Biology subjects

Farber, D. L.

Publications and source records attributed to Farber, D. L..

12 recordsLinked to original sources

bioRxiv2026

Beyond the blood: Tissue-resident immunity shapes SARS-CoV-2 vaccine antibody responses

Infections and vaccinations elicit coordinated humoral and cellular adaptive immune responses that together provide protection. In addition to antibodies, pathogen-specific memory T and Bcells persist in blood and tissues, but it remains unclear how their composition and spatial distribution relate to serum antibody titers, the most common correlate of vaccine-induced protection. Understanding these relationships is essential for predicting vaccine efficacy and optimizing immunization strategies. We analyzed tissues from 58 adult human organ donors vaccinated against SARS-CoV-2, including individuals with and without prior infection. Using multivariate imputation, dimensionality reduction, and correlation, regression, and causal analyses, we identified immune signatures linking memory B cell, CD4 T cell, and CD8 T cell subsets in spleen, lung, and lung-draining lymph nodes with antibody titers and neutralizing activity. Our analyses indicate that humoral immunity is driven primarily by virus-specific B cellsand CD4 T cells in lymphoid tissues rather than blood, whereas tissue-localized CD8 T cell responses, although correlated with antibody levels, develop independently. These findings demonstrate that cross-sectional immune profiling across multiple tissues recapitulates established immunological principles and reveal that serum antibody responses emerge from coordinated cellular immune responses distributed throughout the body.

immunology↗

bioRxiv2026

Age determines NK cell fate and tissue compartmentalization to CMV infection

Cytomegalovirus (CMV), a ubiquitous herpesvirus, establishes persistent infection that is controlled by both NK and CD8 T cells. While immunity to CMV is primarily studied in adult mice and humans, most individuals acquire CMV during the early years of life and virus-specific NK and T cell responses during this vulnerable life stage are understudied. Here, we show distinct responses by infant and adult NK cells to CMV infection in both mice and humans resulting from cell-intrinsic features and host T cell responses. Infant mice sustained higher viral loads compared to adults following MCMV infection and exhibited non-redundant requirements for NK cells. Infant MCMV-reactive (Ly49H+) NK cells preferentially expanded adaptive-like subsets which were maintained in tissues and exhibited a distinct transcriptional profile relative to adult NK cells. This biased differentiation of adaptive-like NK cells was altered over age and controlled in part, by competition with memory T cells. We demonstrate similar dynamics with human NK cells; distinct adaptive-profiles for HCMV-reactive NK cells in early life and childhood that change over age and are inversely associated with anti-viral T cell responses. Together, our results reveal that NK cells develop adaptive-like responses and seed tissues in early life to provide protective memory when T cell immunity is limited. ONE-SENTENCE SUMMARYMemory NK cell generation to cytomegalovirus infection is regulated by age and T cell immunity

immunology↗

bioRxiv2025

Dynamic remodeling of the pancreas immune landscape in obesity.

Obesity is a known risk factor for diseases of the pancreas, including diabetes, pancreatic cancer and pancreatitis, but mechanisms remain unclear. To elucidate how obesity impacts pancreatic immune homeostasis, we performed spatial, transcriptomic and functional profiling of human pancreatic immune cells from obese and non-obese organ donors. Obesity was associated with higher density of tissue resident memory T-cells (TRM) in the exocrine pancreas which display high cytotoxic functions and aggregated around macrophages. Single cell sequencing of pancreatic macrophages revealed two main subsets - FOLR2+ CD11c- fetal-derived macrophages with pro-repair and immunoregulatory function and a FOLR2- CD11c+ monocyte-derived macrophages with greater T-cell interactions and pro-inflammatory function. In obesity, the pancreatic macrophage landscape shifts to lower predominance of FOLR2+ CD11c- macrophages and higher FOLR2- CD11c+ macrophages which interact selectively with the TRM and inflamed exocrine epithelium. Together, these results identify macrophage-T cell circuits and immune epithelial interactions that fuel chronic pancreatic inflammation in obesity - a potential unifying mechanism for obesity-related pancreatic diseases.

immunology↗

bioRxiv2025

Tissue signatures of human macrophages during homeostasis and activation

Human macrophages (M{Phi}s) reside in tissues and develop tissue-specific identities. While studies in mice have identified molecular signatures for site-specific M{Phi} differentiation, we know less about the transcriptional profiles of human M{Phi}s in distinct sites, including mucosal tissues and lymphoid organs during homeostasis and activation. Here, we use multimodal single-cell sequencing and ex vivo stimulation assays to define tissue signatures for populations of human M{Phi}s isolated from lungs, small intestine, spleen, bone marrow, and lymph nodes obtained from individual organ donors. Our results reveal distinct tissue-adapted gene and protein profiles of metabolic, adhesion, and immune interaction pathways, which are specific to M{Phi}s and not monocytes isolated from the same sites. These signatures exhibit homology to murine M{Phi}s from the same sites. Tissue-adapted M{Phi}s remained responsive to polarizing cytokine stimuli ex vivo, with upregulation of expected transcripts and secreted proteins, while retaining tissue-specific profiles. Together, our findings show how human M{Phi} identity is coupled to their site of residence for mucosal and lymphoid organs and is intrinsically maintained during activation and polarization.

immunology↗

bioRxiv2025

The antibacterial factor APOL3 couples lysosomal damage to mitochondrial DNA efflux and type I IFN induction

Lysosomal damage is an endogenous danger signal to the cell, but its significance for innate immunity and how specific signaling pathways are engaged by this stressor remain unclear. Here, we uncover an immune-inducible pathway that connects lysosomal damage to mitochondrial DNA (mtDNA) efflux and type I IFN production. Lysosomal damage elicits mitochondrial outer membrane permeabilization (MOMP) via BAK/BAX macropores; however, the inner mitochondrial membrane (IMM) prevents wholesale mtDNA release in resting cells. Priming with type II IFN (IFN-{gamma}) induced the antibacterial effector apolipoprotein L-3 (APOL3), which upon transient lysosomal damage, targets mitochondria undergoing MOMP and selectively permeabilizes the IMM to enhance mtDNA release and activate cGAS/STING signaling. Biochemical and cellular reconstitution revealed that analogous to its bactericidal detergent-like mechanism, APOL3 solubilizes cardiolipin to permeabilize the IMM. Our findings illustrate how cells use an antibacterial protein to expedite the breakdown of endosymbiosis and facilitate a heightened response to injury and infection.

cell biology↗

bioRxiv2025

Transcriptional control of T cell tissue adaptation and effector function in infants and adults

The first years of life are essential for the development of memory T cells, which rapidly populate the bodys diverse tissue sites during infancy. However, the degree to which tissue memory T cell responses in early life reflect those during adulthood is unclear. Here, we use single cell RNA-sequencing of resting and ex vivo activated T cells from lymphoid and mucosal tissues of infant (aged 2-9 months) and adult (aged 40-65 years) human organ donors to dissect the transcriptional programming of memory T cells over age. Infant memory T cells demonstrate a unique stem-like transcriptional profile and tissue adaptation program, yet exhibit reduced activation capacity and effector function relative to adults. Using CRISPR-Cas9 knockdown, we define Helios (IKZF2) as a critical transcriptional regulator of the infant-specific tissue adaptation program and restricted effector state. Our findings reveal key transcriptional mechanisms that control tissue T cell fate and function in early life.

immunology↗

bioRxiv2024

A variational deep-learning approach to modeling memory T cell dynamics

Mechanistic models of dynamic, interacting cell populations have yielded many insights into the growth and resolution of immune responses. Historically these models have described the behavior of pre-defined cell types based on small numbers of phenotypic markers. The ubiquity of deep pheno-typing therefore presents a new challenge; how do we confront tractable and interpretable mathematical models with high-dimensional data? To tackle this problem, we studied the development and persistence of lung-resident memory CD4 and CD8 T cells (TRM) in mice infected with influenza virus. We developed an approach in which dynamical model parameters and the population structure are inferred simultaneously. This method uses deep learning and stochastic variational inference and is trained on the single-cell flow-cytometry data directly, rather than on the kinetics of pre-identified clusters. We show that during the resolution phase of the immune response, memory CD4 and CD8 T cells within the lung are phenotypically diverse, with subsets exhibiting highly distinct and time-dependent dynamics. TRM heterogeneity is maintained long-term by ongoing differentiation of relatively persistent Bcl-2hi CD4 and CD8 TRM subsets which resolve into distinct functional populations. Our approach yields new insights into the dynamics of tissue-localized immune memory, and is a novel basis for interpreting time series of high-dimensional data, broadly applicable to diverse biological systems.

immunology↗

bioRxiv2024

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years. We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.

immunology↗

bioRxiv2023

Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues

Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and dissecting transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins, as in cells of the immune system. Cellular Indexing of Transcriptomes and Epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes; however, accurate cell type annotation requires a classifier that integrates multimodal data. Here, we describe MultiModal Classifier Hierarchy (MMoCHi), a marker-based approach for classification, reconciling gene and protein expression without reliance on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal novel subset markers. MMoCHi is designed for adaptability and can integrate annotation of cell types and developmental states across diverse lineages, samples, or modalities.

genomics↗

bioRxiv2021

Influence of age on functional memory T cell diversity

Memory T cells exhibit considerable diversity that determines their ability to be protective and their durability. Here, we examined whether changes in T cell heterogeneity contribute to the age-associated failure of immune memory. By screening for age-dependent T cell surface markers, we have identified CD4 and CD8 memory T cell subsets that are unrelated to previously defined subsets of central and effector memory cells. Memory T cells expressing the ecto-5-nucleotidase CD73 constitute a functionally distinct subset of memory T cells that declines with age. They exhibit many features favorable for immune protection, including longevity and polyfunctionality. They have a low turnover, but are poised to display effector functions and to develop into cells resembling tissue-resident memory T cells (TRM). Upstream regulators of differential chromatin accessibility and transcriptomes include transcription factors that are characteristic for conferring these superior memory features as well as facilitating CD73 expression. CD73 is not just a surrogate marker of these regulatory networks but is directly involved in T cell survival and TRM differentiation Interventions preventing the decline of this T cell subset or increasing CD73 expression have the potential to improve immune memory in older adults.

immunology↗

bioRxiv2021

Molecular programs of fibrotic change in aging human lung

Aging is associated with both overt and subclinical lung fibrosis, which increases risk for mortality from viruses and other respiratory pathogens. The molecular programs that induce fibrosis in the aging lung are not well understood. To overcome this knowledge gap, we undertook multimodal profiling of distal lung samples from healthy human donors across the lifespan. Telomere shortening, a cause of cell senescence and fibrosis, was progressive with age in a sample of 86 lungs and was associated with foci of DNA damage. Bulk RNA sequencing confirmed activation of cellular senescence and pro-fibrotic pathways as well as genes necessary for collagen processing with increasing age. These findings were validated in independent datasets for lung and sun-exposed skin, but not other organs including heart, liver and kidney. Cell type deconvolution analysis revealed a progressive loss of lung epithelial cells and an increasing proportion of fibroblasts. Consistent with the observed pro-fibrotic transcriptional profile, second harmonic imaging demonstrated increased density of interstitial collagen in aged human lungs. Furthermore, regions of parenchymal fibrosis were associated with decreased alveolar expansion and surfactant secretion. These findings reveal the transcriptional and structural features of fibrosis and associated physiologic impairments in normal lung aging.

genomics↗

bioRxiv2019

A single-cell reference map for human blood and tissue T cell activation reveals functional states in health and disease

Human T cells coordinate adaptive immunity by localization in diverse tissue sites, though blood T cells are the most readily studied. Here, we used single-cell RNA-seq to define the functional responses of T cells isolated from human lungs, lymph nodes, bone marrow, and blood to TCR-stimulation. We reveal how human T cells in tissues relate to those in blood, and define activation states for CD4+ and CD8+T cells across all sites, including an interferon-response state for CD4+T cells and distinct effector states for CD8+T cells. We further show how profiles of individual tumor-associated T cells can be projected onto this healthy reference map, revealing their functional state.

immunology↗