Integrative systems immunology uncovers molecular networks of the cell cycle that stratify COVID-19 severity.


Caroline Aliane de Souza Prado, Dennyson Leandro M Fonseca, Youvika Singh, Igor Salerno Filgueiras, Gabriela Crispim Baiocchi, Desirée Rodrigues Plaça, Alexandre H C Marques, Raquel Costa Silva Dantas-Komatsu, Júlia N Usuda, Paula Paccielli Freire, Ranieri Coelho Salgado, Sarah Maria da Silva Napoleao, Rodrigo Nalio Ramos, Vanderson Rocha, Guangyan Zhou, Rusan Catar, Guido Moll, Niels Olsen Saraiva Camara, Gustavo Cabral de Miranda, Vera Lúcia Garcia Calich, Lasse M Giil, Neha Mishra, Florian Tran, Andre Ducati Luchessi, Helder I Nakaya, Hans D Ochs, Igor Jurisica, Lena F Schimke, Otavio Cabral-Marques

Year of publication



J. Med. Virol.







Impact factor



Several perturbations in the number of peripheral blood leukocytes, such as neutrophilia and lymphopenia associated with Coronavirus disease 2019 (COVID-19) severity, point to systemic molecular cell cycle alterations during severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the landscape of cell cycle alterations in COVID-19 remains primarily unexplored. Here, we performed an integrative systems immunology analysis of publicly available proteome and transcriptome data to characterize global changes in the cell cycle signature of COVID-19 patients. We found significantly enriched cell cycle-associated gene co-expression modules and an interconnected network of cell cycle-associated differentially expressed proteins (DEPs) and genes (DEGs) by integrating the molecular data of 1469 individuals (981 SARS-CoV-2 infected patients and 488 controls [either healthy controls or individuals with other respiratory illnesses]). Among these DEPs and DEGs are several cyclins, cell division cycles, cyclin-dependent kinases, and mini-chromosome maintenance proteins. COVID-19 patients partially shared the expression pattern of some cell cycle-associated genes with other respiratory illnesses but exhibited some specific differential features. Notably, the cell cycle signature predominated in the patients’ blood leukocytes (B, T, and natural killer cells) and was associated with COVID-19 severity and disease trajectories. These results provide a unique global understanding of distinct alterations in cell cycle-associated molecules in COVID-19 patients, suggesting new putative pathways for therapeutic intervention.