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Journal of Clinical Immunology

, Volume 36, Issue 5, pp 462–471 | Cite as

Dominant Splice Site Mutations in PIK3R1 Cause Hyper IgM Syndrome, Lymphadenopathy and Short Stature

  • Slavé Petrovski
  • Roberta E. Parrott
  • Joseph L. Roberts
  • Hongxiang Huang
  • Jialong Yang
  • Balachandra Gorentla
  • Talal Mousallem
  • Endi Wang
  • Martin Armstrong
  • Duncan McHale
  • Nancie J. MacIver
  • David B. Goldstein
  • Xiao-Ping Zhong
  • Rebecca H. BuckleyEmail author
Original Article

Abstract

The purpose of this research was to use next generation sequencing to identify mutations in patients with primary immunodeficiency diseases whose pathogenic gene mutations had not been identified. Remarkably, four unrelated patients were found by next generation sequencing to have the same heterozygous mutation in an essential donor splice site of PIK3R1 (NM_181523.2:c.1425 + 1G > A) found in three prior reports. All four had the Hyper IgM syndrome, lymphadenopathy and short stature, and one also had SHORT syndrome. They were investigated with in vitro immune studies, RT-PCR, and immunoblotting studies of the mutation’s effect on mTOR pathway signaling. All patients had very low percentages of memory B cells and class-switched memory B cells and reduced numbers of naïve CD4+ and CD8+ T cells. RT-PCR confirmed the presence of both an abnormal 273 base-pair (bp) size and a normal 399 bp size band in the patient and only the normal band was present in the parents. Following anti-CD40 stimulation, patient’s EBV-B cells displayed higher levels of S6 phosphorylation (mTOR complex 1 dependent event), Akt phosphorylation at serine 473 (mTOR complex 2 dependent event), and Akt phosphorylation at threonine 308 (PI3K/PDK1 dependent event) than controls, suggesting elevated mTOR signaling downstream of CD40. These observations suggest that amino acids 435–474 in PIK3R1 are important for its stability and also its ability to restrain PI3K activity. Deletion of Exon 11 leads to constitutive activation of PI3K signaling. This is the first report of this mutation and immunologic abnormalities in SHORT syndrome.

Keywords

PIK3R1 splice site mutations Hyper IgM syndrome lymphadenopathy short stature SHORT syndrome mTOR pathway next generation sequencing 

Notes

Acknowledgments

This study was supported by the following grants: Baxter Healthcare Grant BT13-21694 to R.H.B. and NIH Grant R01 AI101206 to X-P. Z. Partial funding for this study was provided by UCB Celltech, including salary support for D.B.G. M.A. and D.M. are employees of UCB. The other authors declare no conflict of interest. S.P. is a National Health and Medical Research Council (NHMRC) CJ Martin Fellow. We thank our patients and their parents for participating in this study. We also thank B Krueger, J Bridges, Q Wang, N Ren, S Gewalt, S Kisselev, Y-F Lu, K Cronin, and N Walley for excellent technical support. We would like to acknowledge the following individuals for the contributions of control samples: W. B. Gallentine, E.L. Heinzen, A.M. Husain, K. N. Linney, M. A. Mikati, R. A. Radtke, and S. R. Sinha; J.P. McEvoy, A. Need, J. Silver, and M. Silver; D. H. Murdock and The MURDOCK Study Community Registry and Biorepository; G. Cavalleri, N. Delanty, and C. Depondt; J. Burke, C. Hulette, and K. Welsh-Bohmer; J. Milner; J. Hoover-Fong, N. L. Sobreira and D. Valle; E. J. Holtzman; W. L. Lowe; P. Lugar; S. M. Palmer; Z. Farfel, D. Lancet, E. Elon Pras; A. Poduri; M. Hauser; D. Marchuk; D. Koltai Attix, O. Chiba-Falek; E. T. Cirulli, V. Dixon and J. McEvoy; K. Schmader, S. McDonald, H. K. White, M. Yanamadala, and the Carol Woods and Croasdale Retirement Communities; R. Gbadegesin and M. Winn; D. Daskalakis; Q. Zhao; A. Holden and E. Behr; R. Brown; and S. Kerns and H. Oster. The collection of control samples was funded in part by Bryan ADRC NIA P30 AG028377, the Ellison Medical Foundation New Scholar award AG-NS-0441-08, an award from SAIC-Frederick, Inc. (M11-074), funding from Biogen Idec, NIMH awards RC2MH089915, R01MH097971, R01MH099216, and K01MH098126, the Epi4K Gene Discovery in Epilepsy study (NINDS U01-NS077303) and the Epilepsy Genome/Phenome Project (EPGP - NINDS U01-NS053998), and the Center for HIV/AIDS Vaccine Immunology (“CHAVI”) under a grant from the National Institute of Allergy and Infectious Diseases, National Institutes of Health (UO1AIO67854), NIAID (R01AI079088 and R01AI101206). Finally, the authors would also like to thank the Exome Aggregation Consortium and the groups that provided exome variant data for comparison. A full list of contributing groups can be found at http://exac.broadinstitute.org/about.

Supplementary material

10875_2016_281_MOESM1_ESM.jpg (2.5 mb)
ESM 1 Figure S1: Sanger sequencing traces of DNA sequence around the PIK3R1 donor splice site for each patient (1–4) and their parents (M = Mother, F = Father). Both forward (+) and reverse (−) directions are provided. Patients are heterozygous for the variant. The variant was not observed in the unaffected parents. Father of Patient 4 was unavailable. (JPEG 2560 kb)

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Slavé Petrovski
    • 1
  • Roberta E. Parrott
    • 2
  • Joseph L. Roberts
    • 2
  • Hongxiang Huang
    • 2
    • 3
  • Jialong Yang
    • 2
  • Balachandra Gorentla
    • 2
  • Talal Mousallem
    • 2
    • 4
  • Endi Wang
    • 5
  • Martin Armstrong
    • 6
  • Duncan McHale
    • 6
  • Nancie J. MacIver
    • 7
    • 8
  • David B. Goldstein
    • 1
  • Xiao-Ping Zhong
    • 2
    • 8
  • Rebecca H. Buckley
    • 2
    • 8
    Email author
  1. 1.Institute for Genomic MedicineColumbia UniversityNew YorkUSA
  2. 2.Department of Pediatrics, Division of Allergy and ImmunologyDuke University Medical CenterDurhamUSA
  3. 3.Department of Oncology, Nanfang HospitalSouthern Medical UniversityGuangzhouChina
  4. 4.Departments of Internal Medicine and PediatricsWake Forest University School of MedicineWinston-SalemUSA
  5. 5.Department of PathologyDuke University Medical CenterDurhamUSA
  6. 6.UCB NewMedicinesSloughUK
  7. 7.Department of Pediatrics, Division of EndocrinologyDuke University Medical CenterDurhamUSA
  8. 8.Department of ImmunologyDuke University Medical CenterDurhamUSA

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