Microchemistry & Proteomics: Publications

Ronald Hendrickson (Core Head)

Microchemistry & Proteomics: Publications

Ronald Hendrickson (Core Head)

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Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus. Kim SG, Becattini S, Moody TU, Shliaha PV, Littmann ER, Seok R, Gjonbalaj M, Eaton V, Fontana E, Amoretti L, Wright R, Caballero S, Wang ZX, Jung HJ, Morjaria SM, Leiner IM, Qin W, Ramos RJJF, Cross JR, Narushima S, Honda K, Peled JU, Hendrickson RC, Taur Y, van den Brink MRM, Pamer EG. Nature. 2019 Aug;572(7771):665-669. doi: 10.1038/s41586-019-1501-z. Epub 2019 Aug 21.

Sanghvi VR, Leibold J, Mina M, Mohan P, Berishaj M, Li Z, Miele MM, Lailler N, Zhao C, de Stanchina E, Viale A, Akkari L, Lowe SW, Ciriello G, Hendrickson RC, Wendel HG. The Oncogenic Action of NRF2 Depends on De-glycation by Fructosamine-3-Kinase. Cell. 2019 Aug 8;178(4):807-819.e21. doi: 10.1016/j.cell.2019.07.031.

Taylor J, Sendino M, Gorelick AN, Pastore A, Chang MT, Penson AV, Gavrila EI, Stewart C, Melnik EM, Herrejon Chavez F, Bitner L, Yoshimi A, Lee SC, Inoue D, Liu B, Zhang XJ, Mato AR, Dogan A, Kharas MG, Chen Y, Wang D, Soni RK, Hendrickson RC, Prieto G, Rodriguez JA, Taylor BS, Abdel-Wahab O. Altered nuclear export signal recognition as a driver of oncogenesis. Cancer Discov. 2019 Jul 8. pii: CD-19-0298. doi: 10.1158/2159-8290.CD-19-0298. [Epub ahead of print].

Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG. c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma. J Exp Med. 2019 Jul 1;216(7):1509-1524. doi: 10.1084/jem.20181726. Epub 2019 May 29.

Griswold AR, Cifani P, Rao SD, Axelrod AJ, Miele MM, Hendrickson RC, Kentsis A, Bachovchin DA. A Chemical Strategy for Protease Substrate Profiling. Cell Chem Biol. 2019 Jun 20;26(6):901-907.e6. doi: 10.1016/j.chembiol.2019.03.007. Epub 2019 Apr 18.

Hamieh M, Dobrin A, Cabriolu A, van der Stegen SJC, Giavridis T, Mansilla-Soto J, Eyquem J, Zhao Z, Whitlock BM, Miele MM, Li Z, Cunanan KM, Huse M, Hendrickson RC, Wang X, Rivière I, Sadelain M. CAR T cell trogocytosis and cooperative killing regulate tumour antigen escape. Nature. 2019 Apr;568(7750):112-116. doi: 10.1038/s41586-019-1054-1. Epub 2019 Mar 27.

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez, H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B . How many human proteoforms are there? . Nature Chemical Biology . 2018;14(3):206-214 . PMCID: PMC5837046.

Derenzini E, Mondello P, Erazo T, Portelinha A, Liu Y, Scallion M, Asgari Z, Philip J, Hilden P, Valli D, Rossi A, Djaballah H, Ouerfelli O, de Stanchina E, Seshan VE, Hendrickson RC, Younes A . BET inhibition- induced GSK3β feedback enhances lymphoma vulnerability to PI3K inhibitors . Cell Reports . 2018;24(8):2155-2166.

Gala K, Li Q, Sinha A, Razavi P, Dorso M, Sanchez- Vega F, Chung YR, Hendrickson R, Hsieh JJ,Berger M, Schultz N, Pastore A, Abdel-Wahab O, Chandarlapaty S . KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function . Oncogene . 2018;37(34):4692- 4710 . PMCID: PMC6107480.

Rafiq S, Yeku OO, Jackson HJ, Purdon TJ, van Leeuwen DG, Drakes DJ, Song M, Miele MM, Li Z, Wang P, Yan S, Xiang J, Ma X, Seshan VE, Hendrickson RC, Liu C, Brentjens RJ . Targeted delivery of a PD-1-blocking scFV by CAR-T cells enhances anti-tumor efficacy in vivo . Nature Biotechnology . 2018;36(9):847-856 . PMCID: PMC6126939.

Wipperman MF, Heaton BE, Nautiyal A, Adefisayo O, Evans H, Gupta R, van Ditmarsch D, Soni R, Hendrickson R, Johnson J, Krogan N, Glickman MS. Mycobacterial mutagenesis and drug resistance are controlled by phosphorylation- and cardiolipin- mediated inhibition of the RecA coprotease. Molecular Cell. 2018;72(1):152-161 .e7.

Kishinevsky S, Wang T, Rodina A, Chung SY, Xu C, Philip J, Taldone T, Joshi S, Alpaugh ML, Bolaender A, Gutbier S, Sandhu D, Fattahi F, Zimmer B, Shah SK, Chang E, Inda C, Koren J 3rd, Saurat NG, Leist M, Gross SS, Seshan VE, Klein C, Tomishima MJ, Erdjument-Bromage H, Neubert TA, Henrickson RC, Chiosis G, Studer L . HSP90-incorporating chaperome networks as biosensor for disease-related pathways in patient-specific midbrain dopamine neurons. Nature Communications. 2018;9:4345-. PMCID: PMC6195591.

Perna  F,  Berman  SH,  Soni RK,  Mansilla-Soto  J,  Eyquem  J, Hamieh M, Hendrickson RC, Brennan CW, Sadelain M. Integrating  Proteomics  and  Transcriptomics for Systematic Combinatorial Chimeric Antigen Receptor Therapy of AML. Cancer Cell. 2017 Oct 9;32(4):506-519.e5. doi: 10.1016/j.ccell.2017.09.004. PubMed.

Mazzu YZ, Hu Y, Soni RK, Mojica KM, Qin LX, Agius P, Waxman ZM, Mihailovic A, Socci ND, Hendrickson RC, Tuschl T, Singer S. miR-193b-Regulated Signaling Networks Serve as Tumor Suppressors in Liposarcoma and Promote Adipogenesis in Adipose-Derived Stem Cells. Cancer Res. 2017 Nov 1;77(21):5728-5740. doi: 10.1158/0008-5472.CAN-16-2253, Epub 2017 Sep 7. PubMed.

Chang AY, Dao T, Gejman RS, Jarvis CA, Scott  A,  Dubrovsky L, Mathias MO, Korontsvit T, Zakhaleva V, Curcio M, Hendrickson RC, Liu C, Scheinberg DA. A therapeutic T cell receptor mimic  antibody  targets  tumor-associated PRAME peptide/HLA-I antigens. J Clin Invest. 2017 Sep 1;127(9):3557. doi: 10.1172/JCI96860. Epub 2017 Sep 1. PubMed; PubMed Central PMCID: PMC5669580.

Asciolla JJ, Miele MM, Hendrickson RC, Resh MD, An in vitro fatty acylation assay reveals a mechanism for Wnt recognition by the acyltransferase Porcupine. J Biol Chem. 2017 Aug 18;292(33):13507-13513. doi: 10.1074/ jbc.C117.800136, Epub 2017 Jun 27. PubMed; PubMed Central PMCID: PMC5566510.

Total Chemical Synthesis and Folding of All-L and All-D Variants of Oncogenic KRas(G12V). Levinson AM, McGee JH, Roberts AG, Creech G, Wang T, Pete rson MT, Hendrickson RC, Verdine GL, Danishefsky SJ. J Am Chem Soc. 2017 Apr 27. doi: 10.1021/jacs.7b02988. [Epub ahead of print]

PI3K pathway regulates ER-dependent transcription in breast cancer through the epigenetic regulator KMT2D. Toska E, Osmanbeyoglu HU, Castel P, Chan C, Hendrickson RC, Elkabets M, Dickler MN, Scaltriti M, Leslie CS, Armstrong SA, Baselga J. Science. 2017 Mar 24;355(6331):1324-1330. doi: 10.1126/science.aah6893.

Identification, validation, and targeting of the mutant p53-PARP-MCM chromatin axis in triple negative breast cancer. Qiu WG, Polotskaia A, Xiao G, Di L, Zhao Y, Hu W, Philip J, Hendrickson RC, Bargonetti J. NPJ Breast Cancer. 2017;3. pii: 1. doi: 10.1038/s41523-016-0001-7. Epub 2017 Jan 19.

Dual inhibition of histone deacetylases and phosphoinositide 3-kinase enhances therapeutic activity against B cell lymphoma. Mondello P, Derenzini E, Asgari Z, Philip J, Brea EJ, Seshan V, Hendrickson RC, de Stanchina E, Scheinberg DA, Younes A. Oncotarget. 2017 Feb 21;8(8):14017-14028. doi: 10.18632/oncotarget.14876.

Chang, J., Schwer, B., Shuman, S. Structure-function analysis and genetic interactions of the yeast branchpoint binding protein Msl5. Nucleic Acids Res. 2012 Jan 28 [Epub ahead of print]

Beverly, L.J., Lockwood, W.W., Shah, P.P., Erdjument-Bromage, H., Varmus, H. Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1. Proc. Natl. Acad. Sci. U.S.A. 2012 doi:10.1073 EPub January 10, 2012.

Quann, E.J., Lu, X., Altan-Bonnet, G., Huse, M. A cascade of protein kinase C isozymes promotes cytoskeletal polarization in T cells. Nat. Immunol. 2011 12:647-654.

Moulick,K., Ahn, J.H., Zong, H., Rodina, A., Cerchietti, L, Erica M. Gomes DaGama, E.M.G., Caldas-Lopes, E., Beebe, K., Perna, F., Hatzi, K., Ly P. Vu, L.P, Zhao, X., Zatorska, D., Taldone, T., Smith-Jones, P., Alpaugh, M.,, Gross, S.S., Pillarsetty, N., Ku, T., Lewis, J.S., Larson, S.M., Levine, R., Erdjument- Bromage, H., Guzman, M.L., Nimer, S.D., Melnick, A., Neckers, L., Chiosis, G. Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90. Nat. Chem Biol 2011 doi:10.1038/nchembio.670 Epub 2011 September 25.

Somwar, R., Erdjument-Bromage, H., Larsson, E. , Shum, D., Lockwood, W., Yang, G., Sander, C., Ouerfelli, O., Djaballah, H., Tempst, P., Varmus, H. Superoxide dismutase 1 (SOD1) is a target for a small molecule identified in a screen for inhibitors of the growth of lung adenocarcinoma cell Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16375-80. Epub 2011 Sep 19.

Cooper J, Li W, You L, Schiavon G, Pepe-Caprio A, Zhou L, Ishii R, Giovannini M, Hanemann CO, Long SB, Erdjument-Bromage H, Zhou P, Tempst P, Giancotti FG. Merlin/NF2 functions upstream of the nuclear E3 ubiquitin ligase CRL4DCAF1 to suppress oncogenic gene expression. Sci. Signal. 2011 August 30;4 (188) pt6. Epub 2011 Aug 23.

Schvartzman, J.M., Duijf, P.H., Sotillo, R., Coker, C., Benezra, R. Mad2 is a critical mediator of the chromosome instability observed upon Rb and p53 pathway inhibition. Cancer Cell 2011 19:701-4.

Quann, E.J., Liu, X., Altan-Bonnet, G., Huse, M. A cascade of protein kinase C isoenzymes promotes cytoskeletal polarization in T cells. Nat Immunol. 2011 12:647-654.

Schwer, B. Erdjument-Bromage, H. Shuman, S. Composition of yeast snRNPs and snoRNPs in the absence of trimethylguanosine caps reveals nuclear cap binding protein as a gained U1 component implicated in the cold-sensitivity of tgs1{Delta} cells. Nucleic Acid Research, 2011 1-14 doi:10.1093/nar/gkr279.

Abeyweera, T.P., Merino, E., Huse, M. Inhibitory signaling blocks activating receptor clustering and induces cytoskeletal retraction in natural killer cells. J.Cell Biol. 2011, 192:675-90.

Singla, N, Erdjument-Bromage, H, Muir, TW, Nikolov, DB. A semisynthetic Eph receptor tyrosine kinase provides insight into ligand-induced kinase activation. Chem. Biol. 2011, 18:361-71.

Escobar-Alvarez, S. Gardner J, Sheth A, Manfredi G, Yang G, Ouerfelli O, Heaney ML, Scheinberg DA. Inhibition of Human Peptide Deformylase Disrupts Mitochondrial Function. Mol. Cell Biol. 2010, 30:5099-109.

Li W, You L, Cooper J, Schiavon G, Pepe-Caprio A, Zhou L, Ishii R, Giovannini M, Hanemann CO, Long SB, Erdjument-Bromage H, Zhou P, Tempst P, Giancotti FG. Merlin/NF2 suppresses tumorigenesis by inhibiting the E3 ubiquitin ligase CRL4(DCAF1) in the nucleus. Cell 2010, 140:477-90.

Gao Z, Gammoh N, Wong PM, Erdjument-Bromage H, Tempst P, Jiang X. Processing of autophagic protein LC3 by the 20S proteasome. Autophagy 2010, 6:126-37.

Lee, C., Goldberg, J. Structure of Coatomer Cage Proteins and the Relationship among COPI, COPII, and Clathrin Vesicle Coats. Cell 2010, 142:123-132.

O’Reilly RJ, Dao T, Koehne G, Scheinberg D, Doubrovina E. Adoptive transfer of unselected or leukemia-reactive T-cells in the treatment of relapse following allogeneic hematopoietic cell transplantation. Semin Immunol. 2010, 22:162-72.

Villanueva J, Nazarian A, Lawlor K, Tempst P. Monitoring peptidase activities in complex proteomes by MALDI-TOF mass spectrometry. Nat Protoc. 2009;4:1167-83.

Schwer B, Schneider S, Pei Y, Aronova A, Shuman S. Characterization of the Schizosaccharomyces pombe Spt5-Spt4 complex. RNA. 2009, 7:1241-50.

Gao S, Alarcón C, Sapkota G, Rahman S, Chen PY, Goerner N, Macias MJ, Erdjument-Bromage H, Tempst P, Massagué J. Ubiquitin ligase Nedd4L targets activated Smad2/3 to limit TGF-beta signaling. Mol. Cell 2009, 13:457-68.

Lin HK, Wang G, Chen Z, Teruya-Feldstein J, Liu Y, Chan CH, Yang WL, Erdjument-Bromage H, Nakayama KI, Nimer S, Tempst P, Pandolfi PP. Phosphorylation-dependent regulation of cytosolic localization and oncogenic function of Skp2 by Akt/PKB. Nature Cell Biol. 2009, 11:420-32.

Usui T, Foster SS, Petrini JH. Maintenance of the DNA-damage checkpoint requires DNA-damage-induced mediator protein oligomerization. Mol Cell. 2009, 33(2):147-59.

Xiao A, Li H, Shechter D, Ahn SH, Fabrizio LA, Erdjument-Bromage H, Ishibe-Murakami S, Wang B, Tempst P, Hofmann K, Patel DJ, Elledge SJ, Allis CD. WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity. Nature. 2009, 457:57-62.

Parmigiani RB, Xu WS, Venta-Perez G, Erdjument-Bromage H, Yaneva M, Tempst P, Marks PA. HDAC6 is a specific deacetylase of peroxiredoxins and is involved in redox regulation. Proc Natl Acad Sci U S A. 2008, 105:9633-8.

Zhao X, Jankovic V, Gural A, Huang G, Pardanani A, Menendez S, Zhang J, Dunne R, Xiao A, Erdjument-Bromage H, Allis CD, Tempst P, Nimer SD. Methylation of RUNX1 by PRMT1 abrogates SIN3A binding and potentiates its transcriptional activity. Genes Dev. 2008, 22:640-53.

Villanueva J, Nazarian A, Lawlor K, Yi SS, Robbins RJ, Tempst P. A sequence-specific exopeptidase activity test (SSEAT) for “functional” biomarker discovery. Mol Cell Proteomics. 2008, 7:509-18.

Trojer P, Li G, Sims RJ 3rd, Vaquero A, Kalakonda N, Boccuni P, Lee D, Erdjument-Bromage H, Tempst P, Nimer SD, Wang YH, Reinberg D. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell. 2007, 129:915-28.

Tanny JC, Erdjument-Bromage H, Tempst P, Allis CD. Ubiquitylation of histone H2B controls RNA polymerase II transcription elongation independently of histone H3 methylation. Genes Dev. 2007, 21:835-47.

Trotman LC, Wang X, Alimonti A, Chen Z, Teruya-Feldstein J, Yang H, Pavletich NP, Carver BS, Cordon-Cardo C, Erdjument-Bromage H, Tempst P, Chi SG, Kim HJ, Misteli T, Jiang X, Pandolfi PP. Ubiquitination regulates PTEN nuclear import and tumor suppression. Cell. 2007, 128:141-56.

Ooi SK, Qiu C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin SP, Allis CD, Cheng X, Bestor TH. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature. 2007, 448:714-7.

Wang X, Trotman LC, Koppie T, Alimonti A, Chen Z, Gao Z, Wang J, Erdjument-Bromage H, Tempst P, Cordon-Cardo C, Pandolfi PP, Jiang X. NEDD4-1 is a proto-oncogenic ubiquitin ligase for PTEN. Cell. 2007, 128:129-39.

Patke A, Mecklenbräuker I, Erdjument-Bromage H, Tempst P, Tarakhovsky A. BAFF controls B cell metabolic fitness through a PKC beta- and Akt-dependent mechanism. J Exp Med. 2006, 30;203:2551-62.

Scaglioni PP, Yung TM, Cai LF, Erdjument-Bromage H, Kaufman AJ, Singh B, Teruya-Feldstein J, Tempst P, Pandolfi PP. A CK2-dependent mechanism for degradation of the PML tumor suppressor. Cell. 2006, 126:269-83.

Barton WA, Tzvetkova-Robev D, Erdjument-Bromage H, Tempst P, Nikolov DB. Highly efficient selenomethionine labeling of recombinant proteins produced in mammalian cells. Protein Sci. 2006, 15:2008-13.

Yaneva M, Tempst P. Isolation and mass spectrometry of specific DNA binding proteins. Methods Mol Biol. 2006, 338:291-303.

He W, Dorn DC, Erdjument-Bromage H, Tempst P, Moore MA, Massagué J. Hematopoiesis controlled by distinct TIF1gamma and Smad4 branches of the TGFbeta pathway. Cell. 2006, 125:929-41.

Yaneva M, Kippenberger S, Wang N, Su Q, McGarvey M, Nazarian A, Lacomis L, Erdjument-Bromage H, Tempst P. PU.1 and a TTTAAA element in the myeloid defensin-1 promoter create an operational TATA box that can impose cell specificity onto TFIID function. J Immunol. 2006, 176:6906-17.

Villanueva J, Shaffer DR, Philip J, Chaparro CA, Erdjument-Bromage H, Olshen AB, Fleisher M, Lilja H, Brogi E, Boyd J, Sanchez-Carbayo M, Holland EC, Cordon-Cardo C, Scher HI, Tempst P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest. 2006, 116:271-84.

Seitan VC, Banks P, Laval S, Majid NA, Dorsett D, Rana A, Smith J, Bateman A, Krpic S, Hostert A, Rollins RA, Erdjument-Bromage H, Tempst P, Benard CY, Hekimi S, Newbury SF, Strachan T. Metazoan Scc4 homologs link sister chromatid cohesion to cell and axon migration guidance. PLoS Biol. 2006, 4:e242.