Benjamin Garcia – Department of Biochemistry and Molecular Biophysics

Head of Biochemistry and Molecular Biophysics

Phone: 314-362-3075
Email: bagarcia@wustl.edu

Research

The Garcia Lab is focused on the development and application of quantitative mass spectrometry (MS) based proteomics and related computation for understanding dynamic protein and proteome post-translational modifications (PTMs). One particular interest is in investigating epigenetic histone PTMs and their role in regulating gene expression in normal and disease physiology. Our lab utilizes high resolution and high-throughput mass spectrometry and further develops improved sample preparation approaches and advanced instrument methods to sequence intact proteins (Top Down MS) and peptides (Bottom Up MS) with high sensitivity. All of these advances have been employed to study several epigenetic targets involved in processes such as cancer, neurological development, viral infection and cellular reprogramming.

Select Publications

Richard M Searfoss, Rashmi Karki, Zongtao Lin, Faith Robison & Benjamin A Garcia (2023). “An Optimized and High-Throughput Method for Histone Propionylation and Data-Independent Acquisition Analysis for the Identification and Quantification of Histone Post-translational Modifications” J Am Soc Mass Spectrom. 2023 Nov 1;34(11):2508-2517. doi: 10.1021/jasms.3c00223. Epub 2023 Oct 18. (Abstract)

Yixuan Xie, Francisca N. De Luna Vitorino, Ye Chen, Joanna K. Lempiäinen, Chenfeng Zhao, Robert T. Steinbock, Zongtao Lin, Xingyu Liu, Emily Zahn, Arabella L. Garcia, Matthew D. Weitzmancd & Benjamin A Garcia (2023). “SWAMNA: a comprehensive platform for analysis of nucleic acid modifications” Chem Commun. 2023, 59(83):12499-12502. (Abstract)

Peder J Lund, Leah A Gates, Marylene Leboeuf, Sarah A Smith, Lillian Chau, Mariana Lopes, Elliot S Friedman, Yedidya Saiman, Min Soo Kim, Clarissa A Shoffler, Christopher Petucci, C David Allis, Gary D Wu & Benjamin A Garcia (2022). “Stable isotope tracing in vivo reveals a metabolic bridge linking the microbiota to host histone acetylation” Cell Rep. 2022 Dec 13;41(11):111809. doi: 10.1016/j.celrep.2022.111809. (Abstract)

Yixuan Xie, Kevin A Janssen, Alessandro Scacchetti, Elizabeth G Porter, Zongtao Lin, Roberto Bonasio & Benjamin A Garcia (2022). “Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications” Anal Chem. 2022 May 24;94(20):7246-7254. doi: 10.1021/acs.analchem.2c00471. Epub 2022 May 12. (Abstract)

John B Wojcik, Dylan M Marchione, Simone Sidoli, Anissa Djedid, Amanda Lisby, Jacek Majewski & Benjamin A Garcia (2019). “Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors” Cancer Res. 2019 Jul 1;79(13):3205-3219. doi: 10.1158/0008-5472.CAN-18-3704. Epub 2019 Mar 21. (Abstract)

Simone Sidoli, Yekaterina Kori, Mariana Lopes, Zuo-Fei Yuan, Hee Jong Kim, Katarzyna Kulej, Kevin A Janssen, Laura M Agosto, Julia Pinheiro Chagas da Cunha, Andrew J Andrews & Benjamin A Garcia (2019). “One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry” Genome Res. 2019 Jun;29(6):978-987. doi: 10.1101/gr.247353.118. Epub 2019 May 23. (Abstract)

Anumita Saha-Shah, Melody Esmaeili, Simone Sidoli, Hyojeong Hwang, Jing Yang, Peter S Klein & Benjamin A Garcia (2019). “Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis” Anal Chem. 2019 Jul 16;91(14):8891-8899. doi: 10.1021/acs.analchem.9b00327. Epub 2019 Jun 27. (Abstract)

Natarajan V Bhanu, Simone Sidoli, Zuo-Fei Yuan, Rosalynn C Molden & Benjamin A Garcia (2019). “Regulation of proline-directed kinases and the trans-histone code H3K9me3/H4K20me3 during human myogenesis” J Biol Chem. 2019 May 17;294(20):8296-8308. doi: 10.1074/jbc.RA118.004977. Epub 2019 Mar 14. (Abstract)

Kelly R Karch, Mariel Coradin, Levani Zandarashvili, Zhong-Yuan Kan, Morgan Gerace, S Walter Englander, Ben E Black & Benjamin A Garcia (2018). “Hydrogen-Deuterium Exchange Coupled to Top- and Middle-Down Mass Spectrometry Reveals Histone Tail Dynamics before and after Nucleosome Assembly” Structure. 2018 Dec 4;26(12):1651-1663.e3. doi: 10.1016/j.str.2018.08.006. Epub 2018 Oct 4. (Abstract)

Johayra Simithy, Simone Sidoli, Zuo-Fei Yuan, Mariel Coradin, Natarajan V Bhanu, Dylan M Marchione, Brianna J Klein, Gleb A Bazilevsky, Cheryl E McCullough, Robert S Magin, Tatiana G Kutateladze, Nathaniel W Snyder, Ronen Marmorstein & Benjamin A Garcia (2017). “Characterization of histone acylations links chromatin modifications with metabolism” Nat Commun. 2017 Oct 26;8(1):1141. doi: 10.1038/s41467-017-01384-9. (Abstract)

Richard Lauman, Hee Jong Kim, Lindsay K Pino, Alessandro Scacchetti, Yixuan Xie, Faith Robison, Simone Sidoli, Roberto Bonasio & Benjamin A Garcia (2023). “Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography” Anal Chem. 2023 Mar 28;95(12):5187-5195. doi: 10.1021/acs.analchem.2c04114. Epub 2023 Mar 14. (Abstract)

Josue Baeza, Barbara E. Coons, Zongtao Lin, John Riley, Mariel Mendoza, William H. Peranteau & Benjamin A Garcia (2024). “In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development” Cell Rep Methods. 2024 Feb 26;4(2):100713. doi: 10.1016/j.crmeth.2024.100713. (Abstract)