Frank Witzmann, Ph.D.
Full Member of Graduate Faculty
Department of Cellular & Integrative Physiology
Indiana University School of Medicine
635 Barnhill Drive, Room 362A
Indianapolis, Indiana 46202-2111
E-mail: fwitzman @ iupui.edu
Education / Training
1976, B.A., Defiance College, Defiance, Ohio
1978, M.S. in Biology (Human Bioenergetics), Ball State University, Muncie, Indiana
1981, Ph.D. in Biology (Human Physiology), Marquette University, Milwaukee, Wisconsin
Research Biobraphy Summary
Since the mid-1980’s (well before the term proteomics was coined) and throughout my ensuing career, I have applied global protein expression analyses in a variety of research paradigms. I currently direct the use of mass spectrometry-based proteomic approaches in a broad range of collaborative projects where both narrowly focused and comprehensive protein expression profiling and post-translational modification characterization are used to investigate the mechanistic molecular underpinnings of chemical toxicity, renal pathologies, cardiovascular disease, and biomarker discovery in a variety of disease conditions. I also serve as Scientific Director of the Indiana University School of Medicine’s Proteomics Core Facility and my laboratory serves as a proteomics resource for the NIEHS NanoGO and NCNHIR Consortia. I have broad experience in collaborative scientific research and my work is internationally recognized. I will apply my expertise to this Program Project Grant by leading the Proteomic Core component in addressing our overall objective to identify protein molecules that foster and/or result from stone formation. I will coordinate the analysis and bioinformatic interpretation of the proteome of tissues at the plaque-stone interface, plug-stone interface, and interstitium, as well as bulk stone and urine proteomes across the spectrum of highly defined clinical phenotypes and corresponding normal human controls.
In summary, I have a demonstrated record of successful and productive research in broadly applied proteomic applications, specifically in collaborative settings. My expertise and considerable experience enable me to ensure that the various proteomic elements of any project are carried out successfully.
Contribution to Science
Earlier in my career my contributions were related to the technical development and application of large-scale, high-throughput two-dimensional electrophoresis. For many years, as a PI of Department of Defense grants related to Air Force toxicology interests and collaboratively, I applied this technology to both in vivo and in vitro models of toxicity testing and am recognized as one of those that pioneered this application in environmental toxicology.
- Witzmann, F.A., S.A. Bale, S.A. London. (1990). Cellular toxicity as determined by two dimensional polyacrylamide gel electrophoresis. In Vitro Toxicol. 3, 205-218.
- Witzmann, F.A., B.M. Jarnot, D.N. Parker, J.W. Clack. (1994). Modification of hepatic immunoglobulin heavy chain binding protein (BiP/Grp78) following exposure to structurally diverse peroxisome proliferators. Fund. Appl. Toxicol. 23, 1-8. (PMID7958552)
- Witzmann, F.A., C.D. Fultz, J.C. Lipscomb. (1996). Toxicant-induced alterations in two-dimensional electrophoretic patterns of hepatic and renal stress proteins. Electrophoresis 17, 198-202. (PMID8907540)
- Witzmann, F.A., C.D. Fultz, J.F. Wyman. (1997). Two-dimensional electrophoresis of precision-cut testis slices: toxicologic application. Electrophoresis 18, 642-646. (PMID9150954)
To improve the utility of proteomics technologies, I contributed several novel technical methods that have advanced specific aspects of the electrophoretic gel-based proteomic approach.
- Witzmann, F.A., B.M. Jarnot, D.N. Parker. (1991). Dodecyl maltoside detergent improves resolution of hepatic membrane proteins in 2D gels. Electrophoresis 12, 687-688. (PMID1752256)
- Anderson, N.L., R. Esquer-Blasco, J.P. Hofmann, L. Meheus, J. Raymakers, S. Steiner, F.A. Witzmann, N.G. Anderson. (1995). An updated two-dimensional gel database of rat liver proteins useful in gene regulation and drug effects studies. Electrophoresis 16, 1977-1981. (PMID8586073)
- Fultz, C.D., F.A. Witzmann. (1997). Locating Western blotted and immunostained proteins within complex two-dimensional patterns. Anal. Biochem. 251, 288-291. (PMID9299028)
- Bai, F., S. Liu, F.A. Witzmann. (2005). A de-streaking method for two-dimensional electrophoresis using the reducing agent tris(2-carboxyethyl)-phosphine hydrochloride and alkylating agent vinylpyridine. Proteomics 5, 2043-2047. (PMID15846837)
- Richardson, M.R., S. Liu, H.N. Ringham, V. Chan, F.A. Witzmann. (2008). Sample complexity reduction for 2-DE using solution isoelectric focusing (sIEF) prefractionation. Electrophoresis 29, 2637–2644. (PMC2853967)
With advances in both mass spectrometric instrumentation and techniques, along with the inherent limitations of gel-based proteomics, my laboratory became involved in the development and application of label-free quantitative mass spectrometry (LFQMS) as a more powerful means to accomplish our overall goal of comprehensive protein profiling. This led to the development of the IdentiQuantXL™ LFQMS platform (Lai et al. 2011 below) along with sample preparation techniques, and their successful application in studying human disease and the effects of exposure to nanomaterials and ionizing radiation.
- Lai, X., S. Liangpunsakul, D.W. Crabb S., H.N. Ringham, F.A. Witzmann. (2009). A proteomic workflow for discovery of serum carrier protein-bound biomarker candidates of alcohol abuse using liquid chromatography - tandem mass spectrometry. Electrophoresis 30, 2207–2214. (PMC2756771)
- Lai, X., L. Wang, H. Tang, F.A. Witzmann. (2011). A novel alignment method and multiple filters for exclusion of unqualified peptides to enhance label-free quantification using peptide intensity in LC-MS/MS. J. Proteom. Res. 10, 4799-4812. (PMC3216047)
- Blazer-Yost, B.L., A. Banga, A. Amos, E. Chernoff, X. Lai, C. Li, S. Mitra, F.A. Witzmann. (2011). Effect of carbon nanoparticles on renal epithelial cell structure, barrier function, and protein expression. Nanotoxicol. 5, 354-371. (PMC3201737)
- Owen, M.K., F.A. Witzmann, M.L. McKenney, X. Lai, Z.C. Berwick, S.P. Moberly, M. Alloosh, M. Sturek, J.D. Tune. (2013). Perivascular adipose tissue potentiates contraction of coronary vascular smooth muscle: Influence of obesity. Circulation 128, 9-18. (PMC3755741)
- Lai, X., M. Agarwal, Y.M. Lvov, C. Pachpande, K. Varahramyan, F.A. Witzmann. (2013). Proteomic profiling of halloysite clay nanotube exposure in intestinal cell co-culture. J. Appl. Toxicol. 33, 1316–1329. (PMC3789846)
- Rithidech, K., M. Tungjai, W. Jangiam, L. Honikel, C. Gordon, X. Lai, F.A. Witzmann. (2015). Proteomic profiling of hematopoietic stem/progenitor cells after a whole body exposure of CBA/CaJ mice to titanium (48Ti) ions. Proteomes 3, 132-159. doi:10.3390/proteomes3030132
- Rosenfeld, C., M.O. Price, X. Lai, F.A. Witzmann, F.W. Price Jr. (2015). Distinctive and pervasive alterations in aqueous humor protein composition following different types of glaucoma surgery. Molec. Vision 21, 911-918. (PMC4548793)
- Wagner, M.C., S.B. Campos-Bilderback, M. Chowdhury, B. Flores, X. Lai, J. Myslinski, S. Pandit, R.M. Sandoval, S.E. Wean, Y. Wei, L.M. Satlin, R.C. Wiggins, F.A. Witzmann, B.A. Molitoris. (2016). Proximal tubules have the capacity to regulate uptake of albumin. J. Amer. Soc. Nephrol. 27, 482-494. (PMC4731114)
- Witzmann, F.A., A.P. Evan, F.L. Coe, E.M. Worcester, J.E. Lingeman, J.C. Williams Jr. (2016). Label-free proteomic methodology for the analysis of human kidney stone matrix composition. Proteome Sci. 14, 1-10. (PMC4769560)
I have collaboratively applied gel-based and mass spec-based approaches along with bioinformatic analyses, biomarker discovery and/or protein post-translational modification analysis in a variety of other research paradigms.
- Hopper R.K., S. Carroll, A.M. Aponte, D.T. Johnson, S. French, R.F. Shen, F.A. Witzmann, R.A. Harris, R.S. Balaban. (2006). Mitochondrial matrix phosphoproteome: effect of extra mitochondrial calcium. Biochemistry 45, 2524-2536. (PMC1415274)
- Li, J., S. Abraham, F.A. Witzmann, L. Cheng, M. Koch, J. Xie, S.I. Mohammed. (2008). Proteomic-based approach for biomarker discovery in early detection of bladder cancer. Proteomics Clin. Appl. 2, 78-89. (PMID21136781)
- Mason, S.B., X. Lai, R.L. Bacallao, B.L. Blazer-Yost, V.H Gattone II, Wang, K.C., F.A. Witzmann. (2009). The biomarker enriched proteome of adult polycystic kidney disease (ADPKD) cyst fluid. Proteomics Clin. Appl. 3, 1247–1250. (PMC2880522)
- Li, P., X Lai, F.A. Witzmann, B.L. Blazer-Yost. (2013). Bioinformatic analysis of differential protein expression in Calu-3 cells exposed to carbon nanotubes. Proteomes 1, 219-239. (PMC4148817)
- Tilton, S.C., N.J. Karin, A. Tolic, Y. Xie, X. Lai, R.F. Hamilton Jr., K.M. Waters, A. Holian, F.A. Witzmann, G. Orr. (2014). Three human cell types respond to multi-walled carbon nanotubes and titanium dioxide nanobelts with cell-specific transcriptomic and proteomic expression patterns. Nanotoxicol. 8, 533-548. (PMC4226242)
- Lai, X., S. Liangpunsakul, K. Li, F.A. Witzmann. (2015). Proteomic profiling of human sera for discovery of potential biomarkers to monitor abstinence from alcohol abuse. Electrophoresis 36, 556-63. (PMC4492280)
- Waning, D., K. Mohammad , S. Reiken , W. Xie, D. Andersson, S. John, A. Chiechi, L. Wright, A. Umanskaya, M. Niewolna, T. Trivedi, S. Charkhzarrin, P. Khatiwada, A. Wronska, A. Haynes, S. Benassi, F. Witzmann, G. Roodman, A. Marks. (2015). TGFβ mediates muscle weakness associated with bone metastases. Nature Med. 21, 1262-1271. (PMC4636436)
Complete list of 134 PubMed citations related to the topics above are in MyBibliography: http://www.ncbi.nlm.nih.gov/sites/myncbi/1VWJ6gjPucf/bibliography/40432793/public/?sort=date&direction=descending
My research involves the application of proteomic techniques to the detection and analysis of protein expression in a variety of research paradigms. Specific projects include 1) the analysis of differential protein expression by cells and tissues exposed to Engineered Nanomaterials (ENM) in vivo or in vitro, 2) the study of alcohol effects on protein expression in various brain cell types and regions, 3) the characterization of serum proteins associated with alcohol abuse, and 4) assessment of altered protein expression in Polycystic Kidney Disease (PKD) and Acute kidney Injury (AKI).
In conducting these studies, we apply complementary proteomic technologies to address the unique analytical demands associated with each project. We use solution isoelectric focusing, large format one- and two-dimensional gel electrophoretic separations and image analysis coupled to tandem mass spectrometry (LC-MS/MS) to analyze and identify differential protein expression.
As a gel-free alternative, we have developed a label-free, quantitative mass spectrometric platform that exploits both single- and multi-dimensional liquid chromatographic approaches and delivers a global analysis of differential protein expression in complex mixtures. Using both statistical, bioinformatic, and pathway analysis strategies, alterations in either the quantitative expression or post-translational modification of individual proteins or altered protein expression “patterns” from tissues, cells and cell fractions detected by these approaches is assessed. Protein expression information obtained in this way can be used as indicators or “molecular biomarkers” of primary or secondary cellular effects, or used to better understand the molecular mechanisms, as represented by the altered proteome, that trigger altered or impaired physiological function, cellular injury, and disease.
National Institutes of Health, “Proximal Tubule Albumin Transport in Disease States” Co-investigator, 10/01/11 – 09/30/16, RO1DK091623 (Molitoris)
National Institutes of Health, “Nanoparticle Effects on Epithelial Cell Protein Expression and Function” Frank A. Witzmann, Principal Investigator. 06/01/2008 – 04/30/2013. R01GM085218-01