Biology subjects

Pauli, J.

Publications and source records attributed to Pauli, J..

6 recordsLinked to original sources

bioRxiv2026

Deep Visual Proteomics links vascular smooth muscle cell phenotypes to atherosclerotic plaque stability

Vascular smooth muscle cells (VSMCs) drive atherosclerosis through phenotypic switching, yet their spatial organization and protein signatures within plaques remain poorly characterized. Here, we applied Deep Visual Proteomics (DVP) to dissect more than 500 VSMC neighborhoods across 24 human carotid plaques and profile VSMC plasticity in disease. To functionally interpret these tissue proteomes, we built a reference atlas of primary VSMCs driven toward five phenotypes by TGF-{beta}, PDGF-BB, osteogenic stimuli, IL-1{beta}, or cholesterol, quantifying over 10,000 proteins. We integrated tissue and reference proteomes with a deep-learning framework that assigns functional phenotypes to each neighborhood. This revealed spatially distinct phenotype distributions and a shift toward dedifferentiated states in unstable plaques. Knockdown of four candidates (TNC, TNFAIP2, AEBP1, PLK1) validated operational roles during phenotypic switching. Our approach functionally annotates spatial proteomes and links VSMC plasticity to plaque instability in carotid artery disease.

systems biology↗

bioRxiv2025

Single cell spatial transcriptomics integration deciphers the morphological heterogeneity of atherosclerotic carotid arteries

The process of arterial atherosclerosis is characterised by accumulation of lipids and fibrous material with accompanying inflammation. As plaques progress, they restrict blood flow and cause rupture, which results in life threatening organ ischemia and dysfunction. Although extensively studied, a clear understanding of plaque heterogeneity and mechanisms that trigger their destabilization remains elusive. Our study reveals the molecular microarchitecture of human carotid artery plaques, using bulk and single-cell RNA sequencing combined with single cell spatial transcriptomics, for which we present optimized cell segmentation algorithms. We identified distinct plaque morphologies linked to different cell type compositions, impacting early and advanced lesion formation, as well as destabilization. Spatial transcriptomics enabled us further to determine an inflammatory smooth muscle cell subtype, localize regions of neovascularization, and assign hotspots for macrophage activity within distinct cellular neighbourhoods across lesions. For different macrophage substates, we propose gradual and locally contained transdifferentiation of subluminal inflammatory HMOX1+ macrophages into a lipid-handling TREM2+ phenotype within border zones of the fibrous cap and necrotic core. Our findings provide insight into the complex heterogeneity of human atherosclerosis by unravelling location and proximity of different mural and immune cell substates involved in plaque progression and vulnerability.

cell biology↗

bioRxiv2024

Integrated single-cell atlas of human atherosclerotic plaques

Atherosclerosis, a major cause of cardiovascular diseases, is characterized by the buildup of lipids and chronic inflammation in the arteries, leading to plaque formation and potential rupture. The underlying causal immune mechanisms and alterations in structural cell composition and plasticity driving plaque progression remain incompletely defined. Recent advances in single-cell transcriptomics (scRNA-seq) have provided deeper insights into the roles of immune and non-immune cells in atherosclerosis. However, existing public scRNA-seq datasets often lack comprehensive cell type coverage and consistent annotations, posing challenges for downstream analyses. In this study, we present an integrated single-cell atlas of human atherosclerotic plaques, encompassing 261,747 high-quality annotated cells from carotid, coronary, and femoral arteries. By benchmarking and applying the best-performing data integration method, scPoli, we achieved robust cell type annotations validated by expert consensus and surface protein measurements. This comprehensive atlas enables accurate automatic cell type annotation of new datasets, optimal experimental design, and deconvolution of existing as well as novel bulk RNA-seq data to comprehensively determine cell type proportions in human atherosclerotic lesions. It facilitates future studies by providing an interactive WebUI for easy data annotation and experimental design, while supporting various downstream applications, including integration of genetic association studies and experimental planning.

cell biology↗

bioRxiv2023

INKILN is a novel long noncoding RNA promoting vascular smooth muscle inflammation

BackgroundActivation of vascular smooth muscle cells (VSMCs) inflammation is vital to initiate vascular disease. However, the role of human-specific long noncoding RNAs (lncRNAs) in VSMC inflammation is poorly understood. MethodsBulk RNA-seq in differentiated human VSMCs revealed a novel human-specific lncRNA called INflammatory MKL1 Interacting Long Noncoding RNA (INKILN). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation and human atherosclerosis and abdominal aortic aneurysm (AAA) samples. The transcriptional regulation of INKILN was determined through luciferase reporter system and chromatin immunoprecipitation assay. Both loss- and gain-of-function approaches and multiple RNA-protein and protein-protein interaction assays were utilized to uncover the role of INKILN in VSMC proinflammatory gene program and underlying mechanisms. Bacterial Artificial Chromosome (BAC) transgenic (Tg) mice were utilized to study INKLIN expression and function in ligation injury-induced neointimal formation. ResultsINKILN expression is downregulated in contractile VSMCs and induced by human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-{kappa}B site within its proximal promoter. INKILN activates the proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. Mechanistically, INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-{kappa}B pathway. INKILN depletion blocks ILI{beta}-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1, and the luciferase activity of an NF-{kappa}B reporter. Further, INKILN knockdown enhances MKL1 ubiquitination, likely through the reduced physical interaction with the deubiquitinating enzyme, USP10. INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in BAC Tg mice. ConclusionsThese findings elucidate an important pathway of VSMC inflammation involving an INKILN/MKL1/USP10 regulatory axis. Human BAC Tg mice offer a novel and physiologically relevant approach for investigating human-specific lncRNAs under vascular disease conditions.

molecular biology↗

bioRxiv2022

Utilization of an Artery-on-a-chip to unravel novel regulators and therapeutic targets in vascular diseases

IntroductionOrgans-on-chips represent novel in vitro models that have the capacity to emulate aspects of human physiology and pathophysiology by incorporating features like tissue-multicellularity and exposure to organ-relevant physical environment. We developed an artery-on-a-chip with the objective to recapitulate the structure of the arterial wall composed of intimal and medial layers and the relevant hemodynamic forces that affect luminal cells. ResultsBy comparing arteries-on-chips exposed either to in vivo-like shear stress values or kept in static conditions, we identified a panel of novel genes modulated by shear stress. We next measured the expression pattern of shear stress-modulated genes in areas of the vascular tree affected by atherosclerotic plaques and aortic aneurysms, where disease development and progression are induced by alterations of shear stress. We obtained biopsies from patients affected by carotid artery disease (CAD), comprising the atherosclerotic plaque (diseased artery) and the adjacent region (non-diseased artery). From patients with abdominal aortic aneurysms (AAA), we obtained the aneurysmal portion (diseased aorta) and non-dilated adjacent segment (non-diseased aorta). Genes modulated by shear stress followed the same expression pattern in non-diseased segments of human vessels and were expressed by endothelial and smooth muscle cells as evidenced by immunofluorescence analysis and single cell RNA sequencing. Using mice and porcine models of vascular CAD and AAA, we confirmed that shear stress mediated targets are important in discriminating diseased and non-diseased vessel portions in vivo. Furthermore, we showed that our artery-on-a-chip can serve as a platform for drug-testing. We were able to reproduce the effects of a therapeutic agent previously used in AAA animal models in artery-on-a-chip systems and extend our understanding of its therapeutic effect through a multicellular structure. ConclusionsOur novel in vitro model is capable of mimicking important physiological aspects of human arteries, such as the response to shear stress, and can further shed light on the mechanism of action of potential therapeutics before they enter the clinical stage. TeaserThe artery-on-a-chip is a novel in vitro platform that enables the mimicry of human arteries and can be used to gain insights into the development and therapeutic targeting of vascular diseases.

cell biology↗

bioRxiv2022

The circular RNA Ataxia-telangiectasia mutated (cATM) regulates oxidative stress in smooth muscle cells in expanding abdominal aortic aneurysms

An abdominal aortic aneurysm (AAA) is a pathological widening of the aortic wall characterized by loss of smooth muscle cells (SMCs), extracellular matrix degradation, and local inflammation. This condition is often asymptomatic until rupture occurs, leading to high morbidity and mortality rates. Diagnosis is often accidental, and for now, the only available treatment option remains surgical intervention. Circular RNAs (circRNAs) are RNA loops that originated from backsplicing, which have received increasing attention as a novel class of functional non-coding RNAs contributing to cardiovascular physiology and disease. Their high structural stability, combined with a remarkable enrichment in body fluids, make circRNAs promising disease biomarkers. We aimed to investigate the contribution of circRNAs to AAA pathogenesis and their potential application as biomarkers for AAA diagnosis. Combined circRNA array and quantitative real-time PCR analysis revealed the presence of differentially expressed circular transcripts stemming from AAA-relevant gene loci. Among these, the circRNA to the Ataxia-telangiectasia mutated gene (cATM) was upregulated in human AAA tissue specimens, in AAA patient-derived SMCs, and serum samples collected from aneurysm patients. In control primary aortic SMCs, cATM increased upon angiotensin II stimulation, while its silencing triggered apoptosis. Furthermore, doxorubicin could induce cATM expression, supporting a link with acute stress response in SMCs. Constitutively higher cATM expressing AAA patient-derived SMCs were less vulnerable to oxidative stress-induced cell death and survival pathways enriched when compared to control SMCs. Taken together, this data supports the role of cATM in adapting SMCs to oxidative stress in the vascular AAA micromilieu. This molecular signature provides an additional parameter to be included in procedures for AAA screening in combination with already established practices.

molecular biology↗