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Article: Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

TitleRare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19
Authors
Matuozzo, DTalouarn, EMarchal, AZhang, PManry, JSeeleuthner, YZhang, YBolze, AChaldebas, MMilisavljevic, BGervais, ABastard, PAsano, TBizien, LBarzaghi, FAbolhassani, HAbou, Tayoun, AAiuti, AAlavi, Darazam, IAllende, LMAlonso-Arias, RArias, AAAytekin, GBergman, PBondesan, SBryceson, YTBustos, IGCabrera-Marante, OCarcel, SCarrera, PCasari, GChaïbi, KColobran, RCondino-Neto, ACovill, LEDelmonte, OMEl, Zein, LFlores, CGregersen, PKGut, MHaerynck, FHalwani, RHancerli, SHammarström, LHatipoğlu, NKarbuz, AKeles, SKyheng, CLeon-Lopez, RFranco, JLMansouri, DMartinez-Picado, JMetin, Akcan, OMigeotte, IMorange, PEMorelle, GMartin-Nalda, ANovelli, GNovelli, AOzcelik, TPalabiyik, FPan-Hammarström, Qde, Diego, RPPlanas-Serra, LPleguezuelo, DEPrando, CPujol, AReyes, LFRivière, JGRodriguez-Gallego, CRojas, JRovere-Querini, PSchlüter, AShahrooei, MSobh, ASoler-Palacin, PTandjaoui-Lambiotte, YTipu, ITresoldi, CTroya, Jvan, de, Beek, DZatz, MZawadzki, PAl-Muhsen, SZAlosaimi, MFAlsohime, FMBaris-Feldman, HButte, MJConstantinescu, SNCooper, MADalgard, CLFellay, JHeath, JRLau, YLLifton, RPManiatis, TMogensen, THvon Bernuth, HLermine, AVidaud, MBoland, ADeleuze, JFNussbaum, RKahn-Kirby, AMentre, FTubiana, SGorochov, GTubach, FHausfater, PCOVID Human Genetic Effort,COVIDeF Study Group,French COVID Cohort Study Group,CoV-Contact Cohort,COVID-STORM Clinicians,COVID Clinicians,Orchestra Working Group,Amsterdam UMC Covid-19 Biobank,NIAID-USUHS COVID Study Group,Meyts, IZhang, SYPuel, ANotarangelo, LDBoisson-Dupuis, SSu, HCBoisson, BJouanguy, ECasanova, JLZhang, QAbel, LCobat, A
KeywordsCOVID-19
Immunity
Rare variants
Type I interferon
Issue Date5-Apr-2023
PublisherBioMed Central
Citation
Genome Medicine, 2023, v. 15, n. 1 How to Cite?
Abstract

Background

We 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.

Methods

We 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.

Results

No 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).

Conclusions

Rare 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.


Persistent Identifierhttp://hdl.handle.net/10722/331829
ISSN
2023 Impact Factor: 10.4
2023 SCImago Journal Rankings: 4.975
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorMatuozzo, D-
dc.contributor.authorTalouarn, E-
dc.contributor.authorMarchal, A-
dc.contributor.authorZhang, P-
dc.contributor.authorManry, J-
dc.contributor.authorSeeleuthner, Y-
dc.contributor.authorZhang, Y-
dc.contributor.authorBolze, A-
dc.contributor.authorChaldebas, M-
dc.contributor.authorMilisavljevic, B-
dc.contributor.authorGervais, A-
dc.contributor.authorBastard, P-
dc.contributor.authorAsano, T-
dc.contributor.authorBizien, L-
dc.contributor.authorBarzaghi, F-
dc.contributor.authorAbolhassani, H-
dc.contributor.authorAbou, Tayoun, A-
dc.contributor.authorAiuti, A-
dc.contributor.authorAlavi, Darazam, I-
dc.contributor.authorAllende, LM-
dc.contributor.authorAlonso-Arias, R-
dc.contributor.authorArias, AA-
dc.contributor.authorAytekin, G-
dc.contributor.authorBergman, P-
dc.contributor.authorBondesan, S-
dc.contributor.authorBryceson, YT-
dc.contributor.authorBustos, IG-
dc.contributor.authorCabrera-Marante, O-
dc.contributor.authorCarcel, S-
dc.contributor.authorCarrera, P-
dc.contributor.authorCasari, G-
dc.contributor.authorChaïbi, K-
dc.contributor.authorColobran, R-
dc.contributor.authorCondino-Neto, A-
dc.contributor.authorCovill, LE-
dc.contributor.authorDelmonte, OM-
dc.contributor.authorEl, Zein, L-
dc.contributor.authorFlores, C-
dc.contributor.authorGregersen, PK-
dc.contributor.authorGut, M-
dc.contributor.authorHaerynck, F-
dc.contributor.authorHalwani, R-
dc.contributor.authorHancerli, S-
dc.contributor.authorHammarström, L-
dc.contributor.authorHatipoğlu, N-
dc.contributor.authorKarbuz, A-
dc.contributor.authorKeles, S-
dc.contributor.authorKyheng, C-
dc.contributor.authorLeon-Lopez, R-
dc.contributor.authorFranco, JL-
dc.contributor.authorMansouri, D-
dc.contributor.authorMartinez-Picado, J-
dc.contributor.authorMetin, Akcan, O-
dc.contributor.authorMigeotte, I-
dc.contributor.authorMorange, PE-
dc.contributor.authorMorelle, G-
dc.contributor.authorMartin-Nalda, A-
dc.contributor.authorNovelli, G-
dc.contributor.authorNovelli, A-
dc.contributor.authorOzcelik, T-
dc.contributor.authorPalabiyik, F-
dc.contributor.authorPan-Hammarström, Q-
dc.contributor.authorde, Diego, RP-
dc.contributor.authorPlanas-Serra, L-
dc.contributor.authorPleguezuelo, DE-
dc.contributor.authorPrando, C-
dc.contributor.authorPujol, A-
dc.contributor.authorReyes, LF-
dc.contributor.authorRivière, JG-
dc.contributor.authorRodriguez-Gallego, C-
dc.contributor.authorRojas, J-
dc.contributor.authorRovere-Querini, P-
dc.contributor.authorSchlüter, A-
dc.contributor.authorShahrooei, M-
dc.contributor.authorSobh, A-
dc.contributor.authorSoler-Palacin, P-
dc.contributor.authorTandjaoui-Lambiotte, Y-
dc.contributor.authorTipu, I-
dc.contributor.authorTresoldi, C-
dc.contributor.authorTroya, J-
dc.contributor.authorvan, de, Beek, D-
dc.contributor.authorZatz, M-
dc.contributor.authorZawadzki, P-
dc.contributor.authorAl-Muhsen, SZ-
dc.contributor.authorAlosaimi, MF-
dc.contributor.authorAlsohime, FM-
dc.contributor.authorBaris-Feldman, H-
dc.contributor.authorButte, MJ-
dc.contributor.authorConstantinescu, SN-
dc.contributor.authorCooper, MA-
dc.contributor.authorDalgard, CL-
dc.contributor.authorFellay, J-
dc.contributor.authorHeath, JR-
dc.contributor.authorLau, YL-
dc.contributor.authorLifton, RP-
dc.contributor.authorManiatis, T-
dc.contributor.authorMogensen, TH-
dc.contributor.authorvon Bernuth, H-
dc.contributor.authorLermine, A-
dc.contributor.authorVidaud, M-
dc.contributor.authorBoland, A-
dc.contributor.authorDeleuze, JF-
dc.contributor.authorNussbaum, R-
dc.contributor.authorKahn-Kirby, A-
dc.contributor.authorMentre, F-
dc.contributor.authorTubiana, S-
dc.contributor.authorGorochov, G-
dc.contributor.authorTubach, F-
dc.contributor.authorHausfater, P-
dc.contributor.authorCOVID Human Genetic Effort,-
dc.contributor.authorCOVIDeF Study Group,-
dc.contributor.authorFrench COVID Cohort Study Group,-
dc.contributor.authorCoV-Contact Cohort,-
dc.contributor.authorCOVID-STORM Clinicians,-
dc.contributor.authorCOVID Clinicians,-
dc.contributor.authorOrchestra Working Group,-
dc.contributor.authorAmsterdam UMC Covid-19 Biobank,-
dc.contributor.authorNIAID-USUHS COVID Study Group,-
dc.contributor.authorMeyts, I-
dc.contributor.authorZhang, SY-
dc.contributor.authorPuel, A-
dc.contributor.authorNotarangelo, LD-
dc.contributor.authorBoisson-Dupuis, S-
dc.contributor.authorSu, HC-
dc.contributor.authorBoisson, B-
dc.contributor.authorJouanguy, E-
dc.contributor.authorCasanova, JL-
dc.contributor.authorZhang, Q-
dc.contributor.authorAbel, L-
dc.contributor.authorCobat, A-
dc.date.accessioned2023-09-21T06:59:17Z-
dc.date.available2023-09-21T06:59:17Z-
dc.date.issued2023-04-05-
dc.identifier.citationGenome Medicine, 2023, v. 15, n. 1-
dc.identifier.issn1756-994X-
dc.identifier.urihttp://hdl.handle.net/10722/331829-
dc.description.abstract<h3>Background</h3><p>We 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.</p><h3>Methods</h3><p>We 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.</p><h3>Results</h3><p>No gene reached genome-wide significance. Under a recessive model, the most significant gene with at-risk variants was <em>TLR7</em>, with an OR of 27.68 (95%CI 1.5–528.7, <em>P</em> = 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], <em>P</em> = 2.1 × 10−4). This enrichment was further strengthened by (1) adding the recently reported <em>TYK2</em> and <em>TLR7</em> COVID-19 loci, particularly under a recessive model (OR = 19.65[95%CI 2.1–2635.4], <em>P</em> = 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], <em>P</em> = 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; <em>P</em> = 1.68 × 10−5).</p><h3>Conclusions</h3><p>Rare 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.</p>-
dc.languageeng-
dc.publisherBioMed Central-
dc.relation.ispartofGenome Medicine-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectCOVID-19-
dc.subjectImmunity-
dc.subjectRare variants-
dc.subjectType I interferon-
dc.titleRare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19-
dc.typeArticle-
dc.identifier.doi10.1186/s13073-023-01173-8-
dc.identifier.scopuseid_2-s2.0-85160044322-
dc.identifier.volume15-
dc.identifier.issue1-
dc.identifier.eissn1756-994X-
dc.identifier.isiWOS:001022167700001-
dc.identifier.issnl1756-994X-

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