1
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Wang Z, Zhang T, Tang M. Navigating nanotoxicity: Unraveling nanomaterial-induced effects via multi-omics integration. NANOIMPACT 2025; 38:100565. [PMID: 40383513 DOI: 10.1016/j.impact.2025.100565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2025] [Revised: 04/14/2025] [Accepted: 05/12/2025] [Indexed: 05/20/2025]
Abstract
The growing use of nanomaterials in industry and medicine raises significant concerns about their safety, particularly regarding their interactions with biological systems. Traditional toxicological methods, with limited throughput and mechanistic understanding, are increasingly being complemented by omics technologies. Genomics, transcriptomics, proteomics, and metabolomics provide comprehensive insights into the molecular mechanisms of nanomaterial toxicity and enable the identification of potential biomarkers. In addition, single-cell and spatial omics approaches are emerging as powerful tools to assess toxicity at the cellular and tissue levels, revealing heterogeneous responses and spatial distribution of nanomaterials. Despite their advantages, omics technologies face challenges in nanotoxicology, including large, complex data sets, integration difficulties, and a lack of standardized protocols. To address these challenges, we propose the development of new bioinformatics tools, multi-omics integration platforms, and standardized analysis processes to enhance research efficiency and accuracy. These efforts can provide a practical roadmap for integrating the application of omics technologies, including single-cell and spatial approaches, in the study of nanomaterial toxicity studies.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education; School of Public Health, Southeast University, Nanjing 210009, People's Republic of China
| | - Ting Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education; School of Public Health, Southeast University, Nanjing 210009, People's Republic of China.
| | - Meng Tang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education; School of Public Health, Southeast University, Nanjing 210009, People's Republic of China.
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2
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Su P, Hollas MAR, Pla I, Rubakhin S, Butun FA, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL. Proteoform profiling of endogenous single cells from rat hippocampus at scale. Nat Biotechnol 2025:10.1038/s41587-025-02669-x. [PMID: 40374954 DOI: 10.1038/s41587-025-02669-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/04/2025] [Indexed: 05/18/2025]
Abstract
We perform intact proteoform profiling of 10,809 endogenous single cells from the rat hippocampus using single-cell proteoform imaging mass spectrometry (scPiMS). scPiMS directly extracts whole proteins and demonstrates high throughput for MS-based single-cell proteomics compared with existing approaches. We develop an informatics workflow dedicated to this datatype and use it to assign neurons, astrocytes or microglia cell types according to their proteoform signatures.
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Affiliation(s)
- Pei Su
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Michael A R Hollas
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Indira Pla
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Stanislav Rubakhin
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Fatma Ayaloglu Butun
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Joseph B Greer
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Bryan P Early
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Ryan T Fellers
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Michael A Caldwell
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Jonathan V Sweedler
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Chan Zuckerberg Biohub Chicago, Chicago, IL, USA
| | - Jared O Kafader
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Chan Zuckerberg Biohub Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
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3
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Tang C, Xu W, Chen Y, Yu H, Xu L, Zhang C, Zhang Y, Liang Y. DFT calculations guide the design of dual-responsive molecule 9,10-phenanthrenequinone-sydnone. Chem Commun (Camb) 2025. [PMID: 40357574 DOI: 10.1039/d5cc00819k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2025]
Abstract
With the aid of density functional theory (DFT) calculations, we designed and synthesized a dual-responsive molecule 9,10-phenanthrenequinone-sydnone PQ-Syd, enabling tandem orthogonal reactions with furan-2(3H)-one derivatives and bicyclo[6.1.0]nonyne (BCN) for turn-on and fluorescence modulation. The PQ-Syd has been applied for protein labeling, and has potential for rapid screening of cells.
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Affiliation(s)
- Cheng Tang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
| | - Wenyuan Xu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
| | - Hongzhe Yu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
| | - Lixin Xu
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China.
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBi-oMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), ChemBioMed Interdisciplinary Research Center, Nanjing University, Nanjing, 210023, China.
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4
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Leduc A, Xu Y, Shipkovenska G, Dou Z, Slavov N. Limiting the impact of protein leakage in single-cell proteomics. Nat Commun 2025; 16:4169. [PMID: 40324992 PMCID: PMC12053607 DOI: 10.1038/s41467-025-56736-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 01/28/2025] [Indexed: 05/07/2025] Open
Abstract
Limiting artifacts during sample preparation can significantly increase data quality in single-cell proteomics experiments. Towards this goal, we characterize the impact of protein leakage by analyzing thousands of primary single cells from mouse trachea. The cells were prepared either fresh immediately after dissociation or first cryopreserved and prepared at a later date. We directly identify permeabilized cells by imaging a cell permeable dye and use the data to define a signature for protein leakage. This signature is similar across diverse cell types and reflects increased leakage propensities for cytosolic and nuclear proteins compared to membrane and mitochondrial proteins. A classifier based on the signature allowed for the accurate identification of permeabilized cells across cell types and species. The classifier is integrated into QuantQC ( scp.slavovlab.net/QuantQC ) to support its application to diverse samples and workflows.
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Affiliation(s)
- Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA, USA.
| | - Yanxin Xu
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Gergana Shipkovenska
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Zhixun Dou
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, Northeastern University, Boston, MA, USA.
- Parallel Squared Technology Institute, Watertown, MA, USA.
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5
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Petrosius V, Aragon-Fernandez P, Arrey TN, Woessman J, Üresin N, de Boer B, Su J, Furtwängler B, Stewart H, Denisov E, Petzoldt J, Peterson AC, Hock C, Damoc E, Makarov A, Zabrouskov V, Porse BT, Schoof EM. Quantitative Label-Free Single-Cell Proteomics on the Orbitrap Astral MS. Mol Cell Proteomics 2025:100982. [PMID: 40334743 DOI: 10.1016/j.mcpro.2025.100982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 03/26/2025] [Accepted: 04/23/2025] [Indexed: 05/09/2025] Open
Abstract
Single-cell proteomics by mass spectrometry (scp-MS) holds the potential to provide unprecedented insights into molecular features directly linked to the cellular phenotype, while deconvoluting complex organisms into their basic building blocks. Tailored sample preparation that maximizes the extracted amount of material that is introduced into the mass spectrometer has rapidly propelled the field forward. However, the measured signal is still at the lower edge of detection approaching the sensitivity boundary of current instrumentation. Here, we investigate the capacity of the enhanced sensitivity of the Orbitrap Astral mass spectrometer to facilitate deeper proteome profiles from low-input to single-cell samples. We carry out a comprehensive data acquisition method survey to pinpoint which parameters provide most sensitivity. Furthermore, we explore the quantitative accuracy of the obtained measurements to ensure that the obtained abundances are in line with expected ground truth values. We culminate our technical exploration by generating small datasets from two cultured cell lines and a primary bone marrow sample, to showcase obtainable proteome coverage differences from different source materials. Finally, as a proof of concept we explore protein covariation to showcase how information on known protein complexes is captured inherently in our scp-MS data.
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Affiliation(s)
| | | | | | | | - Nil Üresin
- Technical University of Denmark, Lyngby, Denmark; Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Bauke de Boer
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Jinyu Su
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Benjamin Furtwängler
- Technical University of Denmark, Lyngby, Denmark; Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark
| | | | | | | | | | | | - Eugen Damoc
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | - Bo T Porse
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Denmark; The Finsen Laboratory, Rigshospitalet, Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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6
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Kanao E, Ishihama Y. StageTip: a little giant unveiling the potential of mass spectrometry-based proteomics. ANAL SCI 2025; 41:667-675. [PMID: 40138149 PMCID: PMC12064472 DOI: 10.1007/s44211-025-00749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2025] [Accepted: 03/06/2025] [Indexed: 03/29/2025]
Abstract
This review highlights the growing impact of StageTips (Stop and Go Extraction Tips), a pipette tip-based LC column in MS-based proteomics. By packing standard pipette tips with reversed-phase, ion-exchange, or metal oxide materials, StageTips enable efficient peptide desalting, fractionation, selective enrichment, and in-tip reactions with minimal sample loss. Recent improvements, including new resin designs and integrated workflows, have further expanded the applications to phosphoproteomics, protein terminomics, and single-cell proteomics. With their simplicity, high reproducibility, and low cost, StageTips offer a versatile platform that can be seamlessly integrated into automated pipelines, increasing the throughput and the depth of proteome analysis. As materials and protocols continue to evolve, StageTips will continue to develop as an essential keystone for robust sample preparation in next-generation proteomics research.
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Affiliation(s)
- Eisuke Kanao
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.
- Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.
- Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, 567-0085, Japan.
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7
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Gaizley EJ, Chen X, Bhamra A, Enver T, Surinova S. Multiplexed phosphoproteomics of low cell numbers using SPARCE. Commun Biol 2025; 8:666. [PMID: 40287540 PMCID: PMC12033357 DOI: 10.1038/s42003-025-08068-x] [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: 10/18/2024] [Accepted: 04/09/2025] [Indexed: 04/29/2025] Open
Abstract
Understanding cellular diversity and disease mechanisms requires a global analysis of proteins and their modifications. While next-generation sequencing has advanced our understanding of cellular heterogeneity, it fails to capture downstream signalling networks. Ultrasensitive mass spectrometry-based proteomics enables unbiased protein-level analysis of low cell numbers, down to single cells. However, phosphoproteomics remains limited to high-input samples due to sample losses and poor reaction efficiencies associated with processing low cell numbers. Isobaric stable isotope labelling is a promising approach for reproducible and accurate quantification of low abundant phosphopeptides. Here, we introduce SPARCE (Streamlined Phosphoproteomic Analysis of Rare CElls) for multiplexed phosphoproteomic analysis of low cell numbers. SPARCE integrates cell isolation, water-based lysis, on-tip TMT labelling, and phosphopeptide enrichment. SPARCE outperforms traditional methods by enhancing labelling efficiency and phosphoproteome coverage. To demonstrate the utility of SPARCE, we analysed four patient-derived glioblastoma stem cell lines, reliably quantifying phosphosite changes from 1000 FACS-sorted cells. This workflow expands the possibilities for signalling analysis of rare cell populations.
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Affiliation(s)
| | - Xiuyuan Chen
- UCL Cancer Institute, University College London, London, UK
| | | | - Tariq Enver
- UCL Cancer Institute, University College London, London, UK
| | - Silvia Surinova
- UCL Cancer Institute, University College London, London, UK.
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8
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Lin KT, Muneer G, Huang PR, Chen CS, Chen YJ. Mass Spectrometry-Based Proteomics for Next-Generation Precision Oncology. MASS SPECTROMETRY REVIEWS 2025. [PMID: 40269546 DOI: 10.1002/mas.21932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 03/29/2025] [Accepted: 04/01/2025] [Indexed: 04/25/2025]
Abstract
Cancer is the leading cause of death worldwide characterized by patient heterogeneity and complex tumor microenvironment. While the genomics-based testing has transformed modern medicine, the challenge of diverse clinical outcomes highlights unmet needs for precision oncology. As functional molecules regulating cellular processes, proteins hold great promise as biomarkers and drug targets. Mass spectrometry (MS)-based clinical proteomics has illuminated the molecular features of cancers and facilitated discovery of biomarkers or therapeutic targets, paving the way for innovative strategies that enhance the precision of personalized treatment. In this article, we introduced the tools and current achievements of MS-based proteomics, choice of discovery and targeted MS from discovery to validation phases, profiling sensitivity from bulk samples to single-cell level and tissue to liquid biopsy specimens, current regulatory landscape of MS-based protein laboratory-developed tests (LDTs). The challenges, success and future perspectives in translating research MS assay into clinical applications are also discussed. With well-designed validation studies to demonstrate clinical benefits and meet the regulatory requirements for both analytical and clinical performance, the future of MS-based assays is promising with numerous opportunities to improve cancer diagnosis, treatment, and monitoring.
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Affiliation(s)
- Kuen-Tyng Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Ciao-Syuan Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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9
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Nitz A, Giraldez Chavez JH, Eliason ZG, Payne SH. Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses. J Proteome Res 2025; 24:1482-1492. [PMID: 38981598 PMCID: PMC11976870 DOI: 10.1021/acs.jproteome.4c00091] [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: 02/07/2024] [Revised: 05/02/2024] [Accepted: 06/13/2024] [Indexed: 07/11/2024]
Abstract
Single-cell analysis is an active area of research in many fields of biology. Measurements at single-cell resolution allow researchers to study diverse populations without losing biologically meaningful information to sample averages. Many technologies have been used to study single cells, including mass spectrometry-based single-cell proteomics (SCP). SCP has seen a lot of growth over the past couple of years through improvements in data acquisition and analysis, leading to greater proteomic depth. Because method development has been the main focus in SCP, biological applications have been sprinkled in only as proof-of-concept. However, SCP methods now provide significant coverage of the proteome and have been implemented in many laboratories. Thus, a primary question to address in our community is whether the current state of technology is ready for widespread adoption for biological inquiry. In this Perspective, we examine the potential for SCP in three thematic areas of biological investigation: cell annotation, developmental trajectories, and spatial mapping. We identify that the primary limitation of SCP is sample throughput. As proteome depth has been the primary target for method development to date, we advocate for a change in focus to facilitate measuring tens of thousands of single-cell proteomes to enable biological applications beyond proof-of-concept.
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Affiliation(s)
- Alyssa
A. Nitz
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| | | | - Zachary G. Eliason
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel H. Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
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10
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Pang M, Jones JJ, Wang TY, Quan B, Kubat NJ, Qiu Y, Roukes ML, Chou TF. Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples. J Proteome Res 2025; 24:1528-1538. [PMID: 38832920 PMCID: PMC11976869 DOI: 10.1021/acs.jproteome.4c00062] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024]
Abstract
The advancement of sophisticated instrumentation in mass spectrometry has catalyzed an in-depth exploration of complex proteomes. This exploration necessitates a nuanced balance in experimental design, particularly between quantitative precision and the enumeration of analytes detected. In bottom-up proteomics, a key challenge is that oversampling of abundant proteins can adversely affect the identification of a diverse array of unique proteins. This issue is especially pronounced in samples with limited analytes, such as small tissue biopsies or single-cell samples. Methods such as depletion and fractionation are suboptimal to reduce oversampling in single cell samples, and other improvements on LC and mass spectrometry technologies and methods have been developed to address the trade-off between precision and enumeration. We demonstrate that by using a monosubstrate protease for proteomic analysis of single-cell equivalent digest samples, an improvement in quantitative accuracy can be achieved, while maintaining high proteome coverage established by trypsin. This improvement is particularly vital for the field of single-cell proteomics, where single-cell samples with limited number of protein copies, especially in the context of low-abundance proteins, can benefit from considering analyte complexity. Considerations about analyte complexity, alongside chromatographic complexity, integration with data acquisition methods, and other factors such as those involving enzyme kinetics, will be crucial in the design of future single-cell workflows.
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Affiliation(s)
- Marion Pang
- Division
of Biology and Biological Engineering, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Jeff J. Jones
- Division
of Biology and Biological Engineering, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome
Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Ting-Yu Wang
- Division
of Biology and Biological Engineering, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome
Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Baiyi Quan
- Division
of Physics, Mathematics and Astronomy, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Nicole J. Kubat
- Division
of Physics, Mathematics and Astronomy, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Yanping Qiu
- Division
of Biology and Biological Engineering, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome
Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Michael L. Roukes
- Division
of Biology and Biological Engineering, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Division
of Physics, Mathematics and Astronomy, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Division
of Engineering and Applied Science, California
Institute of Technology, 1200 East California Blvd, Pasadena, California 91125, United States
| | - Tsui-Fen Chou
- Division
of Biology and Biological Engineering, California
Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
- Proteome
Exploration Laboratory, Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
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11
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Peters-Clarke TM, Liang Y, Mertz KL, Lee KW, Westphall MS, Hinkle JD, McAlister GC, Syka JEP, Kelly RT, Coon JJ. Boosting the Sensitivity of Quantitative Single-Cell Proteomics with Infrared-Tandem Mass Tags. J Proteome Res 2025; 24:1539-1548. [PMID: 38713017 PMCID: PMC12068060 DOI: 10.1021/acs.jproteome.4c00076] [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] [Indexed: 05/08/2024]
Abstract
Single-cell proteomics is a powerful approach to precisely profile protein landscapes within individual cells toward a comprehensive understanding of proteomic functions and tissue and cellular states. The inherent challenges associated with limited starting material demand heightened analytical sensitivity. Just as advances in sample preparation maximize the amount of material that makes it from the cell to the mass spectrometer, we strive to maximize the number of ions that make it from ion source to the detector. In isobaric tagging experiments, limited reporter ion generation limits quantitative accuracy and precision. The combination of infrared photoactivation and ion parking circumvents the m/z dependence inherent in HCD, maximizing reporter generation and avoiding unintended degradation of TMT reporter molecules in infrared-tandem mass tags (IR-TMT). The method was applied to single-cell human proteomes using 18-plex TMTpro, resulting in 4-5-fold increases in reporter signal compared to conventional SPS-MS3 approaches. IR-TMT enables faster duty cycles, higher throughput, and increased peptide identification and quantification. Comparative experiments showcase 4-5-fold lower injection times for IR-TMT, providing superior sensitivity without compromising accuracy. In all, IR-TMT enhances the dynamic range of proteomic experiments and is compatible with gas-phase fractionation and real-time searching, promising increased gains in the study of cellular heterogeneity.
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Affiliation(s)
- Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yiran Liang
- Department of Chemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Keaton L. Mertz
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kenneth W. Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | | | | | - Ryan T. Kelly
- Department of Chemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, WI, 53515, USA
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12
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Cheung TK, Zhu Y, Rose CM. Offset Mass Carrier Proteome Improves Quantification of Multiplexed Single Cell Proteomics. Mol Cell Proteomics 2025; 24:100959. [PMID: 40180178 PMCID: PMC12090233 DOI: 10.1016/j.mcpro.2025.100959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2024] [Revised: 03/06/2025] [Accepted: 03/30/2025] [Indexed: 04/05/2025] Open
Abstract
Multiplexed single cell proteomics by mass spectrometry (scpMS) approaches currently offer the highest throughput as measured by cells analyzed per day. These methods employ isobaric labels and typically a carrier proteome, a sample added at 20 to 500× the single cell level that improves peptide sampling and identification. Peptides from the carrier and single cell proteomes exist within the same precursor isotopic cluster and are co-isolated for identification and quantification. This represents a challenge as high levels of carrier proteome limit the sampling of peptide ions from single cell samples and can potentially lead to decreased accuracy of quantitative measurements. Here, we address this limitation by introducing a triggered by offset mass acquisition method for scpMS (toma-scpMS) that utilizes a carrier proteome labeled with nonisobaric tags that have the same chemical composition but different mass as the labels used for quantitative multiplexing. Within toma-scpMS, the carrier proteome and single cell proteome are separated at the precursor level, enabling separate isolation, fragmentation, and quantitation of the single cell samples. To enable this workflow, we implemented a custom data acquisition scheme within inSeqAPI, an instrument application programming interface program that performed real-time identification of carrier proteome peptides and subsequent triggering of offset single cell quantification scans. We demonstrate that toma-scpMS is more robust to high levels of carrier proteome and offers superior quantitative accuracy as compared to traditional multiplexed scpMS approaches when similar carrier proteome levels are employed.
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Affiliation(s)
- Tommy K Cheung
- Department of Proteomic and Genomic Technologies, Genentech, Inc, South San Francisco, California, USA
| | - Ying Zhu
- Department of Proteomic and Genomic Technologies, Genentech, Inc, South San Francisco, California, USA
| | - Christopher M Rose
- Department of Proteomic and Genomic Technologies, Genentech, Inc, South San Francisco, California, USA.
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13
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Sanchez-Avila X, de Oliveira RM, Huang S, Wang C, Kelly RT. Trends in Mass Spectrometry-Based Single-Cell Proteomics. Anal Chem 2025; 97:5893-5907. [PMID: 40091206 PMCID: PMC12003028 DOI: 10.1021/acs.analchem.5c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Affiliation(s)
- Ximena Sanchez-Avila
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Raphaela M de Oliveira
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Siqi Huang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Chao Wang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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14
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Mulvey JF, Meyer EL, Svenningsen MS, Lundby A. Integrating -Omic Technologies across Modality, Space, and Time to Decipher Remodeling in Cardiac Disease. Curr Cardiol Rep 2025; 27:74. [PMID: 40116972 PMCID: PMC11928419 DOI: 10.1007/s11886-025-02226-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/11/2025] [Indexed: 03/23/2025]
Abstract
PURPOSE OF REVIEW Despite significant efforts to understand pathophysiological processes underlying cardiac diseases, the molecular causes for the most part remain unresolved. Rapid advancements in -omics technologies, and their application in cardiac research, offer new insight into cardiac remodeling in disease states. This review aims to provide an accessible overview of recent advances in omics approaches for studying cardiac remodeling, catering to readers without extensive prior expertise. RECENT FINDINGS We provide a methodologically focused overview of current methods for performing transcriptomics and proteomics, including their extensions for single-cell and spatial measurements. We discuss approaches to integrate data across modalities, resolutions and time. Key recent applications within the cardiac field are highlighted. Each -omics modality can provide insight, yet each existing experimental method has technical or conceptual limitations. Integrating data across multiple modalities can leverage strengths and mitigate weaknesses, ultimately enhancing our understanding of cardiac pathophysiology.
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Affiliation(s)
- John F Mulvey
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emily L Meyer
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Skjoldan Svenningsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alicia Lundby
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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15
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Xie Y, Chen X, Xu M, Zheng X. Application of the Human Proteome in Disease, Diagnosis, and Translation into Precision Medicine: Current Status and Future Prospects. Biomedicines 2025; 13:681. [PMID: 40149657 PMCID: PMC11940125 DOI: 10.3390/biomedicines13030681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 02/21/2025] [Accepted: 02/28/2025] [Indexed: 03/29/2025] Open
Abstract
This review summarizes the existing studies of human proteomics technology in the medical field with a focus on the development mechanism of a disease and its potential in discovering biomarkers. Through a systematic review of the relevant literature, we found the significant advantages and application scenarios of proteomics technology in disease diagnosis, drug development, and personalized treatment. However, the review also identifies the challenges facing proteomics technologies, including sample preparation of low-abundance proteins, massive amounts of data analysis, and how research results can be better used in clinical practice. Finally, this work discusses future research directions, including the development of more effective proteomics technologies, strengthening the integration of multi-source omics technologies, and promoting the application of AI in the human proteome.
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Affiliation(s)
| | | | - Maokai Xu
- Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou 350001, China; (Y.X.); (X.C.)
| | - Xiaochun Zheng
- Department of Anesthesiology, Fujian Provincial Hospital, Fuzhou 350001, China; (Y.X.); (X.C.)
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16
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Hernandez R, Garcia-Rodriguez NS, Arriaga MA, Perez R, Bala AA, Leandro AC, Diego VP, Almeida M, Parsons JG, Manusov EG, Galan JA. The hepatocellular model of fatty liver disease: from current imaging diagnostics to innovative proteomics technologies. Front Med (Lausanne) 2025; 12:1513598. [PMID: 40109726 PMCID: PMC11919916 DOI: 10.3389/fmed.2025.1513598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2024] [Accepted: 02/06/2025] [Indexed: 03/22/2025] Open
Abstract
Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a prevalent chronic liver condition characterized by lipid accumulation and inflammation, often progressing to severe liver damage. We aim to review the pathophysiology, diagnostics, and clinical care of MASLD, and review highlights of advances in proteomic technologies. Recent advances in proteomics technologies have improved the identification of novel biomarkers and therapeutic targets, offering insight into the molecular mechanisms underlying MASLD progression. We focus on the application of mass spectrometry-based proteomics including single cell proteomics, proteogenomics, extracellular vesicle (EV-omics), and exposomics for biomarker discovery, emphasizing the potential of blood-based panels for noninvasive diagnosis and personalized medicine. Future research directions are presented to develop targeted therapies and improve clinical outcomes for MASLD patients.
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Affiliation(s)
- Renee Hernandez
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Natasha S Garcia-Rodriguez
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marco A Arriaga
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Ricardo Perez
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Auwal A Bala
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Ana C Leandro
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Vince P Diego
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Marcio Almeida
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Jason G Parsons
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Eron G Manusov
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
| | - Jacob A Galan
- Division of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, United States
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17
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Kardassis D, Vindis C, Stancu CS, Toma L, Gafencu AV, Georgescu A, Alexandru-Moise N, Molica F, Kwak BR, Burlacu A, Hall IF, Butoi E, Magni P, Wu J, Novella S, Gamon LF, Davies MJ, Caporali A, de la Cuesta F, Mitić T. Unravelling molecular mechanisms in atherosclerosis using cellular models and omics technologies. Vascul Pharmacol 2025; 158:107452. [PMID: 39667548 DOI: 10.1016/j.vph.2024.107452] [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: 09/27/2024] [Revised: 10/31/2024] [Accepted: 12/02/2024] [Indexed: 12/14/2024]
Abstract
Despite the discovery and prevalent clinical use of potent lipid-lowering therapies, including statins and PCSK9 inhibitors, cardiovascular diseases (CVD) caused by atherosclerosis remain a large unmet clinical need, accounting for frequent deaths worldwide. The pathogenesis of atherosclerosis is a complex process underlying the presence of modifiable and non-modifiable risk factors affecting several cell types including endothelial cells (ECs), monocytes/macrophages, smooth muscle cells (SMCs) and T cells. Heterogeneous composition of the plaque and its morphology could lead to rupture or erosion causing thrombosis, even a sudden death. To decipher this complexity, various cell model systems have been developed. With recent advances in systems biology approaches and single or multi-omics methods researchers can elucidate specific cell types, molecules and signalling pathways contributing to certain stages of disease progression. Compared with animals, in vitro models are economical, easily adjusted for high-throughput work, offering mechanistic insights. Hereby, we review the latest work performed employing the cellular models of atherosclerosis to generate a variety of omics data. We summarize their outputs and the impact they had in the field. Challenges in the translatability of the omics data obtained from the cell models will be discussed along with future perspectives.
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Affiliation(s)
- Dimitris Kardassis
- University of Crete Medical School and Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology of Hellas, Heraklion, Greece.
| | - Cécile Vindis
- CARDIOMET, Center for Clinical Investigation 1436 (CIC1436)/INSERM, Toulouse, France
| | - Camelia Sorina Stancu
- Lipidomics Department, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Laura Toma
- Lipidomics Department, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Anca Violeta Gafencu
- Gene Regulation and Molecular Therapies Department, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Adriana Georgescu
- Pathophysiology and Cellular Pharmacology Department, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Nicoleta Alexandru-Moise
- Pathophysiology and Cellular Pharmacology Department, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Filippo Molica
- Department of Pathology and Immunology, Geneva Center for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Brenda R Kwak
- Department of Pathology and Immunology, Geneva Center for Inflammation Research, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Alexandrina Burlacu
- Department of Stem Cell Biology, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Ignacio Fernando Hall
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Elena Butoi
- Department of Biopathology and Therapy of Inflammation, Institute of Cellular Biology and Pathology Nicolae Simionescu, Bucharest, Romania
| | - Paolo Magni
- Department of Pharmacological and Biomolecular Sciences 'Rodolfo Paoletti', Università degli Studi di Milano, Milano, Italy; IRCCS MultiMedica, Milan, Italy
| | - Junxi Wu
- University of Strathclyde, Glasgow, United Kingdom
| | - Susana Novella
- Department of Physiology, University of Valencia - INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Luke F Gamon
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Caporali
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Fernando de la Cuesta
- Department of Pharmacology and Therapeutics, School of Medicine, Universidad Autónoma de Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Tijana Mitić
- Centre for Cardiovascular Science, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom.
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18
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Li ZP, Du Z, Huang DS, Teschendorff AE. Interpretable deep learning of single-cell and epigenetic data reveals novel molecular insights in aging. Sci Rep 2025; 15:5048. [PMID: 39934290 PMCID: PMC11814351 DOI: 10.1038/s41598-025-89646-1] [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: 11/15/2024] [Accepted: 02/06/2025] [Indexed: 02/13/2025] Open
Abstract
Deep learning (DL) and explainable artificial intelligence (XAI) have emerged as powerful machine-learning tools to identify complex predictive data patterns in a spatial or temporal domain. Here, we consider the application of DL and XAI to large omic datasets, in order to study biological aging at the molecular level. We develop an advanced multi-view graph-level representation learning (MGRL) framework that integrates prior biological network information, to build molecular aging clocks at cell-type resolution, which we subsequently interpret using XAI. We apply this framework to one of the largest single-cell transcriptomic datasets encompassing over a million immune cells from 981 donors, revealing a ribosomal gene subnetwork, whose expression correlates with age independently of cell-type. Application of the same DL-XAI framework to DNA methylation data of sorted monocytes reveals an epigenetically deregulated inflammatory response pathway whose activity increases with age. We show that the ribosomal module and inflammatory pathways would not have been discovered had we used more standard machine-learning methods. In summary, the computational deep learning framework presented here illustrates how deep learning when combined with explainable AI tools, can reveal novel biological insights into the complex process of aging.
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Affiliation(s)
- Zhi-Peng Li
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, Zhejiang, China
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - De-Shuang Huang
- Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, 315201, Zhejiang, China.
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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19
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Dutta S, Pang M, Coughlin GM, Gudavalli S, Roukes ML, Chou TF, Gradinaru V. Molecularly-guided spatial proteomics captures single-cell identity and heterogeneity of the nervous system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.10.637505. [PMID: 39990460 PMCID: PMC11844393 DOI: 10.1101/2025.02.10.637505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Single-cell proteomics is an emerging field with significant potential to characterize heterogeneity within biological tissues. It offers complementary insights to single-cell transcriptomics by revealing unbiased proteomic changes downstream of the transcriptome. Recent advancements have focused on enhancing proteome coverage and depth, mostly in cultured cell lines, and a few recent studies have explored the potential of analyzing tissue micro-samples but were limited to homogenous peripheral tissues. In this current work, we utilize the power of spatial single cell-proteomics through immunostaining-guided laser capture microdissection (LCM) coupled with LC-MS to investigate the heterogenous central nervous system. We used this method to compare neuronal populations from cortex and substantia nigra, two brain regions associated with motor and cognitive function and various neurological disorders. Moreover, we used the technique to understand the neuroimmune changes associated with stab wound injury. Finally, we focus our application on the peripheral nervous system, where we compare the proteome of the myenteric plexus cell ganglion to the nerve bundle. This study demonstrates the utility of spatial single-cell proteomics in neuroscience research toward understanding fundamental biology and the molecular drivers of neurological conditions.
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Affiliation(s)
- Sayan Dutta
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Marion Pang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Gerard M. Coughlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Sirisha Gudavalli
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Michael L. Roukes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, CA 91125
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
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20
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Lecornec N, Duchmann M, Itzykson R. Single-cell sequencing applications in acute myeloid leukemia. Leuk Lymphoma 2025; 66:175-189. [PMID: 39496597 DOI: 10.1080/10428194.2024.2422833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 09/26/2024] [Accepted: 10/23/2024] [Indexed: 11/06/2024]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous group of malignancies with poor prognosis. AML result from the proliferation of immature myeloid cells blocked at a variable stage of differentiation. Beyond inter-patient heterogeneity, AMLs are characterized by genetic and phenotypic intra-patient heterogeneity. Despite major advances in deciphering AML biology with bulk sequencing studies, pivotal questions remain unanswered. Analyses at the single-cell level could thus transform our understanding of these neoplasms. We review recent progresses in single-cell sequencing technologies from cell processing to bioinformatic pipelines. We next discuss how single-cell applications have helped understand the genetic and functional intra-leukemic heterogeneity, emphasizing aspects related to leukemic stem cells, clonal evolution and measurable residual disease (MRD) monitoring. We finally delineate how single-cell technologies could be implemented in routine clinical practice to improve patient management.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Single-Cell Analysis/methods
- Neoplasm, Residual/genetics
- Neoplasm, Residual/diagnosis
- Biomarkers, Tumor/genetics
- High-Throughput Nucleotide Sequencing/methods
- Clonal Evolution
- Neoplastic Stem Cells/pathology
- Neoplastic Stem Cells/metabolism
- Computational Biology/methods
- Prognosis
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Affiliation(s)
- Nicolas Lecornec
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université Paris Cité, Paris, France
- Département d'Immuno-Hématologie Pédiatrique, Hôpital Robert-Debré, Assistance Publique Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Matthieu Duchmann
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université Paris Cité, Paris, France
- Laboratoire d'Hématologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Raphael Itzykson
- Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRS, Université Paris Cité, Paris, France
- Département Hématologie et Immunologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
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21
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Meteling M, Johnbosco C, Wolfel A, Conceição F, Govindaraj K, Moreira Teixeira L, Leijten J. High-Throughput Single-Cell Analysis of Local Nascent Protein Deposition in 3D Microenvironments via Extracellular Protein Identification Cytometry (EPIC). ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2025; 37:e2415981. [PMID: 39629556 PMCID: PMC11817916 DOI: 10.1002/adma.202415981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 11/17/2024] [Indexed: 02/13/2025]
Abstract
Extracellular matrix (ECM) guides cell behavior and tissue fate. Cell populations are notoriously heterogeneous leading to large variations in cell behavior at the single-cell level. Although insights into population heterogeneity are valuable for fundamental biology, regenerative medicine, and drug testing, current ECM analysis techniques only provide either averaged population-level data or single-cell data from a limited number of cells. Here, extracellular protein identification cytometry (EPIC) is presented as a novel platform technology that enables high-throughput measurements of local nascent protein deposition at single-cell level. Specifically, human primary chondrocytes are microfluidically encapsulated in enzymatically crosslinked microgels of 16 picoliter at kHz rates, forming large libraries of discrete 3D single-cell microniches in which ECM can be deposited. ECM proteins are labeled using fluorescence immunostaining to allow for nondestructive analysis via flow cytometry. This approach reveals population heterogeneity in matrix deposition at unprecedented throughput, allowing for the identification and fluorescent activated cell sorting-mediated isolation of cellular subpopulations. Additionally, it is demonstrated that inclusion of a second cell into microgels allows for studying the effect of cell-cell contact on matrix deposition. In summary, EPIC enables high-throughput single-cell analysis of nascent proteins in 3D microenvironments, which is anticipated to advance fundamental knowledge and tissue engineering applications.
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Affiliation(s)
- Marieke Meteling
- Leijten LaboratoryDepartment of Developmental BioengineeringFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
| | - Castro Johnbosco
- Leijten LaboratoryDepartment of Developmental BioengineeringFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
| | - Alexis Wolfel
- Leijten LaboratoryDepartment of Developmental BioengineeringFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
| | - Francisco Conceição
- Department of Advanced Organ bioengineering and TherapeuticsFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
| | - Kannan Govindaraj
- Leijten LaboratoryDepartment of Developmental BioengineeringFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
| | - Liliana Moreira Teixeira
- Department of Advanced Organ bioengineering and TherapeuticsFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
| | - Jeroen Leijten
- Leijten LaboratoryDepartment of Developmental BioengineeringFaculty of Science and Technology, Technical Medical CentreUniversity of TwenteDrienerlolaan 5Enschede7522NBThe Netherlands
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22
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Ai L, Binek A, Zhemkov V, Cho JH, Haghani A, Kreimer S, Israely E, Arzt M, Chazarin B, Sundararaman N, Sharma A, Marbán E, Svendsen CN, Van Eyk JE. Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts. Mol Cell Proteomics 2025:100910. [PMID: 39855627 DOI: 10.1016/j.mcpro.2025.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/08/2025] [Accepted: 01/20/2025] [Indexed: 01/27/2025] Open
Abstract
Single cell proteomics was performed on human induced pluripotent stem cells (iPSCs), iPSC-derived cardiomyocytes, and adult cardiomyocytes. Over 700 proteins could be simultaneously measured in each cell revealing unique subpopulations. A sub-set of iPSCs expressed higher levels of Lin28a and Tra-1-60 towards the outer edge of cell colonies. In the cardiomyocytes, two distinct populations were found that exhibited complementary metabolic profiles. Cardiomyocytes from iPSCs showed a glycolysis profile while adult cardiomyocytes were enriched in proteins involved with fatty acid metabolism. Interestingly, rare single cells also co-expressed markers of both cardiac and neuronal lineages, suggesting there maybe a novel hybrid cell type in the human heart.
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Affiliation(s)
- Lizhuo Ai
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Aleksandra Binek
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048.
| | - Vladimir Zhemkov
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Jae Hyung Cho
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Ali Haghani
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Simion Kreimer
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Edo Israely
- Department of Medicine Research, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Madelyn Arzt
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048
| | - Blandine Chazarin
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Niveda Sundararaman
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Arun Sharma
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048
| | - Eduardo Marbán
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Clive N Svendsen
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048.
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048.
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23
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Gong Y, Dai Y, Wu Q, Guo L, Yao X, Yang Q. Benchmark of Data Integration in Single-Cell Proteomics. Anal Chem 2025; 97:1254-1263. [PMID: 39761355 DOI: 10.1021/acs.analchem.4c04933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2025]
Abstract
Single-cell proteomics (SCP) detected based on different technologies always involves batch-specific variations because of differences in sample processing and other potential biases. How to integrate SCP data effectively has become a great challenge. Integration of SCP data not only requires the conservation of true biological variances, but also realizes the removal of unwanted batch effects. In this study, benchmarking analysis of popular data integration methods was conducted to determine the most suitable method for SCP data. To comprehensively evaluate the performance of these integration methods, a novel evaluation system was proposed for integrating SCP data. This evaluation system consists of three objective measures from different perspectives: category (a), the efficacy of correcting batch effects; category (b), the power of conserving biological variances; and category (c), the ability to identify consistent markers. For this comprehensive evaluation, five benchmark data sets under different scenarios (containing substantial proteins, substantial cells, multiple batches, multiple cell types, and unbalanced data) were utilized for selecting the most suitable data integration method. As a result, three methods, ComBat, Scanorama, and Seurat version 3 CCA, were identified as the most recommended methods for integrating SCP data. Overall, this systematic evaluation might provide valuable guidance in choosing the appropriate method for data integration in the SCP.
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Affiliation(s)
- Yaguo Gong
- School of Pharmacy, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Yangbo Dai
- State Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Qibiao Wu
- School of Pharmacy, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Li Guo
- State Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Xiaojun Yao
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China
| | - Qingxia Yang
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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24
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Zhao Q, Li S, Krall L, Li Q, Sun R, Yin Y, Fu J, Zhang X, Wang Y, Yang M. Deciphering cellular complexity: advances and future directions in single-cell protein analysis. Front Bioeng Biotechnol 2025; 12:1507460. [PMID: 39877263 PMCID: PMC11772399 DOI: 10.3389/fbioe.2024.1507460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 12/19/2024] [Indexed: 01/31/2025] Open
Abstract
Single-cell protein analysis has emerged as a powerful tool for understanding cellular heterogeneity and deciphering the complex mechanisms governing cellular function and fate. This review provides a comprehensive examination of the latest methodologies, including sophisticated cell isolation techniques (Fluorescence-Activated Cell Sorting (FACS), Magnetic-Activated Cell Sorting (MACS), Laser Capture Microdissection (LCM), manual cell picking, and microfluidics) and advanced approaches for protein profiling and protein-protein interaction analysis. The unique strengths, limitations, and opportunities of each method are discussed, along with their contributions to unraveling gene regulatory networks, cellular states, and disease mechanisms. The importance of data analysis and computational methods in extracting meaningful biological insights from the complex data generated by these technologies is also highlighted. By discussing recent progress, technological innovations, and potential future directions, this review emphasizes the critical role of single-cell protein analysis in advancing life science research and its promising applications in precision medicine, biomarker discovery, and targeted therapeutics. Deciphering cellular complexity at the single-cell level holds immense potential for transforming our understanding of biological processes and ultimately improving human health.
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Affiliation(s)
- Qirui Zhao
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Yunnan University, Kunming, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Shan Li
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Yunnan University, Kunming, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Leonard Krall
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Yunnan University, Kunming, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Qianyu Li
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Rongyuan Sun
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yuqi Yin
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyi Fu
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Xu Zhang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Yunnan University, Kunming, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Yonghua Wang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Yunnan University, Kunming, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Mei Yang
- Yunnan Key Laboratory of Cell Metabolism and Diseases, Yunnan University, Kunming, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
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25
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Ryu T, Kim K, Asiimwe N, Na CH. Proteomic Insight Into Alzheimer's Disease Pathogenesis Pathways. Proteomics 2025:e202400298. [PMID: 39791267 DOI: 10.1002/pmic.202400298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 12/21/2024] [Accepted: 12/23/2024] [Indexed: 01/12/2025]
Abstract
Alzheimer's disease (AD) is a leading cause of dementia, but the pathogenesis mechanism is still elusive. Advances in proteomics have uncovered key molecular mechanisms underlying AD, revealing a complex network of dysregulated pathways, including amyloid metabolism, tau pathology, apolipoprotein E (APOE), protein degradation, neuroinflammation, RNA splicing, metabolic dysregulation, and cognitive resilience. This review examines recent proteomic findings from AD brain tissues and biological fluids, highlighting potential biomarkers and therapeutic targets. By examining the proteomic landscape of them, we aim to deepen our understanding of the disease and support developing precision medicine strategies for more effective interventions.
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Affiliation(s)
- Taekyung Ryu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyungdo Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Asiimwe
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chan Hyun Na
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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26
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Calarco JA, Taylor SR, Miller DM. Detecting gene expression in Caenorhabditis elegans. Genetics 2025; 229:1-108. [PMID: 39693264 PMCID: PMC11979774 DOI: 10.1093/genetics/iyae167] [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: 01/20/2024] [Accepted: 09/30/2024] [Indexed: 12/20/2024] Open
Abstract
Reliable methods for detecting and analyzing gene expression are necessary tools for understanding development and investigating biological responses to genetic and environmental perturbation. With its fully sequenced genome, invariant cell lineage, transparent body, wiring diagram, detailed anatomy, and wide array of genetic tools, Caenorhabditis elegans is an exceptionally useful model organism for linking gene expression to cellular phenotypes. The development of new techniques in recent years has greatly expanded our ability to detect gene expression at high resolution. Here, we provide an overview of gene expression methods for C. elegans, including techniques for detecting transcripts and proteins in situ, bulk RNA sequencing of whole worms and specific tissues and cells, single-cell RNA sequencing, and high-throughput proteomics. We discuss important considerations for choosing among these techniques and provide an overview of publicly available online resources for gene expression data.
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Affiliation(s)
- John A Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada, M5S 3G5
| | - Seth R Taylor
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
- Neuroscience Program, Vanderbilt University, Nashville, TN 37240, USA
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27
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2025; 68:5-102. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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28
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Su PR, Chien MP. Functional Single-Cell Proteomics: Technology and Biological Applications. Methods Mol Biol 2025; 2902:145-159. [PMID: 40029601 DOI: 10.1007/978-1-0716-4402-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Single-cell proteomics has the potential to decipher tumor heterogeneity, and methods such as Single-Cell ProtEomics by Mass Spectrometry (SCoPE-MS) allow profiling of several tens of single cells for more than 1,000 proteins per cell. Our laboratory has advanced state-of-the-art single-cell proteomics technology to enable linking proteomes of individual cells with phenotypes of interest. Here, we describe a microscopy-based functional single-cell proteomic profiling technology, called FUNpro, designed for general use in cultured cell lines. FUNpro enables high-throughput, real-time live-cell screening, identification, and isolation of single cells of interest, even when the phenotypes are dynamic or the cells are rare. This chapter outlines a generalized protocol for functional single-cell proteomic profiling and analysis of a standard cancer cell line, including an overview of the microscopy, cell culture, image analysis, photolabeling of cells of interest, fluorescence-activated cell sorting (FACS), and the single-cell proteomics procedures and analyses employed.
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Affiliation(s)
- Pin-Rui Su
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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29
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Nalla LV, Kanukolanu A, Yeduvaka M, Gajula SNR. Advancements in Single-Cell Proteomics and Mass Spectrometry-Based Techniques for Unmasking Cellular Diversity in Triple Negative Breast Cancer. Proteomics Clin Appl 2025; 19:e202400101. [PMID: 39568435 PMCID: PMC11726282 DOI: 10.1002/prca.202400101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/04/2024] [Accepted: 11/08/2024] [Indexed: 11/22/2024]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is an aggressive and complex subtype of breast cancer characterized by a lack of targeted treatment options. Intratumoral heterogeneity significantly drives disease progression and complicates therapeutic responses, necessitating advanced analytical approaches to understand its underlying biology. This review aims to explore the advancements in single-cell proteomics and their application in uncovering cellular diversity in TNBC. It highlights innovations in sample preparation, mass spectrometry-based techniques, and the potential for integrating proteomics into multi-omics platforms. METHODS The review discusses the combination of improved sample preparation methods and cutting-edge mass spectrometry techniques in single-cell proteomics. It emphasizes the challenges associated with protein analysis, such as the inability to amplify proteins akin to transcripts, and examines strategies to overcome these limitations. RESULTS Single-cell proteomics provides a direct link to phenotype and cell behavior, complementing transcriptomic approaches and offering new insights into the mechanisms driving TNBC. The integration of advanced techniques has enabled deeper exploration of cellular heterogeneity and disease mechanisms. CONCLUSION Despite the challenges, single-cell proteomics holds immense potential to evolve into a high-throughput and scalable multi-omics platform. Addressing existing hurdles will enable deeper biological insights, ultimately enhancing the diagnosis and treatment of TNBC.
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Affiliation(s)
- Lakshmi Vineela Nalla
- Department of Pharmacology, GITAM School of PharmacyGITAM (Deemed to be University)VisakhapatnamAndhra PradeshIndia
| | - Aarika Kanukolanu
- Department of Pharmaceutical Analysis, GITAM School of PharmacyGITAM (Deemed to be University)VisakhapatnamAndhra PradeshIndia
| | - Madhuri Yeduvaka
- Department of Pharmacology, GITAM School of PharmacyGITAM (Deemed to be University)VisakhapatnamAndhra PradeshIndia
| | - Siva Nageswara Rao Gajula
- Department of Pharmaceutical Analysis, GITAM School of PharmacyGITAM (Deemed to be University)VisakhapatnamAndhra PradeshIndia
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30
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Capelletti MM, Montini O, Ruini E, Tettamanti S, Savino AM, Sarno J. Unlocking the Heterogeneity in Acute Leukaemia: Dissection of Clonal Architecture and Metabolic Properties for Clinical Interventions. Int J Mol Sci 2024; 26:45. [PMID: 39795903 PMCID: PMC11719665 DOI: 10.3390/ijms26010045] [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: 11/21/2024] [Revised: 12/17/2024] [Accepted: 12/19/2024] [Indexed: 01/13/2025] Open
Abstract
Genetic studies of haematological cancers have pointed out the heterogeneity of leukaemia in its different subpopulations, with distinct mutations and characteristics, impacting the treatment response. Next-generation sequencing (NGS) and genome-wide analyses, as well as single-cell technologies, have offered unprecedented insights into the clonal heterogeneity within the same tumour. A key component of this heterogeneity that remains unexplored is the intracellular metabolome, a dynamic network that determines cell functions, signalling, epigenome regulation, immunity and inflammation. Understanding the metabolic diversities among cancer cells and their surrounding environments is therefore essential in unravelling the complexities of leukaemia and improving therapeutic strategies. Here, we describe the currently available methodologies and approaches to addressing the dynamic heterogeneity of leukaemia progression. In the second section, we focus on metabolic leukaemic vulnerabilities in acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL). Lastly, we provide a comprehensive overview of the most interesting clinical trials designed to target these metabolic dependencies, highlighting their potential to advance therapeutic strategies in leukaemia treatment. The integration of multi-omics data for cancer identification with the metabolic states of tumour cells will enable a comprehensive "micro-to-macro" approach for the refinement of clinical practices and delivery of personalised therapies.
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Affiliation(s)
- Martina Maria Capelletti
- School of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy; (M.M.C.); (O.M.); (E.R.); (A.M.S.)
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Orsola Montini
- School of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy; (M.M.C.); (O.M.); (E.R.); (A.M.S.)
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Emilio Ruini
- School of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy; (M.M.C.); (O.M.); (E.R.); (A.M.S.)
| | - Sarah Tettamanti
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Angela Maria Savino
- School of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy; (M.M.C.); (O.M.); (E.R.); (A.M.S.)
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
| | - Jolanda Sarno
- School of Medicine and Surgery, University of Milan-Bicocca, 20126 Milan, Italy; (M.M.C.); (O.M.); (E.R.); (A.M.S.)
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, 20900 Monza, Italy
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31
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Leduc A, Khoury L, Cantlon J, Khan S, Slavov N. Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP. Nat Protoc 2024; 19:3750-3776. [PMID: 39117766 PMCID: PMC11614709 DOI: 10.1038/s41596-024-01033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/27/2024] [Indexed: 08/10/2024]
Abstract
Single-cell proteomics by mass spectrometry (MS) allows the quantification of proteins with high specificity and sensitivity. To increase its throughput, we developed nano-proteomic sample preparation (nPOP), a method for parallel preparation of thousands of single cells in nanoliter-volume droplets deposited on glass slides. Here, we describe its protocol with emphasis on its flexibility to prepare samples for different multiplexed MS methods. An implementation using the plexDIA MS multiplexing method, which uses non-isobaric mass tags to barcode peptides from different samples for data-independent acquisition, demonstrates accurate quantification of ~3,000-3,700 proteins per human cell. A separate implementation with isobaric mass tags and prioritized data acquisition demonstrates analysis of 1,827 single cells at a rate of >1,000 single cells per day at a depth of 800-1,200 proteins per human cell. The protocol is implemented by using a cell-dispensing and liquid-handling robot-the CellenONE instrument-and uses readily available consumables, which should facilitate broad adoption. nPOP can be applied to all samples that can be processed to a single-cell suspension. It takes 1 or 2 d to prepare >3,000 single cells. We provide metrics and software (the QuantQC R package) for quality control and data exploration. QuantQC supports the robust scaling of nPOP to higher plex reagents for achieving reliable and scalable single-cell proteomics.
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Affiliation(s)
- Andrew Leduc
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
| | - Luke Khoury
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | | | - Saad Khan
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Proteomics Center, and Barnett Institute, Northeastern University, Boston, MA, USA.
- Parallel Squared Technology Institute, Watertown, MA, USA.
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32
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Montes C, Zhang J, Nolan TM, Walley JW. Single-cell proteomics differentiates Arabidopsis root cell types. THE NEW PHYTOLOGIST 2024; 244:1750-1759. [PMID: 38923440 DOI: 10.1111/nph.19923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024]
Abstract
Single-cell proteomics (SCP) is an emerging approach to resolve cellular heterogeneity within complex tissues of multi-cellular organisms. Here, we demonstrate the feasibility of SCP on plant samples using the model plant Arabidopsis thaliana. Specifically, we focused on examining isolated single cells from the cortex and endodermis, which are two adjacent root cell types derived from a common stem cell lineage. From 756 root cells, we identified 3763 proteins and 1118 proteins/cell. Ultimately, we focus on 3217 proteins quantified following stringent filtering. Of these, we identified 596 proteins whose expression is enriched in either the cortex or endodermis and are able to differentiate these closely related plant cell types. Collectivity, this study demonstrates that SCP can resolve neighboring cell types with distinct functions, thereby facilitating the identification of biomarkers and candidate proteins to enable functional genomics.
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Affiliation(s)
- Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Jingyuan Zhang
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Trevor M Nolan
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC, 27708, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA, 50011, USA
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33
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Yang D, Fang Y, Liu X, Ma J, Xu J, Dong H, Ding H, Wang D, Liu Q, Zhang F. Lensless On-Chip Chemiluminescence Imaging for High-Throughput Single-Cell Heterogeneity Analysis. NANO LETTERS 2024; 24:14875-14883. [PMID: 39512117 DOI: 10.1021/acs.nanolett.4c04487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
High-throughput single-cell heterogeneity imaging and analysis is essential for understanding complex biological systems and for advancing personalized precision disease diagnosis and treatment. Here, we present a miniaturized lensless chemiluminescence chip for high-throughput single-cell functional imaging with subcellular resolution. With the sensitive chemiluminescence sensing and wide field of view of contact lensless imaging, we demonstrated the chemiluminescent imaging of over 1000 single cells, and their membrane glycoprotein and the high-throughput single-cell heterogeneity of membrane protein imaging were examined for precision analysis. Furthermore, the functional adhesion and heterogeneity of single live cells were imaged and explored. This miniaturized lensless on-chip CL-CMOS imaging platform enables high-throughput single-cell imaging and analysis with high sensitivity and subcellular resolution, providing new techniques for the cellular study of biological heterogeneity and has potential application in precision disease diagnosis and treatment at the point-of-care settings.
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Affiliation(s)
- Dehong Yang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ying Fang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiaoyin Liu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jinbiao Ma
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiahao Xu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Hao Dong
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Haiying Ding
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Department of Pharmacy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310005, China
| | - Di Wang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Qingjun Liu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Fenni Zhang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
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34
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Qian L, Sun R, Aebersold R, Bühlmann P, Sander C, Guo T. AI-empowered perturbation proteomics for complex biological systems. CELL GENOMICS 2024; 4:100691. [PMID: 39488205 PMCID: PMC11605689 DOI: 10.1016/j.xgen.2024.100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 09/02/2024] [Accepted: 10/06/2024] [Indexed: 11/04/2024]
Abstract
The insufficient availability of comprehensive protein-level perturbation data is impeding the widespread adoption of systems biology. In this perspective, we introduce the rationale, essentiality, and practicality of perturbation proteomics. Biological systems are perturbed with diverse biological, chemical, and/or physical factors, followed by proteomic measurements at various levels, including changes in protein expression and turnover, post-translational modifications, protein interactions, transport, and localization, along with phenotypic data. Computational models, employing traditional machine learning or deep learning, identify or predict perturbation responses, mechanisms of action, and protein functions, aiding in therapy selection, compound design, and efficient experiment design. We propose to outline a generic PMMP (perturbation, measurement, modeling to prediction) pipeline and build foundation models or other suitable mathematical models based on large-scale perturbation proteomic data. Finally, we contrast modeling between artificially and naturally perturbed systems and highlight the importance of perturbation proteomics for advancing our understanding and predictive modeling of biological systems.
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Affiliation(s)
- Liujia Qian
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Rui Sun
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | | | - Chris Sander
- Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Boston, MA, USA; Ludwig Center at Harvard, Boston, MA, USA.
| | - Tiannan Guo
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China; Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China; Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.
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35
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Yang L, Kim J, Chen L, Wei W, Wang J. Detection of >400 Cluster of Differentiation Biomarkers and Pathway Proteins in Single Immune Cells by Cyclic Multiplex In Situ Tagging for Single-Cell Proteomic Studies. Anal Chem 2024; 96:17387-17395. [PMID: 39422499 PMCID: PMC11648578 DOI: 10.1021/acs.analchem.4c04239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
The identification and characterization of immune cell subpopulations are critical to reveal cell development throughout life and immune responses to environmental factors. Next-generation sequencing technologies have dramatically advanced single-cell genomics and transcriptomics for immune cell classification. However, gene expression is often not correlated with protein expression, and immunotyping is mostly accepted in protein format. Current single-cell proteomic technologies are either limited in multiplex capacity or not sensitive enough to detect the critical functional proteins. Herein, we present a single-cell cyclic multiplex in situ tagging (CycMIST) technology to simultaneously measure >400 proteins, a scale of >10 times than similar technologies. Such an ultrahigh multiplexity is achieved by reiterative staining of the single cells coupled with a MIST array for detection. This technology has been thoroughly validated through comparison with flow cytometry and fluorescence immunostaining techniques. Both peripheral blood mononuclear cells (PBMCs) and T cells are analyzed by the CycMIST technology, and almost the entire spectrum of cluster of differentiation (CD) surface markers has been measured. The landscape of fluctuation of CD protein expression in single cells has been uncovered by our technology. Further study found T cell activation signatures and protein-protein networks. This study represents the highest multiplexity of single immune cell marker measurement targeting functional proteins. With additional information from intracellular proteins of the same single cells, our technology can potentially facilitate mechanistic studies of immune responses under various disease conditions.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
| | - Juho Kim
- Institute for Systems Biology, Seattle, WA 98109
| | - Long Chen
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
| | - Wei Wei
- Institute for Systems Biology, Seattle, WA 98109
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
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36
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Senavirathna L, Ma C, Duong VA, Tsai HY, Chen R, Pan S. SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.22.618936. [PMID: 39484511 PMCID: PMC11526955 DOI: 10.1101/2024.10.22.618936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Mass spectrometry (MS)-based single-cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single-cell analysis. The single-cell MS data is acquired by msSIM technique, which sequentially applies multiple isolation cycles with the quadrupole using a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching using a well-defined spectral library. We applied the SLB-msSIM method to interrogate cellular heterogeneity among multiple cell lines and to analyze cellular trajectories during epithelial-mesenchymal transition. Our results demonstrate that SLB-msSIM is a highly sensitive and robust platform applicable to a wide range of single-cell proteomic studies.
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37
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Crouigneau R, Li YF, Auxillos J, Goncalves-Alves E, Marie R, Sandelin A, Pedersen SF. Mimicking and analyzing the tumor microenvironment. CELL REPORTS METHODS 2024; 4:100866. [PMID: 39353424 PMCID: PMC11573787 DOI: 10.1016/j.crmeth.2024.100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 07/22/2024] [Accepted: 09/09/2024] [Indexed: 10/04/2024]
Abstract
The tumor microenvironment (TME) is increasingly appreciated to play a decisive role in cancer development and response to therapy in all solid tumors. Hypoxia, acidosis, high interstitial pressure, nutrient-poor conditions, and high cellular heterogeneity of the TME arise from interactions between cancer cells and their environment. These properties, in turn, play key roles in the aggressiveness and therapy resistance of the disease, through complex reciprocal interactions between the cancer cell genotype and phenotype, and the physicochemical and cellular environment. Understanding this complexity requires the combination of sophisticated cancer models and high-resolution analysis tools. Models must allow both control and analysis of cellular and acellular TME properties, and analyses must be able to capture the complexity at high depth and spatial resolution. Here, we review the advantages and limitations of key models and methods in order to guide further TME research and outline future challenges.
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Affiliation(s)
- Roxane Crouigneau
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yan-Fang Li
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jamie Auxillos
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Eliana Goncalves-Alves
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rodolphe Marie
- Department of Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Albin Sandelin
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Stine Falsig Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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38
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Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024; 4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
Abstract
Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.
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Affiliation(s)
- Zicong Wang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Peng-Kai Liu
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Lachman
Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Wisconsin
Center for NanoBioSystems, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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39
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Stanisheuski S, Ebrahimi A, Vaidya KA, Jang HS, Yang L, Eddins AJ, Marean-Reardon C, Franco MC, Maier CS. Thermal inkjet makes label-free single-cell proteomics accessible and easy. Front Chem 2024; 12:1428547. [PMID: 39233922 PMCID: PMC11371764 DOI: 10.3389/fchem.2024.1428547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/31/2024] [Indexed: 09/06/2024] Open
Abstract
In this study, we adapted an HP D100 Single Cell Dispenser - a novel low-cost thermal inkjet (TIJ) platform with impedance-based single cell detection - for dispensing of individual cells and one-pot sample preparation. We repeatedly achieved label-free identification of up to 1,300 proteins from a single cell in a single run using an Orbitrap Fusion Lumos Mass Spectrometer coupled to either an Acquity UPLC M-class system or a Vanquish Neo UHPLC system. The developed sample processing workflow is highly reproducible, robust, and applicable to standardized 384- and 1536-well microplates, as well as glass LC vials. We demonstrate the applicability of the method for proteomics of single cells from multiple cell lines, mixed cell suspensions, and glioblastoma tumor spheroids. As additional proof of robustness, we monitored the results of genetic manipulations and the expression of engineered proteins in individual cells. Our cost-effective and robust single-cell proteomics workflow can be transferred to other labs interested in studying cells at the individual cell level.
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Affiliation(s)
| | - Arpa Ebrahimi
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Kavi Aashish Vaidya
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, United States
| | | | - Liping Yang
- Department of Chemistry, Oregon State University, Corvallis, OR, United States
| | - Alex Jordan Eddins
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, United States
| | - Carrie Marean-Reardon
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, United States
| | - Maria Clara Franco
- Department of Biochemistry and Biophysics, College of Science, Oregon State University, Corvallis, OR, United States
- Center for Translational Science, Florida International University, Port St. Lucie, FL, United States
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
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40
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Veličković M, Fillmore TL, Attah IK, Posso C, Pino JC, Zhao R, Williams SM, Veličković D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD. Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment. Anal Chem 2024; 96:12973-12982. [PMID: 39089681 PMCID: PMC11325296 DOI: 10.1021/acs.analchem.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 08/04/2024]
Abstract
There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity in a cell-type-specific manner to better understand and predict the function of complex biological systems such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (microdroplet processing in one pot for trace samples), multiplexed isobaric labeling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram levels of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 μm2) and differentiate unique protein abundance patterns in pancreas. Furthermore, the use of the microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.
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Affiliation(s)
- Marija Veličković
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Thomas L. Fillmore
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Isaac Kwame Attah
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Camilo Posso
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - James C. Pino
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Rui Zhao
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Sarah M. Williams
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Jon M. Jacobs
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Kristin E. Burnum-Johnson
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Paul D. Piehowski
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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41
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Cutler R, Corveleyn L, Ctortecka C, Cantlon J, Jacome Vaca SA, Deforce D, Vijg J, Dhaenens M, Papanastasiou M, Carr SA, Sidoli S. Mass Spectrometry-based Profiling of Single-cell Histone Post-translational Modifications to Dissect Chromatin Heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602213. [PMID: 39211145 PMCID: PMC11361047 DOI: 10.1101/2024.07.05.602213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Single-cell proteomics confidently quantifies cellular heterogeneity, yet precise quantification of post-translational modifications, such as those deposited on histone proteins, has remained elusive. Here, we developed a robust mass spectrometry-based method for the unbiased analysis of single-cell histone post-translational modifications (schPTM). schPTM identifies both single and combinatorial histone post-translational modifications (68 peptidoforms in total), which includes nearly all frequently studied histone post-translational modifications with comparable reproducibility to traditional bulk experiments. As a proof of concept, we treated cells with sodium butyrate, a histone deacetylase inhibitor, and demonstrated that our method can i) distinguish between treated and non-treated cells, ii) identify sub-populations of cells with heterogeneous response to the treatment, and iii) reveal differential co-regulation of histone post-translational modifications in the context of drug treatment. The schPTM method enables comprehensive investigation of chromatin heterogeneity at single-cell resolution and provides further understanding of the histone code.
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42
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Gao Y, Shonai D, Trn M, Zhao J, Soderblom EJ, Garcia-Moreno SA, Gersbach CA, Wetsel WC, Dawson G, Velmeshev D, Jiang YH, Sloofman LG, Buxbaum JD, Soderling SH. Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions. Nat Commun 2024; 15:6801. [PMID: 39122707 PMCID: PMC11316102 DOI: 10.1038/s41467-024-51037-x] [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: 02/20/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
One of the main drivers of autism spectrum disorder is risk alleles within hundreds of genes, which may interact within shared but unknown protein complexes. Here we develop a scalable genome-editing-mediated approach to target 14 high-confidence autism risk genes within the mouse brain for proximity-based endogenous proteomics, achieving the identification of high-specificity spatial proteomes. The resulting native proximity proteomes are enriched for human genes dysregulated in the brain of autistic individuals, and reveal proximity interactions between proteins from high-confidence risk genes with those of lower-confidence that may provide new avenues to prioritize genetic risk. Importantly, the datasets are enriched for shared cellular functions and genetic interactions that may underlie the condition. We test this notion by spatial proteomics and CRISPR-based regulation of expression in two autism models, demonstrating functional interactions that modulate mechanisms of their dysregulation. Together, these results reveal native proteome networks in vivo relevant to autism, providing new inroads for understanding and manipulating the cellular drivers underpinning its etiology.
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Affiliation(s)
- Yudong Gao
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Daichi Shonai
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Matthew Trn
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Jieqing Zhao
- Department of Biology, Duke University, Durham, NC, USA
| | - Erik J Soderblom
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, NC, USA
| | | | - Charles A Gersbach
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - William C Wetsel
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Mouse Behavioral and Neuroendocrine Analysis Core Facility, Duke University School of Medicine, Durham, NC, USA
| | - Geraldine Dawson
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Dmitry Velmeshev
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Laura G Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott H Soderling
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
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43
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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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44
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Ctortecka C, Clark NM, Boyle BW, Seth A, Mani DR, Udeshi ND, Carr SA. Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications. Nat Commun 2024; 15:5707. [PMID: 38977691 PMCID: PMC11231172 DOI: 10.1038/s41467-024-49651-w] [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: 01/24/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell remains challenging. To address some of those limitations, we present a dedicated sample preparation chip, the proteoCHIP EVO 96 that directly interfaces with the Evosep One. This, in combination with the Bruker timsTOF demonstrates double the identifications without manual sample handling and the newest generation timsTOF Ultra identifies up to 4000 with an average of 3500 protein groups per single HEK-293T without a carrier or match-between runs. Our workflow spans 4 orders of magnitude, identifies over 50 E3 ubiquitin-protein ligases, and profiles key regulatory proteins upon small molecule stimulation. This study demonstrates that the proteoCHIP EVO 96-based sample preparation with the timsTOF Ultra provides sufficient proteome depth to study complex biology beyond cell-type classifications.
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Affiliation(s)
| | | | - Brian W Boyle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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45
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Weng L, Yan G, Liu W, Tai Q, Gao M, Zhang X. Picoliter Single-Cell Reactor for Proteome Profiling by In Situ Cell Lysis, Protein Immobilization, Digestion, and Droplet Transfer. J Proteome Res 2024; 23:2441-2451. [PMID: 38833655 DOI: 10.1021/acs.jproteome.4c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Global profiling of single-cell proteomes can reveal cellular heterogeneity, thus benefiting precision medicine. However, current mass spectrometry (MS)-based single-cell proteomic sample processing still faces technical challenges associated with processing efficiency and protein recovery. Herein, we present an innovative sample processing platform based on a picoliter single-cell reactor (picoSCR) for single-cell proteome profiling, which involves in situ protein immobilization and sample transfer. PicoSCR helped minimize surface adsorptive losses by downscaling the processing volume to 400 pL with a contact area of less than 0.4 mm2. Besides, picoSCR reached highly efficient cell lysis and digestion within 30 min, benefiting from optimal reagent and high reactant concentrations. Using the picoSCR-nanoLC-MS system, over 1400 proteins were identified from an individual HeLa cell using data-dependent acquisition mode. Proteins with copy number below 1000 were identified, demonstrating this system with a detection limit of 1.7 zmol. Furthermore, we profiled the proteome of circulating tumor cells (CTCs). Data are available via ProteomeXchange with the identifier PXD051468. Proteins associated with epithelial-mesenchymal transition and neutrophil extracellular traps formation (which are both related to tumor metastasis) were observed in all CTCs. The cellular heterogeneity was revealed by differences in signaling pathways within individual cells. These results highlighted the potential of the picoSCR platform to help discover new biomarkers and explore differences in biological processes between cells.
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Affiliation(s)
- Lingxiao Weng
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Guoquan Yan
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Wei Liu
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Qunfei Tai
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
| | - Mingxia Gao
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
- Pharmacy Department, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China
| | - Xiangmin Zhang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200438, China
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46
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Xie X, Truong T, Huang S, Johnston SM, Hovanski S, Robinson A, Webber KGI, Lin HJL, Mun DG, Pandey A, Kelly RT. Multicolumn Nanoflow Liquid Chromatography with Accelerated Offline Gradient Generation for Robust and Sensitive Single-Cell Proteome Profiling. Anal Chem 2024; 96:10534-10542. [PMID: 38915247 PMCID: PMC11482043 DOI: 10.1021/acs.analchem.4c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Peptide separations that combine high sensitivity, robustness, peak capacity, and throughput are essential for extending bottom-up proteomics to smaller samples including single cells. To this end, we have developed a multicolumn nanoLC system with offline gradient generation. One binary pump generates gradients in an accelerated fashion to support multiple analytical columns, and a single trap column interfaces with all analytical columns to reduce required maintenance and simplify troubleshooting. A high degree of parallelization is possible, as one sample undergoes separation while the next sample plus its corresponding mobile phase gradient are transferred into the storage loop and a third sample is loaded into a sample loop. Selective offline elution from the trap column into the sample loop prevents salts and hydrophobic species from entering the analytical column, thus greatly enhancing column lifetime and system robustness. With this design, samples can be analyzed as fast as every 20 min at a flow rate of just 40 nL/min with close to 100% MS utilization time and continuously for as long as several months without column replacement. We utilized the system to analyze the proteomes of single cells from a multiple myeloma cell line upon treatment with the immunomodulatory imide drug lenalidomide.
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Affiliation(s)
- Xiaofeng Xie
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
- MicrOmics Technologies, LLC, Spanish Fork, Utah 84660, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
- MicrOmics Technologies, LLC, Spanish Fork, Utah 84660, United States
| | - Siqi Huang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Simon Hovanski
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Abigail Robinson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, United States
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
- MicrOmics Technologies, LLC, Spanish Fork, Utah 84660, United States
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47
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Ertürk A. Deep 3D histology powered by tissue clearing, omics and AI. Nat Methods 2024; 21:1153-1165. [PMID: 38997593 DOI: 10.1038/s41592-024-02327-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/28/2024] [Indexed: 07/14/2024]
Abstract
To comprehensively understand tissue and organism physiology and pathophysiology, it is essential to create complete three-dimensional (3D) cellular maps. These maps require structural data, such as the 3D configuration and positioning of tissues and cells, and molecular data on the constitution of each cell, spanning from the DNA sequence to protein expression. While single-cell transcriptomics is illuminating the cellular and molecular diversity across species and tissues, the 3D spatial context of these molecular data is often overlooked. Here, I discuss emerging 3D tissue histology techniques that add the missing third spatial dimension to biomedical research. Through innovations in tissue-clearing chemistry, labeling and volumetric imaging that enhance 3D reconstructions and their synergy with molecular techniques, these technologies will provide detailed blueprints of entire organs or organisms at the cellular level. Machine learning, especially deep learning, will be essential for extracting meaningful insights from the vast data. Further development of integrated structural, molecular and computational methods will unlock the full potential of next-generation 3D histology.
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Affiliation(s)
- Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Zentrum München, Neuherberg, Germany.
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University, Munich, Germany.
- School of Medicine, Koç University, İstanbul, Turkey.
- Deep Piction GmbH, Munich, Germany.
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48
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Webel H, Niu L, Nielsen AB, Locard-Paulet M, Mann M, Jensen LJ, Rasmussen S. Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning. Nat Commun 2024; 15:5405. [PMID: 38926340 PMCID: PMC11208500 DOI: 10.1038/s41467-024-48711-5] [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: 02/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Imputation techniques provide means to replace missing measurements with a value and are used in almost all downstream analysis of mass spectrometry (MS) based proteomics data using label-free quantification (LFQ). Here we demonstrate how collaborative filtering, denoising autoencoders, and variational autoencoders can impute missing values in the context of LFQ at different levels. We applied our method, proteomics imputation modeling mass spectrometry (PIMMS), to an alcohol-related liver disease (ALD) cohort with blood plasma proteomics data available for 358 individuals. Removing 20 percent of the intensities we were able to recover 15 out of 17 significant abundant protein groups using PIMMS-VAE imputations. When analyzing the full dataset we identified 30 additional proteins (+13.2%) that were significantly differentially abundant across disease stages compared to no imputation and found that some of these were predictive of ALD progression in machine learning models. We, therefore, suggest the use of deep learning approaches for imputing missing values in MS-based proteomics on larger datasets and provide workflows for these.
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Affiliation(s)
- Henry Webel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Lili Niu
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Annelaura Bach Nielsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Marie Locard-Paulet
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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49
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Orsburn BC. Single cell proteomics by mass spectrometry reveals deep epigenetic insight into the actions of an orphan histone deacetylase inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574437. [PMID: 38260471 PMCID: PMC10802306 DOI: 10.1101/2024.01.05.574437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Epigenetic programming has been shown to play a role in nearly every human system and disease where anyone has thought to look. However, the levels of heterogeneity at which epigenetic or epiproteomic modifications occur at single cell resolution across a population remains elusive. While recent advances in sequencing technology have allowed between 1 and 3 histone post-translational modifications to be analyzed in each single cell, over twenty separate chemical PTMs are known to exist, allowing thousands of possible combinations. Single cell proteomics by mass spectrometry (SCP) is an emerging technology in which hundreds or thousands of proteins can be directly quantified in typical human cells. As the proteins detected and quantified by SCP are heavily biased toward proteins of highest abundance, chromatin proteins are an attractive target for analysis. To this end, I applied SCP to the analysis of cancer cells treated with mocetinostat, a class specific histone deacetylase inhibitor. I find that 16 PTMs can be confidently identified and localized with high site specificity in single cells. In addition, the high abundance of histone proteins allows higher throughput methods to be utilized for SCP than previously described. While quantitative accuracy suffers when analyzing more than 700 cells per day, 9 histone proteins can be measured in single cells analyzed at even 3,500 cells per day, a throughput 10-fold greater than any previous report. In addition, the unbiased global approach utilized herein identifies a previously uncharacterized response to this drug through the S100-A8/S100-A9 protein complex partners. This response is observed in nearly every cell of the over 1,000 analyzed in this study, regardless of the relative throughput of the method utilized. While limitations exist in the methods described herein, current technologies can easily improve upon the results presented here to allow comprehensive analysis of histone PTMs to be performed in any mass spectrometry lab. All raw and processed data described in this study has been made publicly available through the ProteomeXchange/MASSIVE repository system as MSV000093434.
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50
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Rivero-Garcia I, Torres M, Sánchez-Cabo F. Deep generative models in single-cell omics. Comput Biol Med 2024; 176:108561. [PMID: 38749321 DOI: 10.1016/j.compbiomed.2024.108561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
Abstract
Deep Generative Models (DGMs) are becoming instrumental for inferring probability distributions inherent to complex processes, such as most questions in biomedical research. For many years, there was a lack of mathematical methods that would allow this inference in the scarce data scenario of biomedical research. The advent of single-cell omics has finally made square the so-called "skinny matrix", allowing to apply mathematical methods already extensively used in other areas. Moreover, it is now possible to integrate data at different molecular levels in thousands or even millions of samples, thanks to the number of single-cell atlases being collaboratively generated. Additionally, DGMs have proven useful in other frequent tasks in single-cell analysis pipelines, from dimensionality reduction, cell type annotation to RNA velocity inference. In spite of its promise, DGMs need to be used with caution in biomedical research, paying special attention to its use to answer the right questions and the definition of appropriate error metrics and validation check points that confirm not only its correct use but also its relevance. All in all, DGMs provide an exciting tool that opens a bright future for the integrative analysis of single-cell -omics to understand health and disease.
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Affiliation(s)
- Inés Rivero-Garcia
- Universidad Politécnica de Madrid, Madrid, 28040, Spain; Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Miguel Torres
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Fátima Sánchez-Cabo
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain.
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