PAF Awards Initial Research Grant Houten DeVita

PAF Awards $50,000 New Research Grant

PI: Sander Houten, Ph.D., Department of Genetics and Genomic Sciences,

Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, NY, US

Co-PI: Robert J. DeVita, Ph.D., Department of Pharmacological Sciences, Drug Discovery Institute,

Icahn School of Medicine at Mount Sinai, NY, US

“Substrate reduction as a novel therapeutic strategy for propionic acidemia”

Amino acid metabolism and in particular the degradation of valine and isoleucine are a significant source of propionyl-CoA, the substrate of propionyl-CoA carboxylase. Current treatment of propionic acidemia aims to decrease the degradation of valine and isoleucine through medical diets and avoidance of fasting. Drs Houten and DeVita, the investigators on this project, aim to develop a pharmacological substrate reduction therapy for propionic acidemia that limits the degradation of these amino acids. They propose to inhibit short/branched-chain acyl-CoA dehydrogenase (SBCAD) and isobutyryl-CoA dehydrogenase (ACAD8), which are involved in isoleucine and valine degradation, respectively. Inhibition of these enzymes is thought to be safe because in contrast to propionic acidemia, inherited defects of SBCAD and ACAD8 are thought to be benign conditions. In cell line models, inhibition of SBCAD using a genetic KO or an inhibitor was efficacious and led to a pronounced decrease in the propionyl-CoA carboxylase substrate. The investigators anticipate to find a few hit inhibitors of SBCAD and ACAD8 that can be further optimized and serve as a starting point for a broader translational drug discovery program for treatment of propionic acidemia.

Progress Update April 2022

In January 2021, we were grateful to receive a research grant from the PAF, which allowed us to start the development of pharmacological substrate reduction as a novel therapeutic approach for propionic acidemia. For this project, we hypothesize that we can achieve a clinically relevant reduction in the accumulation of propionyl-CoA carboxylase substrates by inhibiting enzymes that play a role in the degradation of branched-chain amino acids. Specifically, we propose to inhibit short/branched-chain acyl-CoA dehydrogenase (SBCAD) and isobutyryl-CoA dehydrogenase (ACAD8), which are involved in isoleucine and valine degradation, respectively. Inhibition of these enzymes is predicted to be safe because inherited defects of SBCAD and ACAD8 are thought to be benign conditions. In cell line models, inhibition of SBCAD using a genetic KO or an inhibitor was efficacious, leading to a pronounced decrease in propionyl-CoA derived metabolites. Inhibition of ACAD8 was less efficacious, which may be explained by overlap in substrate specificity between different acyl-CoA dehydrogenases. The goal of this project is to identify small molecule inhibitors of SBCAD and ACAD8 that can be further validated to serve as starting points for a broader translational drug discovery program for treatment of propionic acidemia. In order to achieve this goal, we used the research grant from the PAF to develop the in vitro biochemical and cellular assays useful to screen for chemical matter to establish if a small molecule has possibility to be an effective SBCAD or ACAD8 inhibitor. We have also performed a virtual screening to generate a list of candidate inhibitor molecules for SBCAD and ACAD8. Of these potential SBCAD inhibitors, 91 were purchased and tested in the SBCAD assay. Unfortunately, none of the compounds were able to inhibit SBCAD with high affinity likely as a result of limitations to the computational modeling of the enzyme structure. This result indicates that a larger unbiased high throughput screening is necessary to identify hit small molecule inhibitors for SBCAD. Our enzyme assay seems well suited for this approach and this approach has been successfully applied to two other enzyme targets under investigation by the team (DHTKD1 [1] and LOR domain of AASS (unpublished)).

The progress made with the PAF funds enabled us to propose this research project for the NIH Small Grant Program (R03) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). This grant was awarded in September 2021, which allowed us to continue this work for the next 2 years. In collaboration with Drs. Vockley and Mohsen (University of Pittsburgh), we also applied for an NIH Research Project Grant (R01; The therapeutic potential of inhibition of acyl-CoA dehydrogenases involved in valine and isoleucine degradation). This proposal is currently under consideration.

PAF Awards $49,953 New Research Grant – Swietach

PAF Awards $49,953 New Research Grant in 2021

PI: Pawel Swietach, Professor of Physiology, Department of Physiology, Anatomy & Genetics, University of Oxford, England

“Aberrant protein propionylation and distinct histone marks in propionic acidemia: new disease mechanisms and risk factors for cardiac disease”

The challenge placed on our hearts – to contract and relax in a correct sequence and with adequate strength – is formidable. The elegant biological solution to this mechanical problem is an organ that pumps millions of liters of blood to support life for many decades. However, the quality and span of a person’s life is strongly linked to cardiac health. Thanks to scientific breakthroughs, better treatments are now available for cardiac disease, allowing patients to live longer and happier lives. Our goal at Oxford University’s British Heart Foundation Centre of Research Excellence is to ensure that scientific progress addresses a wide spectrum of disorders, irrespective of their incidence.

Cardiac problems are common in propionic acidemia (PA). Sadly, dilated cardiomyopathy and long-QT syndrome are often the cause of childhood death. In order to treat and prevent these cardiac problems, we must first understand the underlying mechanisms. Once these processes are described, our aimis to identify targets for drugs or interventions. We believe that this ambition is achievable thanks to the wealth of knowledge about the heart and the vast repertoire of drugs approved for therapy in various other cardiac conditions. Many of these drugs could be “repurposed” for PA-associated disorders, giving hope to many families for a timely treatment.

For this PAF-funded project, we have assembled a consortium of scientists who are eager to devote their expertise to studying PA. My laboratory’s expertise is in cardiac cellular physiology in the context of acid-base disorders. We are joined by Tom Milne who is Associate Professor in Epigenetics at Oxford, Holger Kramer, an expert on proteomics, and Steve Krywawych, principal biochemist at Great Ormond Street Hospital in London. Resources and facilities made available to this project include a mouse model of PA, courtesy of Michael Barry and Lourdes Desviat, methods to characterise cardiac function from the cell to organ level, as well as measurements of changes at the protein and gene level. This interdisciplinary but focused approach allows us to identify potential targets for PA treatment. Indeed, our preliminary findings point to one such enzyme, and the aim of this project is to test and validate our hypothesis.

PA is associated with major metabolic changes, and many of these substances are not merely intermediates in a chain of events, but can have strong biological actions that are not always intuitive to predict. Our project will investigate how the build-up of propionate affects cardiac genes through a chemical reaction that causes DNA scaffolds (called histones) to “open up” genes that should not normally be expressed in a healthy heart. Many genes will be affected by this, but some are more closely linked to the cardiac disorder. After identifying these lead genes, we will test the extent to which blocking these could be curative. In parallel, we will investigate if propionate can also react with other targets in the cell, such as proteins underpinning contraction. Indeed, our work suggests that a promising avenue for research relates to so-called excitation-contraction coupling, a process that converts cardiac electricity to a mechanical response.

We are excited to be part of the PA research family and wish to take this opportunity to invite patients, carers, and supporters to our lab for a visit.

Update 8/2022 – Final Report

ABERRANT PROTEIN PROPIONYLATION AND DISTINCT HISTONE MARKS IN PROPIONIC ACIDEMIA: NEW DISEASE MECHANISMS AND RISK FACTORS FOR

CARDIAC DISEASE
Final Report – August 2022
PI: Pawel Swietach (Oxford University)

Non-confidential report for dissemination

Patients affected by propionic acidemia (PA) present with disturbances in the levels of metabolites, notably propionate. This small (three-carbon) molecule is normally produced
from the breakdown of substances in the diet, such as branched-chain amino acids and odd-numbered fatty acids. In PA, however, genes responsible for propionate processing are
inactivated by inherited mutations. A long-standing view postulates that the ensuing biochemical milieu is responsible for the dysfunction of multiple organs affected in PA.
Understanding how the heart is affected in PA is particularly important, because many childhood deaths have been linked to cardiac disease. However, the precise mechanism
linking the metabolic disturbance with heart disease in PA is unclear. Without this detailed information, it is difficult to propose new cures and improve disease management before
viable gene therapies are available. Moreover, knowledge of the molecular mechanisms has broader impact on cardiac health, because elevations of propionate have also been
described in other diseases, such as diabetes.

The aim of our PAF project was to investigate how the metabolic derangements in PA affect proteins through so-called post-translational modifications, i.e. chemical ‘editing’
that can affect their functions. Using a mouse model of PA, we showed that histones, the protein scaffold of DNA, undergo two types of modifications in the heart: propionylation and acetylation. We then demonstrated how these actions affect the expression of genes in the heart. Strikingly, we found that several genes, previously implicated in cardiac disease, become aberrantly activated in PA, and we speculate that dampening this PA-driven genetic response may alleviate the pathological changes experienced by patients. Through our observations of the mouse model of PA, we identified a novel biochemical pathway that offers an alternative means of processing excess propionate in the heart. Activation of this pathway was associated with a less severe disease presentation in mice. We hypothesize that this pathway could be exploited therapeutically in PA patients, and our immediate aims for the future are to identify the best approach for exploiting this protective reservoir for propionate in the heart.

In summary, the PAF project has (i) delivered novel mechanistic insights into how propionate affects the heart using state-of-the-art methods in metabolomics, transcriptomics,
chromatin biology, and physiology, and (ii) revealed new pathways for propionate processing that by-pass the mutated enzymes in PA patients.

PAF Awards Continuation Grant to Guofang Zhang at Duke University

Guofang Zhang, PhD, Duke University

“Propionyl-CoA and propionylcarnitine mediate cardiac complications in patients with propionic acidemia”

Update March 2023

Cardiac disease has a high prevalence among patients with propionic acidemia (PA). The pathological mechanism remains largely unknown, particularly due to the nature of chronic development. It is challenging to predict the cardiac diseases development in PA patients simply by the PCC mutations, propionyl-CoA carboxylase (PCC) enzyme activity or acute metabolic changes in plasma or urine because no strong correlation between cardiac phenotype (severity of disease) and genotype, metabolic decompensations or residual enzyme activity has been observed from the clinical cases.

Fatty acids with various chain-lengths are major fuels for heart. Our previous data demonstrated that propionate rather than amino acids is a major source of cardiac propionyl-CoA. In addition, the deficiency of PCC reduces the hepatic disposal of microbiome-derived propionate and promotes odd-chain fatty acid synthesis, both of which impose metabolic stress on heart. Propionyl-CoA accumulation derived from propionate and odd-chain fatty acids could interrupt cardiac energy metabolism. The low ATP further inhibits propionyl-CoA carboxylation according to our recent ischemia study. The impaired energy metabolism and propionyl-CoA accumulation forms a vicious circle.

With a third-year grant support from PAF, we will collaborate with Drs Eva Richard Rodríguez and Lourdes R. Desviat from Universidad Autónoma de Madrid on how energy metabolism in PCCA- or PCCB- iPSC-cardiomyocytes derived from human patients is altered by stable isotope analysis, particularly under the stress of propionate and odd-chain fatty acids. Another Aim is to improve cardiac energy metabolism by targeting propionate and odd-chain fatty acid metabolism.

Update August 2020

Cardiac disease is one of complications often associated with propionic acidemia (PA). Understanding the pathological mechanism is essential to prevent the development of complication. Our previous research has shown that propionyl-CoA accumulation inhibits the metabolism of fatty acid which is a major fuel for cardiac energy. The loss of fuel switch flexibility could interfere with cardiac energy metabolism and potentially develop cardiac complications particularly under various stresses. Our research was funded by PAF to investigate the pathological mechanism of cardiomyopathy associated with PA in 2019. In the year 1 of PAF award, we started to map out the metabolic source of propionyl-CoA in heart. Surprisingly, the amino acids (isoleucine, threonine, methionine, valine) and protein which are known to be substrates of propionyl-CoA have negligible contribution to propionyl-CoA production in heart. However, our data does not exclude the possibility that these amino acids substantially contribute to propionyl-CoA production in other organs, like liver. Circulating propionate is a major source of cardiac propionyl-CoA. It also fits the observation that heart prefers fatty acids including short-chain fatty acids as energy substrates. More than 99% propionate originating from microbiome is efficiently removed/metabolized at its first pass through liver in healthy rodents. Therefore, circulating propionate maintains at very low level after liver. The deficiency of PCC attenuates hepatic ability of disposing propionate and increases circulating propionate level, which exacerbates propionyl-CoA accumulation in heart. Our results show the “metabolic filtering” role of liver in maintaining efficient cardiac energy metabolism.

In order to understand the pathological mechanism of cardiac complication associated with PA, a PA-mediated cardiac complication model is essential. In year 2 of PAF award, we will first develop and confirm a mouse model with cardiac complication before pathological mechanism study. With the collaboration with Dr. Michael Barry, we will characterize cardiac function and metabolic phenotype of Pcca-/-(A138T) mouse that is a PA animal model created by Dr. Michael Barry. We will induce cardiac complication with Pcca-/-(A138T) mice by diets or stresses if it is necessary. After that, we will examine how cardiac energy metabolism is disturbed using stable isotope-based metabolic flux and RNA-Seq approaches. Furthermore, we will further investigate how propionylcarnitine expansion in the heart could deplete cardiac acetylcarnitine, acetyl-CoA buffer, and affects cardiac acute energy demanding. The long-term goal of our research is to find a therapeutic target on cardiac propionyl-CoA metabolism to mitigate cardiac complication associated with PA.

Propionic Acidemia Foundation Research Grant – Richard

PAF Awards $33,082.12 Research Grant in 2019

PAF Awards $30,591 Continuation Grant in 2020

Eva Richard, PhD, Universidad Autonoma de Madrid, Spain

“Cardiomyocytes derived from induced pluripotent stem cells as a new model for therapy development in propionic acidemia”

Understanding the cellular and molecular mechanisms that occur in genetic diseases is essential for the investigation of new strategies for their prevention and treatment. In this context, induced pluripotent stem cells (iPSC) offer unprecedented opportunities for modeling human disease. One of the fundamental powers of iPSC technology lies in the competency of these cells to be directed to become any cell type in the body, thus allowing researchers to examine disease mechanisms and identify and test novel therapeutics in relevant cell types.

The main objective of this project is focused on the generation of human iPSC-derived cardiomyocytes (hiPSC-CMs) from propionic acidemia (PA) patients as a new human cellular model for the disease.In PA, cardiac symptoms, namely cardiac dysfunction and arrhythmias, have been recognized as progressive late-onset complications resulting in one of the major causes of disease mortality. Using hiPSC-CMs we will study cellular processes, such as mitochondrial function and oxidative stress which have been recognized as main contributors for PA pathophysiology. In addition, our aim is to unravel novel altered pathways using high-throughput techniques such as RNAseq and miRNA analysis. We will also examine the potential beneficial effects of an antioxidant and a mitochondrial biogenesis activator in PA cardiomyocytes. The results that derive from this project will be relevant for the disease providing insight into the affected biological processes, and thus providing tools and models for the identification of novel adjuvant treatments for PA.

Update April 2020 – Eva Richard PhD

Thanks to propionic acidemia (PA) foundation, we have developed a new cellular model of PA based on induced pluripotent stem cells (iPSC) with the goal of defining new PA pathomechanisms which could be potential therapeutical targets. Traditionally, disease pathophysiology has been studied in immortalized or human cell lines and in animal models. Unfortunately, immortalized cells often do not respond as primary cells and animal models do not exactly recapitulate patients‘ clinical symptoms. So far, patients-derived fibroblasts have been mainly used as cellular models in PA due to their availability and robustness, but they have important limitations. The ability to reprogram somatic cells to iPSCs has revolutionized the way of modeling human disease. To study rare diseases,
stem cell models carrying patient-specific mutations have become highly important as all cell types can be differentiated from iPSCs.

We have generated and characterized two iPSC lines from patients-derived fibroblasts with defects in the PCCA and PCCB genes; and an isogenic control in which the mutation of the PCCB patient was genetically corrected using CRISPR/Cas9 technology. These iPSC lines have been successfully differentiated into cardiomyocytes,
and their presence was easily established by visual observation of spontaneously contracting regions and by the expression of several cardiac markers. PCCA iPSC-derived cardiomyocytes exhibited reduced oxygen consumption, an accumulation of residual bodies and lipid droplets, and increased ribosomal biogenesis. Furthermore, we found increased protein levels of HERP, GRP78, GRP75, SIG-1R and MFN2 suggesting
endoplasmic reticulum stress and calcium perturbations in these cells. We also analysed a series of heart-enriched miRNAs previously found deregulated in heart tissue of a PA murine model and confirmed their altered expression.

The present study represents the first report of the characterization of cardiomyocytes derived from iPSCs generated by PA patients ́ fibroblasts reprogramming. Our results provide evidence that several pathomechanisms may have a relevant role in cardiac dysfunction, a common complication in PA disease. This new cellular PA model offers a powerful tool to unravel disease mechanism and, potentially, to enable drug
screening/drug testing. Despite improved therapy over the past few decades, the outcome of PA patients is still unsatisfactory, highlighting the requirement to evaluate new therapies aimed at preventing or alleviating the clinical symptoms. Additional research is required to determine the contribution of the mechanisms identified in this work to the cardiac phenotype and how this knowledge can help formulating better personalized therapeutic
strategies in the future.

We sincerely thank the Propionic Acidemia Foundation for supporting our investigation, which has resulted in a truly motivating experience for us, feeling we belong to the PA research family. The funding we received has led to important advances in PA pathophysiology, and our aim is to continue this research in the near future.

Update September 2019 – Eva Richard PhD

There is an unmet clinical need to develop effective therapies for propionic acidemia (PA). Advances in supportive treatment based on dietary restriction and carnitine supplementation have allowed patients to live beyond the neonatal period. However, the overall outcome remains poor in most patients, who suffer from numerous complications related to disease progression, among them cardiac alterations, a major cause of PA morbidity and mortality. In our research, we developed a new cellular model of PA based on induced pluripotent stem cells (iPSC) with the goal of defining new molecular pathways involved in the pathophysiology of PA which would be potential treatment targeting.

Traditionally, disease pathophysiology has been studied in immortalized or human cell lines and in animal models. Unfortunately, immortalizedcells often do not respond as primary cells and animal models do not exactly recapitulate patients‘ symptoms. So far, patients-derived fibroblasts have been mainly usedas cellular models in PAdue to theiravailability and robustness, but they have important limitations.

The ability to reprogram somatic cells to iPSCs has revolutionized the way of modeling human disease. To study rare diseases, stem cell models carrying patient-specific mutations have become highly important as all cell types can be differentiated from iPSCs. We have generated and characterized two iPSC lines from patients-derived fibroblasts with defects in PCCA and PCCB genes. These iPSC lines can be differentiated into cardiomyocytes that mimic the tissue-specific hallmarks of the disease. The presence of PA cardiomyocytes has been easily established by visual observation of spontaneously contracting regions, and the expression of several cardiac markers. We have observed that PCCA-deficient cardiomyocytes present an increase in degradation products and in lipid droplets, and exhibit mitochondrial dysfunction compared to control cells. We further discovered the down-regulation of several miRNAs in PCCA cardiomyocytes compared to control ones, and several miRNAs targets are currently being analyzed in order to investigate underlying cellular pathological mechanisms. Interestingly, we have performed several experiments to analyze the effect of the mitochondrial biogenesis activator, MIN-102 compound (PPAR agonist, derivative of pioglitazone) in cardiomyocytes.

Preliminary results showed an increase in the oxygen consumption rateof PCCA and control cells. In our next steps, we plan to complete the analysis in the PCCA cardiomyocyte line, characterize PCCB cardiomyocytes and to study in depth the therapeutic potential of MitoQ and MIN-102 compounds.

We would like to sincerely thank the Propionic Acidemia Foundation for supporting our research.

Update March 2020

“Cardiomyocytes derived from induced pluripotent stem cells as a new model for therapy development in propionic acidemia.”

Eva Richard, Associate Professor

Traditionally, disease pathophysiology has been studied in immortalized or human cell lines and in animal models. Unfortunately, immortalized cells often do not respond as primary cells and animal models do not exactly recapitulate patients‘ symptoms. So far, patients-derived fibroblasts have been mainly used as cellular models in PA due to their availability and robustness, but they have important limitations.

The ability to reprogram somatic cells to iPSCs has revolutionized the way of modeling human disease. To study rare diseases, stem cell models carrying patient-specific mutations have become highly important as all cell types can be differentiated from iPSCs. We have generated and characterized two iPSC lines from patients-derived fibroblasts with defects in the PCCA and PCCB genes. These iPSC lines can be differentiated into cardiomyocytes that mimic the tissue-specific hallmarks of the disease. The presence of cardiomyocytes has been easily established by visual observation of spontaneously contracting regions, and the expression of several cardiac markers. PCCA iPSC-derived cardiomyocytes exhibited an alteration of autophagy process with an accumulation of residual bodies and mitochondrial dysfunction characterized by reduced oxygen consumption and alteration of mitochondrial biogenesis due to a deregulation of PPARGC1A. We also evaluated the expression of heart-enriched miRNAs previously associated with cardiac dysfunction and several miRNAs were found deregulated. Furthermore, we found increased protein levels of Herp, Grp78, Grp75, sigma-1R and Mfn2 suggesting ER stress and calcium perturbations in these cells.

We are planning to analyze PCCB cardiomyocytes to compare the results with PCCA and control data. We are working to obtain mature cardiomyocytes in order to perform electrophysiology studies (K+ currents) using a whole-cell patch clamp method. We are interested in the study of the tissue-specific bioenergetic signature comparing cardiomyocytes derived from control and PA patients´ iPSCs by reverse phase protein microarrays (RPPMA). Future work also includes testing the effect of the mitochondrial biogenesis activator, MIN-102 compound (PPAR agonist, derivative of pioglitazone) and of the mitochondrial targeting antioxidant MitoQ in PA cardiomyocytes.

We would like to sincerely thank the Propionic Acidemia Foundation for supporting our research.

Propionic Acidemia Foundation Research Grant Guofang Zhang

PAF Awards $48,500 Research Grant

Guofang Zhang, PhD, Duke University

“Propionyl-CoA and propionylcarnitine mediate cardiac complications in patients with propionic acidemia”

Energy production is the central cardiac metabolism for continuous mechanical work. An average human adult heart consumes ~ 6 kg ATP/day. ATP storage in the heart is only sufficient to sustain the heart beat for a few seconds. A tightly coupled cardiac energy metabolism from various substrates is critical for sufficient ATP production required by normal heart function.

One molecule of palmitic acid (fatty acid) generates much more ATP than one molecule of glucose does after their complete metabolism.Fatty acids contribute ~70-90% cardiac energy production in normal condition. However, heart still maintains high flexibility of fuel switch in response to various available substrates. Acetyl-CoA is the first convergent metabolite derived from the diverse fuel substrates via different pathways and enters tricarboxylic acid cycle (TCAC) for energy production. Therefore, the level of acetyl-CoA or the ratio of acetyl-CoA/CoA tightly controls the metabolic fluxes from two major fuels, i.e.,glucose and fatty acid, in the heart. Acetyl-CoA or CoA level is also finely tuned by carnitine acetyltransferase (CrAT) that catalyzes the reversible interconversion between short-chain acyl-CoAs and acylcarnitines.Acetylcarnitine level is ~10-100 fold greater than that of acetyl-CoA in heart and is seen as the buffer of acetyl-CoA. CrAT is highly expressed in high energy demanding organs including heart and mediates fatty acid and glucose metabolism possibly by dynamically interconverting acetyl-CoA and acetylcarnitine into each other.The deficiency of CrAT has been shown to change cardiac fuel selection.

Propionic acidemia (PA) is often associated with cardiac complications. However, the pathological mechanism remains unknown. We have demonstrated that high exogenous propionate led to the propionyl-CoA accumulation and cardiac fuel switch from fatty acid to glucose in the perfused normal rat hearts (Am. J Physiol. Endocrinol. Metab.,2018,315:E622-E633). The deficiency of propionyl-CoA carboxylase in PA also induces the accumulation of propionyl-CoA. Next, we will attempt to understand whether and how the elevated propionyl-CoA in the Pcca-/- heart (collaboration with Dr. Michael Barry)could interrupt cardiac energy metabolism by investigating the fuel switch flexibility, CrAT mediated metabolism, and buffer capacity of acetylcarnitine using stable isotope-based metabolic flux analysis (J. Biol. Chem., 2015,290:8121-32). We hope that the outcome of this project will provide meaningful therapeutic recommendation for patients with PA, especially with the cardiac complication.

Novel therapies for Propionic acidemia – update Sept. 2018

Novel therapies for Propionic acidemia

Nicola Brunetti-Pierri, MD, Fondazione Telethon, Italy

This proposal was focused on the characterization of a fish model of propionic acidemia (PA) and on the development of novel therapies. The PA medaka fish model was found to recapitulate several clinical and biochemical features of the human disease, including reduced survival and locomotor activity, hepatic lipid accumulation, increased propionylcarnitine, methylcitrate, and propionate. Moreover, PA fishes showed better survival when fed with low-protein diet.

To gain insight into the disease pathogenesis and to search for potentially novel therapeutic targets, we performed an unbiased 3’-mRNA-Seq and NMR-based metabolome analyses. Both analyses showed global differences between PA and wild-type (wt) medaka. Interestingly, metabolism of glycine and serine resulted affected both at transcriptional and metabolites level and further studies are ongoing to investigate the role of these changes in the disease pathogenesis. Moreover, we found a marked increase in protein propionylation in PA fishes compared to wt controls. Protein propionylation is a post-translational modification occurring under normal conditions but its physiological role is unknown. Like protein acetylation, it is likely involved in regulation of gene expression, protein-protein interactions, and enzyme function. Interestingly, NAD-dependent sirtuins that are responsible of deacetylation of multiple proteins and have also de-propionylating activity, were significantly reduced in PA fishes. We speculated that aberrant protein propionylation in PA is toxic and proteomic studies are ongoing to reveal proteins with aberrant propionylation. With the support of this grant several drug candidates have been also investigated with the goal of developing new pharmacological approaches for PA.

In conclusion, we performed extensive phenotyping of the PA fish model that can be useful to unravel novel disease mechanisms and therapeutic targets.

updated September 2018

Targeting Serine and Thiol Metabolism in Propionic Acidemia

Targeting Serine and Thiol Metabolism in Propionic Acidemia

Hilary Vernon, MD PhD, Johns Hopkins University

While it has been known for several decades that dysfunction of the enzyme propionyl-CoA carboxylase underlies propionic acidemia (PA), many key downstream metabolic adaptions to this primary defect are not well defined. In our research, we developed and studied a new cellular model of PA, with the goals of understanding how the cell is affected in PA, and to identify new pathways for potential treatment targeting.

We initially studied both protein expression in fibroblasts (skin cells) from individuals with PA, and metabolites in urine from individuals with PA, and discovered changes in pathways related to serine metabolism. Serine is an important amino acid that is involved in the synthesis of folate intermediates, glutathione, and other important cellular metabolites. Serine metabolism is of particular interest because it has also been shown recently to be dysregulated in other mitochondrial diseases, and there is a growing interest in how to target this pathway for therapeutic intervention.

In order to more closely study these findings, we developed a new cellular model of propionyl-CoA carboxylase deficiency, where we used CRISPR technology to mutate the PCCA gene in a kidney cell line called HEK293. This new model cell line has important biochemical hallmarks of PA, including absence of the PCCA protein, elevated propionyl-carnitine, very low methylmalonyl-carnitine, and elevated glycine. We discovered that when these cells are in the growth phase, they express genes involved in serine synthesis at higher levels than cells that have normal propionyl-CoA carboxylase activity. We further discovered that the PA cells are very sensitive to deprivation of serine in their culture media, and grow slower than cells with intact propionyl-CoA carboxylase activity. This growth abnormality is not seen when the cells are grown in media that contains serine. Interestingly, we looked at these same pathways in a CRISPR model of methylmalonic acidemia, a closely related disorder to PA, and while we found some overlap in sensitivity to serine, the gene expression patterns we different. This highlights the biochemical uniqueness of PA. Currently, we are completing flux metabolomics studies in these cells, which will determine exactly what this serine is being metabolized to, and we expect these experiments to be completed by the end of August. In our next steps, we plan to study how treating the cells with different metabolites may alleviate this serine growth defect.

We would like to sincerely thank the Propionic Acidemia Foundation for supporting our research. The funding we received has led to important breakthroughs in our work, and we are excited to continue to move this research forward in the coming years.

updated September 2018

PAF Awards grant for Dr. Oleg Shchelochkov and Dr. Charles P. Venditti for $32,912

PAF awarded a $32,912 research grant to Oleg Shchelochkov, M.D. and Charles P. Venditti MD, PhD at National Human Genome Research Institute, National Institutes of Health – 2018

“Diversion of Isoleucine and Valine Oxidative Pathway to Reduce the Propionogenic Load in Propionic Acidemia.”

Patients with propionic acidemia require lifelong protein restriction. In addition to taking a protein restricted diet, many propionic acidemia patients are also prescribed medical formulas. This dietary approach aims to decrease the intake of four amino acids that can become propionic acid. These four amino acids – isoleucine, valine, threonine, and methionine – are called essential, because they cannot be made in the human body and need to be supplied from foods. Too much protein intake creates a situation where excess can lead to a buildup of propionic acid in the body. On the other hand, limiting these four amino acids too much can lead to poor growth. Therefore, patients’ diets are optimized to minimize propionic acid production while encouraging good growth. We wonder whether it is possible to increase dietary protein intake while minimizing the risk of propionic acid buildup.

To answer this question, we are planning to do a series of experiments in zebrafish. Why use zebrafish? Zebrafish share significant similarity to humans in how they process propionic acid. In addition, zebrafish reproduce and mature quickly, which are very important qualities to help search for new drugs that could be used to treat propionic acidemia. Our zebrafish are kept in a special building where the animals are being cared for by a dedicated team that includes scientists, veterinarians, engineers, aquatic specialists, and many others. They check on fish and feed them several times a day, maintain fish tanks, and keep their water very clean.

This type of facility is unique and had enabled our studies of metabolic diseases in zebrafish. Our ongoing studies have shown that zebrafish affected by metabolic diseases have symptoms that are very similar to patients. Even with treatment, affected fish have difficulty growing, get tired easily, have poor appetites and sometimes perish before adulthood. Using special genomic tools, we are planning to change in how the fish processes protein to direct it away from becoming propionic acid. As we make these changes to the biochemical pathways of propionic acidemia zebrafish, we will be carefully watching how these treatments improve their growth, development, appetite and survival. These experiments will help us understand how we can potentially reduce propionic acid toxicity while helping patients achieve a less restrictive diet.

Interview with Joel Pardo – Summer 2020

Can you tell me about yourself and how you became interested in science?

I was always interested in the sciences. I think ultimately what propelled me towards a career in science was my research experience at the University of California, San Diego. The mentorship I received from Dr. Joshua Bloomekatz helped me develop the ability to reason scientifically and appreciate the opportunities to grow professionally. I learned from him how to design experiments to answer important scientific questions. We often had lengthy discussions about the direction of my project. He helped me make sense of the collection of observations coming from different sources and nurtured my own independent thinking.In gaining an appreciation for his analytical method of thinking, I began to see myself as someday contributing to scientific thinking as a physician-scientist.

During your training at NIH, you worked on a project to find new treatments using zebrafish. What did you find exciting and challenging about studying zebrafish?

Most people are familiar with mice, which are often used in science to find and test new drugs. Working with mice requires a lot of work to have enough animals needed for an experiment. Zebrafish, on the other hand, can produce hundreds of offspring after one breeding cycle. Zebrafish lay eggs directly into water, which also makes it easier to study them soon after they hatch. Somewhat surprisingly,the zebrafish enzymes that handle propionic acid are very similar to the enzymes in humans. These two properties of zebrafish make them an exciting model to study a disease like propionic acidemia.

One of the most challenging parts of my research in zebrafish was their size. Zebrafish offspring are very small, measuring less than a quarter of an inch. I had to spend a lot of time looking at zebrafish under the microscope and learn how to move them around without hurting them. This can be difficult as these small animals are fragile at this young age.

Can you tell us about your PA project?

Earlier in my work, we were able to get zebrafish, which had mutations in the genes linked to propionic acidemia. I needed to understand what propionic acidemia does to zebrafish. We were able to show that propionic acidemia in zebrafish looks a lot like the disease we see in patients. Fish with propionic acidemia had poor appetite, did not grow well, and had difficulty moving. Using special genetic tools, we then attempted to change how zebrafish processed propionic acid and helped them survive longer. Our preliminary results are proving promising, but more work is still needed.

What are your plans after you complete your training at NIH?

The NIH postbac program is a full-time research award for students that have recently completed a bachelor’s degree and are considering a career in science or medicine. I was fortunate enough to join Dr. Charles Venditti’s lab 2 years ago to work on the zebrafish project under Dr. Oleg Shchelochkov. I thoroughly enjoyed my post-bac experience. Looking back on the past 2 years, I feel the lab, and in particular the mentorship of Dr. Shchelochkov, has facilitated and nurtured my growth as a future physician-scientist with roots in propionic acidemia research. In 2019 I applied to MD/PhD programs at several US universities. After having traveled to over half a dozen states and interviewing at many fantastic universities, I ultimately decided upon the physician-scientist training program at University of Minnesota. As I plan my transition to the program, I am currently looking for winter coats.