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Mun DG, Bhat FA, Joshi N, Sandoval L, Ding H, Jain A, Peterson JA, Kang T, Pujari GP, Tomlinson JL, Budhraja R, Zenka RM, Kannan N, Kipp BR, Dasari S, Gaspar-Maia A, Smoot RL, Kandasamy RK, Pandey A. Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry. Commun Biol 2024; 7:884. [PMID: 39030393 PMCID: PMC11271535 DOI: 10.1038/s42003-024-06579-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/11/2024] [Indexed: 07/21/2024] Open
Abstract
The rapid evolution of mass spectrometry-based single-cell proteomics now enables the cataloging of several thousand proteins from single cells. We investigated whether we could discover cellular heterogeneity beyond proteome, encompassing post-translational modifications (PTM), protein-protein interaction, and variants. By optimizing the mass spectrometry data interpretation strategy to enable the detection of PTMs and variants, we have generated a high-definition dataset of single-cell and nuclear proteomic-states. The data demonstrate the heterogeneity of cell-states and signaling dependencies at the single-cell level and reveal epigenetic drug-induced changes in single nuclei. This approach enables the exploration of previously uncharted single-cell and organellar proteomes revealing molecular characteristics that are inaccessible through RNA profiling.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Firdous A Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Neha Joshi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Leticia Sandoval
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Anu Jain
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Taewook Kang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ganesh P Pujari
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Roman M Zenka
- Proteomics Core, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nagarajan Kannan
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Alexandre Gaspar-Maia
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Rory L Smoot
- Department of Surgery, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Richard K Kandasamy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L. Spatial top-down proteomics for the functional characterization of human kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580062. [PMID: 38405958 PMCID: PMC10888776 DOI: 10.1101/2024.02.13.580062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.
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Affiliation(s)
- Kevin J. Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - James M. Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Rashmi Kumar
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - David J. Degnan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Logan A. Lewis
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Yen-Chen Liao
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Marija Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Sarah M. Williams
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lisa M. Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
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Truong T, Kelly RT. What's new in single-cell proteomics. Curr Opin Biotechnol 2024; 86:103077. [PMID: 38359605 PMCID: PMC11068367 DOI: 10.1016/j.copbio.2024.103077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
In recent years, single-cell proteomics (SCP) has advanced significantly, enabling the analysis of thousands of proteins within single mammalian cells. This progress is driven by advances in experimental design, with maturing label-free and multiplexed methods, optimized sample preparation, and innovations in separation techniques, including ultra-low-flow nanoLC. These factors collectively contribute to improved sensitivity, throughput, and reproducibility. Cutting-edge mass spectrometry platforms and data acquisition approaches continue to play a critical role in enhancing data quality. Furthermore, the exploration of spatial proteomics with single-cell resolution offers significant promise for understanding cellular interactions, giving rise to various phenotypes. SCP has far-reaching applications in cancer research, biomarker discovery, and developmental biology. Here, we provide a critical review of recent advances in the field of SCP.
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Affiliation(s)
- Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, United States.
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