Journal of Clinical Immunology

, Volume 39, Issue 2, pp 207–215 | Cite as

Alternative Splicing Rescues Loss of Common Gamma Chain Function and Results in IL-21R-like Deficiency

  • David Illig
  • Marta Navratil
  • Jadranka Kelečić
  • Raffaele Conca
  • Iva Hojsak
  • Oleg Jadrešin
  • Marijana Ćorić
  • Jurica Vuković
  • Meino Rohlfs
  • Sebastian Hollizeck
  • Jens Bohne
  • Christoph Klein
  • Daniel KotlarzEmail author
Original Article


Inborn errors in interleukin 2 receptor, gamma (IL2RG) perturb signaling of the common gamma chain family cytokines and cause severe combined immunodeficiency (SCID). Here, we report two brothers suffering from chronic cryptosporidiosis, severe diarrhea, and cholangitis. Pan T, B, and NK cell numbers were normal, but immunophenotyping revealed defective B cell differentiation. Using whole exome sequencing, we identified a base pair deletion in the first exon of IL2RG predicted to cause a frameshift and premature stop. However, flow cytometry revealed normal surface expression of the IL-2Rγ chain. While IL-2, IL-7, and IL-15 signaling showed only mild defects of STAT5 phosphorylation in response to the respective cytokines, IL-4- and IL-21-induced phosphorylation of STAT3 and STAT6 was markedly reduced. Examination of RNA isoforms detected alternative splicing downstream of IL2RG exon 1 in both patients resulting in resolution of the predicted frameshift and 16 mutated amino acids. In silico modeling suggested that the IL-2Rγ mutation reduces the stabilization of IL-4 and IL-21 cytokine binding by affecting the N-terminal domain of the IL-2Rγ. Thus, our study shows that IL2RG deficiency can be associated with differential signaling defects. Confounding effects of alternative splicing may partially rescue genetic defects and should be considered in patients with inborn errors of immunity.


SCID immunodeficiency IL-21R IL-2R splicing 



Our work is dedicated to the patients who sadly succumbed during the course of our studies. We thank the medical staff at the Departments of Pulmonology, Allergology, Rheumatology and Clinical Immunology and the Referral Center for Pediatric Gastroenterology and Nutrition at the Children’s Hospital Zagreb. We acknowledge the assistance of the Next-Generation Sequencing Facility and the Flow Cytometry Core Facility at the Dr. von Hauner Children’s Hospital.

Authorship Contributions

D.I. designed and conducted experiments and analyzed the data. R.C. supported immunophenotypical analysis. M.N., J.K., I.H., and O.J., recruited and clinically characterized the patients and were critical in the interpretation of the human data. M.Ć. performed histological analysis and J.V. performed pre-transplant hepatological evaluation. M.R. conducted whole-exome sequencing and S.H. performed the bioinformatics analysis of sequencing data. J.B. interpreted splicing mechanisms. C.K. and D.K. conceived the study design, supervised D.I., and recruited study participants. D.I., C.K., and D.K. wrote the draft of the manuscript. All authors interpreted the data and approved the final version of manuscript.

Funding Information

This work has been supported by The Leona M. and Harry B. Helmsley Charitable Trust, the Collaborative Research Consortium SFB1054 project A05 (DFG), PID-NET (BMBF), BioSysNet, the European Research Council, the Gottfried–Wilhelm–Leibniz Program (DFG), the DAAD network on ‘Rare Diseases and Personalized Therapies’, the German Center for Infection Research (DZIF), and the Care-for-Rare Foundation. D.I. was funded by the Hanns-Seidel-Stiftung and received ideational support by the Studienstiftung des deutschen Volkes. D.K. has been a scholar funded by the Else Kröner-Fresenius-Stiftung, the Daimler und Benz Stiftung, and the Reinhard Frank-Stiftung.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflicts of interest.

Supplementary material

10875_2019_606_MOESM1_ESM.docx (180 kb)
ESM 1 (DOCX 180 kb)


  1. 1.
    Kalman L, Lindegren ML, Kobrynski L, Vogt R, Hannon H, Howard JT, et al. Mutations in genes required for T-cell development: IL7R, CD45, IL2RG, JAK3, RAG1, RAG2, ARTEMIS, and ADA and severe combined immunodeficiency: HuGE review. Genet Med. 2004;6:16–26.CrossRefGoogle Scholar
  2. 2.
    Stephan JL, Vlekova V, Le Deist F, Blanche S, Donadieu J, De Saint-Basile G, et al. Severe combined immunodeficiency: a retrospective single-center study of clinical presentation and outcome in 117 patients. J Pediatr. 1993;123:564–72.CrossRefGoogle Scholar
  3. 3.
    Buckley RH, Schiff RI, Schiff SE, Markert ML, Williams LW, Harville TO, et al. Human severe combined immunodeficiency: genetic, phenotypic, and functional diversity in one hundred eight infants. J Pediatr. 1997;130:378–87.CrossRefGoogle Scholar
  4. 4.
    Felgentreff K, Perez-Becker R, Speckmann C, Schwarz K, Kalwak K, Markelj G, et al. Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency. Clin Immunol. 2011;141:73–82.CrossRefGoogle Scholar
  5. 5.
    Buckley RH. Molecular defects in human severe combined immunodeficiency and approaches to immune reconstitution. Annu Rev Immunol. 2004;22:625–55.CrossRefGoogle Scholar
  6. 6.
    Rochman Y, Spolski R, Leonard WJ. New insights into the regulation of T cells by gamma(c) family cytokines. Nat Rev Immunol. 2009;9:480–90.CrossRefGoogle Scholar
  7. 7.
    Puck JM, Pepper AE, Henthorn PS, Candotti F, Isakov J, Whitwam T, et al. Mutation analysis of IL2RG in human X-linked severe combined immunodeficiency. Blood. 1997;89:1968–77.Google Scholar
  8. 8.
    Fischer A. Severe combined immunodeficiencies (SCID). Clin Exp Immunol. 2000;122:143–9.CrossRefGoogle Scholar
  9. 9.
    Fuchs S, Rensing-Ehl A, Erlacher M, Vraetz T, Hartjes L, Janda A, et al. Patients with T(+)/low NK(+) IL-2 receptor gamma chain deficiency have differentially-impaired cytokine signaling resulting in severe combined immunodeficiency. Eur J Immunol. 2014;44:3129–40. CrossRefGoogle Scholar
  10. 10.
    Speckmann C, Pannicke U, Wiech E, Schwarz K, Fisch P, Friedrich W, et al. Clinical and immunologic consequences of a somatic reversion in a patient with X-linked severe combined immunodeficiency. Blood. 2008;112:4090–7.CrossRefGoogle Scholar
  11. 11.
    Stephan V, Wahn V, Le Deist F, Dirksen U, Broker B, Muller-Fleckenstein I, et al. Atypical X-linked severe combined immunodeficiency due to possible spontaneous reversion of the genetic defect in T cells. N Engl J Med. 1996;335:1563–7.CrossRefGoogle Scholar
  12. 12.
    Kotlarz D, Marquardt B, Baroy T, Lee WS, Konnikova L, Hollizeck S, et al. Human TGF-beta1 deficiency causes severe inflammatory bowel disease and encephalopathy. Nat Genet. 2018;50:344–8. CrossRefGoogle Scholar
  13. 13.
    Wang X, Rickert M, Garcia KC. Structure of the quaternary complex of interleukin-2 with its alpha, beta, and gammac receptors. Science. 2005;310:1159–63.CrossRefGoogle Scholar
  14. 14.
    LaPorte SL, Juo ZS, Vaclavikova J, Colf LA, Qi X, Heller NM, et al. Molecular and structural basis of cytokine receptor pleiotropy in the interleukin-4/13 system. Cell. 2008;132:259–72.CrossRefGoogle Scholar
  15. 15.
    Ring AM, Lin JX, Feng D, Mitra S, Rickert M, Bowman GR, et al. Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15. Nat Immunol. 2012;13:1187–95.CrossRefGoogle Scholar
  16. 16.
    Kotlarz D, Zietara N, Uzel G, Weidemann T, Braun CJ, Diestelhorst J, et al. Loss-of-function mutations in the IL-21 receptor gene cause a primary immunodeficiency syndrome. J Exp Med. 2013;210:433–43.Google Scholar
  17. 17.
    Kochetov AV. Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays. 2008;30:683–91.CrossRefGoogle Scholar
  18. 18.
    Lalonde S, Stone OA, Lessard S, Lavertu A, Desjardins J, Beaudoin M, et al. Frameshift indels introduced by genome editing can lead to in-frame exon skipping. PLoS One. 2017;12:e0178700.CrossRefGoogle Scholar
  19. 19.
    Wada T, Yasui M, Toma T, Nakayama Y, Nishida M, Shimizu M, et al. Detection of T lymphocytes with a second-site mutation in skin lesions of atypical X-linked severe combined immunodeficiency mimicking Omenn syndrome. Blood. 2008;112:1872–5.CrossRefGoogle Scholar
  20. 20.
    Stauber DJ, Debler EW, Horton PA, Smith KA, Wilson IA. Crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor. Proc Natl Acad Sci U S A. 2006;103:2788–93.CrossRefGoogle Scholar
  21. 21.
    Kumaki S, Ishii N, Minegishi M, Tsuchiya S, Cosman D, Sugamura K, et al. Functional role of interleukin-4 (IL-4) and IL-7 in the development of X-linked severe combined immunodeficiency. Blood. 1999;93:607–12. Google Scholar
  22. 22.
    Scotti MM, Swanson MS. RNA mis-splicing in disease. Nat Rev Genet. 2016;17:19–32.CrossRefGoogle Scholar
  23. 23.
    Rickert M, Wang X, Boulanger MJ, Goriatcheva N, Garcia KC. The structure of interleukin-2 complexed with its alpha receptor. Science. 2005;308:1477–80.CrossRefGoogle Scholar
  24. 24.
    McElroy CA, Dohm JA, Walsh ST. Structural and biophysical studies of the human IL-7/IL-7Ralpha complex. Structure. 2009;17:54–65. CrossRefGoogle Scholar
  25. 25.
    Zhang JL, Foster D, Sebald W. Human IL-21 and IL-4 bind to partially overlapping epitopes of common gamma-chain. Biochem Biophys Res Commun. 2003;300:291–6.CrossRefGoogle Scholar
  26. 26.
    Matthews DJ, Clark PA, Herbert J, Morgan G, Armitage RJ, Kinnon C, et al. Function of the interleukin-2 (IL-2) receptor gamma-chain in biologic responses of X-linked severe combined immunodeficient B cells to IL-2, IL-4, IL-13, and IL-15. Blood. 1995;85:38–42.Google Scholar
  27. 27.
    Matthews DJ, Hibbert L, Friedrich K, Minty A, Callard RE. X-SCID B cell responses to interleukin-4 and interleukin-13 are mediated by a receptor complex that includes the interleukin-4 receptor alpha chain (p140) but not the gamma c chain. Eur J Immunol. 1997;27:116–21.CrossRefGoogle Scholar
  28. 28.
    Lin JX, Migone TS, Tsang M, Friedmann M, Weatherbee JA, Zhou L, et al. The role of shared receptor motifs and common Stat proteins in the generation of cytokine pleiotropy and redundancy by IL-2, IL-4, IL-7, IL-13, and IL-15. Immunity. 1995;2:331–9.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • David Illig
    • 1
  • Marta Navratil
    • 2
    • 3
  • Jadranka Kelečić
    • 4
  • Raffaele Conca
    • 1
  • Iva Hojsak
    • 3
    • 5
    • 6
  • Oleg Jadrešin
    • 5
  • Marijana Ćorić
    • 7
  • Jurica Vuković
    • 8
  • Meino Rohlfs
    • 1
  • Sebastian Hollizeck
    • 1
  • Jens Bohne
    • 9
  • Christoph Klein
    • 1
  • Daniel Kotlarz
    • 1
    Email author
  1. 1.Dr. von Hauner Children’s Hospital, Department of PediatricsUniversity Hospital, LMU MunichMunichGermany
  2. 2.Department of Pulmonology, Allergology, Rheumatology and Clinical ImmunologyChildren’s Hospital ZagrebZagrebCroatia
  3. 3.School of MedicineUniversity J.J. StrossmayerOsijekCroatia
  4. 4.Department of Pediatrics, Division of Clinical Immunology, Allergology, Respiratory Diseases and RheumatologyUniversity Hospital Centre ZagrebZagrebCroatia
  5. 5.Referral Center for Pediatric Gastroenterology and NutritionChildren’s Hospital ZagrebZagrebCroatia
  6. 6.School of MedicineUniversity of ZagrebZagrebCroatia
  7. 7.Department of Pathology and CytologyUniversity Hospital Centre ZagrebZagrebCroatia
  8. 8.Division of Pediatric Gastroenterology, Hepatology and NutritionUniversity Hospital Centre ZagrebZagrebCroatia
  9. 9.Institute for VirologyHannover Medical SchoolHannoverGermany

Personalised recommendations