Richard Beger Ph.D.

Chief, Omics, Models, Imaging and Chemistry Branch — Division of Systems Biology

Richard Beger, Ph.D.
(870) 543-7121
NCTRResearch@fda.hhs.gov

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Background

Dr. Beger received a Ph.D. from Purdue University and completed postdoctoral training at Wesleyan University and Johns Hopkins University Medical School. His Ph.D. research focused on normal mode analysis of DNA under a variety of conditions. His postdoctoral appointments concentrated on using homonuclear and heteronuclear nuclear magnetic resonance (NMR) spectroscopy to solve NMR spectroscopy solution structures of zinc fingers, damaged DNA, and protein-protein complexes. During his second postdoctoral appointment, he developed an in silico method to use 1H, 13C, and 15N NMR assigned chemical shifts of the protein backbone atoms to form dihedral constraints on the backbone of proteins. This method increased the accuracy of the protein structures and permitted larger proteins to be solved by NMR spectroscopic methods. Dr. Beger is currently the branch chief of the Omics, Models, Imaging and Chemistry (OMIC) Branch in the Division of Systems Biology at FDA’s National Center for Toxicological Research (NCTR). OMIC consists of a metabolomics team, proteomics team, tissue imaging, alternative methods team, and chemical modeling of toxicological endpoints.

Research Interests

Dr. Beger’s current research uses cutting-edge systems biology, proteomics, and metabolomics analysis of biofluid and tissues samples from in vitro, nonclinical, and clinical studies to discover and evaluate translational biomarkers of:

drug-induced liver, kidney, heart, or neural toxicity
drug or chemical addiction
disease status

Dr. Beger is participating in national and international quality assurance/quality control metabolomics committees that include the creation of Metabolomics Quality Assurance and Quality Control Consortium (mQACC) and MEtabolomics standaRds Initiative in Toxicology (MERIT) to provide guidance on best practice, quality standards, and the reporting of analytical and computational metabolomics methods. He initiated NCTR and FDA research in tissue imaging with the purchase of MALDI TOF mass spectrometry to image:

drugs
drug metabolites
endogenous metabolites (i.e., neurotransmitters, cholesterol, lipids)
chemicals

Tissue imaging can be directly compared to histopathology and other imaging techniques to identify biomarkers and mechanisms in tissue. Dr. Beger is also the primary inventor of spectroscopic data activity relationship (SDAR) as well as three-dimensional SDAR modeling that has been used to model estrogen receptor binding, opioid binding, human Ether-à-go-go-Related Gene (hERG) inhibition, and other toxicological endpoints.

Professional Societies/National and International Groups

COnsortium of METabolomics Studies (COMETS)
Member
2016 – Present

Metabolomics Quality Assurance and Quality Control Consortium (mQACC)
Member, Coordinating council
2018 – Present

Metabolomics Reporting Framework (MRF)
Member
2017 – 2018

Metabolomics Society
Member
2004 – Present

MEtabolomics standaRds Initiative in Toxicology (MERIT)
Member
2017 – 2018

Society of Toxicology (SOT)
Member
2004 – Present

South Central Chapter, SOT
Member
2014 – Present

Select Publications

Distinct Lipid Signatures are Identified in the Plasma of Rats with Chronic Inflammation Induced by Estradiol Benzoate and Sex Hormones.
Nakamura N., Pence L.M., Cao Z., and Beger R.D.
Metabolomics. 2020, 16(9):95. doi: 10.1007/s11306-020-01715-w.PMID: 32895772.

Dissemination and Analysis of the Quality Assurance (QA) and Quality Control (QC) Practices of LC-MS Based Untargeted Metabolomics Practitioners.
Evans A.M., O'Donovan C., Playdon M., Beecher C., Beger R.D., Bowden J.A., Broadhurst D., Clish C.B., Dasari S., Dunn W.B., Griffin J.L., Hartung T., Hsu P.C., Huan T., Jans J., Jones C.M., Kachman M., Kleensang A., Lewis M.R., Monge M.E., Mosley J.D., Taylor E., Tayyari F., Theodoridis G., Torta F., Ubhi B.K., Vuckovic D., and the Metabolomics Quality Assurance, Quality Control Consortium (mQACC).
Metabolomics. 2020, 16(10):113. doi: 10.1007/s11306-020-01728-5. PMID: 33044703.

Progress Towards an OECD Reporting Framework for Transcriptomics and Metabolomics in Regulatory Toxicology.
Harrill J.A., Viant M.R., Yauk C.L., Sachana M., Gant T.W., Auerbach S.S., Beger R.D., Bouhifd M., O'Brien J., Burgoon L., Caiment F., Carpi D., Chen T., Chorley B.N., Colbourne J., Corvi R., Debrauwer L., O'Donovan C., Ebbels T.M.D., Ekman D.R., Faulhammer F., Gribaldo L., Hilton G.M., Jones S.P., Kende A., Lawson T.N., Leite S.B., Leonards P.E.G., Luijten M., Martin A., Moussa L., Rudaz S., Schmitz O., Sobanski T., Strauss V., Vaccari M., Vijay V., Weber R.J.M., Williams A.J., Williams A., Thomas R.S., and Whelan M.
Regul Toxicol Pharmacol. 2021, 125:105020. doi: 10.1016/j.yrtph.2021.105020. Epub 2021 Jul 29. PMID: 34333066.

Metabolomics as a Truly Translational Tool for Precision Medicine.
Schmidt J.C., Dougherty B.V., Beger R.D., Jones D.P., Schmidt M.A., and Mattes W.B.
Int J Toxicol. 2021, 40(5):413-426. doi: 10.1177/10915818211039436. PMID: 34514887.

Current Concepts in Pharmacometabolomics, Biomarker Discovery, and Precision Medicine.
Beger R.D., Schmidt M.A., and Kaddurah-Daouk R.
Metabolites. 2020, 10(4):129. doi: 10.3390/metabo10040129. PMID: 32230776.

Bile Acid Profile and its Changes in Response to Cefoperazone Treatment in MR1 Deficient Mice.
Sun J., Cao Z., Smith A.D., Carlson P.E. Jr., Coryell M., Chen H., and Beger R.D.
Metabolites. 2020, 10(4):127. doi: 10.3390/metabo10040127. PMID: 32225042.

Hepatic Transcript Profiles of Cytochrome P450 Genes Predict Sex Differences in Drug Metabolism.
Fuscoe J.C., Vijay V., Hanig J.P., Han T., Ren L., Greenhaw J.J., Beger R.D., Pence L.M., and Shi Q.
Drug Metab Dispos. 2020, 48(6):447-458. doi: 10.1124/dmd.119.089367. Epub 2020 Mar 19. PMID: 32193355.

Determination of Structural Factors Affecting Binding to Mu, Kappa and Delta Opioid Receptors.
Slavov S., Mattes W., and Beger R.D.
Arch Toxicol. 2020, 94(4):1215-1227. doi: 10.1007/s00204-020-02684-8. Epub 2020 Feb 27. PMID: 32107589.

Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite.
Bearden D.W., Sheen D.A., Simón-Manso Y., Benner B.A. Jr., Rocha W.F.C., Blonder N., Lippa K.A., Beger R.D., Schnackenberg L.K., Sun J., Mehta K.Y., Cheema A.K., Gu H., Marupaka R., Nagana Gowda G.A., and Raftery D.
Metabolites. 2019, 9(11):270. doi: 10.3390/metabo9110270. PMID: 31703392.

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. doi: 10.1021/acs.jproteome.9b00320. Epub 2019 Sep 12. PMID: 31442052.

Metabolomics-Based Pathway Changes in Testis Fragments Treated with Ethinylestradiol In Vitro.
Sun J., Beger R.D., Sloper D.T., and Nakamura N.
Birth Defects Res. 2019, 111(20):1643-1654. doi: 10.1002/bdr2.1560. Epub 2019 Jul 26. PMID: 31347792.

Use Cases, Best Practice and Reporting Standards for Metabolomics in Regulatory Toxicology.
Viant M.R., Ebbels T.M.D., Beger R.D., Ekman D.R., Epps D.J.T., Kamp H., Leonards P.E.G., Loizou G.D., MacRae J.I., van Ravenzwaay B., Rocca-Serra P., Salek R.M., Walk T., and Weber R.J.M.
Nat Commun. 2019, 10(1):3041. doi: 10.1038/s41467-019-10900-y. PMID: 31292445.

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. doi: 10.1021/acs.jproteome.8b00903. Epub 2019 May 22. PMID: 31074987.

Towards Quality Assurance and Quality Control in Untargeted Metabolomics Studies.
Beger R.D., Dunn W.B., Bandukwala A., Bethan B., Broadhurst D., Clish C.B., Dasari S., Derr L., Evans A., Fischer S., Flynn T., Hartung T., Herrington D., Higashi R., Hsu P.C., Jones C., Kachman M., Karuso H., Kruppa G., Lippa K., Maruvada P., Mosley J., Ntai I., O'Donovan C., Playdon M., Raftery D., Shaughnessy D., Souza A., Spaeder T., Spalholz B., Tayyari F., Ubhi B., Verma M., Walk T., Wilson I., Witkin K., Bearden D.W., and Zanetti K.A.
Metabolomics. 2019, 15(1):4. doi: 10.1007/s11306-018-1460-7. PMID: 30830465.

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. doi: 10.1016/j.ekir.2018.04.012. eCollection 2018 Sep. PMID: 30197987.

Computational Identification of Structural Factors Affecting the Mutagenic Potential of Aromatic Amines: Study Design and Experimental Validation.
Slavov S.H., Stoyanova-Slavova I., Mattes W., Beger R.D., and Brüschweiler B.J.
Arch Toxicol. 2018, 92(7):2369-2384. doi: 10.1007/s00204-018-2216-x. Epub 2018 May 19. PMID: 29779177.

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. doi: 10.1177/1535370217746383. Epub 2017 Dec 9. PMID: 29224368.

Multiple microRNAs Function as Self-Protective Modules in Acetaminophen-Induced Hepatotoxicity in Humans.
Yu D., Wu L., Gill P., Tolleson W.H., Chen S., Sun J., Knox B., Jin Y., Xiao W., Hong H., Wang Y., Ren Z., Guo L., Mei N., Guo Y., Yang X., Shi L., Chen Y., Zeng L., Dreval K., Tryndyak V., Pogribny I., Fang H., Shi T., McCullough S., Bhattacharyya S., Schnackenberg L., Mattes W., Beger R.D., James L., Tong W., and Ning B.
Arch Toxicol. 2018, 92(2):845-858. doi: 10.1007/s00204-017-2090-y. Epub 2017 Oct 24. PMID: 29067470.

Evaluation of Metabolism of Azo Dyes and Their Effects on Staphylococcus aureus Metabolome.
Sun J., Jin J., Beger R.D., Cerniglia C.E., and Chen H.
J Ind Microbiol Biotechnol. 2017. 44(10):1471-1481. doi: 10.1007/s10295-017-1970-8. Epub 2017 Aug 7. PMID: 28786013.

3D-SDAR Modeling of hERG Potassium Channel Affinity: A Case Study in Model Design and Toxicophore Identification.
Stoyanova-Slavova I.B., Slavov S.H., Buzatu D.A., Beger R.D., and Wilkes J.G.
J Mol Graph Model. 2017, 72:246-255. doi: 10.1016/j.jmgm.2017.01.012. Epub 2017 Jan 16. PMID: 28129595.

Metabolomics Enables Precision Medicine: "A White Paper, Community Perspective".
Beger R.D., Dunn W., Schmidt M.A., Gross S.S., Kirwan J.A., Cascante M., Brennan L., Wishart D.S., Oresic M., Hankemeier T., Broadhurst D.I., Lane A.N., Suhre K., Kastenmüller G., Sumner S.J., Thiele I., Fiehn O., Kaddurah-Daouk R., and for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative.
Metabolomics. 2016, 12(10):149. doi: 10.1007/s11306-016-1094-6. Epub 2016 Sep 2. PMID: 27642271.

Translational Biomarkers of Acetaminophen-Induced Acute Liver Injury.
Beger R.D., Bhattacharyya S., Yang X., Gill P.S., Schnackenberg L.K., Sun J., and James L.P.
Arch Toxicol. 2015, 89(9):1497-522. doi: 10.1007/s00204-015-1519-4. Epub 2015 May 17. PMID: 25983262.