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Li M, Zuo J, Yang K, Wang P, Zhou S. Proteomics mining of cancer hallmarks on a single-cell resolution. MASS SPECTROMETRY REVIEWS 2024; 43:1019-1040. [PMID: 37051664 DOI: 10.1002/mas.21842] [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: 03/10/2022] [Revised: 11/25/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated proteome is an essential contributor in carcinogenesis. Protein fluctuations fuel the progression of malignant transformation, such as uncontrolled proliferation, metastasis, and chemo/radiotherapy resistance, which severely impair therapeutic effectiveness and cause disease recurrence and eventually mortality among cancer patients. Cellular heterogeneity is widely observed in cancer and numerous cell subtypes have been characterized that greatly influence cancer progression. Population-averaged research may not fully reveal the heterogeneity, leading to inaccurate conclusions. Thus, deep mining of the multiplex proteome at the single-cell resolution will provide new insights into cancer biology, to develop prognostic biomarkers and treatments. Considering the recent advances in single-cell proteomics, herein we review several novel technologies with particular focus on single-cell mass spectrometry analysis, and summarize their advantages and practical applications in the diagnosis and treatment for cancer. Technological development in single-cell proteomics will bring a paradigm shift in cancer detection, intervention, and therapy.
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Affiliation(s)
- Maomao Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jing Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ping Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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Senavirathna L, Ma C, Chen R, Pan S. Spectral Library-Based Single-Cell Proteomics Resolves Cellular Heterogeneity. Cells 2022; 11:cells11152450. [PMID: 35954294 PMCID: PMC9368228 DOI: 10.3390/cells11152450] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 02/07/2023] Open
Abstract
Dissecting the proteome of cell types and states at single-cell resolution, while being highly challenging, has significant implications in basic science and biomedicine. Mass spectrometry (MS)-based single-cell proteomics represents an emerging technology for system-wide, unbiased profiling of proteins in single cells. However, significant challenges remain in analyzing an extremely small amount of proteins collected from a single cell, as a proteome-wide amplification of proteins is not currently feasible. Here, we report an integrated spectral library-based single-cell proteomics (SLB-SCP) platform that is ultrasensitive and well suited for a large-scale analysis. To overcome the low MS/MS signal intensity intrinsically associated with a single-cell analysis, this approach takes an alternative approach by extracting a breadth of information that specifically defines the physicochemical characteristics of a peptide from MS1 spectra, including monoisotopic mass, isotopic distribution, and retention time (hydrophobicity), and uses a spectral library for proteomic identification. This conceptually unique MS platform, coupled with the DIRECT sample preparation method, enabled identification of more than 2000 proteins in a single cell to distinguish different proteome landscapes associated with cellular types and heterogeneity. We characterized individual normal and cancerous pancreatic ductal cells (HPDE and PANC-1, respectively) and demonstrated the substantial difference in the proteomes between HPDE and PANC-1 at the single-cell level. A significant upregulation of multiple protein networks in cancer hallmarks was identified in the PANC-1 cells, functionally discriminating the PANC-1 cells from the HPDE cells. This integrated platform can be built on high-resolution MS and widely accepted proteomic software, making it possible for community-wide applications.
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Affiliation(s)
- Lakmini Senavirathna
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Cheng Ma
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ru Chen
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sheng Pan
- The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Correspondence:
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Serelli-Lee V, Ito K, Koibuchi A, Tanigawa T, Ueno T, Matsushima N, Imai Y. A State-of-the-Art Roadmap for Biomarker-Driven Drug Development in the Era of Personalized Therapies. J Pers Med 2022; 12:jpm12050669. [PMID: 35629092 PMCID: PMC9143954 DOI: 10.3390/jpm12050669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/30/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
Advances in biotechnology have enabled us to assay human tissue and cells to a depth and resolution that was never possible before, redefining what we know as the “biomarker”, and how we define a “disease”. This comes along with the shift of focus from a “one-drug-fits-all” to a “personalized approach”, placing the drug development industry in a highly dynamic landscape, having to navigate such disruptive trends. In response to this, innovative clinical trial designs have been key in realizing biomarker-driven drug development. Regulatory approvals of cancer genome sequencing panels and associated targeted therapies has brought personalized medicines to the clinic. Increasing availability of sophisticated biotechnologies such as next-generation sequencing (NGS) has also led to a massive outflux of real-world genomic data. This review summarizes the current state of biomarker-driven drug development and highlights examples showing the utility and importance of the application of real-world data in the process. We also propose that all stakeholders in drug development should (1) be conscious of and efficiently utilize real-world evidence and (2) re-vamp the way the industry approaches drug development in this era of personalized medicines.
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Affiliation(s)
- Victoria Serelli-Lee
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Eli Lilly Japan K.K., 5-1-28 Isogamidori, Chuo-ku, Kobe 651-0086, Japan
- Correspondence: (V.S.-L.); (Y.I.)
| | - Kazumi Ito
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan;
| | - Akira Koibuchi
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Astellas Pharma Inc., 2-5-1 Nihonbashi-Honcho, Chuo-ku, Tokyo 103-8411, Japan
| | - Takahiko Tanigawa
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Bayer Yakuhin Ltd., 2-4-9, Umeda, Kita-ku, Osaka 530-0001, Japan
| | - Takayo Ueno
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Bristol Myers Squibb K.K., 6-5-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-1334, Japan
| | - Nobuko Matsushima
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Janssen Pharmaceutical K.K., 3-5-2, Nishikanda, Chiyoda-ku, Tokyo 101-0065, Japan
| | - Yasuhiko Imai
- Clinical Evaluation Sub-Committee, Medicinal Evaluation Committee, Japan Pharmaceuticals Manufacturers Association, 2-3-11, Nihonbashi Honcho, Chuo-ku, Tokyo 103-0023, Japan; (A.K.); (T.T.); (T.U.); (N.M.)
- Bristol Myers Squibb K.K., 6-5-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo 163-1334, Japan
- Correspondence: (V.S.-L.); (Y.I.)
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Yang L, George J, Wang J. Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies. Proteomics 2020; 20:e1900226. [PMID: 31729152 PMCID: PMC7225074 DOI: 10.1002/pmic.201900226] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/14/2019] [Indexed: 12/20/2022]
Abstract
The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single-cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well-established methods for single-cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining-based techniques for single-cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single-cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single-cell proteomic technologies in cell biology and medical research are discussed.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
| | - Justin George
- Department of Chemistry, State University of New York, University at Albany, Albany, NY 12222
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
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Abstract
Cardiovascular diseases are the leading cause of death worldwide. Complex diseases with highly heterogenous disease progression among patient populations, cardiovascular diseases feature multifactorial contributions from both genetic and environmental stressors. Despite significant effort utilizing multiple approaches from molecular biology to genome-wide association studies, the genetic landscape of cardiovascular diseases, particularly for the nonfamilial forms of heart failure, is still poorly understood. In the past decade, systems-level approaches based on omics technologies have become an important approach for the study of complex traits in large populations. These advances create opportunities to integrate genetic variation with other biological layers to identify and prioritize candidate genes, understand pathogenic pathways, and elucidate gene-gene and gene-environment interactions. In this review, we will highlight some of the recent progress made using systems genetics approaches to uncover novel mechanisms and molecular bases of cardiovascular pathophysiological manifestations. The key technology and data analysis platforms necessary to implement systems genetics will be described, and the current major challenges and future directions will also be discussed. For complex cardiovascular diseases, such as heart failure, systems genetics represents a powerful strategy to obtain mechanistic insights and to develop individualized diagnostic and therapeutic regiments, paving the way for precision cardiovascular medicine.
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Affiliation(s)
- Christoph D. Rau
- Departments of Anesthesiology, Medicine, Physiology
- Current address: Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599
| | - Aldons J. Lusis
- Department of Human Genetics and Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, Physiology
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Abstract
Breaking down the silos between disciplines to accelerate the pace of cancer research is a key paradigm for the Cancer Moonshot. Molecular analyses of cancer biology have tended to segregate between a focus on nucleic acids-DNA, RNA, and their modifications-and a focus on proteins and protein function. Proteogenomics represents a fusion of those two approaches, leveraging the strengths of each to provide a more integrated vision of the flow of information from DNA to RNA to protein and eventually function at the molecular level. Proteogenomic studies have been incorporated into multiple activities associated with the Cancer Moonshot, demonstrating substantial added value. Innovative study designs integrating genomic, transcriptomic, and proteomic data, particularly those using clinically relevant samples and involving clinical trials, are poised to provide new insights regarding cancer risk, progression, and response to therapy.
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Prado RC, Borges ER. MICROBIOREACTORS AS ENGINEERING TOOLS FOR BIOPROCESS DEVELOPMENT. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2018. [DOI: 10.1590/0104-6632.20180354s20170433] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- R. C. Prado
- Federal University of Rio de Janeiro, Brazil
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Su Y, Shi Q, Wei W. Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis. Proteomics 2017; 17. [PMID: 28128880 DOI: 10.1002/pmic.201600267] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/11/2022]
Abstract
New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data. The underlying assumptions, unique features, and limitations of the analytical methods with the designated biological questions they seek to answer will be discussed. Particular attention will be given to those information theoretical approaches that are anchored in a set of first principles of physics and can yield detailed (and often surprising) predictions.
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Affiliation(s)
- Yapeng Su
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
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Caen O, Lu H, Nizard P, Taly V. Microfluidics as a Strategic Player to Decipher Single-Cell Omics? Trends Biotechnol 2017. [DOI: 10.1016/j.tibtech.2017.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Protein and lipid kinases are deregulated in most, if not all, cancers and are among the most valuable therapeutic targets in these diseases. Despite the introduction of dozens of effective kinase inhibitors into clinical practice, the development of drug resistance remains a major barrier to treatment because of adaption of cellular signaling pathways to bypass targeted kinases. So that the basal and adaptive responses of kinases in cancer can be better understood, new methods have emerged that allow simultaneous and unbiased measurement of the activation state of a substantial fraction of the entire kinome. Here, we discuss such kinome-profiling methodologies, emphasizing the relative strengths and weaknesses of each approach.
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Affiliation(s)
- Maria Radu
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA
| | - Jonathan Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111-2497, USA
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Lu Y, Yang L, Wei W, Shi Q. Microchip-based single-cell functional proteomics for biomedical applications. LAB ON A CHIP 2017; 17:1250-1263. [PMID: 28280819 PMCID: PMC5459479 DOI: 10.1039/c7lc00037e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical frameworks to extract new biology. In this review article, we highlight a few biological and clinical applications in which microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating a well-controlled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies.
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Affiliation(s)
- Yao Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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