Deep longitudinal immune profiling reveals reprogramming of memory T cells that links to B cell dysregulation with age

Immune aging is a dynamic process shaped by time and external perturbation. Here, we sought to untangle the complexity of the healthy human immunity across age using deep molecular profiling. Applying our new Healthy Immune Cell Atlas, we profiled the transcriptional dynamics of peripheral immune cells in a longitudinal cohort of ~100 healthy young and older adults followed over 2 years, both under homeostasis and perturbation induced by vaccination, building a scRNA-seq dataset of more than 13.5 million PBMCs. From these data, we revealed that T cells exhibit substantially more age-related changes in transcription at homeostasis than other immune cell subsets, which persist both over time and across age and are distinct from those associated with biological sex or CMV infection status. B cells, which demonstrated few age-related differences at homeostasis, had numerous and persistent changes in vaccine-induced responses with age linked to an age- and GATA3-related transcriptional skewing in the central memory CD4 T cell compartment of older adults. Our study collectively highlights that gradual, age-related alterations in the homeostatic transcriptional networks in immune cells leads to shifts in the landscape of immune responsiveness as we age. This rich resource is further provided with data exploration tools at https://explore.allenimmunology.org/. The SoundLife cohort comprised of healthy young adults aged 25–35 years old and older adults aged 55–65 years old were recruited from the greater Seattle, WA area. Longitudinal visits were collected from these subjects prior to (Day 0) and following seasonal influenza vaccination (Day 7, Day 90) for two years. An additional Immune Variation series was collected over the course of 3 months (Day 0, 7, 90) and served as a baseline comparison of no vaccination/perturbation. A single stand-alone blood draw was also collected from these participants over the course of the two year study. Blood was drawn and PBMCs were isolated. PBMCs were assayed for flow cytometry and 10x 3' scRNA-seq (v3.1). *************************************************************** Submitter states that missing raw data are being made available for controlled access in dbGaP. ***************************************************************

免疫衰老（Immune aging）是一类受时间与外界扰动共同塑造的动态生物学过程。本研究旨在通过深度分子谱分析（deep molecular profiling），解析不同年龄段健康人类免疫系统的复杂特征。本研究依托全新构建的健康免疫细胞图谱（Healthy Immune Cell Atlas），对包含约100名健康青年与老年受试者的纵向队列开展了为期2年的随访研究，分别在稳态（homeostasis）与疫苗接种诱导的扰动（perturbation）状态下，对受试者外周免疫细胞的转录动态进行了谱分析，最终构建了包含超过1350万份外周血单个核细胞（Peripheral Blood Mononuclear Cells, PBMCs）的单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据集。
基于该数据集，我们发现相较于其他免疫细胞亚群，T细胞在稳态下的转录组层面表现出更为显著的年龄相关性变化，这类变化会随时间推移与年龄增长持续存在，且与生物性别或巨细胞病毒（Cytomegalovirus, CMV）感染状态无关。
而在稳态下几乎未表现出年龄相关差异的B细胞，其疫苗诱导的应答反应随年龄增长则出现了大量且持久的变化；这类变化与老年人群中枢记忆CD4阳性T细胞亚群中，由年龄与GATA结合蛋白3（GATA binding protein 3, GATA3）介导的转录偏移密切相关。
本研究整体揭示：免疫细胞稳态转录网络随年龄发生的渐进性改变，会随着个体衰老导致免疫应答整体格局发生偏移。
本研究还附带了数据探索工具，可通过https://explore.allenimmunology.org/访问使用。
SoundLife队列的受试者均招募自美国华盛顿州大西雅图地区，包含年龄在25~35岁之间的健康青年，以及年龄在55~65岁之间的健康老年人群。
在为期两年的研究周期内，我们对所有受试者进行了多次纵向随访采样：分别在季节性流感疫苗接种前（第0天）与接种后第7天、第90天采集样本。
此外，我们还在为期3个月的周期内采集了一组免疫变化队列样本（采样时间点为第0天、第7天、第90天），作为未接种疫苗/未受扰动状态下的基线对照数据集。
在整个两年的研究周期内，我们还为所有受试者单独采集了单次外周血样本。
所有血液样本采集后均分离得到外周血单个核细胞，随后对其开展流式细胞术检测与10x 3'端单细胞RNA测序（v3.1版本）分析。
**************************************************************** 提交者说明：缺失的原始数据正通过基因型与表型数据库（Database of Genotypes and Phenotypes, dbGaP）进行受控访问权限下的公开共享。 ****************************************************************