The structural network of Interleukin-10 and its implications in inflammation and cancer

BMC Genomics

Volumn 15, Issue 4, 2014, Pages

  Acuner Ozbabacan, Ece Saliha ^a   Engin, Billur Hatice ^a   Guven Maiorov, Emine ^a   Kuzu, Guray ^a   Muratcioglu, Serena ^a   Baspinar, Alper ^a   Chen, Zhong ^c   Van Waes, Carter ^c   Gursoy, Attila ^a   Keskin, Ozlem ^a   Nussinov, Ruth ^b,d  

^a KOÇ UNIVERSITY   (Turkey)

^b FREDERICK NATIONAL LABORATORY FOR CANCER RESEARCH   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA 2 MACROGLOBULIN; AMYLOID BETA PROTEIN; AMYLOID PRECURSOR PROTEIN; INTERLEUKIN 10; INTERLEUKIN 10 RECEPTOR ALPHA; INTERLEUKIN 10 RECEPTOR BETA; KALLIKREIN 13; A2M PROTEIN, HUMAN; CYSTEINE PROTEINASE; PRORENIN PROCESSING ENZYME; PROTEIN BINDING;

ARTICLE; CELL PROLIFERATION; DISEASE ASSOCIATION; EXTRACELLULAR MATRIX; INFLAMMATION; METASTASIS; MUTATION; NEOPLASM; PATHOGENESIS; PROTEIN DEGRADATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; TUMOR IMMUNITY; BIOLOGY; CHEMISTRY; GENETICS; HUMAN; METABOLISM; MUTAGENESIS; PATHOLOGY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

ALPHA-MACROGLOBULINS; AMYLOID BETA-PROTEIN PRECURSOR; COMPUTATIONAL BIOLOGY; CYSTEINE ENDOPEPTIDASES; DATABASES, PROTEIN; HUMANS; INFLAMMATION; INTERLEUKIN-10; INTERLEUKIN-10 RECEPTOR ALPHA SUBUNIT; INTERLEUKIN-10 RECEPTOR BETA SUBUNIT; MUTAGENESIS; NEOPLASMS; PROTEIN BINDING; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, TERTIARY; SIGNAL TRANSDUCTION; THERMODYNAMICS;

EID: 84907569494     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-S4-S2     Document Type: Article

References (77)

1. Guven Maiorov E, Keskin O, Gursoy A, Nussinov R: The structural network of inflammation and cancer: Merits and challenges. Seminars in cancer biology. 2013, 23 (4): 243-251.
2. Trinchieri G: Cancer and inflammation: an old intuition with rapidly evolving new concepts. Annu Rev Immunol. 2012, 30: 677-706.
3. Trinchieri G: Inflammation in cancer: a therapeutic target?. Oncology (Williston Park). 2011, 25 (5): 418-420.
4. Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell. 2011, 144 (5): 646-674.
5. Vacchelli E, Galluzzi L, Eggermont A, Galon J, Tartour E, Zitvogel L, Kroemer G: Trial Watch: Immunostimulatory cytokines. Oncoimmunology. 2012, 1 (4): 493-506.
6. Balkwill F, Coussens LM: Cancer: an inflammatory link. Nature. 2004, 431 (7007): 405-406.
7. Coussens LM, Werb Z: Inflammation and cancer. Nature. 2002, 420 (6917): 860-867.
8. Bar D, Apte RN, Voronov E, Dinarello CA, Cohen S: A continuous delivery system of IL-1 receptor antagonist reduces angiogenesis and inhibits tumor development. FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 2004, 18 (1): 161-163.
9. Balkwill F, Mantovani A: Inflammation and cancer: back to Virchow?. Lancet. 2001, 357 (9255): 539-545.
10. Robinson SC, Coussens LM: Soluble mediators of inflammation during tumor development. Advances in cancer research. 2005, 93: 159-187.
11. Mantovani A, Allavena P, Sica A, Balkwill F: Cancer-related inflammation. Nature. 2008, 454 (7203): 436-444.
12. Fiorentino DF, Bond MW, Mosmann TR: Two types of mouse T helper cell. IV. Th2 clones secrete a factor that inhibits cytokine production by Th1 clones. The Journal of experimental medicine. 1989, 170 (6): 2081-2095.
13. Moore KW, de Waal Malefyt R, Coffman RL, O'Garra A: Interleukin-10 and the interleukin-10 receptor. Annual review of immunology. 2001, 19: 683-765.
14. Tanikawa T, Wilke CM, Kryczek I, Chen GY, Kao J, Nunez G, Zou W: Interleukin-10 ablation promotes tumor development, growth, and metastasis. Cancer research. 2012, 72 (2): 420-429.
15. Merlo P, Cecconi F: XIAP: inhibitor of two worlds. The EMBO journal. 2013, 32 (16): 2187-2188.
16. Germano G, Allavena P, Mantovani A: Cytokines as a key component of cancer-related inflammation. Cytokine. 2008, 43 (3): 374-379.
17. Allavena P, Germano G, Marchesi F, Mantovani A: Chemokines in cancer related inflammation. Experimental cell research. 2011, 317 (5): 664-673.
18. Wilke CM, Wei S, Wang L, Kryczek I, Kao J, Zou W: Dual biological effects of the cytokines interleukin-10 and interferon-gamma. Cancer immunology, immunotherapy : CII. 2011, 60 (11): 1529-1541.
19. Mocellin S, Marincola FM, Young HA: Interleukin-10 and the immune response against cancer: a counterpoint. Journal of leukocyte biology. 2005, 78 (5): 1043-1051.
20. Kim BG, Joo HG, Chung IS, Chung HY, Woo HJ, Yun YS: Inhibition of interleukin-10 (IL-10) production from MOPC 315 tumor cells by IL-10 antisense oligodeoxynucleotides enhances cell-mediated immune responses. Cancer immunology, immunotherapy : CII. 2000, 49 (8): 433-440.
21. Sun Z, Luo Q, Ye D, Chen W, Chen F: Role of toll-like receptor 4 on the immune escape of human oral squamous cell carcinoma and resistance of cisplatin-induced apoptosis. Molecular cancer. 2012, 11: 33-
22. Sabat R, Grutz G, Warszawska K, Kirsch S, Witte E, Wolk K, Geginat J: Biology of interleukin-10. Cytokine & growth factor reviews. 2010, 21 (5): 331-344.
23. Asadullah K, Sterry W, Volk HD: Interleukin-10 therapy--review of a new approach. Pharmacological reviews. 2003, 55 (2): 241-269.
24. Kotenko SV, Krause CD, Izotova LS, Pollack BP, Wu W, Pestka S: Identification and functional characterization of a second chain of the interleukin-10 receptor complex. The EMBO journal. 1997, 16 (19): 5894-5903.
25. Riley JK, Takeda K, Akira S, Schreiber RD: Interleukin-10 receptor signaling through the JAK-STAT pathway. Requirement for two distinct receptor-derived signals for anti-inflammatory action. The Journal of biological chemistry. 1999, 274 (23): 16513-16521.
26. Donnelly RP, Dickensheets H, Finbloom DS: The interleukin-10 signal transduction pathway and regulation of gene expression in mononuclear phagocytes. Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research. 1999, 19 (6): 563-573.
27. Garber TR, Gonias SL, Webb DJ: Interleukin-4 and IL-10 bind covalently to activated human alpha2-macroglobulin by a mechanism that requires Cys949. Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research. 2000, 20 (2): 125-131.
28. Sheikh AM, Chauhan V, Tsiouris JA, Mehta PD, Burguess K, Fenko MD, Spivack W, Vaughan M, Malik M: Elevated levels of serum alpha(2) macroglobulin in wild black bears during hibernation. Biochimie. 2003, 85 (10): 1027-1032.
29. Rehman AA, Ahsan H, Khan FH: alpha-2-Macroglobulin: a physiological guardian. Journal of cellular physiology. 2013, 228 (8): 1665-1675.
30. Zhevago NA, Samoilova KA: Pro- and anti-inflammatory cytokine content in human peripheral blood after its transcutaneous (in vivo) and direct (in vitro) irradiation with polychromatic visible and infrared light. Photomedicine and laser surgery. 2006, 24 (2): 129-139.
31. Borth W, Scheer B, Urbansky A, Luger TA, Sottrup-Jensen L: Binding of IL-1 beta to alpha-macroglobulins and release by thioredoxin. Journal of immunology. 1990, 145 (11): 3747-3754.
32. Borth W: Alpha 2-macroglobulin. A multifunctional binding and targeting protein with possible roles in immunity and autoimmunity. Annals of the New York Academy of Sciences. 1994, 737: 267-272.
33. Mosca R, Ceol A, Aloy P: Interactome3D: adding structural details to protein networks. Nature methods. 2013, 10 (1): 47-53.
34. Tuncbag N, Gursoy A, Keskin O: Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces. Physical biology. 2011, 8 (3): 035006-
35. Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A: PRISM: protein interactions by structural matching. Nucleic Acids Research. 2005, 33: W331-W336.
36. Tuncbag N, Gursoy A, Nussinov R, Keskin O: Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nature Protocols. 2011, 6 (9): 1341-1354.
37. Tsai CJ, Lin SL, Wolfson HJ, Nussinov R: Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Critical Reviews in Biochemistry and Molecular Biology. 1996, 31 (2): 127-152.
38. Keskin O, Nussinov R, Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways. Protein Engineering Design & Selection. 2005, 18 (1): 11-24.
39. Keskin O, Gursoy A, Ma B, Nussinov R: Principles of protein-protein interactions: What are the preferred ways for proteins to interact?. Chemical Reviews. 2008, 108 (4): 1225-1244.
40. Tuncbag N, Keskin O, Nussinov R, Gursoy A: Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement. Proteins-Structure Function and Bioinformatics. 2012, 80 (4): 1239-1249.
41. Kuzu G, Gursoy A, Nussinov R, Keskin O: Exploiting Conformational Ensembles in Modeling Protein-Protein Interactions on the Proteome Scale. Journal of Proteome Research. 2013, 12 (6): 2641-2653.
42. Ozbabacan SEA, Keskin O, Nussinov R, Gursoy A: Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. Journal of Structural Biology. 2012, 179 (3): 338-346.
43. Kar G, Keskin O, Nussinov R, Gursoy A: Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. J Proteome Res. 2012, 11 (2): 1196-1207.
44. Kuzu G, Keskin O, Gursoy A, Nussinov R: Constructing structural networks of signaling pathways on the proteome scale. Current Opinion in Structural Biology. 2012, 22 (3): 367-377.
45. Engin HB, Keskin O, Nussinov R, Gursoy A: A strategy based on protein-protein interface motifs may help in identifying drug off-targets. J Chem Inf Model. 2012, 52 (8): 2273-2286.
46. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, et al: STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41 (Database): D808-815.
47. Roy A, Kucukural A, Zhang Y, I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010, 5 (4): 725-738.
48. Zhang Y, Skolnick J, TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33 (7): 2302-2309.
49. DuPage M, Jacks T: Genetically engineered mouse models of cancer reveal new insights about the antitumor immune response. Current opinion in immunology. 2013, 25 (2): 192-199.
50. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, et al: COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic acids research. 2011, 39 (Database): D945-950.
51. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et al: The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer discovery. 2012, 2 (5): 401-404.
52. Tuncbag N, Keskin O, Gursoy A: HotPoint: hot spot prediction server for protein interfaces. Nucleic acids research. 2010, 38 (Web Server): W402-406.
53. Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J, Rousseau F: A graphical interface for the FoldX forcefield. Bioinformatics. 2011, 27 (12): 1711-1712.
54. Krieger E, Koraimann G, Vriend G: Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field. Proteins. 2002, 47 (3): 393-402.
55. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR: The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet. 2008, Chapter 10 (Unit 10 11):
56. Schuster-Bockler B, Bateman A: Protein interactions in human genetic diseases. Genome biology. 2008, 9 (1): R9-
57. Chiti F, Dobson CM: Protein misfolding, functional amyloid, and human disease. Annual review of biochemistry. 2006, 75: 333-366.
58. Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H: Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nature biotechnology. 2012, 30 (2): 159-164.
59. Engin HB, Guney E, Keskin O, Oliva B, Gursoy A: Integrating structure to protein-protein interaction networks that drive metastasis to brain and lung in breast cancer. PloS one. 2013, 8 (11): e81035-
60. Acuner Ozbabacan SE, Gursoy A, Nussinov R, Keskin O: The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer. PLOS Comp Biol. 10 (2): e1003470-
61. Yoon SI, Logsdon NJ, Sheikh F, Donnelly RP, Walter MR: Conformational changes mediate interleukin-10 receptor 2 (IL-10R2) binding to IL-10 and assembly of the signaling complex. J Biol Chem. 2006, 281 (46): 35088-35096.
62. Muller UC, Zheng H: Physiological functions of APP family proteins. Cold Spring Harbor perspectives in medicine. 2012, 2 (2): a006288-
63. Narita M, Holtzman DM, Schwartz AL, Bu G: Alpha2-macroglobulin complexes with and mediates the endocytosis of beta-amyloid peptide via cell surface low-density lipoprotein receptor-related protein. Journal of neurochemistry. 1997, 69 (5): 1904-1911.
64. Yerbury JJ, Kumita JR, Meehan S, Dobson CM, Wilson MR: alpha2-Macroglobulin and haptoglobin suppress amyloid formation by interacting with prefibrillar protein species. The Journal of biological chemistry. 2009, 284 (7): 4246-4254.
65. Hansel DE, Rahman A, Wehner S, Herzog V, Yeo CJ, Maitra A: Increased expression and processing of the Alzheimer amyloid precursor protein in pancreatic cancer may influence cellular proliferation. Cancer research. 2003, 63 (21): 7032-7037.
66. Meng JY, Kataoka H, Itoh H, Koono M: Amyloid beta protein precursor is involved in the growth of human colon carcinoma cell in vitro and in vivo. International journal of cancer Journal international du cancer. 2001, 92 (1): 31-39.
67. Takayama K, Tsutsumi S, Suzuki T, Horie-Inoue K, Ikeda K, Kaneshiro K, Fujimura T, Kumagai J, Urano T, Sakaki Y, et al: Amyloid precursor protein is a primary androgen target gene that promotes prostate cancer growth. Cancer research. 2009, 69 (1): 137-142.
68. Pietrzik CU, Hoffmann J, Stober K, Chen CY, Bauer C, Otero DA, Roch JM, Herzog V: From differentiation to proliferation: the secretory amyloid precursor protein as a local mediator of growth in thyroid epithelial cells. Proceedings of the National Academy of Sciences of the United States of America. 1998, 95 (4): 1770-1775.
69. Yousef GM, Chang A, Diamandis EP: Identification and characterization of KLK-L4, a new kallikrein-like gene that appears to be down-regulated in breast cancer tissues. Journal of Biological Chemistry. 2000, 275 (16): 11891-11898.
70. Diamandis EP, Yousef GM: Human tissue kallikreins: A family of new cancer biomarkers. Clinical Chemistry. 2002, 48 (8): 1198-1205.
71. Darling MR, Jackson-Boeters L, Daley TD, Diamandis EP: Human kallikrein 13 expression in salivary gland tumors. International Journal of Biological Markers. 2006, 21 (2): 106-110.
72. Kapadia C, Yousef GM, Mellati AA, Magklara A, Wasney GA, Diamandis EP: Complex formation between human kallikrein 13 and serum protease inhibitors. Clinica Chimica Acta. 2004, 339 (1-2): 157-167.
73. Petraki CD, Gregorakis AK, Papanastasiou PA, Karavana VN, Luo LY, Diamandis EP: Immunohistochemical localization of human kallikreins 6, 10 and 13 in benign and malignant prostatic tissues. Prostate Cancer and Prostatic Diseases. 2003, 6 (3): 223-227.
74. Chang A, Yousef GM, Scorilas A, Grass L, Sismondi P, Ponzone R, Diamandis EP: Human kallikrein gene 13 (KLK13) expression by quantitative RT-PCR: an independent indicator of favourable prognosis in breast cancer. British Journal of Cancer. 2002, 86 (9): 1457-1464.
75. Scorilas A, Borgono CA, Harbeck N, Dorn J, Schmalfeldt B, Schmitt M, Diamandis EP: Human kallikrein 13 protein in ovarian cancer cytosols: A new favorable prognostic marker. Journal of Clinical Oncology. 2004, 22 (4): 678-685.
76. Luo LY, Yousef G, Diamandis EP: Human tissue kallikreins and testicular cancer. Apmis. 2003, 111 (1): 225-233.
77. Planque C, Li L, Zheng YG, Soosaipillai A, Reckamp K, Chia D, Diamandis EP, Goodglick L: A multiparametric serum kallikrein panel for diagnosis of non-small cell lung carcinoma. Clinical Cancer Research. 2008, 14 (5): 1355-1362.