Systems biologic analysis of T regulatory cells genetic pathways in murine primary biliary cirrhosis

Journal of Autoimmunity

Volumn 59, Issue , 2015, Pages 26-37

  Wang, Yin Hu ^a   Yang, Wei ^a   Yang, Jing Bo ^a   Jia, Yan Jie ^a   Tang, Wei ^a   Gershwin, M Eric ^b   Ridgway, William M ^c   Lian, Zhe Xiong ^a,d  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CINCINNATI   (United States)

^d UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Cholangitis; Primary biliary cirrhosis; Regulatory T cells; Transcription profile and pathway analysis

Indexed keywords

AROMATIC HYDROCARBON RECEPTOR; CD24 ANTIGEN; CHEMOKINE RECEPTOR CCR5; CHEMOKINE RECEPTOR CCR6; CHEMOKINE RECEPTOR CCR7; CHEMOKINE RECEPTOR CXCR3; CHEMOKINE RECEPTOR CXCR4; CYTOTOXIC T LYMPHOCYTE ANTIGEN 4; GAMMA INTERFERON; GLUCOCORTICOID INDUCED TUMOR NECROSIS FACTOR RECEPTOR; GRANZYME B; INDUCIBLE T CELL COSTIMULATOR; INTERLEUKIN 10; INTERLEUKIN 2 RECEPTOR ALPHA; KRUPPEL LIKE FACTOR 2; RANTES; SOMATOMEDIN BINDING PROTEIN 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FOXP1; TRANSCRIPTION FACTOR FOXP3; TRANSCRIPTION FACTOR T BET; TRANSFORMING GROWTH FACTOR BETA RECEPTOR 2; UNCLASSIFIED DRUG; VASCULAR CELL ADHESION MOLECULE 1; AUTACOID; FORKHEAD TRANSCRIPTION FACTOR; FOXP3 PROTEIN, MOUSE; GRANZYME; PROTEIN SERINE THREONINE KINASE; TRANSFORMING GROWTH FACTOR BETA RECEPTOR; TRANSFORMING GROWTH FACTOR-BETA TYPE II RECEPTOR;

ANALYSIS; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; APOPTOSIS; ARTICLE; AUTOIMMUNITY; CELL ADHESION; CELL DIFFERENTIATION; CONTROLLED STUDY; DOWN REGULATION; GENE INTERACTION; GENETIC DISORDER; LYMPHOCYTE COUNT; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; PRIMARY BILIARY CIRRHOSIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY T LYMPHOCYTE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; UPREGULATION; ANIMAL; BILIARY CIRRHOSIS; DISEASE MODEL; FEMALE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; IMMUNOLOGY; METABOLISM; MUTANT MOUSE STRAIN; MUTATION;

ANIMALS; CHEMOKINE CCL5; DISEASE MODELS, ANIMAL; FEMALE; FORKHEAD TRANSCRIPTION FACTORS; GENE EXPRESSION REGULATION; GRANZYMES; HUMANS; INFLAMMATION MEDIATORS; INTERFERON-GAMMA; LIVER CIRRHOSIS, BILIARY; MICE; MICE, MUTANT STRAINS; MICROARRAY ANALYSIS; MUTATION; PROTEIN-SERINE-THREONINE KINASES; RECEPTORS, TRANSFORMING GROWTH FACTOR BETA; SIGNAL TRANSDUCTION; T-LYMPHOCYTES, REGULATORY; TRANSCRIPTION FACTORS;

EID: 84928587439     PISSN: 08968411     EISSN: 10959157     Source Type: Journal    
DOI: 10.1016/j.jaut.2015.01.011     Document Type: Article

References (45)

1. Gershwin M.E., Mackay I.R., Sturgess A., Coppel R.L. Identification and specificity of a cDNA encoding the 70 kd mitochondrial antigen recognized in primary biliary cirrhosis. JImmunol 1987, 138:3525-3531.
2. Yang C.Y., Ma X., Tsuneyama K., Huang S., Takahashi T., Chalasani N.P., et al. IL-12/Th1 and IL-23/Th17 biliary microenvironment in primary biliary cirrhosis: implications for therapy. Hepatology 2014, 59:1944-1953.
3. Kawata K., Yang G.X., Ando Y., Tanaka H., Zhang W., Kobayashi Y., et al. Clonality, activated antigen-specific CD8(+) T cells, and development of autoimmune cholangitis in dnTGFbetaRII mice. Hepatology 2013, 58:1094-1104.
4. Rong G.H., Yang G.X., Ando Y., Zhang W., He X.S., Leung P.S., et al. Human intrahepatic biliary epithelial cells engulf blebs from their apoptotic peers. Clin Exp Immunol 2013, 172:95-103.
5. Chen R.C., Naiyanetr P., Shu S.A., Wang J., Yang G.X., Kenny T.P., et al. Antimitochondrial antibody heterogeneity and the xenobiotic etiology of primary biliary cirrhosis. Hepatology 2013, 57:1498-1508.
6. Dhirapong A., Yang G.X., Nadler S., Zhang W., Tsuneyama K., Leung P., et al. Therapeutic effect of cytotoxic T lymphocyte antigen 4/immunoglobulin on a murine model of primary biliary cirrhosis. Hepatology 2013, 57:708-715.
7. Kaplan M.M., Gershwin M.E. Primary biliary cirrhosis. N.Engl J Med 2005, 353:1261-1273.
8. Hirschfield G.M., Gershwin M.E. The immunobiology and pathophysiology of primary biliary cirrhosis. Annu Rev Pathol 2013, 8:303-330.
9. Oertelt S., Lian Z.X., Cheng C.M., Chuang Y.H., Padgett K.A., He X.S., et al. Anti-mitochondrial antibodies and primary biliary cirrhosis in TGF-beta receptor II dominant-negative mice. JImmunol 2006, 177:1655-1660.
10. Selmi C., Meda F., Kasangian A., Invernizzi P., Tian Z., Lian Z., et al. Experimental evidence on the immunopathogenesis of primary biliary cirrhosis. Cell Mol Immunol 2010, 7:1-10.
11. Sakaguchi S., Yamaguchi T., Nomura T., Ono M. Regulatory T cells and immune tolerance. Cell 2008, 133:775-787.
12. Lan R.Y., Cheng C., Lian Z.X., Tsuneyama K., Yang G.X., Moritoki Y., et al. Liver-targeted and peripheral blood alterations of regulatory T cells in primary biliary cirrhosis. Hepatology 2006, 43:729-737.
13. Aoki C.A., Roifman C.M., Lian Z.X., Bowlus C.L., Norman G.L., Shoenfeld Y., et al. IL-2 receptor alpha deficiency and features of primary biliary cirrhosis. JAutoimmun 2006, 27:50-53.
14. Tanaka H., Zhang W., Yang G.X., Ando Y., Tomiyama T., Tsuneyama K., et al. Successful immunotherapy of autoimmune cholangitis by adoptive transfer of forkhead boxprotein 3(+) regulatory T cells. Clin Exp Immunol 2014, 178:253-261.
15. Huang W., Kachapati K., Adams D., Wu Y., Leung P.S., Yang G.X., et al. Murine autoimmune cholangitis requires two hits: cytotoxic KLRG1(+) CD8 effector cells and defective T regulatory cells. JAutoimmun 2014, 50:123-134.
16. Fontenot J.D., Rasmussen J.P., Williams L.M., Dooley J.L., Farr A.G., Rudensky A.Y. Regulatory T cell lineage specification by the forkhead transcription factor foxp3. Immunity 2005, 22:329-341.
17. Yang W., Yao Y., Yang Y.Q., Lu F.T., Li L., Wang Y.H., et al. Differential modulation by IL-17A of cholangitis versus colitis in IL-2Ralpha deleted mice. PloS One 2014, 9:e105351.
18. Kitoh A., Ono M., Naoe Y., Ohkura N., Yamaguchi T., Yaguchi H., et al. Indispensable role of the Runx1-Cbfbeta transcription complex for invivo-suppressive function of FoxP3+ regulatory T cells. Immunity 2009, 31:609-620.
19. Yao Y., Yang W., Yang Y.Q., Ma H.D., Lu F.T., Li L., et al. Distinct from its canonical effects, deletion of IL-12p40 induces cholangitis and fibrosis in interleukin-2Ralpha(-/-) mice. JAutoimmun 2014, 51:99-108.
20. Gene Ontology C. The gene ontology (GO) project in 2006. Nucleic Acids Res 2006, 34:D322-D326.
21. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
22. Cline M.S., Smoot M., Cerami E., Kuchinsky A., Landys N., Workman C., et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2007, 2:2366-2382.
23. Su G., Morris J.H., Demchak B., Bader G.D. Biological network exploration with cytoscape 3. Curr Protoc Bioinforma 2014, 47. 8 13 1-8 24.
24. Chatr-Aryamontri A., Breitkreutz B.J., Heinicke S., Boucher L., Winter A., Stark C., et al. The BioGRID interaction database: 2013 update. Nucleic Acids Res 2013, 41:D816-D823.
25. Maere S., Heymans K., Kuiper M. BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449.
26. Boyle E.I., Weng S., Gollub J., Jin H., Botstein D., Cherry J.M., et al. GO::TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 2004, 20:3710-3715.
27. Benjamini Y., Drai D., Elmer G., Kafkafi N., Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001, 125:279-284.
28. Hosack D.A., Dennis G., Sherman B.T., Lane H.C., Lempicki R.A. Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70.
29. Nolan T., Hands R.E., Bustin S.A. Quantification of mRNA using real-time RT-PCR. Nat Protoc 2006, 1:1559-1582.
30. Hilscher C., Vahrson W., Dittmer D.P. Faster quantitative real-time PCR protocols may lose sensitivity and show increased variability. Nucleic Acids Res 2005, 33:e182.
31. Arvey A., van der Veeken J., Samstein R.M., Feng Y., Stamatoyannopoulos J.A., Rudensky A.Y. Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells. Nat Immunol 2014, 15:580-587.
32. Kang S.S., Bloom S.M., Norian L.A., Geske M.J., Flavell R.A., Stappenbeck T.S., et al. An antibiotic-responsive mouse model of fulminant ulcerative colitis. PLoS Med 2008, 5:e41.
33. Pan F., Yu H., Dang E.V., Barbi J., Pan X., Grosso J.F., et al. Eos mediates Foxp3-dependent gene silencing in CD4+ regulatory T cells. Science 2009, 325:1142-1146.
34. Sharma M.D., Huang L., Choi J.H., Lee E.J., Wilson J.M., Lemos H., et al. An inherently bifunctional subset of Foxp3+ T helper cells is controlled by the transcription factor eos. Immunity 2013, 38:998-1012.
35. Cao Z., Sun X., Icli B., Wara A.K., Feinberg M.W. Role of Kruppel-like factors in leukocyte development, function, and disease. Blood 2010, 116:4404-4414.
36. Hart G.T., Hogquist K.A., Jameson S.C. Kruppel-like factors in lymphocyte biology. JImmunol 2012, 188:521-526.
37. Pabbisetty S.K., Rabacal W., Maseda D., Cendron D., Collins P.L., Hoek K.L., et al. KLF2 is a rate-limiting transcription factor that can be targeted to enhance regulatory T-cell production. Proc Natl Acad Sci U S A 2014, 111:9579-9584.
38. Feng X., Wang H., Takata H., Day T.J., Willen J., Hu H. Transcription factor Foxp1 exerts essential cell-intrinsic regulation of the quiescence of naive T cells. Nat Immunol 2011, 12:544-550.
39. Wang H., Geng J., Wen X., Bi E., Kossenkov A.V., Wolf A.I., et al. The transcription factor Foxp1 is a critical negative regulator of the differentiation of follicular helper T cells. Nat Immunol 2014, 15:667-675.
40. Feng X., Ippolito G.C., Tian L., Wiehagen K., Oh S., Sambandam A., et al. Foxp1 is an essential transcriptional regulator for the generation of quiescent naive T cells during thymocyte development. Blood 2010, 115:510-518.
41. Chang L.Y., Lin Y.C., Kang C.W., Hsu C.Y., Chu Y.Y., Huang C.T., et al. The indispensable role of CCR5 for invivo suppressor function of tumor-derived CD103+ effector/memory regulatory T cells. JImmunol 2012, 189:567-574.
42. Reynolds L.A., Maizels R.M. Cutting edge: in the absence of TGF-beta signaling in T cells, fewer CD103+ regulatory T cells develop, but exuberant IFN-gamma production renders mice more susceptible to helminth infection. JImmunol 2012, 189:1113-1117.
43. Weiss J.M., Bilate A.M., Gobert M., Ding Y., Curotto de Lafaille M.A., Parkhurst C.N., et al. Neuropilin 1 is expressed on thymus-derived natural regulatory T cells, but not mucosa-generated induced Foxp3+ T reg cells. JExp Med 2012, 209:1723-1742. S1.
44. Kar S.P., Seldin M.F., Chen W., Lu E., Hirschfield G.M., Invernizzi P., et al. Pathway-based analysis of primary biliary cirrhosis genome-wide association studies. Genes Immun 2013, 14:179-186.
45. Lleo A., Zhang W., McDonald W.H., Seeley E.H., Leung P.S., Coppel R.L., et al. Shotgun proteomics: identification of unique protein profiles of apoptotic bodies from biliary epithelial cells. Hepatology 2014, 60:1314-1323.