Temporal single-cell profiling uncovers age-associated delays in immune resolution to respiratory viral infection

Sun, J.; Wu, Y.; Li, C.; Tang, J.; Gao, X.; Cheon, I. S.; Zhu, B.; Zhang, R.; Fain, C.; Hu, S.; Narasimhan, H.; de Almeida Santos, G.; Ayasoufi, K.; Johnson, A.; Zong, H.; Zang, C.; Dong, H.

doi:10.64898/2025.12.15.694321

bioRxiv · 10.64898/2025.12.15.694321

Temporal single-cell profiling uncovers age-associated delays in immune resolution to respiratory viral infection

Sun, J.·Wu, Y.·Li, C.·Tang, J.·Gao, X.·Cheon, I. S.·Zhu, B.·Zhang, R.·Fain, C.·Hu, S.·Narasimhan, H.·de Almeida Santos, G.·Ayasoufi, K.·Johnson, A.·Zong, H.·Zang, C.·Dong, H.

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Abstract

Aging is a major risk factor for increased morbidity and mortality following acute respiratory virus infections. To elucidate the immune determinants underlying viral pathogenesis and delayed lung repair in the aged lung, a comprehensive time-course study was conducted. Single-cell RNA sequencing (scRNAseq) and high-dimensional flow cytometry were utilized to compare lungs from young and aged mice infected with influenza A virus (IAV). Aged hosts displayed diminished alveolar macrophage (AM) and dendritic cell (DC) but elevated monocyte-derived macrophage (MoM) and interstitial macrophage (IM) presence following infection. Additionally, enhanced accumulation of adaptive immune cells, including CD4+ tissue-resident helper (TRH) cells, CD8+ tissue-resident memory (TRM) cells, and a B cell subset resembling age-associated B cells, was observed in the memory phase. Pathway analysis revealed that elevated type I and II interferon (IFN/{gamma}) signaling, especially in MoM/IM subsets, distinguished the aged hosts from the young. Inhibition of IFN/{gamma} signaling after viral clearance improved long-term respiratory outcomes and reduced both IM and TRH populations in aged mice. These findings highlight the pivotal role of IFN/{gamma} signaling, likely within MoM/IM subsets, in driving the exuberant persistence of adaptive immune cells and chronic immunopathology in the aged lung following acute viral infection.

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Sun, J., Wu, Y., Li, C., Tang, J., Gao, X., Cheon, I. S., Zhu, B., Zhang, R., Fain, C., Hu, S., Narasimhan, H., de Almeida Santos, G., Ayasoufi, K., Johnson, A., Zong, H., Zang, C., Dong, H.. 2025-12-17. Temporal single-cell profiling uncovers age-associated delays in immune resolution to respiratory viral infection. https://doi.org/10.64898/2025.12.15.694321

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