Arun Padmanabhan, MD, PhD

Assistant Professor

CLINICAL INTERESTS: Dr. Padmanabhan is a cardiologist specializing in general cardiology. His specific interests include preventive cardiology, lamin A/C gene (LMNA) associated cardiomyopathies, and right heart disease in athletes.

RESEARCH INTERESTS: Dr. Padmanabhan’s research focuses on understanding the gene-regulatory and epigenetic pathways that govern cell fate decisions during early cardiac development and cell state transitions in the pathophysiology of heart failure.

Education
2017 - Cardiovascular Disease Fellowship, University of California San Francisco
2014 - Internal Medicine Residency, Massachusetts General Hospital, Harvard Medical School
M.D., 2012 - , University of Pennsylvania
Ph.D., 2010 - Cell & Developmental Biology, University of Pennsylvania
A.B., 2003 - Biochemistry & Molecular Biology, Washington University in St. Louis
Publications

  1. Amrute JM, Zhu A, Pai YL, Hector-Greene M, An Y, Kim KR, Sheth MU, Padmanabhan A, Lee CY, Yamawaki T, Sicklinger F, Hartman N, Bredemeyer A, Lee CJM, Xu V, Bell L, Harmon T, Shin H, Parvathaneni A, Liu L, Dutta AK, Pruitt D, Barreda J, Chen J, Shroff UN, Nadadur R, Nigro J, Weinheimer C, Kovacs A, Cui J, Wang C, Li CM, Kreisel D, Liu Y, Foo RS, Schneider RK, Engreitz JM, Mann DL, Rulifson I, Jackson S, Ason B, Kramann R, Drakos SG, Leuschner F, Alexanian M, Lavine KJ. Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery. bioRxiv : the preprint server for biology 2025. PMID: 40777284


  2. Qin J, Aras MA, Song EJ, Connolly AJ, Zhou L, O'Brien C, Salem JE, Padmanabhan A, Moslehi JJ. Insights Into Recovery From Acute Fulminant Myocarditis Following Successful Treatment With Ruxolitinib by Comprehensive Single-Cell Profiling. Circulation 2025. PMID: 40549846


  3. Busse L, Huth EA, Abraham MR, Abraham T, Padmanabhan A, Wojciak J, Wright G, Aatre R, Campagna R, Jackson E, Kreykes S, Lane K, Sawyer L, Pappas C, Thomas M, VanDyke R, Vedantham V, Higgs EJ. ALPK3 Heterozygous Truncating Variants Cause Late-Onset Hypertrophic Cardiomyopathy With Frequent Apical Involvement and Apical Aneurysm. Circulation. Genomic and precision medicine 2025. PMID: 40469041


  4. Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A, Birth Defects Research Laboratory, Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM. Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart. medRxiv : the preprint server for health sciences 2024. PMID: 39606363


  5. Caudal A, Liu Y, Pang PD, Maison DP, Nakasuka K, Feng J, Schwarzer-Sperber HS, Schwarzer R, Moffatt E, Henrich TJ, Padmanabhan A, Connolly AJ, Wu JC, Tseng ZH. Transcriptomic Profiling of Human Myocardium at Sudden Death to Define Vulnerable Substrate for Lethal Arrhythmias. JACC. Clinical electrophysiology 2024. PMID: 39545913


  6. Alexanian M, Padmanabhan A, Nishino T, Travers JG, Ye L, Pelonero A, Lee CY, Sadagopan N, Huang Y, Auclair K, Zhu A, An Y, Ekstrand CA, Martinez C, Teran BG, Flanigan WR, Kim CK, Lumbao-Conradson K, Gardner Z, Li L, Costa MW, Jain R, Charo I, Combes AJ, Haldar SM, Pollard KS, Vagnozzi RJ, McKinsey TA, Przytycki PF, Srivastava D. Chromatin remodelling drives immune cell-fibroblast communication in heart failure. Nature 2024. PMID: 39443808


  7. Yurk D, Barrios JP, Labrecque Langlais E, Avram R, Aras MA, Abu-Mostafa Y, Padmanabhan A, Tison GH. Automated Assessment of Right Atrial Pressure From Ultrasound Videos Using Machine Learning. JACC. Advances 2024. PMID: 39372459


  8. Thottakara T, Padmanabhan A, Tanriverdi T, Thambidurai T, Diaz-Rg JA, Amonkar SR, Olgin JE, Long CS, Roselle Abraham M. Single-nucleus RNA/ATAC-seq in early-stage HCM models predicts SWI/SNF-activation in mutant-myocytes, and allele-specific differences in fibroblasts. bioRxiv : the preprint server for biology 2024. PMID: 38903075


  9. Padmanabhan A, de Soysa TY, Pelonero A, Sapp V, Shah PP, Wang Q, Li L, Lee CY, Sadagopan N, Nishino T, Ye L, Yang R, Karnay A, Poleshko A, Bolar N, Linares-Saldana R, Ranade SS, Alexanian M, Morton SU, Jain M, Haldar SM, Srivastava D, Jain R. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation. Nature cardiovascular research 2024. PMID: 39196112


  10. Nishino T, Ranade SS, Pelonero A, van Soldt BJ, Ye L, Alexanian M, Koback F, Huang Y, Sadagopan N, Lam A, Zholudeva LV, Li F, Padmanabhan A, Thomas R, van Bemmel JG, Gifford CA, Costa MW, Srivastava D. Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes. Nature cardiovascular research 2023. PMID: 39183978


  11. Chorba JS, Xia VQ, Smith GA, Padmanabhan A. Rapid Multiplexed Flow Cytometric Validation of CRISPRi sgRNAs in Tissue Culture. Bio-protocol 2023. PMID: 36789164


  12. Alexanian M, Padmanabhan A, Nishino T, Travers JG, Ye L, Lee CY, Sadagopan N, Huang Y, Pelonero A, Auclair K, Zhu A, Gonzalez Teran B, Flanigan W, Kim CK, Lumbao-Conradson K, Costa M, Jain R, Charo I, Haldar SM, Pollard KS, Vagnozzi RJ, McKinsey TA, Przytycki PF, Srivastava D. Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis. bioRxiv : the preprint server for biology 2023. PMID: 36711864


  13. Smith GA, Padmanabhan A, Lau BH, Pampana A, Li L, Lee CY, Pelonero A, Nishino T, Sadagopan N, Xia VQ, Jain R, Natarajan P, Wu RS, Black BL, Srivastava D, Shokat KM, Chorba JS. Cold shock domain-containing protein E1 is a posttranscriptional regulator of the LDL receptor. Science translational medicine 2022. PMID: 36103516


  14. Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel JG, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D. Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Circulation 2022. PMID: 35938400


  15. Hsu A, Duan Q, Day DS, Luo X, McMahon S, Huang Y, Feldman ZB, Jiang Z, Zhang T, Liang Y, Alexanian M, Padmanabhan A, Brown JD, Lin CY, Gray NS, Young RA, Bruneau BG, Haldar SM. Targeting transcription in heart failure via CDK7/12/13 inhibition. Nature communications 2022. PMID: 35896549


  16. Seedor RS, Meeker CR, Lewis B, Handorf EA, Filchner KA, Varadarajan R, Hensold J, Padmanabhan A, Negin B, Blankstein K, Chawla NR, Song WF, Epstein J, Winn J, Goldstein LJ, Dotan E. Prospective Comparison of Geriatric Assessment and Provider's Assessment of Older Adults With Metastatic Breast Cancer in the Community. The oncologist 2022. PMID: 35641214


  17. Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Transcription factor protein interactomes reveal genetic determinants in heart disease. 2015 Year Book of Pediatrics. Ed. Cabana MD. (Elsevier; Philadelphia, PA) 2022. PMID: 35182466


  18. Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R. Publisher Correction: BRD4 orchestrates genome folding to promote neural crest differentiation. 2015 Year Book of Pediatrics. Ed. Cabana MD. (Elsevier; Philadelphia, PA) 2021. PMID: 34725478


  19. Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R. BRD4 orchestrates genome folding to promote neural crest differentiation. 2015 Year Book of Pediatrics. Ed. Cabana MD. (Elsevier; Philadelphia, PA) 2021. PMID: 34611363


  20. Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A. Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. Cell systems 2021. PMID: 34352221


  21. Alexanian M, Przytycki PF, Micheletti R, Padmanabhan A, Ye L, Travers JG, Gonzalez-Teran B, Silva AC, Duan Q, Ranade SS, Felix F, Linares-Saldana R, Li L, Lee CY, Sadagopan N, Pelonero A, Huang Y, Andreoletti G, Jain R, McKinsey TA, Rosenfeld MG, Gifford CA, Pollard KS, Haldar SM, Srivastava D. A transcriptional switch governs fibroblast activation in heart disease. Nature 2021. PMID: 34163071


  22. Padmanabhan A, Alexanian M, Linares-Saldana R, González-Terán B, Andreoletti G, Huang Y, Connolly AJ, Kim W, Hsu A, Duan Q, Winchester SAB, Felix F, Perez-Bermejo JA, Wang Q, Li L, Shah PP, Haldar SM, Jain R, Srivastava D. BRD4 Interacts with GATA4 to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes. Circulation 2020. PMID: 33094644


  23. Padmanabhan A, Haldar SM. Drugging transcription in heart failure. The Journal of physiology 2019. PMID: 30927446


  24. Alexanian M, Padmanabhan A, McKinsey TA, Haldar SM. Epigenetic therapies in heart failure. Journal of molecular and cellular cardiology 2019. PMID: 30991033


  25. Muniyappa A, Padmanabhan A, Goldschlager N. A Wide Complex Tachycardia in a Woman During Exercise: Did She Tread Into Dangerous Territory? JAMA internal medicine 2018. PMID: 30419135


  26. Padmanabhan A, Haldar SM. Unusual transcription factor protects against heart failure. Science (New York, N.Y.) 2018. PMID: 30573617


  27. Cedarbaum ER, Padmanabhan A, Goldschlager N. Electrical Alternans in Disguise-A Curious Case of Atrial Flutter. JAMA internal medicine 2018. PMID: 30383080


  28. Morehead-Gee A, Padmanabhan A, Goldschlager N. Not Your Typical ST-Elevation Myocardial Infarction. Volume 178 of Issue 2. JAMA internal medicine 2018. PMID: 29159403


  29. Padmanabhan A, Haldar SM. Plasma MicroRNA Clusters in Human Left Ventricular Remodeling: A Biomarker and Discovery Platform. Volume 11 of Issue 2. 2018. PMID: 29438983


  30. Yzaguirre AD, Padmanabhan A, de Groh ED, Engleka KA, Li J, Speck NA, Epstein JA. Loss of neurofibromin Ras-GAP activity enhances the formation of cardiac blood islands in murine embryos. Volume 4. 2015. PMID: 26460546


  31. Jain R, Li D, Gupta M, Manderfield LJ, Ifkovits JL, Wang Q, Liu F, Liu Y, Poleshko A, Padmanabhan A, Raum JC, Li L, Morrisey EE, Lu MM, Won KJ, Epstein JA. HEART DEVELOPMENT. Integration of Bmp and Wnt signaling by Hopx specifies commitment of cardiomyoblasts. Volume 348 of Issue 6242. 2015. PMID: 26113728


  32. Jain R, Barkauskas CE, Takeda N, Bowie EJ, Aghajanian H, Wang Q, Padmanabhan A, Manderfield LJ, Gupta M, Li D, Li L, Trivedi CM, Hogan BL, Epstein JA. Plasticity of Hopx(+) type I alveolar cells to regenerate type II cells in the lung. Volume 6. 2015. PMID: 25865356


  33. Vaduganathan M, Nagarur A, Kerr DA, Lauter KB, Padmanabhan A, Raghavan S, Pallais JC, Fenves AZ. Metastatic pancreatic neuroendocrine tumor with ectopic adrenocorticotropic hormone production. Volume 28 of Issue 1. 2015. PMID: 25552797


  34. Padmanabhan A, Haldar SM. Neuroprotection in ischemic stroke: AhR we making progress? Volume 130 of Issue 23. Circulation 2014. PMID: 25359167


  35. Takeda N, Jain R, Leboeuf MR, Padmanabhan A, Wang Q, Li L, Lu MM, Millar SE, Epstein JA. Hopx expression defines a subset of multipotent hair follicle stem cells and a progenitor population primed to give rise to K6+ niche cells. Volume 140 of Issue 8. 2013. PMID: 23487314


  36. Shin J, Padmanabhan A, de Groh ED, Lee JS, Haidar S, Dahlberg S, Guo F, He S, Wolman MA, Granato M, Lawson ND, Wolfe SA, Kim SH, Solnica-Krezel L, Kanki JP, Ligon KL, Epstein JA, Look AT. Zebrafish neurofibromatosis type 1 genes have redundant functions in tumorigenesis and embryonic development. Volume 5 of Issue 6. 2012. PMID: 22773753


  37. Zhu C, Smith T, McNulty J, Rayla AL, Lakshmanan A, Siekmann AF, Buffardi M, Meng X, Shin J, Padmanabhan A, Cifuentes D, Giraldez AJ, Look AT, Epstein JA, Lawson ND, Wolfe SA. Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish. Volume 138 of Issue 20. 2011. PMID: 21937602


  38. Lee JS, Padmanabhan A, Shin J, Zhu S, Guo F, Kanki JP, Epstein JA, Look AT. Oligodendrocyte progenitor cell numbers and migration are regulated by the zebrafish orthologs of the NF1 tumor suppressor gene. Volume 19 of Issue 23. 2010. PMID: 20858602


  39. Elden AC, Kim HJ, Hart MP, Chen-Plotkin AS, Johnson BS, Fang X, Armakola M, Geser F, Greene R, Lu MM, Padmanabhan A, Clay-Falcone D, McCluskey L, Elman L, Juhr D, Gruber PJ, Rüb U, Auburger G, Trojanowski JQ, Lee VM, Van Deerlin VM, Bonini NM, Gitler AD. Ataxin-2 intermediate-length polyglutamine expansions are associated with increased risk for ALS. Volume 466 of Issue 7310. 2010. PMID: 20740007


  40. Degenhardt K, Wright AC, Horng D, Padmanabhan A, Epstein JA. Rapid 3D phenotyping of cardiovascular development in mouse embryos by micro-CT with iodine staining. Volume 3 of Issue 3. 2010. PMID: 20190279


  41. Degenhardt KR, Milewski RC, Padmanabhan A, Miller M, Singh MK, Lang D, Engleka KA, Wu M, Li J, Zhou D, Antonucci N, Li L, Epstein JA. Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expressions. Volume 339 of Issue 2. 2010. PMID: 20045680


  42. Padmanabhan A, Lee JS, Ismat FA, Lu MM, Lawson ND, Kanki JP, Look AT, Epstein JA. Cardiac and vascular functions of the zebrafish orthologues of the type I neurofibromatosis gene NFI. Volume 106 of Issue 52. Proceedings of the National Academy of Sciences of the United States of America 2009. PMID: 19966217


  43. Caporini MA, Padmanabhan A, Cardon TB, Lorigan GA. Investigating magnetically aligned phospholipid bilayers with various lanthanide ions for X-band spin-label EPR studies. Volume 1612 of Issue 1. Biochimica et biophysica acta 2003. PMID: 12729929


  44. Cardon TB, Tiburu EK, Padmanabhan A, Howard KP, Lorigan GA. Magnetically aligned phospholipid bilayers at the parallel and perpendicular orientations for X-band spin-label EPR studies. Volume 123 of Issue 12. 2001. PMID: 11456991