Richard Beger Ph.D.

Omics, Models, Imaging, and Chemistry Branch Chief — 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. In 1998, Dr, Beger joined FDA’s National Center for Toxicological Research (NCTR) as a staff scientist and chemist for NMR analysis of drugs and drug metabolites. Dr. Beger is currently the branch chief of the Omics, Models, Imaging and Chemistry (OMIC) Branch in the Division of Systems Biology. OMIC consists of a diverse group of scientists working the fields of metabolomics, proteomics, tissue imaging, and chemical modeling of toxicological endpoints.

Research Interests

Dr. Beger’s current research uses cutting-edge systems biology, proteomics, and metabolomics approaches to analyze samples (e.g., biofluids, tissues, and cell culture mediums) 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 was involved in the creation of, and has continued as an active participant in, national and international QA/QC (quality assurance/quality control) metabolomics committees including the Metabolomics Quality Assurance and Quality Control Consortium (mQACC) and MERIT—which stands for the MEtabolomics standaRds Initiative in Toxicology—to provide guidance on best practices, quality standards, and the reporting of analytical and computational metabolomics methods. He initiated NCTR and FDA research in tissue imaging with the purchase of a matrix-assisted laser desorption/ionization time-of-flight (MALDI TOF) mass spectrometer to image:

drugs
drug metabolites
endogenous metabolites (e.g., neurotransmitters, cholesterol, acylcarnitines, etc.)
protein tags

Tissue imaging can be directly compared to histopathology and other imaging techniques to identify biomarkers and mechanisms in tissue. Dr. Beger has continued to grow the imaging capabilities with the addition of a Fourier Transform mass spectrometer and macro cryostat to allow whole body imaging in nonclinical studies. 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

Quality Assurance and Quality Control Reporting in Untargeted Metabolic Phenotyping: mQACC Recommendations for Analytical Quality Management.
Kirwan J.A., Gika H., Beger R.D., Bearden D., Dunn W.B., Goodacre R., Theodoridis G., Witting M., Yu L.R., and Wilson I.D.; Metabolomics Quality Assurance and Quality Control Consortium (mQACC).
Metabolomics. 2022, 18(9):70. PMID: 36029375.

Evaluating Cefoperazone-Induced Gut Metabolic Functional Changes in MR1-Deficient Mice.
Sun J., Cao Z., Smith A.D., Carlson P.E. Jr, Coryell M., Chen H., and Beger R.D.
Metabolites. 2022, 12(5):380. PMID: 35629884.

Reference Materials for MS-Based Untargeted Metabolomics and Lipidomics: A Review by the Metabolomics Quality Assurance and Quality Control Consortium (mQACC).
Lippa K.A., Aristizabal-Henao J.J., Beger R.D., Bowden J.A., Broeckling C., Beecher C., Clay Davis W., Dunn W.B., Flores R., Goodacre R., Gouveia G.J., Harms A.C., Hartung T., Jones C.M., Lewis M.R., Ntai I., Percy A.J., Raftery D., Schock T.B., Sun J., Theodoridis G., Tayyari F., Torta F., Ulmer C.Z., Wilson I., and Ubhi B.K.
Metabolomics. 2022, 18(4):24. PMID: 35397018.

Emerging Technologies and Their Impact on Regulatory Science.
Anklam E., Bahl M.I., Ball R., Beger R.D., Cohen J., Fitzpatrick S., Girard P., Halamoda-Kenzaoui B., Hinton D., Hirose A., Hoeveler A., Honma M., Hugas M., Ishida S., Kass G.E., Kojima H., Krefting I., Liachenko S., Liu Y., Masters S., Marx U., McCarthy T., Mercer T., Patri A., Pelaez C., Pirmohamed M., Platz S., Ribeiro A.J., Rodricks J.V., Rusyn I., Salek R.M., Schoonjans R., Silva P., Svendsen C.N., Sumner S., Sung K., Tagle D., Tong L., Tong W., Eijnden-van-Raaij J.V.D., Vary N., Wang T., Waterton J., Wang M., Wen H., Wishart D., Yuan Y., and Slikker W. Jr.
Exp Biol Med (Maywood). 2022, 247(1):1-75. PMID: 34783606.

Serum Metabolite Profiles Predict Outcomes in Critically Ill Patients Receiving Renal Replacement Therapy.
Sun J., Cao Z., Schnackenberg L., Pence L., Yu L.R., Choudhury D., Palevsky P.M., Portilla D., and Beger R.D.
J Chromatogr B Analyt Technol Biomed Life Sci. 2021, 1187:123024. PMID: 34815179.

Discovery of Novel Proteomic Biomarkers for the Prediction of Kidney Recovery from Dialysis-Dependent AKI Patients.
Daniels J.R., Ma J.Z., Cao Z., Beger R.D., Sun J., Schnackenberg L., Pence L., Choudhury D., Palevsky P.M., Portilla D., and Yu L.R.
Kidney360. 2021, 2(11):1716-1727. PMID: 34913041.

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. PMID: 34514887.

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. PMID: 34333066.

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., and Vuckovic D.; Metabolomics Quality Assurance, Quality Control Consortium (mQACC).
Metabolomics. 2020, 16(10):113. PMID: 33044703.

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. 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. PMID: 32107589.

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

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. PMID: 31442052.

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. 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. 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. 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. PMID: 30197987.

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., and Kaddurah-Daouk R.; for “Precision Medicine and Pharmacometabolomics Task Group”-Metabolomics Society Initiative.
Metabolomics. 2016, 12(10):149. 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. PMID: 25983262.

A Review of Applications of Metabolomics in Cancer.
Beger R.D.
Metabolites. 2013, 3(3):552-74. PMID: 24958139