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Human Autosomal Recessive DNA Polymerase Delta 3 Deficiency Presenting as Omenn Syndrome

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Abstract

The DNA polymerase δ complex (PolD), comprising catalytic subunit POLD1 and accessory subunits POLD2, POLD3, and POLD4, is essential for DNA synthesis and is central to genome integrity. We identified, by whole exome sequencing, a homozygous missense mutation (c.1118A > C; p.K373T) in POLD3 in a patient with Omenn syndrome. The patient exhibited severely decreased numbers of naïve T cells associated with a restricted T-cell receptor repertoire and a defect in the early stages of TCR recombination. The patient received hematopoietic stem cell transplantation at age 6 months. He manifested progressive neurological regression and ultimately died at age 4 years. We performed molecular and functional analysis of the mutant POLD3 and assessed cell cycle progression as well as replication-associated DNA damage. Patient fibroblasts showed a marked defect in S-phase entry and an enhanced number of double-stranded DNA break-associated foci despite normal expression levels of PolD components. The cell cycle defect was rescued by transduction with WT POLD3. This study validates autosomal recessive POLD3 deficiency as a novel cause of profound T-cell deficiency and Omenn syndrome.

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Data Availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

Abbreviations

CADD:

Combined annotation dependent depletion

DSB:

Double strand breaks

HSCT:

Hematopoietic stem cell transplant

IEI:

Inborn error of immunity

IgH:

Immunoglobulin heavy chain

NHEJ:

Non-homologous end joining

PCNA:

Proliferating cell nuclear antigen

PolD:

Polymerase delta complex

Polζ:

Polymerase zeta complex

TLS:

Translesion synthesis

TRB:

T cell receptor B locus

WES:

Whole exome sequencing

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Acknowledgements

We acknowledge the Centre for Multimodal Oncology Research (C-MORE) at KU Leuven for the use of the ImageStream.We thank Dr Rebeca Perez-De Diego for fruitful discussion. We thank the parents of the patient for their trust.

Funding

This work was supported by UZ Leuven Klinische Onderzoeksraad Funding – KOOR. MRR was supported by an ESID fellowship. LE is supported by a PhD Fellowship from the Research Foundation – Flanders (FWO) (grant 11E0123N). SD is supported by a PhD Fellowship from the Research Foundation – Flanders (FWO) (grant 11F4421N). LDN is supported by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health (grant AI001222). IM is supported by the Jeffrey Modell Foundation.

Author information

Author notes

  1. Maria Rodrigo Riestra and Bethany A. Pillay These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Inborn Errors of Immunity, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium

    Maria Rodrigo Riestra, Bethany A. Pillay, Verena Kienapfel, Lisa Ehlers, Selket Delafontaine, Marjon Wouters, Anneleen Hombrouck, Leen Moens & Isabelle Meyts

  2. Laboratory of Adaptive Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium

    Mathijs Willemsen & Stephanie Humblet-Baron

  3. Laboratory of Onco-Hematology, Hôpital Necker Enfants-Malades, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France

    Antoine Pinton & Aurore Touzart

  4. INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France

    Antoine Pinton & Aurore Touzart

  5. Department of Pediatrics, Pediatric Pulmonology Division, University Hospitals Leuven, Leuven, Belgium

    Kate Sauer

  6. Department of Pediatrics, Pediatric Pulmonology Division, AZ Sint-Jan Brugge, Brugge, Belgium

    Kate Sauer

  7. Clinical and Diagnostic Immunology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium

    Xavier Bossuyt

  8. Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium

    Xavier Bossuyt

  9. Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium

    Arnout Voet

  10. NanoHealth and Optical Imaging Group, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium

    Stefaan J. Soenen

  11. Leuven Cancer Research Institute, Faculty of Medical Sciences, KU Leuven, Leuven, Belgium

    Stefaan J. Soenen

  12. Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria

    Cecilia Dominguez Conde

  13. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

    Cecilia Dominguez Conde

  14. Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven, Belgium

    Giorgia Bucciol & Isabelle Meyts

  15. Department of Pediatric Hematology and Oncology, St. Anna Children’s Hospital, Vienna, Austria

    Kaan Boztug

  16. Department of Pediatrics, Medical University of Vienna, Vienna, Austria

    Kaan Boztug

  17. Université Paris Cité, Institut Imagine, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Paris, France

    Frédéric Rieux-Laucat

  18. Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA

    Luigi D. Notarangelo

Authors
  1. Maria Rodrigo Riestra
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Contributions

Experiments, data collection, and analysis were performed by Maria Rodrigo Riestra, Bethany Pillay, Giorgia Bucciol, Xavier Bossuyt, Kate Sauer, and Leen Moens with assistance from Mathijs Willemsen, Verena Kienapfel, Lisa Ehlers, Selket Delafontaine, Marjon Wouters, Anneleen Hombrouck, Stephanie Humblet-Baron, Frédéric Rieux-Laucat, Cecilia Dominguez Conde, Kaan Boztug, and Luigi D. Notarangelo. Antoine Pinton and Aurore Touzart analyzed TRB and IgH data. Arnout Voet provided structural data. Stefaan J Soenen provided Imagestream facilities. Isabelle Meyts conceptualized and funded the study. The manuscript was written by Maria Rodrigo Riestra, Bethany Pillay, Giorgia Bucciol, and Isabelle Meyts, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Isabelle Meyts.

Ethics declarations

Ethics Approval

The Ethics Committee of the University Hospitals Leuven (UZLeuven) approved this study (S66910, S63807). The study was performed in compliance with the Declaration of Helsinki for research involving human subjects.

Consent to Participate

Written informed consent was obtained from the parents prior to DNA, PBMCs, and fibroblast isolation.

Consent for Publication

Informed consent was provided by the parents for the publication of the images in Fig. 1a and b.

Competing Interests

IM receives funding from CSL Behring and consultancy fees from Boehringer-Ingelheim, unrelated to this submission, paid to KU Leuven.

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Riestra, M.R., Pillay, B.A., Willemsen, M. et al. Human Autosomal Recessive DNA Polymerase Delta 3 Deficiency Presenting as Omenn Syndrome. J Clin Immunol 44, 2 (2024). https://doi.org/10.1007/s10875-023-01627-z

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