Trio-based whole exome sequencing in patients with suspected sporadic inborn errors of immunity: a retrospective cohort study
- Radboud University Nijmegen Medical Centre, Netherlands
- University Medical Center Groningen, Netherlands
- Maastricht University Medical Centre, Netherlands
- Leiden University Medical Center, Netherlands
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
Frank L van de Veerdonk
Alexander Hoischen
Caspar I van der Made
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.
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.
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.
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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
Further reading
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- Medicine
Background: Several fields have described low reproducibility of scientific research and poor accessibility in research reporting practices. Although previous reports have investigated accessible reporting practices that lead to reproducible research in other fields, to date, no study has explored the extent of accessible and reproducible research practices in cardiovascular science literature.
Methods: To study accessibility and reproducibility in cardiovascular research reporting, we screened 639 randomly selected articles published in 2019 in three top cardiovascular science publications: Circulation, the European Heart Journal, and the Journal of the American College of Cardiology (JACC). Of those 639 articles, 393 were empirical research articles. We screened each paper for accessible and reproducible research practices using a set of accessibility criteria including protocol, materials, data, and analysis script availability, as well as accessibility of the publication itself. We also quantified the consistency of open research practices within and across cardiovascular study types and journal formats.
Results: We identified that fewer than 2% of cardiovascular research publications provide sufficient resources (materials, methods, data, and analysis scripts) to fully reproduce their studies. Of the 639 articles screened, 393 were empirical research studies for which reproducibility could be assessed using our protocol, as opposed to commentaries or reviews. After calculating an accessibility score as a measure of the extent to which an article makes its resources available, we also showed that the level of accessibility varies across study types with a score of 0.08 for Case Studies or Case Series and 0.39 for Clinical Trials (p = 5.500E-5) and across journals (0.19 through 0.34, p = 1.230E-2). We further showed that there are significant differences in which study types share which resources.
Conclusion: Although the degree to which reproducible reporting practices are present in publications varies significantly across journals and study types, current cardiovascular science reports frequently do not provide sufficient materials, protocols, data, or analysis information to reproduce a study. In the future, having higher standards of accessibility mandated by either journals or funding bodies will help increase the reproducibility of cardiovascular research.
Funding: Authors Gabriel Heckerman, Arely Campos-Melendez, and Chisomaga Ekwueme were supported by an NIH R25 grant from the National Heart, Lung and Blood Institute (R25HL147666). Eileen Tzng was supported by an AHA Institutional Training Award fellowship (18UFEL33960207).
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- Cell Biology
- Medicine
Background:
It has been reported that loss of PCBP2 led to increased reactive oxygen species (ROS) production and accelerated cell aging. Knockdown of PCBP2 in HCT116 cells leads to significant downregulation of fibroblast growth factor 2 (FGF2). Here, we tried to elucidate the intrinsic factors and potential mechanisms of bone marrow mesenchymal stromal cells (BMSCs) aging from the interactions among PCBP2, ROS, and FGF2.
Methods:
Unlabeled quantitative proteomics were performed to show differentially expressed proteins in the replicative senescent human bone marrow mesenchymal stromal cells (RS-hBMSCs). ROS and FGF2 were detected in the loss-and-gain cell function experiments of PCBP2. The functional recovery experiments were performed to verify whether PCBP2 regulates cell function through ROS/FGF2-dependent ways.
Results:
PCBP2 expression was significantly lower in P10-hBMSCs. Knocking down the expression of PCBP2 inhibited the proliferation while accentuated the apoptosis and cell arrest of RS-hBMSCs. PCBP2 silence could increase the production of ROS. On the contrary, overexpression of PCBP2 increased the viability of both P3-hBMSCs and P10-hBMSCs significantly. Meanwhile, overexpression of PCBP2 led to significantly reduced expression of FGF2. Overexpression of FGF2 significantly offset the effect of PCBP2 overexpression in P10-hBMSCs, leading to decreased cell proliferation, increased apoptosis, and reduced G0/G1 phase ratio of the cells.
Conclusions:
This study initially elucidates that PCBP2 as an intrinsic aging factor regulates the replicative senescence of hBMSCs through the ROS-FGF2 signaling axis.
Funding:
This study was supported by the National Natural Science Foundation of China (82172474).
