Publications | Mirza Group

Selected Publications

Uyar, Denise; Huang, Yi-Wen; Chesnik, Marla A.; Doan, Ninh B.; Mirza, Shama M. 2021. "Comprehensive serum proteomic analysis in early endometrial cancer." Journal of Proteomics vol 234, no. 104099. https://doi.org/10.1016/j.jprot.2020.104099

Rajaratnam, Vilashini †; Islam, Mohammad M. †; Yang, Maixee; Slaby, Rachel; Ramirez, Hilda M.; Mirza, Shama P. 2020. "Glioblastoma: Pathogenesis and Current Status of Chemotherapy and Other Novel Treatments." Cancers 12, no. 4: 937. https://doi.org/10.3390/cancers12040937 (First co-authors †)

L C Stetson, Quinn T Ostrom, Daniela Schlatzer, Peter Liao, Karen Devine, Kristin Waite, Marta E Couce, Peggy L R Harris, Amber Kerstetter-Fogle, Michael E Berens, Andrew E Sloan, Mohammad M Islam, Vilashini Rajaratnam, Shama P Mirza, Mark R Chance, Jill S Barnholtz-Sloan, Proteins inform survival-based differences in patients with glioblastoma, Neuro-Oncology Advances, Volume 2, Issue 1, January-December 2020, vdaa039, https://doi.org/10.1093/noajnl/vdaa039

Ciezki, Kristin., Wesener, Shane., Jaber, Danny., Mirza, Shama., and Forst, Steven. "ngrA-dependent natural products are required for interspecies competition and virulence in the insect pathogenic bacterium Xenorhabdus szentirmaii." Microbiology. 2019 April 2. doi:10.1099/mic.0.000793

Zhang, Qi., Lee, Sang Beom., Chen, Xu., Stevenson, Morgan E., Pan, Jing., Xiong, Donghai., Zhou, Yu., Miller, Mark S., Lubet, Ronald A., Wang, Yian., Mirza, Shama P., and You, Ming. "Optimized Bexarotene Aerosol Formulation Inhibits Major Subtypes of Lung Cancer in Mice."Nano lett.,2019 March 15, 19(4). pp 2231-2242. doi:10.1021/acs.nanolett.8b04309

Labbe, Benjamin D., Hall, Cherisse L., Kellogg, Stephanie L., Chen, Yao., Koehn, Olivia., Pickrum, Adam M., Mirza, Shama P., and Kristich, Christopher J."Reciprocal Regulation of PASTA Kinase Signaling by Differential Modification."Journal of Bacteriology. 2019 March 11. doi:10.1128/JB.00016-19

Doan, Ninh B., Nguyen, Ha S., Alhajala, Hisham S., Jaber, B., Al-Gizawiy, Mona M., Ahn, EE., Mueller, Wade M., Chitambar, Christopher R., Mirza, Shama P., and Schmainda, Kathleen M. "Identification of radiation responsive genes and transcriptome profiling via complete RNA sequencing in a stable radioresistant U87 glioblastoma model."Oncotarget. 2018 May 4;9(34):23532-23542

Yacout,S M., McIlwain, K L., Mirza, S P., Gaillard, E R.,"Characterization of Retinal Pigment Epithelial Melanin and Degraded Synthetic Melanin Using Mass Spectrometry and In Vitro Biochemical Diagnostics."Photochem Photobiol. 2018 May 12

Doan, N B., Alhajala, H., Al-Gizawiy, M M., Mueller, W M., Rand, S D., Connelly, J M., Cochran, E J., Chitambar, C R., Clark, P., Kuo, J., Schmainda, K M., Mirza, S P. "Acid ceramidase and its inhibitors: a de novo drug target and a new class of drugs for killing glioblastoma cancer stem cells with high efficiency."Oncotarget. 2017 Nov 7;8(68):112662-112674

Doan, Ninh B., Nguyen, Ha S., Al-Gizawiy, Mona M., Mueller, Wade M.,Sabbadini, Roger., Rand, Scott D., Connelly, Jennifer M., Chitambar, Christopher R., Schmainda, Kathleen M., and Mirza, Shama P. "Acid ceramidase confers radioresistance to glioblastoma cells."Oncol Rep. 2017 Oct;38(4):1932-1940

Doan, Ninh B., Nguyen, Ha S., Montoure, Andrew, Al-Gizawiy, Mona M., Mueller, Wade M., Kurpad, Shekar, Rand, Scott D., Connelly, Jennifer M., Chitambar, Christopher R., Schmainda, Kathleen M., and Mirza, Shama P. “Acid ceramidase is a novel drug target for pediatric brain tumors.” Oncotarget 8.15 (2017): 24753.

Raphael, Roseanne, Purushotham, Diana, Gastonguay, Courtney, Chesnik, Marla A., Kwok, Wai-Meng, Wu, Hsiang-En, Shah, Sanjiv J., Mirza, Shama P., and Strande, Jennifer L. “Combining patient proteomics and in vitro cardiomyocyte phenotype testing to identify potential mediators of heart failure with preserved ejection fraction.” Journal of translational medicine 14.1 (2016): 18.

Cossette, Stephanie M., Bhute, Vijesh J., Bao, Xiaoping, Harmann, Leanne M., Horswill, Mark A., Sinha, Indranil, Gastonguay, Adam, Pooya, Shabnam, Bordas, Michelle, Kumar, Suresh N., and others, . “Sucrose Non-Fermenting Related Kinase Enzyme Mediated Rho-Associated Kinase Signaling is Responsible for Cardiac Function.” Circulation: Cardiovascular Genetics. (2016): CIRCGENETICSâ116.

Qi, Xiaomei, Xie, Congying, Hou, Songwang, Li, Gang, Yin, Ning, Dong, Lei, Lepp, Adrienne, Chesnik, Marla A., Mirza, Shama P., Szabo, Aniko, and others, . “Identification of a ternary protein-complex as a therapeutic target for K-Ras-dependent colon cancer.” Oncotarget 5.12 (2014): 4269.

Alexanian, Anna, Miller, Bradley, Chesnik, Marla, Mirza, Shama, and Sorokin, Andrey. “Post-translational regulation of COX2 activity by FYN in prostate cancer cells.” Oncotarget 5.12 (2014): 4232â4243.

Heroux, Maxime S., Chesnik, Marla A., Halligan, Brian D., Al-Gizawiy, Mona, Connelly, Jennifer M., Mueller, Wade M., Rand, Scott D., Cochran, Elizabeth J., LaViolette, Peter S., Malkin, Mark G., Schmainda, Kathleen, and Shama, Mirza P. “Comprehensive characterization of glioblastoma tumor tissues for biomarker identification using mass spectrometry-based label-free quantitative proteomics.” Physiological genomics 46.13 (2014): 467â481.

Mesrobian, Hrair-George O., Kryger, John V., Groth, Travis W., Fiscus, Gabriel E., and Mirza, Shama P. “Urinary proteome analysis in patients with stable SFU grade 4 ureteropelvic junction obstruction differs from normal.” Urology 82.3 (2013): 745âe1.

Bigley, Tarin M., Reitsma, Justin M., Mirza, Shama P., and Terhune, Scott S. “Human cytomegalovirus pUL97 regulates the viral major immediate early promoter by phosphorylation-mediated disruption of histone deacetylase 1 binding.” Journal of virology 87.13 (2013): 7393â7408.

Mirza, Shama P. “Quantitative mass spectrometry-based approaches in cardiovascular research.” Circulation: Cardiovascular Genetics 5.4 (2012): 477â477.

Hou, Songwang, Padmanaban, Suresh, Qi, Xiaomei, Lepp, Adrienne, Mirza, Shama P., and Chen, Guan. “p38γ MAPK signals through phosphorylating its phosphatase PTPH1 in regulating Ras oncogenesis and stress response.” Journal of Biological Chemistry. (2012): jbcâM111.

Mesrobian, Hrair-George O., and Mirza, Shama P. “Hydronephrosis: a view from the inside.” Pediatric clinics of North America 59.4 (2012): 839â851.

Chesnik, Marla, Halligan, Brian, Olivier, Michael, and Mirza, Shama P. “Sequential abundant ion fragmentation analysis (SAIFA): An alternative approach for phosphopeptide identification using an ion trap mass spectrometer.” Analytical biochemistry 418.2 (2011): 197â203.

Narayan, Malathi, Mirza, Shama P., and Twining, Sally S. “Identification of phosphorylation sites on extracellular corneal epithelial cell maspin.” Proteomics 11.8 (2011): 1382â1390.

Wu, Cheng-Hsien, Chen, Siyuan, Shortreed, Michael R., Kreitinger, Gloria M., Yuan, Yuan, Frey, Brian L., Zhang, Yi, Mirza, Shama, Cirillo, Lisa A., Olivier, Michael, and others, . “Sequence-specific capture of protein-DNA complexes for mass spectrometric protein identification.” PloS one 6.10 (2011): e26217.

Collins, Lisamarie A., Mirza, Shama P., Kissebah, Ahmed H., and Olivier, Michael. “Integrated approach for the comprehensive characterization of lipoproteins from human plasma using FPLC and nano-HPLC-tandem mass spectrometry.” Physiological genomics 40.3 (2010): 208â215.

Narayan, M, Mirza, SP, and Twining, SS. “Differential Phosphorylation of Intracellular and Secreted Corneal Epithelial Cell Maspin.” Investigative Ophthalmology & Visual Science 51.13 (2010): 1972â1972.

Narayan, M, Mirza, SP, and Twining, SS. “Identification of Phosphorylation Sites on Maspin Secreted by Corneal Epithelial Cells using Tandem Mass Spectrometry.” Investigative Ophthalmology & Visual Science 50.13 (2009): 4603â4603.

Mirza, Shama P., and Olivier, Michael. “Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry.” Physiological genomics 33.1 (2008): 3â11.

Mirza, Shama P., Greene, Andrew S., and Olivier, Michael. “18O labeling over a coffee break: a rapid strategy for quantitative proteomics.” Journal of proteome research 7.7 (2008): 3042â3048.

Lee, Ji E., Mirza, Shama P., Didier, Daniela N., Scalf, Mark, Olivier, Michael, Greene, Andrew S., and Smith, Lloyd M. “Identification of Cell Surface Markers to Differentiate Rat Endothelial and Fibroblast Cells Using Lectin Arrays and LC- ESI-MS/MS.” Analytical chemistry 80.21 (2008): 8269â8275.

Halligan, Brian D., Mirza, Shama P., Pellitteri-Hahn, Molly C., Olivier, Michael, and Greene, Andrew S. “Visualizing quantitative proteomics datasets using treemaps.” Information Visualization, 2007. IV’07. 11th International Conference. (2007): 527â534.

Mirza, Shama P., Halligan, Brian D., Greene, Andrew S., and Olivier, Michael. “Improved method for the analysis of membrane proteins by mass spectrometry.” Physiological genomics 30.1 (2007): 89â94.

Kim, Sung C., Chen, Yue, Mirza, Shama, Xu, Yingda, Lee, Jaeick, Liu, Pingsheng, and Zhao, Yingming. “A clean, more efficient method for in-solution digestion of protein mixtures without detergent or urea.” Journal of proteome research 5.12 (2006): 3446â3452.

Pellitteri-Hahn, MC, Warren, MC, Didier, DN, Winkler, EL, Mirza, SP, Greene, AS, and Olivier, M. “Improved mass spectrometric proteomic profiling of the secretome of rat vascular endothelial cells.” Journal of proteome research 5.10 (2006): 2861â2864.

Prabhakar, S, Radha Kishan, M, Mirza, SP, Raghavan, KV, and Vairamani, M. “Mass spectral study of meso-alkyl and meso-cycloalkyl calix (4) pyrroles under electron impact conditions.” Rapid communications in mass spectrometry 18.18 (2004): 2077â2086.

Mirza, Shama P., Raju, N P., and Vairamani, M. “Estimation of the proton affinity values of fifteen matrix-assisted laser desorption/ionization matrices under electrospray ionization conditions using the kinetic method.” Journal of the American Society for Mass Spectrometry 15.3 (2004): 431â435.

Mirza, Shama P., Raju, N P., Madhavendra, SS, and Vairamani, M. “5-Amino-2-mercapto-1, 3, 4-thiadiazole: a new matrix for the efficient matrix-assisted laser desorption/ionization of neutral carbohydrates.” Rapid communications in mass spectrometry 18.14 (2004): 1666â1674.

Premsingh, Sundarsingh, Venkataramanan, Natarajan S., Rajagopal, Seenivasan, Mirza, Shama P., Vairamani, Mariappanadar, Rao, P S., and Velavan, K. “Electron transfer reaction of oxo (salen) chromium (V) ion with anilines.” Inorganic chemistry 43.18 (2004): 5744â5753.

Mirza, SP, Krishna, P, Prabhakar, S, Vairamani, M, Giblin, D, and Gross, Michael L. “The kinetic method reveals secondary deuterium isotope effects on the proton affinity and gas-phase basicity of glycine and alanine methyl esters.” International Journal of Mass Spectrometry 230.2 (2003): 175â183.

Reddy, T J., Mirza, Shama P., Saradhi, UVR, Rao, V J., and Vairamani, M. “Mass spectral studies of N, N-dialkylaminoethanols.” Rapid communications in mass spectrometry 17.7 (2003): 746â752.

Prabhakar, S, Kar, Paramita, Mirza, SP, Lakshmi, VVS, Nagaiah, K, and Vairamani, M. “Mass spectral study of O-and S-aryl dimethylthiocarbamates under electron impact conditions: Newman-Kwart rearrangement in the gas phase.” Rapid Communications in Mass Spectrometry15.22 (2001): 2127â2134.

Raju, N P., Mirza, Shama P., Vairamani, M, Ramulu, A Raghu, , and Pardhasaradhi, M. “5-Ethyl-2-mercaptothiazole as matrix for matrix-assisted laser desorption/ionization of a broad spectrum of analytes in positive and negative ion mode.” Rapid Communications in Mass Spectrometry15.19 (2001): 1879â1884.

Mirza, Shama P., Prabhakar, S, and Vairamani, M. “Estimation of proton affinity of proline and tryptophan under electrospray ionization conditions using the extended kinetic method.” Rapid Communications in Mass Spectrometry 15.12 (2001): 957â962.

Prabhakar, S, Mirza, SP, Kundu, A, Roy, Sujit, and Vairamani, M. “Claisen rearrangement of allyl phenyl ether and its sulfur and selenium analogues on electron impact.” Rapid Communications in Mass Spectrometry 14.13 (2000): 1116â1122.