High temporal resolution transcriptomic profiling delineates distinct patterns of interferon response following Covid-19 mRNA vaccination and SARS-CoV2 infection

Darawan Rinchai (1) , Sara Deola (1) , Gabriele Zoppoli (2, 3) , Basirudeen Syed Ahamed Kabeer (1) , Sara Taleb (4) , Igor Pavlovski (1) , Selma Maacha (1) , Giusy Gentilcore (1) , Mohammed Toufiq (1) , Lisa Mathew (1) , Li Liu (1) , Fazulur Rehaman Vempalli (1) , Ghada Mubarak (1) , Stephan Lorenz (1) , Irene Sivieri (2, 5) , Gabriella Cirmena (3) , Chiara Dentone (3) , Paola Cuccarolo (2) , Daniele Giacobbe (2, 3) , Federico Baldi (2) , Alberto Garbarino (2) , Benedetta Cigolini (2) , Paolo Cremonesi (6) , Michele Bedognetti , Alberto Ballestrero (2, 3) , Matteo Bassetti (1) , Boris P. Hejblum (7, 8, 9) , Tracy Augustine (10) , Nicholas Van Panhuys (1) , Rodolphe Thiébaut (7, 8, 9) , Ricardo Branco (1) , Tracey Chew (11) , Maryam Shojaei (11, 10) , Kirsty Short (12) , Carl Feng (11) , Susu Zughaier (13) , Andrea De Maria (2, 3) , Benjamin Tang (10) , Ali Ait Hssain , Davide Bedognetti (1) , Jean-Charles Grivel (1) , Damien Chaussabel (1)

1 Sidra Medicine [Doha, Qatar]
2 UniGe - Università degli studi di Genova = University of Genoa
3 IRCCS Istituto Giannina Gaslini [Genoa, Italy]
4 HBKU - Hamad Bin Khalifa University
5 UniFI - Università degli Studi di Firenze = University of Florence = Université de Florence
6 E.O. Ospedali Galliera
7 SISTM - Statistics In System biology and Translational Medicine
8 BPH - Bordeaux population health
9 UB - Université de Bordeaux
10 The Westmead Institute for Medical Research
11 The University of Sydney
12 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
13 Qatar University

Knowledge of the factors contributing to the development of protective immunity after vaccination with COVID-19 mRNA vaccines is fragmentary. Thus we employed high- temporal-resolution transcriptome profiling and in-depth characterization of antibody production approaches to investigate responses to COVID-19 mRNA vaccination. There were marked differences in the timing and amplitude of the responses to the priming and booster doses. Notably, two distinct interferon signatures were identified, that differed based on their temporal patterns of induction. The first signature (S1), which was preferentially induced by type I interferon, peaked at day 2 post-prime and at day 1 post-boost, and in both instances was associated with subsequent development of the antibody response. In contrast, the second interferon signature (S2) peaked at day 1 both post-prime and post- boost but was found to be potently induced only post-boost, where it coincided with a robust inflammation peak. Notably, we also observed “post-prime-like” (S1 ++ ,S2 0/+ ) and “post-boost-like” (S1 ++ ,S2 ++ ) patterns of interferon response among COVID-19 patients. A post-boost-like signature was observed in most severely ill patients at admission to the intensive care unit and was associated with a shorter hospital stay. Interestingly, severely ill patients who stayed hospitalized the longest showed a peculiar pattern of interferon induction (S1 -/0 ,S2 + ), that we did not observe following the administration of mRNA vaccines. In summary, high temporal resolution profiling revealed an elaborate array of immune responses elicited by priming and booster doses of COVID-19 mRNA vaccines. Furthermore, it contributed to the identification of distinct interferon-response phenotypes underpinning vaccine immunogenicity and the course of COVID-19 disease.

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]

Darawan Rinchai, Sara Deola, Gabriele Zoppoli, Basirudeen Syed Ahamed Kabeer, Sara Taleb, et al.. High temporal resolution transcriptomic profiling delineates distinct patterns of interferon response following Covid-19 mRNA vaccination and SARS-CoV2 infection. Science Advances , 2022, 8 (45), eabp9961. ⟨10.1126/sciadv.abp9961⟩. ⟨hal-03530948⟩