Trio-based whole exome sequencing in patients with suspected sporadic inborn errors of immunity: a retrospective cohort study

Abstract

Background: De novo variants (DNVs) are currently not routinely evaluated as part of diagnostic whole exome sequencing (WES) analysis in patients with suspected inborn errors of immunity (IEI).

Methods: This study explored the potential added value of systematic assessment of DNVs in a retrospective cohort of 123 patients with a suspected sporadic IEI that underwent patient-parent trio-based WES.

Results: A (likely) molecular diagnosis for (part) of the immunological phenotype was achieved in 12 patients with the diagnostic in silico IEI WES gene panel. Systematic evaluation of rare, non-synonymous DNVs in coding or splice site regions led to the identification of 14 candidate DNVs in genes with an annotated immune function. DNVs were found in IEI genes (NLRP3 and RELA) and in potentially novel candidate genes, including PSMB10, DDX1, KMT2C and FBXW11. The FBXW11 canonical splice site DNV was shown to lead to defective RNA splicing, increased NF-κB p65 signalling, and elevated IL-1β production in primary immune cells extracted from the patient with autoinflammatory disease.<

Conclusions: Our findings in this retrospective cohort study advocate the implementation of trio-based sequencing in routine diagnostics of patients with sporadic IEI. Furthermore, we provide functional evidence supporting a causal role for FBXW11 loss-of-function mutations in autoinflammatory disease.

Funding: This research was supported by grants from the European Union, ZonMW and the Radboud Institute for Molecular Life Sciences.

Data availability

The code used to filter DNA sequencing data for candidate de novo mutations (DNMs) and to generate output files is provided in Figure 1 - source code 1. Source data linked to Figure 1 - figure supplement 1 is provided as an additional, numerical data file. Source data for candidate DNM evaluation is provided in Figure 1 - source data 2. Source data linked to Figure 2 - figure supplement 1A is an uncropped, raw gel image used to create this figure. Source data linked to Figure 2B-D is provided as an additional, numerical data file. Raw DNA sequencing data of patients are not publicly available as it is confidential human subject data that would compromise anonymity. Researchers that are interested to access the sequencing data of our cohort are advised to contact the corresponding author, A. Hoischen (alexander.hoischen@radboudumc.nl). Anonymized subject data will be shared on request from qualified investigators for the purposes of replicating procedures and results, and for other non-commercial research purposes within the limits of participants' consent. Any data sharing will also require evaluation of the request by the regional Arnhem and Nijmegen Ethics Committee and the signature of a data transfer agreement (DTA).

Article and author information

Author details

  1. Anne Hebert

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8945-015X
  2. Annet Simons

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  3. Janneke HM Schuurs-Hoeijmakers

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  4. Hans JPM Koenen

    Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  5. Evelien Zonneveld-Huijssoon

    Department of Genetics, University Medical Center Groningen, Groningen, Netherlands
    Competing interests
    No competing interests declared.
  6. Stefanie SV Henriet

    Department of Pediatric Infectious Diseases and Immunology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  7. Ellen JH Schatorjé

    Department of Pediatric Rheumatology and Immunology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  8. Esther PAH Hoppenreijs

    Department of Pediatric Rheumatology and Immunology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  9. Erika KSM Leenders

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  10. Etienne JM Janssen

    Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, Netherlands
    Competing interests
    No competing interests declared.
  11. Gijs WE Santen

    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
    Competing interests
    No competing interests declared.
  12. Sonja A de Munnik

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  13. Simon V van Reijmersdal

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  14. Esther van Rijssen

    Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  15. Simone Kersten

    Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0251-5564
  16. Mihai G Netea

    Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2421-6052
  17. Ruben L Smeets

    Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
  18. Frank L van de Veerdonk

    Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    Frank L van de Veerdonk, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1121-4894
  19. Alexander Hoischen

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    For correspondence
    alexander.hoischen@radboudumc.nl
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8072-4476
  20. Caspar I van der Made

    Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0763-4017

Funding

European Research Council (No. 833247)

  • Mihai G Netea

ZonMw (Spinoza Grant)

  • Mihai G Netea

Radboud Institute for Molecular Life Sciences (Internal grant)

  • Mihai G Netea

ZonMw (Vidi)

  • Frank L van de Veerdonk

H2020 European Research Council (HDM-FUN)

  • Frank L van de Veerdonk

H2020 European Research Council (Solve-RD (No. 779257))

  • Alexander Hoischen

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Tony Yuen, Icahn School of Medicine at Mount Sinai, United States

Ethics

Human subjects: Patients and their parents provided written informed consent for in silico inborn errors of immunity whole exome sequencing gene panel analysis with or without exome-wide variant analysis in line with the diagnostic procedure and clinical question, as approved by the Medical Ethics Review Committee Arnhem-Nijmegen (2011/188 and 2020-7142). This research is in compliance with the principles of the Declaration of Helsinki.

Version history

  1. Received: March 8, 2022
  2. Preprint posted: April 18, 2022 (view preprint)
  3. Accepted: October 5, 2022
  4. Accepted Manuscript published: October 17, 2022 (version 1)
  5. Version of Record published: November 4, 2022 (version 2)

Copyright

© 2022, Hebert et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,683
    views
  • 238
    downloads
  • 4
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Anne Hebert
  2. Annet Simons
  3. Janneke HM Schuurs-Hoeijmakers
  4. Hans JPM Koenen
  5. Evelien Zonneveld-Huijssoon
  6. Stefanie SV Henriet
  7. Ellen JH Schatorjé
  8. Esther PAH Hoppenreijs
  9. Erika KSM Leenders
  10. Etienne JM Janssen
  11. Gijs WE Santen
  12. Sonja A de Munnik
  13. Simon V van Reijmersdal
  14. Esther van Rijssen
  15. Simone Kersten
  16. Mihai G Netea
  17. Ruben L Smeets
  18. Frank L van de Veerdonk
  19. Alexander Hoischen
  20. Caspar I van der Made
(2022)
Trio-based whole exome sequencing in patients with suspected sporadic inborn errors of immunity: a retrospective cohort study
eLife 11:e78469.
https://doi.org/10.7554/eLife.78469

Share this article

https://doi.org/10.7554/eLife.78469

Further reading

    1. Medicine
    2. Neuroscience
    Flora Moujaes, Jie Lisa Ji ... Alan Anticevic
    Research Article

    Background:

    Ketamine has emerged as one of the most promising therapies for treatment-resistant depression. However, inter-individual variability in response to ketamine is still not well understood and it is unclear how ketamine’s molecular mechanisms connect to its neural and behavioral effects.

    Methods:

    We conducted a single-blind placebo-controlled study, with participants blinded to their treatment condition. 40 healthy participants received acute ketamine (initial bolus 0.23 mg/kg, continuous infusion 0.58 mg/kg/hr). We quantified resting-state functional connectivity via data-driven global brain connectivity and related it to individual ketamine-induced symptom variation and cortical gene expression targets.

    Results:

    We found that: (i) both the neural and behavioral effects of acute ketamine are multi-dimensional, reflecting robust inter-individual variability; (ii) ketamine’s data-driven principal neural gradient effect matched somatostatin (SST) and parvalbumin (PVALB) cortical gene expression patterns in humans, while the mean effect did not; and (iii) behavioral data-driven individual symptom variation mapped onto distinct neural gradients of ketamine, which were resolvable at the single-subject level.

    Conclusions:

    These results highlight the importance of considering individual behavioral and neural variation in response to ketamine. They also have implications for the development of individually precise pharmacological biomarkers for treatment selection in psychiatry.

    Funding:

    This study was supported by NIH grants DP5OD012109-01 (A.A.), 1U01MH121766 (A.A.), R01MH112746 (J.D.M.), 5R01MH112189 (A.A.), 5R01MH108590 (A.A.), NIAAA grant 2P50AA012870-11 (A.A.); NSF NeuroNex grant 2015276 (J.D.M.); Brain and Behavior Research Foundation Young Investigator Award (A.A.); SFARI Pilot Award (J.D.M., A.A.); Heffter Research Institute (Grant No. 1–190420) (FXV, KHP); Swiss Neuromatrix Foundation (Grant No. 2016–0111) (FXV, KHP); Swiss National Science Foundation under the framework of Neuron Cofund (Grant No. 01EW1908) (KHP); Usona Institute (2015 – 2056) (FXV).

    Clinical trial number:

    NCT03842800

    1. Medicine
    Jinjing Chen, Ruoyu Wang ... Jongsook Kemper
    Research Article

    The nuclear receptor, farnesoid X receptor (FXR/NR1H4), is increasingly recognized as a promising drug target for metabolic diseases, including nonalcoholic steatohepatitis (NASH). Protein-coding genes regulated by FXR are well known, but whether FXR also acts through regulation of long non-coding RNAs (lncRNAs), which vastly outnumber protein-coding genes, remains unknown. Utilizing RNA-seq and global run-on sequencing (GRO-seq) analyses in mouse liver, we found that FXR activation affects the expression of many RNA transcripts from chromatin regions bearing enhancer features. Among these we discovered a previously unannotated liver-enriched enhancer-derived lncRNA (eRNA), termed FXR-induced non-coding RNA (Fincor). We show that Fincor is specifically induced by the hammerhead-type FXR agonists, including GW4064 and tropifexor. CRISPR/Cas9-mediated liver-specific knockdown of Fincor in dietary NASH mice reduced the beneficial effects of tropifexor, an FXR agonist currently in clinical trials for NASH and primary biliary cholangitis (PBC), indicating that amelioration of liver fibrosis and inflammation in NASH treatment by tropifexor is mediated in part by Fincor. Overall, our findings highlight that pharmacological activation of FXR by hammerhead-type agonists induces a novel eRNA, Fincor, contributing to the amelioration of NASH in mice. Fincor may represent a new drug target for addressing metabolic disorders, including NASH.