Daniel B. Rainbow

Background: Regulatory T cells (Tregs) are an important component of adaptive immune regulation and have been implicated in Parkinson’s disease (PD), with previous studies suggesting altered Treg proportions, phenotype and, in some cases, function. However, existing studies have been limited by variable phenotyping approaches and a lack of detailed functional assessment. Given the growing interest in Tregs as potential therapies in PD, better understanding of their phenotype and function in the disease is important. Methods: Circulating FOXP3+ Tregs were characterised in individuals with PD and age-matched healthy controls (HC) using a 24-colour spectral flow cytometry panel. Treg suppressive function was assessed by their ability to inhibit proliferation and cytokine production by polyclonally stimulated autologous T effector cells in vitro . Treg lineage stability was assessed by analysis of FOXP3 TSDR demethylation. Results: The proportions and phenotypic characteristics of circulating CD4 Tregs were broadly similar between individuals with PD and HCs, as were Treg suppressive function and FOXP3 TSDR demethylation. However, naive CD4 Tregs from individuals with PD showed reduced HELIOS expression, with a similar but non-significant trend in FOXP3 expression. Reduced HELIOS expression was also observed in the CD8 naive Treg compartment. Conclusions: Major quantitative or functional abnormalities in circulating Tregs do not appear to be a dominant feature PD. However, reduced HELIOS expression in naive Tregs suggests more subtle phenotypic alterations that warrant further investigation. The broadly preserved suppressive function is reassuring for therapeutic approaches aimed at increasing Treg numbers, although it will be important to establish that expanded Tregs retain a stable phenotype and suppressive function in inflammatory and tissue environments.

Single-cell RNA-sequencing (scRNA-seq) studies have transformed our understanding of cellular diversity in the human intestine, but differences in anatomical sampling, experimental processing and cell-type nomenclature limit comparison across datasets. Here, we present the Human Gut Cell Atlas (HGCA) V1, a community-curated reference of 944,390 healthy and disease-adjacent intestinal cells from 502 samples, 265 donors and 24 landmark studies, linked to detailed anatomical, clinical, and technical metadata. As this metadata is of critical importance to human biology, we developed MetaManager, an open source data management framework for standardized metadata collection and tracking. A five-level consensus taxonomy resolves 94 homeostatic cell identities and enables transferrable, high-resolution annotation of new gut datasets. By assembling cell identity, sampling metadata, and independent spatial validation, intestinal segment and radial tissue depth were revealed to systematically shape cellular composition and transcriptional state, enabling inference of the presence of sampling-dependent tissue niches, including lymphoid follicles. Reference mapping accurately and rapidly recovered cohort-level Crohn’s disease and treatment signatures without de novo annotation, while mapping human intestinal organoids quantified cell-type-specific identity, regional specification, maturation, and transcriptional fidelity to native tissue. The HGCA V1 provides a standardized cellular, anatomical coordinate, and metadata system for reproducible, high-quality analysis of intestinal biology across healthy tissue, disease-associated remodelling, and experimental models, providing a continuously evolving community reference for cumulative discovery in human intestinal biology.

Parkinson’s disease (PD) is a neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TEs) have been linked to inflammation, but their potential role in PD remains unexplored. Using bulk- and single-nuclei RNA-seq of postmortem brain tissue from four brain regions, we studied TE transcription and its correlation with PD neuroinflammation. Over a thousand TEs, including LINE-1 s and ERVs, were expressed in a cell type– and region-specific manner in the human brain. Increased TE expression was found in microglia and neurons in the substantia nigra and putamen of PD brains, but not amygdala or prefrontal cortex, compared to controls. This TE activation correlated with an innate immune response in the same brain regions. The link between an interferon response and TE activation was mechanistically confirmed using human pluripotent stem cell–derived microglia and neurons. Our findings provide insights into TE transcription in the PD brain and suggest that TEs may contribute to neuroinflammation and pathological progression in PD.

Parkinson’s disease (PD) is a common age-related neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TE) have been linked to inflammatory states, but their potential role in PD has not been explored. Using bulk– and single nuclei RNAseq of postmortem brain tissue from four brain regions, we studied TE transcriptional activation and its correlation with neuroinflammation in PD. Over a thousand TE loci, including LINE-1s and ERVs, were highly expressed in a cell-type and region-specific manner in the human brain. Increased TE expression was found in microglia and neurons in the substantia nigra and putamen in the PD brains, but not amygdala or prefrontal cortex, compared to age-matched control tissue. This TE activation correlated with innate immune transcriptional responses, characterized by the expression of interferon-related and viral response genes, in the same brain regions. The link between an interferon response and TE activation was mechanistically confirmed using human pluripotent stem cell-derived microglia and neurons. Our findings provide a unique insight into TE transcription in the PD brain and suggests that TEs play a role in chronic neuroinflammatory processes and the progression of this neurodegenerative disorder.

The immune system comprises multiple cell lineages and subsets maintained in tissues throughout the lifespan, with unknown effects of tissue and age on immune cell function. Here we comprehensively profiled RNA and surface protein expression of over 1.25 million immune cells from blood and lymphoid and mucosal tissues from 24 organ donors aged 20–75 years. We annotated major lineages (T cells, B cells, innate lymphoid cells and myeloid cells) and corresponding subsets using a multimodal classifier and probabilistic modeling for comparison across tissue sites and age. We identified dominant site-specific effects on immune cell composition and function across lineages; age-associated effects were manifested by site and lineage for macrophages in mucosal sites, B cells in lymphoid organs, and circulating T cells and natural killer cells across blood and tissues. Our results reveal tissue-specific signatures of immune homeostasis throughout the body, from which to define immune pathologies across the human lifespan.

During ontogeny, γδ T cells emerge from the thymus and directly seed peripheral tissues for in situ immunity. However, their functional role in humans has largely been defined from blood. Here, we analyzed the phenotype, transcriptome, function, and repertoire of human γδ T cells in blood and mucosal and lymphoid tissues from 176 donors across the life span, revealing distinct profiles in children compared with adults. In early life, clonally diverse Vδ1 subsets predominate across blood and tissues, comprising naïve and differentiated effector and tissue repair functions, whereas cytolytic Vδ2 subsets populate blood, spleen, and lungs. With age, Vδ1 and Vδ2 subsets exhibit clonal expansions and elevated cytolytic signatures, which are disseminated across sites. In adults, Vδ2 cells predominate in blood, whereas Vδ1 cells are enriched across tissues and express residency profiles. Thus, antigenic exposures over childhood drive the functional evolution and tissue compartmentalization of γδ T cells, leading to age-dependent roles in immunity.

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.

For decades, regulatory T cell (Treg) research has focussed on CD4+FOXP3+ Tregs, while characterisation of CD8+FOXP3+ Tregs has been limited due to their scarcity in blood. Here, by analysing 95 tissue samples from 26 deceased transplant organ donors we show that, despite representing less than 5% of circulating Tregs, CD8+ Tregs are enriched in human tissue, particularly in non-lymphoid tissues and bone marrow. We further show that they are fully demethylated at the FOXP3 TSDR, indicating lineage stability, and demonstrate their presence in human thymic tissue and cord blood. Transcriptomic profiling revealed strong similarities to CD4+ Tregs, however at the protein level, they reside in tissue as surface CD25 ^lo /-CD8+CD69+CD103+TLR9+HELIOS+FOXP3+ cells, expressing CD25 intracellularly. Surface CD25 was rapidly regained ex-vivo , allowing us to sort and expand them, and to subsequently demonstrate their therapeutic potential in a humanised mouse model of graft-vs-host disease. Additionally we report increased circulating CD8+Tregs in individuals with SLE and patients early following traumatic brain injury (TBI), underscoring their functional importance. We conclude that these under-studied cells likely play an essential but previously unappreciated role in maintaining peripheral tolerance. One Sentence Summary: FOXP3+CD8+ Tregs, expressing tissue residency markers and intracellular CD25, are enriched in human non-lymphoid tissues.

As the dimensionality, throughput, and complexity of cytometry data increases, so does the demand for user-friendly, interactive analysis tools that leverage high-performance machine learning frameworks. Here we introduce FlowAtlas.jl: an interactive web application that bridges the user-friendly environment of FlowJo and computational tools in Julia developed by the scientific machine learning community. We demonstrate the capabilities of FlowAtlas using a novel human multi-tissue, multi-donor immune cell dataset, highlighting key immunological findings.

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.