Arun Padmanabhan, MD, PhD
Sanchita and Dipten Deb Professor of Cardiovascular Genetics
Assistant Professor of Medicine, Division of Cardiology, UCSF
Research Summary
Dr. Padmanabhan is a cardiologist specializing in general cardiology. His interests include preventive cardiology, lamin A/C gene (LMNA) associated cardiomyopathies, and right heart disease in athletes. His 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
- 2003 - BA
Washington University in St. Louis, Biochemistry & Molecular Biology - 2012 - MD
University of Pennsylvania, Medicine - 2010 - PhD
University of Pennsylvania, ell & Developmental Biology - 2015 - Residency
Massachusetts General Hospital / Harvard Medical School, Internal Medicine - 2017 - Fellowship
UC San Francisco, Cardiovascular Disease - 2021 - Postdoctoral Fellowship
J. David Gladstone Institutes, Cardiovascular Epigenetics
Selected Publications
1. A Pilot Program to Engage, Retain, and Train Physicians as Scientists: Creating and Sustaining a Discovery-Driven Community. J Pediatr. 2026 Jan 19; 114995.Solvik TA, Schnoes AM, Nguyen TA, Behrman SL, Maksoud E, Goodwin SS, Weiss EJ, Padmanabhan A, Cornfield DN. PMID: 41565006.
2. Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest. Elife. 2025 Dec 02; 13.Casey-Clyde T, Liu SJ, Pelonero A, Serrano JAC, Teng C, Jang YG, Vasudevan HN, Padmanabhan A, Bush JO, Raleigh DR. PMID: 41329158; PMCID: PMC12671911.
3. Myocardial reprogramming by HMGN1 underlies heart defects in trisomy 21. Nature. 2025 11; 647(8091):979-987.Ranade SS, Li F, Whalen S, Pelonero A, Ye L, Huang Y, Brand A, Nishino T, Mital R, Boileau RM, Koback F, Padmanabhan A, Yu V, Cimarosti B, Presas-Ramos D, Merriman AF, Wallace LG, Nguyen A, Poulis N, Costa MW, Gifford CA, Pollard KS, Srivastava D. PMID: 41125893; PMCID: PMC12657217.
4. Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery. bioRxiv. 2025 Jul 26.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. PMID: 40777284; PMCID: PMC12330724.
5. Eed controls craniofacial osteoblast differentiation and mesenchymal proliferation from the neural crest. bioRxiv. 2025 Jul 21.Casey-Clyde T, Liu SJ, Pelonero A, Serrano JAC, Teng C, Jang YG, Vasudevan HN, Padmanabhan A, Bush JO, Raleigh DR. PMID: 38558995; PMCID: PMC10979956.
6. Insights Into Recovery From Acute Fulminant Myocarditis Following Successful Treatment With Ruxolitinib by Comprehensive Single-Cell Profiling. Circulation. 2025 Jun 24; 151(25):1814-1817.Qin J, Aras MA, Song EJ, Connolly AJ, Zhou L, O'Brien C, Salem JE, Padmanabhan A, Moslehi JJ. PMID: 40549846; PMCID: PMC12191800.
7. ALPK3 Heterozygous Truncating Variants Cause Late-Onset Hypertrophic Cardiomyopathy With Frequent Apical Involvement and Apical Aneurysm. Circ Genom Precis Med. 2025 Aug; 18(4):e005186.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. PMID: 40469041.
8. Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart. medRxiv. 2024 Nov 22.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. PMID: 39606363; PMCID: PMC11601760.
9. Transcriptomic Profiling of Human Myocardium at Sudden Death to Define Vulnerable Substrate for Lethal Arrhythmias. JACC Clin Electrophysiol. 2025 Jan; 11(1):143-155.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. PMID: 39545913; PMCID: PMC11809765.
10. Chromatin remodelling drives immune cell-fibroblast communication in heart failure. Nature. 2024 11; 635(8038):434-443.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. PMID: 39443808; PMCID: PMC11698514.
11. Automated Assessment of Right Atrial Pressure From Ultrasound Videos Using Machine Learning. JACC Adv. 2024 Sep; 3(9):101192.Yurk D, Barrios JP, Labrecque Langlais E, Avram R, Aras MA, Abu-Mostafa Y, Padmanabhan A, Tison GH. PMID: 39372459; PMCID: PMC11450965.
12. Single-nucleus RNA/ATAC-seq in early-stage HCM models predicts SWI/SNF-activation in mutant-myocytes, and allele-specific differences in fibroblasts. bioRxiv. 2024 Apr 24.Thottakara T, Padmanabhan A, Tanriverdi T, Thambidurai T, Diaz-Rg JA, Amonkar SR, Olgin JE, Long CS, Roselle Abraham M. PMID: 38903075; PMCID: PMC11188105.
13. A genome-wide CRISPR screen identifies BRD4 as a regulator of cardiomyocyte differentiation. Nat Cardiovasc Res. 2024 03; 3(3):317-331.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. PMID: 39196112; PMCID: PMC11361716.
14. Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes. Nat Cardiovasc Res. 2023 12; 2(12):1190-1203.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. PMID: 39183978; PMCID: PMC11343316.
15. Rapid Multiplexed Flow Cytometric Validation of CRISPRi sgRNAs in Tissue Culture. Bio Protoc. 2023 Jan 20; 13(2).Chorba JS, Xia VQ, Smith GA, Padmanabhan A. PMID: 36789164; PMCID: PMC9901452.
16. Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis. bioRxiv. 2023 Jan 07.Alexanian M, Padmanabhan A, Nishino T, Travers JG, Ye L, Lee CY, Sadagopan N, Huang Y, Pelonero A, Auclair K, Zhu A, Teran BG, 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. PMID: 36711864; PMCID: PMC9881961.
17. Cold shock domain-containing protein E1 is a posttranscriptional regulator of the LDL receptor. Sci Transl Med. 2022 09 14; 14(662):eabj8670.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. PMID: 36103516; PMCID: PMC10174261.
18. Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Circulation. 2022 09 06; 146(10):770-787.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. PMID: 35938400; PMCID: PMC9452483.
19. Targeting transcription in heart failure via CDK7/12/13 inhibition. Nat Commun. 2022 07 27; 13(1):4345.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. PMID: 35896549; PMCID: PMC9329381.
20. Prospective Comparison of Geriatric Assessment and Provider's Assessment of Older Adults With Metastatic Breast Cancer in the Community. Oncologist. 2022 03 04; 27(2):e133-e141.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. PMID: 35641214; PMCID: PMC8895742.