Single-cell analysis of aging in lymphoid compartments

Single-cell analysis of aging in lymphoid compartments

Columbia University from New York, USA and the Wellcome Sanger Institute, UK




The age-associated changes in immunity can manifest in diverse ways. There is a marked decline and dysregulation of adaptive immune responses. They include the ability of T and B lymphocytes to specifically recognize and respond to foreign antigens and maintain tolerance to self-antigens. At the same time, there is an increase in low-level systemic inflammation caused by overactive innate immunity—a phenomenon referred to as “inflammaging.” With age, the increased incidence of cancer, infectious disease, and autoimmunity is likely due to innate and adaptive immunity alterations.

Theories about the decline of adaptive immunity include the reduced production of naïve T lymphocytes and progenitor B cells resulting from the degeneration of the primary lymphoid organs (thymus and bone marrow) and a decrease in the activation and responsiveness of T cells to external stimuli. The reduced number of naïve T cells leads to a decreased clonal repertoire. Additionally, exposure to multiple pathogens results in an increased pool of protective memory cells, often with reduced diversity due to chronic exposure to specific pathogens over time.

Most innate and adaptive immune cells reside in tissues rather than blood, with the largest numbers present in primary and secondary lymphoid organs (i.e., bone marrow, thymus, spleen, and lymph nodes). The microenvironment of the primary and secondary lymphoid organs, comprised of various cell types including epithelial cells, fibroblasts, and endothelium, plays a crucial role in the development and activation of the immune cells.

A novel investigation into lymphoid compartment aging is proposed in this collaborative project of the Wellcome Sanger Institute (Cambridge, UK) and Columbia University (New York, USA). In the course of the project, 50 matched samples for primary (bone marrow) and secondary (spleen, lymph node) lymphoid organs along with blood will be taken from individual organ donors representing the entire adult lifespan of a human from 20 to 80 years old. The tissue collection will be split between the Cambridge Biorepository for Translational Medicine (CBTM) in the UK and the LiveOnNY repository in New York, USA. Both places are unique resources that allow access to tissues from deceased organ donors during organ transplant retrieval, which preserves the viability of cells and tissues.

A human lymphoid tissue atlas over space (multiple sites) and time (over 7 decades of life) will be generated using cutting-edge single-cell technologies and innovative computational analysis of these complex datasets. Matched scRNA-seq and scATAC-seq data will be generated for the bone marrow, spleen, lymph node as well as blood whenever possible. These approaches will allow identifying the cell types present and assessing changes in cell-type composition with age. Additionally, CITE-seq will be performed to supplement RNA measurement with protein measurements of the specific immune markers.

For the spleen and lymph node, a high-throughput spatial transcriptomics approach will be applied using tissue sections from 10 young and 10 old donors to gain insight into how aging influences tissue architecture, i.e., localization of different cell types in relation to each other and the interactions between them.

Finally, whole-genome sequencing (WGS) on the blood sample from every donor will be performed. WGS information from every donor will allow us to put our cohort of patients into the perspective of genome sequencing data available from the other human cohorts (UK Biobank, 1000 Genomes, GTEx).

Single-cell analysis of aging in lymphoid compartments - illustration

The following fundamental questions about tissue aging will be addressed:

  1. How do cell identities change during the aging of lymphoid organs? How is the repertoire of genes expressed by specific cell types impacted in aging? Do we observe entirely new cell populations, and if yes, where do they come from? How does cell type composition change in primary and secondary immune organs with age?
  2. What is the role of stromal cell populations (i.e., epithelial cells, fibroblasts, endothelial cells, etc.) in the aging of lymphoid organs?
  3. How does the regulatory circuitry of cells become modified with age? Are there age- and site-specific epigenetic alterations in chromatin?
  4. How does tissue architecture (cell-cell interactions, cell-matrix interactions) change with age across different lymphoid sites?

This collaborative project of Columbia University and the Wellcome Sanger Institute is contributing to the global Human Cell Atlas Initiative, which is creating comprehensive reference maps of all human cells.  The project complements and expands another immune aging project from the Wellcome Sanger Institute, funded as a Chan Zuckerberg Initiative (CZI) Seed Network for the Human Cell Atlas.  The Seed Network project focuses  on age-related changes in specific immune cell lineages across multiple lymphoid and mucosal organs, which will be investigated by means of scRNAseq and CITEseq techniques.

In comparison to the Seed Network project, the collaborative project from Columbia University and the Sanger Institute, funded by ABF-EU and ABF-US, will have more breadth in the sample size, consider donors from across the human lifespan, and study all cell populations within lymphoid tissues. This project will also include experiments to assess chromatin accessibility changes with age (scATAC-Seq) and changes in tissue architecture in two and three dimensions.


The project’s start date is November 1, 2021, for Columbia University from New York and March 1, 2022, for the Wellcome Sanger Institute.