29 apr. 2026
Keywords
•Spatial multi-omics
•Immunosenescence
•Germinal center
Main Findings
Immunosenescence refers to the age-associated decline in immune function and is characterized by increased susceptibility to infections, reduced vaccine efficacy, and the development of chronic low-grade inflammation termed inflammaging. This inflammatory state is driven in part by the senescence-associated secretory phenotype (SASP), in which senescent cells secrete a broad array of pro-inflammatory cytokines, chemokines, and growth factors. Most human studies of immunosenescence have relied on peripheral blood mononuclear cells (PBMCs) or bulk tissue analyses that lack spatial resolution, leaving the cellular identities, functional states, and tissue contexts of senescence-associated immune cells in lymphoid organs poorly characterized. Defining the heterogeneity and spatial organization of these cells in intact human tissue is therefore critical for understanding how immunosenescence emerges and contributes to age-related functional decline.
By integrating spatial multi-omics encompassing high-plex CODEX immunofluorescence with the canonical senescence markers p16, p21, HMGB1, and γ-H2AX, DBiT-seq and CosMx spatial transcriptomics, spatial ATAC-seq, mass-spectrometry proteomics on nanoPOTS-isolated cells, and label-free stimulated Raman scattering (SRS) metabolic imaging, Farzad et al. in this preprint constructed a cellular senescence atlas of human lymph nodes from 51 donors aged 18 to 86 years. They identified approximately 34 immune and stromal cell types across 18 whole lymph nodes and 81 tissue cores, encompassing roughly 20 million single cells. Whereas PBMC-derived senescence signatures concentrated in T cells, NK cells, and classical monocytes, consistent with previous studies, the same analysis in secondary lymphoid organs revealed that senescence-associated programs preferentially accumulated memory, naïve and plasma B cells. In the lymph nodes, CODEX imaging showed that with age, p16+/p21+ cells progressively shifted from extrafollicular regions in young donors to inside germinal center (GC) follicles in aged donors. The spatial reorganization of B cells within follicles marks the formation of hubs of chronic inflammation termed “SenSpots”, that result from senescent B cells reprogrammed to strongly activate stress response and anti-apoptotic pathways.
To probe the functional consequences of this senescence pattern, the authors profiled profiled SenSpot residents in situ. First, they performed spatial proteomics on laser-captured p16+ cells, revealing marked depletion of DKC1, the gene encoding dyskerin, which stabilizes the telomerase RNA component, and pathway enrichment for telomere maintenance dysfunction and rewired T-cell receptor signaling. Second, SRS metabolic imaging showed elevated lipid-to-protein ratios, increased lipid saturation, and a reduced optical redox ratio in p16+ GC B cells, changes that were largely specific to this population and less prominent in other cell types such as endothelial cells. Memory B cells emerged as the dominant senescent population overall, accounting for roughly 75% of all p16+ cells. Next, spatial transcriptomics demonstrated that aged follicular B cells were enriched for NF-κB, p53, and canonical senescence-pathway signaling, while simultaneously downregulating immunoglobulin heavy and light chain transcripts (IGHG1, IGLC3, IGHM), directly linking the spatial accumulation of senescent cells to impaired antibody production. Lastly, spatial ATAC-seq further revealed increased chromatin accessibility at senescence-associated loci (CDKN2A, CDKN1A, H2AFX, HMGB1) in cycling-like and plasma B cells, alongside an epigenomic shift that closed cytoskeletal, transport, and renewal genes while opening oxidative stress, tissue remodeling, and inflammatory programs, consistent with an integrated multi-omic senescence program centered on the B-cell compartment.
Limitations
This work presents a comprehensive investigation that leverages orthogonal spatial modalities to converge on a B-cell-centric senescence program. However, several limitations remain that future experiments could address.
1.The study is largely observational and lacks mechanistic causality. While the convergence of proteomic, metabolic, transcriptomic, and epigenomic signatures demonstrates a tissue-specific B cell senescence program, the paper does not demonstrate that modulating these cells restores humoral function in aged individuals. Senolytic intervention studies in aged mice, or analysis of post-vaccination lymph nodes from older adults treated with experimental senolytics would establish whether follicular SenSpots are causal contributors to declining humoral response.
2.The age distribution of the donor cohort is uneven. Donors aged 41 to 59 years are underrepresented, leaving the middle-aged population largely uncharacterized. This gap limits the ability to trace the temporal trajectory of senescence accumulation and to identify when SenSpots begin to emerge during the aging process.
3.Sample sizes for several multi-omic readouts are small. Some of the most striking findings, including spatial transcriptomics and spatial ATAC-seq, rest on only three to four donors per age group. Validation in larger and more uniformly distributed cohorts is needed to confirm that the SenSpot framework generalizes beyond this initial dataset.
4.Generalizability across anatomical sites and disease contexts remains untested. Lymph nodes were sampled from multiple anatomical sites without explicit matching for infection history or vaccination status. It also remains unclear whether the same B-cell-centric pattern emerges in mucosa-associated lymphoid tissue, spleen, or tumor-draining lymph nodes, where chronic antigen exposure may shape the senescence landscape differently.
Significance/Novelty
This study presents the first integrated multi-omic spatial atlas of cellular senescence in human lymph nodes, localizing immunosenescence to specific GC follicular B cell niches. The identification of focal inflammatory “SenSpots” in aged lymph nodes provides a tissue-level mechanistic framework for the long-recognized clinical observation that humoral immunity and vaccine responsiveness decline with age. By connecting spatial cell heterogeneity, coordinated transcriptomic-proteomic-metabolomic-epigenomic remodeling, and impaired immunoglobulin production into a single coherent story, this work positions follicular senescent B cells as potential therapeutic targets for modulating age-related immune decline and lays the groundwork for testing whether senolytic or senomorphic strategies can rejuvenate humoral immunity in older adults.
Preprint rating
•Scientific quality: 4.5
•Novelty: 5
•Significance: 4.5
Credit
Reviewed by Xiaotian (Tony) Wang as part of a cross-institutional journal club between the Icahn School of Medicine at Mount Sinai, the University of Oxford, the Karolinska Institute, the University of Toronto, and the UT MD Anderson James P. Allison Institute.
The author declares no conflict of interests in relation to their involvement in the review.