Characterization of circadian rhythms in peripheral tissues using experimental and computational modeling approaches
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Circadian rhythms have been implicated in the regulation of various biological processes ranging from molecular functions to behavior. In mammalian systems, the regulation of the central clock present in the suprachiasmatic nucleus is well characterized. However, the regulation of clocks present in peripheral tissues as well as the genes regulated by those clocks is still unclear. This thesis aims at characterizing both circadian rhythms in gene expression in peripheral tissues and relevant physiological measurements. The objective is to gain insight into tissue specific differences in the peripheral clocks and their effects on the physiology and pathophysiology of these tissues. In addition, quantitative mathematical modeling techniques were used to describe the effects of circadian rhythms on gene expression and the effect of perturbing the circadian rhythms with glucocorticoid treatment. An animal experiment was designed and conducted to study circadian rhythms. The experiment consisted of a rich time series involving 54 animals sacrificed at 18 distinct time points on three successive days across the 24 h light-dark cycle. Transcriptomic profiling of mRNA expression in white adipose tissue and lung were carried out using Affymetrix gene array chips. In addition, a wide array of relevant physiological measurements which both complemented and validated the gene expression data were performed. The results demonstrated that 127 genes (190 probe sets) and 646 genes (1006 probe sets) showed circadian oscillations in expression in white adipose tissue and lung respectively. The genes in both tissues were further parsed into distinct temporal clusters. More than 70% of the genes showing circadian oscillations in expression in white adipose tissue peaked during the dark/active period in agreement with other peripheral tissues studied to date. Functional analysis of these circadian regulated genes indicated that they play important roles in regulating adipogenesis, lipid metabolism and immune processes in adipose tissue. In contrast, more than two-thirds of the genes showing circadian oscillations in expression in lung peaked during the light/inactive period and were found to be mainly involved in homeostasis, repair and remodeling of the organ. In addition, genes that are biomarkers or therapeutic targets or are involved in drug metabolism also showed circadian oscillations in expression suggesting an important role for circadian rhythms in regulating the physiology and pathophysiology of the organ and in the emerging science of chronopharmacology. In addition to studying circadian rhythms in normal animals, additional animal experiments were designed to study the perturbation in circadian rhythms induced by treating the animals with a synthetic glucocorticoid. A rich time series was generated by sacrificing subgroups of animals at different time points from 0.25 to 96 h after drug treatment. Perturbations in circadian expression of important adipokines in white adipose tissue along with relevant physiological factors including plasma markers and receptor expression were examined. A mechanistic pharmacokinetic-pharmacodynamic model was developed to quantitatively describe, integrate and provide additional insight into the pharmacological effects of glucocorticoids on the circadian expression of adipokines and the related physiological factors that control these processes. In summary, this dissertation provides insights into tissue specific circadian regulation of the molecular clock, the transcriptomics and its physiological relevance in peripheral tissues. Furthermore, the effect of perturbing the circadian oscillations on adipokines expression by glucocorticoid treatment was quantitatively characterized by employing mathematical modeling strategies.