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

XINA: A Workflow for the Integration of Multiplexed Proteomics Kinetics Data with Network Analysis

Quantitative proteomics experiments, using for instance isobaric tandem mass tagging approaches, are conducive to measuring changes in protein abundance over multiple time points in response to one or more conditions or stimulations. The aim is often to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with coabundance patterns may have common molecular functions related to a given stimulation. In order to facilitate the identification and analyses of coabundance patterns within and across conditions, we previously developed a software inspired by the isobaric mass tagging method itself. Specifically, multiple data sets are tagged in silico and combined for subsequent subgrouping into multiple clusters within a single output depicting the variation across all conditions, converting a typical inter-data-set comparison into an intra-data-set comparison. An updated version of our software, XINA, not only extracts coabundance profiles within and across experiments but also incorporates protein-protein interaction databases and integrative resources such as KEGG to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs. In this report, we compare the kinetics profiles of >5600 unique proteins derived from three macrophage cell culture experiments and demonstrate through intuitive visualizations that XINA identifies key regulators of macrophage activation via their coabundance patterns.

Tissue factor pathway inhibitor in atherosclerosis

Tissue factor pathway inhibitor (TFPI) reduces the development of atherosclerosis by regulating tissue factor (TF) mediated coagulation pathway. In this review, we focus on recent findings on the inhibitory effects of TFPI on endothelial cell activation, vascular smooth muscle cell (VSMC) proliferation and migration, inflammatory cell recruitment and extracellular matrix which are associated with the development of atherosclerosis. Meanwhile, we are also concerned about the impact of TFPI levels and genetic polymorphisms on clinical atherogenesis. This article aims to explain the mechanism in inhibiting the development of atherosclerosis and clinical effects of TFPI, and provide new ideas for the clinical researches and mechanism studies of atherothrombosis.

The Myeloid Cell Compartment-Cell by Cell

Myeloid cells are a major cellular compartment of the immune system comprising monocytes, dendritic cells, tissue macrophages, and granulocytes. Models of cellular ontogeny, activation, differentiation, and tissue-specific functions of myeloid cells have been revisited during the last years with surprising results; for example, most tissue macrophages are yolk sac derived, monocytes and macrophages follow a multidimensional model of activation, and tissue signals have a significant impact on the functionality of all these cells. While these exciting results have brought these cells back to center stage, their enormous plasticity and heterogeneity, during both homeostasis and disease, are far from understood. At the same time, the ongoing revolution in single-cell genomics, with single-cell RNA sequencing (scRNA-seq) leading the way, promises to change this. Prevailing models of hematopoiesis with distinct intermediates are challenged by scRNA-seq data suggesting more continuous developmental trajectories in the myeloid cell compartment. Cell subset structures previously defined by protein marker expression need to be revised based on unbiased analyses of scRNA-seq data. Particularly in inflammatory conditions, myeloid cells exhibit substantially vaster heterogeneity than previously anticipated, and work performed within large international projects, such as the Human Cell Atlas, has already revealed novel tissue macrophage subsets. Based on these exciting developments, we propose the next steps to a full understanding of the myeloid cell compartment in health and diseases.

Macrophages and Cardiovascular Health

Research during the last decade has generated numerous insights on the presence, phenotype, and function of myeloid cells in cardiovascular organs. Newer tools with improved detection sensitivities revealed sizable populations of tissue-resident macrophages in all major healthy tissues. The heart and blood vessels contain robust numbers of these cells; for instance, 8% of noncardiomyocytes in the heart are macrophages. This number and the cell's phenotype change dramatically in disease conditions. While steady-state macrophages are mostly monocyte independent, macrophages residing in the inflamed vascular wall and the diseased heart derive from hematopoietic organs. In this review, we will highlight signals that regulate macrophage supply and function, imaging applications that can detect changes in cell numbers and phenotype, and opportunities to modulate cardiovascular inflammation by targeting macrophage biology. We strive to provide a systems-wide picture, i.e., to focus not only on cardiovascular organs but also on tissues involved in regulating cell supply and phenotype, as well as comorbidities that promote cardiovascular disease. We will summarize current developments at the intersection of immunology, detection technology, and cardiovascular health.

Macrophage Biology, Classification, and Phenotype in Cardiovascular Disease: JACC Macrophage in CVD Series (Part 1)

Macrophages represent one of the most numerous and diverse leukocyte types in the body. Furthermore, they are important regulators and promoters of many cardiovascular disease programs. Their functions range from sensing pathogens to digesting cell debris, modulating inflammation, and producing key cytokines and other regulatory factors throughout the body. Macrophage research has undergone a renaissance in recent years, which has propelled a newfound interest in their heterogeneity as well as a new understanding of ontological differences in their development. In addition, recent technological advances such as single-cell mass-cytometry by time-of-flight have enabled phenotype and functional analyses of individual immune myeloid cells, including macrophages, at unprecedented resolution. In this Part 1 of a 4-part review series covering the macrophage in cardiovascular disease, we focus on the basic principles of macrophage development, heterogeneity, phenotype, tissue-specific differentiation, and functionality as a basis to understand their role in cardiovascular disease.

Inflammation, Immunity, and Infection in Atherothrombosis: JACC Review Topic of the Week

Observations on human and experimental atherosclerosis, biomarker studies, and now a large-scale clinical trial support the operation of immune and inflammatory pathways in this disease. The factors that incite innate and adaptive immune responses implicated in atherogenesis and in lesion complication include traditional risk factors such as protein and lipid components of native and modified low-density lipoprotein, angiotensin II, smoking, visceral adipose tissue, and dysmetabolism. Infectious processes and products of the endogenous microbiome might also modulate atherosclerosis and its complications either directly, or indirectly by eliciting local and systemic responses that potentiate disease expression. Trials with antibiotics have not reduced recurrent cardiovascular events, nor have vaccination strategies yet achieved clinical translation. However, anti-inflammatory interventions such as anticytokine therapy and colchicine have begun to show efficacy in this regard. Thus, inflammatory and immune mechanisms can link traditional and emerging risk factors to atherosclerosis, and offer novel avenues for therapeutic intervention.

Atherosclerosis in the single-cell era

PURPOSE OF REVIEW

The immune system plays a critical role in the development and modulation of atherosclerosis. New high-parameter technologies, including mass cytometry (CyTOF) and single-cell RNA sequencing (scRNAseq), allow for an encompassing analysis of immune cells. Unexplored marker combinations and transcriptomes can define new immune cell subsets and suggest their functions. Here, we review recent advances describing the immune cells in the artery wall of mice with and without atherosclerosis. We compare technologies and discuss limitations and advantages.

RECENT FINDINGS

Both CyTOF and scRNAseq on leukocytes from digested aortae show 10-30 immune cell subsets. Myeloid, T, B and natural killer cells were confirmed. Although cellular functions can be inferred from RNA-Seq data, some subsets cannot be identified based on current knowledge, suggesting they may be new cell types. CyTOF and scRNAseq each identified four B-cell subsets and three macrophage subsets in the atherosclerotic aorta. Limitations include cell death caused by enzymatic digestion and the limited depth of the scRNAseq transcriptomes.

SUMMARY

High-parameter methods are powerful tools for uncovering leukocyte diversity. CyTOF is currently more powerful at discerning leukocyte subsets in the atherosclerotic aorta, whereas scRNAseq provides more insight into their likely functions.

Lipid-driven immunometabolic responses in atherosclerosis

PURPOSE OF REVIEW

Atherosclerosis is a chronic inflammatory disease in which subendothelial infiltration of lipoproteins leads to inflamed lesions in arteries. Despite improvements in secondary prevention, most cardiovascular events cannot be avoided with current therapies. This review focuses on novel mechanistic insights on lipid-driven immune activation, which could pave the way for new anti-inflammatory treatments for atherosclerosis.

RECENT FINDINGS

Immunometabolic interactions can shape the immune response. Within atherosclerotic plaques, macrophages and T cells are the dominant immune cell populations. Using multiple mechanisms, lipoprotein-derived components activate both the innate and adaptive immune systems. Cholesterol crystals and apolipoprotein B-peptides have been shown to activate macrophages and T cells, respectively. Lipoproteins are also important modulators of regulatory T cells that can hamper vascular inflammation. In the liver, T cells can influence hepatic inflammation and lipoprotein metabolism. Hence, there is an intricate crosstalk between the immune system and lipoprotein metabolism.

SUMMARY

Novel treatments are needed to prevent clinical manifestations of atherosclerosis. Improved understanding of lipid-driven immunometabolic responses is likely to reveal new therapeutic targets.

2016 Jeffrey M. Hoeg Award Lecture

Innate and adaptive immune effector mechanisms, in conjunction with hyperlipidemia, are important drivers of atherosclerosis. The interaction between the different immune cells and the secretion of cytokines and chemokines determine the progression of atherosclerosis. The activation or dampening of the immune response is tightly controlled by immune checkpoints. Costimulatory and coinhibitory immune checkpoints represent potential targets for immune modulatory therapies for atherosclerosis. This review will discuss the current knowledge on immune checkpoints in atherosclerosis and the clinical potential of immune checkpoint targeted therapy for atherosclerosis.

Myeloid cell contributions to cardiovascular health and disease

Recent advances in cell tracing and sequencing technologies have expanded our knowledge on leukocyte behavior. As a consequence, inflammatory cells, such as monocyte-derived macrophages, and their actions and products are increasingly being considered as potential drug targets for treatment of atherosclerosis, myocardial infarction and heart failure. Particularly promising developments are the identification of harmful arterial and cardiac macrophage subsets, the cells' altered, sometimes even clonal production in hematopoietic organs, and epigenetically entrained memories of myeloid progenitors and macrophages in the setting of cardiovascular disease. Given the roles of monocytes and macrophages in host defense, intricately understanding the involved cellular subsets, sources and functions is essential for the design of precision therapeutics that preserve protective innate immunity. Here I review how new clinical and preclinical data, often linking the cardiovascular, immune and other organ systems, propel conceptual advances to a point where cardiovascular immunotherapy appears within reach.