1
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Steinbach MK, Leipert J, Matzanke T, Tholey A. Digital Microfluidics for Sample Preparation in Low-Input Proteomics. SMALL METHODS 2024:e2400495. [PMID: 39205538 DOI: 10.1002/smtd.202400495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Low-input proteomics, also referred to as micro- or nanoproteomics, has become increasingly popular as it allows one to elucidate molecular processes in rare biological materials. A major prerequisite for the analytics of minute protein amounts, e.g., derived from low cell numbers, down to single cells, is the availability of efficient sample preparation methods. Digital microfluidics (DMF), a technology allowing the handling and manipulation of low liquid volumes, has recently been shown to be a powerful and versatile tool to address the challenges in low-input proteomics. Here, an overview is provided on recent advances in proteomics sample preparation using DMF. In particular, the capability of DMF to isolate proteomes from cells and small model organisms, and to perform all necessary chemical sample preparation steps, such as protein denaturation and proteolytic digestion on-chip, are highlighted. Additionally, major prerequisites to making these steps compatible with follow-up analytical methods such as liquid chromatography-mass spectrometry will be discussed.
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Affiliation(s)
- Max K Steinbach
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Jan Leipert
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Theo Matzanke
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
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2
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Tan CH, Wang TY, Park H, Lomenick B, Chou TF, Sternberg PW. Single-tissue proteomics in Caenorhabditis elegans reveals proteins resident in intestinal lysosome-related organelles. Proc Natl Acad Sci U S A 2024; 121:e2322588121. [PMID: 38861598 PMCID: PMC11194598 DOI: 10.1073/pnas.2322588121] [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: 12/25/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of biomolecules; lysosome-related organelles known as gut granules are important for many of these functions. Aspects of intestine biology are not well understood, including the export of the nutrients it imports and the molecules it synthesizes, as well as the complete functions and protein content of the gut granules. Here, we report a mass spectrometry (MS)-based proteomic analysis of the intestine of the Caenorhabditis elegans and of its gut granules. Overall, we identified approximately 5,000 proteins each in the intestine and the gonad and showed that most of these proteins can be detected in samples extracted from a single worm, suggesting the feasibility of individual-level genetic analysis using proteomes. Comparing proteomes and published transcriptomes of the intestine and the gonad, we identified proteins that appear to be synthesized in the intestine and then transferred to the gonad. To identify gut granule proteins, we compared the proteome of individual intestines deficient in gut granules to the wild type. The identified gut granule proteome includes proteins known to be exclusively localized to the granules and additional putative gut granule proteins. We selected two of these putative gut granule proteins for validation via immunohistochemistry, and our successful confirmation of both suggests that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single-tissue MS-based proteomic analysis in small organisms and in its future utility.
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Affiliation(s)
- Chieh-Hsiang Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Ting-Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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3
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Zhu T, Li S, Liu D, Zhang X, Zhou L, Zhou R, Yang B. Single-worm quantitative proteomics reveals aging heterogeneity in isogenic Caenorhabditis elegans. Aging Cell 2024; 23:e14055. [PMID: 38044578 PMCID: PMC10928571 DOI: 10.1111/acel.14055] [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: 06/26/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
The heterogeneity of aging has been investigated at cellular and organic levels in the mouse model and human, but the exploration of aging heterogeneity at whole-organism level is lacking. C. elegans is an ideal model organism for studying this question as they are self-fertilized and cultured in the same chamber. Despite the tremendous progress made in single-cell proteomic analysis, there is few single-worm proteomics studies about aging. Here, we apply single-worm quantitative mass spectrometry to quantify the heterogenous proteomic changes during aging across individuals, a total of 3524 proteins from 157 C. eleagns individuals were quantified. A reconstructed C. elegans aging trajectory and proteomic landscape of fast-aging individuals were used to analyze the heterogeneity of C. elegans aging. We characterized inter-individual proteomic variation during aging and revealed contributing factors that distinguish fast-aging individuals from their siblings.
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Affiliation(s)
- Tian‐Yi Zhu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | | | - Dan‐Dan Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Xiajun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Lianqi Zhou
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
| | - Rong Zhou
- Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Bing Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences InstituteZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhouChina
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4
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Yang C, Gan X, Zeng Y, Xu Z, Xu L, Hu C, Ma H, Chai B, Hu S, Chai Y. Advanced design and applications of digital microfluidics in biomedical fields: An update of recent progress. Biosens Bioelectron 2023; 242:115723. [PMID: 37832347 DOI: 10.1016/j.bios.2023.115723] [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: 07/05/2023] [Revised: 09/11/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
Significant breakthroughs have been made in digital microfluidic (DMF)-based technologies over the past decades. DMF technology has attracted great interest in bioassays depending on automatic microscale liquid manipulations and complicated multi-step processing. In this review, the recent advances of DMF platforms in the biomedical field were summarized, focusing on the integrated design and applications of the DMF system. Firstly, the electrowetting-on-dielectric principle, fabrication of DMF chips, and commercialization of the DMF system were elaborated. Then, the updated droplets and magnetic beads manipulation strategies with DMF were explored. DMF-based biomedical applications were comprehensively discussed, including automated sample preparation strategies, immunoassays, molecular diagnosis, blood processing/testing, and microbe analysis. Emerging applications such as enzyme activity assessment and DNA storage were also explored. The performance of each bioassay was compared and discussed, providing insight into the novel design and applications of the DMF technology. Finally, the advantages, challenges, and future trends of DMF systems were systematically summarized, demonstrating new perspectives on the extensive applications of DMF in basic research and commercialization.
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Affiliation(s)
- Chengbin Yang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Xiangyu Gan
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Yuping Zeng
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Zhourui Xu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
| | - Longqian Xu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Chenxuan Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Hanbin Ma
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China; Guangdong ACXEL Micro & Nano Tech Co., Ltd, Foshan, China.
| | - Bao Chai
- Department of Dermatology, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; Department of Dermatology, The 6th Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China.
| | - Siyi Hu
- CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.
| | - Yujuan Chai
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, China.
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5
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von Mikecz A. Elegant Nematodes Improve Our Understanding of Human Neuronal Diseases, the Role of Pollutants and Strategies of Resilience. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16755-16763. [PMID: 37874738 PMCID: PMC10634345 DOI: 10.1021/acs.est.3c04580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
The prevalence of neurodegenerative disorders such as Alzheimer's and Parkinson's disease are rising globally. The role of environmental pollution in neurodegeneration is largely unknown. Thus, this perspective advocates exposome research in C. elegans models of human diseases. The models express amyloid proteins such as Aβ, recapitulate the degeneration of specifically vulnerable neurons and allow for correlated neurobehavioral phenotyping throughout the entire life span of the nematode. Neurobehavioral traits like locomotion gaits, rigidity, or cognitive decline are quantifiable and carefully mimic key aspects of the human diseases. Underlying molecular pathways of neurodegeneration are elucidated in pollutant-exposed C. elegans Alzheimer's or Parkinson's models by transcriptomics (RNA-seq), mass spectrometry-based proteomics and omics addressing other biochemical traits. Validation of the identified disease pathways can be achieved by genome-wide association studies in matching human cohorts. A consistent One Health approach includes isolation of nematodes from contaminated sites and their comparative investigation by imaging, neurobehavioral profiling and single worm proteomics. C. elegans models of neurodegenerative diseases are likewise well-suited for high throughput methods that provide a promising strategy to identify resilience pathways of neurosafety and keep up with the number of pollutants, nonchemical exposome factors, and their interactions.
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Affiliation(s)
- Anna von Mikecz
- IUF − Leibniz Research Institute
of Environmental Medicine GmbH, Auf’m Hennekamp 50, 40225 Duesseldorf, Germany
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6
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Shen J, Liao J, Liu H, Liu C, Li C, Cheng H, Yang H, Chen H. A low-temperature digital microfluidic system used for protein-protein interaction detection. LAB ON A CHIP 2023; 23:4390-4399. [PMID: 37721054 DOI: 10.1039/d3lc00386h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The occurrence, development and prediction of various biological processes and diseases are inseparable from the protein-protein interaction (PPI), so it is extremely meaningful to perfect PPI networks. However, shortcomings of traditional detection methods, such as protein degradation, long detection time, complex operation, poor automation and high cost, restrict the rapid development of PPI networks. Here, a low-temperature digital microfluidic (LTDMF) system-based PPI detection box (LTDMF-PPI-Box) was developed to achieve rapid, lossless and efficient PPI detection. It consists of a PMMA shell, LTDMF-PPI and an integrated temperature control system. LTDMF reduces the PPI detection time from tens of hours to 1.5 hours by programmatically controlling the movement of droplets. Moreover, an integrated thermoelectric cooler (TEC) ensures an operating temperature of 4 °C, resulting in a protein protection up to 90%. The interaction between RILP protein and Rab26 protein which has a close connection to insulin secretion was demonstrated as a prototype to illustrate the feasibility of the LTDMF-PPI-Box. LTDMF with automation characteristics is capable of meeting the requirement of high-throughput screening of interacting proteins; therefore, the LTDMF-PPI-Box is expected to accelerate the establishment of the PPI network in the future.
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Affiliation(s)
- Jienan Shen
- Center for Bionic Sensing and Intelligence, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, P. R. China.
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, Fujian, P. R. China.
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen 518038, Guangdong, P. R. China
| | - Jiaqi Liao
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, Fujian, P. R. China.
| | - Huiying Liu
- The Institute of Translational Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi, P. R. China
| | - Chunyan Liu
- Department of Dermatology, Longgang Central Hospital, Shenzhen 518172, Guangdong, P. R. China
| | - Chonghao Li
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, Fujian, P. R. China.
| | - Hao Cheng
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, Fujian, P. R. China.
| | - Hui Yang
- Center for Bionic Sensing and Intelligence, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, Guangdong, P. R. China.
| | - Hong Chen
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, Fujian, P. R. China.
- Jiujiang Research Institute of Xiamen University, Jiujiang 332000, Jiangxi, P. R. China
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7
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Chan C, Peng J, Rajesh V, Scott EY, Sklavounos AA, Faiz M, Wheeler AR. Digital Microfluidics for Microproteomic Analysis of Minute Mammalian Tissue Samples Enabled by a Photocleavable Surfactant. J Proteome Res 2023; 22:3242-3253. [PMID: 37651704 DOI: 10.1021/acs.jproteome.3c00281] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Proteome profiles of precious tissue samples have great clinical potential for accelerating disease biomarker discovery and promoting novel strategies for early diagnosis and treatment. However, tiny clinical tissue samples are often difficult to handle and analyze with conventional proteomic methods. Automated digital microfluidic (DMF) workflows facilitate the manipulation of size-limited tissue samples. Here, we report the assessment of a DMF microproteomics workflow enabled by a photocleavable surfactant for proteomic analysis of minute tissue samples. The surfactant 4-hexylphenylazosulfonate (Azo) was found to facilitate fast droplet movement on DMF and enhance the proteomics analysis. Comparisons of Azo and n-Dodecyl β-d-maltoside (DDM) using small samples of HeLa digest standards and MCF-7 cell digests revealed distinct differences at the peptide level despite similar results at the protein level. The DMF microproteomics workflow was applied for the sample preparation of ∼3 μg biopsies from murine brain tissue. A total of 1969 proteins were identified in three samples, including established neural biomarkers and proteins related to synaptic signaling. Going forward, we propose that the Azo-enabled DMF workflow has the potential to advance the practical clinical application of DMF for the analysis of size-limited tissue samples.
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Affiliation(s)
- Calvin Chan
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 3G9, Ontario, Canada
| | - Vigneshwar Rajesh
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
| | - Erica Y Scott
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 3G9, Ontario, Canada
- Department of Surgery, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Ontario, Canada
| | - Maryam Faiz
- Department of Surgery, University of Toronto, Toronto M5S 1A8, Ontario, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto M5S 3G9, Ontario, Canada
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8
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Anastasi F, Botto A, Immordino B, Giovannetti E, McDonnell LA. Proteomics analysis of circulating small extracellular vesicles: Focus on the contribution of EVs to tumor metabolism. Cytokine Growth Factor Rev 2023; 73:3-19. [PMID: 37652834 DOI: 10.1016/j.cytogfr.2023.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
The term small extracellular vesicle (sEV) is a comprehensive term that includes any type of cell-derived, membrane-delimited particle that has a diameter < 200 nm, and which includes exosomes and smaller microvesicles. sEVs transfer bioactive molecules between cells and are crucial for cellular homeostasis and particularly during tumor development, where sEVs provide important contributions to the formation of the premetastic niche and to their altered metabolism. sEVs are thus legitimate targets for intervention and have also gained increasing interest as an easily accessible source of biomarkers because they can be rapidly isolated from serum/plasma and their molecular cargo provides information on their cell-of origin. To target sEVs that are specific for a given cell/disease it is essential to identify EV surface proteins that are characteristic of that cell/disease. Mass-spectrometry based proteomics is widely used for the identification and quantification of sEV proteins. The methods used for isolating the sEVs, preparing the sEV sample for proteomics analysis, and mass spectrometry analysis, can have a strong influence on the results and requires careful consideration. This review provides an overview of the approaches used for sEV proteomics and discusses the inherent compromises regarding EV purity versus depth of coverage. Additionally, it discusses the practical applications of the methods to unravel the involvement of sEVs in regulating the metabolism of pancreatic ductal adenocarcinoma (PDAC). The metabolic reprogramming in PDAC includes enhanced glycolysis, elevated glutamine metabolism, alterations in lipid metabolism, mitochondrial dysfunction and hypoxia, all of which are crucial in promoting tumor cell growth. A thorough understanding of these metabolic adaptations is imperative for the development of targeted therapies to exploit PDAC's vulnerabilities.
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Affiliation(s)
- Federica Anastasi
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; National Enterprise for NanoScience and NanoTechnology, Scuola Normale Superiore, Pisa, Italy; BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | - Asia Botto
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Benoit Immordino
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; Scuola Superiore Sant'Anna, Pisa, Italy
| | - Elisa Giovannetti
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy; Department of Medical Oncology, Amsterdam UMC, Cancer Center Amsterdam, Vrije Universiteit, Amsterdam, the Netherlands
| | - Liam A McDonnell
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, PI, Italy.
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9
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Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler AR, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. CELL REPORTS METHODS 2023; 3:100511. [PMID: 37426761 PMCID: PMC10326451 DOI: 10.1016/j.crmeth.2023.100511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.
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Affiliation(s)
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Zhaoguan Wu
- CHU Sainte Justine Research Center, Montreal, QC, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Department of Chemistry, University of Montreal, Montreal, QC, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Etienne Caron
- CHU Sainte Justine Research Center, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, QC, Canada
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10
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Gebreyesus ST, Muneer G, Huang CC, Siyal AA, Anand M, Chen YJ, Tu HL. Recent advances in microfluidics for single-cell functional proteomics. LAB ON A CHIP 2023; 23:1726-1751. [PMID: 36811978 DOI: 10.1039/d2lc01096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.
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Affiliation(s)
- Sofani Tafesse Gebreyesus
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | | | - Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
| | - Mihir Anand
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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11
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Peng J, Chan C, Zhang S, Sklavounos AA, Olson ME, Scott EY, Hu Y, Rajesh V, Li BB, Chamberlain MD, Zhang S, Peng H, Wheeler AR. All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis. Chem Sci 2023; 14:2887-2900. [PMID: 36937585 PMCID: PMC10016607 DOI: 10.1039/d3sc00560g] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Highly sensitive and reproducible analysis of samples containing low amounts of protein is restricted by sample loss and the introduction of contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic sample reduction, alkylation, digestion, isotopic labeling and analysis. The system features end-to-end automation, with integrated thermal control for digestion, optimized droplet additives for sample manipulation and analysis, and an automated interface to liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Dimethyl labeling was integrated into the pipeline to allow for relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, and AKR1C2) and pathways were observed between model breast cancer cell lines related to hormone response, cell metabolism, and cell morphology. Furthermore, differentially quantified proteins (such as PGS2, UGDH, ASPN, LUM, COEA1, and PRELP) were found in comparisons of healthy and cancer breast tissues, suggesting potential utility of the All-in-One pipeline for the emerging application of proteomic cancer sub-typing. In sum, the All-in-One pipeline represents a powerful new tool for automated proteome processing and analysis, with the potential to be useful for evaluating mass-limited samples for a wide range of applications.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Calvin Chan
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Shuailong Zhang
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Mechatronical Engineering, Beijing Institute of Technology Beijing 100081 China
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, Beijing Institute of Technology Beijing 100081 China
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
| | - Maxwell E Olson
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Erica Y Scott
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Yechen Hu
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Vigneshwar Rajesh
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Bingyu B Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
- Saskatchewan Cancer Agency, University of Saskatchewan 107 Wiggins Road Saskatoon SK S7N 5E5 Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue Toronto ON M5G 1X5 Canada
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha Hunan 410000 China
| | - Hui Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Environment, University of Toronto 33 Willcocks Street Toronto ON M5S 3E8 Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
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