Rare variants in Toll-like receptor 7 results in functional impairment and downregulation of cytokine-mediated signaling in COVID-19 patients

Stefania Mantovani,Pier Giorgio Scotton,Maria Palmieri,David Bennett,Miriana D’Alessandro,Antonella D’Arminio Monforte,Davide Romani,Anna Gallì,Alessandra Vergori,Andrea Tommasi,Giuseppe Fiorentino,Agostino Ognibene,Ilaria Meloni,Margherita Baldassarri,Arianna Gabrieli,Anna Canaccini,Daniela Francisci,Silvia Zibellini,Paolo Piacentini,Mario Tumbarello,Maria Bandini,Carmelo Piscopo,Sara Amitrano,Elisabetta Schiaroli,Stefano Rusconi,Renzo Scaggiante,Stefano Baratti,Francesca Gatti,Elisa Benetti,Mario Capasso,Alessandra Renieri,Federico Franchi,Nicola Picchiotti,Sophie Venturelli,Silvia Cappelli,Valentina Anemoli,Francesca Mari,Roberta Russo,Luca Cantarini,Francesco Castelli,Achille Iolascon,Bruno Frediani,Matteo Siano,Eugenia Quirós-Roldán ,Arianna Emiliozzi,Raffaele Bruno,Agnese Verzuri,Sandro Panese,Cesira Nencioni,Laura Bergantini,Chiara Spertilli Raffaelli,Edoardo Conticini,Susanna Guerrini,Simona Marcantonio,Leonardo Croci,Maria Antonietta Mazzei,Andrea Antinori,Marco Feri,Matteo Della Monica,Diana Alaverdian,Marta Corridi,Federica Gaia Miraglia,Saverio Giuseppe Parisi,Danilo Tacconi,Susanna Croci,Mirella Bruttini,Alessandro Pancrazzi,Francesca Fava,Mario U Mondelli,Manola Pisani,Simone Furini,Federico Anedda,Barbara Rossetti,Immacolata Andolfo,Massimo Carella,Massimo Girardis,Alice Donati,Maria Lorubbio,Francesca Andretta,Isabella Zanella,Elena Desanctis,Gian Piero Caldarelli,Marco Castori,Null Author_Id ,Raffaele Scala,Sabino Scolletta,Melania Degli Antoni,Katia Capitani,Andrea Cossarizza,Massimo Vaghi,Sergio Daga,Marco Vecchia,Paolo Cameli,Chiara Fallerini,Luca Guidelli,Francesco Paciosi,Stefano Busani,Genni Spargi,Agostino Riva,Filippo Aucella

doi:10.1038/s41435-021-00157-1

Stefania Mantovani, Pier Giorgio Scotton + Show 98 more

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https://doi.org/10.1038/s41435-021-00157-1

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Toll-like receptors (TLR) are crucial components in the initiation of innate immune responses to a variety of pathogens, triggering the production of pro-inflammatory cytokines and type I and II interferons, which are responsible for innate antiviral responses. Among the different TLRs, TLR7 recognizes several single-stranded RNA viruses including SARS-CoV-2. We and others identified rare loss-of-function variants in X-chromosomal TLR7 in young men with severe COVID-19 and with no prior history of major chronic diseases, that were associated with impaired TLR7 signaling as well as type I and II IFN responses. Here, we performed RNA sequencing to investigate transcriptome variations following imiquimod stimulation of peripheral blood mononuclear cells isolated from patients carrying previously identified hypomorphic, hypofunctional, and loss-of-function TLR7 variants. Our investigation revealed a profound impairment of the TLR7 pathway in patients carrying loss-of-function variants. Of note, a failure in IFNγ upregulation following stimulation was also observed in cells harboring the hypofunctional and hypomorphic variants. We also identified new TLR7 variants in severely affected male patients for which a functional characterization of the TLR7 pathway was performed demonstrating a decrease in mRNA levels in the IFNα, IFNγ, RSAD2, ACOD1, IFIT2, and CXCL10 genes.

Highlights

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1], has rapidly developed into a global pandemic of enormous consequences
TLR7 stimulation induced a strong response in healthy donors (HDs) with 211 genes significantly upregulated (log2 fold change (FC) ≥ 1.5; adjusted p value ≤ 0.05) and 19 downregulated genes compared with unstimulated peripheral blood mononuclear cells (PBMC)
RNAseq analysis in patients carrying LOF variants showed that none had genes with an adjusted p value ≤ 0.05 (Fig. 1C), suggesting a profound impairment of the TLR7 pathway

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Introduction

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1], has rapidly developed into a global pandemic of enormous consequences. To gain insight into TLR7-linked mechanisms of severe COVID19, we performed RNA sequencing (RNA-Seq) to carefully characterize transcriptome variations following IMQ stimulation of peripheral blood mononuclear cells (PBMC) isolated from patients carrying previously identified LOF TLR7 variants [5]. We found new TLR7 variants in severely affected males for which functional characterization of the pathway was performed.

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