Donald F. Hunt
- Email: dfh@virginia.edu
- Phone: 434-924-3610
Primary Appointment
Professor, Chemistry
Education
- BS, Chemistry, University of Massachusetts, Amherst, MA
- PhD, Organic Chemistry, University of Massachusetts, Amherst, MA
- Postdoc, Mass Spectrometry, MIT, Cambridge, MA (Klaus Biemann)
Research Disciplines
Biophysics, Biotechnology
Research Interests
Analytical Biochemistry
Research Description
(A) Mass spectrometry applied to immunology:
Cells in the human body communicate their health status to the immune system by degrading cellular proteins and presenting fragments of each on the cell surface in association class I MHC proteins. Appropriately educated, cytotoxic T-lymphocytes (CTL) (CD8+ T-cells) bind to the class I MHC molecules on the cell surface, sample the protein fragments (peptides) being presented and kill those cells that express new peptides as a result of viral, bacterial and parasitic infection, tissue transplantation and cellular transformation (cancer). Since dysregulation of cell signaling pathways is one of the hallmarks of cancer, we hypothesized that class I MHC phosphopeptides that result from these pathways should be excellent candidates for use in the immunotherapy of cancer. Class I MHC phosphopeptides identified in preliminary work on leukemia, melanoma, and colorectal cancers elicit pre-existing, central-memory, T-cell-recall responses in multiple, healthy blood donors. Central memory recall responses to phosphopeptide antigens is absent in some leukemia patients and correlates with clinical outcome. The response is restored following allogenic stem cell transplantation. These results suggest strongly that class I MHC phosphopeptides are tumor targets of immune surveillance in humans and, therefore, are likely candidates for immunotherapy of cancer. Three of the discovered phosphopeptides will be the subject of a phase I clinical trial on melanoma later this spring. Proposed here is additional research to complete our studies on melanoma, leukemia, and colorectal cancer and to begin an effort to characterize class I MHC phosphopetides presented on esophageal, liver and ovarian cancer. Additional research will be conducted to identify the repertoire of altered class I or class II self-peptides that are induced by prescription drugs or environmental agents and lead to life threatening autoimmune disease.
B) Mass spectrometry applied characterization of protein post-translational modifications and antibody sequences.
Proposed here is research to develop a combination of mass spectrometry instrumentation and techniques plus chemical and biochemical methods that will facilitate identification and near complete amino acid sequence analysis of intact proteins or large protein fragments on a chromatographic time scale. This research will make it possible to characterize multiple post-translational modifications, particularly those that exist on the same protein molecule and together regulate its biological activity. This research is driven by five major innovations in my lab: development of (a) electron transfer dissociation (ETD) for fragmentation of intact proteins, (b) ETD and IIPT (ion-ion proton transfer) chemistry to obtain n- and c-terminal sequence information from intact proteins, (c) front end ETD (FETD) that facilitates a 10-50 fold increase in sensitivity for intact proteins, (d) micro-column enzyme reactors that generate 3-10 KDa proteins fragments and provide 96% sequence coverage for monoclonal antibodies and (e) methodology for enrichment of O-GlcNAcylated peptides by boronic acid chemistry in non-aqueous solvents. Going forward, we will implement new IIPT reagents to extend the usable mass range to m/z 4,000, employ a combination of IIPT and parallel ion parking strategies to concentrate multiple charge states observed in protein ESI into a single lower charge state for protein identification by CAD, develop parallel ion parking strategies to minimize second generation ETD reactions and thus allow us to read complete protein sequences from both the n- and c- termini of intact proteins, build a longer linear ion trap to increase the number of protein ions that can be stored for analysis, extend the micro-column enzyme reactor concept to other proteases and solvents and then apply all of this development to the analysis of proteins in outer membrane vesicles secreted by the antibiotic resistant, gram negative bacteria, Neisseria gonorrhoeae. The ultimate goal is to be able to identify bacterial, virulence-factor proteins on a chromatographic time scale. The above technology will also be employed to characterize (a) proteolytic cleavage events on histones that alter the epigenetic code, (b) O-GlcNAc sites on ribosomal proteins, mitochondrial proteins in the heart, and all known human kinases, and (c) protein binding partners for RSK1 (ribosomal protein S6 Kinase) that plays a major role in breast cancer.
Personal Statement
Professor Hunt has also been a pioneer in characterizing protein post-translational modifications. In 1991, he identified the regulatory phosphorylation sites on MAP kinase. In 1988, he pioneered the use of immobilized metal affinity chromatography to enrich samples for phosphopeptides and reported methodology for the global characterization of phosphopeptides in a yeast cell lysate in 2002. This approach is now the basis for large scale efforts to monitor cell signaling pathways in a variety of biological systems. Professor Hunt also developed instrumentation and chemical derivatization methods that made it possible to elucidate the âhistone codeâ and to characterize the combinatorial nature of histone post-translational modifications on a genome wide scale. Since 2000, his group has published 46 papers on this topic.
Perhaps the most significant of Professor Huntâs recent achievements is the development of instrumentation that makes it possible to use ion-ion chemistry inside the mass spectrometer to determine the sequence of amino acids at both the n-terminus and c-terminus of intact proteins. This technique, electron transfer dissociation (ETD), facilitates identification of proteins in complex mixtures on a chromatographic time-scale (500 msec/protein), and allows one to detect the presence of both splice variants and post-translational modifications. This technology is likely to revolutionize the whole field of proteomics. ETD is also a breakthrough technology for the identification of O-GlcNAcylated peptides. This posttranslational modification on Ser and Thr residues rivals phosphorylation in abundance and constitutes a whole new field of signal transduction. Professor Hunt has now trained more than 120 graduate students and postdoctoral fellows. Many hold academic positions. The list includes: John Yates (Scripps), Andrea Cox (Johns Hopkins), Jarrod Marto (Harvard), Forest White (MIT), Murray Hackett (U. of Washington), Josh Coon (University of Wisconsin), Pat Griffin (Scripps), Nathan Yates, U of Pittsburgh, Beatrix Ueberheide NYU, and Ben Garcia (U. of Pennsylvania Medical School). Professor Hunt is an inventor on more than 30 patents and patent applications and has over 390 scholarly publications to his credit. His Goggle Scholar h-index of 100, (100 papers with 100 or more citations, total citations = 37,000, i10-index = 320) ranks him among the top 130 living chemists in the world. An RG score of 48.82 on ResearchGate places him in the top 97.5% of all members in this scientific community.
Training
- Training in Molecular Biophysics
Selected Publications
Papazyan R, Voronina E, Chapman JR, Luperchio TR, Gilbert TM, Meier E, Mackintosh SG, Shabanowitz J, Tackett AJ, Reddy KL, Coyne RS, Hunt DF, Liu Y, Taverna SD, Methylation of histone H3K23 blocks DNA damage in pericentric heterochromatin during meiosis., 2014; eLife. 3() e02996. PMID: 25161194 | PMCID: PMC4141274
Mothé BR, Southwood S, Sidney J, English AM, Wriston A, Hoof I, Shabanowitz J, Hunt DF, Sette A, Peptide-binding motifs associated with MHC molecules common in Chinese rhesus macaques are analogous to those of human HLA supertypes and include HLA-B27-like alleles., 2013; Immunogenetics. 65(5) 371-86. PMID: 23417323 | PMCID: PMC3633659
Abreu CM, Kumar R, Hamilton D, Dawdy AW, Creavin K, Eivers S, Finn K, Balsbaugh JL, O'Connor R, Kiely PA, Shabanowitz J, Hunt DF, Grenon M, Lowndes NF, Site-specific phosphorylation of the DNA damage response mediator rad9 by cyclin-dependent kinases regulates activation of checkpoint kinase 1., 2013; PLoS genetics. 9(4) e1003310. PMID: 23593009 | PMCID: PMC3616908
Pérez Jde, Udeshi ND, Shabanowitz J, Ciordia S, Juárez S, Scott CL, Olszewski NE, Hunt DF, GarcÃa JA, O-GlcNAc modification of the coat protein of the potyvirus Plum pox virus enhances viral infection., 2013; Virology. 442(2) 122-31. PMID: 23639873
Earley L, Anderson LC, Bai DL, Mullen C, Syka JE, English AM, Dunyach JJ, Stafford GC, Shabanowitz J, Hunt DF, Compton PD, Front-end electron transfer dissociation: a new ionization source., 2013; Analytical chemistry. 85(17) 8385-90. PMID: 23909443 | PMCID: PMC3822909
Bailey AO, Panchenko T, Sathyan KM, Petkowski JJ, Pai PJ, Bai DL, Russell DH, Macara IG, Shabanowitz J, Hunt DF, Black BE, Foltz DR, Posttranslational modification of CENP-A influences the conformation of centromeric chromatin., 2013; Proceedings of the National Academy of Sciences of the United States of America. 110(29) 11827-32. PMID: 23818633 | PMCID: PMC3718089
Wu D, Chapman JR, Wang L, Harris TE, Shabanowitz J, Hunt DF, Fu Z, Intestinal cell kinase (ICK) promotes activation of mTOR complex 1 (mTORC1) through phosphorylation of Raptor Thr-908., 2012; The Journal of biological chemistry. 287(15) 12510-9. PMID: 22356909 | PMCID: PMC3321000
Petkowski JJ, Schaner Tooley CE, Anderson LC, Shumilin IA, Balsbaugh JL, Shabanowitz J, Hunt DF, Minor W, Macara IG, Substrate Specificity of Mammalian N-Terminal α-Amino Methyltransferase NRMT., 2012; Biochemistry. 51(30) 5942-50. PMID: 22769851 | PMCID: PMC3447998
Compton PD, Strukl JV, Bai DL, Shabanowitz J, Hunt DF, Optimization of electron transfer dissociation via informed selection of reagents and operating parameters., 2011; Analytical chemistry. 84(3) 1781-5. PMID: 22182179 | PMCID: PMC3277643
Hao Y, Du Q, Chen X, Zheng Z, Balsbaugh JL, Maitra S, Shabanowitz J, Hunt DF, Macara IG, Par3 controls epithelial spindle orientation by aPKC-mediated phosphorylation of apical Pins., 2010; Current biology : CB. 20(20) 1809-18. PMID: 20933426 | PMCID: PMC2963683
Gordon V, Bhadel S, Wunderlich W, Zhang J, Ficarro SB, Mollah SA, Shabanowitz J, Hunt DF, Xenarios I, Hahn WC, Conaway M, Carey MF, Gioeli D, CDK9 regulates AR promoter selectivity and cell growth through serine 81 phosphorylation., 2010; Molecular endocrinology (Baltimore, Md.). 24(12) 2267-80. PMID: 20980437 | PMCID: PMC2999477
Tooley CE, Petkowski JJ, Muratore-Schroeder TL, Balsbaugh JL, Shabanowitz J, Sabat M, Minor W, Hunt DF, Macara IG, NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein., 2010; Nature. 466(7310) 1125-8. PMID: 20668449 | PMCID: PMC2939154
Baker SP, Phillips J, Anderson S, Qiu Q, Shabanowitz J, Smith MM, Yates JR, Hunt DF, Grant PA, Histone H3 Thr 45 phosphorylation is a replication-associated post-translational modification in S. cerevisiae., 2010; Nature cell biology. 12(3) 294-8. PMID: 20139971 | PMCID: PMC2856316
Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW, Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis., 2010; Science signaling. 3(104) ra2. PMID: 20068230 | PMCID: PMC2866299
Shechter D, Chitta RK, Xiao A, Shabanowitz J, Hunt DF, Allis CD, A distinct H2A.X isoform is enriched in Xenopus laevis eggs and early embryos and is phosphorylated in the absence of a checkpoint., 2009; Proceedings of the National Academy of Sciences of the United States of America. 106(3) 749-54. PMID: 19131518 | PMCID: PMC2630098
Ishibashi T, Dryhurst D, Rose KL, Shabanowitz J, Hunt DF, Ausió J, Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome., 2009; Biochemistry. 48(22) 5007-17. PMID: 19385636 | PMCID: PMC2850812
Depontieu FR, Qian J, Zarling AL, McMiller TL, Salay TM, Norris A, English AM, Shabanowitz J, Engelhard VH, Hunt DF, Topalian SL, Identification of tumor-associated, MHC class II-restricted phosphopeptides as targets for immunotherapy., 2009; Proceedings of the National Academy of Sciences of the United States of America. 106(29) 12073-8. PMID: 19581576 | PMCID: PMC2715484
Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB, Proteome-wide prediction of acetylation substrates., 2009; Proceedings of the National Academy of Sciences of the United States of America. 106(33) 13785-90. PMID: 19666589 | PMCID: PMC2728972
Wang Z, Udeshi ND, O'Malley M, Shabanowitz J, Hunt DF, Hart GW, Enrichment and site mapping of O-linked N-acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation mass spectrometry., 2009; Molecular & cellular proteomics : MCP. 9(1) 153-60. PMID: 19692427 | PMCID: PMC2808261
Eisinger-Mathason TS, Andrade J, Groehler AL, Clark DE, Muratore-Schroeder TL, Pasic L, Smith JA, Shabanowitz J, Hunt DF, Macara IG, Lannigan DA, Codependent functions of RSK2 and the apoptosis-promoting factor TIA-1 in stress granule assembly and cell survival., 2008; Molecular cell. 31(5) 722-36. PMID: 18775331 | PMCID: PMC2654589
Bernstein E, Muratore-Schroeder TL, Diaz RL, Chow JC, Changolkar LN, Shabanowitz J, Heard E, Pehrson JR, Hunt DF, Allis CD, A phosphorylated subpopulation of the histone variant macroH2A1 is excluded from the inactive X chromosome and enriched during mitosis., 2008; Proceedings of the National Academy of Sciences of the United States of America. 105(5) 1533-8. PMID: 18227505 | PMCID: PMC2234179
Housley MP, Rodgers JT, Udeshi ND, Kelly TJ, Shabanowitz J, Hunt DF, Puigserver P, Hart GW, O-GlcNAc regulates FoxO activation in response to glucose., 2008; The Journal of biological chemistry. 283(24) 16283-92. PMID: 18420577 | PMCID: PMC2423255
Prickett TD, Ninomiya-Tsuji J, Broglie P, Muratore-Schroeder TL, Shabanowitz J, Hunt DF, Brautigan DL, TAB4 stimulates TAK1-TAB1 phosphorylation and binds polyubiquitin to direct signaling to NF-kappaB., 2008; The Journal of biological chemistry. 283(28) 19245-54. PMID: 18456659 | PMCID: PMC2443674
Duncan EM, Muratore-Schroeder TL, Cook RG, Garcia BA, Shabanowitz J, Hunt DF, Allis CD, Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation., 2008; Cell. 135(2) 284-94. PMID: 18957203 | PMCID: PMC2579750
Mohammed F, Cobbold M, Zarling AL, Salim M, Barrett-Wilt GA, Shabanowitz J, Hunt DF, Engelhard VH, Willcox BE, Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self., 2008; Nature immunology. 9(11) 1236-43. PMID: 18836451 | PMCID: PMC2596764
Goldfinger LE, Ptak C, Jeffery ED, Shabanowitz J, Han J, Haling JR, Sherman NE, Fox JW, Hunt DF, Ginsberg MH, An experimentally derived database of candidate Ras-interacting proteins., 2007; Journal of proteome research. 6(5) 1806-11. PMID: 17439166
Chi A, Bai DL, Geer LY, Shabanowitz J, Hunt DF, Analysis of intact proteins on a chromatographic time scale by electron transfer dissociation tandem mass spectrometry., 2007; International journal of mass spectrometry. 259(1) 197-203. PMID: 17364019 | PMCID: PMC1826913
Taverna SD, Ueberheide BM, Liu Y, Tackett AJ, Diaz RL, Shabanowitz J, Chait BT, Hunt DF, Allis CD, Long-distance combinatorial linkage between methylation and acetylation on histone H3 N termini., 2007; Proceedings of the National Academy of Sciences of the United States of America. 104(7) 2086-91. PMID: 17284592 | PMCID: PMC1892956
Luo W, Peterson A, Garcia BA, Coombs G, Kofahl B, Heinrich R, Shabanowitz J, Hunt DF, Yost HJ, Virshup DM, Protein phosphatase 1 regulates assembly and function of the beta-catenin degradation complex., 2007; The EMBO journal. 26(6) 1511-21. PMID: 17318175 | PMCID: PMC1829374
Frum R, Busby SA, Ramamoorthy M, Deb S, Shabanowitz J, Hunt DF, Deb SP, HDM2-binding partners: interaction with translation elongation factor EF1alpha., 2007; Journal of proteome research. 6(4) 1410-7. PMID: 17373842
Chen T, Muratore TL, Schaner-Tooley CE, Shabanowitz J, Hunt DF, Macara IG, N-terminal alpha-methylation of RCC1 is necessary for stable chromatin association and normal mitosis., 2007; Nature cell biology. 9(5) 596-603. PMID: 17435751
Udeshi ND, Shabanowitz J, Hunt DF, Rose KL, Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS., 2007; The FEBS journal. 274(24) 6269-76. PMID: 18021239
Calvert ME, Keck KM, Ptak C, Shabanowitz J, Hunt DF, Pemberton LF, Phosphorylation by casein kinase 2 regulates Nap1 localization and function., 2007; Molecular and cellular biology. 28(4) 1313-25. PMID: 18086883 | PMCID: PMC2258750
Hunt DF, Henderson RA, Shabanowitz J, Sakaguchi K, Michel H, Sevilir N, Cox AL, Appella E, Engelhard VH, Pillars article: Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 1992. 255: 1261-1263., 2007; Journal of immunology (Baltimore, Md. : 1950). 179(5) 2669-71. PMID: 17709476
Mayhew MW, Jeffery ED, Sherman NE, Nelson K, Polefrone JM, Pratt SJ, Shabanowitz J, Parsons JT, Fox JW, Hunt DF, Horwitz AF, Identification of phosphorylation sites in betaPIX and PAK1., 2007; Journal of cell science. 120(0) 3911-8. PMID: 17989089
Harris TE, Huffman TA, Chi A, Shabanowitz J, Hunt DF, Kumar A, Lawrence JC, Insulin controls subcellular localization and multisite phosphorylation of the phosphatidic acid phosphatase, lipin 1., 2006; The Journal of biological chemistry. 282(1) 277-86. PMID: 17105729
Herlevsen M, Oxford G, Ptak C, Shabanowitz J, Hunt DF, Conaway M, Theodorescu D, A novel model to identify interaction partners of the PTEN tumor suppressor gene in human bladder cancer., 2006; Biochemical and biophysical research communications. 352(2) 549-55. PMID: 17126809 | PMCID: PMC1933505
Webb DJ, Mayhew MW, Kovalenko M, Schroeder MJ, Jeffery ED, Whitmore L, Shabanowitz J, Hunt DF, Horwitz AF, Identification of phosphorylation sites in GIT1., 2006; Journal of cell science. 119(0) 2847-50. PMID: 16825424
Garcia BA, Shabanowitz J, Hunt DF, Characterization of histones and their post-translational modifications by mass spectrometry., 2006; Current opinion in chemical biology. 11(1) 66-73. PMID: 17157550
Morris SA, Rao B, Garcia BA, Hake SB, Diaz RL, Shabanowitz J, Hunt DF, Allis CD, Lieb JD, Strahl BD, Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification., 2006; The Journal of biological chemistry. 282(10) 7632-40. PMID: 17189264 | PMCID: PMC2811852
Altrich-VanLith ML, Ostankovitch M, Polefrone JM, Mosse CA, Shabanowitz J, Hunt DF, Engelhard VH, Processing of a class I-restricted epitope from tyrosinase requires peptide N-glycanase and the cooperative action of endoplasmic reticulum aminopeptidase 1 and cytosolic proteases., 2006; Journal of immunology (Baltimore, Md. : 1950). 177(8) 5440-50. PMID: 17015730
Chi A, Valencia JC, Hu ZZ, Watabe H, Yamaguchi H, Mangini NJ, Huang H, Canfield VA, Cheng KC, Yang F, Abe R, Yamagishi S, Shabanowitz J, Hearing VJ, Wu C, Appella E, Hunt DF, Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes., 2006; Journal of proteome research. 5(11) 3135-44. PMID: 17081065
Harris TE, Chi A, Shabanowitz J, Hunt DF, Rhoads RE, Lawrence JC, mTOR-dependent stimulation of the association of eIF4G and eIF3 by insulin., 2006; The EMBO journal. 25(8) 1659-68. PMID: 16541103 | PMCID: PMC1440840
Zarling AL, Polefrone JM, Evans AM, Mikesh LM, Shabanowitz J, Lewis ST, Engelhard VH, Hunt DF, Identification of class I MHC-associated phosphopeptides as targets for cancer immunotherapy., 2006; Proceedings of the National Academy of Sciences of the United States of America. 103(40) 14889-94. PMID: 17001009 | PMCID: PMC1595446
Li Y, Kao GD, Garcia BA, Shabanowitz J, Hunt DF, Qin J, Phelan C, Lazar MA, A novel histone deacetylase pathway regulates mitosis by modulating Aurora B kinase activity., 2006; Genes & development. 20(18) 2566-79. PMID: 16980585 | PMCID: PMC1578679
Mosoian A, Teixeira A, High AA, Christian RE, Hunt DF, Shabanowitz J, Liu X, Klotman M, Novel function of prothymosin alpha as a potent inhibitor of human immunodeficiency virus type 1 gene expression in primary macrophages., 2006; Journal of virology. 80(18) 9200-6. PMID: 16940531 | PMCID: PMC1563913
Goldfinger LE, Ptak C, Jeffery ED, Shabanowitz J, Hunt DF, Ginsberg MH, RLIP76 (RalBP1) is an R-Ras effector that mediates adhesion-dependent Rac activation and cell migration., 2006; The Journal of cell biology. 174(6) 877-88. PMID: 16966426 | PMCID: PMC2064341
Auphan-Anezin N, Mazza C, Guimezanes A, Barrett-Wilt GA, Montero-Julian F, Roussel A, Hunt DF, Malissen B, Schmitt-Verhulst AM, Distinct orientation of the alloreactive monoclonal CD8 T cell activation program by three different peptide/MHC complexes., 2006; European journal of immunology. 36(7) 1856-66. PMID: 16761314
Brickner AG, Evans AM, Mito JK, Xuereb SM, Feng X, Nishida T, Fairfull L, Ferrell RE, Foon KA, Hunt DF, Shabanowitz J, Engelhard VH, Riddell SR, Warren EH, The PANE1 gene encodes a novel human minor histocompatibility antigen that is selectively expressed in B-lymphoid cells and B-CLL., 2006; Blood. 107(9) 3779-86. PMID: 16391015 | PMCID: PMC1895781
Martin KH, Jeffery ED, Grigera PR, Shabanowitz J, Hunt DF, Parsons JT, Cortactin phosphorylation sites mapped by mass spectrometry., 2006; Journal of cell science. 119(0) 2851-3. PMID: 16825425