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Primitive macrophages enable long-term vascularization of human heart-on-a-chip platforms
... Employing a fibrin hydrogel matrix, we co-cultured human umbilical vein endothelial cells (HUVECs) alongside human dental pulp stem cells (DPSCs). DPSCs were chosen for their enhanced efficacy in supporting vessel formation and stabilization compared to other stromal supporting cells like MSCs or fibroblasts [15][16][17]. Control tissues without CM, termed 'EC/DPSC' , were seeded with equal numbers of GFP+ HUVEC and DPSC as supporting cells for vascular formation. ...
... Control tissues without CM, termed 'EC/DPSC' , were seeded with equal numbers of GFP+ HUVEC and DPSC as supporting cells for vascular formation. In parallel, hydrogels containing the aforementioned cell mixture were used as a base with the addition of human iPSC-derived CM to create a cardiac vasculogenesis group, termed 'EC/DPSC/CM' , at a cellular composition in line with previous studies shown to create functionally robust cardiac tissues [17,18]. Representative flow cytometry analysis of iPSC-CM differentiation cultures indicated that a conservative estimate of 51.3% of differentiated cells were cTnT+ (supplemental figure S2(f)). ...
... Since our findings from transfection efficiency screening suggest that a significant proportion of supplemental EVs may have been internalized by DPSCs and not directly by ECs, it is possible that our observations of enhanced vascularization could be mediated by EC-EVs reinforcing a more pro-vasculogenic phenotype in DPSCs. We demonstrated a similar mechanism previously through a combination of single cell sequencing and secretomics in cardiac tissues incorporating primitive macrophages [17]. Specifically, primitive macrophages in co-culture acted on DPSCs to enhance their pro-vasculogenic signaling and thereby stabilize the vasculature in cardiac tissues in vitro [17]. ...
The fabrication of complex and stable vasculature in engineered cardiac tissues represents a significant hurdle towards building physiologically relevant models of the heart. Here, we implemented a 3D model of cardiac vasculogenesis, incorporating endothelial cells (EC), stromal cells, and human induced pluripotent stem cell (iPSC)-derived cardiomyocytes (CM) in a fibrin hydrogel. The presence of CMs disrupted vessel formation in 3D tissues, resulting in the upregulation of endothelial activation markers and altered extracellular vesicle (EV) signaling in engineered tissues as determined by the proteomic analysis of culture supernatant. miRNA sequencing of CM- and EC-secreted EVs highlighted key EV-miRNAs that were postulated to play differing roles in cardiac vasculogenesis, including the let-7 family and miR-126-3p in EC-EVs. In the absence of CMs, the supplementation of CM-EVs to EC monolayers attenuated EC migration and proliferation and resulted in shorter and more discontinuous self-assembling vessels when applied to 3D vascular tissues. In contrast, supplementation of EC-EVs to the tissue culture media of 3D vascularized cardiac tissues mitigated some of the deleterious effects of CMs on vascular self-assembly, enhancing the average length and continuity of vessel tubes that formed in the presence of CMs. Direct transfection validated the effects of the key EC-EV miRNAs let-7b-5p and miR-126-3p in improving the maintenance of continuous vascular networks. EC-EV supplementation to biofabricated cardiac tissues and microfluidic devices resulted in tissue vascularization, illustrating the use of this approach in the engineering of enhanced, perfusable, microfluidic models of the myocardium.
... They play a role in cardiac development (Xu et al., 2024), maintain cardiac tissue homeostasis (Nicolas-Avila et al., 2020), support electric conduction (Hulsmans et al., 2017), and contribute to the repair and regeneration of cardiac tissue (Zaman and Epelman, 2022). Moreover, recent studies have demonstrated improved contractile force, tissue functionality, and long-term vascularization when macrophages are incorporated into engineered heart tissues (Landau et al., 2024) (Lock et al., 2024) . Therefore, macrophages, included into cardiac organoids, would create a more physiologic model that better mimics the complex interactions within the heart. ...
... All these findings show that tissue-resident macrophages play an important role in maintaining functional cardiac tissue and are probably also involved in cardiac development and tissue maturation. This assumption is supported by recent studies showing that adding macrophages to engineered heart tissue improves contractile strength, functionality, and long-term vascularization (Landau et al., 2024) (Lock et al., 2024) . Whether macrophages fulfill similar functions in the described cardiac organoids, leading to more mature and functional tissue models with properties like the heart in vivo, needs to be carefully investigated in future studies and is beyond the scope of this brief report. ...
The heart is the first functional organ to develop during embryogenesis, forming in parallel with the vasculature and hematopoietic cell lineages. To advance our understanding of human cardiac development and disease, human induced pluripotent stem cell-derived cardiomyocytes offer a promising in vitro model. However, conventional 2D culture systems lack the complexity required to recapitulate the intricate interactions of different cell types leading to fully functional and mature cardiac tissue. Here, we present a cardiac organoid model that mimics several aspects of cardiogenesis. The cardiac organoids develop a complex tissue architecture, including functional myocardium consisting of cardiomyocytes and fibroblasts capable of spontaneous rhythmic contractions. The myocardium is interspersed with a branched endothelial network. Additionally, macrophages develop within the organoids and integrate into the myocardium.
In summary, we describe a complex 3D cell culture platform to study human heart tissue development with all the involved cell types (cardiomyocytes, fibroblasts, endothelial cells, macrophages), paving the way for new insights into the role of macrophages in cardiac development and disease.
... 82 To generate stably vascularized tissues, with microvasculature comparable to the size of capillaries, it was necessary to incorporate primitive macrophages, that fulfill the roles similar to those of resident macrophages, into a co-culture consisting of iPSC-derived CM, endothelial cells, and stromal cells. 83 Ultimately, developing functional vascularized heart-on-a-chip systems may provide immune cell circulation, thereby enhancing our understanding of systemic infection and inflammation observed in myocarditis and other related conditions. ...
... Current models have recapitulated the anisotropic architecture of cardiac tissue using substrate microfabrication techniques and have achieved fundamental electromechanical coupling functions through the integration of electroconductive materials. Although current inflammatory heart-on-a-chip models have successfully incorporated monocytes and primitive macrophages, 83 these innate immunogenic cells only partially recapitulate the immune response. Albeit challenging, future models would benefit from incorporating relevant cells, including dendritic cells, neutrophils, and adaptive immune cells such as T lymphocytes and B lymphocytes, into current coculture systems to achieve a more comprehensive understanding of the immune response observed in COVID-19 patients. ...
Cardiovascular diseases are the leading cause of morbidity and mortality worldwide with numerous inflammatory cell etiologies associated with impaired cardiac function and heart failure. Inflammatory cardiomyopathy, also known as myocarditis, is an acquired cardiomyopathy characterized by inflammatory cell infiltration into the myocardium with a high risk of progression to deteriorated cardiac function. Recently, amidst the ongoing COVID-19 pandemic, the emergence of acute myocarditis as a complication of SARS-CoV-2 has garnered significant concern. Given its mechanisms remain elusive in conjunction with the recent withdrawal of previously FDA-approved antiviral therapeutics and prophylactics due to unexpected cardiotoxicity, there is a pressing need for human-mimetic platforms to investigate disease pathogenesis, model dysfunctional features, and support pre-clinical drug screening. Traditional in vitro models for studying cardiovascular diseases have inherent limitations in recapitulating the complexity of the in vivo microenvironment. Heart-on-a-chip technologies, combining microfabrication, microfluidics, and tissue engineering techniques, have emerged as a promising approach for modeling inflammatory cardiac diseases like myocarditis. This review outlines the established and emerging conditions of inflamed myocardium, identifying key features essential for recapitulating inflamed myocardial structure and functions in heart-on-a-chip models, highlighting recent advancements, including the integration of anisotropic contractile geometry, cardiomyocyte maturity, electromechanical functions, vascularization, circulating immunity, and patient/sex specificity. Finally, we discuss the limitations and future perspectives necessary for the clinical translation of these advanced technologies.
... We anticipate that TRACE could be a versatile tool to be used in new cardiac research that involves engineered cardiac tissues. 7,8,16 The tissue strip is a basic geometry that could be a part of many complex geometries. As such, we initially printed cardiac strips. ...
Advancing cardiac tissue engineering requires innovative fabrication techniques, including 3D bioprinting and tissue maturation, to enable the generation of new muscle for repairing or replacing damaged heart tissue. Recent advances in tissue engineering have highlighted the need for rapid, high-resolution bioprinting methods that preserve cell viability and maintain structural fidelity. Traditional collagen-based bioinks gel slowly, limiting their use in bioprinting. Here, we implement TRACE (tunable rapid assembly of collagenous elements), a macromolecular crowding-driven bioprinting technique that enables the immediate gelation of collagen bioinks infused with cells. This overcomes the need for extended incubation, allowing for direct bioprinting of engineered cardiac tissues with high fidelity. Unlike methods that rely on high-concentration acidic collagen or fibrin for gelation, TRACE achieves rapid bioink stabilization without altering the biochemical composition. This ensures greater versatility in bioink selection while maintaining functional tissue outcomes. Additionally, agarose slurry provides stable structural support, preventing tissue collapse while allowing nutrient diffusion. This approach better preserves complex tissue geometries during culture than gelatin-based support baths or polydimethylsiloxane (PDMS) molds. Our results demonstrate that TRACE enables the bioprinting of structurally stable cardiac tissues with high resolution. By supporting the fabrication of biomimetic tissues, TRACE represents a promising advancement in bioprinting cardiac models and other engineered tissues.
... Therefore, the mechanism of persistence of bacteria and escape of elimination by immune cells was highlighted. Landau et al. (2024) used human primitive macrophages differentiated from pluripotent stem cells in a commercially available BioWire and iFlow platforms for hearton-a-chip modelingto demonstrate a strongly positive role of macrophages in the heart tissue microvascularization and perfusion. Lung-on-a-chip models with incorporated murine macrophages were used to study inflammatory processes of viral or bacterial nature in the lungs (Thacker et al., 2021(Thacker et al., , 2020. ...
Macrophages play crucial roles in immune responses and tissue homeostasis. Despite the fact that macrophages were described more than a century ago, they continue to be the cells of intensive interest. Advanced understanding of phenotypic diversity in macrophages holds great promise for development of cell-based therapeutic strategies. The introduction of innovative approaches in cell biology greatly enhances our ability to investigate the unique characteristics of macrophages. The review considers both classical methods to study macrophages and high-tech approaches, including single-cell sequencing, single-cell mass spectrometry, droplet microfluidics, scanning probe microscopy and atomic force spectroscopy. This review will be valuable both to specialists beginning their study of macrophages and to experienced scientists seeking to deepen their understanding of methods at the intersection of biological and physical sciences.
... Recent advancements have been achieved in the development of microscale engineered heart tissue, colloquially known as heart-on-a-chip systems, dedicated to exploring heart physiology and pathology. These heart models are constructed by amalgamating human cells, micromachining technology, and state-of-the-art sensors to emulate the human heart's architecture and functionality within a microfluidic setting [88,89]. Anticipated to catalyze a paradigm shift in drug testing, disease modeling, personalized medicine, and the management of cardiovascular diseases, these systems promise to unveil novel pathways for efficacious interventions. ...
Microfluidic technology plays a crucial role in organ-on-a-chip (OoC) systems by replicating human physiological processes and disease states, significantly advancing biomedical research and drug discovery. This article reviews the design and fabrication processes of microfluidic devices. It also explores how these technologies are integrated into OoC platforms to simulate human physiological environments, highlighting key principles, technological advances, and diverse applications. Through case studies involving the simulation of multiple organs such as the heart, liver, and lungs, the article evaluates the impact of OoC systems’ integrated microfluidic technology on drug screening, toxicity assessment, and personalized medicine. In addition, this article considers technical challenges, ethical issues, and future directions, and looks ahead to further optimizing the functionality and biomimetic precision of OoCs through innovation, emphasizing its critical role in promoting personalized medicine and precision treatment strategies.
... Recent studies have also demonstrated the potential of macrophages to address the dearth of vascularization observed in cardiac organoids. Landau et al. incorporated hiPSC-derived macrophages into heart-on-achip, observing the formation of stable and perfusable microvasculature within cardiac tissue [118]. RNA-seq analysis revealed an upregulation of pro-angiogenic and cardiac maturation markers. ...
Cardiac organoids offer sophisticated 3D structures that emulate key aspects of human heart development and function. This review traces the evolution of cardiac organoid technology, from early stem cell differentiation protocols to advanced bioengineering approaches. We discuss the methodologies for creating cardiac organoids, including self-organization techniques, biomaterial-based scaffolds, 3D bioprinting, and organ-on-chip platforms, which have significantly enhanced the structural complexity and physiological relevance of in vitro cardiac models. We examine their applications in fundamental research and medical innovations, highlighting their potential to transform our understanding of cardiac biology and pathology. The integration of multiple cell types, vascularization strategies, and maturation protocols has led to more faithful representations of the adult human heart. However, challenges remain in achieving full functional maturity and scalability. We critically assess the current limitations and outline future directions for advancing cardiac organoid technology. By providing a comprehensive analysis of the field, this review aims to catalyze further innovation in cardiac tissue engineering and facilitate its translation to clinical applications.
... Landau et al. developed a 3D fibrin hydrogel system mixing macrophages, cardiomyocytes, human umbilical vein endothelial cells, and dental pulp stem cells. Using Biowire and iFlow Organ Chip systems, they assessed functionality and found that macrophages significantly enhanced cardiac tissue function by promoting angiogenic factors and cell-cell interactions, thus stabilizing microvascular structures and improving long-term perfusion capabilities of the cardiac chip [46]. Wu et al. fabricated a nanocomposite material using thermoplastic elastomers and quantum dots for a 3D bioprinted chip. ...
Globally, cardiovascular diseases remain among the leading causes of mortality, highlighting the urgent need for innovative research models. Consequently, the development of accurate models that simulate cardiac function holds significant scientific and clinical value for both disease research and therapeutic interventions. Cardiac organoids, which are three-dimensional structures derived from the induced differentiation of stem cells, are particularly promising. These organoids not only replicate the autonomous beating and essential electrophysiological properties of the heart but are also widely employed in studies related to cardiac diseases, drug efficacy testing, and regenerative medicine. This review comprehensively surveys the various fabrication techniques used to create cardiac organoids and their diverse applications in modeling a range of cardiac diseases. We emphasize the role of advanced technologies in enhancing the maturation and functionality of cardiac cells, ensuring that these models closely resemble native cardiac tissue. Furthermore, we discuss monitoring techniques and evaluation parameters critical for assessing the performance of cardiac organoids, considering the complex interactions within multi-organ systems. This approach is vital for enhancing precision and efficiency in drug development, allowing for more effective therapeutic strategies. Ultimately, this review aims to provide a thorough and innovative perspective on both fundamental research and clinical treatment of cardiovascular diseases, offering insights that could pave the way for future advancements in understanding and addressing these prevalent health challenges.
Graphical abstract
... Many immune cells are also embedded in human myometrium, 81 which are key regulators of cytokine signaling and should also be integrated in future models of the myometrium, similar to recent work in engineered cardiac tissue models. 82 We also anticipate that 3-D engineered myometrium models, 83 which can also be selectively doped with supporting cell types, may demonstrate enhanced maturity and sensitivity to small molecules, as observed in other engineered muscle systems. 84,85 Other tissues in the female reproductive system, such as the placenta, fetal membrane, and decidua, also produce and are impacted by cytokines [86][87][88] and prostaglandins. ...
Preterm labor is a prevalent public health problem and occurs when the myometrium, the smooth muscle layer of the uterus, begins contracting before the fetus reaches full term. Abnormal contractions of the myometrium also underlie painful menstrual cramps, known as dysmenorrhea. Both disorders have been associated with increased production of prostaglandins and cytokines, yet the functional impacts of inflammatory mediators on the contractility of human myometrium have not been fully established, in part due to a lack of effective model systems. To address this, we engineered human myometrial microtissues (μmyometrium) on compliant hydrogels designed for traction force microscopy. We then measured μmyometrium contractility in response to a panel of compounds with known contractile effects and inflammatory mediators. We observed that prostaglandin F2α, interleukin 6, and interleukin 8 induced contraction, while prostaglandin E1 and prostaglandin E2 induced relaxation. Our data suggest that inflammation may be a key factor modulating uterine contractility in conditions including, but not limited to, preterm labor or dysmenorrhea. More broadly, our μmyometrium model can be used to systematically identify the functional impact of many small molecules on human myometrium.
... The convergence of -omics and imaging techniques is powering advanced assessments of cellular phenotypes in basic science 1,2 , drug testing 3 , and regenerative medicine 4 . Further, reference human induced pluripotent stem cells (hiPSCs) and robust protocols for multilineage differentiation (e.g., cardiac muscle cells, hiPSC-CM) strengthened reproducibility 5 and extended phenotyping efforts to organoids 6,7 and organs-on-chips 8,9 . However, the cell cycle (CC) can confound these studies because gene expression, morphology, and behavior change as cells grow after division (G1 phase), duplicate their DNA (S), grow before subsequent divisions (G2), or divide (M) 10 . ...
Measuring cell structure and function along with cell cycle progression in live cell imaging has been challenging because Fluorescence Ubiquitin Cell Cycle Indicators (FUCCI) and most phenotypic sensors both utilize green (GFP) and red (RFP) fluorescence proteins. We introduce CALIPERS, a cell cycle-aware live-cell imaging method, using a custom FUCCI that spectrally multiplexes with GFP and RFP-based sensors. We validate CALIPERS in multi-color reporter epithelial and human induced pluripotent stem cell lines, co-expressing structural and functional fluorescent sensors. We demonstrate FUCCIplex's broad applications in live-cell imaging experiments, covering proliferation, migration, cardiac drug testing, and regenerative medicine.
... Having seen excellent interactions between iCMs and iMacs in a 2D setting, our next focus was to study the effect of iMacs addition on ECTs. Although majority of conventional ECT models only focused on cardiomyocytes, or a combination of cardiomyocytes and cardiac fibroblasts [58,87,88], newer studies underline the immense benefits of adding iMacs into ECTs in terms of improving tissue function [23] and vascularisation [89]. In line with these findings, addition of iMacs significantly reduced the variability in the beat rate of the tissues, improved cell alignment and iCM elongation, as well as remarkably increased tissue compaction. ...
Cardiovascular disease stands as the leading cause of death globally, claiming approximately 19 million lives in 2020. On the contrary, the development of cardiovascular drugs is experiencing a decline, largely due to the bottleneck in understanding the pathophysiology of various heart diseases and assessing the effects of drugs on healthy human hearts. The development of induced pluripotent stem cell (iPSC) technology and the availability of cardiac cell types in vitro, has resulted in a surge in efforts to fabricate human cardiac models for disease modelling and drug discovery applications. Although numerous attempts evidence successful fabrication of 3 dimensional (3D) engineered heart tissues, the innate immune cell population of the myocardium ;particularly cardiac macrophages, was until recently, overlooked. With increasing appreciation of the interactions between cardiomyocytes and macrophages in the myocardium, in this work, isogenic populations of cardiac resident-like macrophages and cardiomyocytes were generated using iPSCs, to understand the interactions between the two cell types in both 2D and 3D settings, and subjected to electric stimulation. After characterizing iPSC-derived macrophages (iMacs) and iPSC-derived cardiomyocytes (iCMs) in depth, the conditioning of iMacs to align to a cardiac resident macrophage-like phenotype in the presence of iCMs in 2D culture was explored. In coculture with iCMs, iMacs upregulated known genes expressed by cardiac resident macrophages. Additionally, in co-culture with iMacs, iCMs displayed an elongated morphology, improved calcium function and an increase in known maturation genes such as the ratio between MYH7 and MYH6 as well as SERCA2. In a 2D setting, iMacs showed the ability to electrically couple with iCMs and facilitate synchronous beating in iCM cultures. The 2D characterisation was translated into an engineered cardiac tissue model, wherein, improvement in tissue characteristics in the presence of iMacs was demonstrated in terms of increased cell alignment, enhanced cardiomyocyte elongation, physiologically relevant beat rates and improved tissue compaction. Taken together, these findings may open new avenues to use iMacs in engineered cardiac tissue models, not only as an innate immune cell source, but also as a support cell type to improve cardiomyocyte function and maturation.
... Additionally, embryonic stem cells can generate LYVE1 + macrophages that mitigate myocardial stress by clearing apoptotic cells ). These differentiated macrophages also contribute to angiogenesis in engineered heart tissue models (Landau et al. 2024). ...
Macrophages are crucial in the heart’s development, function, and injury. As part of the innate immune system, they act as the first line of defense during cardiac injury and repair. After events such as myocardial infarction or myocarditis, numerous macrophages are recruited to the affected areas of the heart to clear dead cells and facilitate tissue repair. This review summarizes the roles of resident and recruited macrophages in developing cardiovascular diseases. We also describe how macrophage phenotypes dynamically change within the cardiovascular disease microenvironment, exhibiting distinct pro-inflammatory and anti-inflammatory functions. Recent studies reveal the values of targeting macrophages in cardiovascular diseases treatment and the novel bioengineering technologies facilitate engineered macrophages as a promising therapeutic strategy. Engineered macrophages have strong natural tropism and infiltration for cardiovascular diseases aiming to reduce inflammatory response, inhibit excessive fibrosis, restore heart function and promote heart regeneration. We also discuss recent studies highlighting therapeutic strategies and new approaches targeting engineered macrophages, which can aid in heart injury recovery.
Cardiovascular-kidney-metabolic syndrome is a progressive disorder driven by perturbed interorgan crosstalk among adipose, liver, kidney, and heart, leading to multiorgan dysfunction. Capturing the complexity of human cardiovascular-kidney-metabolic syndrome pathophysiology using conventional models has been challenging. Multi-organ-on-a-chip platforms offer a versatile means to study underlying interorgan signaling at different stages of cardiovascular-kidney-metabolic syndrome and bolster clinical translation.
The microvasculature, a complex network of small blood vessels, connects systemic circulation with local tissues, facilitating the nutrient and oxygen exchange that is critical for homeostasis and organ function. Engineering these structures is paramount for advancing tissue regeneration, disease modeling, and drug testing. However, replicating the intricate architecture of native vascular systems—characterized by diverse vessel diameters, cellular constituents, and dynamic perfusion capabilities—presents significant challenges. This complexity is compounded by the need to precisely integrate biomechanical, biochemical, and cellular cues. Recent breakthroughs in microfabrication, organoids, bioprinting, organ-on-a-chip platforms, and in vivo vascularization techniques have propelled the field toward faithfully replicating vascular complexity. These innovations not only enhance our understanding of vascular biology but also enable the generation of functional, perfusable tissue constructs. Here, we explore state-of-the-art technologies and strategies in microvascular engineering, emphasizing key advancements and addressing the remaining challenges to developing fully functional vascularized tissues.
Cardiac development is a complex and intricate process involving numerous molecular signals and pathways. Researchers have explored cardiac development through a long journey, starting with early studies observing morphological changes and progressing to the exploration of molecular mechanisms using various molecular biology methods. Currently, advancements in stem cell technology and sequencing technology, such as the generation of human pluripotent stem cells and cardiac organoids, multi-omics sequencing, and artificial intelligence (AI) technology, have enabled researchers to understand the molecular mechanisms of cardiac development better. Many molecular signals regulate cardiac development, including various growth and transcription factors and signaling pathways, such as WNT signaling, retinoic acid signaling, and Notch signaling pathways. In addition, cilia, the extracellular matrix, epigenetic modifications, and hypoxia conditions also play important roles in cardiac development. These factors play crucial roles at one or even multiple stages of cardiac development. Recent studies have also identified roles for autophagy, metabolic transition, and macrophages in cardiac development. Deficiencies or abnormal expression of these factors can lead to various types of cardiac development abnormalities. Nowadays, congenital heart disease (CHD) management requires lifelong care, primarily involving surgical and pharmacological treatments. Advances in surgical techniques and the development of clinical genetic testing have enabled earlier diagnosis and treatment of CHD. However, these technologies still have significant limitations. The development of new technologies, such as sequencing and AI technologies, will help us better understand the molecular mechanisms of cardiac development and promote earlier prevention and treatment of CHD in the future.
The heart, with its complex structural and functional characteristics, plays a critical role in sustaining life by pumping blood throughout the entire body to supply nutrients and oxygen. Engineered heart tissues have been introduced to reproduce heart functions to understand the pathophysiological properties of the heart and to test and develop potential therapeutics. Although numerous studies have been conducted in various fields to increase the functionality of heart tissue to be similar to reality, there are still many difficulties in reproducing the blood-pumping function of the heart. In this review, we discuss advancements in cells, biomaterials, and biofabrication in cardiac tissue engineering to achieve cardiac models that closely mimic the pumping function. Moreover, we provide insight into future directions by proposing future perspectives to overcome remaining challenges, such as scaling up and biomimetic patterning of blood vessels and nerves through bioprinting.
This Review explores the rapidly evolving field of bioengineered vasculature, a key area of focus in tissue engineering and regenerative medicine. The broad relevance of this topic is attributed to its impacts on a wide range of biological processes, enabling studies in tissue development, fundamental biology and drug discovery, and the applications in tissue engineering and regenerative medicine. We outline the design criteria for bioengineered vasculature and the methodologies for constructing these systems by self-assembly and in microfluidics, organs-on-a-chip and macroscale tubular systems that often rely on biofabrication approaches such as 3D printing. We discuss existing challenges in developing functional vasculature that closely mirrors its native equivalent, including achieving hierarchical branching with organ and vessel-specific endothelial and supporting cells, providing perusable vasculature within organoids and scaling the systems for implantation and direct vascular anastomosis.
3D in vitro engineered heart tissue (EHT) models recapitulate aspects of native cardiac physiology but are often limited by scalability, cost, and reproducibility. Here, we report a simple, one-step method for rapid fabrication of molds using digital light processing (DLP)-based 3D printing that support the formation of EHTs by human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) with high reproducibility (>95% efficiency) and varied designs (e.g., length, aspect ratio). Compared to 2D iPSC-CMs, 3D EHTs display enhanced maturity, including increased expression of B-oxidation genes, higher concentrations of sarcomeric myosins, improved sarcomere density and alignment, and enrichment of cardiac pathways (e.g., upregulation of sodium channels, action potentials, contraction). The technology is applied to model pathological cardiac hypertrophy in vitro, using either (i) acute adrenergic agonism or (ii) chronic culture within stiff hydrogel molds. Treated EHTs exhibit increased levels of pathology-associated gene expression and activation of signaling cascades involved in pathological remodeling compared to untreated controls or treated 2D iPSC-CMs. Thus, our method results in robust yet simpler, cheaper, and faster EHTs to study cardiac disease.
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce ‘bridge integration’, a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a ‘dictionary’, which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit (http://www.satijalab.org/seurat), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
In this study, we report static and perfused models of human myocardial-microvascular interaction. In static culture, we observe distinct regulation of electrophysiology of human induced pluripotent stem cell derived-cardiomyocytes (hiPSC-CMs) in co-culture with human cardiac microvascular endothelial cells (hCMVECs) and human left ventricular fibroblasts (hLVFBs), including modification of beating rate, action potential, calcium handling, and pro-arrhythmic substrate. Within a heart-on-a-chip model, we subject this three-dimensional (3D) co-culture to microfluidic perfusion and vasculogenic growth factors to induce spontaneous assembly of perfusable myocardial microvasculature. Live imaging of red blood cells within myocardial microvasculature reveals pulsatile flow generated by beating hiPSC-CMs. This study therefore demonstrates a functionally vascularized in vitro model of human myocardium with widespread potential applications in basic and translational research.
Organ-on-a-chip systems that recapitulate tissue-level functions have been proposed to improve in vitro-in vivo correlation in drug development. Significant progress has been made to control the cellular microenvironment with mechanical stimulation and fluid flow. However, it has been challenging to introduce complex 3D tissue structures due to the physical constraints of microfluidic channels or membranes in organ-on-a-chip systems. Inspired by 4D bioprinting, we develop a subtractive manufacturing technique where a flexible sacrificial material can be patterned on a 2D surface, swell and shape change when exposed to aqueous hydrogel, and subsequently degrade to produce perfusable networks in a natural hydrogel matrix that can be populated with cells. The technique is applied to fabricate organ-specific vascular networks, vascularized kidney proximal tubules, and terminal lung alveoli in a customized 384-well plate and then further scaled to a 24-well plate format to make a large vascular network, vascularized liver tissues, and for integration with ultrasound imaging. This biofabrication method eliminates the physical constraints in organ-on-a-chip systems to incorporate complex ready-to-perfuse tissue structures in an open-well design.
Heart failure represents a major cause of morbidity and mortality worldwide. Single-cell transcriptomics have revolutionized our understanding of cell composition and associated gene expression. Through integrated analysis of single-cell and single-nucleus RNA-sequencing data generated from 27 healthy donors and 18 individuals with dilated cardiomyopathy, here we define the cell composition of the healthy and failing human heart. We identify cell-specific transcriptional signatures associated with age and heart failure and reveal the emergence of disease-associated cell states. Notably, cardiomyocytes converge toward common disease-associated cell states, whereas fibroblasts and myeloid cells undergo dramatic diversification. Endothelial cells and pericytes display global transcriptional shifts without changes in cell complexity. Collectively, our findings provide a comprehensive analysis of the cellular and transcriptomic landscape of human heart failure, identify cell type-specific transcriptional programs and disease-associated cell states and establish a valuable resource for the investigation of human heart failure.
Resident macrophages orchestrate homeostatic, inflammatory, and reparative activities. It is appreciated that different tissues instruct specialized macrophage functions. However, individual tissues contain heterogeneous subpopulations, and how these subpopulations are related is unclear. We asked whether common transcriptional and functional elements could reveal an underlying framework across tissues. Using single-cell RNA sequencing and random forest modeling, we observed that four genes could predict three macrophage subsets that were present in murine heart, liver, lung, kidney, and brain. Parabiotic and genetic fate mapping studies revealed that these core markers predicted three unique life cycles across 17 tissues. TLF+ (expressing TIMD4 and/or LYVE1 and/or FOLR2) macrophages were maintained through self-renewal with minimal monocyte input; CCR2+ (TIMD4−LYVE1−FOLR2−) macrophages were almost entirely replaced by monocytes, and MHC-IIhi macrophages (TIMD4−LYVE1−FOLR2−CCR2−), while receiving modest monocyte contribution, were not continually replaced. Rather, monocyte-derived macrophages contributed to the resident macrophage population until they reached a defined upper limit after which they did not outcompete pre-existing resident macrophages. Developmentally, TLF+ macrophages were first to emerge in the yolk sac and early fetal organs. Fate mapping studies in the mouse and human single-cell RNA sequencing indicated that TLF+ macrophages originated from both yolk sac and fetal monocyte precursors. Furthermore, TLF+ macrophages were the most transcriptionally conserved subset across mouse tissues and between mice and humans, despite organ- and species-specific transcriptional differences. Here, we define the existence of three murine macrophage subpopulations based on common life cycle properties and core gene signatures and provide a common starting point to understand tissue macrophage heterogeneity.
In the mouse, the first hematopoietic cells are generated in the yolk sac from the primitive, erythro-myeloid progenitor (EMP) and lymphoid programs that are specified before the emergence of hematopoietic stem cells. While many of the yolk sac-derived populations are transient, specific immune cell progeny seed developing tissues, where they function into adult life. To access the human equivalent of these lineages, we modeled yolk sac hematopoietic development using pluripotent stem cell differentiation. Here, we show that the combination of Activin A, BMP4, and FGF2 induces a population of KDR+CD235a/b+ mesoderm that gives rise to the spectrum of erythroid, myeloid, and T lymphoid lineages characteristic of the mouse yolk sac hematopoietic programs, including the Vδ2+ subset of γ/δ T cells that develops early in the human embryo. Through clonal analyses, we identified a multipotent hematopoietic progenitor with erythroid, myeloid, and T lymphoid potential, suggesting that the yolk sac EMP and lymphoid lineages may develop from a common progenitor.
Rationale: The initial hypertrophy response to cardiac pressure overload is considered compensatory, but with sustained stress, it eventually leads to heart failure. Recently, a role for recruited macrophages (mψs) in determining the transition from compensated to decompensated hypertrophy has been established. However, whether cardiac-resident immune cells influence the early phase of hypertrophy development has not been established.
Objective: To assess the role of cardiac immune cells in the early hypertrophy response to cardiac pressure overload-induced by transverse aortic constriction (TAC).
Methods and Results: We performed cytometry-by-time-of-flight to determine the identity and abundance of immune cells in the heart at 1 and 4 weeks after TAC. We observed a substantial increase in cardiac mψs 1 week after TAC. We then conducted Cite-Seq single-cell RNA sequencing of cardiac immune cells isolated from 4 sham and 6 TAC hearts. We identified 12 clusters of monocytes and mψs, categorized as either resident or recruited mψs, that showed remarkable changes in their abundance between sham and TAC conditions. To determine the role of cardiac-resident mψs early in the response to a hypertrophic stimulus, we used a blocking antibody against macrophage colony-stimulating factor 1 receptor (CD115). As blocking CD115 initially depletes all macrophages, we allowed the replenishment of recruited mψs by monocytes before performing TAC. This preferential depletion of resident mψs resulted in enhanced fibrosis and a blunted angiogenesis response to TAC. Mψ-depletion in CCR2 knockout mice showed that aggravated fibrosis was primarily caused by the recruitment of monocyte-derived mψs. Finally, 6 weeks after TAC these early events lead to depressed cardiac function and enhanced fibrosis, despite complete restoration of cardiac immune cells.
Conclusions: Cardiac resident mψs are a heterogeneous population of immune cells with key roles in stimulating angiogenesis and inhibiting fibrosis in response to cardiac pressure overload.
Fibroblasts and macrophages are universal cell types across all mammalian tissues. These cells differ in many ways including their cellular origins; dynamics of renewal, recruitment, and motility within tissues; roles in tissue structure and secretion of signaling molecules; and contributions to the activation and progression of immune responses. However, many of the features that make these two cell types unique are not opposing, but instead complementary. This review will present cell‐cell communication in this context and discuss how complementarity makes fibroblasts and macrophages highly compatible partners in the maintenance of tissue homeostasis.
The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce “weighted-nearest neighbor” analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.
A new source of mesenchymal stem cells has recently been discovered, the so-called dental pulp derived stem cells (DPSCs) which therefore could represent potentially tools for regenerative medicine. DPSC originate from the neural crest and are physiologically involved in dentin homeostasis; moreover, they contribute to bone remodeling and differentiation into several tissues including cartilage, bone, adipose and nervous tissues. DPSCs have also been shown to influence the angiogenesis process, for example through the release of secretory factors or by differentiating into vascular and/or perivascular cells. Angiogenesis, that has a pivotal role in tissue regeneration and repair, is defined as the formation of new vessels from preexisting vessels and is mediated by mutual and reciprocal interactions between endothelial cells and perivascular cells. It is also known that co-cultures of perivascular and endothelial cells (ECs) can form a vascular network in vitro and also in vivo. Since DPSCs seem to have characteristics similar to pericytes, understanding the possible mechanism of interaction between DPSCs and ECs during neo-angiogenesis is dramatically important for the development of advanced clinical application in the field of regeneration.
Graphical abstract
Cardiac arrhythmias are a primary contributor to sudden cardiac death, a major unmet medical need. Because right ventricular (RV) dysfunction increases the risk for sudden cardiac death, we examined responses to RV stress in mice. Among immune cells accumulated in the RV after pressure overload-induced by pulmonary artery banding, interfering with macrophages caused sudden death from severe arrhythmias. We show that cardiac macrophages crucially maintain cardiac impulse conduction by facilitating myocardial intercellular communication through gap junctions. Amphiregulin (AREG) produced by cardiac macrophages is a key mediator that controls connexin 43 phosphorylation and translocation in cardiomyocytes. Deletion of Areg from macrophages led to disorganization of gap junctions and, in turn, lethal arrhythmias during acute stresses, including RV pressure overload and β-adrenergic receptor stimulation. These results suggest that AREG from cardiac resident macrophages is a critical regulator of cardiac impulse conduction and may be a useful therapeutic target for the prevention of sudden death.
Background: Despite in-depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about the signals governing postnatal maturation of the human heart.
Methods: Single nucleus RNA-sequencing (snRNA-seq) of 54,140 nuclei from 9 human donors was used to profile transcriptional changes in diverse cardiac cell types during maturation from fetal stages to adulthood. Bulk RNA-sequencing and the assay for transposase-accessible chromatin using sequencing (ATAC-seq) were used to further validate transcriptional changes and to profile alterations in the chromatin accessibility landscape in purified cardiomyocyte nuclei from 21 human donors. Functional validation studies of sex steroids implicated in cardiac maturation were performed in human pluripotent stem cell-derived cardiac organoids and mice.
Results: Our data identify the progesterone receptor as a key mediator of sex-dependent transcriptional programs during cardiomyocyte maturation. Functional validation studies in human cardiac organoids and mice demonstrate the progesterone receptor drives sex-specific metabolic programs and maturation of cardiac contractile properties.
Conclusions: These data provide a blueprint for understanding human heart maturation in both sexes and reveal an important role for the progesterone receptor in human heart development.
Background
Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-free RNA constitutes a background contamination that confounds the biological interpretation of single-cell transcriptomic data.
Results
We demonstrate that contamination from this "soup" of cell-free RNAs is ubiquitous, with experiment-specific variations in composition and magnitude. We present a method, SoupX, for quantifying the extent of the contamination and estimating "background-corrected" cell expression profiles that seamlessly integrate with existing downstream analysis tools. Applying this method to several datasets using multiple droplet sequencing technologies, we demonstrate that its application improves biological interpretation of otherwise misleading data, as well as improving quality control metrics.
Conclusions
We present SoupX, a tool for removing ambient RNA contamination from droplet-based single-cell RNA sequencing experiments. This tool has broad applicability, and its application can improve the biological utility of existing and future datasets.
Cardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and therapeutic strategies require a deeper understanding of the molecular processes involved in the healthy heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavour. Here, using state-of-the-art analyses of large-scale single-cell and single-nucleus transcriptomes, we characterize six anatomical adult heart regions. Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, and reveal distinct atrial and ventricular subsets of cells with diverse developmental origins and specialized properties. We define the complexity of the cardiac vasculature and its changes along the arterio-venous axis. In the immune compartment, we identify cardiac-resident macrophages with inflammatory and protective transcriptional signatures. Furthermore, analyses of cell-to-cell interactions highlight different networks of macrophages, fibroblasts and cardiomyocytes between atria and ventricles that are distinct from those of skeletal muscle. Our human cardiac cell atlas improves our understanding of the human heart and provides a valuable reference for future studies.
The regeneration of injured spinal cord is hampered by the lack of vascular supply and neurotrophic support. Transplanting tissue‐engineered constructs with developed vascular networks and neurotrophic factors, and further understanding the pattern of vessel growth in the remodeled spinal cord tissue are greatly desired. To this end, highly vascularized scaffolds embedded with human dental pulp stem cells (DPSCs) are fabricated, which possess paracrine‐mediated angiogenic and neuroregenerative potentials. The potent pro‐angiogenic effect of the prevascularized scaffolds is first demonstrated in a rat femoral bundle model, showing robust vessel growth and blood perfusion induced within these scaffolds postimplantation, as evidenced by laser speckle contrast imaging and 3D microCT dual imaging modalities. More importantly, in a rat complete spinal cord transection model, the implantation of these scaffolds to the injured spinal cords can also promote revascularization, as well as axon regeneration, myelin deposition, and sensory recovery. Furthermore, 3D microCT imaging and novel morphometric analysis on the remodeled spinal cord tissue demonstrate substantial regenerated vessels, more significantly in the sensory tract regions, which correlates with behavioral recovery following prevascularization treatment. Taken together, prevascularized DPSC‐embedded constructs bear angiogenic and neurotrophic potentials, capable of augmenting and modulating SCI repair.
Angiogenesis and vascular maturation play important roles in tumorigenesis and tumor development. The expression of neuropilin 1 (NRP1) is closely associated with angiogenesis in tumors; however, the molecular mechanisms of action in angiogenesis and tumor maturation, as well as the potential clinical value of NRP1 remain unclear. The importance of NRP1 expression in tumor progression was determined using The Cancer Genome Atlas (TCGA) database analysis. Gain‑ and loss‑of‑function experiments of NRP1 were performed in vascular endothelial cells (ECs) to investigate the functions in angiogenesis. CCK‑8, flow cytometry, Transwell experiments and a series of in vitro experiments were used to detect cell functions. A combination of angiogenesis antibody arrays and RNA‑Seq analyses were performed to reveal the proangiogenic mechanisms of action. The function of semaphorin 4D (SEMA4D) was also investigated separately. NRP1 mRNA levels were significantly increased in primary tumors compared with normal tissues based on TCGA data (P<0.01) and were associated with tumor development in patients. Gain‑ and loss‑of‑function experiments highlighted the function of NRP1 in promoting EC proliferation, motility and capillary‑like tube formation and in reducing apoptosis. NRP1 overexpression led to significantly decreased EC markers (PECAM‑1, angiogenin, PIGF and MMP‑9) expression levels and reduced the vascular maturity. MAPK7, TPM1, RRBP1, PTPRK, HSP90A, PRKD2, PFKFB3, RGS4 and SPARC were revealed to play important roles in this process. SEMA4D was revealed to be a key protein associated with NRP1 in ECs. These data indicated that NRP1‑promoted angiogenesis may be induced at the cost of reducing maturity of the ECs. NRP1 may also be a therapeutic target for antiangiogenic strategies and a candidate prognostic marker for tumors.
Cardiovascular disease (CVD) is the leading cause of death worldwide, and extensive research has been performed to understand this disease better, using various experimental models. The endothelium plays a crucial role in the development of CVD, since it is an interface between bloodstream components, such as monocytes and platelets, and other arterial wall components. Human umbilical vein endothelial cell (HUVEC) isolation from umbilical cord was first described in 1973. To date, this model is still widely used because of the high HUVEC isolation success rate, and because HUVEC are an excellent model to study a broad array of diseases, including cardiovascular and metabolic diseases. We here review the history of HUVEC isolation, the HUVEC model over time, HUVEC culture characteristics and conditions, advantages and disadvantages of this model and finally, its applications in the area of cardiovascular diseases.
Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet (https://github.com/saeyslab/nichenetr), a method that predicts ligand–target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks. We applied NicheNet to tumor and immune cell microenvironment data and demonstrate that NicheNet can infer active ligands and their gene regulatory effects on interacting cells.
The emerging diversity of single-cell RNA-seq datasets allows for the full transcriptional characterization of cell types across a wide variety of biological and clinical conditions. However, it is challenging to analyze them together, particularly when datasets are assayed with different technologies, because biological and technical differences are interspersed. We present Harmony (https://github.com/immunogenomics/harmony), an algorithm that projects cells into a shared embedding in which cells group by cell type rather than dataset-specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. In six analyses, we demonstrate the superior performance of Harmony to previously published algorithms while requiring fewer computational resources. Harmony enables the integration of ~10⁶ cells on a personal computer. We apply Harmony to peripheral blood mononuclear cells from datasets with large experimental differences, five studies of pancreatic islet cells, mouse embryogenesis datasets and the integration of scRNA-seq with spatial transcriptomics data.
Upon inflammation, monocyte-derived macrophages (MΦ) infiltrate blood vessels to regulate several processes involved in vascular pathophysiology. However, little is known about the mediators involved. Macrophage polarization is crucial for a fast and efficient initial response (GM-MΦ) and a good resolution (M-MΦ) of the inflammatory process. The functional activity of polarized MΦ is exerted mainly through their secretome, which can target other cell types, including endothelial cells. Endoglin (CD105) is a cell surface receptor expressed by endothelial cells and MΦ that is markedly upregulated in inflammation and critically involved in angiogenesis. In addition, a soluble form of endoglin with anti-angiogenic activity has been described in inflammation-associated pathologies. The aim of this work was to identify components of the MΦ secretome involved in the shedding of soluble endoglin. We find that the GM-MΦ secretome contains metalloprotease 12 (MMP-12), a GM-MΦ specific marker that may account for the anti-angiogenic activity of the GM-MΦ secretome. Cell surface endoglin is present in both GM-MΦ and M-MΦ, but soluble endoglin is only detected in GM-MΦ culture supernatants. Moreover, MMP-12 is responsible for the shedding of soluble endoglin in vitro and in vivo by targeting membrane-bound endoglin in both MΦ and endothelial cells. These data demonstrate a direct correlation between GM-MΦ polarization, MMP-12, and soluble endoglin expression and function. By targeting endothelial cells, MMP-12 may represent a novel mediator involved in vascular homeostasis.
Generation of thick vascularized tissues that fully match the patient still remains an unmet challenge in cardiac tissue engineering. Here, a simple approach to 3D‐print thick, vascularized, and perfusable cardiac patches that completely match the immunological, cellular, biochemical, and anatomical properties of the patient is reported. To this end, a biopsy of an omental tissue is taken from patients. While the cells are reprogrammed to become pluripotent stem cells, and differentiated to cardiomyocytes and endothelial cells, the extracellular matrix is processed into a personalized hydrogel. Following, the two cell types are separately combined with hydrogels to form bioinks for the parenchymal cardiac tissue and blood vessels. The ability to print functional vascularized patches according to the patient's anatomy is demonstrated. Blood vessel architecture is further improved by mathematical modeling of oxygen transfer. The structure and function of the patches are studied in vitro, and cardiac cell morphology is assessed after transplantation, revealing elongated cardiomyocytes with massive actinin striation. Finally, as a proof of concept, cellularized human hearts with a natural architecture are printed. These results demonstrate the potential of the approach for engineering personalized tissues and organs, or for drug screening in an appropriate anatomical structure and patient‐specific biochemical microenvironment. A small biopsy of an omental tissue is taken from patients. While the cells are reprogrammed to induce pluripotent stem cells and differentiate to cardiac and endothelial cells, the extra‐cellular matrix is processed into a thermoresponsive, hydrogel‐based bioink. These components are used to 3D‐print functional vascularized cardiac patches and even small scale, whole cellularized human hearts.
Macrophages promote both injury and repair after myocardial infarction, but discriminating functions within mixed populations
remains challenging. Here we used fate mapping, parabiosis and single-cell transcriptomics to demonstrate that at steady state,
TIMD4+LYVE1+MHC-IIloCCR2− resident cardiac macrophages self-renew with negligible blood monocyte input. Monocytes partially
replaced resident TIMD4–LYVE1–MHC-IIhiCCR2− macrophages and fully replaced TIMD4−LYVE1−MHC-IIhiCCR2+ macrophages,
revealing a hierarchy of monocyte contribution to functionally distinct macrophage subsets. Ischemic injury reduced
TIMD4+ and TIMD4– resident macrophage abundance, whereas CCR2+ monocyte-derived macrophages adopted multiple cell
fates within infarcted tissue, including those nearly indistinguishable from resident macrophages. Recruited macrophages did
not express TIMD4, highlighting the ability of TIMD4 to track a subset of resident macrophages in the absence of fate mapping.
Despite this similarity, inducible depletion of resident macrophages using a Cx3cr1-based system led to impaired cardiac
function and promoted adverse remodeling primarily within the peri-infarct zone, revealing a nonredundant, cardioprotective
role of resident cardiac macrophages.
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
Paradigm-shifting studies in the mouse have identified tissue macrophage heterogeneity as a critical determinant of immune responses. In contrast, surprisingly little is known regarding macrophage heterogeneity in humans. Macrophages within the mouse heart are partitioned into CCR2- and CCR2+ subsets with divergent origins, repopulation mechanisms, and functions. Here, we demonstrate that the human myocardium also contains distinct subsets of CCR2- and CCR2+ macrophages. Analysis of sex-mismatched heart transplant recipients revealed that CCR2- macrophages are a tissue-resident population exclusively replenished through local proliferation, whereas CCR2+ macrophages are maintained through monocyte recruitment and proliferation. Moreover, CCR2- and CCR2+ macrophages have distinct functional properties, analogous to reparative CCR2- and inflammatory CCR2+ macrophages in the mouse heart. Clinically, CCR2+ macrophage abundance is associated with left ventricular remodeling and systolic function in heart failure patients. Collectively, these observations provide initial evidence for the functional importance of macrophage heterogeneity in the human heart.
Today, in vitro vessel network systems frequently serve as models for investigating cellular and functional mechanisms underlying angiogenesis and vasculogenesis. Understanding the cues triggering the observed cell migration, organization, and differentiation, as well as the time frame of these processes, can improve the design of engineered microvasculature. Here, we present first evidence of the migration of endothelial cells into the depths of the scaffold, where they formed blood vessels surrounded by extracellular matrix and supporting cells. The supporting cells presented localization-dependent phenotypes, where cells adjacent to blood vessels displayed a more mature phenotype, with smooth muscle cell characteristics, whereas cells on the scaffold surface showed a pericyte-like phenotype. Yes-associated protein (YAP), a transcription activator of genes involved in cell proliferation and tissue growth, displayed spatially dependent expression, with cells on the surface showing more nuclear YAP than cells situated deeper within the scaffold.
Drug screening with simplified 2D cell culture and relevant animal testing fail to
predict clinical outcomes. With the rising cost of drug development, predictive
3D tissue models with human cells are in urgent demand. Establishing vascular
perfusion of 3D tissues has always been a challenge, but it is necessary to
mimic drug transport and to capture complex interorgan crosstalk. Here, a
versatile multiwell plate is presented empowered by built-in microfabricated
vascular scaffolds that define the vascular space and support self-assembly of
various parenchymal tissues. In this configuration, assembly and organ-specific
function of a metabolically active liver, a free-contracting cardiac muscle, and
a metastatic solid tumor are demonstrated, tracking organ function using
noninvasive analysis techniques. By linking the 3D tumor and the liver tissue
in series, it is demonstrated that the presence of liver tissue is crucial to correctly
reveal the efficacy of a chemotherapeutic drug, Tegafur. Furthermore, the
complete cancer metastasis cascade is demonstrated across multiple organs,
where cancer cells escaping from the solid tumor can invade a distant liver
tissue connected through a continuous vascular interface. This combinatory
use of microfabricated scaffold onto a standard cell culturing platform can offer
important insights into the mechanics of complex interorgan biological events.
A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
We report the fabrication of a scaffold (hereafter referred to as AngioChip) that supports the assembly of parenchymal cells on a mechanically tunable matrix surrounding a perfusable, branched, three-dimensional microchannel network coated with endothelial cells. The design of AngioChip decouples the material choices for the engineered vessel network and for cell seeding in the parenchyma, enabling extensive remodelling while maintaining an open-vessel lumen. The incorporation of nanopores and micro-holes in the vessel walls enhances permeability, and permits intercellular crosstalk and extravasation of monocytes and endothelial cells on biomolecular stimulation. We also show that vascularized hepatic tissues and cardiac tissues engineered by using AngioChips process clinically relevant drugs delivered through the vasculature, and that millimetre-thick cardiac tissues can be engineered in a scalable manner. Moreover, we demonstrate that AngioChip cardiac tissues implanted with direct surgical anastomosis to the femoral vessels of rat hindlimbs establish immediate blood perfusion.
Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.
We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets' elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.
InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net .
Despite the advances that have been made in developing new therapeutics, cardiovascular disease remains the leading cause of worldwide mortality. Therefore, understanding the mechanisms underlying cardiovascular tissue injury and repair is of prime importance. Following cardiac tissue injury, the immune system has an important and complex role in driving both the acute inflammatory response and the regenerative response. This Review summarizes the role of the immune system in cardiovascular disease - focusing on the idea that the immune system evolved to promote tissue homeostasis following injury and/or infection, and that the inherent cost of this evolutionary development is unwanted inflammatory damage.
Crosstalk between cardiac cells is critical for heart performance. Here we show that vascular cells within human cardiac organoids (hCOs) enhance their maturation, force of contraction, and utility in disease modeling. Herein we optimize our protocol to generate vascular populations in addition to epicardial, fibroblast, and cardiomyocyte cells that self-organize into in-vivo-like structures in hCOs. We identify mechanisms of communication between endothelial cells, pericytes, fibroblasts, and cardiomyocytes that ultimately contribute to cardiac organoid maturation. In particular, (1) endothelial-derived LAMA5 regulates expression of mature sarcomeric proteins and contractility, and (2) paracrine platelet-derived growth factor receptor β (PDGFRβ) signaling from vascular cells upregulates matrix deposition to augment hCO contractile force. Finally, we demonstrate that vascular cells determine the magnitude of diastolic dysfunction caused by inflammatory factors and identify a paracrine role of endothelin driving dysfunction. Together this study highlights the importance and role of vascular cells in organoid models.
Hypertension affects one-third of the world's population, leading to cardiac dysfunction that is modulated by resident and recruited immune cells. Cardiomyocyte growth and increased cardiac mass are essential to withstand hypertensive stress; however, whether immune cells are involved in this compensatory cardioprotective process is unclear. In normotensive animals, single-cell transcriptomics of fate-mapped self-renewing cardiac resident macrophages (RMs) revealed transcriptionally diverse cell states with a core repertoire of reparative gene programs, including high expression of insulin-like growth factor-1 (Igf1). Hypertension drove selective in situ proliferation and transcriptional activation of some cardiac RM states, directly correlating with increased cardiomyocyte growth. During hypertension, inducible ablation of RMs or selective deletion of RM-derived Igf1 prevented adaptive cardiomyocyte growth, and cardiac mass failed to increase, which led to cardiac dysfunction. Single-cell transcriptomics identified a conserved IGF1-expressing macrophage subpopulation in human cardiomyopathy. Here we defined the absolute requirement of RM-produced IGF-1 in cardiac adaptation to hypertension.
To examine the role of fibronectin in vivo, we have generated mice in which the fibronectin gene is inactivated. Heterozygotes have one half normal levels of plasma fibronectin, yet appear normal. When homozygous, the mutant allele causes early embryonic lethality, proving that fibronectin is required for embryogenesis. However, homozygous mutant embryos implant and initiate gastrulation normally including extensive mesodermal movement. Neural folds also form but the mutant embryos subsequently display shortened anterior-posterior axes, deformed neural tubes and severe defects in mesodermally derived tissues. Notochord and somites are absent; the heart and embryonic vessels are variable and deformed, and the yolk sac, extraembryonic vasculature and amnion are also defective. These abnormalities can be interpreted as arising from fundamental deficits in mesodermal migration, adhesion, proliferation or differentiation as a result of the absence of fibronectin. The nature of these embryonic defects leads to reevaluation of suggested roles for fibronectin during early development based on results obtained in vitro and in embryos of other species.
Heart disease is one of the largest burdens to human health worldwide and has very limited therapeutic options. Engineered three-dimensional (3D) vascularized cardiac tissues have shown promise in rescuing cardiac function in diseased hearts and may serve as a whole organ replacement in the future. One of the major obstacles in reconstructing these thick myocardial tissues to a clinically applicable scale is the integration of functional vascular networks capable of providing oxygen and nutrients throughout whole engineered constructs. Without perfusion of oxygen and nutrient flow throughout the entire engineered tissue, not only is tissue viability compromised, but overall tissue functionality is lost. There are many supporting technologies and approaches that have been developed to create vascular networks such as 3D bioprinting, co-culturing hydrogels, and incorporation of soluble angiogenic factors. In this state-of-the-art review we discuss some of the most current engineered vascular cardiac tissues reported in the literature and future directions in the field.
Cardiomyocytes are subjected to the intense mechanical stress and metabolic demands of the beating heart. It is unclear whether these cells, which are long-lived and rarely renew, manage to preserve homeostasis on their own. While analyzing macrophages lodged within the healthy myocardium, we discovered that they actively took up material, including mitochondria, derived from cardiomyocytes. Cardiomyocytes ejected dysfunctional mitochondria and other cargo in dedicated membranous particles reminiscent of neural exophers, through a process driven by the cardiomyocyte’s autophagy machinery that was enhanced during cardiac stress. Depletion of cardiac macrophages or deficiency in the phagocytic receptor Mertk resulted in defective elimination of mitochondria from the myocardial tissue, activation of the inflammasome, impaired autophagy, accumulation of anomalous mitochondria in cardiomyocytes, metabolic alterations, and ventricular dysfunction. Thus, we identify an immune-parenchymal pair in the murine heart that enables transfer of unfit material to preserve metabolic stability and organ function.
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Single-cell transcriptomics has transformed our ability to characterize cell states, but deep biological understanding requires more than a taxonomic listing of clusters. As new methods arise to measure distinct cellular modalities, a key analytical challenge is to integrate these datasets to better understand cellular identity and function. Here, we develop a strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities. After demonstrating improvement over existing methods for integrating scRNA-seq data, we anchor scRNA-seq experiments with scATAC-seq to explore chromatin differences in closely related interneuron subsets and project protein expression measurements onto a bone marrow atlas to characterize lymphocyte populations. Lastly, we harmonize in situ gene expression and scRNA-seq datasets, allowing transcriptome-wide imputation of spatial gene expression patterns. Our work presents a strategy for the assembly of harmonized references and transfer of information across datasets.
Recent therapeutic success of large-molecule biologics has led to intense interest in assays to measure with precision their transport across the vascular endothelium and into the target tissue. Most current in vitro endothelial models show unrealistically large permeability coefficients due to a non-physiological paracellular transport. Thus, more advanced systems are required to better recapitulate and discern the important contribution of transcellular transport (transcytosis), particularly of pharmaceutically-relevant proteins. Here, a robust platform technology for the measurement of transport through a human endothelium is presented, which utilizes in vitro microvascular networks (MVNs). The self-assembled MVNs recapitulate the morphology and junctional complexity of in vivo capillaries, and express key endothelial vesicular transport proteins. This results in measured permeabilities to large molecules comparable to those observed in vivo, which are orders of magnitude lower than those measured in transwells. The permeability of albumin and immunoglobulin G (IgG), biopharmaceutically-relevant proteins, is shown to occur primarily via transcytosis, with passage of IgG regulated by the receptor FcRn. The physiological relevance of the MVNs make it a valuable tool to assess the distribution of biopharmaceuticals into tissues, and may be used to prioritize candidate molecules from this increasingly important class of therapeutics.
Tissue engineering using cardiomyocytes derived from human pluripotent stem cells holds a promise to revolutionize drug discovery, but only if limitations related to cardiac chamber specification and platform versatility can be overcome. We describe here a scalable tissue-cultivation platform that is cell source agnostic and enables drug testing under electrical pacing. The plastic platform enabled on-line noninvasive recording of passive tension, active force, contractile dynamics, and Ca2+ transients, as well as endpoint assessments of action potentials and conduction velocity. By combining directed cell differentiation with electrical field conditioning, we engineered electrophysiologically distinct atrial and ventricular tissues with chamber-specific drug responses and gene expression. We report, for the first time, engineering of heteropolar cardiac tissues containing distinct atrial and ventricular ends, and we demonstrate their spatially confined responses to serotonin and ranolazine. Uniquely, electrical conditioning for up to 8 months enabled modeling of polygenic left ventricular hypertrophy starting from patient cells.
Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics dataset, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp.
Cell communication within tissues is mediated by multiple paracrine signals including growth factors, which control cell survival and proliferation. Cells and the growth factors they produce and receive constitute a circuit with specific properties that ensure homeostasis. Here, we used computational and experimental approaches to characterize the features of cell circuits based on growth factor exchange between macrophages and fibroblasts, two cell types found in most mammalian tissues. We found that the macrophage-fibroblast cell circuit is stable and robust to perturbations. Analytical screening of all possible two-cell circuit topologies revealed the circuit features sufficient for stability, including environmental constraint and negative-feedback regulation. Moreover, we found that cell-cell contact is essential for the stability of the macrophage-fibroblast circuit. These findings illustrate principles of cell circuit design and provide a quantitative perspective on cell interactions.
Cardiac tissue engineering is currently being pursued with three different applications in mind: drug safety screening, disease modeling, and cardiac repair. Mini- and microengineered heart tissues are well suitable for drug safety screening and disease modeling. But generation of large cardiac patches of clinically relevant thickness, to functionally support the injured heart after myocardial infarction, still needs improvement. The high oxygen and nutrient demand request prevascularization of the engineered tissues in vitro prior to implantation. Vascularization and cardiac tissue development are influenced by several factors such as perfusion velocity, shear stress, coculture, extracellular matrix, mechanical strain, electrical stimulation, and many more. As engineering approaches get ever more sophisticated and bioreactors increasingly complex, cardiac tissue engineering evolves and quality control becomes more prominent. This chapter will focus on different perfusion bioreactors that aim at cultivating highly vascularized and functional engineered heart tissues by, e.g., direct perfusion through the tissue or cultivation on top of an engineered vascular bed.
Vascularization is a fundamental aspect of tissue engineering and is one of the main challenges in the field when trying to construct thick tissues. Co-culture systems have demonstrated promising potential in construction of vascularized tissues, and in enhancing graft viability and persistence in vivo. In this chapter, we discuss pivotal studies integrating co-cultures of endothelial with various types of supporting cells, aimed to generate vascularized and functional tissue. The influence of different biomaterial components, construct geometry and external mechanical stimulations on the forming vasculature, is reviewed. A comprehensive understanding of the processes leading to the formation of mature and stable vessel networks within engineered tissues will provide guidelines to enhance current protocols, which will ultimately improve integration prospects and enable the fabrication of clinically relevant, large engineered tissues.
Organ-specific functions of tissue-resident macrophages in the steady-state heart are unknown. Here, we show that cardiac macrophages facilitate electrical conduction through the distal atrioventricular node, where conducting cells densely intersperse with elongated macrophages expressing connexin 43. When coupled to spontaneously beating cardiomyocytes via connexin-43-containing gap junctions, cardiac macrophages have a negative resting membrane potential and depolarize in synchrony with cardiomyocytes. Conversely, macrophages render the resting membrane potential of cardiomyocytes more positive and, according to computational modeling, accelerate their repolarization. Photostimulation of channelrhodopsin-2-expressing macrophages improves atrioventricular conduction, whereas conditional deletion of connexin 43 in macrophages and congenital lack of macrophages delay atrioventricular conduction. In the Cd11bDTR mouse, macrophage ablation induces progressive atrioventricular block. These observations implicate macrophages in normal and aberrant cardiac conduction.
MaxQuant is one of the most frequently used platforms for mass-spectrometry (MS)-based proteomics data analysis. Since its first release in 2008, it has grown substantially in functionality and can be used in conjunction with more MS platforms. Here we present an updated protocol covering the most important basic computational workflows, including those designed for quantitative label-free proteomics, MS1-level labeling and isobaric labeling techniques. This protocol presents a complete description of the parameters used in MaxQuant, as well as of the configuration options of its integrated search engine, Andromeda. This protocol update describes an adaptation of an existing protocol that substantially modifies the technique. Important concepts of shotgun proteomics and their implementation in MaxQuant are briefly reviewed, including different quantification strategies and the control of false-discovery rates (FDRs), as well as the analysis of post-translational modifications (PTMs). The MaxQuant output tables, which contain information about quantification of proteins and PTMs, are explained in detail. Furthermore, we provide a short version of the workflow that is applicable to data sets with simple and standard experimental designs. The MaxQuant algorithms are efficiently parallelized on multiple processors and scale well from desktop computers to servers with many cores. The software is written in C# and is freely available at http://www.maxquant.org.
Macrophages inhabit all major organs, and are capable of adapting their functions to meet the needs of their home tissues. The recent recognition that tissue macrophages derive from different sources, coupled with the notion that environmental cues and inflammatory stimuli can sculpt and agitate homeostasis, provides a frame of reference from which we can decipher the breadth and depth of macrophage activity. Here we discuss macrophages residing in the cardiovascular system, focusing particularly on their development and function in steady state and disease. Central to our discussion is the tension between macrophage ontogeny as a determinant of macrophage function, and the idea that tissues condition macrophage activities and supplant the influence of macrophage origins in favor of environmental demands.
Construction of three-dimensional (3D) tissues with pre-isolated cells is a promising achievement for novel medicine and drug-discovery research. Our laboratory constructs 3D tissues with an innovative and unique method for layering multiple cell sheets. Cell sheets maintain a high-efficiently regenerating function, because of the higher cell density and higher transplantation efficiency, compared to other cell-delivery methods. Cell sheets have already been applied in clinical applications for regenerative medicine in treating patients with various diseases. Therefore, in our search to develop a more efficient treatment with cell sheets, we are constructing 3D tissues by layering cell sheets. Native animal tissues and organs have an abundance of capillaries to supply oxygen and nutrients, and to remove waste molecules. In our investigation of vascularized cardiac cell sheets, we have found that endothelial cells within cell sheets spontaneously form blood vessel networks as in vivo capillaries. To construct even thicker 3D tissues by layering multiple cell sheets, it is critical to have medium or blood flow within the vascular networks of the cell sheets. Therefore, to perfuse medium or blood in the cell sheet vascular network to maintain the viability of all cells, we developed two types of vascular beds; (1) a femoral muscle-based vascular bed, and (2) a synthetic collagen gel-based vascular bed. Both vascular beds successfully provide the critical flow of culture medium, which allows 12-layer cell sheets to survive. Such bioreactor systems, when combined with cell sheet engineering techniques, have produced functional vascularized 3D tissues. Here we explain and discuss the various processes to obtain vascular networks by properly connecting cell sheets and the engineering of 3D tissues.
Copyright © 2014. Published by Elsevier B.V.
Significance
This study addresses a fundamentally important and widely debated issue in the field of inflammation, which is why inflammation can be simultaneously deleterious after injury and yet is essential for tissue repair. Recently, an important new paradigm has emerged in the macrophage field: Organs are replete with resident macrophages of embryonic origin, distinct from monocyte-derived macrophages. In this article, we use a new model of cardiac injury and show that distinct macrophage populations derived from embryonic and adult lineages are important determinants of tissue repair and inflammation, respectively. Our data suggest that therapeutics, which inhibit monocyte-derived macrophages and/or selectively harness the function of embryonic-derived macrophages, may serve as novel treatments for heart failure.