Justin J Brumbaugh
Title | Asst Professor |
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Institution | University of Colorado Boulder |
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Department | Biology-MCD Instruction |
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Biography Harvard Medical School/Massachusetts General Hospital, Boston, MA, USA | Postdoctoral | 12/2018 | Stem Cell Biology | University of Wisconsin, Madison, WI, USA | PhD | 12/2011 | Biochemistry | European Molecular Biology Laboratory (EMBL), Heidelberg, Germany | | 08/2006 | Biochemistry | Penn State University, State College, PA, USA | BS | 05/2004 | Biochemistry and Molecular Biology |
2020 | Boettcher Foundation Webb-Waring Biomedical Research Award, Boettcher Foundation | 2019 | Next Generation Leader, The International Society for Stem Cell Research | 2014 - 2017 | NRSA Kirchstein Postdoctoral Fellowship, NIH | 2014 | Tosteson & Fund for Medical Discovery Postdoctoral Fellowship, Massachusetts General Hospital Executive Committee on Research | 2006 - 2009 | NSF Graduate Research Fellowship, National Science Foundation | 2004 | Fulbright Scholar, Fulbright Program | 2000 - 2004 | Schreyer Honors Scholar, Penn State Honors College |
Overview Development is extraordinary feat in complex organisms. Numerous cell types with highly specific functions arise from a single cell, the zygote. During this process, the embryo must strike a fine balance between replenishing stem cell populations (i.e., self-renewal) and appropriate induction of specialized cells (differentiation). Remarkably, all of these decisions take place largely without changing the genomic content of the cells involved, which underscores the importance of intricate and dynamic regulatory mechanisms in development. Understanding these mechanisms is crucial for both basic science and medicine. Our lab seeks to develop and apply novel and innovative tools to study the molecular determinants of cell fate.
Bibliographic
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Brumbaugh J, Aguado BA, Lysaght T, Goldstein LSB. Human fetal tissue is critical for biomedical research. Stem Cell Reports. 2023 12 12; 18(12):2300-2312. PMID: 37977142.
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Serdyukova K, Swearingen AR, Coradin M, Nevo M, Tran H, Bajric E, Brumbaugh J. Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development. Development. 2023 11 01; 150(21). PMID: 37846748.
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Scott AK, Casas E, Schneider SE, Swearingen AR, Van Den Elzen CL, Seelbinder B, Barthold JE, Kugel JF, Stern JL, Foster KJ, Emery NC, Brumbaugh J, Neu CP. Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential. Biophys J. 2023 04 18; 122(8):1428-1444. PMID: 36871159.
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Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi KC, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng. 2021 12; 5(12):1500-1516. PMID: 34857921.
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Brumbaugh J, Di Stefano B, Sardina JL. Editorial: Chromatin Regulation in Cell Fate Decisions. Front Cell Dev Biol. 2021; 9:734020. PMID: 34540846.
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Brumbaugh J, Di Stefano B, Hochedlinger K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development. 2019 12 02; 146(23). PMID: 31792064.
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Brumbaugh J, Kim IS, Ji F, Huebner AJ, Di Stefano B, Schwarz BA, Charlton J, Coffey A, Choi J, Walsh RM, Schindler JW, Anselmo A, Meissner A, Sadreyev RI, Bernstein BE, Hock H, Hochedlinger K. Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nat Cell Biol. 2019 11; 21(11):1449-1461. PMID: 31659274.
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Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jim?nez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell. 2019 11 07; 25(5):622-638.e13. PMID: 31588046.
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Schiebinger G, Shu J, Tabaka M, Cleary B, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Cell. 2019 02 07; 176(4):928-943.e22. PMID: 30712874.
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Sardina JL, Collombet S, Tian TV, G?mez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T. Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate. Cell Stem Cell. 2018 11 01; 23(5):727-741.e9. PMID: 30220521.
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Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner AJ, Sahakyan A, Clement K, Clowers KJ, Erickson AR, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, Plath K, Hochedlinger K. Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nat Methods. 2018 09; 15(9):732-740. PMID: 30127506.
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Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell. 2018 01 11; 172(1-2):106-120.e21. PMID: 29249356.
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Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature. 2017 08 10; 548(7666):219-223. PMID: 28746311.
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Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K. DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell. 2017 05 04; 20(5):706-719.e7. PMID: 28366588.
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Liu LL, Brumbaugh J, Bar-Nur O, Smith Z, Stadtfeld M, Meissner A, Hochedlinger K, Michor F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep. 2016 12 20; 17(12):3395-3406. PMID: 28009305.
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Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K. A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2. Stem Cell Reports. 2016 05 10; 6(5):704-716. PMID: 26947976.
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Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10; 528(7581):218-24. PMID: 26659182.
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Bar-Nur O, Verheul C, Sommer AG, Brumbaugh J, Schwarz BA, Lipchina I, Huebner AJ, Mostoslavsky G, Hochedlinger K. Lineage conversion induced by pluripotency factors involves transient passage through an iPSC stage. Nat Biotechnol. 2015 Jul; 33(7):761-8. PMID: 26098450.
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Bar-Nur O, Brumbaugh J, Verheul C, Apostolou E, Pruteanu-Malinici I, Walsh RM, Ramaswamy S, Hochedlinger K. Small molecules facilitate rapid and synchronous iPSC generation. Nat Methods. 2014 Nov; 11(11):1170-6. PMID: 25262205.
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Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports. 2014 Jan 14; 2(1):18-25. PMID: 24678451.
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Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RL, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ. F-box protein FBXL16 binds PP2A-B55a and regulates differentiation of embryonic stem cells along the FLK1+ lineage. Mol Cell Proteomics. 2014 Mar; 13(3):780-91. PMID: 24390425.
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Brumbaugh J, Hochedlinger K. Removing reprogramming roadblocks: Mbd3 depletion allows deterministic iPSC generation. Cell Stem Cell. 2013 Oct 03; 13(4):379-81. PMID: 24094318.
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Van Etten J, Schagat TL, Hrit J, Weidmann CA, Brumbaugh J, Coon JJ, Goldstrohm AC. Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem. 2012 Oct 19; 287(43):36370-83. PMID: 22955276.
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Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Wenger CD, Westphall MS, Thomson JA, Coon JJ. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8411-6. PMID: 22586074.
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Brumbaugh J, Hou Z, Russell JD, Howden SE, Yu P, Ledvina AR, Coon JJ, Thomson JA. Phosphorylation regulates human OCT4. Proc Natl Acad Sci U S A. 2012 May 08; 109(19):7162-8. PMID: 22474382.
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Brumbaugh J, Rose CM, Phanstiel DH, Thomson JA, Coon JJ. Proteomics and pluripotency. Crit Rev Biochem Mol Biol. 2011 Dec; 46(6):493-506. PMID: 21999516.
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Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11; 8(10):821-7. PMID: 21983960.
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McAlister GC, Phanstiel DH, Brumbaugh J, Westphall MS, Coon JJ. Higher-energy collision-activated dissociation without a dedicated collision cell. Mol Cell Proteomics. 2011 May; 10(5):O111.009456. PMID: 21393638.
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Laketa V, Zarbakhsh S, Morbier E, Subramanian D, Dinkel C, Brumbaugh J, Zimmermann P, Pepperkok R, Schultz C. Membrane-permeant phosphoinositide derivatives as modulators of growth factor signaling and neurite outgrowth. Chem Biol. 2009 Nov 25; 16(11):1190-6. PMID: 19942142.
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Brumbaugh J, Phanstiel D, Coon JJ. Unraveling the histone's potential: a proteomics perspective. Epigenetics. 2008 Sep; 3(5):254-7. PMID: 18849650.
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Phanstiel D, Brumbaugh J, Berggren WT, Conard K, Feng X, Levenstein ME, McAlister GC, Thomson JA, Coon JJ. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4093-8. PMID: 18326628.
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Brumbaugh J, Schleifenbaum A, Gasch A, Sattler M, Schultz C. A dual parameter FRET probe for measuring PKC and PKA activity in living cells. J Am Chem Soc. 2006 Jan 11; 128(1):24-5. PMID: 16390103.
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Brumbaugh J, Schleifenbaum A, Stier G, Sattler M, Schultz C. Single- and dual-parameter FRET kinase probes based on pleckstrin. Nat Protoc. 2006; 1(2):1044-55. PMID: 17406341.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
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Year | Publications |
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2006 | 2 | 2008 | 2 | 2009 | 1 | 2011 | 3 | 2012 | 3 | 2013 | 1 | 2014 | 3 | 2015 | 2 | 2016 | 2 | 2017 | 3 | 2018 | 2 | 2019 | 4 | 2021 | 2 | 2023 | 3 |
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