05), that represent distinct molecular profiles of MNs generated at brachial and thoracic levels which may be used to further characterize MNs involved in forelimb and thoracic innervation. Conclusions: Our study represents a detailed transcriptional analysis of embryonic spinal motor neurons and revealed a number of novel motor neuron-specific genes that are under transcriptional regulation of Pbx genes.
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Project description:Familial amyotrophic lateral sclerosis (ALS) represents about 10% of ALS cases. In about 20% of familial ALS patients, a mutation in superoxide dismutase-1 (SOD1) can be found. The ubiquitous SOD1 protein converts superoxide radical anions to oxygen and hydrogen peroxide. Patients with familial ALS caused by mutations in SOD1 can show comorbidity with frontotemporal dementia and develop cognitive impairment, including apathy, inattention, verbal deficits, and hypersexuality. At the cellular level, pathological signs of ALS may include tau immunoreactive astrocytic and neuronal inclusions, suggesting that cognitive dysfunction in ALS may also reflect abnormal protein metabolism of the microtubule associated protein (MAP), tau. To identify cell-specific expression changes, we performed laser capture microdissection (LCM) to isolate anterior horn motor neurons and surrounding cells. 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RNA isolation from LCM collected cells was performed using the Qiagen RNeasy Micro Kit. Only RNA with RNA Integrity Numbers (RIN) above 7.5 were taken for further analysis (Agilent Bioanalyzer 2100). A two-round T7-based amplification and labeling protocol (Agilent Low RNA Input Linear Amplification Kit PLUS) was used to generate high quality labeled cRNA. Agilent Whole Mouse Genome Microarray comparisons of motor neurons and surrounding glia were performed between transgenic (SOD1G93A and TAUP301L) and corresponding nontransgenic (control) littermate animals, producing four independent comparison groups: SOD1G93A motor neurons versus control motor neurons (SOD1mn), SOD1G93A motor neuron surrounding glia versus control glia (SOD1gl), TAUP301L motor neurons versus control motor neurons (TAUmn) and TAUP301L glia versus control glia (TAUgl). Each comparison used four pairs of transgenic (SOD1G93A or TAUP301L) vs. corresponding control littermate animals, producing four biological replicates. Raw microarray data were acquired using the Agilent DNA Microarray scanner and processed with the accompanying Agilent Feature Extraction 10.5 Image Analysis software using default settings. Normalized signal intensities were used to identify gene expression changes in SOD1G93A and TAUP301L motor neurons and surrounding glial cells, generating four partially overlapping sets of data. For the identification of differential expression, the genes were required to pass two conservative criteria: a ratio beyond the 99.5% confidence interval observed in homotypic comparisons, which corresponded to an approximately 1.5-fold expression change, and a paired t-test (P<0.01) computed using 100 permutations of the data for each gene. Correction for multiple comparisons was performed using the adjusted Bonferroni test. The analysis was performed in the TM4: Microarray Software Suite. These techniques identified 251 transcripts representing 186 known genes for which expression was altered in at least one of the four comparisons. Four-condition experiment, SOD1G93A motor neurons versus control motor neurons (SODmn), SOD1G93A motor neuron surrounding glia versus control glia (SODgl), TAUP301L motor neurons versus control motor neurons (TAUmn) and TAUP301L glia versus control glia (TAUgl). Each comparison used four pairs of transgenic (SOD1G93A or TAUP301L) vs. corresponding control littermate animals, producing four biological replicates. Biological replicates: 4 SOD1G93A motor neurons (SODmn), 4 non SOD littermate motor neurons (nonSODmn), 4 SOD1G93A motor neuron surrounding glia (SODgl), 4 non SOD littermate motor neuron surrounding glia (nonSODgl), 4 TAUP301L motor neurons (TAUmn), 4 non TAU littermate motor neurons (nonTAUmn), 4 TAUP301L motor neuron surrounding glia (TAUgl), 4 non TAU littermate motor neuron surrounding glia (nonTAUgl). Four independent comparison groups were generated: SOD1G93A motor neurons versus control nonSOD motor neurons, SOD1G93A motor neuron surrounding glia versus control nonSOD glia, TAUP301L motor neurons versus control nonTAU motor neurons and TAUP301L glia versus control nonTAU glia. Each comparison used four pairs of transgenic (SOD1G93A or TAUP301L) vs. corresponding control littermate animals, producing four biological replicates. Each replicate was repeated twice with dye flip to correct for unequal dye incorporation rates. 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Project description:New roles for Hoxc8 in the establishment and maintenance of motor neuron identity
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