Current Funded Research

A Pilot Study for Managing Depressive Symptoms in Autosomal Dominant Polycystic Kidney Disease

Depression is common in chronic conditions such as ADPKD. We know that having depression can accelerate loss of kidney function in chronic kidney disease. In this proposal we will first evaluate whether or not having a diagnosis of depression affects the loss of kidney function in our ADPKD patients at Mayo Clinic. Given that depression is common in ADPKD, we will also conduct a small pilot study comparing 2 different non-medication techniques for treating depression, either digital neurotherapy or capacity coaching to see if we are able to improve symptoms of depression and pain in those with ADPKD. Digital neurotherapy is a web-based treatment somewhat similar to playing a video game, that improves the connections within various parts of the brain thus helping the brain function better. Capacity coaching teaches resilience in managing both the disease and treatment burden associated with ADPKD. This clinical trial will be conducted virtually making it accessible to those at remote distances from Mayo Clinic. 

Dr. Neera Dahl is a Professor of Medicine in the Division of Nephrology and Hypertension at Mayo Clinic Rochester. She is a member of the Scientific Advisory Committee for the Polycystic Kidney Disease Foundation, and Director of the PKD Center of Excellence at Mayo Clinic Rochester. Dr. Dahl is an Associate Director of the Mayo Clinic Translational PKD Center and co-chair of the KDOQI ADPKD Workgroup on the KDIGO Guidelines for ADPKD.

Developing a Vascularized Human Kidney Organoid Model for ARPKD Research and Therapeutic Screening

Autosomal recessive polycystic kidney disease (ARPKD) is a rare genetic condition that causes fluid-filled cysts to form in the kidneys from a young age, often leading to kidney failure early in life. Our research aims to create a better way to study and treat this disease by using tiny, three-dimensional “mini-kidneys” grown in the lab. These mini-kidneys, called organoids, are made from the urine of ARPKD patients. Using a novel method developed in our lab, we collect cells that naturally shed into the urine, expand them, and grow them under specialized 3D conditions to form patient-specific kidney organoids. Using urine a source for organoids makes this process entirely non-invasive . Once we have these ARPKD organoids, we aim to establish a large collection and build a biobank – a living organoid library that reflects the variety of disease presentations seen in ARPKD. Moreover, to make these models more realistic, we add engineered blood vessels into organoids so they now harbor a perfusable vascular network and behave more like a real human kidney. This vascularized ARPKD organoid system allows us to study how cysts form and expand, and how diseased kidney cells communicate with each other. With this platform, we can analyze each organoid by multi-omics to identify key changes in genes and proteins that drive cyst growth and disease progression. Based on the changes we then test existing drugs and their combinations to see if they can be repurposed to shrink or prevent cysts in our lab-grown ARPKD models. Alternatively, if such do not exist for the molecular aberrations observed we will start planning new approaches. By combining patient-derived organoids, blood vessel networks, and molecular analysis, we hope to discover new treatments that can slow or stop ARPKD progression and ultimately improve outcomes for children and families facing this challenging disease. 

Prof. Benjamin Dekel leads a pioneering research program at the Pediatric Stem Cell Research Institute and the Division of Pediatric Nephrology, Sheba Medical Center, dedicated to advancing the understanding and treatment of autosomal recessive polycystic kidney disease (ARPKD). The Dekel lab utilizes innovative patient-specific kidney organoids, non-invasively derived from urine samples of multiple donors, to establish a biobank, complemented by engineered vascular networks to closely mimic the kidney’s physiological environment. By integrating innovative laboratory techniques, cutting-edge bioinformatics, and advanced vascularization technologies, the lab seeks to uncover critical mechanisms underlying ARPKD, identify novel therapeutic targets, and facilitate precision medicine approaches to ARPKD and related cystic kidney diseases.

Bempedoic Acid as a Novel Therapy for Polycystic Kidney and Liver Disease

New ADPKD treatment strategies are desperately needed, including therapies targeting both kidney and liver cystic disease (PKD and PLD). Tolvaptan, the only FDA-approved drug for ADPKD, slows PKD progression but does not affect PLD, and side effects limit its tolerability, including thirst, frequent urination, and rare liver toxicity that requires close clinical monitoring. In this project we will test repurposing of bempedoic acid (BA), FDA-approved to treat high cholesterol, as a new potential therapy in the PCK rat model featuring both PKD and PLD. We recently showed that BA was effective in the treatment of ADPKD in mouse kidneys where it inhibited cyst growth and improved energy usage in ADPKD cells. Importantly, we found that in ADPKD mouse liver tissue, BA improved the health of mitochondria (major energy-generating structures in cells) while dramatically inhibiting liver cell death both in mice treated with BA alone or together with tolvaptan. Based on these exciting findings, we hypothesized that repurposing BA as a therapy for ADPKD would be beneficial in improving both liver and kidney disease manifestations and may limit tolvaptan-induced liver cell stress and injury. For this project we will investigate the dose-dependent effects of BA alone and its potentially additive effects in combination with tolvaptan on kidney and liver cystic disease features at early and late disease time points and the effects of BA on markers of tolvaptan-induced liver stress and injury in the PCK rat model. Results obtained from this study will complement and help inform pending ADPKD clinical trials. 

Effective July 2025, Dr. Hallows is transitioning from the University of Southern California (USC) to the University of Vermont (UVM), where he will be Professor of Medicine and Chief of Nephrology for the UVM Health Network. After completing his undergraduate training at Brown University, Dr. Hallows earned his PhD and MD degrees from the University of Rochester. He then went on to complete residency in internal medicine and then a fellowship in nephrology at the Hospital of the University of Pennsylvania. After spending a year as an instructor at the University of Pennsylvania, Dr. Hallows moved to the University of Pittsburgh as an assistant professor, then associate professor of medicine. He moved to the Keck School of Medicine of USC in 2015 where he has served as Chief of the Division of Nephrology and Hypertension, Director of the USC/UKRO Kidney Research Center, and more recently Director of the USC Keck PKD Clinic, a PKD Foundation Center of Excellence. Dr. Hallows’ broad research interests are in studying the metabolic control of kidney epithelial salt and water transport mechanisms with applications to therapeutics for various kidney diseases, including ADPKD. In the ADPKD field, he has spearheaded preclinical, translational, and clinical studies relevant to dysregulated metabolism, new therapeutic target identification, and the repurposing of metformin, bempedoic acid, and other FDA-approved drugs for ADPKD. He was Co-PI of the Dept. of Defense (DoD)-funded ADPKD clinical trial (TAME-PKD), where he led the biomarker discovery aims of the grant. He is currently the overall PI for an approved DoD-funded placebo-controlled multicenter clinical trial that will be launched to investigate bempedoic acid as a new ADPKD therapy (BEAT-PKD). 

Activation of endogenous renal exercise mimetics to treat ADPKD in mice.

Polycystic kidney disease (PKD) is a genetic condition where fluid-filled cysts grow in the kidneys, eventually leading to kidney failure. Studies have shown that being overweight and overeating can make PKD worse, while healthy habits like regular exercise and reduced calorie intake may help slow the disease. However, maintaining these lifestyle changes over a lifetime can be difficult for many people. 

Our research aims to find a way to mimic the effects of exercise and calorie restriction using medicine. In other words, we’re looking for a drug that can “trick” kidney cells into acting as if the person is exercising—even when they aren’t. This could help slow the growth of cysts and protect kidney function. 

One drug we are testing, called AICAR, activates a part of the cell’s metabolism that is usually turned on during exercise. In early studies using a mouse model of PKD, AICAR helped kidney cells burn energy more efficiently. By boosting the activity of mitochondria—the energy-producing “powerhouse” of the cell—we believe we can reduce the energy available for cysts to grow. 

This project builds on years of promising research and is led by a team with deep experience in kidney disease and metabolism. Our goal is to develop new therapies that can improve the lives of people with PKD by slowing disease progression in a way that doesn’t depend solely on diet and exercise. 

Dr. Miguel A. Lanaspa is an experienced investigator with a strong background in metabolism and nutrient sensing, with a focus on fructose, glucose, and purine metabolism in the context of obesity, diabetes, and kidney disease. His recent interest in polycystic kidney disease (PKD) stems from emerging data linking metabolic dysregulation to cyst growth. Leveraging his expertise in metabolic pathways, Dr. Lanaspa is now investigating how alterations in glucose and purine metabolism may contribute to PKD progression, with the goal of identifying novel therapeutic targets. 

Role of netrin-1 in cyst growth

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder, affecting about 600,000 people in the U.S. and 4 to 6 million worldwide. In this disease, genetic mutations—mostly in a gene called PKD1—cause kidney cells to behave abnormally. Instead of functioning normally, these cells grow excessively and form numerous fluid-filled sacs called cysts. Over time, these cysts grow larger and damage the kidneys, often leading to kidney failure. In fact, ADPKD is responsible for 7–10% of patients who end up needing dialysis to survive. Currently, there is only one FDA-approved medication, Tolvaptan, but its side effects can make long-term use difficult. A key challenge in developing better treatments is that scientists still don’t fully understand what causes these cysts to grow. 

Our research focuses on a protein called netrin-1, which is known to play a role in cell proliferation, cell migration, and tumor growth. Our laboratory recently discovered that netrin-1 is significantly increased in the kidneys of animal models with ADPKD. When we increased netrin-1 levels in mice, their kidney cells grew more rapidly and formed more cysts. On the other hand, when we blocked netrin-1, cyst growth slowed down in ADPKD animal models. This suggests that netrin-1 plays a major role in worsening ADPKD. However, we still don’t know exactly how it does this. The long-term goal of our project is to better understand how and when netrin-1 contributes to cyst growth and PKD progression. Successful completion of our proposed studies will increase our understanding of the role of netrin-1 in cyst growth and provide the pre-clinical foundation needed to identify netrin-1 as a novel therapeutic target for the treatment of PKD. 

Riyaz Mohamed, PhD, is a Research Scientist in the Department of Physiology at Augusta University in Augusta, Georgia. He has extensive training and expertise in cardiovascular and renal physiology and pathophysiology, with a particular focus on kidney injury/regeneration and hypertension. Dr. Mohamed’s research centers on characterizing signaling pathways and identifying therapeutic targets by utilizing a broad range of biochemical, cellular, immunological, molecular biology techniques and whole animal physiology. Dr. Mohamed earned his PhD in Biochemistry from the University of Mysore, India, and completed a postdoctoral fellowship in vascular biology and renal physiology at Augusta University. His long-term research interests involve understanding the complex relationships between hypertension, acute kidney injury (AKI), and the progression to chronic kidney disease (CKD), as well as exploring the cellular mechanisms underlying polycystic kidney disease (PKD) in both males and females. Recently, Dr. Mohamed’s studies have focused mainly on elucidating the cellular and molecular mechanisms driving PKD progression. Dr. Mohamed recently published that neuronal guidance cue netrin-1 is significantly upregulated in the kidneys of rodent models of PKD. Overexpression of netrin-1 in renal tubules promotes tubular epithelial cell proliferation, stimulates cyst growth, and activates signaling pathways known to be involved in human PKD. Conversely, suppression or neutralization of netrin-1 was found to reduce cyst growth in both aggressive and slowly progressive PKD mouse models. Dr. Mohamed’s current grant application aims to address a critical knowledge gap by investigating the functional role of netrin-1 in cyst development and PKD progression. This research will help uncover the underlying mechanisms by which netrin-1 promotes cyst growth and will provide a preclinical foundation for targeting netrin-1 and its receptor as a novel therapeutic strategy for PKD. 

Signaling components of the polycystin pathway in cilia and extracellular vesicles

Understanding hidden communication in Polycystic Kidney Disease Polycystic kidney disease (PKD) is a serious genetic condition where fluid-filled cysts grow in the kidneys, often leading to kidney failure. It’s caused by problems in two specific genes, PKD1 and PKD2, which produce proteins called polycystins. How changes in these proteins actually lead to cysts is still a mystery. Our research focuses on understanding how polycystins normally help cells “talk” to each other. We study this using a tiny transparent worm called C. elegans, which shares many biological features with humans. Think of C. elegans as a simple but powerful model that helps us zoom in on the fine details of how cells work, faster and at a much lower cost than in mice or humans. In C. elegans and humans, cells shed polycystins on tiny bubbles called extracellular vesicles (EVs). These EVs carry signals that may play a key role in starting or worsening PKD. Using advanced imaging and genetic tools, we’re now uncovering what exactly these vesicles carry and how those signals go wrong in disease. By figuring out the basic principles of polycystin EV cell-to-cell communication, our research lays the scientific groundwork that larger clinical projects can build on, bringing us closer to better outcomes for patients and families living with PKD. 

Dr. Inna Nikonorova is an Assistant Research Professor in the Department of Genetics at Rutgers University, where she explores the molecular roots of polycystic kidney disease using an unexpected but powerful model, the tiny nematode Caenorhabditis elegans. Her work has led to the identification of conserved signaling components in the polycystin pathway and opened new ways for the dissection of polycystin function on extracellular vesicles, tiny membrane-bound organelles that cells use to communicate, and which may hold the key to understanding disease progression. Dr. Nikonorova earned her undergraduate degree in Biochemistry and Molecular Biology from Lomonosov Moscow State University in Russia and her Ph.D. in Cellular and Molecular Pharmacology at Rutgers University. She studied the molecular regulation of ion channel production and then trained in mouse models of liver health as a postdoctoral researcher in Nutritional Sciences. With this multi-disciplinary background, Dr. Nikonorova is poised to solve complex biomedical questions with the ultimate goal of improving outcomes for patients with polycystic kidney disease. 

Dr. Patricia Outeda is an Assistant Professor in the Division of Nephrology at the University of Maryland, Baltimore, and Director of the Mouse Models and Biobank Core at the NIH-funded Maryland Polycystic Kidney Disease Research and Translation Core Center (MPKD-RTCC). She received her PhD from the School of Medicine at the University of Santiago de Compostela in Spain and completed postdoctoral training at Johns Hopkins University and the University of Maryland. Dr. Outeda’s research is dedicated to understanding the molecular mechanisms of polycystic kidney disease (PKD), with a specific focus on both autosomal dominant (ADPKD) and autosomal recessive (ARPKD) forms. She has developed and characterized innovative Pkd2 and Pkhd1 mouse models that have become essential tools for studying disease progression and testing potential therapies in preclinical trials. 
Since 2020, she has served as co-chair of the In Vivo Models Subcommittee of the PKD Research Resource Consortium (PKD-RRC), where she plays a key role in standardizing and expanding access to PKD mouse models across the research community. 

A flow nanocytometry based assay for the diagnosis and monitoring of ADPKD

This application will develop a technique to diagnose autosomal dominant polycystic kidney disease (ADPKD) using a urine sample. No needles, MRI, or ultrasound scanning! The test will be able to tell who in an affected family has the disease and how bad the disease will be before cysts develop in the kidney. This will allow a physician to start treatment before the kidney has become damaged and thus preserve renal function. This test relies on the finding that the proteins encoded by the PKD1 and PKD2 genes, polycystin-1 and polycystin-2 are both present on tiny structures present in urine termed extracellular vesicles (EVs). We have made antibodies to these proteins that can be modified to glow brightly when illuminated by laser light. We will use a machine called a flow Nanocytometer (Kinetic River) that can detect EVs in the urine and can measure how much polycystin-1 antibody is attached to the EV as it passes an intense laser. The degree to which the EV glows indicates the amount of polycystin-1 on the EV as well as the number of EVs per unit volume of urine. The number of polycystin-1 positive EVs per milliliter of urine is low in people with ADPKD and the lower the number of EVs the worse the disease will be. The results are available immediately and the test will be inexpensive compared to MRI or ultrasound. Hopefully, this will allow future generations to be diagnosed early and their disease stopped before kidney damage sets in. 

Development of gene therapy for polycystic liver disease 

The research team at UCSF is working on reversing cysts in the liver, and the negative effects they can have on liver function and health, by gene therapy. For this, the researchers are using AAV vectors, which are FDA approved for liver-directed gene therapy of bleeding disorders. They took the first hurdle by targeting AAV vectors to the cells that form the biliary system, which are also the source of liver cysts. They will now test in mice whether liver cysts caused by a gene defect found in humans can be reversed by delivering a normal copy of that gene with AAV vectors. To make gene therapy of liver cysts as useful as possible, the researchers need to overcome another hurdle, which is that in humans many defects occur in genes that are too large to be delivered with AAV vectors. For this, they will build on other researchers’ work that showed that liver cysts can be reversed by inactivating genes that execute the effects of the defective gene. Using their AAV vectors, the researchers will screen a large group of these candidate genes for those whose inactivation most efficiently and safely reverses liver cysts in mice. In summary, the researchers aim to establish the know-how and tools for gene therapy of liver cysts impairing liver function and health. 

Pharmacological reprogramming of the epithelial and stromal compartments to treat PLD

Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD) develop cysts in their kidneys, but 9-in-10 patients also live with cysts in their livers (called polycystic liver disease; PLD). Like water balloons, cysts fill with liquid and swell. This makes livers bigger, causing them to press on other organs in the body, resulting in pain and discomfort. Like water balloons, cysts can burst leading to infections if not treated quickly. Because of this, patients with PLD experience a poor quality of life. 

Despite liver cysts being often found in patients with ADPKD, research to understand how liver cysts form has been neglected, meaning there are no approved therapies to treat PLD. There is a desperate need within the PKD-patient community to develop therapies that can shrink liver cysts or stop them from forming in the first place. We know from other human diseases that different types of cells contribute to disease: tumors, for example, not only contain cancer cells but also immune cells whose normal job is to fight infection. Using medicines that both kill cancer cells and turn-on nearby immune system cells to attack the cancer has revolutionized how cancer patients are treated. This project will focus on studying how medicines that are currently used to treat patients with cancer can be used to stop cyst cells growing, while also telling nearby immune cells to discourage cyst growth. 

Scott Waddell completed his PhD with Luke Boulter & Pleasantine Mill at the MRC Human Genetics Unit at the University of Edinburgh (UK). During his doctoral studies, Scott investigated the role of primary cilia in hepatobiliary diseases, which led him to research the cellular and tissue dynamics underpinning polycystic liver disease (PLD). 
 
PLD is the most common extra-renal manifestation in Autosomal Dominant Polycystic Kidney Disease (ADPKD), yet research into PLD is largely neglected. Further research is required to understand what promotes cyst development and progression in the liver such that new therapeutics can be discovered. 
 
Scott has previously shown that hepatic cyst cells modulate and signal through the surrounding extracellular matrix to promote cyst growth. In his PKD Foundation-funded project, he will continue to investigate the intracellular response to a cyst-associated matrix, as well as investigate how different cells of the cyst microenvironment use common signaling pathways to promote PLD progression. 

Refining ADPKD Risk Prediction: The Utility of Machine Learning Approaches

Autosomal dominant polycystic kidney disease (ADPKD), characterized by fluid-filled cysts growing in the kidneys, is the most common cause of genetic kidney disease leading to kidney replacement therapy. However, the disease does not progress in the same way for everyone. Some people present a rapid decline in their kidney function, while others remain stable for many years. This makes it hard for physicians to predict the risk of progression for each person and to know who could benefit from treatment. As new treatments emerge, many of which can be costly and not without side effects, it is crucial to identify people at high risk who could potentially benefit from them. Our project aims to improve the prediction of the course of ADPKD by combining several types of tools: medical data, advanced imaging of the kidneys, and a wide range of genetic information. We will study about 2,000 people with ADPKD using modern tools like artificial intelligence to identify patterns that may be missed by traditional methods. In addition to kidney size and single gene tests, we will also analyze complex genetic patterns and new types of imaging data to better understand this risk. In the end, our goal is to create a tool that helps physicians to give more personalized advice: who is likely to progress and needs to start treatment early, and who can avoid unneeded medication. Ultimately, this will lead to better care, reduce unnecessary exposure to medication side effects, and support smarter use of healthcare resources. 

 IFT172 as a minor ADPKD gene and identifying disease modifiers 

Autosomal Dominant Polycystic kidney disease (ADPKD) is one of the most common inherited kidney diseases, often leading to kidney failure. ADPKD is mostly caused by changes in the PKD1 and PKD2 genes, but in this project we aim to look beyond those genes to study other lesser-known genes that can cause or modify ADPKD. 

One focus of this project is on a group of genes that encode intraflagellar transport (IFT) proteins, especially those in the B complex, which help cells form tiny hair-like structures called cilia, which are essential for normal kidney development. Particularly, our preliminary analysis indicates that genetic changes in the IFT-B gene IFT172 can cause ADPKD. We will use mouse models of IFT172 to see how loss affects cilia and the Pkd1 disease course. We will also study if other IFT-B genes are associated with ADPKD. 

Another part of the project involves less understood ADPKD genes, such as ALG8, ALG9, GANAB, and DNAJB11. A question we aim to address is why some individuals with changes in these genes develop multiple kidney cysts and severe symptoms, while others have only mild disease or even no cysts. To explore this, we will analyze large genetic databases and clinical data to identify other genetic factors that modify disease severity. We will also use mouse models of these modifying genes to mimic genetic interactions. By understanding these genetic modifiers, we aim to identify high-risk individuals earlier and discover new treatment targets. 

Dr. Doaa E. Elbarougy is a postdoctoral fellow at the Mayo Clinic’s Translational Polycystic Kidney Disease Center, under the mentorship of Dr. Peter Harris. Her research utilizes population-based biobanks to identify novel genetic causes and modifiers associated with Autosomal Dominant Polycystic Kidney Disease. She received her medical degree from Al-Azhar University in Egypt and then joined Mayo Clinic for training in PKD genetics. She is committed to a career as a physician-scientist, aiming to advance understanding of polycystic kidney diseases and improve patient outcomes.

Polycystic Kidney Disease (PKD) is a common genetic disorder that causes fluid-filled sacs, called cysts, to grow inside the kidneys. Over time, the growth of these cysts causes the kidneys to become very large and they damage healthy kidney tissue. Patients may pain, high blood pressure, and even kidney failure, requiring renal replacement therapy such as dialysis or renal transplantation. Currently, the only drug treatment that is available to slow the disease, comes with side effects that many patients are unable to tolerate. There is a pressing need for better, more targeted therapies. 

My research is focused on finding a better way to slow PKD progression. 

We discovered a protein called periostin that acts like a “bad signal” in PKD kidneys. This protein tells the kidneys to stay inflamed, creating more scar tissue. Another protein listens to that signal and makes things worse. Together, they help the cysts to grow and the kidneys to become damaged. We use advanced tools to determine if blocking these proteins in human PKD kidney cells and in PKD mouse models slow down or even stop the damage before it becomes permanent. If we succeed, this could lead to a new treatment that protects kidneys, reduces the need for dialysis, and gives people with PKD a better future. Ultimately, this research could pave the way for precision therapies that target the root causes of the disease, offering hope for ADPKD patients and others suffering from fibrosis-related conditions. This work brings hope not just for managing PKD, but for truly fighting back against it. 

Cardiovascular and renal effects of mitochondrial-targeted antioxidant therapy in ADPKD

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease and accounts for 5-10% of cases of end-stage kidney disease worldwide. Importantly, because ADPKD involves a genetic mutation that affects tissues throughout the body, it is accompanied by abnormalities in organs besides the kidney, known as “extra-renal manifestations”. A major site of extra-renal manifestations of ADPKD is the cardiovascular (CV) system. Consequently, patients with ADPKD are at greatly elevated risk of CV diseases and events, including heart attacks, aneurysms, and sudden cardiac death. Some therapies are currently available to treat CV manifestations of ADPKD, including blood pressure medications. However, CV diseases remain the leading cause of death in ADPKD despite these treatments. Therefore, new therapies are needed.

CV manifestations of ADPKD include dysfunction of the arteries, high blood pressure (hypertension), and an impaired ability of the heart to pump blood efficiently. All of these can directly cause CV diseases. Of these, artery dysfunction shows up very early in the disease course, as early as childhood and before other CV manifestations are detectible. Artery dysfunction is also likely a cause of high blood pressure and heart problems in ADPKD. Therefore, therapies that target the arteries may be the most effective for reducing risk of CV diseases in ADPKD. In addition, artery dysfunction can cause damage to the kidneys and our preliminary data suggest that this could contribute to the growth of kidney cysts. Therefore, therapies that improve artery function could not only reduce CV risk in ADPKD but also have the potential to slow kidney disease progression, which could have a major impact on the lives of patients with ADPKD.

We use a mouse model of ADPKD that has one of the most common mutations in the Pkd1 gene found in human patients, the C57Bl/6J Pkd1RC/RC mouse. As a result, these mice develop cysts in their kidneys in a way that mimics the slowly progressing nature of ADPKD in humans. We have also found that these mice have many of the same abnormalities in the CV system as patients with ADPKD. In our preliminary studies using this mouse model, we have identified the dietary supplement MitoQ as promising new therapy to treat artery dysfunction in ADPKD. We have also seen that MitoQ can slow the growth of kidney cysts and that it may improve heart function. MitoQ is an antioxidant that targets the mitochondria, organelles in cells that use oxygen and fuel from food to produce energy. The mitochondria become dysfunctional in ADPKD and over produce free radicals that cause damage to cells, which we have shown is a key mechanism of artery dysfunction in ADPKD and which can be suppressed by MitoQ.

Therefore, the purpose of this PKD Foundation Grant is to perform a preclinical trial in our mouse model of ADPKD in which we will rigorously test the effectiveness of oral supplementation with MitoQ for improving artery function, slowing kidney cyst growth, and improving other CV manifestations of ADPKD (lowering blood pressure and improving heart function). Importantly, because artery dysfunction develops so early in the disease course but because patients are typically not diagnosed until later, we will compare the effectiveness of MitoQ between when it is initiated early vs. later in PKD progression. This will provide unique insight into the population of patients with ADPKD for whom MitoQ may be most beneficial. We will also perform various measures to identify the molecular mechanisms linking improvements in artery function to effects on the kidney, which could be relevant not only for understanding the effects of MitoQ but also for developing other therapies for slowing kidney disease progression. Importantly, studies that have dual emphasis on both the CV system and the kidney are rare in PKD research. Thus, our approach is highly innovative.

This will be the first study assessing the effectiveness of MitoQ supplementation in ADPKD. As such, a preclinical study in mice is needed first. However, we have designed our studies with translation to human patients in mind as the next step. For example, supplementing MitoQ to mice in their drinking water mimics giving a dietary supplement in humans. MitoQ is currently available as a dietary supplement in humans and has been shown to be safe with minimal side effects in initial clinical trials in humans in other disease populations. As such, our studies will provide strong support for rapid translation of MitoQ to young and adult patients with ADPKD as the next step.

Comprehensive analysis of the transition to the cystic state using a novel organoid system

ADPKD poses unique challenges for both those affected by the condition and those seeking to develop treatments. The disease is usually slowly progressive, taking decades before it causes the kidneys to fail, though this process can often be marked by episodes of recurrent pain, bleeding and/or infection. About half of those who have the disease progress to end stage kidney disease. Unfortunately, our ability to identify those at most risk of severe disease or rapid progression are limited, relying either on genotype (PKD1 truncating mutations are associated with most severe disease), phenotype (kidney volume adjusted for height, age, potentially other factors like hypertension), or some combination of these factors. None of these predictive algorithms are perfect, and those that rely on phenotype identify those who already have significant progressive disease. Ideally, one would like to intervene before such a stage.

PKD science has made considerable progress since identification of the causative genes, culminating in the first approved therapy for ADPKD. Despite these encouraging steps, the therapy is expensive, not well-tolerated by many, and at best offers modest benefit. The field clearly needs new therapies informed by the biology of the disease, but the challenge is in identifying treatments that can be given safely. Both the slowly progressive nature of the disease and the variability in its severity necessitate that treatments be both effective AND safe since they may need to be given for decades.

Therapeutic development could take multiple tracks:

a) correct the underlying genetic abnormality: The obvious solution for a genetic condition would be to correct the underlying genetic abnormality, and incredible developments in gene editing and gene delivery have certainly heralded a new age of genetic treatments. But the kidney poses real challenges for gene delivery and/or delivery of gene editing agents. Furthermore, separate treatment would likely be required for the liver, and we are not even sure what the appropriate target would be for vascular structures (ie. to prevent aneurysms).

b) correct the mutant gene or protein’s abnormality: Some mutations introduce a “stop codon” into the gene which causes the protein translation machinery to stop prematurely. Classes of drugs in development can override this feature, though their long-term efficacy and safety are unestablished with many uncertain about their likely value. Similarly, drugs have been developed for other conditions (eg cystic fibrosis (CF)) that can partially overcome the effects of mutations that reduce but do not eliminate a protein’s function. In the case of CF, investigators used a cell-based system to screen for efficacious agents. In ADPKD, this class of mutations is most often associated with milder disease, potentially limiting their value.

c) replace the mutant gene’s function or target some of its downstream pathways: Even if one can’t replace or correct mutant protein function, one might be able to replace its activity partially or in full if it is known. This approach requires a detailed understanding of PKD proteins and their effector pathways. This is an area where there are large gaps in our knowledge. Despite knowing for decades the major genes and proteins that result in ADPKD when disrupted, we still have a very incomplete understanding of the proteins’ normal functions. Importantly, we have even less of a consensus on how disruption of their function ultimately triggers cyst formation. These large gaps in our fundamental knowledge about normal function and pathobiology greatly hinder our ability to develop effective therapies for this condition.

d) target some of the aberrant signaling pathways driving disease: In this approach, one studies mutant cells and tissues to identify targets. While this may be helpful as treatments could slow disease progression or reduce some of its worst effects, they are not curative and often incompletely effective. Tolvaptan, which blocks the vasopressin-2 receptor, is an example. It provides very modest benefit, and it is not tolerated by all and has significant side effects.

Most of the strategies listed above would greatly benefit from three resources: a) a detailed knowledge of PKD protein function and downstream pathways; b) a detailed understanding of the steps between gene dysfunction and cyst formation and growth; c) a simple system for studying disease and testing or screening for therapies.

Our central hypothesis is that a simple, robust, cell-based system can be used to partially meet all three goals, and the project proposed in this application was developed to meet this need.

We have developed a simple, mouse-based cyst-forming organoid system that reliably (100%) develops cysts in <10 days. An important feature is that they also appear to be properly oriented, with primary cilia that face into the cyst lumen as occurs in vivo. This offers several distinct advantages. It allows very intensive interrogation of the signaling systems and pathways that go awry when Pkd genes are mutated since the process is very quick and predictable. Cyst formation is easily visualized since the organoid is in vitro, and the system can be easily and quickly manipulated to introduce reporters or modify downstream pathways. The system is scalable, and because the in vitro system is derived from mice, any findings can be relatively easily validated in an in vivo setting using the same mouse line. Finally, it is unique in that it is the first organoid system with correct ciliary orientation, a limitation of others that has been repeatedly raised in PKD RRC Conferences.

In this application, we propose to use this system to deeply query the cellular phenotype during the very earliest stages of Pkd1 cyst formation using a variety of “omic” technologies and determine if the findings are shared by the Pkd2 cyst model, as would be predicted.

Prioritizing drug repurposing candidates for PKD with machine learning and multimodal networks

Most autosomal dominant polycystic kidney disease (ADPKD) patients have both reduced quality and length of life (1). While tolvaptan was approved as the first and only ADPKD therapy for adults with a high risk of renal cystic disease progression (3). It reduces the rate of renal function decline by 30% (3-5), it does not cure ADPKD, shows no benefit for other PKD manifestations, is associated with liver toxicity, and costs ~$170,000 per patient per year (3). As new drug development typically requires years and billions of dollars, identifying drug repurposing candidates (new uses for already approved drugs) to stop, slow, or reverse ADPKD without severe adverse events is particularly promising. However, efforts to identify these drugs or drug combinations for ADPKD have largely been due to prior knowledge of perturbed pathways. They are further complicated by the challenge of modeling the complexity and high degree of interindividual heterogeneity in ADPKD. Despite advances in using preclinical models for human disease, most therapies still fail in phase III clinical trials (6).

Here, we propose to develop innovative machine learning and data science approaches for secondary data analyses utilizing existing ADPKD database resources. We will test the hypothesis that we can predict drug repurposing candidates or combinations of candidates targeting ADPKD kidney manifestations and prioritize those candidates for future testing by their predicted ability to succeed in both preclinical and clinical trials, as well as attributes known to be critical for clinical success (e.g., drug similarity, side effects). Our proposed research is innovative because it will 1) leverage cutting-edge machine learning and network approaches capable of detecting global patterns to identify drug targets, 2) identify drug combinations (shown to increase therapeutic efficacy while reducing toxicity in other diseases), and 3) prioritize drugs by predicted perturbation of both preclinical model and human kidney profiles while avoiding potential adverse events. The proposed research is significant because of the potential for identifying already approved drugs to bypass lengthy and costly drug development and because, by making version-controlled code to reproduce all analyses and prioritized drug candidates available as FAIR (Findable, Accessible, Interoperable, for Reuse) research products, we will enable the community to build upon our findings most effectively. This would impact ADPKD patient care more rapidly than developing novel drug targets and is responsive to the special consideration areas of innovative approaches to machine learning. As the Lasseigne Lab closely collaborates with the UAB PKD research community and Dr. Lasseigne serves as the Associate Director of the Center for Precision Animal Modeling Bioinformatics section, where her team leads efforts to identify drug targets and repurpose candidates for Mendelian diseases, they are uniquely positioned to execute the research proposed here, as well as follow-on proposals to evaluate prioritized repurposing candidates in preclinical models. While not the primary focus of this application, the computational approaches and prioritized drugs may also translate to other special consideration areas of interest to the PKD Foundation, including Autosomal Recessive PKD, ADPKD in children, lifestyle interventions (e.g., lifestyle mimetics), or extra-renal manifestations of PKD.

Brittany N. Lasseigne, PhD is an Assistant Professor in the Cell, Developmental and Integrative Biology department, an Associate Scientist in the Nephrology Research & Training Center, the Center for Neurodegeneration and Experimental Therapeutics, the Experimental Therapeutics section of the O’Neal Comprehensive Cancer Center, the Precision Medicine Institute, and the Informatics Institute at The University of Alabama at Birmingham (UAB) Heersink School of Medicine. Before joining UAB, Dr. Lasseigne trained in Biotechnology, Science, and Engineering at Mississippi State University (B.S.) and the University of Alabama in Huntsville (Ph.D.) and completed a postdoctoral fellowship in genetics and genomics at the HudsonAlpha Institute for Biotechnology. Her lab develops and applies genomic- and data-driven strategies to discover biological signatures that might be used to improve patient care and provide insight into the cellular and molecular processes contributing to disease, particularly polycystic kidney disease (PKD) and other diseases impacting the kidney. Their recent work includes prioritizing drug repurposing candidates for PKD, discovering sex-biased transcript expression, identifying sex-biased gene expression and regulatory patterns of drug targets and enzymes associated with sex-biased adverse events, and evaluating preclinical models and cross-species transcriptomic signatures for improving Mendelian disease research. The Lasseigne Lab is currently supported by funds from the National Institutes of Health and UAB and is focused on integrating genomics data, functional annotations, and patient information with machine learning and regulatory network approaches to discover novel mechanisms in disease etiology and progression, identify genome-driven therapeutic targets and opportunities for drug repositioning and repurposing, determine clinically relevant biomarkers, and understand how cellular context contributes to these diseases. By developing and applying single-cell, long-read sequencing, and advanced computational approaches to human diseases, they hope to accelerate future research. Dr. Lasseigne also serves as a program director and student research mentor for the NHGRI R25 Summer Undergraduate Research Experiences in Genomic Medicine (SURE-GM) program.

Development of targeted nanoparticle-based tethered agonist peptide mimetics for treatment of PKD

Autosomal dominant polycystic kidney disease (ADPKD) is the most common potentially lethal genetic disease. Our long-term goal is to develop safe and effective treatments for this disease. The predominant cause of ADPKD is mutation of the PKD1 or PKD2 genes, which encode the proteins polycystin-1 (PC1) and polycystin-2 (PC2). Together, PC1 and PC2 form a combined signaling receptor (PC1) and ion channel (PC2) complex within cellular membranes whose critical activity within the kidney is to maintain the normal structure and function of renal tubules. Importantly, PC1 and PC2 appear to be mutually dependent on each other for appropriate maturation, trafficking and functional activity or regulation. One of the leading ideas is that kidney cysts initiate when renal tubule cells have insufficient functional levels of this complex as a result of inherited and/or acquired mutations within their genes.

We know approximately 80% of the cases of ADPKD are due to mutations within the PKD1 gene, two-thirds of which result in a truncated and completely non-functional PC1 protein. However, up to one-third of the PKD1 gene mutations can produce PC1 protein but at reduced amounts (i.e., haploinsufficient) or with compromised function (i.e., hypomorphic) such that there are insufficient levels of PC1 activity to maintain a normal renal tubular structure. Excitingly, recent studies suggest that some PKD1 mutations may be amenable to therapies that increase the expression levels of PC1 protein. In a similar fashion, we believe that it is feasible to directly stimulate and augment residual PC1 activity as a treatment for ADPKD resulting from insufficient levels of either PC1 or PC2 protein. However, this type of therapeutic approach will not be possible without a better understanding of PC1 function(s) in preventing cystogenesis.

One of the proposed signaling functions of PC1 is as an unusual type of G protein-coupled receptor (GPCR). This is based on studies demonstrating that loss or alteration of PC1-mediated regulation of G protein signaling results in PKD in mouse and frog models. Unfortunately, we know very little about the mechanism by which PC1 functions as a signaling receptor or its immediate biological effects. We believe that understanding how PC1 functions as a signaling receptor will enable us to target and augment or regulate this activity as a treatment for ADPKD. We and others in the field have noted that PC1 shares multiple structural and functional features with the Adhesion family of GPCRs. Importantly, the mechanisms of signaling regulation have been uncovered for the Adhesion GPCRs, which provides clues for revealing PC1 function and its regulation. By using this analogy, we have investigated and shown that PC1 utilizes an Adhesion GPCR-like mechanism involving a tethered peptide agonist, or ‘TAP’ as we abbreviate it, which binds intramolecularly and activates the signaling function of PC1. The TAP is a short, ~20-amino acid sequence (i.e., peptide) located at the N-terminal end of the membrane-embedded portion of PC1, which can literally ‘bend backwards’ to interact with the remainder of the protein, resulting in activation of PC1 signaling.

In cell culture studies, we have now shown that synthetic peptides consisting of short stretches of the PC1 TAP sequence can be used to activate signaling (in trans) of PC1 that is missing its tethered agonist. Furthermore, we have found that treatment with the synthetic tethered agonist peptides (TAPs) can ameliorate cystogenesis (ex vivo) in embryonic kidney organ cultures from a mouse model with a hypomorphic Pkd1 mutation, thus supporting the physiological relevance of a PC1 tethered peptide agonist mechanism in cystic disease and the feasibility of activating it therapeutically. By partnering with a leading expert in nanotechnology, bioengineering and drug delivery, we will develop and characterize a nanoparticle-based therapeutic agent, i.e., ‘peptide nanosponges’ carrying our lead TAP. These ‘nanoTAPs’ will be synthesized with a covalently attached folate molecule to ensure their targeted delivery specifically to the kidney and cystic renal tubules. We will treat mice with a hypomorphic mutation of Pkd1 as a pre-clinical test of the therapeutic potential of our lead nanoTAP on cystic kidney disease. In the short term, successful completion of this project will demonstrate that nanosponges carrying a PC1 tethered agonist peptide can be specifically delivered to cystic kidneys and will provide ‘proof of concept’ that stimulation of PC1 signaling activity ameliorates cystic renal disease in vivo. Such results will also support the tethered agonist-mediated activation of PC1 signaling as a critical function and provide a strong foundation for the continued development of this novel therapeutic approach as a treatment for ADPKD which will be the focus of future research. Finally, if successful, this strategy is likely to be beneficial not only for ADPKD arising from PKD1, but also from PKD2 and other genes associated with cyst development in the liver and kidneys as a result of defects in the ER biogenesis of membrane proteins since these gene products reduce the level of PC1 protein and hence, PC1 activity.

Early biomarkers for stratification of disease progression in ADPKD children

In the previous years, our group has contributed to challenging the paradigm for the management of Autosomal Dominant Polycystic Kidney Disease (ADPKD) by demonstrating that this disorder manifests itself already in childhood. Spotlighting this simple but critical insight implies that in order to prevent progression of the disease to kidney failure (KF), treatment of ADPKD must start early, before a point of no return has been reached. For this purpose, new targets for safe and efficacious drugs need to be identified, but also novel biomarkers of disease progression in young ADPKD patients with early disease stages. Applying these biomarkers to a comprehensive classification system including imaging and clinical data for pediatric ADPKD patients would mean a significant breakthrough in the early ADPKD field and will lead to new insights into predicting outcome, designing trials and selecting the patients who are most eligible for therapeutic interventions for early stage ADPKD disease. By making this classification tool accessible to clinicians worldwide and easily applicable, it will have an essential impact on its management and will help in counseling families. In addition, the development of this classification system will shed light on the clinical phenotype of early ADPKD. This knowledge is essential to identify the best timepoint for intervention in the disease, and to delineate early events in disease progression.

Finally, by identifying known and novel biomarkers in the early stages of the disease, it will contribute to the identification of novel underlying players in the proximal events in cystogenesis, and potentially form a basis for novel drug target discovery in early ADPKD.

Effect of Pregnancy and Lactation on PKD

Autosomal dominant polycystic kidney disease is a common genetic disorder affecting 1 in 500-1000 individuals. Although the disease is inherited genetically, progression is variable within the patient population and is likely affected by diverse factors including diet, lifestyle, and epigenetic factors.

We have generated a mouse model with a slowly progressive form of cystic disease that mimics ADPKD. In our experience with this model we have obtained preliminary evidence that suggests that pregnancy exacerbates PKD progression. There is good evidence that the rate of PKD progression is different between males and females, but there has surprisingly been no investigations into pregnancy as a driver of cystic disease. The availability of this new mouse model allows the opportunity to study this possibility in a controlled environment. Furthermore, the increasing volume of clinical patient data from long-term imaging studies, such as CRISP, provide the opportunity to retrospectively address this question in human patients as well.

This proposal will merge basic science and clinical data-mining approaches to determine whether pregnancy is a risk factor for ADPKD patients. The information gained from this study will hopefully help patients make important lifestyle decisions with regard to their choices related to pregnancy.

Dr. Stephen Parnell, PhD, is a Research Associate Professor in the Department of Biochemistry and Molecular Biology, and a member of the Jared Grantham Kidney Institute at the University of Kansas Medical Center. His specific research interests are in polycystin-1 structure/function and aberrant cell signaling mechanisms that contribute to cystic disease progression. He has enjoyed working with many friends and colleagues in the area of PKD research since his introduction to the field in the mid 90’s, but was familiar with the disease for many years prior on account of having a parent with ADPKD. Dr. Parnell is deeply appreciative of the Foundation’s commitment to patient advocacy and financial support for research. Outside of the lab, Dr. Parnell enjoys hiking in the mountains (and other outdoor locations) and getting new summit photos in his ENDPKD shirt.

Mitochondrial Role of Fibrocystin/Polyductin in Cyst Formation Through Its Cleavage Product ICD15

Fibrocystin/Polyductin (FPC) is the protein encoded by PKHD1, the principal gene responsible for autosomal recessive polycystic kidney disease (ARPKD). ARPKD is a severe neonatal nephropathy characterized by cystic dilation of collecting ducts and congenital hepatic fibrosis. Despite its significance, the exact function of FPC and its role in cyst formation remain elusive, posing challenges to the development of effective therapeutic strategies for ARPKD. Unexpectedly, Pkhd1 mutant mice exhibit only minimal renal disease, further restricting the study of FPC in ARPKD pathogenesis.

We recently published a study unveiling a crucial connection between FPC and mitochondria in cyst formation (Walker et al. 2023). This connection is likely mediated by proteolytic cleavage of FPC, releasing a novel intracellular C-terminal domain product known as ICD15. Our findings indicate that ICD15 enters the mitochondrion—the cellular organelle responsible for producing ATP for cellular energy currency and producing small molecular building blocks for larger molecules. Pkhd1 knockout (KO) mice exhibit structural and functional abnormalities in the mitochondria of kidney tubules. Moreover, Pkhd1 KO greatly worsens PKD in the Pkd1 mouse mutant known as Pkd1V/V. These digenic mouse mutants mimic ARPKD, particularly those severely affected due to biallelic mutations in PKHD1 with coinheritance of changes in an ADPKD gene. Furthermore, removing the ICD15 sequence from FPC aggravates PKD in Pkd1V/V mice. Our findings indicate that dysfunction of ICD15 could be a key factor in cyst growth

Our discoveries offer intriguing insights. First, the identification of mitochondrial abnormalities in Pkhd1 KO kidney tubules, even in the absence of cyst formation, rules out the possibility of them being a consequence of cyst formation. Instead, they likely result directly from FPC inactivation, establishing a pro-cystic state that operates synergistically with the Pkd1-dependent cystic pathway to promote cyst development. Second, the absence of ICD15 alone is the likely cause of mitochondrial dysfunction contributing to this pro-cystic state. The importance of ICD15 in pathogenesis is underscored by the identification of various mutations in PKHD1’s final exon (exon 67, encoding ICD15) in severely affected ARPKD patients. Third, ICD15, therefore, may normally play a crucial role in regulating mitochondrial function, potentially facilitating tubular adaptation in response to environmental cues. Fourth, our digenic mouse mutants mimicking ARPKD provide a valuable model for investigating FPC function in cystogenesis.

We hypothesize that ICD15 of FPC participates in a mitochondrial signaling pathway that is linked to cystogenesis operating synergistically with the Pkd1-dependent cystic pathway. Consequently, introducing an extra copy of ICD15 may alleviate cystic development in PKD. This concept addresses a knowledge gap in comprehending FPC function and its involvement in ARPKD. Validation of the hypothesis will likely provide novel insights into FPC’s function and its role in cyst growth through its ICD15 product and open new avenues for novel ICD15-based therapeutic interventions in ARPKD. Accordingly, our proposed research is designed with the following two main aims.

1. Elucidate the role of FPC in mitochondrial signaling via ICD15. We hypothesize that FPC-ICD15 interacts with other mitochondrial regulatory proteins and affects mitochondrial metabolism. Recognizing oxidative stress as a key contributor to ADPKD pathogenesis, we will determine the effect of Pkhd1 inactivation on the levels of reactive oxygen species (ROS), oxidative stress, and antioxidant defenses in the kidneys and cells, and assess if ICD15 expression may alleviate these effects. Furthermore, we will investigate the ICD15 signaling pathways associated with the disease through an unbiased approach, employing mitochondrial proteome and protein network analysis.
2. Assess suppressive effects and mechanism of ICD15 on renal cyst growth in Pkd1V/V mice. This will involve the development of a new transgenic mouse line expressing ICD15 and testing its effect in mitigating the cystic phenotype of Pkd1V/V mice. Additionally, we will use the MITO-Tag mice to facilitate mitochondria isolation from their kidneys. The isolated mitochondria will be subjected to mitochondrial proteomic and bioinformatic analyses to gain novel insights into the cyst-suppressive mechanisms of ICD15.

The anticipated results may yield significant impacts.

THE SHORT-TERM/IMMEDIATE IMPACT. This study may advance our understanding in several key areas:

• Defining the role of FPC and its ICD15 in regulating ROS and oxidative stress.
• Identifying the effect of FPC and the role of ICD15 on changing the mitochondrial proteome.
• Determining ICD15 binding partners in mitochondria and its protein interaction network
• Characterizing the ICD15 signaling pathway and the contributors to the pro-cystic state.
• Developing a transgenic mouse line expressing ICD15.
• Assessing whether transgenic ICD15 mitigates the cystic phenotype of Pkd1V/V mice.
• Delineating cyst-suppressive mechanisms of ICD15 through mitochondrial proteome analysis and functional annotation.

THE LONG-TERM IMPACT. The insights gained may pave the way for the development of interventions and therapeutic strategies based on ICD15 expression to mitigate cyst growth. Our findings may establish a foundation for innovative interventions, including small molecules, peptides, and nanobodies, designed to enhance the release of ICD15 from full-length FPC. Alternatively, small molecules that can enhance the function of the mitochondrial electron transport chain may be effective in compensating for the loss of ICD15. These FPC-directed therapeutic strategies hold considerable promise compared to previous attempted approaches that primarily focused on targeting altered signaling pathways associated with the disease.

I am a Professor of Medicine specializing in Polycystic Kidney Disease (PKD) research with a particular focus on the intricate biology of PKD proteins, including Polycystin-1 (PC-1), Polycystin-2 (PC-2), and fibrocystin/polyductin (FPC). With a robust foundation in molecular biology, biochemistry, animal models, and human PKD, I have firmly established myself as a principal investigator or co-investigator on numerous grants, generously funded by prestigious organizations including the NIH/NIDDK and various foundations including the PKD Foundation. Over the span of 25 years, my contributions to the PKD field have been profoundly impactful. A defining achievement was my pivotal role in sequencing the PKD1 genomic locus, a foundational step that underpinned the establishment of the two-hit model of cystogenesis. Moreover, I spearheaded the discovery of the interaction between PC-1 and PC-2, specifically elucidating their interactions through their C-termini. My laboratory’s findings have highlighted the critical role of PC-1’s autoproteolytic cleavage at its GPCR Proteolysis Site (GPS) in controlling the protein’s biogenesis, ciliary trafficking, and signaling properties. These accomplishments collectively provide me with an extensive grasp of polycystin protein biochemistry. In addition to my research efforts, I also serve as the director of the Molecular Core of the NIH U54-funded Polycystic Kidney Disease Research Resource Consortium. This pivotal role entails the development and dissemination of various PKD antibodies, alongside a rich array of reagents and expertise, contributing valuably to the expansive research community. Of particular note is the development of a distinguished collection of FPC-specific antibodies, as well as various FPC expression constructs.

Role of BRAF on renal cyst formation in PKD

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited disorder with a diagnosed prevalence of 4.3 per 10,000 individuals affecting ~144,000 people in the US. The disease is characterized by the relentless growth of numerous fluid-filled cysts causing kidney injury, tissue inflammation, fibrosis (scar tissue), and progressive decline in kidney function. Approximately, one-half of ADPKD patients reach end-stage kidney disease by the 6th decade of life, accounting for 6-10% of patients on renal replacement therapy. Over the past two decades, there have been major advancements in PKD research; however, the lack of understanding of cellular pathways involved in initial cyst formation has limited our ability to design and develop effective therapies to prevent or halt renal cystic disease in ADPKD patients. Tolvaptan (Jynarque) is an important first therapeutic for the treatment of ADPKD; however, its side-effects, including polyurea (excessive urination), nocturia (excess urination at night), polydipsia (excessive thirst), and liver complications, limit its use in some patients.

Our research has shown that BRAF, a kinase upstream of the ERK pathway, is the key intermediate in the proliferation of human ADPKD cells. BRAF is normally inhibited or repressed in the kidneys. Mutations genes that cause ADPKD lead to de-repression of BRAF in the cystic cells such that hormones such as vasopressin, an antidiuretic hormone that works through a cell signaling molecule cAMP, stimulates BRAF and ERK-dependent cell proliferation. Recently, we generated a novel mouse that expresses a constitutively active BRAFV600E, a common activating mutation found in cancer, in the renal collecting ducts (CD)s of otherwise normal mice. These BRAFCD mice formed cysts in the CDs, which is a prominent site for cyst formation in human ADPKD. It is well established that cysts can form in all segments of the nephron; therefore, we will express active BRAF in all nephron segments of normal kidneys and identify which segments form cysts due to BRAF activation. In a preliminary experiment, we found that changes in gene expression during initial cyst formation in BRAFCD kidneys were similar to those activated during initial cyst formation in PKD mice, suggesting that the same pathways are activated in both models. Pathways analysis indicated that the top pathways affected were tissue remodeling and inflammation, which are also affected in human ADPKD kidneys.

Our hypothesis is that BRAF activation is sufficient and required for the initiation of cyst formation in ADPKD and that targeting BRAF prevents the initiation of cyst formation and halts disease progression in PKD mice.

In Aim 1, we will determine if the expression of active BRAF induces in vitro cyst formation of human kidney cells, and if active BRAF induces cyst formation throughout the nephron causing early inflammation of the kidneys. We will express an inducible BRAFV600E in primary normal human kidney (NHK) cells to determine if active BRAF drives ERK-dependent cell proliferation and in vitro cyst formation of cells seeded within a collagen matrix. Using the BRAFV600E mouse, we will express active BRAF throughout the entire nephron of wildtype mice, identify the nephron segments that form cysts, and evaluate changes in markers of cell proliferation, inflammation, fibrosis, and renal function.

In Aim 2, we will use novel gene editing approaches to knockout BRAF in human ADPKD cells to determine if the loss of BRAF prevents cell proliferation and in vitro cyst formation. A conditional BRAF knockout mouse will be used to determine if the loss of BRAF in the nephrons of Pkd1RC/RC mice prevents renal cyst formation and inflammation, and reverses gene expression and cellular pathways that were identified to be activated during initial cyst formation.

We think that these studies are important to the PKD field to understand initial cyst formation and activation of pathways involved in tissue remodeling and inflammation, and to the PKD patients. FDA-approved Raf inhibitors show efficacy on inhibition of the BRAFV600E protein in metastatic melanoma; however, resistance develops, in part, due to dimerization of RAF proteins making the drugs ineffective. There is growing interest in the development of next-generation RAF inhibitors that target both monomers and dimers of the RAF proteins. We think that a better understanding of the role of BRAF on the initiation of renal cystic disease in ADPKD is timely with the emergence of new BRAF inhibitors.

Darren Wallace is a Professor in the Department of Internal Medicine and a member of the Jared Grantham Kidney Institute at the University of Kansas Medical Center. Dr. Wallace earned his PhD from the Department of Molecular and Integrative Physiology and completed postdoctoral training in renal physiology and polycystic kidney disease (PKD) at the University of Kansas Medical Center. His contributions to the PKD field include research on the molecular mechanisms for cAMP-dependent cell proliferation and Cl–dependent fluid secretion using primary cultures of human PKD cyst epithelial cells. His laboratory discovered that periostin, a matricellular protein, is highly overexpressed by cyst-lining cells of PKD kidneys, where it binds to integrins and stimulates tissue repair pathways, leading to aberrant cell proliferation and matrix production, driving progressive cyst growth and fibrosis. Recently, his research has focused on the pivotal role of BRAF, a kinase upstream of the mitogen-activated protein kinase ERK, on cyst initiation in PKD. Dr. Wallace is the Director of the Kansas PKD Research and Translational Core Center and Director of PKD Biomarkers, Biomaterials and Cellular Models Core, which are part of the national PKD Research Resource Consortium (PKD-RRC). He also served as a member of the PKD Foundation Scientific Advisory Committee from 2008 to 2019.

Understanding mechanisms of senescence in promoting cyst growth in ADPKD

The roles of cellular senescence in ADPKD have become the focus of scientific investigation. However, whether senescent cells can directly drive ADPKD-related pathology and be therapeutically targeted is still unclear. To address these fundamental questions, we investigate whether senescence plays a fundamental and mechanistic role in the pathophysiology of ADPKD, identify key SASPs secreted by senescent Pkd1 null renal epithelial cells, and investigate the role of one candidate SASP in the regulation of cyst growth in ADPKD mouse models. Completion of this project will provide strong pre-clinical mechanistic data supporting the role of senescence in the pathophysiology of ADPKD and identify novel therapeutics that target fundamental senescence processes to improve both immediate and long-term outcomes related to ADPKD. Thus, this study is highly significance and therapeutically relevant with exciting potential for translation.

The PC2-dependent activation and regulation of the Aquaporin 2 signaling pathway

The kidney represents a unique environment where cells are exposed to a variety of different stimuli. Cellular homeostasis is critical for kidney cells as dysregulation of any signaling pathway can trigger the progression of kidney disease. The ability of renal cells to adapt to changes in their environment is critical for cell survival. Autosomal Dominant Polycystic Kidney Disease is the leading genetic cause of renal failure affecting ~1:1,000 people and has no cure. ADPKD is caused by loss-of-function mutations to PC2 where it causes the formation of renal cysts being the most damaging one in the collecting duct (CD) of the nephron where urine concentration is finalized. I have shown in my pre-published manuscript that deletion of PC2 in the CD leads to the activation of hyperosmotic dependent signaling pathways like the incorporation of Aquaporin 2 (AQP2) in the apical membrane of CD cells. However, it has not been previously characterized how do the polycystin proteins regulate and activate the osmotically induced AQP2 signaling pathway. This proposal aims to characterize how PC2 activates and regulates the osmotically induced AQP2 signaling pathway. The characterization of this signaling pathway provides an early intervention point for ADPKD patients and new signaling pathways that can be targeted for therapeutic development.

Dr. Márquez-Nogueras is a postdoctoral researcher in Dr. Ivana Kuo’s laboratory in the Department of Cell and Molecular Physiology at Loyola University Chicago. She earned her bachelor’s degree in Industrial Microbiology and her master’s degree in Microbiology from the University of Puerto Rico, Mayagüez and received her PhD in Microbiology from the University of Georgia. Dr. Márquez Nogueras’s research combines the use of molecular approaches, high-resolution live cell imaging, cell culture and animal models to undestand how breakdown of cellular communication in the PC2 signaling pathway can lead to defects in urine concentration. In the proposed study, Dr. Márquez-Nogueras will aim to characterize how PC2 activates and regulates the osmotically induced AQP2 signaling pathway.

The role of adipose tryptophan metabolism in obesity-driven PKD progression

Autosomal dominant polycystic kidney disease (ADPKD) is characterized by growth of fluid-filled cysts in the kidney, resulting in loss of kidney function and kidney failure. To date, Jynarque is the only approved therapy that slows kidney cyst growth progression in patients with ADPKD. However, it is only approved for a subset of patients and lowers quality of life; as such, understanding mechanisms that drive PKD and finding new treatment options is vital. Obesity is a growing public health problem of which the ADPKD population is not spared. Work from our group has shown that, in patients with ADPKD, being overweight or obese increases the rate at which kidney disease progresses. In my preliminary studies, I developed an overweight mouse model with ADPKD that presents with more rapid disease progression compared to normal weight mice, mimicking human findings. As it is difficult to acquire kidney, blood, and adipose tissue from patients with ADPKD, this model uniquely allows us to decipher mechanisms that link adiposity and rapid kidney cyst growth. Importantly, overweight/obesity results in the global dysregulation of multiple signaling pathways, including metabolism and organ inflammation, which have been shown to influence kidney cyst growth in mouse models of ADPKD. This includes metabolism of the amino acid tryptophan (TRP). I have recently published a paper linking tryptophan, its metabolizing enzyme IDO1, and its metabolites kynurenines to the progression of ADPKD in normal weight mice. Of significance, in overweight non-diseased mice, I found increased expression of IDO1 on adipose immune cells (macrophages) and increased levels of kidney kynurenine compared to normal weight mice. Plasma collected from patients with ADPKD and overweight/obesity shows that kynurenine levels rise with increasing body mass index. In this application, I hope to achieve a detailed characterization of adipose TRP metabolism as overweight/obesity progresses with a focus on understanding which cells within this secretory organ are critical to the dysregulation of the pathway, as well as its impact on systemic/kidney inflammation and subsequent kidney cyst growth. I will also test whether returning from an obese to a lean state resolves dysregulated TRP metabolism and slows kidney cyst growth. To increase the translational potential of my studies I will assess if IDO1 loss in adipose macrophages slows adipose-driven kidney cyst growth and whether blocking IDO1 with an FDA approved inhibitor corrects the pathogenic function of these macrophages in cell culture. These findings will provide foundational and mechanistic data that allow testing of an FDA approved inhibitor of TRP metabolism as a therapeutic option for patients with overweight/obesity and ADPKD. These findings could augment the progression of this common, detrimental, and economically costly diseases as well as inhibit its obesity-associated accentuation.

Mayo ADPKD Mutation Database

In other genetic diseases, such as cystic fibrosis, all patients are routinely molecularly screened so that families know their disease causing mutations. At present this does not happen for ADPKD, partly because the value of the data for diagnostics and prognostics is not generally recognized, and because molecular testing is specialized and expensive due to the complex genomic situation of the PKD1 gene. However, as specialized next generation sequencing panels for ADPKD become available and there is more competition to offer testing, the price of testing is likely to decrease. In addition, the value of the patient knowing their specific mutation is likely to be more widely appreciated as the prognostic value of this data is realized, and genetic data is increasing used to select patients for treatment and clinical trials. In cystic fibrosis, therapies geared to specific mutations are being developed. ADPKD is more complex because of the high level of family specific mutations, but mutation focused treatment strategies are still likely to be tested in this disorder in the next few years. For instance, chaperone treatment may be of value for some missense substitutions and read-through drugs help patients with nonsense mutations, while therapies to overcome splicing defects have also been proposed. Hence, the database will play an increasingly important role as a repository of the accumulating genetic data (paired with clinical and in vitro data), allowing the penetrance of specific mutations to be better determined. In addition, it will function as a source of information about patients that (through their nephrologist) can be selected for treatments and specific clinical trials, including targeting specific mutation groups.

Visit Mayo ADPKD Mutation Database website