Richard R. Drake, PhD
Director, MUSC Proteomics Center
SmartState Endowed Chair of Proteomics
1990 Ph.D., University of Kentucky
Office: CRI 305
MALDI Imaging Mass Spectrometry and Glycoprotein Biomarkers of Cancer
In my laboratory, we are applying a variety of mass spectrometry-based approaches to identify molecular diagnostic and prognostic biomarkers of cancer, using the resources within the MUSC Proteomics Center and Mass Spectrometry Facility. Our emphasis is on the application of these resources for analysis of clinically derived tissues, fluids and exosomes to develop proteomic-based or small molecule diagnostic assays, with a particular focus on glycosylation and its role in disease. A new state-of-the-art, translational MALDI Imaging Research Center has been created. The facility is anchored by a dual-source Bruker Daltonic 7T Solarix FTICR mass spectrometer, two Bruker AutoFlex III MALDI instruments and an HTX sprayer. These are complemented by a Thermo Orbitrap Elite mass spectrometer and an Agilent Triversa Nanomate with LESA-MS for direct analysis of post-translational modifications to proteins. This instrumentation is being applied to multiple translational cancer research projects within my laboratory, as well as collaborations within the department and throughout the NCI-designated Hollings Cancer Center . These projects combine the capabilities of the MUSC Proteomics Center with clinical research, lipidomic, biorepository and molecular pathology resources, as well as strong collaborations with other Center researchers, Peggi Angel, Anand Mehta and Lauren Ball. Current types of cancer being targeted include prostate, breast, liver, colon, kidney, lung and pancreatic cancers. The major research areas of the Drake laboratory are summarized as follows.
MALDI Mass Spectrometry Tissue Imaging of Glycans, Lipids, Proteins and Drug Metabolites - MALDI imaging mass spectrometry (MALDI-IMS) is an established method used primarily to spatially profile proteins, lipids, drug and small molecule metabolites in tissues. Using the resources of the MUSC Proteomics Center and MALDI Imaging Research Center, our group has recently developed a glycobiology approach using on-tissue peptide N-glycanase F (PNGaseF) digestion to directly profile released N-linked glycans in their local microenvironment. This method, co-developed with another MUSC investigator, Anand Mehta, has recently been optimized for use with formalin-fixed paraffin-embedded tissues obtained directly from pathology collections. The approach is being applied to map the two-dimensional N-linked glycomes associated with prostate, breast, pancreatic, liver, colon and lung cancers. Several prostate cancer tissue glycome analyses are ongoing with multiple MUSC investigators, including Jennifer Wu, Michael Lilly, Sebastiano Gattoni-Celli, Steve Savage and Chanita Hughes-Halbert. A new collaboration with Elizabeth Yeh at MUSC is focused on identifying glycan biomarkers of breast cancer drug resistance and sensitivity. Mapping of the liver cancer glycome is being done in collaboration with Anand Mehta, and multiple pancreatic cancer glycome projects are ongoing with Brian Haab (Van Andel Research Institute). The approach also works well with tissue microarrays representing prostate, lung, breast and pancreatic cancers in efforts to identify glycan biomarker panels indicative of disease state. A longer term goal is to use the N-linked glycome maps to link these glycans back to their original glycoprotein carriers, which represents a second tier of biomarker targets. New publications with collaborators (Manfred Wuhrer and Liam McDonnell) highlight the feasibility of this approach. Recent NIH funding will support the expansion of these glycomic approaches to develop new MALDI imaging methods to tissue profile O-glycans and glycosaminoglycans.
Another research emphasis is the development of methods to spatially profile bioactive ceramide, sphingosine and glycolipid specie distribution in tissues of clinical interest, supported in part by an NCI program project with Besim Ogretmen and other lipidomic researchers at MUSC. A reference database of ceramide and glycosphingolipid masses for use in tissue imaging analysis has been created using tissues derived from lysosomal storage disease models (in collaboration with Jeffrey Medin, Medical College of Wisconsin). Drug uptake and metabolism in tissues derived from pre-clinical model systems is also ongoing, working in conjunction with researchers in the Hollings Cancer Center and the Developmental Cancer Therapeutics program. The method has been applied to multiple frozen tissues types, with emphasis on human lung, renal, prostate and pancreatic cancer tissues matched for tumor and non-tumor regions, and tissues from different therapeutic mouse xenograft models of cancer. For clear cell renal cancer and lung tissues, defining biomolecules that are unique to the non-tumor and tumor margin interface are being assessed. Current MALDI imaging analysis of these margin regions have identified multiple glycan, phospholipid, ceramide and protein species differentially expressed relative to non-tumor and tumor regions. Linking these biomolecular differences to known mediators of epithelial-to-mesenchymal transitions, pathology correlates and tumor metastasis are ongoing.
Identification of Prostate and Lung Cancer Glycoprotein Biomarkers of Aggressive Disease - Our overall research goal is the identification of glycoprotein biomarkers that will improve clinical decision-making in the detection and management of prostate and lung cancers, particularly for the most lethal and metastatic types that require aggressive treatment. My laboratory has been part of a systemic effort to characterize and identify potential biomarker targets in proximal fluids of the prostate, including direct prostatic fluids obtained just prior to prostatectomy, and expressed prostatic secretions in urine obtained in the urology clinic following digital rectal exam. Our recent publications cumulatively describe the identification of over 1100 proteins identified in post-DRE expressed prostatic secretions in urine (EPS-urine) and prostatic fluids termed direct EPS obtained at the time of prostatectomy. Lastly, we have completed the proteome analysis of exosomes from pooled EPS samples from benign, indolent and aggressive cancers. These lists are being combined with prostate tissue-based glycomic studies that are ongoing with different collaborators, Jennifer Wu at MUSC, Joseph Ippolito at Washington University, Donna Peehl at Stanford University and biotech collaborators at Ymir Genomics. For lung cancers, NSCLC tissue and bronchoalveolar lavage samples were obtained from the Lung Cancer Biospecimen Resource Network and in collaboration with Dr. Chad Denlinger at MUSC. New HCD-PD-ETD workflows for direct analysis of EPS and bronchoalveolar lavage fluids, exosomes and tissue glycopeptides associated with disease status are in progress. Corresponding glycomic and lipidomic analyses of the same fluids and samples are also in progress.
A complementary biomarker discovery approach is being done using metabolic labeling with sugar-azides and alkyne-bead click chemistry to capture secreted and cell surface glycoproteins in human-derived prostate, pancreatic, breast and lung cancer cell line models. A current emphasis is with cell lines associated with the epithelial-to-mesenchymal cell transition. The current workflow uses N-acetylgalactosamine (GalNAc-Az) or sialic acid (ManNAc-Az) analogs for metabolic labeling, cell lysis or concentration of conditioned media, and Click chemistry conjugation to alkyne beads. The bead-bound azide-modified glycoproteins can be extensively washed prior to direct protease digestion on the beads, which significantly reduces the background of non-specific, unmodified proteins identified at the mass spectrometry stage. Captured glycoproteins are digested directly from the beads and the resulting peptides analyzed on the Orbitrap Elite for protein identification and development of HCD-ETD glycopeptide analysis workflows. The bound peptides can also be released by PNGaseF to identify specific sites of glycosylation. Bioinformatic pathway analysis is then done to link the proteins to molecular function and cancer biology. This biomarker selection step is being coupled with the EPS protein lists, and more recently bronchoalveolar lavage fluids. The glycoproteins identified are being linked with glycoproteins identified in proximal fluids and tissues derived from the same cancer types as part of a further biomarker candidate verification strategy.
Recent Publications | Additional Publications
1. Powers, T.W. Holst, S., Wuhrer, M.,Mehta, A.S., and Drake, R.R. (2015) Two-Dimensional N-Glycan Distribution Mapping of Hepatocellular Carcinoma Tissues by MALDI-Imaging Mass Spectrometry. Biomolecules, 7, 2611-2619.
2. Neely, B.A., Wilkins, C.E., Marlow, L.A., Malyarenko, D., Kim, Y., Ignatchenko, A., Sasinowska, H., Sasinowski, M., Nyalwidhe, J.O., Kislinger, T., Copland, J.A., and Drake, R.R. (2016) Proteotranscriptomic Analysis Reveals Stage Specific Changes in the Molecular Landscape of Clear-Cell Renal Cell Carcinoma. PLoS One. 11, e0154074.
3. Kim, Y., Jeon, J., Mejia, S., Yao, C.Q., Ignatchenko, V., Nyalwidhe, J.O., Gramolini, A.O., Lance, R.S, Troyer, D.A., Drake, R.R., Boutros, P.C., Semmes, O.J., and Kislinger T. (2016) Targeted proteomics identifies liquid-biopsy signatures for extracapsular prostate cancer. Nature Comm.. 7,11906.
4. Heijs, B., Holst, S., Briaire-de Bruijn, I.H., van Pelt, G.W., de Ru, A.H., van Veelen, P.A., Drake, R.R., Mehta, A.S., Mesker, W.E., Tollenaar, R.A., Bovée, J.V., Wuhrer, M., and McDonnell, L.A. (2016) Multimodal Mass Spectrometry Imaging of N-Glycans and Proteins from the Same Tissue Section. Anal Chem., 88, 7745-7753.
5. Holst, S., Heijs, B., de Haan, N., van Zeijl, R.J., Briaire-de Bruijn, I.H., van Pelt, G.W., Mehta, A.S., Angel, P.M., Mesker, W.E., Tollenaar, R.A., Drake, R.R., Bovee, J.V., McDonnell, L.A.,,and Wuhrer, M. (2016) Linkage-specific in-situ sialic acid derivatization for N-glycan mass spectrometry imaging of FFPE tissues. Anal Chem, 88, 5904-5913.
6. Drake R.R., Jones, E.E., Powers, T.W., and Nyalwidhe, J.O. (2015) Altered glycosylation in prostate cancer. Adv Cancer Res., 126, 345-382.
7. Powers, T.W., Neely, B.A., Shao, Y., Tang, H., Troyer, D.A., Mehta, A.S., Haab, B.B., and Drake, R.R. (2014) MALDI Imaging Mass Spectrometry Profiling of N-Glycans in Formalin-Fixed Paraffin Embedded Clinical Tissue Blocks and Tissue Microarrays. PLoS One, 9, e106255.
8. Jones, E.E., Dworski, S., Canals, D., Casas, J., Fabrias, G., Schoenling, D., Levade, T., Denlinger, C., Hannun, Y.A., Medin, J.A., and Drake, R.R. (2014) On-Tissue Localization of Ceramides and other Sphingolipids by MALDI Mass Spectrometry Imaging. Anal. Chem., 86, 8303-8311.
9. Drake, R.R. and Kislinger, T. (2014) The Proteomics of Prostate Cancer Exosomes. Expert Rev. Proteomics, 11, 167-177.
10. Jones, E.E., Powers, T.W., Neely, B.A., Cazares, L.H., Troyer, D.A., Parker, A.S., and Drake, R.R. (2014) MALDI Imaging Mass Spectrometry Profiling of Proteins and Lipids in Clear Cell Renal Cell Carcinoma. Proteomics, 14, 924-935.
11. Powers, T.W., Jones, E.E., Betesh, L.R., Romano, P., Gao, P., Copland, J.A., Mehta, A.S., Drake, R.R. (2013) A MALDI Imaging Mass Spectrometry Workflow for Spatial Profiling Analysis of N-linked Glycan Expression in Tissues. Anal. Chem., 85, 9799-9806.
12. Nyalwidhe, J.O., Betesh, L.R., Powers, T.W., Jones, E.E., White, K.Y., Burch, T.C., Brooks, J., Watson, M.T.,, Lance, R.S., Troyer, D.A., Semmes, O.J., Mehta, A.., Drake, R.R. (2013) Increased bisecting N-acetylglucosamine and decreased branched chain glycans of N-linked glycoproteins in expressed prostatic secretions associated with prostate cancer progression.. Proteomics Clin App., doi: 10.1002/prca.201200134.
13. Roper, S.M., Zemskova, M., Neely, B.A., Martin, A., Gao, P., Jones, E.E., Kraft, A.S., Drake R.R. (2013) Targeted Glycoprotein Enrichment and Identification in Stromal Cell Secretomes using Azido Sugar Metabolic Labeling. Proteomics Clin App., 7, 367-371.
14. Drake R.R., Boggs, S.R., Drake, S.K. (2011) Pathogen identification using mass spectrometry in the clinical microbiology laboratory. J Mass Spectrom., 46, 1223-1232.