Advertisement

Pediatric Cardiology

, Volume 37, Issue 6, pp 1003–1012 | Cite as

Identification of Differentially Expressed Genes in Kawasaki Disease Patients as Potential Biomarkers for IVIG Sensitivity by Bioinformatics Analysis

  • Lan He
  • Youyu Sheng
  • Chunyun Huang
  • Guoying HuangEmail author
Original Article

Abstract

Kawasaki disease (KD) is a leading cause of acquired heart disease predominantly affecting infants and young children. Intravenous immunoglobulin (IVIG) is applied as the most favorable treatment against KD, but IVIG resistant remains exist. Although several clinical scoring systems have been developed to identify children at highest risk of IVIG resistance, there is a need to identify sufficiently sensitive biomarkers for IVIG treatment. Some differentially expressed genes (DEGs) could be the promising potential biomarkers for IVIG-related sensitivity diagnosis. We employed a systematic and integrative bioinformatics framework to identify such kind of genes. The performance of the candidate genes was evaluated by hierarchical clustering, ROC analysis and literature mining. By analyzing three datasets of KD patients, 34 DEGs of the three groups have been found to be associated with IVIG-related sensitivity. A module of 12 genes could predict resistant group patients with high accuracy, and a module of ten genes could predict responsive group patients effectively with accuracy of 96 %. And three of them are most likely to serve as drug targets or diagnostic biomarkers in the future. Compared with unsupervised hierarchical clustering analysis, our modules could distinct IVIG-resistant patients efficiently. Two groups of DEGs could predict IVIG-related sensitivity with high accuracy, which are potential biomarkers for the clinical diagnosis and prediction of IVIG treatment response in KD patients, improving the prognosis of patients.

Keywords

Kawasaki disease Differentially expressed genes (DEGs) Biomarker IVIG-related sensitivity 

Abbreviations

DAVID

Database for Annotation, Visualization and Integrated Discovery

DEGs

Differentially expressed genes

GEO

Gene expression omnibus

GO

Gene ontology

IVIG

Intravenous immunoglobulin

BH FDR

Hochberg false discovery rate

KD

Kawasaki disease

KEGG

Kyoto encyclopedia of genes and genomes

NCBI

National Center for Biotechnology Information

ROC

Receiver operating characteristic curve

SVM

Supported vector machine

Notes

Acknowledgments

On the completion of my thesis, I should like to express my deepest gratitude to all those whose kindness and advice have made this work possible. I am greatly indebted to my advisor Guoying Huang who gave me valuable instructions and has improved me in language. His effective advice and shrewd comments have kept the thesis in the right direction. I would like to thank my partners for their friendship and constructive suggestions, and they constantly encouraged me when I felt frustrated with this dissertation.

Funding

This research received no grant from any funding agency in the public, commercial or not-for-profit sectors.

Compliance with Ethical Standards

Conflict of interest

The authors disclose no conflicts of interest.

Supplementary material

246_2016_1381_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 14 kb)

References

  1. 1.
    Gerding R (2011) Kawasaki disease: a review. J Pediatr Health Care 25(6):379–387. doi: 10.1016/j.pedhc.2011.07.007 CrossRefPubMedGoogle Scholar
  2. 2.
    Kuo HC, Yang KD, Chang WC, Ger LP, Hsieh KS (2012) Kawasaki disease: an update on diagnosis and treatment. Pediatr Neonatol 53(1):4–11. doi: 10.1016/j.pedneo.2011.11.003 CrossRefPubMedGoogle Scholar
  3. 3.
    Sandrine B, Goebeler M (2014) Vasculitis in childhood—a dermatological approach. J Ger Soc Dermatol JDDG 12(2):124–129. doi: 10.1111/ddg.12252_suppl Google Scholar
  4. 4.
    Dajani AS, Taubert KA, Gerber MA, Shulman ST, Ferrieri P, Freed M, Takahashi M, Bierman FZ, Karchmer AW, Wilson W et al (1993) Diagnosis and therapy of Kawasaki disease in children. Circulation 87(5):1776–1780CrossRefPubMedGoogle Scholar
  5. 5.
    Kuo HC, Liang CD, Wang CL, Yu HR, Hwang KP, Yang KD (2010) Serum albumin level predicts initial intravenous immunoglobulin treatment failure in Kawasaki disease. Acta Paediatr 99(10):1578–1583. doi: 10.1111/j.1651-2227.2010.01875.x CrossRefPubMedGoogle Scholar
  6. 6.
    Rowley AH, Duffy CE, Shulman ST (1988) Prevention of giant coronary artery aneurysms in Kawasaki disease by intravenous gamma globulin therapy. J Pediatr 113(2):290–294CrossRefPubMedGoogle Scholar
  7. 7.
    Dominguez SR, Anderson MS (2013) Advances in the treatment of Kawasaki disease. Curr Opin Pediatr 25(1):103–109. doi: 10.1097/MOP.0b013e32835c1122 CrossRefPubMedGoogle Scholar
  8. 8.
    Stiehm ER (2006) Lessons from Kawasaki disease: all brands of IVIG are not equal. J Pediatr 148(1):6–8. doi: 10.1016/j.jpeds.2005.09.019 CrossRefPubMedGoogle Scholar
  9. 9.
    Soltner E, Neel A, Tiab M, Varin S, Cormier G, Maisonneuve H, Maugars Y, Tanguy G, Hamidou M, Berthelot JM (2009) Chronic, eventually fatal, Kawasaki-like disease in an adult with spondylarthropathy responding to IVIG therapy. Joint Bone Spine Revue Rhum 76(5):559–561. doi: 10.1016/j.jbspin.2009.01.006 CrossRefGoogle Scholar
  10. 10.
    Ogihara Y, Ogata S, Nomoto K, Ebato T, Sato K, Kokubo K, Kobayashi H, Ishii M (2014) Transcriptional regulation by infliximab therapy in Kawasaki disease patients with immunoglobulin resistance. Pediatr Res 76(3):287–293. doi: 10.1038/pr.2014.92 CrossRefPubMedGoogle Scholar
  11. 11.
    Newburger JW, Takahashi M, Gerber MA, Gewitz MH, Tani LY, Burns JC, Shulman ST, Bolger AF, Ferrieri P, Baltimore RS, Wilson WR, Baddour LM, Levison ME, Pallasch TJ, Falace DA, Taubert KA (2004) Diagnosis, treatment, and long-term management of Kawasaki disease: a statement for health professionals from the Committee on Rheumatic Fever, Endocarditis and Kawasaki Disease, Council on Cardiovascular Disease in the Young, American Heart Association. Circulation 110(17):2747–2771. doi: 10.1161/01.cir.0000145143.19711.78 CrossRefPubMedGoogle Scholar
  12. 12.
    Weng KP, Ou SF, Lin CC, Hsieh KS (2011) Recent advances in the treatment of Kawasaki disease. J Chin Med Assoc JCMA 74(11):481–484. doi: 10.1016/j.jcma.2011.09.001 CrossRefPubMedGoogle Scholar
  13. 13.
    Tremoulet AH, Best BM, Song S, Wang S, Corinaldesi E, Eichenfield JR, Martin DD, Newburger JW, Burns JC (2008) Resistance to intravenous immunoglobulin in children with Kawasaki disease. J Pediatr 153(1):117–121. doi: 10.1016/j.jpeds.2007.12.021 CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Ashouri N, Takahashi M, Dorey F, Mason W (2008) Risk factors for nonresponse to therapy in Kawasaki disease. J Pediatr 153(3):365–368. doi: 10.1016/j.jpeds.2008.03.014 CrossRefPubMedGoogle Scholar
  15. 15.
    Kobayashi T, Inoue Y, Takeuchi K, Okada Y, Tamura K, Tomomasa T, Kobayashi T, Morikawa A (2006) Prediction of intravenous immunoglobulin unresponsiveness in patients with Kawasaki disease. Circulation 113(22):2606–2612. doi: 10.1161/circulationaha.105.592865 CrossRefPubMedGoogle Scholar
  16. 16.
    Egami K, Muta H, Ishii M, Suda K, Sugahara Y, Iemura M, Matsuishi T (2006) Prediction of resistance to intravenous immunoglobulin treatment in patients with Kawasaki disease. J Pediatr 149(2):237–240. doi: 10.1016/j.jpeds.2006.03.050 CrossRefPubMedGoogle Scholar
  17. 17.
    Sano T, Kurotobi S, Matsuzaki K, Yamamoto T, Maki I, Miki K, Kogaki S, Hara J (2007) Prediction of non-responsiveness to standard high-dose gamma-globulin therapy in patients with acute Kawasaki disease before starting initial treatment. Eur J Pediatr 166(2):131–137. doi: 10.1007/s00431-006-0223-z CrossRefPubMedGoogle Scholar
  18. 18.
    Sleeper LA, Minich LL, McCrindle BM, Li JS, Mason W, Colan SD, Atz AM, Printz BF, Baker A, Vetter VL, Newburger JW (2011) Evaluation of Kawasaki disease risk-scoring systems for intravenous immunoglobulin resistance. J Pediatr 158(5):831.e833–835.e833. doi: 10.1016/j.jpeds.2010.10.031 CrossRefGoogle Scholar
  19. 19.
    Seki M, Kobayashi T, Kobayashi T, Morikawa A, Otani T, Takeuchi K, Ayusawa M, Tsuchiya K, Yasuda K, Suzuki T, Shimoyama S, Ikeda K, Ishii Y, Arakawa H (2011) External validation of a risk score to predict intravenous immunoglobulin resistance in patients with Kawasaki disease. Pediatr Infect Dis J 30(2):145–147. doi: 10.1097/INF.0b013e3181f386db CrossRefPubMedGoogle Scholar
  20. 20.
    Ogawa S (2014) Biomarker. Jpn J Clin Med 72(9):1578–1584Google Scholar
  21. 21.
    Abe J, Matsuda A (2013) [Biomarkers associated with unresponsiveness to IVIG in children with Kawasaki disease]. Nihon Rinsho Men’eki Gakkai kaishi = Japanese. J Clin Immunol 36(1):27–34CrossRefGoogle Scholar
  22. 22.
    Fury W, Tremoulet AH, Watson VE, Best BM, Shimizu C, Hamilton J, Kanegaye JT, Wei Y, Kao C, Mellis S, Lin C, Burns JC (2010) Transcript abundance patterns in Kawasaki disease patients with intravenous immunoglobulin resistance. Hum Immunol 71(9):865–873. doi: 10.1016/j.humimm.2010.06.008 CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Davies S, Sutton N, Blackstock S, Gormley S, Hoggart CJ, Levin M, Herberg JA (2015) Predicting IVIG resistance in UK Kawasaki disease. Arch Dis Child 100(4):366–368. doi: 10.1136/archdischild-2014-307397 CrossRefPubMedGoogle Scholar
  24. 24.
    Ogata S, Ogihara Y, Nomoto K, Akiyama K, Nakahata Y, Sato K, Minoura K, Kokubo K, Kobayashi H, Ishii M (2009) Clinical score and transcript abundance patterns identify Kawasaki disease patients who may benefit from addition of methylprednisolone. Pediatr Res 66(5):577–584. doi: 10.1203/PDR.0b013e3181baa3c2 CrossRefPubMedGoogle Scholar
  25. 25.
    Hoang LT, Shimizu C, Ling L, Naim AN, Khor CC, Tremoulet AH, Wright V, Levin M, Hibberd ML, Burns JC (2014) Global gene expression profiling identifies new therapeutic targets in acute Kawasaki disease. Genome Med 6(11):541. doi: 10.1186/s13073-014-0102-6 CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Diboun I, Wernisch L, Orengo CA, Koltzenburg M (2006) Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genome 7:252. doi: 10.1186/1471-2164-7-252 CrossRefGoogle Scholar
  27. 27.
    da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57. doi: 10.1038/nprot.2008.211 CrossRefGoogle Scholar
  28. 28.
    Wang Y, Rekaya R (2010) LSOSS: detection of cancer outlier differential gene expression. Biomark Insights 5:69–78CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    da Huang W, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucl Acids Res 37(1):1–13. doi: 10.1093/nar/gkn923 CrossRefGoogle Scholar
  30. 30.
    Joyseeree R, Abou Sabha R, Mueller H (2015) Applying machine learning to gait analysis data for disease identification. Stud Health Technol Inform 210:850–854PubMedGoogle Scholar
  31. 31.
    Ren X, Li Y, Liu X, Shen X, Gao W, Li J (2015) Computational identification of antigenicity-associated sites in the hemagglutinin protein of A/H1N1 seasonal influenza virus. PLoS One 10(5):e0126742. doi: 10.1371/journal.pone.0126742 CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Chang EJ, Kim HJ, Ha J, Kim HJ, Ryu J, Park KH, Kim UH, Lee ZH, Kim HM, Fisher DE, Kim HH (2007) Hyaluronan inhibits osteoclast differentiation via Toll-like receptor 4. J Cell Sci 120(Pt 1):166–176. doi: 10.1242/jcs.03310 PubMedGoogle Scholar
  33. 33.
    Hedrich CM, Hofmann SR, Pablik J, Morbach H, Girschick HJ (2013) Autoinflammatory bone disorders with special focus on chronic recurrent multifocal osteomyelitis (CRMO). Pediatr Rheumatol Online J 11(1):47. doi: 10.1186/1546-0096-11-47 CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Choe CH, Park IS, Park J, Yu KY, Jang H, Kim J, Jang YS (2015) Transmembrane protein 173 inhibits RANKL-induced osteoclast differentiation. FEBS Lett 589(7):836–841. doi: 10.1016/j.febslet.2015.02.018 CrossRefPubMedGoogle Scholar
  35. 35.
    Mori M, Tomono N, Yokota S (1995) [Coronary arteritis of Kawasaki disease unresponsive to high-dose intravenous gammaglobulin successfully treated with plasmapheresis]. Nihon Rinsho Men’eki Gakkai kaishi = Japanese. J Clin Immunol 18(3):282–288CrossRefGoogle Scholar
  36. 36.
    Wang Y, Wang W, Gong F, Fu S, Zhang Q, Hu J, Qi Y, Xie C, Zhang Y (2013) Evaluation of intravenous immunoglobulin resistance and coronary artery lesions in relation to Th1/Th2 cytokine profiles in patients with Kawasaki disease. Arthr Rheum 65(3):805–814. doi: 10.1002/art.37815 CrossRefGoogle Scholar
  37. 37.
    Shangguan W, Du Z, Yang H, Zhang Y, Song M, Dong W (2014) Effects of intravenous immunoglobulin upon the overexpression and over-activation of nuclear factor-kappaB and matrix metalloproteinase-9 in murine model of Kawasaki disease. Zhonghua yi xue za zhi 94(12):938–943PubMedGoogle Scholar
  38. 38.
    Wang CL, Wu YT, Liu CA, Kuo HC, Yang KD (2005) Kawasaki disease: infection, immunity and genetics. Pediatr Infect Dis J 24(11):998–1004CrossRefPubMedGoogle Scholar
  39. 39.
    Guo MM, Tseng WN, Ko CH, Pan HM, Hsieh KS, Kuo HC (2015) Th17- and Treg-related cytokine and mRNA expression are associated with acute and resolving Kawasaki disease. Allergy 70(3):310–318. doi: 10.1111/all.12558 CrossRefPubMedGoogle Scholar
  40. 40.
    Kim DS (2006) Kawasaki disease. Yonsei Med J 47(6):759–772CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Galeotti C, Kaveri SV, Bayry J (2015) Molecular and immunological biomarkers to predict IVIg response. Trends Mol Med 21(3):145–147. doi: 10.1016/j.molmed.2015.01.005 CrossRefPubMedGoogle Scholar
  42. 42.
    Liu R, He B, Gao F, Liu Q, Yi Q (2012) Association of the resistin gene promoter region polymorphism with Kawasaki disease in Chinese children. Med Inflamm 2012:356362. doi: 10.1155/2012/356362 Google Scholar
  43. 43.
    Mahachie John JM, Baurecht H, Rodriguez E, Naumann A, Wagenpfeil S, Klopp N, Mempel M, Novak N, Bieber T, Wichmann HE, Ring J, Illig T, Cattaert T, Van Steen K, Weidinger S (2010) Analysis of the high affinity IgE receptor genes reveals epistatic effects of FCER1A variants on eczema risk. Allergy 65(7):875–882. doi: 10.1111/j.1398-9995.2009.02297.x CrossRefPubMedGoogle Scholar
  44. 44.
    Roosild TP, Castronovo S, Villoso A, Ziemba A, Pizzorno G (2011) A novel structural mechanism for redox regulation of uridine phosphorylase 2 activity. J Struct Biol 176(2):229–237. doi: 10.1016/j.jsb.2011.08.002 CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Khor CC, Davila S, Breunis WB, Lee YC, Shimizu C, Wright VJ, Yeung RS, Tan DE, Sim KS, Wang JJ, Wong TY, Pang J, Mitchell P, Cimaz R, Dahdah N, Cheung YF, Huang GY, Yang W, Park IS, Lee JK, Wu JY, Levin M, Burns JC, Burgner D, Kuijpers TW, Hibberd ML (2011) Genome-wide association study identifies FCGR2A as a susceptibility locus for Kawasaki disease. Nat Genet 43(12):1241–1246. doi: 10.1038/ng.981 CrossRefPubMedGoogle Scholar
  46. 46.
    Kuo HC, Chao MC, Hsu YW, Lin YC, Huang YH, Yu HR, Hou MF, Liang CD, Yang KD, Chang WC, Wang CL (2012) CD40 Gene polymorphisms associated with susceptibility and coronary artery lesions of Kawasaki disease in the Taiwanese population. Sci World J 2012:520865. doi: 10.1100/2012/520865 CrossRefGoogle Scholar
  47. 47.
    Onouchi Y, Gunji T, Burns JC, Shimizu C, Newburger JW, Yashiro M, Nakamura Y, Yanagawa H, Wakui K, Fukushima Y, Kishi F, Hamamoto K, Terai M, Sato Y, Ouchi K, Saji T, Nariai A, Kaburagi Y, Yoshikawa T, Suzuki K, Tanaka T, Nagai T, Cho H, Fujino A, Sekine A, Nakamichi R, Tsunoda T, Kawasaki T, Nakamura Y, Hata A (2008) ITPKC functional polymorphism associated with Kawasaki disease susceptibility and formation of coronary artery aneurysms. Nat Genet 40(1):35–42. doi: 10.1038/ng.2007.59 CrossRefPubMedGoogle Scholar
  48. 48.
    Onouchi Y, Ozaki K, Burns JC, Shimizu C, Terai M, Hamada H, Honda T, Suzuki H, Suenaga T, Takeuchi T, Yoshikawa N, Suzuki Y, Yasukawa K, Ebata R, Higashi K, Saji T, Kemmotsu Y, Takatsuki S, Ouchi K, Kishi F, Yoshikawa T, Nagai T, Hamamoto K, Sato Y, Honda A, Kobayashi H, Sato J, Shibuta S, Miyawaki M, Oishi K, Yamaga H, Aoyagi N, Iwahashi S, Miyashita R, Murata Y, Sasago K, Takahashi A, Kamatani N, Kubo M, Tsunoda T, Hata A, Nakamura Y, Tanaka T (2012) A genome-wide association study identifies three new risk loci for Kawasaki disease. Nat Genet 44(5):517–521. doi: 10.1038/ng.2220 CrossRefPubMedGoogle Scholar
  49. 49.
    Kuo HC, Yu HR, Juo SH, Yang KD, Wang YS, Liang CD, Chen WC, Chang WP, Huang CF, Lee CP, Lin LY, Liu YC, Guo YC, Chiu CC, Chang WC (2011) CASP3 gene single-nucleotide polymorphism (rs72689236) and Kawasaki disease in Taiwanese children. J Hum Genet 56(2):161–165. doi: 10.1038/jhg.2010.154 CrossRefPubMedGoogle Scholar
  50. 50.
    Onouchi Y, Suzuki Y, Suzuki H, Terai M, Yasukawa K, Hamada H, Suenaga T, Honda T, Honda A, Kobayashi H, Takeuchi T, Yoshikawa N, Sato J, Shibuta S, Miyawaki M, Oishi K, Yamaga H, Aoyagi N, Iwahashi S, Miyashita R, Murata Y, Ebata R, Higashi K, Ozaki K, Sasago K, Tanaka T, Hata A (2013) ITPKC and CASP3 polymorphisms and risks for IVIG unresponsiveness and coronary artery lesion formation in Kawasaki disease. Pharmacogenomics J 13(1):52–59. doi: 10.1038/tpj.2011.45 CrossRefPubMedGoogle Scholar
  51. 51.
    Eleftheriou D, Levin M, Shingadia D, Tulloh R, Klein NJ, Brogan PA (2014) Management of Kawasaki disease. Arch Dis Child 99(1):74–83. doi: 10.1136/archdischild-2012-302841 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Lan He
    • 1
  • Youyu Sheng
    • 2
  • Chunyun Huang
    • 2
  • Guoying Huang
    • 1
    Email author
  1. 1.Pediatric Heart Center, Children’s Hospital, Fudan UniversityShanghaiChina
  2. 2.Department of DermatologyHuashan Hospital, Fudan UniversityShanghaiChina

Personalised recommendations