Research Projects | Overview
Heart disease is the leading cause of death worldwide, posing an immense burden on global health. A significant roadblock to effective cardiac disease treatment lies in the limited capacity of the adult heart to regenerate. In contrast, the newborn mouse heart can effectively regrow the damaged tissue. Our lab aims to use systems-level approaches to discover the basic biological mechanisms underlying neonatal heart regeneration. We are interested in studying how cells in the neonatal heart detect injury signals and initiate dedifferentiation, proliferation, and eventually redifferentiation to form functional new cells? How do different cell types within the heart interact and guide each other in reconstructing the damaged tissue with appropriate cellular composition and tissue architecture? How is genetic information regulated in space and time to instruct a three-dimensional organization of cells within the regenerated heart tissue? We leverage the information learned by answering those questions to identify therapeutic targets and translate our findings into studies of human cells and therapies for heart disease patients. The long-term goal of our research program is to understand the mechanisms underlying the distinct reparative abilities of different cardiac cell types during neonatal heart regeneration vs. pathological remodeling in adults, and ultimately to generate a comprehensive cellular and molecular blueprint for targeting cardiac regeneration in patients.
The origin and identity of regenerative cardiomyocytes
Determining which CMs are regenerative is a crucial first step in understanding the molecular processes that enable their regenerative capabilities. Using single-nucleus RNA-seq, we identified a novel CM population, CM4, that is unique to newborn mice and exhibits regeneration features following injury population (Fig. 1A, B). We found that CM4 cells expressed embryonic genes that are associated with cell cycle progression (Fig. 1C) and were localized in the infarct region of the heart after injury (Fig. 1D). These characteristics suggest that CM4 cells are regenerative CMs that are responsible for tissue regrowth during regeneration. We will further demonstrate their role in regeneration using lineage tracing models and identify the molecular mechanisms that are responsible for their regeneration phenotype. We will also use multiple orthogonal approaches in parallel to most accurately construct the lineage relationship of regenerative CMs. Our hypothesis is that regenerative CMs have an inherent capacity to regenerate after injury and are characterized by a distinct transcriptome state. By identifying and manipulating this transcriptome state, we hope to be able to promote regeneration in human CMs
Plasticity of cardiac stromal cells in regeneration and disease
Stromal cells, once believed to only provide structural support, are now acknowledged as key regulators in various tissues, including the heart. Cardiac stromal cells play a crucial role in maintaining tissue homeostasis through their control of extracellular matrix remodeling, paracrine signaling, and communication with the immune system. They also play a significant role in heart regeneration, as well as the development and progression of various heart diseases. Despite this, our understanding of the dynamic facets of the cardiac stroma and the mechanisms underlying their ability to differentially regulate cardiac regeneration and disease is still limited. Our single-cell transcriptomic studies have provided insight into the phenotypic plasticity of cardiac stromal cells in response to injury, revealing distinct transcriptional profiles in regeneration and disease remodeling. We are studying the regulatory mechanisms underlying their plasticity (Fig. 2), with the goal to identify novel molecular targets to guide these cells in supporting heart repair and regeneration in adults.
Role of adaptive stress response in tissue regeneration and repair
The specific mechanisms by which cells in regenerative tissues adapt to stress conditions caused by injury during the regeneration process are still not fully understood. In our previous work (Cui, et al. Nat. Commun, 2021), we demonstrated that regenerative cardiomyocytes (CMs) not only undergo cell-cycle activation but also upregulate cell survival pathways. This finding suggests a potential co-regulation between cardioprotection and heart regeneration. Traditionally, cardioprotection and heart regeneration were believed to involve distinct mechanisms. However, protecting cardiomyocytes from injury or disease stimuli is an essential prerequisite for any meaningful regenerative response. Our research focuses on exploring the unique stress adaptive mechanisms of neonatal regenerative CMs and investigating how these mechanisms can be harnessed to enhance the reparative potential of adult hearts. We aim to demonstrate the therapeutic potential of these approaches using AAV (adeno-associated virus) and modified RNA molecules.
High-throughput functional screens for regeneration essential factors
We employ methods of network analyses incorporating single cell-transcriptome and chromatin accessibility as well as cutting-edge machine learning approaches to identify essential regulatory nodes for heart regeneration. We further study the pro-regenerative effects of these network elements through AAV-based in vivo loss- and gain-of-function screening approaches. The results will provide a high-resolution molecular framework of regenerative responses in CMs and uncover many gene targets that can inform development of new strategies for promoting regeneration in human hearts.
