Light-dark oscillations in the lung transcriptome: implications for lung homeostasis, repair, metabolism, disease, and drug action

Abstract

Diurnal-nocturnal, or circadian-like, rhythms are 24-h variations in biological processes, evolved for the efficient functioning of living organisms. Such oscillations and their regulation in many peripheral tissues are still unclear. In this study, we used Affymetrix gene chips in a rich time-series experiment involving 54 animals killed at 18 time points within the 24-h cycle to examine light-dark cycle patterns of gene expression in rat lungs. Data mining identified 646 genes (represented by 1,006 probe sets) showing robust oscillations in expression in lung that were parsed into 8 distinct temporal clusters. Surprisingly, more than two-thirds of the probe sets showing cyclic expression peaked during the animal's light/inactive period. Six core clock genes and nine clock-related genes showed rhythmic oscillations in their expression in lung. Many of the genes that peaked during the inactive period included genes related to extracellular matrix, cytoskeleton, and protein processing and trafficking, which appear to be mainly involved in the repair and remodeling of the organ. Genes coding for growth factor ligands and their receptors, which play important roles in maintaining normal lung function, also showed rhythmic expression. In addition, genes involved in the metabolism and transport of endogenous compounds, xenobiotics, and therapeutic drugs, along with genes that are biomarkers or potential therapeutic targets for many lung diseases, also exhibited 24-h cyclic oscillations, suggesting an important role for such rhythms in regulating various aspects of the physiology and pathophysiology of lung.

Fig. 1.

Quality threshold (QT) clustering of genes showing circadian-like oscillations in expression in lung. For each probe set, Pearson's correlation (R²) >0.75; centroid curve of the cluster (average curve) is shown in white. Shaded areas indicate dark periods; unshaded areas indicate light periods.

Fig. 2.

Expression patterns of core clock transcription factors in lung as a function of circadian time. ●, Mean data; error bars, SD; solid lines, curves fitted to a sine function.

Fig. 3.

Expression patterns of clock-related and clock-controlled transcription factors in lung as a function of circadian time. ●, Mean data; error bars, SD; solid lines, curves fitted to a sine function.

Fig. 4.

Expression patterns of selected extracellular matrix components and processing proteins in lung as a function of circadian time. ●, Mean data; error bars, SD; solid lines, curves fitted to a sine function.

Fig. 5.

Expression patterns of selected signaling ligand molecules and receptors in lung as a function of circadian time. ●, Mean data; error bars, SD; solid lines, curves fitted to a sine function.

Fig. 6.

Expression patterns of genes coding for enzymes involved in endogenous and exogenous compound metabolism in lung as a function of circadian time. ●, Mean data; error bars, SD; solid lines, curves fitted to a sine function.

Fig. 7.

Expression patterns of Adrb2 and Pde5a in lung as a function of circadian time. ●, Mean data; error bars, SD; solid lines, curves fitted to a sine function.

Fig. 8.

Cyclic pattern of expression of glucocorticoid receptor (GR) and glutamine synthase (GS) quantified by quantitative real-time PCR and Affymetrix gene chips. Solid lines, curves fitted to a sine function.

Fig. 9.

Summary of select physiological functions (A) and targets of drug action (B) in relation to circadian time. PH, pulmonary hypertension; NSCLC, non-small cell lung carcinoma; COPD, chronic obstructive pulmonary disorder; ALI, acute lung injury.