Abstract
Clinical variability in COVID-19 is partly explained by host genetic factors, including inborn errors of immunity. We investigated a patient with a heterozygous nonsense mutation in the TLR3 gene (p.Trp769*) by generating human-induced pluripotent stem cells (hiPSCs) and differentiating them into lung organoids (hLORGs). TLR3-mutated hLORGs showed reduced basal expression of TLR3 and downstream signaling genes. Following infection with a pseudotyped SARS-CoV-2 virus and live SARS-CoV-2, RNA-Seq and qPCR analyses revealed significant upregulation of fibrinogen genes (FGA, FGG), which are associated with severe COVID-19. Interestingly, TLR3 expression remained inducible upon infection, despite the loss-of-function mutation. Our patient-derived hLORG model recapitulates the pathophysiological features of the patient and provides a platform to investigate host–virus interactions and test targeted therapies for genetically at-risk individuals.
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The authors declare that RNA sequencing data are not publicly available due to patient privacy, but all other data supporting the findings of this study are available within the article and its supplementary material files, or from the corresponding author upon reasonable request.
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Acknowledgements
We thank the A. family individuals who participated in this study and gratefully acknowledge the support of NEGEDIA srl NEGEDIA for sequencing and data analysis services. We are grateful to the COVID Human Genetic Effort Consortium (https://www.covidhge.com/) for the ongoing exchange of information and for the scientific input. The authors acknowledge the valuable funding provided by the EU-Horizon-HLTH-2021 (ID: 101057100, UNDINE), Fondazione Telethon Core Grant, Armenise-Harvard Foundation Career Development Award, Italian Ministry of Health (Piano Operativo Salute Traiettoria 3, T3-AN-09, ‘Genomed’; Ricerca Finalizzata 2021, ‘genOMICA’; MCNT2 2023, ‘EUCARDIS’), the Italian Ministry of University and Research and the European Union (Next Generation EU – MUR-PRIN-2022, CUP 2022T7XP29 and 2022HM5LFW; Project PNC 0000001 D3-4-Health); LV was supported by an AIRC fellowship for Italy.
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Conceptualization: GN; Methodology: AL, PS, FC, and BR; Formal analysis: AL, PS, FC, BR and LV; Investigation: AL, PS, FC, BR, DA, GG, RDS, LV and GP; Resources: VLC, AMN, EC, LS, MB and PR; Writing—original draft: AL, PS, FC, and BR; Writing—reviewing & editing: GN; Visualization: AL, PS, FC, BR and DA; Supervision: DC, AN, FS, FL, GN; Funding acquisition: DC and GN. All authors read and approved the final manuscript.
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Davide Cacchiarelli is founder, shareholder, and consultant of NEGEDIA S.r.l.
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Latini, A., Spitalieri, P., Centofanti, F. et al. Modelling severe COVID-19 in TLR3-mutated hiPSCs-derived lung organoids. Cell Death Discov. (2025). https://doi.org/10.1038/s41420-025-02936-5
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DOI: https://doi.org/10.1038/s41420-025-02936-5
