1
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Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. Nat Commun 2024; 15:5888. [PMID: 39003254 PMCID: PMC11246512 DOI: 10.1038/s41467-024-50046-0] [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: 09/04/2023] [Accepted: 06/27/2024] [Indexed: 07/15/2024] Open
Abstract
Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.
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Affiliation(s)
- Yang Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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2
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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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3
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Dutta T, Vlassakis J. Microscale measurements of protein complexes from single cells. Curr Opin Struct Biol 2024; 87:102860. [PMID: 38848654 DOI: 10.1016/j.sbi.2024.102860] [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: 03/08/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Proteins execute numerous cell functions in concert with one another in protein-protein interactions (PPI). While essential in each cell, such interactions are not identical from cell to cell. Instead, PPI heterogeneity contributes to cellular phenotypic heterogeneity in health and diseases such as cancer. Understanding cellular phenotypic heterogeneity thus requires measurements of properties of PPIs such as abundance, stoichiometry, and kinetics at the single-cell level. Here, we review recent, exciting progress in single-cell PPI measurements. Novel technology in this area is enabled by microscale and microfluidic approaches that control analyte concentration in timescales needed to outpace PPI disassembly kinetics. We describe microscale innovations, needed technical capabilities, and methods poised to be adapted for single-cell analysis in the near future.
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Affiliation(s)
- Tanushree Dutta
- Department of Bioengineering, Rice University, Houston, TX 77005, USA. https://twitter.com/duttatanu1717
| | - Julea Vlassakis
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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4
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Islam MN, Liu Y, Herr AE. Electromigration of Charged Analytes Through Immiscible Fluids in Multiphasic Electrophoresis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596534. [PMID: 38853831 PMCID: PMC11160796 DOI: 10.1101/2024.05.29.596534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Multiphasic buffer systems have been of greatest interest in electrophoresis and liquid-liquid electrotransfer; this study extends that foundation by exploring the interplay of the geometric and viscous properties of an interleaving oil layer on the electrotransfer of a charged analyte from an aqueous solution into a hydrogel. We utilized finite element analysis to examine two complementary configurations: one being electrotransfer of a charged analyte (protein) in an aqueous phase into a surrounding hydrogel layer and another being electrotransfer of the protein from that originating aqueous phase - through an interleaving oil layer of predetermined viscosity and thickness - and into a surrounding hydrogel layer. Results indicate that the presence of an oil layer leads to increased skew of the injected peak. To explain this difference in injection dispersion, we utilize Probstein's framework and compare the Péclet (Pe) number with the ratio between length scales characteristic to the axial and radial dispersion, respectively. The formulation assigns electrotransfer conditions into six different dispersion regimes. We show that the presence or absence of an interleaving oil layer moves the observed peak dispersion into distinct electrotransfer regimes; the presence of an oil layer augments the electrophoretic mobility mismatch between the different phases, resulting in a five-fold increase in Pe and a six-fold increase in the ratio between the axial to radial dispersion characteristic lengths. We further show that oil viscosity significantly influences resultant injection dispersion. A decrease in oil-layer viscosity from 0.08 Pa·s to 0.02 Pa·s results in a >100% decrease in injection dispersion. Our theoretical predictions were experimentally validated by comparing the electrotransfer regimes of three different mineral oil samples. We show that lowering the oil viscosity to 0.0039 Pa·s results in an injection regime similar to that of the absence of an oil layer. Additionally, we measure the migration distance and show that average electromigration velocity over the transit duration is inversely proportional to the viscosity of an interleaving oil layer. Understanding of the impact of electrotransfer of charged species across multiple immiscible fluid layers on peak dispersion informs the design of multiphasic electrophoresis systems.
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Affiliation(s)
- Md Nazibul Islam
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Yang Liu
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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5
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Merteroglu M, Santoro MM. Exploiting the metabolic vulnerability of circulating tumour cells. Trends Cancer 2024; 10:541-556. [PMID: 38580535 DOI: 10.1016/j.trecan.2024.03.004] [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: 11/22/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Metastasis has a major part in the severity of disease and lethality of cancer. Circulating tumour cells (CTCs) represent a reservoir of metastatic precursors in circulation, most of which cannot survive due to hostile conditions in the bloodstream. Surviving cells colonise a secondary site based on a combination of physical, metabolic, and oxidative stress protection states required for that environment. Recent advances in CTC isolation methods and high-resolution 'omics technologies are revealing specific metabolic pathways that support this selection of CTCs. In this review, we discuss recent advances in our understanding of CTC biology and discoveries of adaptations in metabolic pathways during their selection. Understanding these traits and delineating mechanisms by which they confer acquired resistance or vulnerability in CTCs is crucial for developing successful prognostic and therapeutic strategies in cancer.
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Huang CH, Lai YJ, Chen LN, Hung YH, Tu HY, Cheng CJ. Label-Free Three-Dimensional Morphological Characterization of Cell Death Using Holographic Tomography. SENSORS (BASEL, SWITZERLAND) 2024; 24:3435. [PMID: 38894226 PMCID: PMC11174527 DOI: 10.3390/s24113435] [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: 04/10/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
This study presents a novel label-free approach for characterizing cell death states, eliminating the need for complex molecular labeling that may yield artificial or ambiguous results due to technical limitations in microscope resolution. The proposed holographic tomography technique offers a label-free avenue for capturing precise three-dimensional (3D) refractive index morphologies of cells and directly analyzing cellular parameters like area, height, volume, and nucleus/cytoplasm ratio within the 3D cellular model. We showcase holographic tomography results illustrating various cell death types and elucidate distinctive refractive index correlations with specific cell morphologies complemented by biochemical assays to verify cell death states. These findings hold promise for advancing in situ single cell state identification and diagnosis applications.
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Affiliation(s)
- Chung-Hsuan Huang
- Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
| | - Yun-Ju Lai
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; (L.-N.C.); (Y.-H.H.)
| | - Li-Nian Chen
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; (L.-N.C.); (Y.-H.H.)
| | - Yu-Hsuan Hung
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan; (L.-N.C.); (Y.-H.H.)
| | - Han-Yen Tu
- Department of Electrical Engineering, Chinese Culture University, Taipei 11114, Taiwan;
| | - Chau-Jern Cheng
- Institute of Electro-Optical Engineering, National Taiwan Normal University, Taipei 11677, Taiwan;
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7
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Xie H, Guo W, Jiang H, Zhang T, Zhao L, Hu J, Gao S, Song S, Xu J, Xu L, Sun X, Ding Y, Jiang L, Ding X. Photosensitive Hydrogel with Temperature-Controlled Reversible Nano-Apertures for Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308569. [PMID: 38483955 PMCID: PMC11109651 DOI: 10.1002/advs.202308569] [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: 11/09/2023] [Revised: 02/15/2024] [Indexed: 05/23/2024]
Abstract
Single cell western blot (scWB) is one of the most important methods for cellular heterogeneity profiling. However, current scWB based on conventional photoactive polyacrylamide hydrogel material suffers from the tradeoff between in-gel probing and separation resolution. Here, a highly sensitive temperature-controlled single-cell western blotting (tc-scWB) method is introduced, which is based on a thermo/photo-dualistic-sensitive polyacrylamide hydrogel, namely acrylic acid-functionalized graphene oxide (AFGO) assisted, N-isopropylacrylamide modified polyacrylamide (ANP) hydrogel. The ANP hydrogel is contracted at high-temperature to constrain protein band diffusion during microchip electrophoretic separation, while the gel aperture is expanded under low-temperature for better antibody penetration into the hydrogel. The tc-scWB method enables the separation and profiling of small-molecule-weight proteins with highly crosslinked gel (12% T) in SDS-PAGE. The tc-scWB is demonstrated on three metabolic and ER stress-specific proteins (CHOP, MDH2 and FH) in four pancreatic cell subtypes, revealing the expression of key enzymes in the Krebs cycle is upregulated with enhanced ER stress. It is found that ER stress can regulate crucial enzyme (MDH2 and FH) activities of metabolic cascade in cancer cells, boosting aerobic respiration to attenuate the Warburg effect and promote cell apoptosis. The tc-scWB is a general toolbox for the analysis of low-abundance small-molecular functional proteins at the single-cell level.
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Affiliation(s)
- Haiyang Xie
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Wenke Guo
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Hui Jiang
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Ting Zhang
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Lei Zhao
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jinjuan Hu
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Shuxin Gao
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Sunfengda Song
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Jiasu Xu
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Li Xu
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xinyi Sun
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Yi Ding
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care UnitXinhua HospitalSchool of Medicine and School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200092China
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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8
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Lim J, Park C, Kim M, Kim H, Kim J, Lee DS. Advances in single-cell omics and multiomics for high-resolution molecular profiling. Exp Mol Med 2024; 56:515-526. [PMID: 38443594 PMCID: PMC10984936 DOI: 10.1038/s12276-024-01186-2] [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: 08/30/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
Single-cell omics technologies have revolutionized molecular profiling by providing high-resolution insights into cellular heterogeneity and complexity. Traditional bulk omics approaches average signals from heterogeneous cell populations, thereby obscuring important cellular nuances. Single-cell omics studies enable the analysis of individual cells and reveal diverse cell types, dynamic cellular states, and rare cell populations. These techniques offer unprecedented resolution and sensitivity, enabling researchers to unravel the molecular landscape of individual cells. Furthermore, the integration of multimodal omics data within a single cell provides a comprehensive and holistic view of cellular processes. By combining multiple omics dimensions, multimodal omics approaches can facilitate the elucidation of complex cellular interactions, regulatory networks, and molecular mechanisms. This integrative approach enhances our understanding of cellular systems, from development to disease. This review provides an overview of the recent advances in single-cell and multimodal omics for high-resolution molecular profiling. We discuss the principles and methodologies for representatives of each omics method, highlighting the strengths and limitations of the different techniques. In addition, we present case studies demonstrating the applications of single-cell and multimodal omics in various fields, including developmental biology, neurobiology, cancer research, immunology, and precision medicine.
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Affiliation(s)
- Jongsu Lim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Chanho Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Minjae Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Hyukhee Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Junil Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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9
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Thakkar PV. Immunoblot Analysis from Single Cells Using Milo™ Single-Cell Western Platform. Methods Mol Biol 2024; 2752:201-214. [PMID: 38194036 DOI: 10.1007/978-1-0716-3621-3_13] [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: 01/10/2024]
Abstract
In this new era of precision medicine, characterization of single-cell subpopulations to better understand disease etiology is paramount. It is thus an opportune time to explore techniques that allow molecular analysis of single cells and to better understand the basis of pathogenesis of diseases like cancer. Single-cell western blotting is one such method that allows analysis of single cells at the protein level. In contrast to traditional western blotting, which relies heavily on bulk analysis of lysates generated from tissues and is often indicative of the population average, this technique allows analysis of lysates from single-cell subpopulations thereby providing a glimpse into cell heterogeneity. The method entails the use of a chip containing 30 μm thick photoactivated polyacrylamide gel spotted with nearly 6400 microwells. Single cells loaded on the chip are captured in the microwells by passive gravity and are then lysed and electrophoresed using the MILO™ single-cell western platform. This method forgoes the use of transfer of proteins on a PVDF and a nitrocellulose membrane, as performed in traditional western blotting, and all other steps including probing of primary and fluorescent secondary antibodies against the protein of interest are performed directly on the chip. The proteins of interest can then be visualized by scanning a chip with the use of a microarray scanner. The entire procedure can be performed in as less as 4-6 h, and thus this method provides several advantages over traditional western blotting.
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Affiliation(s)
- Prashant V Thakkar
- Department of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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10
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Xu Z, Zou R, Horn NC, Kitata RB, Shi T. Robust Surfactant-Assisted One-Pot Sample Preparation for Label-Free Single-Cell and Nanoscale Proteomics. Methods Mol Biol 2024; 2817:85-96. [PMID: 38907149 DOI: 10.1007/978-1-0716-3934-4_8] [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: 06/23/2024]
Abstract
With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell-to-cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in the recent 5 years, there has been a surge of small sample preparation methods developed for robust and effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: methods based on specific devices and those based on standard PCR tubes or multi-well plates. In this chapter, we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of an MS-compatible surfactant, n-dodecyl-β-D-maltoside (DDM), and standard low-bind PCR tube or multi-well plate for "all-in-one" one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in biological and biomedical research.
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Affiliation(s)
- Zhangyang Xu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rongge Zou
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nina C Horn
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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11
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Alibekova Long M, Benman WKJ, Petrikas N, Bugaj LJ, Hughes AJ. Enhancing Single-Cell Western Blotting Sensitivity Using Diffusive Analyte Blotting and Antibody Conjugate Amplification. Anal Chem 2023; 95:17894-17902. [PMID: 37974303 DOI: 10.1021/acs.analchem.3c04130] [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: 11/19/2023]
Abstract
While there are many techniques to achieve highly sensitive, multiplex detection of RNA and DNA from single cells, detecting protein content often suffers from low limits of detection and throughput. Miniaturized, high-sensitivity Western blots on single cells (scWesterns) are attractive because they do not require advanced instrumentation. By physically separating analytes, scWesterns also uniquely mitigate limitations to target protein multiplexing posed by the affinity reagent performance. However, a fundamental limitation of scWesterns is their limited sensitivity for detecting low-abundance proteins, which arises from transport barriers posed by the separation gel against detection species. Here we address the sensitivity by decoupling the electrophoretic separation medium from the detection medium. We transfer scWestern separations to a nitrocellulose blotting medium with distinct mass transfer advantages over traditional in-gel probing, yielding a 5.9-fold improvement in the limit of detection. We next amplify probing of blotted proteins with enzyme-antibody conjugates, which are incompatible with traditional in-gel probing to achieve further improvement in the limit of detection to 1000 molecules, a 120-fold improvement. This enables us to detect 100% of cells in an EGFP-expressing population using fluorescently tagged and enzyme-conjugated antibodies compared to 84.5% of cells using in-gel detection. These results suggest the compatibility of nitrocellulose-immobilized scWesterns with a variety of affinity reagents─not previously accessible for in-gel use─for further signal amplification and detection of low-abundance targets.
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Affiliation(s)
- Mariia Alibekova Long
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William K J Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
| | - Nathan Petrikas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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Zhang A, Guo Z, Ge G, Liu Z. Insights into In Vivo Environmental Effects on Quantitative Biochemistry in Single Cells. Anal Chem 2023; 95:17246-17255. [PMID: 37963214 DOI: 10.1021/acs.analchem.3c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Biomacromolecules exist and function in a crowded and spatially confined intracellular milieu. Single-cell analysis has been an essential tool for deciphering the molecular mechanisms of cell biology and cellular heterogeneity. However, a sound understanding of in vivo environmental effects on single-cell quantification has not been well established. In this study, via cell mimicking with giant unilamellar vesicles and single-cell analysis by an approach called plasmonic immunosandwich assay (PISA) that we developed previously, we investigated the effects of two in vivo environmental factors, i.e., molecular crowding and spatial confinement, on quantitative biochemistry in the cytoplasm of single cells. We find that molecular crowding greatly affects the biomolecular interactions and immunorecognition-based detection while the effect of spatial confinement in cell-sized space is negligible. Without considering the effect of molecular crowding, the results by PISA were found to be apparently under-quantitated, being only 29.5-50.0% of those by the calibration curve considering the effect of molecular crowding. We further demonstrated that the use of a calibration curve established with standard solutions containing 20% (wt) polyethylene glycol 6000 can well offset the effect of intracellular crowding and thereby provide a simple but accurate calibration for the PISA measurement. Thus, this study not only sheds light on how intracellular environmental factors influence biomolecular interactions and immunorecognition-based single-cell quantification but also provides a simple but effective strategy to make the single-cell analysis more accurate.
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Affiliation(s)
- Anqi Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhanchen Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Ge Ge
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
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13
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Zhao Q, Shen Y, Li X, Li Y, Tian F, Yu X, Liu Z, Tong R, Park H, Yobas L, Huang P. Nanobead-based single-molecule pulldown for single cells. Heliyon 2023; 9:e22306. [PMID: 38027957 PMCID: PMC10679481 DOI: 10.1016/j.heliyon.2023.e22306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Investigation of cell-to-cell variability holds critical physiological and clinical implications. Thus, numerous new techniques have been developed for studying cell-to-cell variability, and these single-cell techniques can also be used to investigate rare cells. Moreover, for studying protein-protein interactions (PPIs) in single cells, several techniques have been developed based on the principle of the single-molecule pulldown (SiMPull) assay. However, the applicability of these single-cell SiMPull (sc-SiMPull) techniques is limited because of their high technical barrier and special requirements for target cells and molecules. Here, we report a highly innovative nanobead-based approach for sc-SiMPull that is based on our recently developed microbead-based, improved version of SiMPull for cell populations. In our sc-SiMPull method, single cells are captured in microwells and lysed in situ, after which commercially available, pre-surface-functionalized magnetic nanobeads are placed in the microwells to specifically capture proteins of interest together with their binding partners from cell extracts; subsequently, the PPIs are examined under a microscope at the single-molecule level. Relative to previously published methods, nanobead-based sc-SiMPull is considerably faster, easier to use, more reproducible, and more versatile for distinct cell types and protein molecules, and yet provides similar sensitivity and signal-to-background ratio. These crucial features should enable universal application of our method to the study of PPIs in single cells.
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Affiliation(s)
- Qirui Zhao
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yusheng Shen
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaofen Li
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yulin Li
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Fang Tian
- Department of Physics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiaojie Yu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhengzhao Liu
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Rongbiao Tong
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | - Hyokeun Park
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Physics, Hong Kong University of Science and Technology, Hong Kong, China
| | - Levent Yobas
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Hong Kong, China
| | - Pingbo Huang
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- HKUST Shenzhen Research Institute, Hong Kong University of Science and Technology, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Cao Y, Chen X, Pan F, Wang M, Zhuang H, Chen J, Lu L, Wang L, Wang T. Xinmaikang-mediated mitophagy attenuates atherosclerosis via the PINK1/Parkin signaling pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 119:154955. [PMID: 37572567 DOI: 10.1016/j.phymed.2023.154955] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 05/19/2023] [Accepted: 07/06/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND The Chinese herbal compound Xinmaikang (XMK) is effective in treating atherosclerosis (AS), although the associated mechanisms of action remain unclear. We hypothesize that XMK increases mitophagy via the PINK1/Parkin signaling pathway and decreases reactive oxygen species (ROS), thus treating AS. PURPOSE To explore the above-mentioned mechanisms of action of XMK in AS. MATERIALS AND METHODS Ultra-performance liquid chromatography assay was performed to clarify the composition of XMK. A 16-week high-fat diet was fed to APOE-/- mice to form an AS model. Next, mice were given XMK(0.95 g/kg/d, 1.99 g/kg/d, 3.98 g/kg/d, i.g.) or Atorvastatin(3 mg/kg/d, i.g.) or Rapamycin(4 mg/kg/d, i.p.) or XMK with Mdivi-1(40 mg/kg/d, i.p.) or an equivalent amount of normal saline for 4 weeks. Then mice were examined for AS plaque area, lesion area, collagen fiber, pro-inflammatory cytokines, lipid level, ROS level and mitophagy level. We assessed AS using Oil Red O, hematoxylin and eosin, and Sirius red staining, as well as ROS measurements. Mitophagy was evaluated by transmission electron microscopy, real-time quantitative polymerase chain reaction (RT-qPCR), Western blot, single-cell Western blot, and immunofluorescence staining. In vitro, by oxidizing low-density lipoprotein, formation of RAW264.7 macrophage-derived foam cells induced. we induced foam cell formation in RAW264.7 macrophages. Then cells were incubated with XMK-medicated serum with or without Mdivi-1. We examined foam cell formation, ROS level, mitophagy level in cells. Finally, we knocked down the PINK1, and examined foam cell formation and PINK1/Parkin level in RAW264.7 macrophages. RESULTS UPLC analysis revealed 102 main ingredients in XMK. In vivo, XMK at medium-dose or high-dose significantly reduced AS plaques, lipids, pro-inflammatory cytokines, and ROS and increased mitophagy. In further study, Single-cell western blot showed that mitophagy level in macrophages sorted from AS mice was lower than the control mice. While XMK improved mitophagy level. In vitro, XMK reduced foam cell formation and ROS and increased mitophagy. When PINK1 was knocked down, XMK's effects on foam cell formation and PINK1/Parkin pathway activation were reduced. CONCLUSION The study shows that XMK is effective against AS by mediating macrophage mitophagy via the PINK1/Parkin signaling pathway. For the treatment of AS and drug discovery, it provides an experimental basis and target.
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Affiliation(s)
- Yanhong Cao
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan 523000, China; The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangzhou Key Laboratory of Chinese Medicine for Prevention and Treatment of Chronic Heart Failure, Guangzhou 510405, China
| | - Xin Chen
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan 523000, China; The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangzhou Key Laboratory of Chinese Medicine for Prevention and Treatment of Chronic Heart Failure, Guangzhou 510405, China
| | - Fuqiang Pan
- Liwan District People's Hospital of Guangzhou, Guangzhou 510405, China
| | - Mingyang Wang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangzhou Key Laboratory of Chinese Medicine for Prevention and Treatment of Chronic Heart Failure, Guangzhou 510405, China
| | - Haowen Zhuang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangzhou Key Laboratory of Chinese Medicine for Prevention and Treatment of Chronic Heart Failure, Guangzhou 510405, China
| | - Jiangna Chen
- Zhongshan Ophthalmic Center, Sun Yan-Sen University, 510006, China
| | - Lu Lu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangzhou Key Laboratory of Chinese Medicine for Prevention and Treatment of Chronic Heart Failure, Guangzhou 510405, China
| | - Lingjun Wang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; The First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China; Guangzhou Key Laboratory of Chinese Medicine for Prevention and Treatment of Chronic Heart Failure, Guangzhou 510405, China
| | - Ting Wang
- Dongguan Hospital, Guangzhou University of Chinese Medicine, Dongguan 523000, China.
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15
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Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556277. [PMID: 37732260 PMCID: PMC10508777 DOI: 10.1101/2023.09.04.556277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
To further realize proteomics of archived tissues for translational research, we introduce a hybrid microfluidic platform for high-specificity, high-sensitivity protein detection from individual chemically fixed cells. To streamline processing-to-analysis workflows and minimize signal loss, DropBlot serially integrates sample preparation using droplet-based antigen retrieval from single fixed cells with unified analysis-on-a-chip comprising microwell-based antigen extraction followed by chip-based single-cell western blotting. A water-in-oil droplet formulation proves robust to the harsh chemical (SDS, 6M urea) and thermal conditions (98°C, 1-2 hr.) required for sufficient antigen retrieval, and the electromechanical conditions required for electrotransfer of retrieved antigen from microwell-encapsulated droplets to single-cell electrophoresis. Protein-target retrieval was demonstrated for unfixed, paraformaldehyde-(PFA), and methanol-fixed cells. We observed higher protein electrophoresis separation resolution from PFA-fixed cells with sufficient immunoreactivity confirmed for key targets (HER2, GAPDH, EpCAM, Vimentin) from both fixation chemistries. Multiple forms of EpCAM and Vimentin were detected, a hallmark strength of western-blot analysis. DropBlot of PFA-fixed human-derived breast tumor specimens (n = 5) showed antigen retrieval from cells archived frozen for 6 yrs. DropBlot could provide a precision integrated workflow for single-cell resolution protein-biomarker mining of precious biospecimen repositories.
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16
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Sule R, Rivera G, Gomes AV. Western blotting (immunoblotting): history, theory, uses, protocol and problems. Biotechniques 2023; 75:99-114. [PMID: 36971113 DOI: 10.2144/btn-2022-0034] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Western blotting (immunoblotting) is a powerful and commonly used technique that is capable of detecting or semiquantifying an individual protein from complex mixtures of proteins extracted from cells or tissues. The history surrounding the origin of western blotting, the theory behind the western blotting technique, a comprehensive protocol and the uses of western blotting are presented. Lesser known and significant problems in the western blotting field and troubleshooting of common problems are highlighted and discussed. This work is a comprehensive primer and guide for new western blotting researchers and those interested in a better understanding of the technique or getting better results.
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Affiliation(s)
- Rasheed Sule
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Gabriela Rivera
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology & Behavior, University of California, Davis, Davis, CA 95616, USA
- Department of Physiology & Membrane Biology, University of California, Davis, Davis, CA 95616, USA
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17
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Zhu Z, Jiang L, Ding X. Advancing Breast Cancer Heterogeneity Analysis: Insights from Genomics, Transcriptomics and Proteomics at Bulk and Single-Cell Levels. Cancers (Basel) 2023; 15:4164. [PMID: 37627192 PMCID: PMC10452610 DOI: 10.3390/cancers15164164] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/23/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer continues to pose a significant healthcare challenge worldwide for its inherent molecular heterogeneity. This review offers an in-depth assessment of the molecular profiling undertaken to understand this heterogeneity, focusing on multi-omics strategies applied both in traditional bulk and single-cell levels. Genomic investigations have profoundly informed our comprehension of breast cancer, enabling its categorization into six intrinsic molecular subtypes. Beyond genomics, transcriptomics has rendered deeper insights into the gene expression landscape of breast cancer cells. It has also facilitated the formulation of more precise predictive and prognostic models, thereby enriching the field of personalized medicine in breast cancer. The comparison between traditional and single-cell transcriptomics has identified unique gene expression patterns and facilitated the understanding of cell-to-cell variability. Proteomics provides further insights into breast cancer subtypes by illuminating intricate protein expression patterns and their post-translational modifications. The adoption of single-cell proteomics has been instrumental in this regard, revealing the complex dynamics of protein regulation and interaction. Despite these advancements, this review underscores the need for a holistic integration of multiple 'omics' strategies to fully decipher breast cancer heterogeneity. Such integration not only ensures a comprehensive understanding of breast cancer's molecular complexities, but also promotes the development of personalized treatment strategies.
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Affiliation(s)
- Zijian Zhu
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, China;
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200025, China;
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200030, China;
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200025, China;
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18
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Xu L, Xie H, Wang B, Zhu Z, Jiang H, Duan X, Deng S, Xu J, Jiang L, Ding X. Multiplex Protein Profiling by Low-Signal-Loss Single-Cell Western Blotting with Fluorescent-Quenching Aptamers. Anal Chem 2023; 95:11399-11409. [PMID: 37458448 DOI: 10.1021/acs.analchem.3c01577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Single-cell western blotting (scWB) is a prevalent technique for high-resolution protein analysis on low-abundance cell samples. However, the extensive signal loss during repeated antibody stripping precludes multiplex protein detection. Herein, we introduce Fluorescent-quenching Aptamer-based Single-cell Western Blotting (FAS-WB) for multiplex protein detection at single-cell resolution. The minimal size of aptamer probes allows rapid in-gel penetration, diffusion, and elution. Meanwhile, the fluorophore-tagged aptamers, coordinated with complementary quenching strands, avoid the massive signal loss conventionally caused by antibody stripping during repeated staining. Such a strategy also facilitates multiplex protein analysis with a limited number of fluorescent tags. We demonstrated FAS-WB for co-imaging four biomarker proteins (EpCAM, PTK7, HER2, CA125) at single-cell resolution with lower signal loss and enhanced signal-to-noise ratio compared to conventional antibody-based scWB. Being more time-saving (less than 25 min per cycle) and economical (1/1000 cost of conventional antibody probes), FAS-WB offers a highly efficient platform for profiling multiplex proteins at single-cell resolution.
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Affiliation(s)
- Li Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Haiyang Xie
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Boqian Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Zijian Zhu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Hui Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Xiaoqian Duan
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Shuxin Deng
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Jiasu Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200230, China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200230, China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai 200230, China
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Rathore D, Marino MJ, Nita-Lazar A. Omics and systems view of innate immune pathways. Proteomics 2023; 23:e2200407. [PMID: 37269203 DOI: 10.1002/pmic.202200407] [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: 02/14/2023] [Revised: 04/16/2023] [Accepted: 05/23/2023] [Indexed: 06/04/2023]
Abstract
Multiomics approaches to studying systems biology are very powerful techniques that can elucidate changes in the genomic, transcriptomic, proteomic, and metabolomic levels within a cell type in response to an infection. These approaches are valuable for understanding the mechanisms behind disease pathogenesis and how the immune system responds to being challenged. With the emergence of the COVID-19 pandemic, the importance and utility of these tools have become evident in garnering a better understanding of the systems biology within the innate and adaptive immune response and for developing treatments and preventative measures for new and emerging pathogens that pose a threat to human health. In this review, we focus on state-of-the-art omics technologies within the scope of innate immunity.
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Affiliation(s)
- Deepali Rathore
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Matthew J Marino
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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20
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Long MA, Benman W, Petrikas N, Bugaj LJ, Hughes AJ. Enhancing single-cell western blotting sensitivity using diffusive analyte blotting and antibody conjugate amplification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544857. [PMID: 37398364 PMCID: PMC10312704 DOI: 10.1101/2023.06.13.544857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
While there are many techniques to achieve highly sensitive, multiplex detection of RNA and DNA from single cells, detecting protein contents often suffers from low limits of detection and throughput. Miniaturized, high-sensitivity western blots on single cells (scWesterns) are attractive since they do not require advanced instrumentation. By physically separating analytes, scWesterns also uniquely mitigate limitations to target protein multiplexing posed by affinity reagent performance. However, a fundamental limitation of scWesterns is their limited sensitivity for detecting low-abundance proteins, which arises from transport barriers posed by the separation gel against detection species. Here we address sensitivity by decoupling the electrophoretic separation medium from the detection medium. We transfer scWestern separations to a nitrocellulose blotting medium with distinct mass transfer advantages over traditional in-gel probing, yielding a 5.9-fold improvement in limit of detection. We next amplify probing of blotted proteins with enzyme-antibody conjugates which are incompatible with traditional in-gel probing to achieve further improvement in the limit of detection to 103 molecules, a 520-fold improvement. This enables us to detect 85% and 100% of cells in an EGFP-expressing population using fluorescently tagged and enzyme-conjugated antibodies respectively, compared to 47% of cells using in-gel detection. These results suggest compatibility of nitrocellulose-immobilized scWesterns with a variety of affinity reagents - not previously accessible for in-gel use - for further signal amplification and detection of low abundance targets.
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Affiliation(s)
- Mariia Alibekova Long
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
| | - Nathan Petrikas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Currently at Tempus Labs Inc., Chicago, IL, USA
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alex J. Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA, 19104, USA
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21
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Augustin D, Lambert B, Wang K, Walz AC, Robinson M, Gavaghan D. Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data. PLoS Comput Biol 2023; 19:e1011135. [PMID: 37216399 DOI: 10.1371/journal.pcbi.1011135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 04/26/2023] [Indexed: 05/24/2023] Open
Abstract
Variability is an intrinsic property of biological systems and is often at the heart of their complex behaviour. Examples range from cell-to-cell variability in cell signalling pathways to variability in the response to treatment across patients. A popular approach to model and understand this variability is nonlinear mixed effects (NLME) modelling. However, estimating the parameters of NLME models from measurements quickly becomes computationally expensive as the number of measured individuals grows, making NLME inference intractable for datasets with thousands of measured individuals. This shortcoming is particularly limiting for snapshot datasets, common e.g. in cell biology, where high-throughput measurement techniques provide large numbers of single cell measurements. We introduce a novel approach for the estimation of NLME model parameters from snapshot measurements, which we call filter inference. Filter inference uses measurements of simulated individuals to define an approximate likelihood for the model parameters, avoiding the computational limitations of traditional NLME inference approaches and making efficient inferences from snapshot measurements possible. Filter inference also scales well with the number of model parameters, using state-of-the-art gradient-based MCMC algorithms such as the No-U-Turn Sampler (NUTS). We demonstrate the properties of filter inference using examples from early cancer growth modelling and from epidermal growth factor signalling pathway modelling.
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Affiliation(s)
- David Augustin
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Ben Lambert
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Ken Wang
- Research and Early Development, F. Hoffmann-La Roche AG, Basel, Switzerland
| | | | - Martin Robinson
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - David Gavaghan
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
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22
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Tuncay A, Crabtree DR, Muggeridge DJ, Husi H, Cobley JN. Performance benchmarking microplate-immunoassays for quantifying target-specific cysteine oxidation reveals their potential for understanding redox-regulation and oxidative stress. Free Radic Biol Med 2023; 204:252-265. [PMID: 37192685 DOI: 10.1016/j.freeradbiomed.2023.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 05/18/2023]
Abstract
The antibody-linked oxi-state assay (ALISA) for quantifying target-specific cysteine oxidation can benefit specialist and non-specialist users. Specialists can benefit from time-efficient analysis and high-throughput target and/or sample n-plex capacities. The simple and accessible "off-the-shelf" nature of ALISA brings the benefits of oxidative damage assays to non-specialists studying redox-regulation. Until performance benchmarking establishes confidence in the "unseen" microplate results, ALISA is unlikely to be widely adopted. Here, we implemented pre-set pass/fail criteria to benchmark ALISA by evaluating immunoassay performance in diverse contexts. ELISA-mode ALISA assays were accurate, reliable, and sensitive. For example, the average inter-assay CV for detecting 20%- and 40%-oxidised PRDX2 or GAPDH standards was 4.6% (range: 3.6-7.4%). ALISA displayed target-specificity. Immunodepleting the target decreased the signal by ∼75%. Single-antibody formatted ALISA failed to quantify the matrix-facing alpha subunit of the mitochondrial ATP synthase. However, RedoxiFluor quantified the alpha subunit displaying exceptional performance in the single-antibody format. ALISA discovered that (1) monocyte-to-macrophage differentiation amplified PRDX2-oxidation in THP-1 cells and (2) exercise increased GAPDH-specific oxidation in human erythrocytes. The "unseen" microplate data were "seen-to-be-believed" via orthogonal visually displayed immunoassays like the dimer method. Finally, we established target (n = 3) and sample (n = 100) n-plex capacities in ∼4 h with 50-70 min hands-on time. Our work showcases the potential of ALISA to advance our understanding of redox-regulation and oxidative stress.
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Affiliation(s)
- Ahmet Tuncay
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | - Daniel R Crabtree
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | | | - Holger Husi
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK
| | - James N Cobley
- Division of Biomedical Science, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK; Cysteine Redox Technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, IV2 5NA, Scotland, UK.
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23
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Cobley JN. Oxiforms: Unique cysteine residue- and chemotype-specified chemical combinations can produce functionally-distinct proteoforms: Like how mixing primary colours creates new shades, cysteine residue- and chemotype-specified chemical combinations can produce functionally-distinct proteoforms called oxiforms: Like how mixing primary colours creates new shades, cysteine residue- and chemotype-specified chemical combinations can produce functionally-distinct proteoforms called oxiforms. Bioessays 2023:e2200248. [PMID: 37147790 DOI: 10.1002/bies.202200248] [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: 12/21/2022] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
A single protein molecule with one or more cysteine residues can occupy a plurality of unique residue and oxidation-chemotype specified proteoforms that I term oxiforms. In binary reduced or oxidised terms, one molecule with three cysteines will adopt one of eight unique oxiforms. Residue-defined sulfur chemistry endows specific oxiforms with distinct functionally-relevant biophysical properties (e.g., steric effects). Their emergent complexity means a functionally-relevant effect may only manifest when multiple cysteines are oxidised. Like how mixing colours makes new shades, combining discrete redox chemistries-colours-can create a kaleidoscope of oxiform hues. The sheer diversity of oxiforms co-existing within the human body provides a biological basis for redox heterogeneity. Of evolutionary significance, oxiforms may enable individual cells to mount a broad spectrum of responses to the same stimulus. Their biological significance, however plausible, is speculative because protein-specific oxiforms remain essentially unexplored. Excitingly, pioneering new techniques can push the field into uncharted territory by quantifying oxiforms. The oxiform concept can advance our understanding of redox-regulation in health and disease.
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Affiliation(s)
- James N Cobley
- Cysteine Redox Technology Group, Life Science Innovation Centre, University of the Highlands and Islands, Inverness, Scotland, UK
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24
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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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25
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Wälchli T, Bisschop J, Carmeliet P, Zadeh G, Monnier PP, De Bock K, Radovanovic I. Shaping the brain vasculature in development and disease in the single-cell era. Nat Rev Neurosci 2023; 24:271-298. [PMID: 36941369 PMCID: PMC10026800 DOI: 10.1038/s41583-023-00684-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2023] [Indexed: 03/23/2023]
Abstract
The CNS critically relies on the formation and proper function of its vasculature during development, adult homeostasis and disease. Angiogenesis - the formation of new blood vessels - is highly active during brain development, enters almost complete quiescence in the healthy adult brain and is reactivated in vascular-dependent brain pathologies such as brain vascular malformations and brain tumours. Despite major advances in the understanding of the cellular and molecular mechanisms driving angiogenesis in peripheral tissues, developmental signalling pathways orchestrating angiogenic processes in the healthy and the diseased CNS remain incompletely understood. Molecular signalling pathways of the 'neurovascular link' defining common mechanisms of nerve and vessel wiring have emerged as crucial regulators of peripheral vascular growth, but their relevance for angiogenesis in brain development and disease remains largely unexplored. Here we review the current knowledge of general and CNS-specific mechanisms of angiogenesis during brain development and in brain vascular malformations and brain tumours, including how key molecular signalling pathways are reactivated in vascular-dependent diseases. We also discuss how these topics can be studied in the single-cell multi-omics era.
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Affiliation(s)
- Thomas Wälchli
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, and Division of Neurosurgery, University and University Hospital Zurich, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland.
- Group of Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada.
| | - Jeroen Bisschop
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, and Division of Neurosurgery, University and University Hospital Zurich, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Group of Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB & Department of Oncology, KU Leuven, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, People's Republic of China
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Philippe P Monnier
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Donald K. Johnson Research Institute, Krembil Research Institute, Krembil Discovery Tower, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Katrien De Bock
- Laboratory of Exercise and Health, Department of Health Science and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Ivan Radovanovic
- Group of Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, Toronto, ON, Canada
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26
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Breukers J, Ven K, Struyfs C, Ampofo L, Rutten I, Imbrechts M, Pollet F, Van Lent J, Kerstens W, Noppen S, Schols D, De Munter P, Thibaut HJ, Vanhoorelbeke K, Spasic D, Declerck P, Cammue BPA, Geukens N, Thevissen K, Lammertyn J. FLUIDOT: A Modular Microfluidic Platform for Single-Cell Study and Retrieval, with Applications in Drug Tolerance Screening and Antibody Mining. SMALL METHODS 2023; 7:e2201477. [PMID: 36642827 DOI: 10.1002/smtd.202201477] [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: 11/11/2022] [Revised: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Advancements in lab-on-a-chip technologies have revolutionized the single-cell analysis field. However, an accessible platform for in-depth screening and specific retrieval of single cells, which moreover enables studying diverse cell types and performing various downstream analyses, is still lacking. As a solution, FLUIDOT is introduced, a versatile microfluidic platform incorporating customizable microwells, optical tweezers and an interchangeable cell-retrieval system. Thanks to its smart microfluidic design, FLUIDOT is straightforward to fabricate and operate, rendering the technology widely accessible. The performance of FLUIDOT is validated and its versatility is subsequently demonstrated in two applications. First, drug tolerance in yeast cells is studied, resulting in the discovery of two treatment-tolerant populations. Second, B cells from convalescent COVID-19 patients are screened, leading to the discovery of highly affine, in vitro neutralizing monoclonal antibodies against SARS-CoV-2. Owing to its performance, flexibility, and accessibility, it is foreseen that FLUIDOT will enable phenotypic and genotypic analysis of diverse cell samples and thus elucidate unexplored biological questions.
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Affiliation(s)
- Jolien Breukers
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
- LISCO, KU Leuven Institute for Single Cell Omics, ON4 Herestraat 49, Leuven, 3000, Belgium
| | - Karen Ven
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
- LISCO, KU Leuven Institute for Single Cell Omics, ON4 Herestraat 49, Leuven, 3000, Belgium
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
| | - Caroline Struyfs
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Leuven, 3001, Belgium
| | - Louanne Ampofo
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, ON 2 Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, ON2 Herestraat 49, Leuven, 3000, Belgium
| | - Iene Rutten
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
- LISCO, KU Leuven Institute for Single Cell Omics, ON4 Herestraat 49, Leuven, 3000, Belgium
| | - Maya Imbrechts
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, ON 2 Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, ON2 Herestraat 49, Leuven, 3000, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
| | - Julie Van Lent
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
| | - Winnie Kerstens
- Translational Platform Virology and Chemotherapy, Rega Institute, KU Leuven, Rega - Herestraat 49, Leuven, 3000, Belgium
| | - Sam Noppen
- Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Rega - Herestraat 49, Leuven, 3000, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Rega - Herestraat 49, Leuven, 3000, Belgium
| | - Paul De Munter
- Department of Internal Medicine, University Hospitals Leuven, UZ Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Clinical Infectious and Inflammatory Disorders, KU Leuven, UZ Herestraat 49, Leuven, 3000, Belgium
| | - Hendrik Jan Thibaut
- Translational Platform Virology and Chemotherapy, Rega Institute, KU Leuven, Rega - Herestraat 49, Leuven, 3000, Belgium
| | - Karen Vanhoorelbeke
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, ON 2 Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Thrombosis Research, KU Leuven Campus Kulak Kortrijk, Etienne Sabbelaan 53, Kortrijk, 8500, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
| | - Paul Declerck
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, ON 2 Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, ON2 Herestraat 49, Leuven, 3000, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Leuven, 3001, Belgium
| | - Nick Geukens
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, ON 2 Herestraat 49, Leuven, 3000, Belgium
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, ON2 Herestraat 49, Leuven, 3000, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Leuven, 3001, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors group, KU Leuven, Willem de Croylaan 42, Leuven, 3001, Belgium
- LISCO, KU Leuven Institute for Single Cell Omics, ON4 Herestraat 49, Leuven, 3000, Belgium
- MabMine: KU Leuven Single B Cell Mining Platform, KU Leuven, ON2 Herestraat 49, 3000, Leuven, Belgium
- LIMNI, KU Leuven Institute for Micro- and Nanoscale Integration, Celestijnenlaan 200F, Leuven, 3001, Belgium
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27
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Zhang J, Xue J, Luo N, Chen F, Chen B, Zhao Y. Microwell array chip-based single-cell analysis. LAB ON A CHIP 2023; 23:1066-1079. [PMID: 36625143 DOI: 10.1039/d2lc00667g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell profiling is key to uncover the cellular heterogeneity and drives deep understanding of cell fate. In recent years, microfluidics has become an ideal tool for single-cell profiling owing to its benefits of high throughput and automation. Among various microfluidic platforms, microwell has the advantages of simple operation and easy integration with in situ analysis ability, making it an ideal technique for single-cell studies. Herein, recent advances of single-cell analysis based on microwell array chips are summarized. We first introduce the design and preparation of different microwell chips. Then microwell-based cell capture and lysis strategies are discussed. We finally focus on advanced microwell-based analysis of single-cell proteins, nucleic acids, and metabolites. The challenges and opportunities for the development of microwell-based single-cell analysis are also presented.
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Affiliation(s)
- Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Ningfeng Luo
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Badong Chen
- Institute of Artificial Intelligence and Robotics and the College of Artificial Intelligence, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
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28
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Desire CT, Arrua RD, Strudwick XL, Kopecki Z, Cowin AJ, Hilder EF. The development of microfluidic-based western blotting: Technical advances and future perspectives. J Chromatogr A 2023; 1691:463813. [PMID: 36709548 DOI: 10.1016/j.chroma.2023.463813] [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: 12/14/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Over the past two decades significant technical advancement in the field of western blotting has been made possible through the utilization of microfluidic technologies. In this review we provide a critical overview of these advancements, highlighting the advantages and disadvantages of each approach. Particular attention is paid to the development of now commercially available systems, including those for single cell analysis. This review also discusses more recent developments, including algorithms for automation and/or improved quantitation, the utilization of different materials/chemistries, use of projection electrophoresis, and the development of triBlots. Finally, the review includes commentary on future advances in the field based on current developments, and the potential of these systems for use as point-of-care devices in healthcare.
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Affiliation(s)
- Christopher T Desire
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - R Dario Arrua
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Xanthe L Strudwick
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Zlatko Kopecki
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Allison J Cowin
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Emily F Hilder
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia.
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29
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Yang T, Li D, Yan Y, Ettoumi FE, Wu RA, Luo Z, Yu H, Lin X. Ultrafast and absolute quantification of SARS-CoV-2 on food using hydrogel RT-LAMP without pre-lysis. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130050. [PMID: 36182888 PMCID: PMC9507997 DOI: 10.1016/j.jhazmat.2022.130050] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/12/2022] [Accepted: 09/21/2022] [Indexed: 05/13/2023]
Abstract
With rapid growing of environmental contact infection, more and more attentions are focused on the precise and absolute quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus on cold chain foods via point-of-care test (POCT). In this work, we propose a hydrogel-mediated reverse transcription loop-mediated isothermal amplification (RT-LAMP) for ultrafast and absolute quantification of SARS-CoV-2. Cross-linked hydrogel offers opportunities for digital single molecule amplification in nanoconfined spaces, facilitating the virus lysis, RNA reverse transcription and amplification process, which is about 3.4-fold faster than conventional bulk RT-LAMP. Ultrafast quantification of SARS-CoV-2 is accomplished in 15 min without virus pre-lysis and RNA extraction. The sensitivity can accurately quantify SARS-CoV-2 down to 0.5 copy/μL. Furthermore, the integrated system has an excellent specificity, reproducibility and storage stability, which can be also used to test SARS-CoV-2 on various cold chain fruits. The developed ultrafast and simple hydrogel RT-LAMP will be an enormous potential for surveillance of virus or other hazardous microbes in environmental, agricultural and food industry.
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Affiliation(s)
- Tao Yang
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Dong Li
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Yuhua Yan
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Fatima-Ezzahra Ettoumi
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Ricardo A Wu
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China; Ningbo Research Institute, Zhejiang University, 310058, China
| | - Hanry Yu
- Critical Analytics for Manufacturing Personalized Medicine Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 138602, Singapore
| | - Xingyu Lin
- College of Biosystems Engineering & Food Science, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, 310058, China; Ningbo Research Institute, Zhejiang University, 310058, China.
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30
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Zhu F, Liu S, Bai X, Liu X, Lin B, Lu Y. Point‐of‐care multiplexed single‐cell protein secretion analysis based on tyramide signal amplification. VIEW 2022. [DOI: 10.1002/viw.20220033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Fengjiao Zhu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
- University of Chinese Academy of Sciences Beijing China
| | - Songnan Liu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
- University of Chinese Academy of Sciences Beijing China
| | - Xue Bai
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - Xianming Liu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - Bingcheng Lin
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
| | - Yao Lu
- Department of Biotechnology Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian China
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31
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Thakur B, Saha L, Bhatia A. Relative refractoriness of breast cancer cells to tumour necrosis factor-α induced necroptosis. Clin Exp Pharmacol Physiol 2022; 49:1294-1306. [PMID: 36054417 DOI: 10.1111/1440-1681.13711] [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: 03/22/2022] [Revised: 06/22/2022] [Accepted: 08/09/2022] [Indexed: 01/31/2023]
Abstract
Necroptosis, a recently identified programmed cell death pathway, has attracted attention as an alternative route to target apoptosis-resistant cancer cells. The status of the necroptosis pathway in different subtypes of breast cancer has not been well explored. Stimulating the cells by TNF-α can trigger cell survival or death depending on the combination of downstream players involved. In this work, we attempted to induce necroptosis in them using a combination of TNF-α and Z-VAD-FMK with and without chemotherapy. Cell viability, apoptosis, and necroptosis were assessed using MTT and Annexin-V/PI assays, respectively. Gene and protein expression was analysed by qPCR and immunophenotyping. Both the cell lines were resistant to induction of cell death by necroptosis. There was no enhancement in cell death when chemotherapeutic drugs were combined with necroptosis induction. Expression studies showed reduced translational expression of key necroptosis molecules like RIP kinases and MLKL in breast cancer cells compared to positive control cell line L929. Also, cell survival molecules were expressed more in MDA-MB-231 in contrast to death pathway molecules which were expressed more in T47D cells. In this work, the two breast cancer cell lines were observed to be resistant to TNF-α induced necroptosis with or without chemotherapy. Expression of key necroptosis players revealed relative insufficiency of the molecular machinery involved in the above pathway. In our opinion this may be the cause for resistance to necroptosis and novel strategies to upregulate these molecules need to be developed to sensitize the breast cancer cells towards cell death by necroptosis.
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Affiliation(s)
- Banita Thakur
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Lekha Saha
- Department of Pharmacology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Bhatia
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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32
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Solt LA. Emerging insights and challenges for understanding T cell function through the proteome. Front Immunol 2022; 13:1028366. [DOI: 10.3389/fimmu.2022.1028366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
T cells rapidly transition from a quiescent state into active proliferation and effector function upon exposure to cognate antigen. These processes are tightly controlled by signal transduction pathways that influence changes in chromatin remodeling, gene transcription, and metabolism, all of which collectively drive specific T cell memory or effector cell development. Dysregulation of any of these events can mediate disease and the past several years has shown unprecedented novel approaches to understand these events, down to the single-cell level. The massive explosion of sequencing approaches to assess the genome and transcriptome at the single cell level has transformed our understanding of T cell activation, developmental potential, and effector function under normal and various disease states. Despite these advances, there remains a significant dearth of information regarding how these events are translated to the protein level. For example, resolution of protein isoforms and/or specific post-translational modifications mediating T cell function remains obscure. The application of proteomics can change that, enabling significant insights into molecular mechanisms that regulate T cell function. However, unlike genomic approaches that have enabled exquisite visualization of T cell dynamics at the mRNA and chromatin level, proteomic approaches, including those at the single-cell level, has significantly lagged. In this review, we describe recent studies that have enabled a better understanding of how protein synthesis and degradation change during T cell activation and acquisition of effector function. We also highlight technical advances and how these could be applied to T cell biology. Finally, we discuss future needs to expand upon our current knowledge of T cell proteomes and disease.
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33
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Mukherjee P, Park SH, Pathak N, Patino CA, Bao G, Espinosa HD. Integrating Micro and Nano Technologies for Cell Engineering and Analysis: Toward the Next Generation of Cell Therapy Workflows. ACS NANO 2022; 16:15653-15680. [PMID: 36154011 DOI: 10.1021/acsnano.2c05494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The emerging field of cell therapy offers the potential to treat and even cure a diverse array of diseases for which existing interventions are inadequate. Recent advances in micro and nanotechnology have added a multitude of single cell analysis methods to our research repertoire. At the same time, techniques have been developed for the precise engineering and manipulation of cells. Together, these methods have aided the understanding of disease pathophysiology, helped formulate corrective interventions at the cellular level, and expanded the spectrum of available cell therapeutic options. This review discusses how micro and nanotechnology have catalyzed the development of cell sorting, cellular engineering, and single cell analysis technologies, which have become essential workflow components in developing cell-based therapeutics. The review focuses on the technologies adopted in research studies and explores the opportunities and challenges in combining the various elements of cell engineering and single cell analysis into the next generation of integrated and automated platforms that can accelerate preclinical studies and translational research.
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Affiliation(s)
- Prithvijit Mukherjee
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - So Hyun Park
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Nibir Pathak
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Cesar A Patino
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Gang Bao
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, Texas 77030, United States
| | - Horacio D Espinosa
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Theoretical and Applied Mechanics Program, Northwestern University, Evanston, Illinois 60208, United States
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34
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Ma G, Zhang P, Zhou X, Wan Z, Wang S. Label-Free Single-Molecule Pulldown for the Detection of Released Cellular Protein Complexes. ACS CENTRAL SCIENCE 2022; 8:1272-1281. [PMID: 36188347 PMCID: PMC9523780 DOI: 10.1021/acscentsci.2c00602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 06/16/2023]
Abstract
Precise and sensitive detection of intracellular proteins and complexes is key to the understanding of signaling pathways and cell functions. Here, we present a label-free single-molecule pulldown (LFSMP) technique for the imaging of released cellular protein and protein complexes with single-molecule sensitivity and low sample consumption down to a few cells per mm2. LFSMP is based on plasmonic scattering imaging and thus can directly image the surface-captured molecules without labels and quantify the binding kinetics. In this paper, we demonstrate the detection principle for LFSMP, study the phosphorylation of protein complexes involved in a signaling pathway, and investigate how kinetic analysis can be used to improve the pulldown specificity. We wish our technique can contribute to uncovering the molecular mechanisms in cells with single-molecule resolution.
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Affiliation(s)
- Guangzhong Ma
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
| | - Pengfei Zhang
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
| | - Xinyu Zhou
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Zijian Wan
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Shaopeng Wang
- Biodesign
Center for Biosensors and Bioelectronics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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35
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Zadeh C, Huggins JR, Sarmah D, Westbury BC, Interiano WR, Jordan MC, Phillips SA, Dodd WB, Meredith WO, Harold NJ, Erdem C, Birtwistle MR. Mesowestern Blot: Simultaneous Analysis of Hundreds of Submicroliter Lysates. ACS OMEGA 2022; 7:28912-28923. [PMID: 36033686 PMCID: PMC9404195 DOI: 10.1021/acsomega.2c02201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Western blotting is a widely used technique for molecular-weight-resolved analysis of proteins and their posttranslational modifications, but high-throughput implementations of the standard slab gel arrangement are scarce. The previously developed Microwestern requires a piezoelectric pipetting instrument, which is not available for many labs. Here, we report the Mesowestern blot, which uses a 3D-printable gel casting mold to enable high-throughput Western blotting without piezoelectric pipetting and is compatible with the standard sample preparation and small (∼1 μL) sample sizes. The main tradeoffs are reduced molecular weight resolution and higher sample-to-sample CV, making it suitable for qualitative screening applications. The casted polyacrylamide gel contains 336, ∼0.5 μL micropipette-loadable sample wells arranged within a standard microplate footprint. Polyacrylamide % can be altered to change molecular weight resolution profiles. Proof-of-concept experiments using both infrared-fluorescent molecular weight protein ladder and cell lysate (RIPA buffer) demonstrate that the protein loaded in Mesowestern gels is amenable to the standard Western blotting steps. The main difference between Mesowestern and traditional Western is that semidry horizontal instead of immersed vertical gel electrophoresis is used. The linear range of detection is at least 32-fold, and at least ∼500 attomols of β-actin can be detected (∼29 ng of total protein from mammalian cell lysates: ∼100-300 cells). Because the gel mold is 3D-printable, users with access to additive manufacturing cores have significant design freedom for custom layouts. We expect that the technique could be easily adopted by any typical cell and molecular biology laboratory already performing Western blots.
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Affiliation(s)
- Cameron
O. Zadeh
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Jonah R. Huggins
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Deepraj Sarmah
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Baylee C. Westbury
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - William R. Interiano
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Micah C. Jordan
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - S. Ashley Phillips
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - William B. Dodd
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Wesley O. Meredith
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Nicholas J. Harold
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Cemal Erdem
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | - Marc R. Birtwistle
- Department
of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
- Department
of Bioengineering, Clemson University, Clemson, South Carolina 29634, United States
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36
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Yu H, Tai Q, Yang C, Weng L, Gao M, Zhang X. Counting Protein Number in a Single Cell by a Picoliter Liquid Operating Technology. Anal Chem 2022; 94:11925-11933. [PMID: 35980697 DOI: 10.1021/acs.analchem.2c02701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultra-low-copy number proteins play a crucial role in exploring cellular heterogeneity and the insight of protein biomarkers in a single cell. However, counting ultra-low-copy number target proteins in a single cell remains a grand challenge. Herein, we developed a so-called single-cell picoliter liquid operating technology for counting target proteins in a single cell. An ingenious volume-controllable sampling technique was employed to capture a single cell for subsequent analysis. Remarkably, 50 pL of sample volume was employed for sample preparation, single-cell capture, in-droplet lysis, and target protein immobilization on a functionalized coverslip in a monolayer. Then, target protein antibodies coupled with quantum dots were added and incubated to label those immobilized proteins. After clean-up, a single-view image under 100× objective was taken, and the 80 × 80 μm2 view image was then applied to count the precise copy number of the target proteins in the single cell. Furthermore, good linearity and repeatability were achieved for ultra-low-copy number proteins, ranging from 1 to 1500. Finally, the expression level of human epidermal growth factor receptor 2 in single cells from both MCF-7 and MDA-MB-231 cell lines was also analyzed. In a word, this work stimulated the development of capillary-based single-cell analysis and updated the connotation of counting ultra-low-copy number proteins.
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Affiliation(s)
- Hailong Yu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Qunfei Tai
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chenjie Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Lingxiao Weng
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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37
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Garg T, Weiss CR, Sheth RA. Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology. Cancers (Basel) 2022; 14:3628. [PMID: 35892890 PMCID: PMC9332307 DOI: 10.3390/cancers14153628] [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: 07/08/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/07/2022] Open
Abstract
In recent years there has been increased interest in using the immune contexture of the primary tumors to predict the patient's prognosis. The tumor microenvironment of patients with cancers consists of different types of lymphocytes, tumor-infiltrating leukocytes, dendritic cells, and others. Different technologies can be used for the evaluation of the tumor microenvironment, all of which require a tissue or cell sample. Image-guided tissue sampling is a cornerstone in the diagnosis, stratification, and longitudinal evaluation of therapeutic efficacy for cancer patients receiving immunotherapies. Therefore, interventional radiologists (IRs) play an essential role in the evaluation of patients treated with systemically administered immunotherapies. This review provides a detailed description of different technologies used for immune assessment and analysis of the data collected from the use of these technologies. The detailed approach provided herein is intended to provide the reader with the knowledge necessary to not only interpret studies containing such data but also design and apply these tools for clinical practice and future research studies.
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Affiliation(s)
- Tushar Garg
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Clifford R. Weiss
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Rahul A. Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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38
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Abstract
Single-cell proteomics is a promising field to provide direct yet comprehensive molecular insights into cellular functions without averaging effects. Here, we address a grand technical challenge impeding the maturation of single-cell proteomics─protein adsorption loss (PAL). Even though widely known, there is currently no quantitation on how profoundly and selectively PAL has affected single-cell proteomics. Therefore, the mitigations to this challenge have been generic, and their efficacy was only evaluated by the size of the resolved proteome with no specificity on individual proteins. We use the existing knowledge of PAL, protein expression, and the typical surface area used in single-cell proteomics to discuss the severity of protein loss. We also summarize the current solutions to this challenge and briefly review the available methods to characterize the physical and chemical properties of protein surface adsorption. By citing successful strategies in single-cell genomics for measurement errors in individual transcripts, we pinpoint the urgency to benchmark PAL at the proteome scale with individual protein resolution. Finally, orthogonal single-cell proteomic techniques that have the potential to cross validate PAL are proposed. We hope these efforts can promote the fruition of single-cell proteomics in the near future.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Sharwan Kumar
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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39
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Wang Y, Lih TSM, Chen L, Xu Y, Kuczler MD, Cao L, Pienta KJ, Amend SR, Zhang H. Optimized data-independent acquisition approach for proteomic analysis at single-cell level. Clin Proteomics 2022; 19:24. [PMID: 35810282 PMCID: PMC9270744 DOI: 10.1186/s12014-022-09359-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/26/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Single-cell proteomic analysis provides valuable insights into cellular heterogeneity allowing the characterization of the cellular microenvironment which is difficult to accomplish in bulk proteomic analysis. Currently, single-cell proteomic studies utilize data-dependent acquisition (DDA) mass spectrometry (MS) coupled with a TMT labelled carrier channel. Due to the extremely imbalanced MS signals among the carrier channel and other TMT reporter ions, the quantification is compromised. Thus, data-independent acquisition (DIA)-MS should be considered as an alternative approach towards single-cell proteomic study since it generates reproducible quantitative data. However, there are limited reports on the optimal workflow for DIA-MS-based single-cell analysis. METHODS We report an optimized DIA workflow for single-cell proteomics using Orbitrap Lumos Tribrid instrument. We utilized a breast cancer cell line (MDA-MB-231) and induced drug resistant polyaneuploid cancer cells (PACCs) to evaluate our established workflow. RESULTS We found that a short LC gradient was preferable for peptides extracted from single cell level with less than 2 ng sample amount. The total number of co-searching peptide precursors was also critical for protein and peptide identifications at nano- and sub-nano-gram levels. Post-translationally modified peptides could be identified from a nano-gram level of peptides. Using the optimized workflow, up to 1500 protein groups were identified from a single PACC corresponding to 0.2 ng of peptides. Furthermore, about 200 peptides with phosphorylation, acetylation, and ubiquitination were identified from global DIA analysis of 100 cisplatin resistant PACCs (20 ng). Finally, we used this optimized DIA approach to compare the whole proteome of MDA-MB-231 parental cells and induced PACCs at a single-cell level. We found the single-cell level comparison could reflect real protein expression changes and identify the protein copy number. CONCLUSIONS Our results demonstrate that the optimized DIA pipeline can serve as a reliable quantitative tool for single-cell as well as sub-nano-gram proteomic analysis.
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Affiliation(s)
- Yuefan Wang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | | | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Yuanwei Xu
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Morgan D Kuczler
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Liwei Cao
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kenneth J Pienta
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Sarah R Amend
- Cancer Ecology Center, The Brady Urological Institute, Johns Hopkins School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, 21287, USA.
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40
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Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL. New Views of Old Proteins: Clarifying the Enigmatic Proteome. Mol Cell Proteomics 2022; 21:100254. [PMID: 35654359 PMCID: PMC9256833 DOI: 10.1016/j.mcpro.2022.100254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/09/2022] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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Affiliation(s)
- Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.
| | - Thomas P Conrads
- Inova Women's Service Line, Inova Health System, Falls Church, Virginia, USA
| | - Richard R Drake
- Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Emma Lundberg
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute in the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Marc Vidal
- Department of Genetics, Harvard University, Cambridge, Massachusetts, USA
| | - Christine Vogel
- New York University Center for Genomics and Systems Biology, New York University, New York, New York, USA
| | - David R Walt
- Department of Pathology, Harvard Medical School, Brigham and Women's Hospital, Wyss Institute at Harvard University, Boston, Massachusetts, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, Illinois, USA.
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41
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Abstract
Western blotting (WB), also known as immunoblotting, is a well-known molecular biology method that biologists often use to investigate many features of the protein, ranging from basic protein analysis to disease detection. WB is simple, unique, rapid, widely used routine tool with easy interpretation and definite results. It is being used in various fields of science, research and development, diagnostic labs and hospitals. The principle of WB is to accomplish the separation of proteins based on molecular weight and charge. This review addresses in detail the individual steps involved in the WB technique, its troubleshooting, internal loading controls, total protein staining and its diverse applications in scientific research and clinical settings, along with its future perspectives.
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42
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Källberg J, Xiao W, Van Assche D, Baret JC, Taly V. Frontiers in single cell analysis: multimodal technologies and their clinical perspectives. LAB ON A CHIP 2022; 22:2403-2422. [PMID: 35703438 DOI: 10.1039/d2lc00220e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single cell multimodal analysis is at the frontier of single cell research: it defines the roles and functions of distinct cell types through simultaneous analysis to provide unprecedented insight into cellular processes. Current single cell approaches are rapidly moving toward multimodal characterizations. It replaces one-dimensional single cell analysis, for example by allowing for simultaneous measurement of transcription and post-transcriptional regulation, epigenetic modifications and/or surface protein expression. By providing deeper insights into single cell processes, multimodal single cell analyses paves the way to new understandings in various cellular processes such as cell fate decisions, physiological heterogeneity or genotype-phenotype linkages. At the forefront of this, microfluidics is key for high-throughput single cell analysis. Here, we present an overview of the recent multimodal microfluidic platforms having a potential in biomedical research, with a specific focus on their potential clinical applications.
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Affiliation(s)
- Julia Källberg
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - Wenjin Xiao
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - David Van Assche
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France.
| | - Jean-Christophe Baret
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France.
- Institut Universitaire de France, Paris 75005, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
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43
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Yang L, Ball A, Liu J, Jain T, Li YM, Akhter F, Zhu D, Wang J. Cyclic microchip assay for measurement of hundreds of functional proteins in single neurons. Nat Commun 2022; 13:3548. [PMID: 35729174 PMCID: PMC9213506 DOI: 10.1038/s41467-022-31336-x] [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: 06/07/2021] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Despite the fact that proteins carry out nearly all cellular functions and mark the differences of cells, the existing single-cell tools can only analyze dozens of proteins, a scale far from full characterization of cells and tissue yet. Herein, we present a single-cell cyclic multiplex in situ tagging (CycMIST) technology that affords the comprehensive functional proteome profiling of single cells. We demonstrate the technology by detecting 182 proteins that include surface markers, neuron function proteins, neurodegeneration markers, signaling pathway proteins, and transcription factors. Further studies on cells derived from the 5XFAD mice, an Alzheimer’s Disease (AD) model, validate the utility of our technology and reveal the deep heterogeneity of brain cells. Through comparison with control mouse cells, we have identified differentially expressed proteins in AD pathology. Our technology could offer new insights into cell machinery and thus may advance many fields including drug discovery, molecular diagnostics, and clinical studies. Current single-cell tools are limited by the number of proteins they can analyse. Here the authors report a single-cell cyclic multiplex in situ tagging (CycMIST) method for functional proteome profiling of single cells, allowing multiple rounds of multiplexing of the same single cells on a microchip.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Avery Ball
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jesse Liu
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA.,Programs of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, USA
| | - Firoz Akhter
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Donghui Zhu
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
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Abstract
Over the years, the engineering aspect of nanotechnology has been significantly exploited. Medical intervention strategies have been developed by leveraging existing molecular biology knowledge and combining it with nanotechnology tools to improve outcomes. However, little attention has been paid to harnessing the strengths of nanotechnology as a biological discovery tool. Fundamental understanding of controlling dynamic biological processes at the subcellular level is key to developing personalized therapeutic and diagnostic interventions. Single-cell analyses using intravital microscopy, expansion microscopy, and microfluidic-based platforms have been helping to better understand cell heterogeneity in healthy and diseased cells, a major challenge in oncology. Also, single-cell analysis has revealed critical signaling pathways and biological intracellular components with key biological functions. The physical manipulation enabled by nanotools can allow real-time monitoring of biological changes at a single-cell level by sampling intracellular fluid from the same cell. The formation of intercellular highways by nanotube-like structures has important clinical implications such as metastasis development. The integration of nanomaterials into optical and molecular imaging techniques has rendered valuable morphological, structural, and biological information. Nanoscale imaging unravels mechanisms of temporality by enabling the visualization of nanoscale dynamics never observed or measured between individual cells with standard biological techniques. The exceptional sensitivity of nanozymes, artificial enzymes, make them perfect components of the next-generation mobile diagnostics devices. Here, we highlight these impactful cancer-related biological discoveries enabled by nanotechnology and producing a paradigm shift in cancer research and oncology.
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Affiliation(s)
- Carolina Salvador-Morales
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20850, United States
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, Maryland 20850, United States
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45
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Wang L, Abdulla A, Wang A, Warden AR, Ahmad KZ, Xin Y, Ding X. Sickle-like Inertial Microfluidic System for Online Rare Cell Separation and Tandem Label-Free Quantitative Proteomics (Orcs-Proteomics). Anal Chem 2022; 94:6026-6035. [PMID: 35380437 DOI: 10.1021/acs.analchem.2c00679] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Label-free proteomics with trace clinical samples provides a wealth of actionable insights for personalized medicine. Clinically acquired primary cells, such as circulating tumor cells (CTCs), are usually with low abundance that is prohibitive for conventional label-free proteomics analysis. Here, we present a sickle-like inertial microfluidic system for online rare cell separation and tandem label-free proteomics (namely, Orcs-proteomics). Orcs-proteomics adopts a buffer system with 0.1% N-dodecyl β-d-maltoside (DDM), 1 mM Tris (2-carboxyethyl) phosphine (TCEP), and 2 mM 2-chloroacetamide (CAA) for cell lysis and reductive alkylation. We demonstrate the application of Orcs-proteomics with 293T cells and manage to identify 913, 1563, 2271, and 2770 protein groups with 4, 13, 68, and 119 cells, respectively. We then spike MCF7 cells with white blood cells (WBCs) to simulate the patient's blood sample. Orcs-proteomics identifies more than 2000 protein groups with an average of 61 MCF7 cells. We further recruit two advanced breast cancer patients and collect 5 and 7 CTCs from each patient through minimally invasive blood drawing. Orcs-proteomics manages to identify 973 and 1135 protein groups for each patient. Therefore, Orcs-proteomics empowers rare cells simultaneously to be separated and counted for proteomics and provides technical support for personalized treatment decision making with rare primary patient samples.
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Affiliation(s)
- Liping Wang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Aynur Abdulla
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Aiting Wang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Antony R Warden
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Khan Zara Ahmad
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yufang Xin
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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46
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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47
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Klein P, Kallenberger SM, Roth H, Roth K, Ly-Hartig TBN, Magg V, Aleš J, Talemi SR, Qiang Y, Wolf S, Oleksiuk O, Kurilov R, Di Ventura B, Bartenschlager R, Eils R, Rohr K, Hamprecht FA, Höfer T, Fackler OT, Stoecklin G, Ruggieri A. Temporal control of the integrated stress response by a stochastic molecular switch. SCIENCE ADVANCES 2022; 8:eabk2022. [PMID: 35319985 PMCID: PMC8942376 DOI: 10.1126/sciadv.abk2022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response by integrating quantitative experiments with mathematical modeling and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2α, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 messenger RNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.
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Affiliation(s)
- Philipp Klein
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Stefan M. Kallenberger
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
- Medical Oncology, National Center for Tumor Diseases, Heidelberg University, Heidelberg, Germany
| | - Hanna Roth
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Karsten Roth
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Thi Bach Nga Ly-Hartig
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Vera Magg
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Janez Aleš
- HCI/IWR, Heidelberg University, Heidelberg, Germany
| | - Soheil Rastgou Talemi
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yu Qiang
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany
| | - Steffen Wolf
- HCI/IWR, Heidelberg University, Heidelberg, Germany
| | - Olga Oleksiuk
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Roma Kurilov
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Di Ventura
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, Berlin, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Heidelberg, Germany
| | | | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
| | - Georg Stoecklin
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Diseases Research, Heidelberg University, Heidelberg, Germany
- Corresponding author.
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48
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Circulating tumour cells in the -omics era: how far are we from achieving the 'singularity'? Br J Cancer 2022; 127:173-184. [PMID: 35273384 PMCID: PMC9296521 DOI: 10.1038/s41416-022-01768-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/27/2022] [Accepted: 02/17/2022] [Indexed: 12/22/2022] Open
Abstract
Over the past decade, cancer diagnosis has expanded to include liquid biopsies in addition to tissue biopsies. Liquid biopsies can result in earlier and more accurate diagnosis and more effective monitoring of disease progression than tissue biopsies as samples can be collected frequently. Because of these advantages, liquid biopsies are now used extensively in clinical care. Liquid biopsy samples are analysed for circulating tumour cells (CTCs), cell-free DNA, RNA, proteins and exosomes. CTCs originate from the tumour, play crucial roles in metastasis and carry information on tumour heterogeneity. Multiple single-cell omics approaches allow the characterisation of the molecular makeup of CTCs. It has become evident that CTCs are robust biomarkers for predicting therapy response, clinical development of metastasis and disease progression. This review describes CTC biology, molecular heterogeneity within CTCs and the involvement of EMT in CTC dynamics. In addition, we describe the single-cell multi-omics technologies that have provided insights into the molecular features within therapy-resistant and metastasis-prone CTC populations. Functional studies coupled with integrated multi-omics analyses have the potential to identify therapies that can intervene the functions of CTCs.
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49
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Abstract
Hydrogels are important structural and operative components of microfluidic systems, finding diverse utility in biological sample preparation and interrogation. One inherent challenge for integrating hydrogels into microfluidic tools is thermodynamic molecular partitioning, which reduces the in-gel concentration of molecular solutes (e.g., biomolecular regents), as compared to the solute concentration in an applied solution. Consequently, biomolecular reagent access to in-gel scaffolded biological samples (e.g., encapsulated cells, microbial cultures, target analytes) is adversely impacted in hydrogels. Further, biomolecular reagents are typically introduced to the hydrogel via diffusion. This passive process requires long incubation periods compared to active biomolecular delivery techniques. Electrotransfer is an active technique used in Western blots and other gel-based immunoassays that overcomes limitations of size exclusion (increasing the total probe mass delivered into gel) and expedites probe delivery, even in millimeter-thick slab gels. While compatible with conventional slab gels, electrotransfer has not been adapted to thin gels (50-250 μm thick), which are of great interest as components of open microfluidic devices (vs enclosed microchannel-based devices). Mechanically delicate, thin gels are often mounted on rigid support substrates (glass, plastic) that are electrically insulating. Consequently, to adapt electrotransfer to thin-gel devices, we replace rigid insulating support substrates with novel, mechanically robust, yet electrically conductive nanoporous membranes. We describe grafting nanoporous membranes to thin-polyacrylamide-gel layers via silanization, characterize the electrical conductivity of silane-treated nanoporous membranes, and report the dependence of in-gel immunoprobe concentration on transfer duration for passive diffusion and active electrotransfer. Alternative microdevice component layers─including the mechanically robust, electrically conductive nanoporous membranes reported here─provide new functionality for integration into an increasing array of open microfluidic systems.
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Affiliation(s)
- Andoni P Mourdoukoutas
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720, United States
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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50
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Wei J, Zhao Z, Lan K, Wang Z, Qin G, Chen R. Highly sensitive detection of multiple proteins from single cells by MoS 2-FET biosensors. Talanta 2022; 236:122839. [PMID: 34635229 DOI: 10.1016/j.talanta.2021.122839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/29/2021] [Accepted: 08/31/2021] [Indexed: 12/25/2022]
Abstract
Single-cell analysis of proteins is critical to gain precise information regarding the mechanisms that dictate the heterogeneity in cellular phenotypes and their differential response to internal and external stimuli. However, tools that allow sensitive and easy measurement of proteins in individual cells are still limited. The emerging semiconductor-based bioelectronics may provide a new approach to overcome the challenges in this field, however its utility in single-cell protein analysis has not been explored. In this study, we investigated multiple protein detection in single cells by MoS2 field effect transistors (MoS2-FETs) modified with specific biological probes. First, β-actin antibody was connected to the surface of MoS2-FETs by covalent bonds, and the fabricated device was tested using β-actin solution with concentrations from 10-9 to 10-3 μg/μL. Next, we examined the application of MoS2-FET for protein analysis in complex biological samples, and the device showed electrical signal response to human embryonic kidney cell line HEK293T in a dose-dependent manner. Furthermore, we applied this method to analyze individual liver cancer MHCC-97L cells, targeting four cellular proteins, including β-actin, epidermal growth factor receptor, sirtuin-2, and glyceraldehyde-3-phosphate dehydrogenase. The devices modified with corresponding probes could identify the target proteins and showed cell number-dependent responses. As a proof of principle, we demonstrated sensitive and multiplexed detection of proteins in single cells using MoS2-FETs. The biosensor and this detection method are cost-efficient and user-friendly with broad application prospects in biological studies and clinical diagnosis.
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Affiliation(s)
- Junqing Wei
- School of Microelectronics & Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Zhihan Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Kuibo Lan
- School of Microelectronics & Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Zhi Wang
- School of Microelectronics & Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Guoxuan Qin
- School of Microelectronics & Tianjin Key Laboratory of Imaging and Sensing Microelectronic Technology, Tianjin University, Tianjin, 300072, P. R. China.
| | - Ruibing Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China.
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