Skip to content

Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.10.09.681522

Stage-resolved Spatial Multi-omics Reveals Myeloid Niches in Human Atherosclerotic Plaques

Hou, P.·Cai, H.·Liu, Z.·Fang, J.·Wang, Z.·Wang, S.·Lyu, Q.·Li, P.·Shao, C.·Melino, G.·Ley, K.·Hu, B.·Shi, Y.

View original source ↗Export metadata ↓

Abstract

BackgroundAtherosclerosis, a leading cause of heart attack and stroke, involves intricate immune cell dynamics within arterial plaques, yet their spatial organization and functional roles remain elusive. MethodsWe combined Visium HD spatial transcriptomics, imaging mass cytometry, and single-cell RNA-seq across fatty-streak, advanced, and restenotic plaques to map myeloid architectures and relate them to lesion geography and extracellular matrix features. Slingshot trajectory analysis resolved macrophages differentiation path. In vitro, we tested microenvironmental and lipid cues separately: fibronectin (FN) exposure during PMA-driven THP-1 differentiation and oxidized LDL (oxLDL)-induced foam cell formation in murine bone-marrow derived macrophages (BMDMs). ResultsOur analysis identified seven macrophage subsets and two neutrophil populations with distinct spatial distribution and functional roles. In early lesions, neutrophils expressing MMP9, MPO, p47phox, TGF-{beta}1 and arachidonate 5-lipoxygenase (ALOX5), aligned with proteolysis, inflammatory processes, and endothelial-mesenchymal transition features. In advanced plaques, macrophage subsets exhibit specialized functions: Ki67+ proliferative macrophages localized near necrotic cores, sustaining local population; SPP1+ macrophages, enriched in lipid handling and tissue remodeling, are prone to apoptosis/ferroptosis, potentially promoting necrotic core expansion; and C3aR+ macrophages form antigen-presenting niches with elevated HLA-DR and CD74, engaging T cells possibly through CXCL12-CXCR4 signaling. Slingshot trajectories indicated progression from C3aR toward SPP1 remodeling states concentrated at fibronectin-rich rims. In vitro, FN increased MMP9 and TIMP1 in THP-1-derived macrophages, consistent with FN imprinting remodeling features characteristic of SPP1 macrophages in situ. Concurrently, oxLDL-treated BMDMs showed enhanced lipid-handling and remodeling modules consistent with the SPP1 program. ConclusionsThese findings define conserved myeloid niches and support a microenvironment-imprinting model that links ECM composition and lipid loading to macrophage state transitions, providing a framework for microenvironment-targeted therapies to stabilize plaques and mitigate cardiovascular risk.

Explore related subjects

pathology Preprint

Keep this discovery

Explore connections, maps & timelines

Hou, P., Cai, H., Liu, Z., Fang, J., Wang, Z., Wang, S., Lyu, Q., Li, P., Shao, C., Melino, G., Ley, K., Hu, B., Shi, Y.. 2025-10-11. Stage-resolved Spatial Multi-omics Reveals Myeloid Niches in Human Atherosclerotic Plaques. https://doi.org/10.1101/2025.10.09.681522

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

SilencioM: silencing connected interfering oligonucleotides against MAPT as a potential disease modifying therapeutic for tauopathies

Tauopathies are a diverse group of neurodegenerative diseases whose pathogenesis involves brain accumulation of misfolded, pathological tau (Microtubule Associated Protein Tau, MAPT). More than twenty tauopathies have been identified thus far that collectively impact millions of people worldwide, of which the most common is Alzheimer's disease (AD). Despite substantial efforts to develop drugs for tauopathies, no effective treatments currently exist, highlighting the urgent need for therapeutics to combat these prevalent and ruinous neurodegenerative diseases. Strategies that target tau are likely to have the greatest impact since tau is the proximal cause of their pathogenesis. Small interfering RNAs (siRNAs) have emerged as a powerful class of precision therapeutics that silence disease-causing genes through RNA interference with favorable safety profiles. Delivery challenges are rapidly being addressed, and siRNA-based approaches are poised to transform the therapeutic landscape of neurological diseases. In this study, we describe SilencioM (Silencing connected interfering oligonucleotides against MAPT) and show its efficacy in markedly reducing tau pathology after a single intracerebroventricular injection in PS19 mice, a mouse model of severe tauopathy. SilencioM targets human, primate, rat and mouse ortholog genes; thus, the same compound can proceed from efficacy studies to Investigational New Drug Application (IND)-enabling studies. SilencioM is simple to manufacture and is administered without encapsulation in lipid nanoparticles and without requirements for lipophilic conjugation, making it a promising candidate for further development as a novel therapeutic for tauopathies, including AD.

pathology↗

bioRxiv2026

SilencioMA: A single compound that targets both MAPT and APP as a potential disease modifying therapeutic for Alzheimer's Disease

Alzheimer's Disease (AD) is the most common age-related neurodegenerative disease and the leading cause of dementia worldwide. AD pathogenesis involves aggregation of amyloid-beta (A{beta}), produced from amyloidogenic proteolytic processing of Amyloid Precursor Protein (APP), and accumulation of misfolded, pathological tau (Microtubule Associated Protein Tau, MAPT). Current efforts focus on developing disease modifying therapeutics (DMTs) against single targets: A{beta} or tau. However, DMTs that concurrently target both tau and A{beta} are likely to have the greatest impact since they target both culprits of AD pathogenesis. Here we describe the development of SilencioMA, a single compound that targets both MAPT and APP messenger RNAs (mRNAs) based on silencing connected interfering oligonucleotides against MAPT and APP. Cerebrospinal fluid (CSF) administration of SilencioMA reduces A{beta} and tau and pathology after a single intracerebroventricular injection in 5XFAD/PS19 mice, an animal model of severe amyloidosis and tauopathy. SilencioMA does not rely on lipid nanoparticles or lipophilic conjugates for CSF administration. At the same time its modular design permits conjugation of ligands that facilitate transcytosis through the blood brain barrier, allowing systemic administration. Our findings provide proof-of-concept for a strategy that targets the dual A{beta} and tau pathologies of AD, and establishes a compelling foundation for further development of SilencioMA as a next-generation DMT for AD.

pathology↗

bioRxiv2026

TREM2-stimulated, PDGF-dependent macrophage-fibroblast crosstalk induces beneficial plaque remodeling in clonal hematopoiesis

Background: In Jak2V617F clonal hematopoiesis, inflammatory signaling suppresses macrophage TREM2 and promotes features of plaque instability, while therapeutic TREM2 agonism reverses plaque instability by increasing fibroblasts and fibrous cap formation. We tested whether macrophage-derived PDGFB and stromal cell PDGFR? signaling mediate this response. Methods: Low allele burden (LAB) Jak2V617F atherosclerosis models were combined with inducible Pdgfb deletion in CX3CR1-lineage monocytes/macrophages or Pdgfra deletion in Col1a2-lineage fibroblast-enriched stromal cells. Mice were treated with the TREM2 agonist 4D9. Plaque composition, macrophage-fibroblast interactions, and aortic stromal cell populations were analyzed. Human WT and JAK2V617F iPSC-derived macrophages were used for validation. Results: TREM2 activation with 4D9 increased macrophage PDGFB production and promoted fibrous cap formation in LAB Jak2V617F atherosclerosis. Deletion of Pdgfb in CX3CR1-lineage cells markedly attenuated the 4D9-mediated increase in fibrous cap area and lesional PDGFR?+ cells, establishing macrophage-derived PDGFB as a key signal for the stromal response. Consistently, Col1a2-lineage Pdgfra deletion abolished the 4D9-induced fibrous cap response without significantly altering lesion or necrotic core area. Single cell RNA-seq identified increased Fmod+ and CD26/Dpp4+ fibroblast populations associated with 4D9 treatment. Fmod+ fibroblasts represented an abundant matrix-associated population, whereas CD26+ fibroblasts showed greatest enrichment, prominent extracellular matrix, collagen organization, and matrix-remodeling programs that were enhanced by 4D9 and attenuated by Pdgfra deletion. The stromal response was also associated with reduced macrophage migration-related programs and predicted chemokine communication from CD26+ fibroblasts to macrophages which was verified by macrophage migration studies. Moreover, stromal Pdgfra deletion increased lesional CCR2+ and CCR5+ macrophages. Conclusions: In a CH model of inflammatory atherosclerosis, TREM2 activation promotes a macrophage PDGFB-stromal PDGFR? pathway that expands Fmod+ and CD26+ fibroblast populations and increases fibrous cap matrix formation. CD26+ fibroblasts impair macrophage chemotaxis in a DPP4-dependent manner, suggesting reciprocal macrophage-fibroblast communication that coordinates matrix remodeling and inflammatory cell trafficking in the plaque.

pathology↗