Thomas Vallim*
Websites:
Research Interests:
gene regulation, cholesterol, MASLD, atherosclerosis, nuclear receptor, bile acids, lipids, metabolism, RNA Binding Proteins,Publications:
Panzitt K, Jungwirth E, Vosko LE, Madreiter-Sokolowski CT, Madl T, Tawfik I, Habisch H, Krstic J, Prokesch A, Karitnig R, Sucher R, Erdogan CY, Vallim TA, Trauner M, Fickert P, Al-Dury S, Molinaro A, Moore DD, Thallinger GG, Marschall HU, Wagner M. FXR adapts hepatic mitochondrial function to increased substrate oxidation in patients with obesity. Sci Transl Med. 2025 Aug 13; 17(811):eadn4558. view on PubMed
Bae H, Jung S, Le J, Tamburini I, Kim J, Wang E, Song WS, Choi W, Jang KH, Kang T, Lopez ML, Ramirez C, Mohanty I, Kelly ME, Kim J, Kim R, Park SH, Baek J, Mendez B, Petrus P, de Aguiar Vallim TQ, Nicholas DA, Smith Q, Lee G, Seldin M, Jang C. Cross-organ metabolite production and consumption in healthy and atherogenic conditions. Cell. 2025 Aug 07; 188(16):4441-4455.e16. view on PubMed
Zhou Z, Moore TM, Strumwasser AR, Ribas V, Iwasaki H, Morrow N, Ma A, Tran PH, Wanagat J, de Aguiar Vallim TQ, Clifford B, Zhang Z, Sallam T, Parks BW, Reue K, Shirihai O, Acin-Perez R, Morselli M, Pellegrini M, Mahata SK, Norheim F, Zhou M, Seldin MM, Lusis AJ, Lee CC, Goodarzi MO, Rotter JI, Hansen JR, Drucker B, Sagendorf TJ, Adkins JN, Sanford JA, DeMayo FJ, Hewitt SC, Korach KS, Hevener AL. Muscle metabolic resilience and enhanced exercise adaptation by Esr1-induced remodeling of mitochondrial cristae-nucleoid architecture in males. Cell Rep Med. 2025 May 20; 6(5):102116. view on PubMed
Schmidt HM, Jarrett KE, de Aguiar Vallim TQ, Tarling EJ. Pathways and Molecular Mechanisms Governing LDL Receptor Regulation. Circ Res. 2025 Apr 11; 136(8):902-919. view on PubMed
Ayala I, Hebbale SK, Mononen J, Brearley-Sholto MC, Shannon CE, Valdez I, Fourcaudot M, Bakewell TM, Zagorska A, Romero G, Asmis M, Musa FA, Sily JT, Smelter AA, Hinostroza EA, Freitas Lima LC, de Aguiar Vallim TQ, Heikkinen S, Norton L. The Spatial Transcriptional Activity of Hepatic TCF7L2 Regulates Zonated Metabolic Pathways that Contribute to Liver Fibrosis. Nat Commun. 2025 Apr 10; 16(1):3408. view on PubMed
Rauckhorst AJ, Sheldon RD, Pape DJ, Ahmed A, Falls-Hubert KC, Merrill RA, Brown RF, Deshmukh K, Vallim TA, Deja S, Burgess SC, Taylor EB. A hierarchical hepatic de novo lipogenesis substrate supply network utilizing pyruvate, acetate, and ketones. Cell Metab. 2025 Jan 07; 37(1):255-273.e6. view on PubMed
Lee E, Williams KJ, McCarthy C, Bridges JP, Redente EF, de Aguiar Vallim TQ, Barrington RA, Wang T, Tarling EJ. Alveolar macrophage lipid burden correlates with clinical improvement in patients with pulmonary alveolar proteinosis. J Lipid Res. 2024 02; 65(2):100496. view on PubMed
Sunshine HL, Cicchetto AC, Kaczor-Urbanowicz KE, Ma F, Pi D, Symons C, Turner M, Shukla V, Christofk HR, Vallim TA, Iruela-Arispe ML. Endothelial Jagged1 levels and distribution are post-transcriptionally controlled by ZFP36 decay proteins. Cell Rep. 2024 01 23; 43(1):113627. view on PubMed
Bendixen SM, Jakobsgaard PR, Hansen D, Hejn KH, Terkelsen MK, Bjerre FA, Thulesen AP, Eriksen NG, Hallenborg P, Geng Y, Dam TV, Larsen FT, Wernberg CW, Vijayathurai J, Scott EAH, Marcher AB, Detlefsen S, Grøntved L, Dimke H, Berdeaux R, de Aguiar Vallim TQ, Olinga P, Lauridsen MM, Krag A, Blagoev B, Ravnskjaer K. Single cell-resolved study of advanced murine MASH reveals a homeostatic pericyte signaling module. J Hepatol. 2024 03; 80(3):467-481. view on PubMed
Zhang S, Williams KJ, Verlande-Ferrero A, Chan AP, Su GB, Kershaw EE, Cox JE, Maschek JA, Shapira SN, Christofk HR, de Aguiar Vallim TQ, Masri S, Villanueva CJ. Acute activation of adipocyte lipolysis reveals dynamic lipid remodeling of the hepatic lipidome. J Lipid Res. 2024 02; 65(2):100434. view on PubMed
Cicchetto AC, Jacobson EC, Sunshine H, Wilde BR, Krall AS, Jarrett KE, Sedgeman L, Turner M, Plath K, Iruela-Arispe ML, de Aguiar Vallim TQ, Christofk HR. ZFP36-mediated mRNA decay regulates metabolism. Cell Rep. 2023 05 30; 42(5):112411. view on PubMed
Clifford BL, Jarrett KE, Cheng J, Cheng A, Seldin M, Morand P, Lee R, Chen M, Baldan A, de Aguiar Vallim TQ, Tarling EJ. RNF130 Regulates LDLR Availability and Plasma LDL Cholesterol Levels. Circ Res. 2023 03 31; 132(7):849-863. view on PubMed
Xiao X, Kennelly JP, Ferrari A, Clifford BL, Whang E, Gao Y, Qian K, Sandhu J, Jarrett KE, Brearley-Sholto MC, Nguyen A, Nagari RT, Lee MS, Zhang S, Weston TA, Young SG, Bensinger SJ, Villanueva CJ, de Aguiar Vallim TQ, Tontonoz P. Hepatic nonvesicular cholesterol transport is critical for systemic lipid homeostasis. Nat Metab. 2023 01; 5(1):165-181. view on PubMed
Ilacqua N, Anastasia I, Aloshyn D, Ghandehari-Alavijeh R, Peluso EA, Brearley-Sholto MC, Pellegrini LV, Raimondi A, de Aguiar Vallim TQ, Pellegrini L. Expression of Synj2bp in mouse liver regulates the extent of wrappER-mitochondria contact to maintain hepatic lipid homeostasis. Biol Direct. 2022 12 01; 17(1):37. view on PubMed
Doerfler AM, Han J, Jarrett KE, Tang L, Jain A, Saltzman A, De Giorgi M, Chuecos M, Hurley AE, Li A, Morand P, Ayala C, Goodlett DR, Malovannaya A, Martin JF, de Aguiar Vallim TQ, Shroyer N, Lagor WR. Intestinal Deletion of 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase Promotes Expansion of the Resident Stem Cell Compartment. Arterioscler Thromb Vasc Biol. 2022 04; 42(4):381-394. view on PubMed
De Giorgi M, Jarrett KE, de Aguiar Vallim TQ, Lagor WR. In Vivo Gene Editing in Lipid and Atherosclerosis Research. Methods Mol Biol. 2022; 2419:673-713. view on PubMed
Mukherjee P, Chattopadhyay A, Grijalva V, Dorreh N, Lagishetty V, Jacobs JP, Clifford BL, Vallim T, Mack JJ, Navab M, Reddy ST, Fogelman AM. Oxidized phospholipids cause changes in jejunum mucus that induce dysbiosis and systemic inflammation. J Lipid Res. 2022 Jan; 63(1):100153. view on PubMed
Ilacqua N, Anastasia I, Raimondi A, Lemieux P, de Aguiar Vallim TQ, Toth K, Koonin EV, Pellegrini L. A three-organelle complex made by wrappER contacts with peroxisomes and mitochondria responds to liver lipid flux changes. J Cell Sci. 2022 03 01; 135(5). view on PubMed
Clifford BL, Sedgeman LR, Williams KJ, Morand P, Cheng A, Jarrett KE, Chan AP, Brearley-Sholto MC, Wahlström A, Ashby JW, Barshop W, Wohlschlegel J, Calkin AC, Liu Y, Thorell A, Meikle PJ, Drew BG, Mack JJ, Marschall HU, Tarling EJ, Edwards PA, de Aguiar Vallim TQ. FXR activation protects against NAFLD via bile-acid-dependent reductions in lipid absorption. Cell Metab. 2021 08 03; 33(8):1671-1684.e4. view on PubMed
de Aguiar Vallim TQ, Tarling EJ. mInd the gAP: Intestinal Alkaline Phosphatase Puts the Breaks on Atherosclerosis. Circ Res. 2021 05 28; 128(11):1660-1662. view on PubMed
Zhuang A, Calkin AC, Lau S, Kiriazis H, Donner DG, Liu Y, Bond ST, Moody SC, Gould EAM, Colgan TD, Carmona SR, Inouye M, de Aguiar Vallim TQ, Tarling EJ, Quaife-Ryan GA, Hudson JE, Porrello ER, Gregorevic P, Gao XM, Du XJ, McMullen JR, Drew BG. Loss of the long non-coding RNA OIP5-AS1 exacerbates heart failure in a sex-specific manner. iScience. 2021 Jun 25; 24(6):102537. view on PubMed
Anastasia I, Ilacqua N, Raimondi A, Lemieux P, Ghandehari-Alavijeh R, Faure G, Mekhedov SL, Williams KJ, Caicci F, Valle G, Giacomello M, Quiroga AD, Lehner R, Miksis MJ, Toth K, de Aguiar Vallim TQ, Koonin EV, Scorrano L, Pellegrini L. Mitochondria-rough-ER contacts in the liver regulate systemic lipid homeostasis. Cell Rep. 2021 03 16; 34(11):108873. view on PubMed
von Scheidt M, Zhao Y, de Aguiar Vallim TQ, Che N, Wierer M, Seldin MM, Franzén O, Kurt Z, Pang S, Bongiovanni D, Yamamoto M, Edwards PA, Ruusalepp A, Kovacic JC, Mann M, Björkegren JLM, Lusis AJ, Yang X, Schunkert H. Transcription Factor MAFF (MAF Basic Leucine Zipper Transcription Factor F) Regulates an Atherosclerosis Relevant Network Connecting Inflammation and Cholesterol Metabolism. Circulation. 2021 05 04; 143(18):1809-1823. view on PubMed
Bond ST, King EJ, Henstridge DC, Tran A, Moody SC, Yang C, Liu Y, Mellett NA, Nath AP, Inouye M, Tarling EJ, de Aguiar Vallim TQ, Meikle PJ, Calkin AC, Drew BG. Deletion of Trim28 in committed adipocytes promotes obesity but preserves glucose tolerance. Nat Commun. 2021 01 04; 12(1):74. view on PubMed
Pradas-Juni M, Hansmeier NR, Link JC, Schmidt E, Larsen BD, Klemm P, Meola N, Topel H, Loureiro R, Dhaouadi I, Kiefer CA, Schwarzer R, Khani S, Oliverio M, Awazawa M, Frommolt P, Heeren J, Scheja L, Heine M, Dieterich C, Büning H, Yang L, Cao H, Jesus DF, Kulkarni RN, Zevnik B, Tröder SE, Knippschild U, Edwards PA, Lee RG, Yamamoto M, Ulitsky I, Fernandez-Rebollo E, Vallim TQA, Kornfeld JW. A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism. Nat Commun. 2020 01 31; 11(1):644. view on PubMed
Cheng J, Cheng A, Clifford BL, Wu X, Hedin U, Maegdefessel L, Pamir N, Sallam T, Tarling EJ, de Aguiar Vallim TQ. MicroRNA-144 Silencing Protects Against Atherosclerosis in Male, but Not Female Mice. Arterioscler Thromb Vasc Biol. 2020 02; 40(2):412-425. view on PubMed
Parker BL, Calkin AC, Seldin MM, Keating MF, Tarling EJ, Yang P, Moody SC, Liu Y, Zerenturk EJ, Needham EJ, Miller ML, Clifford BL, Morand P, Watt MJ, Meex RCR, Peng KY, Lee R, Jayawardana K, Pan C, Mellett NA, Weir JM, Lazarus R, Lusis AJ, Meikle PJ, James DE, de Aguiar Vallim TQ, Drew BG. An integrative systems genetic analysis of mammalian lipid metabolism. Nature. 2019 03; 567(7747):187-193. view on PubMed
Sullivan WJ, Mullen PJ, Schmid EW, Flores A, Momcilovic M, Sharpley MS, Jelinek D, Whiteley AE, Maxwell MB, Wilde BR, Banerjee U, Coller HA, Shackelford DB, Braas D, Ayer DE, de Aguiar Vallim TQ, Lowry WE, Christofk HR. Extracellular Matrix Remodeling Regulates Glucose Metabolism through TXNIP Destabilization. Cell. 2018 09 20; 175(1):117-132.e21. view on PubMed
Lee JM, Ong JR, Vergnes L, de Aguiar Vallim TQ, Nolan J, Cantor RM, Walters JRF, Reue K. Diet1, bile acid diarrhea, and FGF15/19: mouse model and human genetic variants. J Lipid Res. 2018 03; 59(3):429-438. view on PubMed
Mack JJ, Mosqueiro TS, Archer BJ, Jones WM, Sunshine H, Faas GC, Briot A, Aragón RL, Su T, Romay MC, McDonald AI, Kuo CH, Lizama CO, Lane TF, Zovein AC, Fang Y, Tarling EJ, de Aguiar Vallim TQ, Navab M, Fogelman AM, Bouchard LS, Iruela-Arispe ML. NOTCH1 is a mechanosensor in adult arteries. Nat Commun. 2017 11 20; 8(1):1620. view on PubMed
Zhang L, Rajbhandari P, Priest C, Sandhu J, Wu X, Temel R, Castrillo A, de Aguiar Vallim TQ, Sallam T, Tontonoz P. Inhibition of cholesterol biosynthesis through RNF145-dependent ubiquitination of SCAP. Elife. 2017 10 25; 6. view on PubMed
Tarling EJ, Clifford BL, Cheng J, Morand P, Cheng A, Lester E, Sallam T, Turner M, de Aguiar Vallim TQ. RNA-binding protein ZFP36L1 maintains posttranscriptional regulation of bile acid metabolism. J Clin Invest. 2017 Oct 02; 127(10):3741-3754. view on PubMed
Rong X, Wang B, Palladino EN, de Aguiar Vallim TQ, Ford DA, Tontonoz P. ER phospholipid composition modulates lipogenesis during feeding and in obesity. J Clin Invest. 2017 Oct 02; 127(10):3640-3651. view on PubMed
de Aguiar Vallim TQ, Lee E, Merriott DJ, Goulbourne CN, Cheng J, Cheng A, Gonen A, Allen RM, Palladino END, Ford DA, Wang T, Baldán Á, Tarling EJ. ABCG1 regulates pulmonary surfactant metabolism in mice and men. J Lipid Res. 2017 05; 58(5):941-954. view on PubMed
Zhang H, de Aguiar Vallim TQ, Martel C, Early Career Committee. Translational and Therapeutic Approaches to the Understanding and Treatment of Dyslipidemia. Arterioscler Thromb Vasc Biol. 2016 07; 36(7):e56-61. view on PubMed
Lusis AJ, Seldin MM, Allayee H, Bennett BJ, Civelek M, Davis RC, Eskin E, Farber CR, Hui S, Mehrabian M, Norheim F, Pan C, Parks B, Rau CD, Smith DJ, Vallim T, Wang Y, Wang J. The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits. J Lipid Res. 2016 06; 57(6):925-42. view on PubMed
Ribas V, Drew BG, Zhou Z, Phun J, Kalajian NY, Soleymani T, Daraei P, Widjaja K, Wanagat J, de Aguiar Vallim TQ, Fluitt AH, Bensinger S, Le T, Radu C, Whitelegge JP, Beaven SW, Tontonoz P, Lusis AJ, Parks BW, Vergnes L, Reue K, Singh H, Bopassa JC, Toro L, Stefani E, Watt MJ, Schenk S, Akerstrom T, Kelly M, Pedersen BK, Hewitt SC, Korach KS, Hevener AL. Skeletal muscle action of estrogen receptor α is critical for the maintenance of mitochondrial function and metabolic homeostasis in females. Sci Transl Med. 2016 Apr 13; 8(334):334ra54. view on PubMed
Baldán Á, de Aguiar Vallim TQ. miRNAs and High-Density Lipoprotein metabolism. Biochim Biophys Acta. 2016 12; 1861(12 Pt B):2053-2061. view on PubMed
Vergnes L, Chin RG, de Aguiar Vallim T, Fong LG, Osborne TF, Young SG, Reue K. SREBP-2-deficient and hypomorphic mice reveal roles for SREBP-2 in embryonic development and SREBP-1c expression. J Lipid Res. 2016 Mar; 57(3):410-21. view on PubMed
de Aguiar Vallim TQ, Tarling EJ, Ahn H, Hagey LR, Romanoski CE, Lee RG, Graham MJ, Motohashi H, Yamamoto M, Edwards PA. MAFG is a transcriptional repressor of bile acid synthesis and metabolism. Cell Metab. 2015 Feb 03; 21(2):298-311. view on PubMed
Tarling EJ, Ahn H, de Aguiar Vallim TQ. The nuclear receptor FXR uncouples the actions of miR-33 from SREBP-2. Arterioscler Thromb Vasc Biol. 2015 Apr; 35(4):787-95. view on PubMed
Shih DM, Wang Z, Lee R, Meng Y, Che N, Charugundla S, Qi H, Wu J, Pan C, Brown JM, Vallim T, Bennett BJ, Graham M, Hazen SL, Lusis AJ. Flavin containing monooxygenase 3 exerts broad effects on glucose and lipid metabolism and atherosclerosis. J Lipid Res. 2015 Jan; 56(1):22-37. view on PubMed
de Aguiar Vallim TQ, Tarling EJ, Edwards PA. Pleiotropic roles of bile acids in metabolism. Cell Metab. 2013 May 07; 17(5):657-69. view on PubMed
de Aguiar Vallim TQ, Tarling EJ, Kim T, Civelek M, Baldán Á, Esau C, Edwards PA. MicroRNA-144 regulates hepatic ATP binding cassette transporter A1 and plasma high-density lipoprotein after activation of the nuclear receptor farnesoid X receptor. Circ Res. 2013 Jun 07; 112(12):1602-12. view on PubMed
Tarling EJ, de Aguiar Vallim TQ, Edwards PA. Role of ABC transporters in lipid transport and human disease. Trends Endocrinol Metab. 2013 Jul; 24(7):342-50. view on PubMed
Bennett BJ, de Aguiar Vallim TQ, Wang Z, Shih DM, Meng Y, Gregory J, Allayee H, Lee R, Graham M, Crooke R, Edwards PA, Hazen SL, Lusis AJ. Trimethylamine-N-oxide, a metabolite associated with atherosclerosis, exhibits complex genetic and dietary regulation. Cell Metab. 2013 Jan 08; 17(1):49-60. view on PubMed
Lee FY, de Aguiar Vallim TQ, Chong HK, Zhang Y, Liu Y, Jones SA, Osborne TF, Edwards PA. Activation of the farnesoid X receptor provides protection against acetaminophen-induced hepatic toxicity. Mol Endocrinol. 2010 Aug; 24(8):1626-36. view on PubMed
