학술논문
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19
Document Type
article
Author
Matuozzo, Daniela; Talouarn, Estelle; Marchal, Astrid; Zhang, Peng; Manry, Jeremy; Seeleuthner, Yoann; Zhang, Yu; Bolze, Alexandre; Chaldebas, Matthieu; Milisavljevic, Baptiste; Gervais, Adrian; Bastard, Paul; Asano, Takaki; Bizien, Lucy; Barzaghi, Federica; Abolhassani, Hassan; Abou Tayoun, Ahmad; Aiuti, Alessandro; Alavi Darazam, Ilad; Allende, Luis M; Alonso-Arias, Rebeca; Arias, Andrés Augusto; Aytekin, Gokhan; Bergman, Peter; Bondesan, Simone; Bryceson, Yenan T; Bustos, Ingrid G; Cabrera-Marante, Oscar; Carcel, Sheila; Carrera, Paola; Casari, Giorgio; Chaïbi, Khalil; Colobran, Roger; Condino-Neto, Antonio; Covill, Laura E; Delmonte, Ottavia M; El Zein, Loubna; Flores, Carlos; Gregersen, Peter K; Gut, Marta; Haerynck, Filomeen; Halwani, Rabih; Hancerli, Selda; Hammarström, Lennart; Hatipoğlu, Nevin; Karbuz, Adem; Keles, Sevgi; Kyheng, Christèle; Leon-Lopez, Rafael; Franco, Jose Luis; Mansouri, Davood; Martinez-Picado, Javier; Metin Akcan, Ozge; Migeotte, Isabelle; Morange, Pierre-Emmanuel; Morelle, Guillaume; Martin-Nalda, Andrea; Novelli, Giuseppe; Novelli, Antonio; Ozcelik, Tayfun; Palabiyik, Figen; Pan-Hammarström, Qiang; de Diego, Rebeca Pérez; Planas-Serra, Laura; Pleguezuelo, Daniel E; Prando, Carolina; Pujol, Aurora; Reyes, Luis Felipe; Rivière, Jacques G; Rodriguez-Gallego, Carlos; Rojas, Julian; Rovere-Querini, Patrizia; Schlüter, Agatha; Shahrooei, Mohammad; Sobh, Ali; Soler-Palacin, Pere; Tandjaoui-Lambiotte, Yacine; Tipu, Imran; Tresoldi, Cristina; Troya, Jesus; van de Beek, Diederik; Zatz, Mayana; Zawadzki, Pawel; Al-Muhsen, Saleh Zaid; Alosaimi, Mohammed Faraj; Alsohime, Fahad M; Baris-Feldman, Hagit; Butte, Manish J; Constantinescu, Stefan N; Cooper, Megan A; Dalgard, Clifton L; Fellay, Jacques; Heath, James R; Lau, Yu-Lung; Lifton, Richard P; Maniatis, Tom; Mogensen, Trine H; von Bernuth, Horst; Lermine, Alban; Vidaud, Michel
Source
Genome Medicine. 15(1)
Subject
Language
Abstract
BackgroundWe previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases of life-threatening COVID-19 in unvaccinated patients. Therefore, the determinants of life-threatening COVID-19 remain to be identified in ~ 80% of cases.MethodsWe report here a genome-wide rare variant burden association analysis in 3269 unvaccinated patients with life-threatening COVID-19, and 1373 unvaccinated SARS-CoV-2-infected individuals without pneumonia. Among the 928 patients tested for autoantibodies against type I IFN, a quarter (234) were positive and were excluded.ResultsNo gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was TLR7, with an OR of 27.68 (95%CI 1.5-528.7, P = 1.1 × 10-4) for biochemically loss-of-function (bLOF) variants. We replicated the enrichment in rare predicted LOF (pLOF) variants at 13 influenza susceptibility loci involved in TLR3-dependent type I IFN immunity (OR = 3.70[95%CI 1.3-8.2], P = 2.1 × 10-4). This enrichment was further strengthened by (1) adding the recently reported TYK2 and TLR7 COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1-2635.4], P = 3.4 × 10-3), and (2) considering as pLOF branchpoint variants with potentially strong impacts on splicing among the 15 loci (OR = 4.40[9%CI 2.3-8.4], P = 7.7 × 10-8). Finally, the patients with pLOF/bLOF variants at these 15 loci were significantly younger (mean age [SD] = 43.3 [20.3] years) than the other patients (56.0 [17.3] years; P = 1.68 × 10-5).ConclusionsRare variants of TLR3- and TLR7-dependent type I IFN immunity genes can underlie life-threatening COVID-19, particularly with recessive inheritance, in patients under 60 years old.