Junmin Peng, PhD
Junmin Peng, PhD

Junmin Peng, PhD

Member, St. Jude Faculty

  • Director, Center for Proteomics and Metabolomics

Departments

Education

BS – Wuhan University, China (1991)
PhD – University of Iowa (1999)
Postdoctoral Fellowship – Harvard Medical School (1999-2002)

Research Interests

Lab Website: http://www.stjuderesearch.org/site/lab/peng

  • Mass Spectrometry-based Proteomics and Metabolomics
  • Systems Biology of Cancer
  • Molecular Pathogenesis of Alzheimer’s Disease
  • Ubiquitin and Proteome Turnover

Our mission is to develop novel mass spectrometry-based proteomics and metabolomics technologies, systems biology approaches, and to apply these tools to biomedical challenges (e.g. Alzheimer’s disease, cancer and immunity). We seek to obtain the full spectra of temporal and spatial omics data at bulk and single-cell-type levels from animal models and human clinical specimens. The multi-omics data include genome, transcriptome, proteome (the whole proteome and modified proteomes such as phosphoproteome and ubiquitinome), metabolome, and interactome. Network analysis and integration of such multi-omics data with phenotypic information offer a systems or holistic view, for unbiased identification of central disease gene/protein/metabolite networks, functional modules and master regulators. Beyond the big data analysis, we develop mouse models for functional and mechanistic studies to validate the derived hypotheses. These studies provide novel insights into the pathogenesis for therapeutic intervention, and may discover disease biomarkers for precision medicine.

Selected Publications

Google Scholar Citations:  http://scholar.google.com/citations?user=vFzS-awAAAAJ&hl=en

Bai B, Wang X, Li Y, Chen PC, Yu K, Dey KK, Yarbro JM, Han X, Lutz BM, Rao S, Jiao Y, Sifford JM, Han J, Wang M, Tan H, Shaw TI, Cho JH, Zhou S, Wang H, Niu M, Mancieri A, Messler KA, Sun X, Wu Z, Pagala V, High AA, Bi W, Zhang H, Chi H, Haroutunian V, Zhang B, Beach TG, Yu G, Peng J. Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression. Neuron 2020. [Epub]

Wang H, Diaz AK, Shaw TI, Li Y, Niu M, Cho JH, Paugh BS, Zhang Y, Sifford J, Bai B, Wu Z, Tan H, Zhou S, Hover LD, Tillman HS, Shirinifard A, Thiagarajan S, Sablauer A, Pagala V, High AA, Wang X, Li C, Baker SJ, Peng J. Deep multiomics profiling of brain tumors identifies signaling networks downstream of cancer driver genes. Nat Commun 10:3718, 2019.

Dey KK, Wang H, Niu M, Bai B, Wang X, Li Y, Cho JH, Tan H, Mishra A, High AA, Chen PC, Wu Z, Beach TG, Peng J. Deep undepleted human serum proteome profiling toward biomarker discovery for Alzheimer's disease. Clin Proteomics 2019.

Xie B, Wang Y, Jones DR, Dey KK, Wang X, Li Y, Cho JH, Shaw TI, Tan H, Peng J. Isotope Labeling-Assisted Evaluation of Hydrophilic and Hydrophobic Liquid Chromatograph-Mass Spectrometry for Metabolomics Profiling. Anal Chem 90:8538-45, 2018.

Wang Z, Ma J, Miyoshi C, Li Y, Sato M, Ogawa Y, Lou T, Ma C, Gao X, Lee C, Yang X, Zhou S, Hotta-Hirashima N, Klewe-Nebenius D, Ikkyu A, Kakizaki M, Kanno S, Cao L, Peng J, Yu Y, Funato H, Yanagisawa M, Liu Q. Quantitative phosphoproteomic analysis of the molecular substrates of sleep need. Nature 558:435-9, 2018.

Du X, Wen J, Wang Y, Karmaus PWF, Khatamian A, Tan H, Li Y, Guy C, Nguyen TM, Dhungana Y, Neale G, Peng J, Yu J, Chi H. Hippo/Mst signalling couples metabolic state and immune function of CD8α+ dendritic cells. Nature 558:141-5, 2018.

Stewart E, McEvoy J, Wang H, Chen X, Honnell V, Ocarz M, Gordon B, Dapper J, Blankenship K, Yang Y, Li Y, Shaw TI, Cho JH, Wang X, Xu B, Gupta P, Fan Y, Liu Y, Rusch M, Griffiths L, Jeon J, Freeman BB 3rd, Clay MR, Pappo A, Easton J, Shurtleff S, Shelat A, Zhou X, Boggs K, Mulder H, Yergeau D, Bahrami A, Mardis ER, Wilson RK, Zhang J, Peng J, Downing JR, Dyer MA; St. Jude Children's Research Hospital – Washington University Pediatric Cancer Genome Project. Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses. Cancer Cell 34:411-26, 2018.

Tan H, Yang K, Li Y, Shaw TI, Wang Y, Blanco DB, Wang X, Cho JH, Wang H, Rankin S, Guy C, Peng J (co-corresponding author), Chi H. Integrative proteomics and phosphoproteomics profiling reveals dynamic signaling networks and bioenergetics pathways underlying T cell activation. Immunity 46:488-50, 2017.

Lee KH, Zhang P, Kim HJ, Mitrea DM, Sarkar N, Freibaum BD, Cika J, Coughlin M, Messing J, Molliex A,  Maxwell BA,  Kim NC, Temirov J, Moore J, Kolaitis RM, Shaw TI, Bai B, Peng J, Kriwacki RW, Taylor JP. C9orf72 dipeptide repeats impair the assembly, dynamics, and function of membrane-less organelles. Cell 167:774-88, 2016.

Martinez J, Malireddi RK, Lu Q, Cunha LD, Pelletier S, Gingras S, Orchard R, Guan JL, Tan H, Peng J, Kanneganti TD, Virgin HW, Green DR. Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins. Nat Cell Biol 17:893-906, 2015.

Wang X, Li Y, Wu Z, Wang H, Tan H and Peng J. JUMP: a tag-based database search tool for peptide identification with high sensitivity and accuracy. Mol Cell Proteomics 13:3663-73, 2014.

Jones DR, Wu Z, Chauhan D, Anderson KC, Peng J. A nano Ultra-Performance Liquid Chromatography - High Resolution Mass Spectrometry Approach for Global Metabolomic Profiling and Case Study on Drug-Resistant Multiple Myeloma. Anal Chem 86:3667-75, 2014.

Bai B, Hales CM, Chen PC, Gozal Y, Dammer EB, Fritz JJ, Wang X, Xia Q, Duong DM, Street C, Cantero G, Cheng D, Jones DR, Wu Z, Li Y, Diner I, Heilman CJ, Rees HD, Wu H, Lin L, Szulwach KE, Gearing M, Mufson EJ, Bennett DA, Montine TJ, Seyfried NT, Wingo TS, Sun YE, Jin P, Hanfelt J, Willcock DM, Levey A, Lah JJ, Peng J. U1 Small Nuclear Ribonucleoprotein Complex and RNA Splicing Alterations in Alzheimer’s Disease. Proc Natl Acad Sci U S A. 110:16562-7, 2013.

Willmund F, Del Alamo M, Pechmann S, Chen T, Albanèse V, Dammer EB, Peng J, Frydman J. The cotranslational function of ribosome-associated hsp70 in eukaryotic protein homeostasis. Cell 152:196-209, 2013.

Na CH, Jones DR, Yang Y, Wang X, Xu Y, Peng J. Synaptic protein ubiquitination in rat brain revealed by antibody-based ubiquitome analysis J Proteome Res 11:4722-32, 2012.

Dammer EB, Na CH, Xu P, Seyfried NT, Duong DM, Cheng D, Gearing M, Rees H, Lah JJ, Levey AI, Rush J, Peng J. Polyubiquitin linkage profiles in three models of proteolytic stress suggest etiology of Alzheimer disease. J Biol Chem 286:10457-65, 2011.

Bingol B, Wang CF, Arnott D, Cheng D, Peng J, Sheng M. Autophosphorylated CaMKIIalpha acts as a scaffold to recruit proteasomes to dendritic spines. Cell 140:567-578, 2010.

Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137:133-145, 2009.

Liu Y, Ye X, Jiang F, Liang C, Cheng D, Peng J, Kinch L, Grishin N, Liu Q. C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation. Science 325:750-753, 2009.

Qi HH, Ongusaha PP, Myllyharju J, Cheng D, Pakkanen O, Shi Y, Lee SW, Peng J, Shi Y. Prolyl 4-hydroxylation regulates Argonaute 2 stability. Nature 455:421-4, 2008.

Choe EA, Liao L, Zhou, JY, Cheng D, Duong DM, Jin P, Tsai LH, Peng J. Neuronal morphogenesis is regulated by the interplay between cyclin-dependent kinase 5 and the ubiquitin ligase mind bomb 1. J Neurosci 27:9503-9512, 2007.

Cheng D, Hoogenraad CC, Rush J, Ramm E, Schlager MA, Duong DM, Xu P, Wijayawardana SR, Hanfelt J, Nakagawa T, Sheng M, Peng J. Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics 5:1158-1170, 2006.

Liao L, Cheng D, Wang J, Duong DM, Losik TG, Gearing M, Rees HD, Lah JJ, Levey AI, Peng J. Proteomic characterization of postmortem amyloid plaques isolated by laser capture microdissection. J Biol Chem 279:37061-37068, 2004.

Peng J, Elias JE, Schwartz D, Thoreen CC, Cheng D, Marshiscky G, Roelofs J, Finley D, and Gygi SP. A proteomics approach to protein ubiquitination. Nat Biotechnol 21:921-926, 2003.

Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res 2:43-50, 2003.

Lee MS, Kwon YT, Li M, Peng J, Friedlander RM, Tsai LH. Neurotoxicity induces calpain cleavage of p35 to p25. Nature 405:360-4, 2000.

Peng J, Zhu Y, Milton J, Price DH. Identification of multiple cyclin subunits of human P-TEFb. Genes Dev 12:755-62, 1998.

Last update: February 2020