{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T20:21:18Z","timestamp":1792095678033,"version":"4.4.0"},"posted":{"date-parts":[[2025,5,23]]},"group-title":"Molecular Biology","reference-count":38,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T00:00:00Z","timestamp":1747958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,5,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Vascular smooth muscle cells (VSMCs) play a central role in atherosclerosis by undergoing phenotypic modulation from a quiescent, contractile state to a range of synthetic phenotypes, including fibroblast-like, macrophage-like, and lipid-laden foam cell\u2013like states. However, a comprehensive multimodal characterization and understanding of the transcriptional programs driving these transitions remain incomplete.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>To comprehensively define the phenotypic diversity of VSMCs during atherosclerosis progression, we performed in-depth profiling using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and bulk RNA sequencing in a VSMC lineage-tracing atherosclerotic mouse model. Insights from these datasets guided the design of targeted in vitro experiments to investigate candidate regulatory mechanisms.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Single-cell multi-omics revealed extensive cellular heterogeneity within atherosclerotic plaques, including a rare population of VSMC-derived macrophage-like cells, whose presence was confirmed by histological analysis. These studies also identified a substantial population of VSMC-derived foam cells, comprising approximately 70% of all foam cells in the lesions. These cells exhibited activation of gene programs associated with lipid metabolism, proliferation, and tumor-like features. The transcription factor Bhlhe40 emerged as a key regulator of this phenotypic transition, with elevated expression in VSMC-derived foam cells during disease progression. Functional knockdown of Bhlhe40 suppressed VSMC phenotypic switching and foam cell characteristics, underscoring its potential role as a driver of VSMC modulation.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>These findings advance our understanding of VSMC phenotypic modulation in atherosclerosis and highlight Bhlhe40 as a key regulator of this process. Elucidating the mechanisms governing VSMC plasticity may offer new therapeutic opportunities to reduce cardiovascular risk by targeting disease-driving cellular transitions.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.05.20.655228","type":"posted-content","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T20:35:16Z","timestamp":1748032516000},"source":"Crossref","is-referenced-by-count":2,"title":["Comprehensive Multimodal Profiling of Atherosclerosis Reveals Bhlhe40 as a Potential Regulator of Vascular Smooth Muscle Cell Phenotypic Modulation"],"prefix":"10.64898","author":[{"given":"Chinyere O.","family":"Ibikunle","sequence":"first","affiliation":[{"name":"Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, New York, NY"},{"name":"Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine Columbia University Irving Medical Center, New York, NY"},{"name":"Department of Biological Sciences, Columbia University, New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8829-7659","authenticated-orcid":false,"given":"Chenyi","family":"Xue","sequence":"additional","affiliation":[{"name":"Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, New York, NY"},{"name":"Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine Columbia University Irving Medical Center, New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9749-9930","authenticated-orcid":false,"given":"Eunyoung","family":"Kim","sequence":"additional","affiliation":[{"name":"Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, New York, NY"},{"name":"Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine Columbia University Irving Medical Center, New York, 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