Harnessing Single-Cell RNA Sequencing to Better Understand How Diseased Cells Behave the Way They Do in Cardiovascular Disease

Innate and adaptive immunity in cardiovascular calcification

(2020) Livia SA. Passos et al.   ATHEROSCLEROSIS

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Endothelial heterogeneity across distinct vascular beds during homeostasis and inflammation

(2020) Ankit Jambusaria et al.   eLife

Aortic Valve Stenosis

(2020) Philip Roger Goody et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

Single-cell gene profiling and lineage tracing analyses revealed novel mechanisms of endothelial repair by progenitors

(2020) Jiacheng Deng et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcriptional and Cellular Diversity of the Human Heart

(2020) Nathan R. Tucker et al.   CIRCULATION

Single Cell RNA Sequencing in Atherosclerosis Research

(2020) Jesse W. Williams et al.   CIRCULATION RESEARCH

Sex as a Biological Variable in Atherosclerosis

(2020) Joshua J. Man et al.   CIRCULATION RESEARCH

Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing

(2020) Miao Cui et al.   DEVELOPMENTAL CELL

Vulnerable plaques and patients: state-of-the-art

(2020) Mariusz Tomaniak et al.   EUROPEAN HEART JOURNAL

Dissecting cellular crosstalk by sequencing physically interacting cells

(2020) Amir Giladi et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Integrating lineage tracing and single-cell analysis

(2020) Lin Tang   NATURE METHODS

Single-cell RNA sequencing in cardiovascular development, disease and medicine

(2020) David T. Paik et al.   Nature Reviews Cardiology

T cell subsets and functions in atherosclerosis

(2020) Ryosuke Saigusa et al.   Nature Reviews Cardiology

Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

(2020) Eddie Cano-Gamez et al.   Nature Communications

Meta-Analysis of Leukocyte Diversity in Atherosclerotic Mouse Aortas

(2020) Alma Zernecke et al.   CIRCULATION RESEARCH

Progress and applications of single-cell sequencing techniques

(2020) Aimaiti Yasen et al.   INFECTION GENETICS AND EVOLUTION

Clonally expanding smooth muscle cells promote atherosclerosis by escaping efferocytosis and activating the complement cascade

(2020) Ying Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

(2020) Hamim Zafar et al.   Nature Communications

Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination

(2020) Lars Muhl et al.   Nature Communications

Annexin A1–dependent tethering promotes extracellular vesicle aggregation revealed with single–extracellular vesicle analysis

(2020) Maximillian A. Rogers et al.   Science Advances

Immunity and Inflammation in Atherosclerosis

(2019) Dennis Wolf et al.   CIRCULATION RESEARCH

Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart

(2019) Yueli Cui et al.   Cell Reports

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Multiplexed profiling of single-cell extracellular vesicles secretion

(2019) Yahui Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Maturation of heart valve cell populations during postnatal remodeling

(2019) Alexia Hulin et al.   DEVELOPMENT

Smooth Muscle Cells Contribute the Majority of Foam Cells in ApoE (Apolipoprotein E)-Deficient Mouse Atherosclerosis

(2019) Ying Wang et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Single-Cell Transcriptional Profiling of Aortic Endothelium Identifies a Hierarchy from Endovascular Progenitors to Differentiated Cells

(2019) Samuel W. Lukowski et al.   Cell Reports

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Smooth Muscle Cell Phenotypic Diversity

(2019) Mingjun Liu et al.   ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY

Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations

(2019) Aditya S. Kalluri et al.   CIRCULATION

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis

(2019) Robert C. Wirka et al.   NATURE MEDICINE

Vascular smooth muscle cells in atherosclerosis

(2019) Gemma L. Basatemur et al.   Nature Reviews Cardiology

Comparison of Rapidly Proliferating, Multipotent Aortic Valve-Derived Stromal Cells and Valve Interstitial Cells in the Human Aortic Valve

(2019) Yuming Huang et al.   Stem Cells International

Atherosclerosis

(2019) Peter Libby et al.   Nature Reviews Disease Primers

Fibroblasts and Their Pathological Functions in the Fibrosis of Aortic Valve Sclerosis and Atherosclerosis

(2019) Singh et al.   Biomolecules

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

Single-cell immune landscape of human atherosclerotic plaques

(2019) Dawn M. Fernandez et al.   NATURE MEDICINE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data

(2019) Erica A.K. DePasquale et al.   Cell Reports

Arterial Sca1+ Vascular Stem Cells Generate De Novo Smooth Muscle for Artery Repair and Regeneration

(2019) Juan Tang et al.   Cell Stem Cell

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Immune monitoring using mass cytometry and related high-dimensional imaging approaches

(2019) Felix J. Hartmann et al.   Nature Reviews Rheumatology

Multiplexed Profiling of Single Extracellular Vesicles

(2018) Kyungheon Lee et al.   ACS Nano

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

Histone Variant H2A.Z is Required for the Maintenance of Smooth Muscle Cell Identity as Revealed by Single-Cell Transcriptomics

(2018) Fang Yao et al.   CIRCULATION

Spatiotemporal Multi-omics Mapping Generates a Molecular Atlas of the Aortic Valve and Reveals Networks Driving Disease

(2018) Florian Schlotter et al.   CIRCULATION

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine AtherosclerosisNovelty and Significance

(2018) Clément Cochain et al.   CIRCULATION RESEARCH

Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass CytometryNovelty and Significance

(2018) Holger Winkels et al.   CIRCULATION RESEARCH

Shedding light on the cell biology of extracellular vesicles

(2018) Guillaume van Niel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-Cell DNA Methylation Profiling: Technologies and Biological Applications

(2018) Ino D. Karemaker et al.   TRENDS IN BIOTECHNOLOGY

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Single-Cell Transcriptional Profiling Reveals Cellular Diversity and Intercommunication in the Mouse Heart

(2018) Daniel A. Skelly et al.   Cell Reports

Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry

(2018) Guojun Han et al.   Nature Protocols

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

DNA methylation processes in atheosclerotic plaque

(2018) Einari Aavik et al.   ATHEROSCLEROSIS

Uremic Toxin Indoxyl Sulfate Promotes Proinflammatory Macrophage Activation Via the Interplay of OATP2B1 and Dll4-Notch Signaling

(2018) Toshiaki Nakano et al.   CIRCULATION

Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models

(2018) Kyeongdae Kim et al.   CIRCULATION RESEARCH

Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels

(2018) Lina Dobnikar et al.   Nature Communications

Increased mesenchymal podoplanin expression is associated with calcification in aortic valves

(2018) Juha Näpänkangas et al.   CARDIOVASCULAR PATHOLOGY

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

Antiinflammatory Therapy with Canakinumab for Atherosclerotic Disease

(2017) Paul M Ridker et al.   NEW ENGLAND JOURNAL OF MEDICINE

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

Inflammation in atherosclerosis

(2016) Soraya Taleb   Archives of Cardiovascular Diseases

Comparison of calcification potential of valvular interstitial cells isolated from individual aortic valve cusps

(2016) Shirin Masjedi et al.   CARDIOVASCULAR PATHOLOGY

Vascular Smooth Muscle Cells in Atherosclerosis

(2016) Martin R. Bennett et al.   CIRCULATION RESEARCH

Differentiated Smooth Muscle Cells Generate a Subpopulation of Resident Vascular Progenitor Cells in the Adventitia Regulated by Klf4Novelty and Significance

(2016) Mark W. Majesky et al.   CIRCULATION RESEARCH

Atherosclerosis-Driven Treg Plasticity Results in Formation of a Dysfunctional Subset of Plastic IFNγ + Th1/TregsNovelty and Significance

(2016) Matthew J. Butcher et al.   CIRCULATION RESEARCH

Abandoning M1/M2 for a Network Model of Macrophage Function

(2016) Matthias Nahrendorf et al.   CIRCULATION RESEARCH

Endothelial Cell Dysfunction and the Pathobiology of Atherosclerosis

(2016) Michael A. Gimbrone et al.   CIRCULATION RESEARCH

Sortilin mediates vascular calcification via its recruitment into extracellular vesicles

(2016) Claudia Goettsch et al.   JOURNAL OF CLINICAL INVESTIGATION

Live cell imaging to understand monocyte, macrophage, and dendritic cell function in atherosclerosis

(2016) Sara McArdle et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Simulation of early calcific aortic valve disease in a 3D platform: A role for myofibroblast differentiation

(2016) Jesper Hjortnaes et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

(2016) Suguna Rani Krishnaswami et al.   Nature Protocols

Spectral Cytometry Has Unique Properties Allowing Multicolor Analysis of Cell Suspensions Isolated from Solid Tissues

(2016) Sandrine Schmutz et al.   PLoS One

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

PARP9 and PARP14 cross-regulate macrophage activation via STAT1 ADP-ribosylation

(2016) Hiroshi Iwata et al.   Nature Communications

Beyond vascular inflammation—recent advances in understanding atherosclerosis

(2015) Dennis Wolf et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

KLF4-dependent phenotypic modulation of smooth muscle cells has a key role in atherosclerotic plaque pathogenesis

(2015) Laura S Shankman et al.   NATURE MEDICINE

Pathophysiology of native coronary, vein graft and in-stent atherosclerosis

(2015) Kazuyuki Yahagi et al.   Nature Reviews Cardiology

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap

(2015) Sylvia T. Nurnberg et al.   PLoS Genetics

Multiple potential roles for B cells in atherosclerosis

(2014) Andrew P. Sage et al.   ANNALS OF MEDICINE

Contribution of Intimal Smooth Muscle Cells to Cholesterol Accumulation and Macrophage-Like Cells in Human Atherosclerosis

(2014) Sima Allahverdian et al.   CIRCULATION

Macrophage Activation and Polarization: Nomenclature and Experimental Guidelines

(2014) Peter J. Murray et al.   IMMUNITY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Valvular osteoclasts in calcification and aortic valve stenosis severity

(2013) Edit Nagy et al.   INTERNATIONAL JOURNAL OF CARDIOLOGY

B lymphocytes trigger monocyte mobilization and impair heart function after acute myocardial infarction

(2013) Yasmine Zouggari et al.   NATURE MEDICINE

Cellular Mechanisms of Aortic Valve Calcification

(2012) Jane A. Leopold   Circulation-Cardiovascular Interventions

A platinum-based covalent viability reagent for single-cell mass cytometry

(2012) Harris G. Fienberg et al.   CYTOMETRY PART A

Generation of human vascular smooth muscle subtypes provides insight into embryological origin–dependent disease susceptibility

(2012) Christine Cheung et al.   NATURE BIOTECHNOLOGY

The aortic valve microenvironment and its role in calcific aortic valve disease

(2011) Cindy Ying Yin Yip et al.   CARDIOVASCULAR PATHOLOGY

Comparison of gene expression profiles between human and mouse monocyte subsets

(2009) M. A. Ingersoll et al.   BLOOD

Refining Molecular Pathways Leading to Calcific Aortic Valve Stenosis by Studying Gene Expression Profile of Normal and Calcified Stenotic Human Aortic Valves

(2009) Yohan Bossé et al.   Circulation-Cardiovascular Genetics

Evolving Concepts of Cardiac Valve Dynamics

(2008) Frederick J. Schoen   CIRCULATION

The pathophysiology of vascular calcification: are osteoclast-like cells the missing link?

(2008) Z.A. Massy et al.   DIABETES & METABOLISM