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Palmer JA, Rosenthal N, Teichmann SA, Litvinukova M. Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics. Circ Res 2024; 134:1681-1702. [PMID: 38843288 PMCID: PMC11149945 DOI: 10.1161/circresaha.124.323672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 06/09/2024]
Abstract
Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.
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Affiliation(s)
- Jack A. Palmer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
| | - Nadia Rosenthal
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME (N.R.)
- National Heart and Lung Institute, Imperial College London, United Kingdom (N.R.)
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom (J.A.P., S.A.T.)
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus (J.A.P., S.A.T.), University of Cambridge, United Kingdom
- Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory (S.A.T.), University of Cambridge, United Kingdom
| | - Monika Litvinukova
- University Hospital Würzburg, Germany (M.L.)
- Würzburg Institute of Systems Immunology, Max Planck Research Group at the Julius-Maximilians-Universität Würzburg, Germany (M.L.)
- Helmholtz Pioneer Campus, Helmholtz Munich, Germany (M.L.)
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2
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Salido E, de Medeiros Vieira C, Verdezoto-Mosquera J, Zade R, Miller CL, Sardo VL. The 9p21.3 coronary artery disease risk locus drives vascular smooth muscle cells to osteochondrogenic state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595888. [PMID: 38853913 PMCID: PMC11160673 DOI: 10.1101/2024.05.25.595888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Genome-wide association studies have identified common genetic variants at approximately 300 human genomic loci linked to CAD susceptibility. Among these genomic regions, the most impactful is the 9p21.3 CAD risk locus, which spans a 60 kb gene desert, encompasses about ~80 SNPs in high linkage disequilibrium, and has no defined function. We used induced pluripotent stem cell (iPSC) lines from risk and non-risk donors at 9p21.3, as well as isogenic lines with a full haplotype deletion. iPSC-derived vascular smooth muscle cells (iPSC-VSMCs) were used for single-cell transcriptomics. iPSC-VSMCs resemble the heterogeneity observed in human coronary arteries, establishing the robustness of this model. Our analysis revealed that the 9p21.3 risk haplotype prompts VSMCs to acquire a novel cellular state showing osteochondrogenic features, and we identified a set of signature genes crucial for defining this transcriptional program. Our study provides new insights into the 9p21.3 risk locus and its role in driving disease-prone states in VSMCs.
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Affiliation(s)
- Elsa Salido
- Department of Cell and Regenerative Biology; University of Wisconsin-Madison; Madison, WI 53705 USA
| | | | | | - Rohan Zade
- Department of Cell and Regenerative Biology; University of Wisconsin-Madison; Madison, WI 53705 USA
| | - Clint L Miller
- Department of Public Health Science; University of Virginia; Charlottesville, VA 22904 USA
| | - Valentina Lo Sardo
- Department of Cell and Regenerative Biology; University of Wisconsin-Madison; Madison, WI 53705 USA
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Rademakers T, Manca M, Jin H, Orban T, Perisic LM, Frissen HJM, Rühle F, Hautvast P, van Rijssel J, van Kuijk K, Mees BME, Peutz-Kootstra CJ, Heeneman S, Daemen MJAP, Pasterkamp G, Stoll M, van Zandvoort MAMJ, Hedin U, Dequiedt F, van Buul JD, Sluimer JC, Biessen EAL. Human atherosclerotic plaque transcriptomics reveals endothelial beta-2 spectrin as a potential regulator a leaky plaque microvasculature phenotype. Angiogenesis 2024:10.1007/s10456-024-09921-z. [PMID: 38780883 DOI: 10.1007/s10456-024-09921-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
The presence of atherosclerotic plaque vessels is a critical factor in plaque destabilization. This may be attributable to the leaky phenotype of these microvessels, although direct proof for this notion is lacking. In this study, we investigated molecular and cellular patterns of stable and hemorrhaged human plaque to identify novel drivers of intraplaque vessel dysfunction. From transcriptome data of a human atherosclerotic lesion cohort, we reconstructed a co-expression network, identifying a gene module strongly and selectively correlated with both plaque microvascular density and inflammation. Spectrin Beta Non-Erythrocytic 1 (sptbn1) was identified as one of the central hubs of this module (along with zeb1 and dock1) and was selected for further study based on its predominant endothelial expression. Silencing of sptbn1 enhanced leukocyte transmigration and vascular permeability in vitro, characterized by an increased number of focal adhesions and reduced junctional VE-cadherin. In vivo, sptbn1 knockdown in zebrafish impaired the development of the caudal vein plexus. Mechanistically, increased substrate stiffness was associated with sptbn1 downregulation in endothelial cells in vitro and in human vessels. Plaque SPTBN1 mRNA and protein expression were found to correlate with an enhanced presence of intraplaque hemorrhage and future cardiovascular disease (CVD) events during follow-up. In conclusion, we identify SPTBN1 as a central hub gene in a gene program correlating with plaque vascularisation. SPTBN1 was regulated by substrate stiffness in vitro while silencing blocked vascular development in vivo, and compromised barrier function in vitro. Together, SPTBN1 is identified as a new potential regulator of the leaky phenotype of atherosclerotic plaque microvessels.
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Affiliation(s)
- Timo Rademakers
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Plasma Proteins, Laboratory for Molecular Cell Biology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Marco Manca
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Han Jin
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Tanguy Orban
- Laboratory of Protein Signaling and Interactions, GIGA, Liège Université, Liège, Belgium
| | - Ljubica Matic Perisic
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institutet and Karolinska Hospital, Stockholm, Sweden
| | - Hubertus J M Frissen
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Frank Rühle
- Genetic Epidemiology, Institute of Human Genetics, University of Münster, Münster, Germany
| | - Petra Hautvast
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Jos van Rijssel
- Department of Plasma Proteins, Laboratory for Molecular Cell Biology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Kim van Kuijk
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Barend M E Mees
- Department of Vascular Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Carine J Peutz-Kootstra
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Sylvia Heeneman
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Mat J A P Daemen
- Department of Pathology, Academic Medical Center (AMC), Amsterdam, The Netherlands
| | - Gerard Pasterkamp
- Laboratory of Clinical Chemistry and Haematology, University Medical Center Utrecht, University of Utrecht, Utrecht, The Netherlands
| | - Monika Stoll
- Genetic Epidemiology, Institute of Human Genetics, University of Münster, Münster, Germany
- Maastricht Center for Systems Biology (MaCSBio, Cardiovascular Research Institute Maastricht (CARIM), Maastricht, The Netherlands
- Department of Biochemistry, Maastricht University, Maastricht, The Netherlands
| | - Marc A M J van Zandvoort
- Department of Molecular Cell Biology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - Ulf Hedin
- Division of Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institutet and Karolinska Hospital, Stockholm, Sweden
| | - Franck Dequiedt
- Laboratory of Protein Signaling and Interactions, GIGA, Liège Université, Liège, Belgium
| | - Jaap D van Buul
- Department of Plasma Proteins, Laboratory for Molecular Cell Biology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands
| | - Judith C Sluimer
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
- Department for Renal and Hypertensive, Rheumatological and Immunological Diseases (Medical Clinic II), RWTH Aachen, Aachen, Germany
| | - Erik A L Biessen
- Department of Pathology, Experimental Vascular Pathology Group, Maastricht University, PO box 5800, 6202 AZ, Maastricht, The Netherlands.
- Institute for Molecular Cardiovascular Research, RWTH Aachen, Aachen, Germany.
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Malhi NK, Luo Y, Tang X, Chadha RS, Tapia A, Liu X, Chen M, Yuan D, Qi M, Wei L, Cooke JP, Natarajan R, Southerland KW, Chen ZB. Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594235. [PMID: 38798611 PMCID: PMC11118321 DOI: 10.1101/2024.05.14.594235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Vasculopathies occur 15 years earlier in individuals with diabetes mellitus (DM) as compared to those without, but the underlying mechanisms driving diabetic vasculopathy remain incompletely understood. Endothelial cells (ECs) and macrophages (MΦ) are critical players in vascular wall and their crosstalk is crucial in diabetic vasculopathy. In diabetes, EC activation enables monocyte recruitment, which transmigrate into the intima and differentiate into macrophages (MΦ). Beyond this established model of diapedesis, EC-MΦ interplay is highly intricate and heterogenous. To capture these highly context dependent EC-MΦ interactions, we leveraged single-cell (sc)RNA-seq in conjunction with spatial transcriptome (ST)-seq profiling to analyze human mesenteric arteries from non-diabetic (ND) and type 2 diabetic (T2D) donors. We provide in this study a transcriptomic map encompassing major arterial vascular cells, e.g., EC, mononuclear phagocyte (MP), and T cells, and their interactions associated with human T2D. Furthermore, we identified Triggering Receptor Expressed on Myeloid Cells 2 ( TREM2) as a top T2D-induced gene in MP, with concomitant increase of TREM2 ligands in ECs. TREM2 induction was confirmed in mouse models of T2D and monocyte/MΦ subjected to DM-mimicking stimuli. Perturbing TREM2 with either an antibody or silencing RNA in MPs led to decreased pro-inflammatory responses in MPs and ECs and increased EC migration in vitro . In a mouse model of diabetes, TREM2 expression and its interaction with ECs are increased in the ischemic, as compared to non-ischemic muscles. Importantly, neutralization of TREM2 using a neutralizing antibody enhanced ischemic recovery and flow reperfusion in the diabetic mice, suggesting a role of TREM2 in promoting diabetic PAD. Finally, we verified that both TREM2 expression and the TREM2-EC-interaction are increased in human patients with DM-PAD. Collectively, our study presents the first atlas of human diabetic vessels with a focus on EC-MP interactions. Exemplified by TREM2, our study provides valuable insights into EC-MΦ interactions, key processes contributing to diabetic vasculopathies and the potential of targeting these interactions for therapeutic development.
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Wu X, Zhang H. Omics Approaches Unveiling the Biology of Human Atherosclerotic Plaques. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:482-498. [PMID: 38280419 PMCID: PMC10988765 DOI: 10.1016/j.ajpath.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 12/16/2023] [Accepted: 12/20/2023] [Indexed: 01/29/2024]
Abstract
Atherosclerosis is a chronic inflammatory disease of the arterial wall, characterized by the buildup of plaques with the accumulation and transformation of lipids, immune cells, vascular smooth muscle cells, and necrotic cell debris. Plaques with collagen-poor thin fibrous caps infiltrated by macrophages and lymphocytes are considered unstable because they are at the greatest risk of rupture and clinical events. However, the current histologic definition of plaque types may not fully capture the complex molecular nature of atherosclerotic plaque biology and the underlying mechanisms contributing to plaque progression, rupture, and erosion. The advances in omics technologies have changed the understanding of atherosclerosis plaque biology, offering new possibilities to improve risk prediction and discover novel therapeutic targets. Genomic studies have shed light on the genetic predisposition to atherosclerosis, and integrative genomic analyses expedite the translation of genomic discoveries. Transcriptomic, proteomic, metabolomic, and lipidomic studies have refined the understanding of the molecular signature of atherosclerotic plaques, aiding in data-driven hypothesis generation for mechanistic studies and offering new prospects for biomarker discovery. Furthermore, advancements in single-cell technologies and emerging spatial analysis techniques have unveiled the heterogeneity and plasticity of plaque cells. This review discusses key omics-based discoveries that have advanced the understanding of human atherosclerotic plaque biology, focusing on insights derived from omics profiling of human atherosclerotic vascular specimens.
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Affiliation(s)
- Xun Wu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.
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Ravindran A, Holappa L, Niskanen H, Skovorodkin I, Kaisto S, Beter M, Kiema M, Selvarajan I, Nurminen V, Aavik E, Aherrahrou R, Pasonen-Seppänen S, Fortino V, Laakkonen JP, Ylä-Herttuala S, Vainio S, Örd T, Kaikkonen MU. Translatome profiling reveals Itih4 as a novel smooth muscle cell-specific gene in atherosclerosis. Cardiovasc Res 2024:cvae028. [PMID: 38289873 DOI: 10.1093/cvr/cvae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 12/01/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024] Open
Abstract
AIMS Vascular smooth muscle cells (SMCs) and their derivatives are key contributors to the development of atherosclerosis. However, studying changes in SMC gene expression in heterogeneous vascular tissues is challenging due to the technical limitations and high cost associated with current approaches. In this paper, we apply Translating Ribosome Affinity Purification sequencing (TRAP-Seq) to profile SMC-specific gene expression directly from tissue. METHODS AND RESULTS To facilitate SMC-specific translatome analysis, we generated SMCTRAP mice, a transgenic mouse line expressing EGFP-tagged ribosomal protein L10a (EGFP-L10a) under the control of the SMC-specific αSMA promoter. These mice were further crossed with the atherosclerosis model Ldlr-/-, ApoB100/100 to generate SMCTRAP-AS mice and used to profile atherosclerosis-associated SMCs in thoracic aorta samples of 15-month-old SMCTRAP and SMCTRAP-AS mice. Our analysis of SMCTRAP-AS mice showed that EGFP-L10a expression was localized to SMCs in various tissues, including the aortic wall and plaque. The TRAP fraction demonstrated high enrichment of known SMC-specific genes, confirming the specificity of our approach. We identified several genes, including Cemip, Lum, Mfge8, Spp1, and Serpina3, that are known to be involved in atherosclerosis-induced gene expression. Moreover, we identified several novel genes not previously linked to SMCs in atherosclerosis, such as Anxa4, Cd276, Itih4, Myof, Pcdh11x, Rab31, Serpinb6b, Slc35e4, Slc8a3, and Spink5. Among them, we confirmed the SMC-specific expression of Itih4 in atherosclerotic lesions using immunofluorescence staining of mouse aortic roots and spatial transcriptomics of human carotid arteries. Furthermore, our more detailed analysis of Itih4 showed its link to coronary artery disease (CAD) through the colocalization of GWAS, splice-QTL, and protein-QTL signals. CONCLUSIONS We generated a SMC-specific TRAP mouse line to study atherosclerosis and identified Itih4 as a novel SMC-expressed gene in atherosclerotic plaques, warranting further investigation of its putative function in extracellular matrix stability and genetic evidence of causality.
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Affiliation(s)
- Aarthi Ravindran
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Lari Holappa
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Henri Niskanen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Ilya Skovorodkin
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Susanna Kaisto
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Mustafa Beter
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Miika Kiema
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Ilakya Selvarajan
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Valtteri Nurminen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Einari Aavik
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Rédouane Aherrahrou
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
- Institute for Cardiogenetics, Universität zu Lübeck; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Germany; University Heart Centre Lübeck, 23562 Lübeck, Germany
| | - Sanna Pasonen-Seppänen
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Vittorio Fortino
- Institute of Biomedicine, School of Medicine, Faculty of Health Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Johanna P Laakkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Seppo Ylä-Herttuala
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Seppo Vainio
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
| | - Tiit Örd
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Minna U Kaikkonen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
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