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

Journal of Applied Physiology

Volumn 110, Issue 6, 2011, Pages 1732-1747

  Sukumaran, Siddharth ^a   Jusko, William J ^a   DuBois, Debra C ^a   Almon, Richard R ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Circadian rhythms; Drug metabolism; Growth factors; Lung repair; Microarrays

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR CLOCK;

ANIMAL; ARTICLE; CIRCADIAN RHYTHM; CLUSTER ANALYSIS; DATA MINING; DNA MICROARRAY; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HOMEOSTASIS; LUNG; LUNG DISEASE; MALE; METABOLISM; METHODOLOGY; PHOTOPERIODICITY; POLYMERASE CHAIN REACTION; RAT; REGENERATION; TIME; TRANSPORT AT THE CELLULAR LEVEL; WISTAR RAT;

ANIMALS; BIOLOGICAL TRANSPORT; CIRCADIAN RHYTHM; CLOCK PROTEINS; CLUSTER ANALYSIS; DATA MINING; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HOMEOSTASIS; LUNG; LUNG DISEASES; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOTOPERIOD; POLYMERASE CHAIN REACTION; RATS; RATS, WISTAR; REGENERATION; RNA, MESSENGER; TIME FACTORS;

EID: 79959351684     PISSN: 87507587     EISSN: 15221601     Source Type: Journal    
DOI: 10.1152/japplphysiol.00079.2011     Document Type: Article

References (69)

1. Adamczyk W, Tafil-Klawe M, Siekierka M, Zlomanczuk P, Weber P, Klawe JJ. Daily pattern of breathing in healthy young men. J Physiol Pharmacol 59 Suppl 6:115-122, 2008.
2. Almon RR, Yang E, Lai W, Androulakis IP, DuBois DC, Jusko WJ. Circadian variations in rat liver gene expression: relationships to drug actions. J Pharmacol Exp Ther 326:700-716, 2008.
3. Almon RR, Yang E, Lai W, Androulakis IP, Ghimbovschi S, Hoffman EP, Jusko WJ, DuBois DC. Relationships between circadian rhythms and modulation of gene expression by glucocorticoids in skeletal muscle. Am J Physiol Regul Integr Comp Physiol 295:R1031-R1047, 2008.
4. Bailey MJ, Coon SL, Carter DA, Humphries A, Kim JS, Shi Q, Gaildrat P, Morin F, Ganguly S, Hogenesch JB, Weller JL, Rath MF, Moller M, Baler R, Sugden D, Rangel ZG, Munson PJ, Klein DC. Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling. J Biol Chem 284:7606-7622, 2009.
5. Bartness TJ, Song CK, Demas GE. SCN efferents to peripheral tissues: implications for biological rhythms. J Biol Rhythms 16:196-204, 2001. (Pubitemid 32516194)
6. Boer F. Drug handling by the lungs. Br J Anaesth 91:50-60, 2003. (Pubitemid 36857315)
7. Bowden DH. Cell turnover in the lung. Am Rev RespirDis 128:S46-S48, 1983. (Pubitemid 13039291)
8. Boyton RJ, Openshaw PJ. Pulmonary defences to acute respiratory infection. Br Med Bull 61:1-12, 2002. (Pubitemid 34477552)
9. Burger JA, Stewart DJ. CXCR4 chemokine receptor antagonists: perspectives in SCLC. Expert Opin Investig Drugs 18:481-490, 2009.
10. Chinoy MR, Graybill MM, Miller SA, Lang CM, Kauffman GL. Angiopoietin-1 and VEGF in vascular development and angiogenesis in hypoplastic lungs. Am J Physiol Lung Cell Mol Physiol 283:L60-L66, 2002. (Pubitemid 34764542)
11. Chrastina A, Valadon P, Massey KA, Schnitzer JE. Lung vascular targeting using antibody to aminopeptidase P: CT-SPECT imaging, biodistribution and pharmacokinetic analysis. J Vasc Res 47:531-543, 2010.
12. Desai TJ, Cardoso WV. Growth factors in lung development and disease: friends or foe? Respir Res 3:2, 2002.
13. Duffy JF, Czeisler CA. Effect of light on human circadian physiology. Sleep Med Clin 4:165-177, 2009.
14. Dunlap JC. Molecular bases for circadian clocks. Cell 96:271-290, 1999. (Pubitemid 29059356)
15. Dunsmore SE, Rannels DE. Extracellular matrix biology in the lung. Am J Physiol Lung Cell Mol Physiol 270:L3-L27, 1996.
16. Fan Chung K. Phosphodiesterase inhibitors in airways disease. Eur J Pharmacol 533:110-117, 2006. (Pubitemid 43348344)
17. Foth H. Role of the lung in accumulation and metabolism of xenobiotic compounds-implications for chemically induced toxicity. Crit Rev Toxicol 25:165-205, 1995.
18. Gachon F. Physiological function of PARbZip circadian clock-controlled transcription factors. Ann Med 39:562-571, 2007. (Pubitemid 350175305)
19. Gibbons GH, Dzau VJ. The emerging concept of vascular remodeling. N Engl J Med 330:1431-1438, 1994. (Pubitemid 24139238)
20. Gordon MS, Sweeney CS, Mendelson DS, Eckhardt SG, Anderson A, Beaupre DM, Branstetter D, Burgess TL, Coxon A, Deng H, Kaplan-Lefko P, Leitch IM, Oliner KS, Yan L, Zhu M, Gore L. Safety, pharmacokinetics, and pharmacodynamics of AMG 102, a fully human hepatocyte growth factor-neutralizing monoclonal antibody, in a first-inhuman study of patients with advanced solid tumors. Clin Cancer Res 16:699-710, 2010.
21. Hassoun PM, Mouthon L, Barbera JA, Eddahibi S, Flores SC, Grimminger F, Jones PL, Maitland ML, Michelakis ED, Morrell NW, Newman JH, Rabinovitch M, Schermuly R, Stenmark KR, Voelkel NF, Yuan JX, Humbert M. Inflammation, growth factors, and pulmonary vascular remodeling. J Am Coll Cardiol 54:S10-S19, 2009.
22. Hazra A, Pyszczynski N, DuBois DC, Almon RR, Jusko WJ. Modeling receptor/gene-mediated effects of corticosteroids on hepatic tyrosine aminotransferase dynamics in rats: dual regulation by endogenous and exogenous corticosteroids. J Pharmacokinet Pharmacodyn 34:643-667, 2007. (Pubitemid 47477037)
23. Heinemann HO, Ryan JW, Ryan US. Is the lung a para-endocrine organ? Am J Med 63:595-603, 1977. (Pubitemid 8214933)
24. Herd KA, Nelson M, Mahalingam S, Tindle RW. Pulmonary infection of mice with human metapneumovirus induces local cytotoxic T-cell and immunoregulatory cytokine responses similar to those seen with human respiratory syncytial virus. J Gen Virol 91:1302-1310, 2010.
25. Jetten AM. Retinoid-related orphan receptors (RORs): critical roles in development, immunity, circadian rhythm, and cellular metabolism. Nucl Recept Signal 7:e003, 2009.
26. Johnson M. The β-adrenoceptor. Am J Respir Crit Care Med 158:S146-S153, 1998.
27. Kalscheuer S, Zhang X, Zeng Y, Upadhyaya P. Differential expression of microRNAs in early-stage neoplastic transformation in the lungs of F344 rats chronically treated with the tobacco carcinogen 4-(methylnitrosamino)-1-β- pyridyl)-1-butanone. Carcinogenesis 29:2394-2399, 2008.
28. Keith IM. The role of endogenous lung neuropeptides in regulation of the pulmonary circulation. Physiol Res 49:519-537, 2000.
29. Kim KJ, Malik AB. Protein transport across the lung epithelial barrier. Am J Physiol Lung Cell Mol Physiol 284:L247-L259, 2003. (Pubitemid 36164359)
30. Kim SR, Lee KS, Park SJ, Min KH, Lee KY, Choe YH, Hong SH, Koh GY, Lee YC. Angiopoietin-1 variant, COMP-Ang1 attenuates hydrogen peroxide-induced acute lung injury. Exp Mol Med 40:320-331, 2008.
31. Lemmer B. The clinical relevance of chronopharmacology in therapeutics. Pharmacol Res 33:107-115, 1996. (Pubitemid 26275874)
32. Lindsay CD. Novel therapeutic strategies for acute lung injury induced by lung damaging agents: the potential role of growth factors as treatment options. Hum Exp Toxicol. In press.
33. + mononuclear phagocytes and T lymphocytes in the lungs during cigarette smoke-induced emphysema. Am J Pathol 173:949-961, 2008.
34. McDonald DM. Angiogenesis and remodeling of airway vasculature in chronic inflammation. Am J Respir Crit Care Med 164:S39-S45, 2001.
35. McFadden ER Jr. Inhaled glucocorticoids and acute asthma: therapeutic breakthrough or nonspecific effect? Am J Respir Crit Care Med 157:677-678, 1998.
36. McGowan SE. Extracellular matrix and the regulation of lung development and repair. FASEB J 6:2895-2904, 1992.
37. Mirsky HP, Liu AC, Welsh DK, Kay SA, Doyle FJ 3rd. A model of the cell-autonomous mammalian circadian clock. Proc Natl Acad Sci USA 106:11107-11112, 2009.
38. Nakamura T, Nakanishi T, Haruta T, Shirasaka Y, Keogh JP, Tamai I. Transport of ipratropium, an anti-chronic obstructive pulmonary disease drug, is mediated by organic cation/carnitine transporters in human bronchial epithelial cells: implications for carrier-mediated pulmonary absorption. Mol Pharm 7:187-195, 2010.
39. Negrete-Garcia MC, Velazquez JR, Popoca-Coyotl A, Montes-Vizuet AR, Juarez-Carvajal E, Teran LM. Chemokine (C-X-C motif) ligand 12/stromal cell-derived factor-1 is associated with leukocyte recruitment in asthma. Chest 138:100-106, 2010.
40. Nomura N, Asano M, Saito T, Sasaki S, Suzuki H, Manabe T, Mishima A. Cardiotrophin-1 is a prophylactic against the development of chronic hypoxic pulmonary hypertension in rats. Ann Thorac Surg 76:237-243, 2003. (Pubitemid 36819749)
41. Okunishi K, Sasaki O, Okasora T, Nakagome K, Imamura M, Harada H, Matsumoto T, Tanaka R, Yamamoto K, Tabata Y, Dohi M. Intratracheal delivery of hepatocyte growth factor directly attenuates allergic airway inflammation in mice. Int Arch Allergy Immunol 149 Suppl 1:14-20, 2009.
42. Prakash J, de Jong E, Post E, Gouw AS, Beljaars L, Poelstra K. A novel approach to deliver anticancer drugs to key cell types in tumors using a PDGF receptor-binding cyclic peptide containing carrier. J Control Release 145:91-101, 2010.
43. Preitner N, Damiola F, Lopez-Molina L, Zakany J, Duboule D, Albrecht U, Schibler U. The orphan nuclear receptor REV-ERBα controls circadian transcription within the positive limb of the mammalian circadian oscillator. Cell 110:251-260, 2002. (Pubitemid 34876552)
44. Reppert SM, Weaver DR. Coordination of circadian timing in mammals. Nature 418:935-941, 2002. (Pubitemid 34976023)
45. Reynolds HY. Lung host defenses: a status report. Chest 75:239-242, 1979.
46. Roman J. Extracellular matrix and lung inflammation. Immunol Res 15:163-178, 1996. (Pubitemid 26232482)
47. Roman J, Limper AH, McDonald JA. Lung extracellular matrix: physiology and pathophysiology. Hosp Pract (Off Ed) 25:125-128, 131-125, 139-140, 1990.
48. Scotton CJ, Chambers RC. Molecular targets in pulmonary fibrosis: the myofibroblast in focus. Chest 132:1311-1321, 2007. (Pubitemid 47621009)
49. Siepka SM, Yoo SH, Park J, Song W, Kumar V, Hu Y, Lee C, Takahashi JS. Circadian mutant Overtime reveals F-box protein FBXL3 regulation of cryptochrome and period gene expression. Cell 129:1011-1023, 2007. (Pubitemid 46802705)
50. Sixt SU, Peters J. Extracellular alveolar proteasome: possible role in lung injury and repair. Proc Am Thorac Soc 7:91-96, 2010.
51. Smolensky MH, Reinberg AE, Martin RJ, Haus E. Clinical chronobiology and chronotherapeutics with applications to asthma. Chronobiol Int 16:539-563, 1999. (Pubitemid 29463828)
52. Somers GI, Lindsay N, Lowdon BM, Jones AE, Freathy C, Ho S, Woodrooffe AJ, Bayliss MK, Manchee GR. A comparison of the expression and metabolizing activities of phase I and II enzymes in freshly isolated human lung parenchymal cells and cryopreserved human hepatocytes. Drug Metab Dispos 35:1797-1805, 2007. (Pubitemid 47481571)
53. Sorokin L. The impact of the extracellular matrix on inflammation. Nat Rev Immunol 10:712-723, 2010.
54. Spengler CM, Czeisler CA, Shea SA. An endogenous circadian rhythm of respiratory control in humans. J Physiol 526:683-694, 2000. (Pubitemid 30649625)
55. Spengler CM, Shea SA. Endogenous circadian rhythm of pulmonary function in healthy humans. Am J Respir Crit Care Med 162:1038-1046, 2000.
56. Spurzem JR. Function at the junction: dynamic interactions between lung cells and extracellular matrix. Thorax 51:956-958, 1996. (Pubitemid 26289040)
57. Strieter RM, Keeley EC, Hughes MA, Burdick MD, Mehrad B. The role of circulating mesenchymal progenitor cells (fibrocytes) in the pathogenesis of pulmonary fibrosis. J Leukoc Biol 86:1111-1118, 2009.
58. Sukumaran S, Almon RR, DuBois DC, Jusko WJ. Circadian rhythms in gene expression: relationship to physiology, disease, drug disposition and drug action. Adv Drug Deliv Rev 62:904-917, 2010.
59. Sukumaran S, Xue B, Jusko WJ, DuBois DC, Almon RR. Circadian variations in gene expression in rat abdominal adipose tissue and relationship to physiology. Physiol Genomics 42 A: 141-152, 2010.
60. Suzuki T, Chow CW, Downey GP. Role of innate immune cells and their products in lung immunopathology. Int J Biochem Cell Biol 40:1348-1361, 2008.
61. Ueda HR, Hayashi S, Chen W, Sano M, Machida M, Shigeyoshi Y, Iino M, Hashimoto S. System-level identification of transcriptional circuits underlying mammalian circadian clocks. Nat Genet 37:187-192, 2005.
62. Visoni S, Meireles N, Monteiro L, Rossini A, Pinto LF. Different modes of inhibition of mouse Cyp2a5 and rat CYP2A3 by the food-derived 8-methoxypsoralen. Food Chem Toxicol 46:1190-1195, 2008.
63. Warburton D, Bellusci S, Del Moral PM, Kaartinen V, Lee M, Tefft D, Shi W. Growth factor signaling in lung morphogenetic centers: automaticity, stereotypy and symmetry. Respir Res 4:5, 2003.
64. Ware LB, Matthay MA. Keratinocyte and hepatocyte growth factors in the lung: roles in lung development, inflammation, and repair. Am J Physiol Lung Cell Mol Physiol 282:L924-L940, 2002. (Pubitemid 34654608)
65. Weng DE, Usman N. Angiozyme: a novel angiogenesis inhibitor. Curr Oncol Rep 3:141-146, 2001.
66. Yao Z, DuBois DC, Almon RR, Jusko WJ. Modeling circadian rhythms of glucocorticoid receptor and glutamine synthetase expression in rat skeletal muscle. Pharm Res 23:670-679, 2006.
67. Yasuda S, Idell S, Fu J, Carter G, Snow R, Liu MC. Cigarette smoke toxicants as substrates and inhibitors for human cytosolic SULTs. Toxicol Appl Pharmacol 221:13-20, 2007. (Pubitemid 46702277)
68. Zhang EE, Kay SA. Clocks not winding down: unravelling circadian networks. Nat Rev Mol Cell Biol 11:764-776.
69. Zhou D, Zheng X, Wang L, Stelmack G, Halayko AJ, Dorscheid D, Bai TR. Expression and effects of cardiotrophin-1 (CT-1) in human airway smooth muscle cells. Br J Pharmacol 140:1237-1244, 2003. (Pubitemid 38117428)