Kelly Laboratory

Daniel P. Kelly, M.D.

Willard and Rhoda Ware Professor
Perelman School of Medicine
Children’s Hospital of Philadelphia (CHOP) Rachel Ash Presidential Chair
Director, Penn and CHOP Cardiovascular Institutes

Location: Smilow TRC 11-122
Phone: 215-898-0768
Email: dankelly@pennmedicine.upenn.edu

Admin: Teresa C. Leone
Phone: 215-898-0768
Email: terleone@pennmedicine.upenn.edu

Mitochondrial Biogenesis and Remodeling

Kelly Lab Research

A. HEART PROJECTS

Project 1: Cardiac Nuclear Receptor Signaling in Health and Disease

We are interested in the fuel and energy metabolic disturbances that contribute to the worldwide health problem of heart failure. Early studies by our group delineated the molecular genetic basis of inherited defects in mitochondrial fatty acid oxidation (FAO) that cause childhood sudden death and heart failure. These studies prompted us to determine whether similar metabolic alterations occur in common forms of heart failure due to disease drivers such as hypertension, coronary artery disease, and diabetes. We, and others, found that common acquired forms of heart failure are associated with re-programming of cardiac fuel metabolism and mitochondrial function. Importantly, significant genetic and experimental evidence indicates that fuel and energy metabolic disturbances contribute to the pathogenesis of heart failure. We have defined transcriptional regulatory events that underlie mitochondrial biogenesis and maturation during normal cardiac development, and how this regulatory circuitry becomes altered in the hypertrophied and failing heart. We discovered that members of the nuclear receptor superfamily, including peroxisome proliferator-activated receptors (PPARs) and estrogen-related receptors (ERRs), are necessary and sufficient for mitochondrial biogenesis and maturation along with the development of specialized fuel utilization programs in the developing heart. This circuitry is controlled, in part, by the PPARg coactivator-1 (PGC-1) coregulators (PGC-1a and PGC-1b). Current projects in the lab are focused on PGC-1/ERR signaling in heart. Using human induced pluripotent cardiac myocytes (hiPSC-CM), gene edited mouse models, and assessment of cardiac tissue from well-characterized humans with heart failure, we have shown a master regulatory role for the ERRs in the coordinate control of mitochondrial function and energy-utilizing processes such as contractility, ion transport, and myocyte calcium homeostasis. These findings have led to studies aimed at assessing the potential for activation of ERR signaling as a treatment for heart failure. We also seek to investigate mechanisms involved in mitochondrial signaling to the nucleus via metabolite-mediated epigenomic events. The long-term goal of these studies is to determine whether these factors or selected downstream responses will serve as suitable targets for novel metabolic modulator therapy aimed at heart failure.

Project 2: Systems-based Deep Interrogation of Mitochondrial Re-programming During Development of Cardiac Hypertrophy and Heart Failure

This project began by employing unbiased molecular profiling (-OMIC) to probe mitochondrial phenotypic programming during the development of heart failure in well-defined mouse models and in humans. To this end, we have conducted integrated whole genome RNA sequencing, quantitative targeted metabolomics, and mitochondrial proteomics. Our profiling has led to a series of discoveries that have spawned new projects including: 1) mitochondrial protein lysine acylation is increased in the failing heart, likely due to altered short-chain carbon balance in the mitochondrial matrix. We seek to determine the functional significance of this interesting post-translational modification; 2) surprisingly, the failing heart shifts to burning ketone bodies as a fuel. Studies are ongoing to determine if this fuel switch is adaptive. If so, we seek to develop strategies to increase ketone utilization as a new heart failure treatment; and 3) mitochondrial proteins undergo dynamic changes in phosphorylation status. We seek to determine how both acylation and phosphorylation status impacts mitochondrial function, and if such post-translational modifications are relevant to the pathogenesis of heart failure.

B. MUSCLE PROJECTS

Project 3: Delineation of Mechanisms and Signaling Pathways Involved in Muscle Metabolic Fitness

The broad goal of this project is to identify energy metabolic “checkpoints” relevant to muscle function and insulin sensitivity. It is well known that accumulation of intramyocellular lipid (IMCL) is tightly associated with the development of insulin resistance in obese individuals. However, the mechanisms involved in this linkage are poorly understood. Delineation of pathways that coordinately control muscle lipid depots and insulin signaling would be very useful for the field of diabetes, given that there are few therapeutic approaches that directly target muscle insulin resistance and myocellular lipotoxicity in pre-diabetic and diabetic states. This project began with an unbiased, small molecule screen of myocytes in culture that had been loaded with lipid. We sought to identify molecular probes that reduced lipid levels while increasing glucose uptake. Once such probe was identified, and through a series of transcriptional profiling and cellular metabolic studies in human skeletal myotubes, we found that the small molecule inhibited the transcription factor, MondoA. MondoA is a skeletal muscle-enriched factor that is highly related to MondoB, also known as carbohydrate response element binding protein (ChREBP), a liver-enriched factor that controls hepatic glucose and lipid metabolism. The results of our recent studies strongly suggest that MondoA regulates enzymes and pathways that control the amount of fuel available for combustion in myocytes. Specifically, MondoA increases triglyceride synthesis in order to store excess fatty acid and inhibits insulin signaling to reduce the amount of glucose (fuel) entering the cell. In other words, we believe that MondoA serves as a “brake” or checkpoint on nutrient uptake during times of “plenty”. Further, we hypothesize that under conditions of chronic nutrient excess (obesity), MondoA is chronically activated, driving excessive myocyte lipid accumulation and chronic insulin resistance. We are testing these hypotheses using skeletal muscle-specific and generalized MondoA knockout mice. We will also assess the role of MondoA in liver and heart. In addition, we are undertaking RNA sequencing and whole genome chromatin immunoprecipitation-sequencing (ChIP-seq) with MondoA antibodies to define downstream targets in human skeletal myotubes. We will also conducting studies to determine whether MondoA is necessary for storing fuel in muscle in preparation for repeated bouts of exercise and in disease states such as disuse atrophy and sarcopenia.

A second project has evolved based on an interesting phenotype of muscle specific PPAR (MCK-PPARa and MCK-PPARd) transgenic mice generated in our laboratory. MCK-PPARa mice have very high rates of fatty acid oxidation (FAO) in muscle and are completely resistant to diet-induced obesity (DIO). We have shown that the resistance to DIO is due at least in part to increased energy expenditure due to the incredibly high rates of FAO. The fatty acids that supply the muscle FAO pathway in the transgenic mice come from lipolysis of adipose tissue. These results strongly suggest a communication mediated by signals between muscle and fat tissue. We hypothesize that factors secreted by skeletal muscle downstream of PPAR signaling serve this signaling function. We have identified a candidate list of such factors using RNA sequence analysis, and are testing them using loss- and gain-of-function in mice and in cells in culture. Delineation of such “crosstalk” factors could lead to new therapeutic approaches for obesity and muscle fitness.

C. CANCER PROJECTS

Project 4: The Role of Mitochondrial Metabolism in the Development of Resistant Melanoma

Significant evidence implicates adaptive changes in mitochondrial metabolism as an important determinant of the behavior of certain cancers. Recently, the development of therapeutic resistance in melanoma has been linked to changes in mitochondrial function downstream of the transcriptional coactivator PGC-1a. Given our longstanding interest in the PGC-1/ERR regulatory axis in heart, we are well-positioned to apply our knowledge and reagents to study melanoma metabolism. To this end, we have recently joined a group of cancer biologists to probe the potential roles of PGC-1 and ERR in the development of melanoma drug resistance. We are preparing CRISPR-based functional genomic screens to identify genes involved in the mitochondrial-mediated therapeutic resistance in human melanoma cell lines.

Selected Publications

Gan Z, Burkart-Hartman EM, Han D-H, Finck B, Leone TC, Smith EY, Ayala JE, Holloszy J, Kelly DP: Nuclear receptor PPARβ/δ programs muscle glucose metabolism in cooperation with AMPK and MEF2. Genes Dev. 2011; 25:2619-2630. PMCID: PMC3248683
Kim C, Wen J, Wong J, Wang S, Wang C, Spiering S, Kan NG, Forcales S, Puri PL, Leone TC, Marine JE, Calkins H, Kelly DP, Judge DP, Chen H-SV: Studying arrhythmogenic right ventricular dysplasia with patient-specific iPSCs. Nature. 2013; Feb 7;494:105-110. PMCID: PMC3573229
Gan Z, Rumsey J, Hazen BC, Lai L, Leone TC, Vega RB, Xie H, Conley KE, Auwerx J, Smith SR, Olson EN, Kralli A, Kelly DP: Nuclear receptor/microRNA circuitry links muscle fiber type to energy metabolism. J Clin Invest. 2013; Jun 3;123(6):2564-2575. PMCID: PMC3668841
Lai L, Leone TC, Keller MP, Martin OJ, Broman AT, Nigro J, Kapoor K, Koves TR, Stevens R, Ilkayeva OR, Vega RB, Attie AD, Muoio DM, Kelly DP: Energy metabolic re-programming in the hypertrophied and early stage failing heart: A multi-systems approach. Circ Heart Fail. 2014; 7:1022-1031. PMCID: PMC4241130
Aubert G, Martin OJ, Horton JL, Lai L, Vega RB, Leone TC, Koves T, Gardell SJ, Krüger M, Lewandowski ED, Crawford PA, Muoio DM, Kelly DP: The failing heart relies on ketone bodies as a fuel. Circulation. 2016 Feb 23;133(8):698-705. PMCID: PMC4766035
Ahn B, Soundarapandian MM, Sessions H, Peddibholta S, Roth G, Li J-L, Sugarman E, Koo A, Malany S, Wang M, Yea K, Brooks J, Leone TC, Han X, Vega RB, Kelly DP: MondoA coordinately regulates skeletal myocyte lipid homeostasis and insulin signaling. J Clin Invest. 2016 Sep 1;126(9):3567-3579. PMCID: PMC5004938
Vega RB, Konhilas J, Kelly DP, Leinwand L: Molecular mechanisms underlying cardiac adaptation to exercise. Cell Metab. 2017; May 2;25(5):1012-1026.
Yurista SR, Matsuura TR, Silljé HHW, Nijholt KT, McDaid KS, Shewale SV, Leone TC, Newman JC, Verdin E, Oberdorf-Maass SU, van Veldhuisen DJ, de Boer RA, Kelly DP, Westenbrink BD: Ketone ester treatment improves cardiac function and reduces pathologic remodeling in pre-clinical models of heart failure. Circ HF 2021 Jan; 14(1): e007684. PMCID: PMC7819534
Sakamoto T, Batmanov K, Wan S, Guo Y, Lai L, Vega RB, Kelly DP: The nuclear receptor ERRg cooperates with the cardiogenic factor GATA4 to orchestrate cardiomyocyte maturation. Nat Commun, 2022 Apr 13;13(1):1991. PMCID: PMC9008061.
Yamamoto T, Maurya SK, Pruzinsky E, Batmanov K, Xiao Y, Sulon SM, Sakamoto T, Wang Y, Lai L, McDaid KS, Shewale SV, Leone TC, Koves TR, Muoi DM, Dierickx P, Lazar MA, Lewandowski ED, Kelly DP: RIP140 deficiency enhances cardiac fuel metabolism and protects mice from heart failure. JCI. 2023 Mar 16;e162309. PMCID: PMC: 36927960
Matsuura TR, Puchalska P, Crawford PA, Kelly DP: Ketones and the heart: Metabolic principles and therapeutic implications. Circ Res. 2023 Mar 31;132(7):882-898. PMID: 36996176
Sakamoto T and Kelly DP: Cardiac Maturation. JMCC, 2023, Dec 30:187:38-50. PMID: 38160640