PDXNet Portal: Patient-Derived Xenograft Model, Data, Workflow and Tool Discovery
Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H, Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal-Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH PDXNet Consortium (Contributors include: Held J)
NAR Cancer 2022 Apr 22;4(2):zcac014
Malic Enzyme 1 Absence in Synovial Sarcoma Shifts Antioxidant System Dependence and Increases Sensitivity to Ferroptosis Induction With ACXT3102
Brashears CB, Prudner BC, Rathore R, Caldwell KE, Dehner CA, Buchanan JL, Lange SES, Poulin N, Sehn JK, Roszik J, Spitzer D, Jones KB, O'Keefe RJ, Nielsen TO, Taylor EB, Held JM, Hawkins W, Van Tine BA
Clin Cancer Res 2022 Apr 14:clincanres04702022; [ahead of print]
Comprehensive Characterization of 536 Patient-Derived Xenograft Models Prioritizes Candidates For Targeted Treatment
Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, DiPersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L NCI PDXNet Consortium (Contributors include: Held J)
Nat Commun 2021 Aug 24;12(1):5086
ProteoSushi: A Software Tool to Biologically Annotate and Quantify Modification-Specific, Peptide-Centric Proteomics Data Sets
Seymour RW, van der Post S, Mooradian AD, Held JM
J Proteome Res 2021 Jul 2;20(7):3621-3628
NOX1-Dependent Redox Signaling Potentiates Colonic Stem Cell Proliferation to Adapt to the Intestinal Microbiota by Linking EGFR and TLR Activation
van der Post S, Birchenough GMH, Held JM
Cell Rep 2021 Apr 6;35(1):108949
Cancer-Associated Exportin-6 Upregulation Inhibits the Transcriptionally Repressive and Anticancer Effects of Nuclear Profilin-1
Zhu C, Kim SJ, Mooradian A, Wang F, Li Z, Holohan S, Collins PL, Wang K, Guo Z, Hoog J, Ma CX, Oltz EM, Held JM, Shao J
Cell Rep 2021 Feb 16;34(7):108749
A Clickable Probe for Versatile Characterization of S-Nitrosothiols
Clements JL, Pohl F, Muthupandi P, Rogers SC, Mao J, Doctor A, Birman VB, Held JM
Redox Biol 2020 Oct;37:101707
Systems Level Profiling of Arginine Starvation Reveals MYC and ERK Adaptive Metabolic Reprogramming
Brashears CB, Barlin M, Ehrhardt WR, Rathore R, Schultze M, Tzeng SC, Van Tine BA, Held JM
Cell Death Dis 2020 Aug 20;11(8):662
Phospho-Ser(784)-VCP Is Required for DNA Damage Response and Is Associated With Poor Prognosis of Chemotherapy-Treated Breast Cancer
Zhu C, Rogers A, Asleh K, Won J, Gao D, Leung S, Li S, Vij KR, Zhu J, Held JM, You Z, Nielsen TO, Shao J
Cell Rep 2020 Jun 9;31(10):107745
Spatial and Temporal Alterations in Protein Structure by EGF Regulate Cryptic Cysteine Oxidation
Behring JB, van der Post S, Mooradian AD, Egan MJ, Zimmerman MI, Clements JL, Bowman GR, Held JM
Sci Signal 2020 Jan 21;13(615)
Regulated Phosphosignaling Associated With Breast Cancer Subtypes and Druggability
Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held JM, Payne SH, Davies S, Dar A, Kinsinger CR, Mesri M, Rodriguez H, Ellis MJ, Townsend RR, Chen F, Fenyo D, Li S, Liu T, Carr SA, Ding L
Mol Cell Proteomics 2019 Aug;18(8):1630-1650
Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers
Mundt F, Rajput S, Li S, Ruggles KV, Mooradian AD, Mertins P, Gillette MA, Krug K, Guo Z, Hoog J, Erdmann-Gilmore P, Primeau T, Huang S, Edwards DP, Wang X, Wang X, Kawaler E, Mani DR, Clauser KR, Gao F, Luo J, Davies SR, Johnson GL, Huang KL, Yoon CJ, Ding L, Fenyo D, Ellis MJ, Townsend RR, Held JM, Carr SA, Ma CX
Cancer Res 2018 May 15;78(10):2732-2746
Multi-Laboratory Assessment of Reproducibility, Qualitative and Quantitative Performance of SWATH-Mass Spectrometry
Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R
Nat Commun 2017 Aug 21;8(1):291
Breast Tumors Educate the Proteome of Stromal Tissue in an Individualized but Coordinated Manner
Wang X, Mooradian AD, Erdmann-Gilmore P, Zhang Q, Viner R, Davies SR, Huang KL, Bomgarden R, Van Tine BA, Shao J, Ding L, Li S, Ellis MJ, Rogers JC, Townsend RR, Fenyo D, Held JM* (*corresponding author)
Sci Signal 2017 Aug 8;10(491)
Proteogenomic Integration Reveals Therapeutic Targets in Breast Cancer Xenografts
Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, Wyczalkowski MA, Erdmann-Gilmore P, Snider JE, Hoog J, Singh P, Niu B, Guo Z, Sun SQ, Sanati S, Kawaler E, Wang X, Scott A, Ye K, McLellan MD, Wendl MC, Malovannaya A, Held JM, Gillette MA, Fenyo D, Kinsinger CR, Mesri M, Rodriguez H, Davies SR, Perou CM, Ma C, Reid Townsend R, Chen X, Carr SA, Ellis MJ, Ding L
Nat Commun 2017 Mar 28;8:14864
Arginine Deprivation Inhibits the Warburg Effect and Upregulates Glutamine Anaplerosis and Serine Biosynthesis in ASS1-Deficient Cancers
Kremer JC, Prudner BC, Lange SE, Bean GR, Schultze MB, Brashears CB, Radyk MD, Redlich N, Tzeng SC, Kami K, Shelton L, Li A, Morgan Z, Bomalaski JS, Tsukamoto T, McConathy J, Michel LS, Held JM, Van Tine BA
Cell Rep 2017 Jan 24;18(4):991-1004
Synthetic Ligands of Cannabinoid Receptors Affect Dauer Formation in the Nematode Caenorhabditis Elegans
Reis Rodrigues P, Kaul TK, Ho JH, Lucanic M, Burkewitz K, Mair WB, Held JM, Bohn LM, Gill MS
G3 (Bethesda) 2016 Jun 1;6(6):1695-705
Multiplexed, Scheduled, High-Resolution Parallel Reaction Monitoring on a Full Scan QqTOF Instrument With Integrated Data-Dependent and Targeted Mass Spectrometric Workflows
Schilling B, MacLean B, Held JM, Sahu AK, Rardin MJ, Sorensen DJ, Peters T, Wolfe AJ, Hunter CL, MacCoss MJ, Gibson BW
Anal Chem 2015 Oct 20;87(20):10222-9
Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma
Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA
Mol Cell Proteomics 2015 Sep;14(9):2357-74
Comparative Analyses of Proteins From Haemophilus Influenzae Biofilm and Planktonic Populations Using Metabolic Labeling and Mass Spectrometry
Post DM, Held JM, Ketterer MR, Phillips NJ, Sahu A, Apicella MA, Gibson BW
BMC Microbiol 2014 Dec 31;14:329
RPL24: A Potential Therapeutic Target Whose Depletion or Acetylation Inhibits Polysome Assembly and Cancer Cell Growth
Wilson-Edell KA, Kehasse A, Scott GK, Yau C, Rothschild DE, Schilling B, Gabriel BS, Yevtushenko MA, Hanson IM, Held JM, Gibson BW, Benz CC
Oncotarget 2014 Jul 15;5(13):5165-76
Variation and Quantification Among a Target Set of Phosphopeptides in Human Plasma by Multiple Reaction Monitoring and SWATH-MS2 Data-Independent Acquisition
Zawadzka AM, Schilling B, Held JM, Sahu AK, Cusack MP, Drake PM, Fisher SJ, Gibson BW
Electrophoresis 2014 Dec;35(24):3487-3497
Targeted Quantitation of Acetylated Lysine Peptides by Selected Reaction Monitoring Mass Spectrometry
Rardin MJ, Held JM, Gibson BW
Methods Mol Biol 2013;1077:121-31
Design, Implementation and Multisite Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in Liquid Chromatography-Multiple Reaction Monitoring-MS (LC-MRM-MS)
Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA
Mol Cell Proteomics 2013 Sep;12(9):2623-39
Label-Free Quantitative Proteomics of the Lysine Acetylome in Mitochondria Identifies Substrates of SIRT3 in Metabolic Pathways
Rardin MJ, Newman JC, Held JM, Cusack MP, Sorensen DJ, Li B, Schilling B, Mooney SD, Kahn CR, Verdin E, Gibson BW
Proc Natl Acad Sci U S A 2013 Apr 16;110(16):6601-6
Label-Free Quantitation and Mapping of the ErbB2 Tumor Receptor by Multiple Protease Digestion With Data-Dependent (MS1) and Data-Independent (MS2) Acquisitions Held JM*, Schilling B, D'Souza AK, Srinivasan T, Behring JB, Sorensen DJ, Benz CC, Gibson BW (*corresponding author)
Int J Proteomics 2013;2013:791985
Ligand Binding Promotes CDK-Dependent Phosphorylation of ER-Alpha on Hinge Serine 294 but Inhibits Ligand-Independent Phosphorylation of Serine 305 Held JM, Britton DJ, Scott GK, Lee EL, Schilling B, Baldwin MA, Gibson BW, Benz CC
Mol Cancer Res 2012 Aug;10(8):1120-32
Inhibition of Lipid Signaling Enzyme Diacylglycerol Kinase Epsilon Attenuates Mutant Huntingtin Toxicity
Zhang N, Li B, Al-Ramahi I, Cong X, Held JM, Kim E, Botas J, Gibson BW, Ellerby LM
J Biol Chem 2012 Jun 15;287(25):21204-13
Lectin Chromatography/Mass Spectrometry Discovery Workflow Identifies Putative Biomarkers of Aggressive Breast Cancers
Drake PM, Schilling B, Niles RK, Prakobphol A, Li B, Jung K, Cho W, Braten M, Inerowicz HD, Williams K, Albertolle M, Held JM, Iacovides D, Sorensen DJ, Griffith OL, Johansen E, Zawadzka AM, Cusack MP, Allen S, Gormley M, Hall SC, Witkowska HE, Gray JW, Regnier F, Gibson BW, Fisher SJ
J Proteome Res 2012 Apr 6;11(4):2508-20
Mass Spectrometric Identification of Novel Lysine Acetylation Sites in Huntingtin
Cong X, Held JM, DeGiacomo F, Bonner A, Chen JM, Schilling B, Czerwieniec GA, Gibson BW, Ellerby LM
Mol Cell Proteomics 2011 Oct;10(10):M111009829
N-Acylethanolamine Signalling Mediates the Effect of Diet on Lifespan in Caenorhabditis Elegans
Lucanic M, Held JM, Vantipalli MC, Klang IM, Graham JB, Gibson BW, Lithgow GJ, Gill MS
Nature 2011 May 12;473(7346):226-9
Confident Identification of 3-Nitrotyrosine Modifications in Mass Spectral Data Across Multiple Mass Spectrometry Platforms
Li B, Held JM, Schilling B, Danielson SR, Gibson BW
J Proteomics 2011 Oct 19;74(11):2510-21
Quantitative Mapping of Reversible Mitochondrial Complex I Cysteine Oxidation in a Parkinson Disease Mouse Model
Danielson SR, Held JM, Oo M, Riley R, Gibson BW, Andersen JK
J Biol Chem 2011 Mar 4;286(9):7601-8
ErbB2 Trafficking and Degradation Associated With K48 and K63 Polyubiquitination
Marx C, Held JM, Gibson BW, Benz CC
Cancer Res 2010 May 1;70(9):3709-17
Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach Held JM, Danielson SR, Behring JB, Atsriku C, Britton DJ, Puckett RL, Schilling B, Campisi J, Benz CC, Gibson BW
Mol Cell Proteomics 2010 Jul;9(7):1400-10
Preferentially Increased Nitration of Alpha-Synuclein at Tyrosine-39 in a Cellular Oxidative Model of Parkinson's Disease
Danielson SR, Held JM, Schilling B, Oo M, Gibson BW, Andersen JK
Anal Chem 2009 Sep 15;81(18):7823-8
Systematic Mapping of Posttranslational Modifications in Human Estrogen Receptor-Alpha With Emphasis on Novel Phosphorylation Sites
Atsriku C*, Britton DJ*, Held JM*, Schilling B, Scott GK, Gibson BW, Benz CC, Baldwin MA (*co-first author)
Mol Cell Proteomics 2009 Mar;8(3):467-80
Multi-Site Assessment of the Precision and Reproducibility of Multiple Reaction Monitoring-Based Measurements of Proteins in Plasma
Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H, Hall SC, Allen S, Blackman RK, Borchers CH, Buck C, Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, Hiltke T, Jackson A, Johansen EB, Kinsinger CR, Li J, Mesri M, Neubert TA, Niles RK, Pulsipher TC, Ransohoff D, Rodriguez H, Rudnick PA, Smith D, Tabb DL, Tegeler TJ, Variyath AM, Vega-Montoto LJ, Wahlander A, Waldemarson S, Wang M, Whiteaker JR, Zhao L, Anderson NL, Fisher SJ, Liebler DC, Paulovich AG, Regnier FE, Tempst P, Carr SA
Nat Biotechnol 2009 Jul;27(7):633-41
A Novel Serine Phosphorylation Site Detected in the N-Terminal Domain of Estrogen Receptor Isolated From Human Breast Cancer Cells
Britton DJ, Scott GK, Schilling B, Atsriku C, Held JM, Gibson BW, Benz CC, Baldwin MA
J Am Soc Mass Spectrom 2008 May;19(5):729-40
DAF-12-Dependent Rescue of Dauer Formation in Caenorhabditis Elegans by (25S)-Cholestenoic Acid Held JM, White MP, Fisher AL, Gibson BW, Lithgow GJ, Gill MS
Aging Cell 2006 Aug;5(4):283-91
Vitamin K3 (Menadione)-Induced Oncosis Associated With Keratin 8 Phosphorylation and Histone H3 Arylation
Scott GK, Atsriku C, Kaminker P, Held J, Gibson B, Baldwin MA, Benz CC
Mol Pharmacol 2005 Sep;68(3):606-15
Lipophilic Regulator of a Developmental Switch in Caenorhabditis Elegans
Gill MS, Held JM, Fisher AL, Gibson BW, Lithgow GJ
Aging Cell 2004 Dec;3(6):413-21
Invited Publications
Informatics Solutions for Selected Reaction Monitoring
Schilling B, Maclean B, Held JM, Gibson BW
Proteome Informatics 2016:178-199
Regulatory Control or Oxidative Damage? Proteomic Approaches to Interrogate the Role of Cysteine Oxidation Status in Biological Processes Held JM, Gibson BW
Mol Cell Proteomics 2012 Apr;11(4):R111013037