Identification of a truncated splice variant of IL-18 receptor alpha in the human and rat, with evidence of wider evolutionary conservation

PeerJ

Volumn 2014, Issue 1, 2014, Pages

  Booker, Chris S ^a   Grattan, David R ^a  

^a UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

Comparative genomics; Interleukin 18; Splice variant; Toll like receptor

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 18 RECEPTOR ALPHA; TOLL LIKE RECEPTOR;

ADULT; AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENETIC CONSERVATION; HUMAN; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; RAT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA EXTRACTION; SEQUENCE ALIGNMENT;

RATTUS;

EID: 84907711068     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.560     Document Type: Article

References (66)

1. Adachi O, Kawai T, Takeda K, Matsumoto M, Tsutsui H, Sakagami M, Nakanishi K, Akira S 1998. Targeted disruption of the MyD88 gene results in loss of IL-1-and IL-18-mediated function. Immunity 9(1):143-150 DOI 10.1016/S1074-7613(00)80596-8
2. Alboni S, Cervia D, Ross B, Montanari C, Gonzalez ASS, Sanchez-Alavez M, Marcondes MCGC, De Vries D, Sugama S, Brunello N, BlomJ, Tascedda F, Conti B. 2009. Mapping of the full length and the truncated interleukin-18 receptor alpha in the mouse brain. Journal of Neuroimmunology 214(1-2):43-54 DOI 10.1016/j.jneuroim.2009.06.016
3. Amin MA, Rabquer BJ, Mansfield PJ, Ruth JH, Marotte H, Haas CS, Reamer EN, Koch AE. 2010 Interleukin 18 induces angiogenesis in vitro and in vivo via Src and Jnk kinases. Annals of the Rheumatic Diseases 69(12):2204-2212 DOI 10.1136/ard.2009.127241
4. Bakri Hassan A, Rönnelid J, Gunnarsson I, Karlsson G, Berg L, Lundberg I. 1998. Increased serum levels of immunoglobulins, C-reactive protein, type 1 and type 2 cytokines in patients with mixed connective tissue disease. Journal of Autoimmunity 11(5):503-508 DOI 10.1006/jaut.1998.0236
5. Batzer MA, Deininger PL. 2002. Alu repeats and human genomic diversity. Nature Reviews Genetics 3(5):370-379 DOI 10.1038/nrg798
6. Berg MG, Singh LN, Younis I, Liu Q, Pinto AM, Kaida D, Zhang Z, Cho S, Sherrill-Mix S, Wan L, Dreyfuss G. 2012. U1 snRNP determines mRNA length and regulates isoform expression. Cell 150(1):53-64 DOI 10.1016/j.cell.2012.05.029
7. Bergthorsson U, Andersson DI, Roth JR. 2007. Ohno's dilemma: evolution of new genes under continuous selection. Proceedings of the National Academy of Sciences of the United States of America 104(43):17004-17009 DOI 10.1073/pnas.0707158104
8. Bhangale TR, Rieder MJ, Livingston RJ, Nickerson DA. 2005. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes Human Molecular Genetics 14(1):59-69 DOI 10.1093/hmg/ddi006
9. Bodolay E, Aleksza M, Antal-Szalmás P, Végh J, Szodoray P, Soltész P, Szegedi A, Szekanecz Z 2002. Serum cytokine levels and type 1 and type 2 intracellular T cell cytokine profiles in mixed connective tissue disease. Journal of Rheumatology 29(10):2136-2142
10. Boraschi D, Lucchesi D, Hainzl S, Leitner M, Maier E, Mangelberger D, Oostingh GJ, Pfaller T, Pixner C, Posselt G, Italiani P, Nold MF, Nold-Petry CA, Bufler P, Dinarello CA. 2011. IL-37: a new anti-inflammatory cytokine of the IL-1 family. European Cytokine Network 22(3):127-147 DOI 10.1684/ecn.2011.0288
11. Breda L, Nozzi M, De Sanctis S, Chiarelli F. 2010. Laboratory tests in the diagnosis and follow-up of pediatric rheumatic diseases: an update. Seminars in Arthritis and Rheumatism 40(1):53-72 DOI 10.1016/j.semarthrit.2008.12.001
12. Byun H-M, Nordio F, Coull BA, Tarantini L, Hou L, Bonzini M, Apostoli P, Bertazzi PA, Baccarelli A. 2012. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PLoS ONE 7(6):e39220 DOI 10.1371/journal.pone.0039220
13. Chandrasekar B, Mummidi S, Valente AJ, Patel DN, Bailey SR, Freeman GL, Hatano M, Tokuhisa T, Jensen LE. 2005. The pro-atherogenic cytokine interleukin-18 induces CXCL16 expression in rat aortic smooth muscle cells via MyD88, interleukin-1 receptor-associated kinase, tumor necrosis factor receptor-associated factor 6, c-Src, phosphatidylinositol 3-kinase, Akt, c-Jun N-terminal kinase, and activator protein-1 signaling. Journal of Biological Chemistry 280(28):26263-26277 DOI 10.1074/jbc. M502586200
14. Civeira F, Genest J, Pocovi M, SalemDN, Herbert PN, Wilson PW, Schaefer EJ, Ordovas JM 1992. The MspI restriction fragment length polymorphism 3′ to the apolipoprotein A-II gene: relationships with lipids, apolipoproteins, and premature coronary artery disease. Atherosclerosis 92(2-3):165-176 DOI 10.1016/0021-9150(92)90275-L
15. Colotta F, Dower SK, Sims JE, Mantovani A. 1994. The type II 'decoy' receptor: a novel regulatory pathway for interleukin-1. Immunology Today 15(12):562-566 DOI 10.1016/0167-5699(94)90217-8
16. Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human genome evolution Nature Reviews Genetics 10(10):691-703 DOI 10.1038/nrg2640
17. Dinarello CA. 1998. Interleukin-1 beta, interleukin-18, and the interleukin-1 beta converting enzyme. Annals of the New York Academy of Sciences 856:1-11 DOI 10.1111/j.1749-6632.1998.tb08307.x
18. Dinarello CA. 2006. Interleukin 1 and interleukin 18 as mediators of inflammation and the aging process. American Journal of Clinical Nutrition 83(2):447S-455S
19. Dinarello C. 2009. Immunological and inflammatory functions of the interleukin-1 family. Annual Review of Immunology 27:519-550 DOI 10.1146/annurev.immunol.021908.132612
20. Dinarello CA, Fantuzzi G. 2003. Interleukin-18 and host defense against infection. Journal of Infectious Diseases 187(Suppl 2):S370-S384 DOI 10.1086/374751
21. Dunne A, O'Neill LAJ. 2003. The interleukin-1 receptor/Toll-like receptor superfamily: signal transduction during inflammation and host defense. Science's STKE: Signal Transduction Knowledge Environment 2003(171):re3
22. Ebihara M, Ohba H, Ohno S, Yoshikawa T. 2002. Genomic organization and promoter analysis of the human nicotinic acetylcholine receptor alpha6 subunit (CHNRA6) gene: Alu and other elements direct transcriptional repression. Gene 298(1):101-108 DOI 10.1016/S0378-1119(02)00925-3
23. Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics 41(5):563-571 DOI 10.1038/ng.368
24. Favilli F, Anzilotti C, Martinelli L, Quattroni P, DeMartino S, Pratesi F, Neumann D, Beermann S, Novick D, Dinarello CA, Boraschi D, Migliorini P. 2009. IL-18 activity in systemic lupus erythematosus. Annals of the New York Academy of Sciences 1173:301-309 DOI 10.1111/j.1749-6632.2009.04742.x
25. Feschotte C. 2008. Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics 9(5):397-405 DOI 10.1038/nrg2337
26. GlaxoSmithKline. 2008. Combination study of SB-485232 (interleukin 18) and doxil for advanced stage epithelial ovarian cancer. ClinicalTrials.gov identifier: NCT00659178. Available at http://www.clinicaltrials.gov/ct2/show/NCT00659178(accessed 16 July 2012)
27. Gong C, Maquat LE. 2011. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 470(7333):284-288 DOI 10.1038/nature09701
28. Hambor JE, Mennone J, Coon ME, Hanke JH, Kavathas P. 1993. Identification and characterization of an Alu-containing, T-cell-specific enhancer located in the last intron of the human CD8 alpha gene. Molecular and Cellular Biology 13(11):7056-7070
29. Hivert M, Sun Q, Shrader P, Mantzoros C, Meigs J, Hu F. 2009. Circulating IL-18 and the risk of type 2 diabetes in women. Diabetologia 52(10):2101-2108 DOI 10.1007/s00125-009-1455-z
30. Ho E, Fard A, Maisel A. 2010. Evolving use of biomarkers for kidney injury in acute care settings Current Opinion in Critical Care 16(5):399-407 DOI 10.1097/MCC.0b013e32833e10bc
31. Hwu HR, Roberts JW, Davidson EH, Britten RJ. 1986. Insertion and/or deletion of many repeated DNA sequences in human and higher ape evolution. Proceedings of the National Academy of Sciences of the United States of America 83(11):3875-3879 DOI 10.1073/pnas.83.11.3875
32. Jacobsen BM, Jambal P, Schittone SA, Horwitz KB. 2009. ALU repeats in promoters are position-dependent co-response elements (coRE) that enhance or repress transcription by dimeric and monomeric progesterone receptors. Molecular Endocrinology 23(7):989-1000 DOI 10.1210/me.2009-0048
33. Jefferis BJ, Papacosta O, Owen CG, Wannamethee SG, Humphries SE, Woodward M, Lennon LT, Thomson A, Welsh P, Rumley A, Lowe GDO, Whincup PH. 2011. Interleukin 18 and coronary heart disease: prospective study and systematic review. Atherosclerosis 217(1):227-233 DOI 10.1016/j.atherosclerosis.2011.03.015
34. Kaida D, Berg MG, Younis I, Kasim M, Singh LN, Wan L, Dreyfuss G. 2010. U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation. Nature 468(7324):664-668 DOI 10.1038/nature09479
35. Kattah NH, Kattah MG, Utz PJ. 2010. The U1-snRNP complex: structural properties relating to autoimmune pathogenesis in rheumatic diseases. Immunological Reviews 233(1):126-145 DOI 10.1111/j.0105-2896.2009.00863.x
36. Khan JA, Brint EK, O'Neill LAJ, Tong L. 2004. Crystal structure of the Toll/interleukin-1 receptor domain of human IL-1RAPL. Journal of Biological Chemistry 279(30):31664-31670 DOI 10.1074/jbc. M403434200
37. Knott TJ, Wallis SC, Robertson ME, Priestley LM, Urdea M, Rall LB, Scott J. 1985. The human apolipoprotein AII gene: structural organization and sites of expression. Nucleic Acids Research 13(17):6387-6398 DOI 10.1093/nar/13.17.6387
38. Laperriere D, Wang T-T, White JH, Mader S. 2007. Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics 8(1):23 DOI 10.1186/1471-2164-8-23
39. Le GoffW, Guerin M, Chapman MJ, Thillet J. 2003. A CYP7A promoter binding factor site and Alu repeat in the distal promoter region are implicated in regulation of human CETP gene expression. Journal of Lipid Research 44(5):902-910 DOI 10.1194/jlr. M200423-JLR200
40. Lewis E, Dinarello C. 2006. Responses of IL-18-and IL-18 receptor-deficient pancreatic islets with convergence of positive and negative signals for the IL-18 receptor. Proceedings of the National Academy of Sciences of the United States of America 103(45):16852-16857 DOI 10.1073/pnas.0607917103
41. Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, CuffJ, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Worley KC, Kovar CL, Muzny DM, Gibbs RA, WarrenWC, Mardis ER, Weinstock GM, Wilson RK, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478(7370):476-482 DOI 10.1038/nature10530
42. Ma Y, Zhang B, Tang R-K, Liu Y, Peng G-G. 2012. Interleukin-18 promoter polymorphism and asthma risk: a meta-analysis. Molecular Biology Reports 39(2):1371-1376 DOI 10.1007/s11033-011-0871-6
43. Matsunaga H, Hokari R, Ueda T, Kurihara C, Hozumi H, Higashiyama M, Okada Y, Watanabe C, Komoto S, Nakamura M, Kawaguchi A, Nagao S, Sekiyama A, Miura S. 2011 Physiological stress exacerbates murine colitis by enhancing proinflammatory cytokine expression that is dependent on IL-18. American Journal of Physiology-Gastrointestinal and Liver Physiology 301(3):G555-G564 DOI 10.1152/ajpgi.00482.2010
44. Merkhofer EC, Johnson TL. 2012. U1 snRNA rewrites the 'script'. Cell 150(1):9-11 DOI 10.1016/j.cell.2012.06.017
45. Nold-Petry CA, Nold MF, Nielsen JW, Bustamante A, Zepp JA, StormKA, Hong J-W, Kim S-H, Dinarello CA. 2009. Increased cytokine production in interleukin-18 receptor α-deficient cells is associated with dysregulation of suppressors of cytokine signaling. Journal of Biological Chemistry 284(38):25900-25911 DOI 10.1074/jbc. M109.004184
46. Novick D, Kim SH, Fantuzzi G, Reznikov LL, Dinarello CA, Rubinstein M. 1999. Interleukin-18 binding protein: a novel modulator of the Th1 cytokine response. Immunity 10(1):127-136 DOI 10.1016/S1074-7613(00)80013-8
47. Pandey R, Mandal AK, Jha V, Mukerji M. 2011. Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. Genome Biology 12(11):R117 DOI 10.1186/gb-2011-12-11-r117
48. Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, Dubinsky MC, Brant SR, Silverberg MS, Duerr RH, Altshuler D, Gabriel S, Lettre G, Franke A, D'Amato M, McGovern DPB, Cho JH, Rioux JD, Xavier RJ, Daly MJ. 2011. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nature Genetics 43(11):1066-1073 DOI 10.1038/ng.952
49. Sahar S, Dwarakanath R, Reddy M, Lanting L, Todorov I, Natarajan R. 2005. Angiotensin II enhances interleukin-18 mediated inflammatory gene expression in vascular smooth muscle cells: a novel cross-talk in the pathogenesis of atherosclerosis. Circulation Research 96(10):1064-1071 DOI 10.1161/01.RES.0000168210.10358.f4
50. Schrago CG, Russo CAM. 2003. Timing the origin of New World monkeys. Molecular Biology and Evolution 20(10):1620-1625 DOI 10.1093/molbev/msg172
51. Seenu Reddy V, Prabhu SD, Mummidi S, Valente AJ, Venkatesan B, Shanmugam P, Delafontaine P, Chandrasekar B. 2010. Interleukin-18 induces EMMPRIN expression in primary cardiomyocytes via JNK/Sp1 signaling, and MMP9 in part via EMMPRIN, and through AP-1 and NF-κB activation. American Journal of Physiology-Heart and Circulatory Physiology 299(4):H1242-H1254 DOI 10.1152/ajpheart.00451.2010
52. Siegmund B. 2010. Interleukin-18 in intestinal inflammation: friend and foe? Immunity 32(3):300-302 DOI 10.1016/j.immuni.2010.03.010
53. Slack JL, Schooley K, Bonnert TP, Mitcham JL, QwarnstromEE, Sims JE, Dower SK. 2000 Identification of two major sites in the type I interleukin-1 receptor cytoplasmic region responsible for coupling to pro-inflammatory signaling pathways. Journal of Biological Chemistry 275(7):4670-4678 DOI 10.1074/jbc.275.7.4670
54. Smit A, Hubley R, Green P. 2012. RepeatMasker Open-3.0. 1996-2010. Available at http://wwwrepeatmasker.org/(accessed 13 July 2012)
55. Smyth DJ, Plagnol V, Walker NM, Cooper JD, Downes K, Yang JH, Howson JM, Stevens H, Mcmanus R, Wijmenga C, Heap GA, Dubois PC, Clayton DG, Hunt KA, Van Heel DA, Todd JA. 2008. Shared and distinct genetic variants in type 1 diabetes and celiac disease. New England Journal of Medicine 359(26):2767-2777 DOI 10.1056/NEJMoa0807917
56. Srivastava S, Salim N, Robertson MJ. 2010. Interleukin-18: biology and role in the immunotherapy of cancer. Current Medicinal Chemistry 17(29):3353-3357 DOI 10.2174/092986710793176348
57. Steiper ME, Young NM. 2006. Primate molecular divergence dates. Molecular Phylogenetics and Evolution 41(2):384-394 DOI 10.1016/j.ympev.2006.05.021
58. Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YSN, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJM, Marra MA. 2002. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 99(26):16899-16903 DOI 10.1073/pnas.242603899
59. Thorand B, Kolb H, Baumert J, Koenig W, Chambless L, Meisinger C, Illig T, Martin S, Herder C. 2005. Elevated levels of interleukin-18 predict the development of type 2 diabetes: results from the MONICA/KORA Augsburg Study, 1984-2002. Diabetes 54(10):2932-2938 DOI 10.2337/diabetes.54.10.2932
60. Trujillo MA, Sakagashira M, Eberhardt NL. 2006. The human growth hormone gene contains a silencer embedded within an Alu repeat in the 3′-flanking region. Molecular Endocrinology 20(10):2559-2575 DOI 10.1210/me.2006-0147
61. Vansant G, Reynolds WF. 1995. The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proceedings of the National Academy of Sciences of the United States of America 92(18):8229-8233 DOI 10.1073/pnas.92.18.8229
62. Wang X, Fan J, Liu D, Fu S, Ingvarsson S, Chen H. 2011. Spreading of Alu methylation to the promoter of the MLH1 gene in gastrointestinal cancer. PloS ONE 6(10):e25913 DOI 10.1371/journal.pone.0025913
63. Watanabe M, Goto N, Watanabe Y, Nishiguchi S, Shimada K, Yasunga T, Yamanishi H. 2005 Evolution of interleukin-18 binding proteins and interleukin-1 receptor, type II proteins International Journal of Molecular Medicine 15(4):561-566
64. Watanabe M, Kaneko H, Shikano H, Aoki M, Sakaguchi H, Matsui E, Inoue R, Kato Z, Kasahara K, Fukutomi O, Kondo T, Kondo N. 2002. Predominant expression of 950delCAG of IL-18R alpha chain cDNA is associated with reduced IFN-gamma production and high serum IgE levels in atopic Japanese children. Journal of Allergy and Clinical Immunology 109(4):669-675 DOI 10.1067/mai.2002.122158
65. Xiang S, Liu Z, Zhang B, Zhou J, Zhu B-D, Ji J, Deng D. 2010. Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas. BMC Cancer 10:44 DOI 10.1186/1471-2407-10-44
66. Xu Y, Tao X, Shen B, Horng T, Medzhitov R, Manley JL, Tong L. 2000. Structural basis for signal transduction by the Toll/interleukin-1 receptor domains. Nature 408(6808):111-115 DOI 10.1038/35047056