Background: Coronary artery disease is an incurable, life-threatening disease that was once considered primarily a disorder of lipid deposition. Coronary artery disease is now also characterized by chronic inflammation‚ notable for the buildup of atherosclerotic plaques containing immune cells in various states of activation and differentiation. Understanding how these immune cells contribute to disease progression may lead to the development of novel therapeutic strategies. Methods: We used single-cell technology and in vitro assays to interrogate the immune microenvironment of human coronary atherosclerotic plaque at different stages of maturity. Results: In addition to macrophages, we found a high proportion of αβ T cells in the coronary plaques. Most of these T cells lack high expression of CCR7 and L-selectin , indicating that they are primarily antigen-experienced memory cells. Notably, nearly one-third of these cells express the HLA-DRA surface marker, signifying activation through their TCRs (T-cell receptors). Consistent with this, TCR repertoire analysis confirmed the presence of activated αβ T cells (CD4<CD8), exhibiting clonal expansion of specific TCRs. Interestingly, we found that these plaque T cells had TCRs specific for influenza, coronavirus, and other viral epitopes, which share sequence homologies to proteins found on smooth muscle cells and endothelial cells, suggesting potential autoimmune-mediated T-cell activation in the absence of active infection. To better understand the potential function of these activated plaque T cells, we then interrogated their transcriptome at the single-cell level. Of the 3 T-cell phenotypic clusters with the highest expression of the activation marker HLA-DRA , 2 clusters expressed a proinflammatory and cytolytic signature characteristic of CD8 cells, while the other expressed AREG (amphiregulin), which promotes smooth muscle cell proliferation and fibrosis, and, thus, contributes to plaque progression. Conclusions: Taken together, these findings demonstrate that plaque T cells are clonally expanded potentially by antigen engagement, are potentially reactive to self-epitopes, and may interact with smooth muscle cells and macrophages in the plaque microenvironment.

The response of gamma delta (γδ) T cells in the acute versus chronic phases of the same infection is unclear. How γδ T cells function in acute Mycobacterium tuberculosis (Mtb) infection is well characterized, but their response during persistent Mtb infection is not well understood, even though most infections with Mtb manifest as a chronic, clinically asymptomatic state. Here, we analyze peripheral blood γδ T cells from a South African adolescent cohort and show that a unique CD8 ⁺ γδ T cell subset with features of “memory inflation” expands in chronic Mtb infection. These cells are hyporesponsive to T cell receptor (TCR)–mediated signaling but, like NK cells, can mount robust CD16-mediated cytotoxic responses. These CD8 ⁺ γδ T cells comprise a highly focused TCR repertoire, with clonotypes that are Mycobacterium specific but not phosphoantigen reactive. Using multiparametric single-cell pseudo-time trajectory analysis, we identified the differentiation paths that these CD8 ⁺ γδ T cells follow to develop into effectors in this infection state. Last, we found that circulating CD8 ⁺ γδ T cells also expand in other chronic inflammatory conditions, including cardiovascular disease and cancer, suggesting that persistent antigenic exposure may drive similar γδ T cell effector programs and differentiation fates.

Background: The triglyceride-glucose (TyG) index, an insulin resistance marker linked to the progression of metabolic dysfunction-associated steatotic liver disease (MASLD), underscores the redox imbalance-mediated crosstalk between MASLD and cardiovascular-liver-metabolic health (CLMH), although its causal mechanisms and molecular drivers remain unresolved. Methods: We employed a multi-omics framework to integrate Mendelian randomization (MR) and transcriptome-wide association studies (TWAS). MR leveraged 192 genome-wide significant single-nucleotide polymorphisms for TyG from the UK Biobank, employing inverse-variance weighted (IVW) and generalized summary-data MR (GSMR). Transcriptomic integration utilized four approaches: Multi-marker Analysis of GenoMic Annotation for gene-set enrichment; Joint-Tissue Imputation PrediXcan (JTI-PrediXcan) for tissue-specific expression; Sparse Multi-Tissue Imputation Xcan (SMulTiXcan) for cross-tissue meta-analysis; and Fine-mapping of Causal Gene Sets (FOCUS) for Bayesian fine-mapping. Comorbid genes were validated using Functional Summary-based Imputation (FUSION) and prioritized based on the Polygenic Priority Score (PoPS). Single-cell spatial transcriptomics (sc-ST) in embryonic mice (E16.5) mapped tissue-specific expression via genetically informed spatial mapping (gsMap). Results: The MR analysis demonstrated a causal effect of TyG on MASLD risk [IVW: odds ratio (OR) = 1.58, 95% CI = 1.04–2.38, P = 0.030; GSMR: OR = 1.43, 95% CI = 1.27–1.61, P = 5.20 × 10 ⁻⁹ ]. TWAS identified 12 comorbid genes (C2orf16/SPATA31H1, FNDC4, GCKR, GMIP, HAPLN4, LPAR2, MAU2, MEF2B, NDUFA13, NRBP1, TM6SF2, and ZNF513). Independent validation using the FUSION framework confirmed nine TyG-MASLD comorbid genes with genome-wide significant false discovery rate-adjusted associations. Notably, TM6SF2 (TyG-PoPS = 7.2491) and GCKR (TyG-PoPS = 6.7102) showed strong positive associations in TyG, whereas NDUFA13 exhibited negative scores in MASLD (PoPS = −0.5028). Spatial mapping revealed conserved enrichment of APOA1, APOB, and APOC4 (sc-ST, P < 0.001) in murine liver and vascular tissues. Organ-specific analysis showed significant MASLD signals including the liver (sc-ST, P = 6.43 × 10 ⁻⁵ ), adrenal gland (Cauchy P = 0.0064), and connective tissue (sc-ST, P = 3.29 × 10 ⁻⁵ ). Conclusion: This study establishes TyG as a causal MASLD driver mediated by redox-sensitive hubs and evolutionarily conserved apolipoproteins, linking hepatic lipid peroxidation to systemic metabolic dysregulation. Targeting these pathways may mitigate dual hepatic-cardiovascular risks, advancing precision therapies for CLMH.

Ambient air pollution aggravates cardiovascular-kidney-metabolic (CKM) disorders and sarcopenia, yet the shared genetic and epigenetic mechanisms that underlie their frequent co-occurrence remain poorly understood. We integrated genome-wide association study (GWAS) data for CKM components (cardiovascular disease [CVD], chronic kidney disease [CKD], metabolic syndrome), CKM-related cardiovascular events, and sarcopenia diagnostic criteria from European-ancestry cohorts, and conducted meta-analyses harmonizing each phenotype across at least three studies. We employed Mendelian Randomization (MR) to assess potential causal links and genetic correlation analyses (global and local) to quantify shared heritability. Multi-omics analyses included two sequential phases: Phase 1 identified and validated novel shared CKM-sarcopenia genes through integrated methylation (n = 1980) and expression (n = 31,684) analyses, followed by cross-validation using two complementary transcriptome-wide association studies (TWAS). Phase 2 prioritized druggable targets through proteomic analysis across five independent cohorts (deCODE, n = 35,559; UK Biobank Pharma Proteomics Project (UKB-PPP), n = 54,219; Fenland, n = 10,708; FinnGen Olink, n = 619; FinnGen Somascan, n = 828) and integrated colocalization. MR suggested genetically predicted associations between sarcopenia and CKM; genetically slower walking pace was associated with higher CVD risk (OR = 0.85, P = 9.56 × 10^-6) and metabolic syndrome risk (OR = 0.43, P = 3.90 × 10^-17), while conversely, genetically predicted lower appendicular lean mass exhibited inverse associations with heart failure with heart failure and atrial fibrillation. Multi-omics identified key shared genes (ANAPC4, UNC50, TPO), with ANAPC4 methylation sites linked to CVD (cg13918811, P_adj = 0.0212) and reduced muscle mass (cg04009456, P_adj = 0.0049). Blood-based analyses identified 13 air pollution-associated comorbid genes, primarily responsive to PM_2.5/NO₂, with 11 confirmed by cross-tissue validation. Proteomics (F-statistics > 10) revealed potential targets linking CKM/sarcopenia (HP, FCGR3B, GALNT2) and CKM-events/sarcopenia (SERPINA1, FER). Ambient air pollution likely promotes CKM-sarcopenia comorbidity chiefly via inflammatory signaling and epigenetic modifications. Our multi-omics integration reveals convergent pathways, candidate driver genes, and differential methylation sites that link these conditions. We propose these targets for environmental mitigation and molecular intervention, which require validation in diverse populations.

Background: Migraine, a debilitating neurological disorder with distinct subtypes (migraine with aura [MA] and migraine without aura [MO]), exhibits genetic and spatial heterogeneity that remains poorly understood. While genetic correlations between subtypes are established, spatially resolved molecular mechanisms driving their divergent clinical phenotypes—particularly in tissue microenvironments—are unclear, limiting targeted therapeutic development. Methods: We integrated genome-wide association study (GWAS) data from FinnGen R11 and international cohorts with transcriptomic, epigenomic, and spatially resolved single-cell spatial transcriptomics (sc-ST) profiles. Genetic correlations and functional annotations were assessed using Linkage Disequilibrium Score Regression (LDSC), High-Definition Likelihood (HDL), and partitioned heritability analyses. A multi-omics framework combined Summary Mendelian Randomization (SMR) for expression and methylation quantitative trait loci (eQTL/mQTL), Functional Summary-based Imputation (FUSION), Multi-marker Analysis of GenoMic Annotation (MAGMA), Joint-Tissue Imputation Enhanced PrediXcan Analysis (JTI-PrediXcan), and the Polygenic Priority Score (PoPS) to systematically prioritize genes based on methodological robustness (≥ 2 analytical approaches) and cross-subtype consistency. Tissue-enriched specificity was validated via genetically informed spatial mapping of cells for complex traits (gsMap), a novel algorithm integrating sc-ST and GWAS data to map subtype-associated cellular architectures at single-cell resolution across embryonic tissues. Results: LDSC and HDL confirmed strong genetic correlations between MA and MO. But they showed divergent functional architectures in functional genomic annotations, with MA enriched in conserved regulatory elements (e.g., Backgrd_Selection_StatL2_0, enrichment = 1.38, P = 5.47 × 10⁻⁶) and MO in vascular pathways (e.g., GERP.NSL2_0, enrichment = 2.12, P = 1.04 × 10⁻⁶). Sc-ST revealed spatially divergent niches: MA showed prenatal enrichment in neural crest-derived tissues (jaw primordium, p = 0.0039) and hypothalamic microglial adjacencies, aligning with neuroimmune regulation, while MO exhibited peripheral tropism in vascular smooth muscle and gut-brain interfaces, corroborated by LDSC-SEG/MAGMA vascular pathways. Multi-omics integration identified high-confidence cross-subtype genes (LRP1 [PoPS: Overall = 3.67, MO = 0.80], PHACTR1 [PoPS: Overall = 2.65, MA = 0.33, MO = 1.28], STAT6 [PoPS: Overall = 3.00, MO = 2.29], RDH16, TTC24, ZBTB39, FHL5, MEF2D, NAB2, UFL1, and REEP3) supported by ≥ 2 methods. Subtype-specific genes included MA-associated neuronal regulators (CACNA1A, KLHDC8B) and MO-specific vascular/metabolic genes (e.g., ACO2, BCAR1, CCDC134). Conclusion: Our study delineates spatially constrained mechanisms underlying migraine heterogeneity: MA arises from neuroimmune-epigenetic dysregulation, while MO is driven by vascular-metabolic perturbations. Key genes and pathways provide actionable targets for subtype-specific therapies. By bridging genetic architecture with spatial biology, we redefine migraine pathogenesis and precision intervention strategies.

Background: Peripheral vascular disease remains a leading cause of vascular morbidity and mortality worldwide despite advances in medical and surgical therapy. Besides traditional approaches, which can only restore blood flow to native arteries, an alternative approach is to enhance the growth of new vessels, thereby facilitating the physiological response to ischemia. Methods: The Actin ^CreER /R26 ^VT2/GK3 Rainbow reporter mouse was used for unbiased in vivo survey of injury-responsive vasculogenic clonal formation. Prospective isolation and transplantation were used to determine vessel-forming capacity of different populations. Single-cell RNA-sequencing was used to characterize distinct vessel-forming populations and their interactions. Results: Two populations of distinct vascular stem/progenitor cells (VSPCs) were identified from adipose-derived mesenchymal stromal cells: VSPC1 is CD45-Ter119-Tie2+PDGFRa-CD31+CD105 ^high Sca1 ^low , which gives rise to stunted vessels (incomplete tubular structures) in a transplant setting, and VSPC2 which is CD45-Ter119-Tie2+PDGFRa+CD31-CD105 ^low Sca1 ^high and forms stunted vessels and fat. Interestingly, cotransplantation of VSPC1 and VSPC2 is required to form functional vessels that improve perfusion in the mouse hindlimb ischemia model. Similarly, VSPC1 and VSPC2 populations isolated from human adipose tissue could rescue the ischemic condition in mice. Conclusions: These findings suggest that autologous cotransplantation of synergistic VSPCs from nonessential adipose tissue can promote neovascularization and represents a promising treatment for ischemic disease.