Multi-omic profiling reveals age-related immune dynamics in healthy adults
Qiuyu Gong, Mehul Sharma, Marla C. Glass, Emma L. Kuan, Aishwarya Chander, Mansi Singh, Lucas T. Graybuck, Zachary Thomson, Christian M. LaFrance, Samir Rachid Zaim, Tao Peng, Lauren Okada, Palak C. Genge, Katherine E. Henderson, Elisabeth M. Dornisch, Erik D. Layton, Peter J. Wittig, Alexander T. Heubeck, Nelson Mukuka, Julian Reading, Garrett Strawn, Teminijesu Titus-Adewunmi, Kathleen Abadie, Charles R. Roll, Veronica Hernandez, Vaishnavi Parthasarathy, Tyanna Stuckey, Blessing Musgrove, Elliott Swanson, Cara Lord, Morgan Weiss, Cole Phalen, R Mettey, Kevin J. Lee, John B. Johanneson, Erin K. Kawelo, Jessica Garber, Upaasana Krishnan, Megan E. Smithmyer, E. John Wherry, Laura A. Vella, Sarah E. Henrickson, Mackenzie Kopp, Adam K. Savage, Lynne A. Becker, Paul Meijer, Ernest M. Coffey, Jörg J. Goronzy, Mikael Sigvardsson, Cate Speake, Thomas F. Bumol, Ananda W. Goldrath, Troy R. Torgerson, Xiaojun Li, Peter J. Skene, Jane H. Buckner, Claire E. Gustafson
Abstract
The generation and maintenance of immunity is a dynamic process that is dependent on age1–3. Here, to better understand its progression, we profiled peripheral immunity in more than 300 healthy adults (25 to 90 years of age) using single-cell RNA sequencing, proteomics and flow cytometry, following 96 adults longitudinally across 2 years with seasonal influenza vaccination. The resulting resource generated a single-cell RNA-sequencing dataset of more than 16 million peripheral blood mononuclear cells with 71 immune cell subsets from our Human Immune Health Atlas and enabled us to interrogate how immune cell composition and states shift with age, chronic viral infection and vaccination. From these data, we demonstrate robust, non-linear transcriptional reprogramming in T cell subsets with age that is not driven by systemic inflammation or chronic cytomegalovirus infection. This age-related reprogramming led to a functional T helper 2 (TH2) cell bias in memory T cells that is linked to dysregulated B cell responses against highly boosted antigens in influenza vaccines. Collectively, this study reveals unique features of the immune ageing process that occur prior to advanced age and provides novel targets for age-related immune modulation. We provide interactive tools for exploring this extensive human immune health resource at https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/ . This multi-omic longitudinal analysis of the healthy human peripheral immune system constructs the Human Immune Health Atlas and assembles data on immune cell composition and state changes with age, including responses to cytomegalovirus infection and influenza vaccination.