Whole transcriptome analysis reveals a role for OGG1-initiated DNA repair signaling in airway remodeling

Abstract

Reactive oxygen species (ROS) generated by environmental exposures, and endogenously as by-products of respiration, oxidatively modify biomolecules including DNA. Accumulation of ROS-induced DNA damage has been implicated in various diseases that involve inflammatory processes, and efficient DNA repair is considered critical in preventing such diseases. One of the most abundant DNA base lesions is 7,8-dihydro-8-oxoguanine (8-oxoG), which is repaired by the 8-oxoguanine DNA glycosylase 1 (OGG1)-initiated base-excision repair (OGG1-BER) pathway. Recent studies have shown that the OGG1-BER byproduct 8-oxoG base forms a complex with cytosolic OGG1, activating small GTPases and downstream cell signaling in cultured cells and lungs. This implies that persistent OGG1-BER could result in signaling leading to histological changes in airways. To test this, we mimicked OGG1-BER by repeatedly challenging airways with its repair product 8-oxoG base. Gene expression was analyzed by RNA sequencing (RNA-Seq) and qRT-PCR, and datasets were evaluated by gene ontology and statistical tools. RNA-Seq analysis identified 3252 differentially expressed transcripts (2435 up- and 817 downregulated, Z3-fold change). Among the upregulated transcripts, 2080 mRNAs were identified whose encoded protein products were involved in modulation of the actin family cytoskeleton, extracellular matrix, cell adhesion, cadherin, and cell junctions, affecting biological processes such as tissue development, cell-to-cell adhesion, cell communication, and the immune system. These data are supported by histological observations showing epithelial alterations, subepithelial fibrosis, and collagen deposits in the lungs. These data imply that continuous challenge by the environment and consequent OGG1-BER-driven signaling trigger gene expression consistent with airway remodeling.

8-Oxoguanine DNA glycosylase1–driven DNA repair—A paradoxical role in lung aging

“…Next whether 8-oxoG challenge-induced KRAS signaling in airways resembles that of aging-associated gene expression was also queried. RNAs were isolated at 0, 30, 60 and 120 min after challenge and subjected to RNA-sequencing and gene ontology analysis (Materials and Methods) (Aguilera-Aguirre et al, 2015; Aguilera-Aguirre, 2015). …”

“…Utilizing gene identification programs and NCBI’s mouse data base (Materials and Methods) we identified 3252 differentially expressed transcripts (2435 up- and 817 down-regulated) including 2080 protein-coding mRNAs, 144 microRNAs, and 326 non-coding, full-length RNAs as we published previously (Aguilera-Aguirre, 2015). To identify genes associated with lung aging, a ranked list was generated from the GeneCards gene data base based on the key words “lung” and “aging.” The search generated a 4956-gene-ranked list.…”

“…Activation of these kinases were prerequisite events in induction of biological processes including positive/negative regulation of signal transduction, intracellular signal transduction, cell communication and others (Aguilera-Aguirre et al, 2015). Studies have also shown that OGG1·8-oxoG → small GTPases significantly upregulated signaling pathways including cadherin, integrin, Rho GTPase, transforming growth factor beta (TGFβ), and those modulated by wingless type (Wnt) family growth factors as well as cytokines/chemokines ( P values are between 7.61E-04 and P = 7.61E-09) (Aguilera-Aguirre, 2015). These signaling pathways have previously been related to airway remodeling --well characterized changes in aged and diseased lungs (Chilosi et al, 2013; Ijaz et al, 2014).…”

Pathophysiology of bronchoconstriction

“…RNAs were isolated after the last challenge at 0, 30, 60 and 120 min (Fig. 2A) [78**,79**]. In controls, lungs were challenged once and RNAs were isolated at the same time points (Fig.…”

“…Changes in gene expression were determined by RNA sequencing (RNA-Seq; GEO Series accession number: GSE61095 and GSE65031), and the data were analyzed by gene ontology (GO) and statistical tools. A single exposure of airways to 8-oxoG induced gene expressions primarily related to the immune system; macrophage activation, mediated by chemokines, cytokines, and integrin; and interleukin signaling pathways [79**]. In contrast, repeated challenge induced gene expression potentially involved in modulation of the actin family cytoskeleton, extracellular matrix, cell adhesion, cell junction, and cell communication.…”