Research
We aim to discover the molecular secrets that make organ regeneration possible, enabling a future where we can grow and repair any organ in the body.
Overview
Every year, millions of people suffer from diseases of irreversible organ damage, including neurodegeneration, stroke, heart attack, and diabetes. All of these diseases owe their lifelong morbidity to the loss of specialized cells required for organ function, and the inability of organs like the brain, heart, and pancreas to replace these cells. A means of stimulating these organs to regenerate would provide much-needed cures for numerous debilitating conditions. Unfortunately, despite decades of effort, this longstanding goal of regenerative medicine remains elusive to this day.
In pursuit of this goal, the liver emerges as a remarkable and highly informative exception to other organs. Unlike all other solid organs, our liver can completely regenerate itself after damage. Following liver injury–even injuries that exceed over half of liver mass–the liver’s remaining specialized cells re-enter the cell cycle and proliferate to restore liver size and function in a matter of days. The liver thus harbors the secrets for how to make an organ regenerate, and offers the exciting possibility that by learning these secrets we could someday engineer other organs to do the same.
Although the liver’s remarkable regenerative capacity has been appreciated for decades, we still do not fully understand how the liver is able to regenerate itself when all other organs cannot. Answers to these questions have been limited in part by a lack of tools to investigate regeneration in the living organism. Our lab’s mission is to gain molecular insight into the differential regenerative ability of mammalian organs so that we can modulate the regenerative capacity of any organ in the setting of disease. To this end, we are pursuing two parallel but complementary agendas. First, we are developing tools for high-throughput functional genomics in living mice to bring experimental tractability to these longstanding questions. Second, we are leveraging these new technologies alongside other approaches to uncover the molecular rules governing permissive and restrictive contexts for regeneration. By uncovering the molecular switches that control regeneration throughout the body, we aim for a future in which diseases of organ damage are readily cured.
Functional genomics
Bringing high-throughput functional genomics into the organism
Our ability to understand mammalian physiology and disease has long been limited by a lack of tools for high-throughput genetic dissection in the living organism. Historically, interrogating gene function in mammals required generating single-gene knockout animals, effectively precluding unbiased and comprehensive investigation of physiology and disease. To overcome this technical barrier, our lab recently pioneered genome-wide CRISPR screening directly in the mouse liver (Keys and Knouse 2022). While we leverage this platform to investigate diverse aspects of liver physiology and regeneration, we are keen to extend this powerful technology to other organs and applications. We are currently working to establish efficient transgene delivery and genome-scale CRISPR screening in other organs of interest. Through these collective efforts, we aim to bring the experimental tractability once restricted to cell culture into the living organism, enabling comprehensive investigation of mammalian physiology and disease.
Cell biology
What are the molecular requirements for organ regeneration?
Liver regeneration is particularly remarkable because it is driven not by a stem cell population, but rather by the re-awakening and proliferation of the liver’s differentiated cells. This includes the hepatocytes, which are responsible for the bulk of liver mass and function. Hepatocytes, by virtue of their ability to re-enter the cell cycle, are considered quiescent, as opposed to most other differentiated cells, which are permanently arrested. Importantly, this critical functional distinction between quiescence and permanent arrest still lacks a molecular explanation. It is unclear how hepatocytes are able to re-awaken from a non-proliferative state and re-enter the cell cycle while other differentiated cells like cardiomyocytes and neurons cannot. We are leveraging our genome-wide screening platform to identify the genes required for hepatocytes to re-enter the cell cycle and regenerate the liver. In parallel, we are expanding our genome-wide screening platforms to non-regenerative organs to identify molecular barriers to proliferation in their cells. By uncovering the molecular rules governing permissive and restrictive contexts for regeneration, we hope to bring our goal of tuning regenerative capacity across tissues into the realm of possibility.
Organismal physiology
How does the organism monitor organ size and function?
Organismal viability requires that regeneration occur always when necessary and never when unnecessary—it must always start and stop at the right time. This requires that the organism sense when an organ is insufficient and needs to start regenerating, and when an organ is sufficient and needs to stop regenerating. Although several studies have revealed signals and pathways that are activated during liver regeneration, it is unclear how any of these pathways sense liver size and function to regulate the timing of regeneration. We are working to understand how organ size and function are transduced at the molecular level to ensure that regeneration starts and stops at the right time. By identifying the extracellular signals that communicate organ size and function, we open up the exciting possibility of modulating organ size and function on demand.
Disease
From regeneration to cancer
The majority of cancer deaths can be attributed to metastatic tumors that develop up to decades after diagnosis and treatment of the primary tumor. These metastases arise from cells that disseminate from the primary tumor, colonize sites throughout the body, and lie in a quiescent state until stimulated to resume proliferation and form a metastasis. By virtue of their quiescent state, these cells evade the many therapies designed to target rapidly proliferating cells. Our ability to achieve lasting cancer cures hinges on eradicating these disseminated dormant cancer cells and preventing metastatic tumors. In order to achieve this, we must discover vulnerabilities of disseminated dormant cancer cells that can be targeted without consequence to the many other quiescent cell types in the body. We are extending our genome-wide screens of quiescent hepatocytes to quiescent cancer cells in order to uncover genetic requirements of quiescence that are specific to quiescent cancer cells. By uncovering genetic vulnerabilities of dormant cancer cells, we hope to lay the foundation for targeting disseminated cancer cells and preventing metastatic disease.
