Advertisement

International Journal of Hematology

, Volume 108, Issue 3, pp 319–328 | Cite as

Comprehensive molecular diagnosis of Epstein–Barr virus-associated lymphoproliferative diseases using next-generation sequencing

  • Shintaro Ono
  • Manabu Nakayama
  • Hirokazu Kanegane
  • Akihiro Hoshino
  • Saeko Shimodera
  • Hirofumi Shibata
  • Hisanori Fujino
  • Takahiro Fujino
  • Yuta Yunomae
  • Tsubasa Okano
  • Motoi Yamashita
  • Takahiro Yasumi
  • Kazushi Izawa
  • Masatoshi Takagi
  • Kohsuke Imai
  • Kejian Zhang
  • Rebecca Marsh
  • Capucine Picard
  • Sylvain Latour
  • Osamu Ohara
  • Tomohiro Morio
Original Article

Abstract

Epstein–Barr virus (EBV) is associated with several life-threatening diseases, such as lymphoproliferative disease (LPD), particularly in immunocompromised hosts. Some categories of primary immunodeficiency diseases (PIDs) including X-linked lymphoproliferative syndrome (XLP), are characterized by susceptibility and vulnerability to EBV infection. The number of genetically defined PIDs is rapidly increasing, and clinical genetic testing plays an important role in establishing a definitive diagnosis. Whole-exome sequencing is performed for diagnosing rare genetic diseases, but is both expensive and time-consuming. Low-cost, high-throughput gene analysis systems are thus necessary. We developed a comprehensive molecular diagnostic method using a two-step tailed polymerase chain reaction (PCR) and a next-generation sequencing (NGS) platform to detect mutations in 23 candidate genes responsible for XLP or XLP-like diseases. Samples from 19 patients suspected of having EBV-associated LPD were used in this comprehensive molecular diagnosis. Causative gene mutations (involving PRF1 and SH2D1A) were detected in two of the 19 patients studied. This comprehensive diagnosis method effectively detected mutations in all coding exons of 23 genes with sufficient read numbers for each amplicon. This comprehensive molecular diagnostic method using PCR and NGS provides a rapid, accurate, low-cost diagnosis for patients with XLP or XLP-like diseases.

Keywords

Epstein–Barr virus Hemophagocytic lymphohistiocytosis Lymphoproliferative disease Next-generation sequencing Primary immunodeficiency disease X-linked lymphoproliferative syndrome 

Notes

Acknowledgements

We thank the patients and their parents as well as the doctors who provided the samples. This study was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan, the Ministry of Health, Labour, and Welfare of Japan, and the Japan Blood Products Organization.

Compliance with ethical standards

Conflict of interest

We have no financial or other potential conflicts of interest to declare.

Supplementary material

12185_2018_2475_MOESM1_ESM.docx (155 kb)
Supplementary material 1 (DOCX 154 KB)

References

  1. 1.
    Young LS, Rickinson AB. Epstein–Barr virus: 40 years on. Nat Rev Cancer. 2004;4:757–68.CrossRefPubMedGoogle Scholar
  2. 2.
    Hislop AD, Taylor GS, Sauce D, Rickinson AB. Cellular responses to viral infection in humans: lessons from Epstein–Barr virus. Annu Rev Immunol. 2007;25:587–617.CrossRefPubMedGoogle Scholar
  3. 3.
    Taylor GS, Long HM, Brooks JM, Rickinson AB, Hislop AD. The immunology of Epstein–Barr virus-induced disease. Annu Rev Immunol. 2015;33:787–821.CrossRefPubMedGoogle Scholar
  4. 4.
    Thorley-Lawson DA, Gross A. Persistence of the Epstein–Barr virus and the origins of associated lymphomas. N Engl J Med. 2004;350:1328–37.CrossRefPubMedGoogle Scholar
  5. 5.
    Raab-Traub N, Flynn K. The structure of the termini of the Epstein–Barr virus as a marker of clonal cellular proliferation. Cell. 1986;47:883–9.CrossRefPubMedGoogle Scholar
  6. 6.
    Neria BF, Inghirami G, Knowles DM, Neequaye J, Magrath IT, et al. Epstein–Barr virus infection precedes clonal expansion in Burkitt’s and acquired immunodeficiency syndrome-associated lymphoma. Blood. 1991;77:1092–5.Google Scholar
  7. 7.
    Jones JF, Shurin S, Abramowsky C, Tubbs RR, Sciotto CG, Wahl R, et al. T-cell lymphomas containing Epstein–Barr viral DNA in patients with chronic Epstein–Barr virus infections. N Engl J Med. 1988;318:733–41.CrossRefPubMedGoogle Scholar
  8. 8.
    Andersson-Anvret M, Forsby N, Klein G, Henle W. Relationship between the Epstein–Barr virus and undifferentiated nasopharyngeal carcinoma: correlated nucleic acid hybridization and histopathological examination. Int J Cancer. 1977;20:486–94.CrossRefPubMedGoogle Scholar
  9. 9.
    Sullivan J, Sullivan L. Epstein–Barr virus-associated hemophagocytic syndrome: virological and immunopathological studies. Blood. 1985;65:1097–104.PubMedGoogle Scholar
  10. 10.
    Palendira U, Rickinson AB. Primary immunodeficiencies and the control of Epstein–Barr virus infection. Ann N Y Acad Sci. 2015;1356:22–44.CrossRefPubMedGoogle Scholar
  11. 11.
    Tangye SG, Palendira U, Edwards ESJ. Human immunity against EBV-lessons from the clinic. J Exp Med. 2017;214:269–83.CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Seemayer TA, Gross TG, Egeler RM, Pirruccello SJ, Davis JR, Kelly CM, et al. X-linked lymphoproliferative disease: twenty-five years after the discovery. Pediatr Res. 1995;38:471–8.CrossRefPubMedGoogle Scholar
  13. 13.
    Tangye SG. XLP: Clinical features and molecular etiology due to mutations in SH2D1A encoding SAP. J Clin Immunol 2014;34:772–9.CrossRefPubMedGoogle Scholar
  14. 14.
    Coffey AJ, Brooksbank RA, Brandau O, Oohashi T, Howell GR, Bye JM, et al. Host response to EBV infection in X-linked lymphoproliferative disease results from mutations in an SH2-domain encoding gene. Nat Genet. 1998;20:129–35.CrossRefPubMedGoogle Scholar
  15. 15.
    Sayos J, Wu C, Morra M, Wang N, Zhang X, Allen D, et al. The X-linked lymphoproliferative-disease gene product SAP regulates signals induced through the co-receptor SLAM. Nature. 1998;395:462–9.CrossRefPubMedGoogle Scholar
  16. 16.
    Rigaud S, Fondanèche M-C, Lambert N, Pasquier B, Mateo V, Soulas P, et al. XIAP deficiency in humans causes an X-linked lymphoproliferative syndrome. Nature. 2006;444:110–4.CrossRefPubMedGoogle Scholar
  17. 17.
    Ono S, Okano T, Hoshino A, Yanagimachi M, Hamamoto K, Nakazawa Y, et al. Hematopoietic stem cell transplantation for XIAP deficiency in Japan. J Clin Immunol. 2017;37:85–91.CrossRefPubMedGoogle Scholar
  18. 18.
    Rusmini M, Federici S, Caroli F, Grossi A, Baldi M, Obici L, et al. Next-generation sequencing and its initial applications for molecular diagnosis of systemic auto-inflammatory diseases. Ann Rheum Dis. 2016;75:1550–7.CrossRefPubMedGoogle Scholar
  19. 19.
    Nakayama M, Oda H, Nakagawa K, Yasumi T, Kawai T, Izawa K, et al. Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSEq. Biochem Biophys Rep. 2017;9:146–52.PubMedGoogle Scholar
  20. 20.
    Izawa K, Martin E, Soudais C, Bruneau J, Boutboul D, Rodriguez R, et al. Inherited CD70 deficiency in humans reveals a critical role for the CD70–CD27 pathway in immunity to Epstein–Barr virus infection. J Exp Med. 2017;214:73–89.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Abolhassani H, Edwards ESJ, Ikinciogullari A, Jing H, Borte S, Buggert M, et al. Combined immunodeficiency and Epstein–Barr virus-induced B cell malignancy in humans with inherited CD70 deficiency. J Exp Med. 2017;214:91–106.CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Kuehn HS, Ouyang W, Lo B, Deenick EK, Niemela JE, Avery DT, et al. Immune dysregulation in human subjects with heterozygous germline mutations in CTLA4. Science. 2014;345:1623–7.CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Schubert D, Bode C, Kenefeck R, Hou TZ, Wing JB, Kennedy A, et al. Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations. Nat Med. 2014;20:1410–6.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Greil C, Roether F, La Rosée P, Grimbacher B, Duerschmied D, Warnatz K. Rescue of cytokine storm due to HLH by hemoadsorption in a CTLA4-deficient patient. J Clin Immunol. 2017;37:273–6.CrossRefPubMedGoogle Scholar
  25. 25.
    zur Stadt U, Rohr J, Seifert W, Koch F, Grieve S, Pagel J, et al. Familial hemophagocytic lymphohistiocytosis type 5 (FHL-5) is caused by mutations in Munc18-2 and impaired binding to syntaxin 11. Am J Hum Genet. 2009;85:482–92.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Côte M, Ménager MM, Burgess A, Mahlaoui N, Picard C, Schaffner C, et al. Munc18-2 deficiency causes familial hemophagocytic lymphohistiocytosis type 5 and impairs cytotoxic granule exocytosis in patient NK cells. J Clin Invest. 2009;119:3765–73.CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Kreins AY, Ciancanelli MJ, Okada S, Kong X-F, Ramírez-Alejo N, Kilic SS, et al. Human TYK2 deficiency: mycobacterial and viral infections without hyper-IgE syndrome. J Exp Med. 2015;212:1641–62.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3-new capabilities and interfaces. Nucleic Acids Res 2012;40:e115CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Stepp SE, Dufourcq-Lagelouse R, Le Deist F, Bhawan S, Certain S, Mathew PA, et al. Perforin gene defects in familial hemophagocytic lymphohistiocytosis. Science. 1999;286:1957–9.CrossRefPubMedGoogle Scholar
  30. 30.
    Boztug H, Hirschmugl T, Holter W, Lakatos K, Kager L, Trapin D, et al. NF-κB1 haploinsufficiency causing immunodeficiency and EBV-driven lymphoproliferation. J Clin Immunol. 2016;36:533–40.CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Salzer E, Cagdas D, Hons M, Mace EM, Garncarz W, Petronczki ÖY, et al. RASGRP1 deficiency causes immunodeficiency with impaired cytoskeletal dynamics. Nat Immunol. 2016;17:1352–60.CrossRefPubMedGoogle Scholar
  32. 32.
    Schober T, Magg T, Laschinger M, Rohlfs M, Linhares ND, Puchalka J, et al. A human immunodeficiency syndrome caused by mutations in CARMIL2. Nat Commun. 2017;8:14209.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© The Japanese Society of Hematology 2018

Authors and Affiliations

  • Shintaro Ono
    • 1
    • 2
  • Manabu Nakayama
    • 3
  • Hirokazu Kanegane
    • 1
  • Akihiro Hoshino
    • 1
    • 4
  • Saeko Shimodera
    • 5
  • Hirofumi Shibata
    • 5
  • Hisanori Fujino
    • 6
  • Takahiro Fujino
    • 7
  • Yuta Yunomae
    • 8
  • Tsubasa Okano
    • 1
  • Motoi Yamashita
    • 1
  • Takahiro Yasumi
    • 5
  • Kazushi Izawa
    • 5
  • Masatoshi Takagi
    • 9
  • Kohsuke Imai
    • 9
  • Kejian Zhang
    • 10
  • Rebecca Marsh
    • 11
  • Capucine Picard
    • 12
    • 13
  • Sylvain Latour
    • 13
  • Osamu Ohara
    • 2
    • 3
  • Tomohiro Morio
    • 1
  1. 1.Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
  2. 2.Laboratory for Integrative GenomicsRIKEN Center for Integrative Medical Sciences (IMS)YokohamaJapan
  3. 3.Department of Technology DevelopmentKazusa DNA Research InstituteChibaJapan
  4. 4.Department of Lifetime Clinical ImmunologyTokyo Medical and Dental University (TMDU)TokyoJapan
  5. 5.Department of PediatricsKyoto University Graduate School of MedicineKyotoJapan
  6. 6.Department of PediatricsJapanese Red Cross Osaka HospitalOsakaJapan
  7. 7.Department of HematologyJapanese Red Cross Kyoto Daiichi HospitalKyotoJapan
  8. 8.Center for Stem Cell and Regenerative MedicineTokyo Medical and Dental University (TMDU)TokyoJapan
  9. 9.Department of Community Pediatrics, Perinatal and Maternal Medicine, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University (TMDU)TokyoJapan
  10. 10.Division of Human GeneticsCincinnati Children’s Hospital Medical CenterCincinnatiUSA
  11. 11.Division of Bone Marrow Transplantation and Immune DeficiencyCincinnati Children’s Hospital Medical CenterCincinnatiUSA
  12. 12.Study Center for Primary ImmunodeficienciesNecker-Enfants Malades Hospital, Assistance Publique Hôpitaux de Paris (APHP), Necker Medical SchoolParisFrance
  13. 13.Laboratory of Lymphocyte Activation and Susceptibility to EBV InfectionInstitut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Imagine InstitutParisFrance

Personalised recommendations