1
|
Saei AA, Lundin A, Lyu H, Gharibi H, Luo H, Teppo J, Zhang X, Gaetani M, Végvári Á, Holmdahl R, Gygi SP, Zubarev RA. Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401502. [PMID: 39120068 DOI: 10.1002/advs.202401502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 07/24/2024] [Indexed: 08/10/2024]
Abstract
Multifaceted interrogation of the proteome deepens the system-wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, the first high-throughput redox proteomics approach integrated with expression analysis (REX) is devised and combined with the Proteome Integral Solubility Alteration (PISA) assay. The whole PISA-REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, HCT116 cells treated with auranofin are analyzed, showing great improvement compared with previous studies. PISA-REX is then applied to study proteome remodeling upon stimulation of human monocytes by interferon α (IFN-α). Applying this tool to study the proteome changes in plasmacytoid dendritic cells (pDCs) isolated from wild-type versus Ncf1-mutant mice treated with interferon α, shows that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility, and redox state of interferon-induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA-REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease.
Collapse
Affiliation(s)
- Amir A Saei
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- Biozentrum, University of Basel, Basel, 4056, Switzerland
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Albin Lundin
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Hezheng Lyu
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Huqiao Luo
- Division of Immunology, Medical Inflammation Research Group, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, SE-17 177, Sweden
| | - Jaakko Teppo
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Helsinki, FI-00014, Finland
| | - Xuepei Zhang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Massimiliano Gaetani
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- SciLifeLab, Stockholm, SE-17 177, Sweden
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
| | - Rikard Holmdahl
- Division of Immunology, Medical Inflammation Research Group, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, SE-17 177, Sweden
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17 177, Sweden
- SciLifeLab, Stockholm, SE-17 177, Sweden
| |
Collapse
|
3
|
Végvári Á, Rodriguez JE, Zubarev RA. Single-Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death. Anal Chem 2022; 94:9261-9269. [PMID: 35731985 PMCID: PMC9260713 DOI: 10.1021/acs.analchem.2c00413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/08/2022] [Indexed: 12/04/2022]
Abstract
Chemical proteomics studies the effects of drugs upon a cellular proteome. Due to the complexity and diversity of tumors, the response of cancer cells to drugs is also heterogeneous, and thus, proteome analysis at the single-cell level is needed. Here, we demonstrate that single-cell proteomics techniques have become quantitative enough to tackle the drug effects on target proteins, enabling single-cell chemical proteomics (SCCP). Using SCCP, we studied here the time-resolved response of individual adenocarcinoma A549 cells to anticancer drugs methotrexate, camptothecin, and tomudex, revealing the early emergence of cellular subpopulations committed and uncommitted to death. As a novel and useful approach to exploring the heterogeneous response to drugs of cancer cells, SCCP may prove to be a breakthrough application for single-cell proteomics.
Collapse
Affiliation(s)
- Ákos Végvári
- Division of Physiological
Chemistry I, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Biomedicum A9, Solnavägen 9, SE-171 77 Stockholm, Sweden
| | - Jimmy E. Rodriguez
- Division of Physiological
Chemistry I, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Biomedicum A9, Solnavägen 9, SE-171 77 Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Physiological
Chemistry I, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Biomedicum A9, Solnavägen 9, SE-171 77 Stockholm, Sweden
| |
Collapse
|
4
|
Arias-Hidalgo C, Juanes-Velasco P, Landeira-Viñuela A, García-Vaquero ML, Montalvillo E, Góngora R, Hernández ÁP, Fuentes M. Single-Cell Proteomics: The Critical Role of Nanotechnology. Int J Mol Sci 2022; 23:6707. [PMID: 35743151 PMCID: PMC9224324 DOI: 10.3390/ijms23126707] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022] Open
Abstract
In single-cell analysis, biological variability can be attributed to individual cells, their specific state, and the ability to respond to external stimuli, which are determined by protein abundance and their relative alterations. Mass spectrometry (MS)-based proteomics (e.g., SCoPE-MS and SCoPE2) can be used as a non-targeted method to detect molecules across hundreds of individual cells. To achieve high-throughput investigation, novel approaches in Single-Cell Proteomics (SCP) are needed to identify and quantify proteins as accurately as possible. Controlling sample preparation prior to LC-MS analysis is critical, as it influences sensitivity, robustness, and reproducibility. Several nanotechnological approaches have been developed for the removal of cellular debris, salts, and detergents, and to facilitate systematic sample processing at the nano- and microfluidic scale. In addition, nanotechnology has enabled high-throughput proteomics analysis, which have required the improvement of software tools, such as DART-ID or DO-MS, which are also fundamental for addressing key biological questions. Single-cell proteomics has many applications in nanomedicine and biomedical research, including advanced cancer immunotherapies or biomarker characterization, among others; and novel methods allow the quantification of more than a thousand proteins while analyzing hundreds of single cells.
Collapse
Affiliation(s)
- Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
| | - Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
| | - Marina L. García-Vaquero
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
| | - Enrique Montalvillo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
| | - Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
- Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, 37007 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; (C.A.-H.); (P.J.-V.); (A.L.-V.); (M.L.G.-V.); (E.M.); (R.G.)
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| |
Collapse
|