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  8. Li-Rong Yu
  1. Science & Research (NCTR)

Li-Rong Yu Ph.D.

Team Leader — Division of Systems Biology

Dr. Li-Rong Yu
Li-Rong Yu, Ph.D.
(870) 543-7121
NCTRResearch@fda.hhs.gov  

Back to NCTR Principal Investigator page

 About  |  Publications  |  Lab Members

Background

Dr. Li-Rong Yu received his B.S. in biology from Hangzhou Teachers College in 1991 and M.S. in hydrobiology from the Institute of Hydrobiology, Chinese Academy of Sciences in 1994. He then received a Ph.D. in biochemistry and molecular biology from the Shanghai Institute of Biochemistry, Chinese Academy of Sciences in 2000. His Ph.D. research focused on liver cancer proteomics using 2D-PAGE and mass spectrometry. Dr. Yu completed postdoctoral research training in quantitative proteomics and biological mass spectrometry under Dr. Richard Smith at the Pacific Northwest National Laboratory in 2002. From 2002 to 2007, Dr. Yu worked at the Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., National Cancer Institute in Frederick, Maryland. He worked as a scientist, senior scientist, and group head with studies focusing on the development of mass spectrometry-based quantitative proteomic technologies and their application to cancer biology. In 2007, Dr. Yu joined NCTR as a team leader and director for proteomics. His current research has been on the development of proteomic biomarkers and understanding the mechanisms of drug-induced organ toxicity at the proteome level. Dr. Yu has authored or co-authored more than 90 peer-reviewed publications or book chapters and has served on editorial boards of professional journals and committees of international working groups.

Research Interests

Dr. Yu’s current research focuses on biomarker development and mechanisms of drug-induced toxicity using cutting-edge proteomics technologies and assays in both nonclinical models and clinical settings. He has developed mass spectrometry-based quantitative proteomics and phosphoproteomics approaches for better understanding of drug-induced liver injury (DILI) and cardiotoxicity in rodent models. His investigation in these areas has resulted in identification of nonclinical proteomic biomarker candidates of DILI or cardiac injury, and discovery of hepatotoxicity and mitochondrial dysfunction promoted by c-Jun N-terminal protein kinase (JNK) mediated phosphorylation of mitochondrial proteins. Translation of preclinical/nonclinical biomarkers to clinical use is a critical step in translational biomarker development. Dr. Yu evaluates and uses high throughput multiplex proteomic assays, including SOMAscan and Olink assays, to identify and verify predictive biomarkers of chemotherapy-induced cardiotoxicity in cancer patients. He has also conducted clinical studies and identified mortality-associated serum biomarkers in dialysis-dependent acute kidney injury (AKI-D) patients. While clinical biomarker development relies on quality clinical samples, pre-analytical variables may affect sample quality, thus confounding biomarker discovery and validation. Using SOMAscan assays, multiplex immunoassays, and mass spectrometry, Dr. Yu has identified potential metabolomic and proteomic biomarkers for quality assessment of human plasma samples processed and stored under variable pre-analytical conditions. Dr. Yu is participating in the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) to provide guidance on best practice and reporting standards of quality control in metabolomics.     


Professional Societies/National and International Groups

Metabolomics Quality Assurance and Quality Control Consortium (mQACC)
Member
2019-present

Society of Toxicology
Member
2014-present

International Cardioncology Society
Member
2014 – Present 
 
Journal of Proteomics
Editorial Board Member
2009 – Present

American Society for Mass Spectrometry
Member
2002 – Present

 

Selected Publications

Stability of the Human Plasma Proteome to Pre-analytical Variability as Assessed by an Aptamer-Based Approach.
Daniels J.R., Cao Z., Maisha M., Schnackenberg L.K., Sun J., Pence L., Schmitt T.C., Kamlage B,, Rogstad S., Beger R.D., and Yu L.R.
J Proteome Res. 2019, 18(10):3661-3670.

An Integrated Analysis of Metabolites, Peptides, and Inflammation Biomarkers for Assessment of Preanalytical Variability of Human Plasma.
Cao Z., Kamlage B., Wagner-Golbs A., Maisha M., Sun J., Schnackenberg L.K., Pence L., Schmitt T.C., Daniels J.R., Rogstad S., Beger R.D., and Yu L.R.
J Proteome Res. 2019, 18(6):2411-2421.

Aptamer-Based Proteomics Identifies Mortality-Associated Serum Biomarkers in Dialysis-Dependent AKI Patients.
Yu L.R., Sun J., Daniels J.R., Cao Z., Schnackenberg L., Choudhury D., Palevsky P.M., Ma J.Z., Beger R.D., and Portilla D.
Kidney Int Rep. 2018, 3(5):1202-1213.

Apoptosis of Enterocytes and Nitration of Junctional Complex Proteins Promote Alcohol-Induced Gut Leakiness and Liver Injury.
Cho Y.E., Yu L.R., Abdelmegeed M.A., Yoo S.H., and Song B.J.
J Hepatol. 2018, 69(1):142-153.

Immune Response Proteins as Predictive Biomarkers of Doxorubicin-Induced Cardiotoxicity in Breast Cancer Patients.
Yu L.R., Cao Z., Makhoul I., Daniels J.R., Klimberg S., Wei J.Y., Bai J.P., Li J., Lathrop J.T., Beger R.D., and Todorova V.K.
Exp Biol Med (Maywood). 2018, 243(3):248-255.

CHD4 Has Oncogenic Functions in Initiating and Maintaining Epigenetic Suppression of Multiple Tumor Suppressor Genes.
Xia L., Huang W., Bellani M., Seidman M.M., Wu K., Fan D., Nie Y., Cai Y., Zhang Y.W., Yu L.R., Li H., Zahnow C.A., Xie W., Chiu Yen R.W., Rassool F.V., and Baylin S.B.
Cancer Cell. 2017, 31(5):653-668.e7.

Proteomic Analysis of Acetaminophen-Induced Hepatotoxicity and Identification of Heme Oxygenase 1 as a Potential PPlasma Biomarker of Liver Injury.
Gao Y., Cao Z., Yang X., Abdelmegeed M.A., Sun J., Chen S., Beger R.D., Davis K., Salminen W.F., Song B.J., Mendrick D.L., and Yu L.R.
Proteomics Clin Appl. 2017, 11(1-2):10.1002/prca.201600123.

Early Metabolomics Changes in Heart and Plasma During Chronic Doxorubicin Treatment in B6C3F1 Mice.
Schnackenberg L.K., Pence L., Vijay V., Moland C.L., George N., Cao Z., Yu L.R., Fuscoe J.C., Beger R.D., and Desai V.G.
J Appl Toxicol. 2016, 36(11):1486-95.

Proteomic Analysis of Acetaminophen-Induced Hepatotoxicity and Identification of Heme Oxygenase 1 as a Potential Plasma Biomarker of Liver Injury.
Gao Y, Cao Z, Yang X, Abdelmegeed MA, Sun J, Chen S, Beger RD, Davis K, Salminen WF, Song BJ, Mendrick DL, Yu LR.
Proteomics Clin Appl. 2016, doi: 10.1002/prca.201600123.

Early Transcriptional Changes in Cardiac Mitochondria During Chronic Doxorubicin Exposure and Mitigation by Dexrazoxane in Mice.
Vijay V, Moland CL, Han T, Fuscoe JC, Lee T, Herman EH, Jenkins GR, Lewis SM, Cummings CA, Gao Y, Cao Z, Yu LR, Desai VG.
Toxicol Appl Pharmacol. 2016 Mar 15; 295:68-84.

Critical Role of C-Jun N-Terminal Protein Kinase in Promoting Mitochondrial Dysfunction and Acute Liver Injury.
Jang S, Yu LR, Abdelmegeed MA, Gao Y, Banerjee A, Song BJ.
Redox Biol. 2015 Dec; 6:552-64.

Integrated MicroRNA, mRNA, and Protein Expression Profiling Reveals MicroRNA Regulatory Networks in Rat Kidney Treated with a Carcinogenic Dose of Aristolochic Acid.
Li Z, Qin T, Wang K, Hackenberg M, Yan J, Gao Y, Yu LR, Shi L, Su Z, Chen T.
BMC Genomics. 2015 May 8; 16:365.

Proteomics Quality and Standard: from a Regulatory Perspective.
Gu Q, Yu LR.
J Proteomics. 2014 Jan 16; 96:353-9.

Phosphopeptide Enrichment Using Offline Titanium Dioxide Columns for Phosphoproteomics.
Yu LR, Veenstra T.
Methods Mol Biol. 2013; 1002:93-103.

Functional Robustness of a Polycyclic Aromatic Hydrocarbon Metabolic Network Examined in a nidA Aromatic Ring-Hydroxylating Oxygenase Mutant of Mycobacterium Vanbaalenii PYR-1.
Kim SJ, Song J, Kweon O, Holland RD, Kim DW, Kim J, Yu LR, Cerniglia CE.
Appl Environ Microbiol. 2012 May; 78(10):3715-23.

Pharmacoproteomics and Toxicoproteomics: the Field of Dreams.
Yu LR.
J Proteomics. 2011 Nov 18; 74(12):2549-53. doi: 10.1016/j.jprot.2011.10.001. Epub 2011 Oct 8. Review.

Proteomic Analysis of Early Response Lymph Node Proteins in Mice Treated with Titanium Dioxide Nanoparticles.
Gao Y, Gopee NV, Howard PC, Yu LR.
J Proteomics. 2011 Nov 18; 74(12):2745-59.

Regulation of Microtubule-Based Microtubule Nucleation by Mammalian Polo-Like Kinase 1.
Johmura Y, Soung NK, Park JE, Yu LR, Zhou M, Bang JK, Kim BY, Veenstra TD, Erikson RL, Lee KS.
Proc Natl Acad Sci U S A. 2011 Jul 12; 108(28):11446-51.

Distinct Roles of GCN5/PCAF-Mediated H3K9ac and CBP/p300-Mediated H3K18/27ac in Nuclear Receptor Transactivation.
Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE, Wang C, Brindle PK, Dent SY, Ge K.
EMBO J. 2011 Jan 19; 30(2):249-62.

Oxidant-Induced Apoptosis is Mediated by Oxidation of the Actin-Regulatory Protein Cofilin.
Klamt F, Zdanov S, Levine RL, Pariser A, Zhang Y, Zhang B, Yu LR, Veenstra TD, Shacter E.
Nat Cell Biol. 2009 Oct; 11(10):1241-6.

Quantitative Proteomics for Drug Toxicity.
Gao Y, Holland RD, Yu LR.
Brief Funct Genomic Proteomic. 2009 Mar; 8(2):158-66.

Improved Titanium Dioxide Enrichment of Phosphopeptides from HeLa Cells and High Confident Phosphopeptide Identification by Cross-Validation of MS/MS and MS/MS/MS Spectra.
Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD.
J Proteome Res. 2007 Nov; 6(11):4150-62.

Phosphoproteomics for the Discovery of Kinases as Cancer Biomarkers and Drug Targets.
Yu LR, Issaq HJ, Veenstra TD.
Proteomics Clin Appl. 2007 Sep; 1(9):1042-57.

Self-Regulated Plk1 Recruitment to Kinetochores by the Plk1-PBIP1 Interaction is Critical for Proper Chromosome Segregation.
Kang YH, Park JE, Yu LR, Soung NK, Yun SM, Bang JK, Seong YS, Yu H, Garfield S, Veenstra TD, Lee KS.
Mol Cell. 2006 Nov 3; 24(3):409-22.

Regulation of Androgen Receptor Activity by Tyrosine Phosphorylation.
Guo Z, Dai B, Jiang T, Xu K, Xie Y, Kim O, Nesheiwat I, Kong X, Melamed J, Handratta VD, Njar VC, Brodie AM, Yu LR, Veenstra TD, Chen H, Qiu Y.
Cancer Cell. 2006 Oct; 10(4):309-19.

Global Analysis of the Cortical Neuron Proteome.
Yu LR, Conrads TP, Uo T, Kinoshita Y, Morrison RS, Lucas DA, Chan KC, Blonder J, Issaq HJ, Veenstra TD.
Mol Cell Proteomics. 2004 Sep; 3(9):896-907.

Evaluation of the Acid-Cleavable Isotope-Coded Affinity Tag Reagents: Application to Camptothecin-Treated Cortical Neurons.
Yu LR, Conrads TP, Uo T, Issaq HJ, Morrison RS, Veenstra TD.
J Proteome Res. 2004 May-Jun; 3(3):469-77.

 

Lab Members

Contact information for all lab members:
(870) 543-7121
NCTRResearch@fda.hhs.gov   

Zhijun Cao, Ph.D.
Staff Fellow

Contact Information
Li-Rong Yu
(870) 543-7121
Expertise
Expertise
Approach
Domain
Technology & Discipline
Toxicology
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