Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Apr:81:107-18.
doi: 10.1016/j.freeradbiomed.2015.01.004. Epub 2015 Jan 19.

Whole transcriptome analysis reveals an 8-oxoguanine DNA glycosylase-1-driven DNA repair-dependent gene expression linked to essential biological processes

Leopoldo Aguilera-Aguirre  1 , Koa Hosoki  2 , Attila Bacsi  1 , Zsolt Radák  1 , Thomas G Wood  3 , Steven G Widen  4 , Sanjiv Sur  5 , Bill T Ameredes  2 , Alfredo Saavedra-Molina  1 , Allan R Brasier  5 , Xueqing Ba  1 , Istvan Boldogh  6
Affiliations

Whole transcriptome analysis reveals an 8-oxoguanine DNA glycosylase-1-driven DNA repair-dependent gene expression linked to essential biological processes

Leopoldo Aguilera-Aguirre et al. Free Radic Biol Med. 2015 Apr.

Abstract

Reactive oxygen species inflict oxidative modifications on various biological molecules, including DNA. One of the most abundant DNA base lesions, 8-oxo-7,8-dihydroguanine (8-oxoG) is repaired by 8-oxoguanine DNA glycosylase-1 (OGG1) during DNA base excision repair (OGG1-BER). 8-OxoG accumulation in DNA has been associated with various pathological and aging processes, although its role is unclear. The lack of OGG1-BER in Ogg1(-/-) mice resulted in decreased inflammatory responses and increased susceptibility to infections and metabolic disorders. Therefore, we proposed that OGG1 and/or 8-oxoG base may have a role in immune and homeostatic processes. To test our hypothesis, we challenged mouse lungs with OGG1-BER product 8-oxoG base and changes in gene expression were determined by RNA sequencing and data were analyzed by Gene Ontology and statistical tools. RNA-Seq analysis identified 1592 differentially expressed (≥ 3-fold change) transcripts. The upregulated mRNAs were related to biological processes, including homeostatic, immune-system, macrophage activation, regulation of liquid-surface tension, and response to stimulus. These processes were mediated by chemokines, cytokines, gonadotropin-releasing hormone receptor, integrin, and interleukin signaling pathways. Taken together, these findings point to a new paradigm showing that OGG1-BER plays a role in various biological processes that may benefit the host, but when in excess could be implicated in disease and/or aging processes.

Keywords: 8-Oxoguanine; Biological processes; Gene expression; OGG1-BER.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Whole-transcriptome profile induced by 8-oxoG challenge. (A) Graphical depiction of results from hierarchical clustering showing whole-transcriptome profile. Total RNA isolated from challenged lungs at 30, 60 and 120 min were subjected to RNA-Seq, heat maps were generated using GENE-E (http://www.broadinstitute.org/cancer/software/GENE-E/), and transcripts were clustered according to their expression patterns. Transcript levels (RPKM) were normalized to control (time 0 min). Rows represent identified transcripts and columns at time points after 8-oxoG challenge. The intensity of the red or green colors shows the degree of upregulation or downregulation, respectively. (B) The total number of upregulated (≥3-fold) transcripts (red bars) and downregulated (≤3-fold) transcripts (green bars) in each cluster. (C) Number of unique and shared transcripts altered by 8-oxoG challenge. Venn diagrams were constructed by using online software Venny (Materials and Methods). (D) Kinetic changes in transcript levels induced by 8-oxoG challenge.
Fig. 2
Fig. 2
Gene ontology categories represented by the upregulated genes induced after introduction of the OGG1-BER product 8-oxoG into mouse lungs. Overrepresentation test of the genes upregulated (≥ 3 fold) at 60 min was performed by using PANTHER (http://www.pantherdb.org). (A) Biological process. (B) Protein class. (C) Cellular component. (D) Molecular function. X axis represent −log(P value).
Fig. 3
Fig. 3
Signaling pathways induced by OGG1-BER product, 8-oxoG in mouse lungs. Pie chart was generated by using PANTHER (Materials and Methods). Pathway analysis included only those genes with expression levels ≥ 3-fold at 60 min.
Fig. 4
Fig. 4
Validation of RNA-Seq data. (A) Fold changes in RPKM of selected genes as determined by RNA-Seq analysis. RNA was isolated from lungs at 60 min post challenge and pooled (n = 5) or kept separately. One μg of pooled RNA was subjected to RNA-Seq as in Materials and Methods. (B) qRT-PCR confirmation of RNA-Seq data. One μg RNA isolated from individual control and challenged mice (n = 5) was reverse transcribed, and cDNAs were amplified by using specific primer pairs as described in Materials and Methods.
Fig. 5
Fig. 5
OGG1-BER alters expression of RAS signature genes. Effect of 8-oxoG challenge on the expression of genes reported to be up-regulated (A) or down regulated (B) by RAS signaling. (C) Differentially expressed RAS signature genes with ≥ 3-fold expression levels. Upregulated genes are shown in red bars and down regulated ones in green bars. (D) Activation of RAS-GTPase by 8-oxoG challenge in lungs (upper panel) and dependency on OGG1 expression in 8-oxoG-exposed lungs. (E) Down-regulation of Ogg1 in mouse airway epithelium by RNAi. (F) Decreased expression of Cxcl1 and Cxcl2 in Ogg1-depleted airways. **p < 0.01, ***p < 0.001.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. David SS, O'Shea VL, Kundu S. Base-excision repair of oxidative DNA damage. Nature. 2007;447:941–950. - PMC - PubMed
    1. Jacob KD, Noren Hooten N, Trzeciak AR, Evans MK. Markers of oxidant stress that are clinically relevant in aging and age-related disease. Mech Ageing Dev. 2013;134:139–157. - PMC - PubMed
    1. Kanvah S, Joseph J, Schuster GB, Barnett RN, Cleveland CL, Landman U. Oxidation of DNA: damage to nucleobases. Acc Chem Res. 2010;43:280–287. - PubMed
    1. Steenken S, Jovanovic S. How Easily Oxidizable Is DNA? One-Electron Reduction Potentials of Adenosine and Guanosine Radicals in Aqueous Solution. J Am Chem Soc. 1997;119:617–618.
    1. Mitra S, Hazra TK, Roy R, Ikeda S, Biswas T, Lock J, Boldogh I, Izumi T. Complexities of DNA base excision repair in mammalian cells. Mol Cells. 1997;7:305–312. - PubMed

Publication types

MeSH terms

-