Transcriptional landscapes of emerging autoimmunity: Transient aberrations in the targeted tissue's extracellular milieu precede immune responses in Sjögren's syndrome

Arthritis Research and Therapy

Volumn 15, Issue 5, 2013, Pages

  Delaleu, Nicolas ^a   Nguyen, Cuong Q ^b   Tekle, Kidane M ^c   Jonsson, Roland ^a,d   Peck, Ammon B ^b  

^a UNIVERSITY OF BERGEN   (Norway)

^b University of Florida   (United States)

^c Uni Research AS   (Norway)

^d HAUKELAND UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID; ACETYLCHOLINE; COLLAGEN TYPE 1; COLLAGEN TYPE 3; CYSTEINE LOOP LIGAND GATED ION CHANNEL RECEPTOR; DOUBLE STRANDED RNA; FIBRILLIN 1; FIBRILLIN 2; GLYCINE; INSULIN RECEPTOR; INTERFERON INDUCED HELICASE C DOMAIN CONTAINING PROTEIN 1; INTERFERON REGULATORY FACTOR 3; LAMININ; MATRIX METALLOPROTEINASE; NEUROTRANSMITTER RECEPTOR; PATTERN RECOGNITION RECEPTOR; PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN KINASE B; SOMATOMEDIN C; STAT1 PROTEIN; TOLL LIKE RECEPTOR 3; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG; UVOMORULIN; VERSICAN;

ADAPTIVE IMMUNITY; ALGORITHM; ANIMAL EXPERIMENT; ANIMAL TISSUE; ANTIGEN PRESENTING CELL; ARTICLE; AUTOIMMUNITY; BIOINFORMATICS; CELL DIFFERENTIATION; CELL FATE; CELL HOMING; CELL JUNCTION; CELL MOTILITY; CELL PROLIFERATION; CHRONOLOGY; CONSENSUS; DATA ANALYSIS; DOWN REGULATION; ENRICHMENT CULTURE; EXTRACELLULAR MATRIX; FOCAL ADHESION; GENE DELETION; GENE EXPRESSION PROFILING; INNATE IMMUNITY; INTRACELLULAR SIGNALING; MALE; MOUSE; NATURAL KILLER CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA VIRUS; SALIVARY GLAND; SJOEGREN SYNDROME; UPREGULATION; ANIMAL; C57BL MOUSE; CLUSTER ANALYSIS; DISEASE MODEL; DNA MICROARRAY; FEMALE; GENE REGULATORY NETWORK; GENETIC PREDISPOSITION; GENETICS; HUMAN; IMMUNOLOGY; METABOLISM; NONOBESE DIABETIC MOUSE; TIME;

ALGORITHMS; ANIMALS; AUTOIMMUNITY; CLUSTER ANALYSIS; DISEASE MODELS, ANIMAL; EXTRACELLULAR MATRIX; FEMALE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MALE; MICE; MICE, INBRED C57BL; MICE, INBRED NOD; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SALIVARY GLANDS; SJOGREN'S SYNDROME; TIME FACTORS;

EID: 84886737842     PISSN: 14786354     EISSN: 14786362     Source Type: Journal    
DOI: 10.1186/ar4362     Document Type: Article

References (48)

1. Ziegler AG, Nepom GT. Prediction and pathogenesis in type 1 diabetes. Immunity 2010, 32:468-478. 10.1016/j.immuni.2010.03.018, 2861716, 20412757.
2. Arbuckle MR, McClain MT, Rubertone MV, Scofield RH, Dennis GJ, James JA, Harley JB. Development of autoantibodies before the clinical onset of systemic lupus erythematosus. N Engl J Med 2003, 349:1526-1533. 10.1056/NEJMoa021933, 14561795.
3. Rai E, Wakeland EK. Genetic predisposition to autoimmunity-What have we learned?. Semin Immunol 2011, 23:67-83. 10.1016/j.smim.2011.01.015, 21288738.
4. Barbalat R, Ewald SE, Mouchess ML, Barton GM. Nucleic acid recognition by the innate immune system. Annu Rev Immunol 2011, 29:185-214. 10.1146/annurev-immunol-031210-101340, 21219183.
5. Swamy M, Jamora C, Havran W, Hayday A. Epithelial decision makers: in search of the 'epimmunome'. Nat Immunol 2010, 11:656-665. 10.1038/ni.1905, 2950874, 20644571.
6. Kollias G, Papadaki P, Apparailly F, Vervoordeldonk MJ, Holmdahl R, Baumans V, Desaintes C, Di Santo J, Distler J, Garside P, Hegen M, Huizinga TWJ, Jüngel A, Klareskog L, McInnes I, Ragoussis I, Schett G, t' Hart B, Tak PP, Toes R, van den Berg W, Wurst W, Gay S. Animal models for arthritis: innovative tools for prevention and treatment. Ann Rheum Dis 2011, 70:1357-1362. 10.1136/ard.2010.148551, 21628308.
7. Delaleu N, Nguyen CQ, Peck AB, Jonsson R. Sjögren's syndrome: studying the disease in mice. Arthritis Res Ther 2011, 13:217. 10.1186/ar3313, 3218871, 21672284.
8. Cha S, Nagashima H, Brown VB, Peck AB, Humphreys-Beher MG. Two NOD Idd-associated intervals contribute synergistically to the development of autoimmune exocrinopathy (Sjögren's syndrome) on a healthy murine background. Arthritis Rheum 2002, 46:1390-1398. 10.1002/art.10258, 12115247.
9. Delaleu N, Manoussakis MN, Moutsopoulos HM, Jonsson R. Etiology and pathogenesis of Sjögren's syndrome with special emphasis on the salivary glands. Sjögren's Syndrome 2011, 243-268. New York: Springer, Fox RI, Fox C, 1.
10. Tobón GJ, Pers JO, Youinou P, Saraux A. B cell-targeted therapies in Sjögren's syndrome. Autoimmun Rev 2010, 9:224-228. 10.1016/j.autrev.2009.08.001, 19671451.
11. Båve U, Nordmark G, Lövgren T, Rönnelid J, Cajander S, Eloranta ML, Alm GV, Rönnblom L. Activation of the type I interferon system in primary Sjögren's syndrome: a possible etiopathogenic mechanism. Arthritis Rheum 2005, 52:1185-1195. 10.1002/art.20998, 15818675.
12. Low HZ, Witte T. Aspects of innate immunity in Sjögren's syndrome. Arthritis Res Ther 2011, 13:218. 10.1186/ar3318, 3218872, 21635716.
13. Ewert P, Aguilera S, Alliende C, Kwon YJ, Albornoz A, Molina C, Urzúa U, Quest AF, Olea N, Pérez P, Castro I, Barrera MJ, Romo R, Hermoso M, Leyton C, González MJ. Disruption of tight junction structure in salivary glands from Sjögren's syndrome patients is linked to proinflammatory cytokine exposure. Arthritis Rheum 2010, 62:1280-1289. 10.1002/art.27362, 20131287.
14. Sequeira SJ, Larsen M, DeVine T. Extracellular matrix and growth factors in salivary gland development. Front Oral Biol 2010, 14:48-77.
15. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
16. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinforma 2011, 12:436.
17. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432. 10.1093/bioinformatics/btq675, 3031041, 21149340.
18. Nguyen CQ, Sharma A, She JX, McIndoe RA, Peck AB. Differential gene expressions in the lacrimal gland during development and onset of keratoconjunctivitis sicca in Sjögren's syndrome (SJS)-like disease of the C57BL/6.NOD-Aec1Aec2 mouse. Exp Eye Res 2009, 88:398-409. 10.1016/j.exer.2008.10.006, 2699904, 19103199.
19. Nguyen CQ, Sharma A, Lee BH, She JX, McIndoe RA, Peck AB. Differential gene expression in the salivary gland during development and onset of xerostomia in Sjögren's syndrome-like disease of the C57BL/6.NOD-Aec1Aec2 mouse. Arthritis Res Ther 2009, 11:R56. 10.1186/ar2676, 2688207, 19379516.
20. Horvath S, Nazmul-Hossain ANM, Pollard RPE, Kroese FGM, Vissink A, Kallenberg CGM, Spijkervet FKL, Bootsma H, Michie SA, Gorr SU, Peck AB, Cai C, Zhou H, Wong DTW. Systems analysis of primary Sjögren's syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model. Arthritis Res Ther 2012, 14:R238. 10.1186/ar4081, 3674589, 23116360.
21. http://www.sanger.ac.uk/resources/databases/pfam.html.
22. Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 2010, 5:e13984. 10.1371/journal.pone.0013984, 2981572, 21085593.
23. Glez-Peña D, Gómez-López G, Pisano DG, Fdez-Riverola F. WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis. Nucleic Acids Res 2009, 37:W329-W334. 10.1093/nar/gkp263, 2703947, 19406925.
24. Oesper L, Merico D, Isserlin R, Bader GD. WordCloud: a Cytoscape plugin to create a visual semantic summary of networks. Source Code Biol Med 2011, 6:7. 10.1186/1751-0473-6-7, 3083346, 21473782.
25. Vallabhapurapu S, Karin M. Regulation and function of NF-κB transcription factors in the immune system. Annu Rev Immunol 2009, 27:693-733. 10.1146/annurev.immunol.021908.132641, 19302050.
26. Gentry JJ, Barker PA, Carter BD. The p75 neurotrophin receptor: multiple interactors and numerous functions. Prog Brain Res 2004, 146:25-39.
27. Johnstone RW, Frew AJ, Smyth MJ. The TRAIL apoptotic pathway in cancer onset, progression and therapy. Nat Rev Cancer 2008, 8:782-798. 10.1038/nrc2465, 18813321.
28. Conway K, Price P, Harding KG, Jiang WG. The molecular and clinical impact of hepatocyte growth factor, its receptor, activators, and inhibitors in wound healing. Wound Repair Regen 2006, 14:2-10. 10.1111/j.1524-475X.2005.00081.x, 16476066.
29. Caron E, Ghosh S, Matsuoka Y, Ashton-Beaucage D, Therrien M, Lemieux S, Perreault C, Roux PP, Kitano H. A comprehensive map of the mTOR signaling network. Mol Syst Biol 2010, 6:453. 3018167, 21179025.
30. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell 2008, New York: Garland Science, 5.
31. Geiger B, Spatz JP, Bershadsky AD. Environmental sensing through focal adhesions. Nat Rev Mol Cell Biol 2009, 10:21-33. 10.1038/nrm2593, 19197329.
32. Brooks PC, Klemke RL, Schon S, Lewis JM, Schwartz MA, Cheresh DA. Insulin-like growth factor receptor cooperates with integrin αv β5 to promote tumor cell dissemination in vivo. J Clin Invest 1997, 99:1390-1398. 10.1172/JCI119298, 507955, 9077549.
33. Ivaska J, Heino J. Cooperation between integrins and growth factor receptors in signaling and endocytosis. Annu Rev Cell Dev Biol 2011, 27:291-320. 10.1146/annurev-cellbio-092910-154017, 21663443.
34. Shoulders MD, Raines RT. Collagen structure and stability. Annu Rev Biochem 2009, 78:929-958. 10.1146/annurev.biochem.77.032207.120833, 2846778, 19344236.
35. Georgiadis D, Yiotakis A. Specific targeting of metzincin family members with small-molecule inhibitors: progress toward a multifarious challenge. Bioorg Med Chem 2008, 16:8781-8794. 10.1016/j.bmc.2008.08.058, 18790648.
36. Neuroscience 2012, Sunderland, MA: Sinauer Associates, Purves D, Augustine GJ, Fitzpatrick D, Hall WC, LaMantia AS, White LE, 5.
37. Ren K, Dubner R. Interactions between the immune and nervous systems in pain. Nat Med 2010, 16:1267-1276. 10.1038/nm.2234, 3077564, 20948535.
38. Murphy K. Janeway's Immunobiology 2012, New York: Garland Science, 8.
39. Vivier E, Tomasello E, Baratin M, Walzer T, Ugolini S. Functions of natural killer cells. Nat Immunol 2008, 9:503-510. 10.1038/ni1582, 18425107.
40. Mackay F, Schneider P. Cracking the BAFF code. Nat Rev Immunol 2009, 9:491-502. 10.1038/nri2572, 19521398.
41. van der Greef J, Martin S, Juhasz P, Adourian A, Plasterer T, Verheij ER, McBurney RN. The art and practice of systems biology in medicine: mapping patterns of relationships. J Proteome Res 2007, 6:1540-1559. 10.1021/pr0606530, 17373844.
42. Zhernakova A, van Diemen CC, Wijmenga C. Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat Rev Genet 2009, 10:43-55. 10.1038/nrg2489, 19092835.
43. Campbell SJ, Gaulton A, Marshall J, Bichko D, Martin S, Brouwer C, Harland L. Visualizing the drug target landscape. Drug Discov Today 2010, 15:3-15. 10.1016/j.drudis.2009.09.011, 19840866.
44. Bach JF, Chatenoud L. A historical view from thirty eventful years of immunotherapy in autoimmune diabetes. Semin Immunol 2011, 23:174-181. 10.1016/j.smim.2011.07.009, 21846589.
45. Samy ET, Wheeler KM, Roper RJ, Teuscher C, Tung KS. Cutting edge: autoimmune disease in day 3 thymectomized mice is actively controlled by endogenous disease-specific regulatory T cells. J Immunol 2008, 180:4366-4370.
46. Ideker T, Dutkowski J, Hood L. Boosting signal-to-noise in complex biology: prior knowledge is power. Cell 2011, 144:860-863. 10.1016/j.cell.2011.03.007, 3102020, 21414478.
47. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nat Methods 2010, 7:S56-S68. 10.1038/nmeth.1436, 20195258.
48. Chen C, McGarvey PB, Huang H, Wu CH. Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput " omics" data. Adv Bioinformatics 2010, 2010:423589.