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Series GSE39252 Query DataSets for GSE39252
Status Public on May 03, 2013
Title Expression changes in Caenorhabditis elegans xpa-1 mutant
Organism Caenorhabditis elegans
Experiment type Expression profiling by array
Summary Background: The ability of an organism to repair DNA damage is implicated in carcinogenesis and aging. Interestingly expression profiling of Nucleotide Excision Repair (NER) deficient segmental progeroid mice revealed gene expression changes resembling these observed in aged wild type animals. Our previous transcriptional profiling of NER-deficient C. elegans xpa-1 mutant showed overrepresentation of genes involved in lifespan determination and upregulation of several oxidative stress response genes (Fensgard et al. Aging 2010). However, since an independent study performed by Boyd and coworkers (Boyd et al. Mut Res 2010) showed limited number of changes in xpa-1 mutant. Therefore to independently validate that transcriptome modulation does take place in xpa-1 mutants, we performed another global gene expression profiling based on 5 independent biological replicates allowing more stringent statistical analysis. Results: In agreement with what was observed by Boyd and coworkers (Boyd et al. Mut Res 2010) current transcriptomic analysis detected fewer changes in xpa-1 C. elegans mutant with only a few genes regulated more than 4-fold. Nevertheless, Gene Ontology (GO) enrichment analysis performed on statistically significantly regulated unique protein coding genes revealed overrepresentation of aging gene cluster. Moreover, as before, overexpression of several genes involved in oxidative stress responses was detected. Conclusion: More stringent statistical analysis predictably resulted in a smaller number of regulated genes and thus overrepresented GOs comparing to the earlier paper. However, major conclusions of the previous study can be still regarded as valid, as the most important aging GO is still overrepresented.
Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response to persistent transcription-blocking DNA damage, although the relevant lesions have not been identified. Here we provide evidence for transcriptional reprogramming in NER-deficient C. elegans xpa-1 by transcriptomic and proteomic approaches. This reprograming is accompanied by increased intracellular ROS and ATP levels and lifespan shortening in xpa-1 mutant. Moreover we show that Base Excision Repair DNA glycosylase NTH-1 is upstream form the signaling events leading to transcriptomic changes, as its downregulation reverses overexpression of sod-3, gst-4 and aqp-1 genes, reduces intracellular ROS and ATP levels and reverses lifespan shortening observed in xpa-1 mutant. Surprisingly, however, these responses appear to not depend on cyclopurine levels, since these lesions are lower in xpa-1 C. elegans mutant than in the wild type. Finally, we also explore here which other upstream factors are necessary for transcriptional reprograming in xpa-1 mutant.
Overall design Untreated Caenorhabditis elegans mutant deficient in xpa-1 and the wild type N2 strain were subjected to transcriptome analysis using Affymetrix platform. For each sample group five replicates were analyzed.
Contributor(s) Arczewska KD, Tomazella GG, Lindvall JM, Kassahun H, Schiavi A, Marquis BJ, Holmberg-Still C, Ventura N, Thiede B, Nilsen H
Citation(s) 23580547
Submission date Jul 11, 2012
Last update date Jul 06, 2016
Contact name Jessica Margareta Lindvall
Organization name SciLifeLab. Stockholm University
Department NBIS
Street address Tomtebodavägen 23A
City Solna
ZIP/Postal code 11111
Country Sweden
Platforms (1)
GPL200 [Celegans] Affymetrix C. elegans Genome Array
Samples (10)
GSM958827 N2_rep1
GSM958828 N2_rep2
GSM958829 N2_rep3
BioProject PRJNA170380

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Supplementary file Size Download File type/resource
GSE39252_RAW.tar 16.5 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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