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Veličković M, Fillmore TL, Attah IK, Posso C, Pino JC, Zhao R, Williams SM, Veličković D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD. Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment. Anal Chem 2024. [PMID: 39089681 DOI: 10.1021/acs.analchem.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity in a cell-type-specific manner to better understand and predict the function of complex biological systems such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (microdroplet processing in one pot for trace samples), multiplexed isobaric labeling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram levels of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 μm2) and differentiate unique protein abundance patterns in pancreas. Furthermore, the use of the microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.
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Affiliation(s)
- Marija Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Isaac Kwame Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Camilo Posso
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - James C Pino
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jon M Jacobs
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Paul D Piehowski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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2
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Veličković M, Wu R, Gao Y, Thairu MW, Veličković D, Munoz N, Clendinen CS, Bilbao A, Chu RK, Lalli PM, Zemaitis K, Nicora CD, Kyle JE, Orton D, Williams S, Zhu Y, Zhao R, Monroe ME, Moore RJ, Webb-Robertson BJM, Bramer LM, Currie CR, Piehowski PD, Burnum-Johnson KE. Mapping microhabitats of lignocellulose decomposition by a microbial consortium. Nat Chem Biol 2024; 20:1033-1043. [PMID: 38302607 PMCID: PMC11288888 DOI: 10.1038/s41589-023-01536-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
The leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.
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Affiliation(s)
- Marija Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Margaret W Thairu
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dušan Veličković
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chaevien S Clendinen
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Aivett Bilbao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Rosalie K Chu
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Priscila M Lalli
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Zemaitis
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarai Williams
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ying Zhu
- Department of Microchemistry, Proteomics, Lipidomics, and Next Generation Sequencing, Genentech, San Francisco, CA, USA
| | - Rui Zhao
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry & Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Paul D Piehowski
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
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3
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Dong M, Sun Y, Dunstan DJ, Young RJ, Papageorgiou DG. Mechanical reinforcement from two-dimensional nanofillers: model, bulk and hybrid polymer nanocomposites. NANOSCALE 2024; 16:13247-13299. [PMID: 38940686 DOI: 10.1039/d4nr01356e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Thanks to their intrinsic properties, multifunctionality and unique geometrical features, two-dimensional nanomaterials have been used widely as reinforcements in polymer nanocomposites. The effective mechanical reinforcement of polymers is, however, a multifaceted problem as it depends not only on the intrinsic properties of the fillers and the matrix, but also upon a number of other important parameters. These parameters include the processing method, the interfacial properties, the aspect ratio, defects, orientation, agglomeration and volume fraction of the fillers. In this review, we summarize recent advances in the mechanical reinforcement of polymer nanocomposites from two-dimensional nanofillers with an emphasis on the mechanisms of reinforcement. Model, bulk and hybrid polymer nanocomposites are reviewed comprehensively. The use of Raman and photoluminescence spectroscopies is examined in light of the distinctive information they can yield upon stress transfer at interfaces. It is shown that the very diverse family of 2D nanofillers includes a number of materials that can attribute distrinctive features to a polymeric matrix, and we focus on the mechanical properties of both graphene and some of the most important 2D materials beyond graphene, including boron nitride, molybdenum disulphide, other transition metal dichalcogenides, MXenes and black phosphorous. In the first part of the review we evaluate the mechanical properties of 2D nanoplatelets in "model" nanocomposites. Next we examine how the performance of these materials can be optimised in bulk nanocomposites. Finally, combinations of these 2D nanofillers with other 2D nanomaterials or with nanofillers of other dimensions are assessed thoroughly, as such combinations can lead to additive or even synergistic mechanical effects. Existing unsolved problems and future perspectives are discussed.
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Affiliation(s)
- Ming Dong
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK.
| | - Yiwei Sun
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK.
| | - David J Dunstan
- School of Physics and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Robert J Young
- National Graphene Institute, Department of Materials, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, UK.
| | - Dimitrios G Papageorgiou
- School of Engineering and Materials Science, Queen Mary University of London, London E1 4NS, UK.
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Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583367. [PMID: 38496682 PMCID: PMC10942300 DOI: 10.1101/2024.03.04.583367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ~3500 proteins at a spatial resolution of 50 µm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah M. Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Department of Proteomic and Genomic Technologies, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
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5
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Nitz AA, Giraldez Chavez JH, Eliason ZG, Payne SH. Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses. J Proteome Res 2024. [PMID: 38981598 DOI: 10.1021/acs.jproteome.4c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Single-cell analysis is an active area of research in many fields of biology. Measurements at single-cell resolution allow researchers to study diverse populations without losing biologically meaningful information to sample averages. Many technologies have been used to study single cells, including mass spectrometry-based single-cell proteomics (SCP). SCP has seen a lot of growth over the past couple of years through improvements in data acquisition and analysis, leading to greater proteomic depth. Because method development has been the main focus in SCP, biological applications have been sprinkled in only as proof-of-concept. However, SCP methods now provide significant coverage of the proteome and have been implemented in many laboratories. Thus, a primary question to address in our community is whether the current state of technology is ready for widespread adoption for biological inquiry. In this Perspective, we examine the potential for SCP in three thematic areas of biological investigation: cell annotation, developmental trajectories, and spatial mapping. We identify that the primary limitation of SCP is sample throughput. As proteome depth has been the primary target for method development to date, we advocate for a change in focus to facilitate measuring tens of thousands of single-cell proteomes to enable biological applications beyond proof-of-concept.
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Affiliation(s)
- Alyssa A Nitz
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| | | | - Zachary G Eliason
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
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6
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Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L. Spatial top-down proteomics for the functional characterization of human kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580062. [PMID: 38405958 PMCID: PMC10888776 DOI: 10.1101/2024.02.13.580062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.
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Affiliation(s)
- Kevin J. Zemaitis
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - James M. Fulcher
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Rashmi Kumar
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - David J. Degnan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Logan A. Lewis
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Yen-Chen Liao
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Marija Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Sarah M. Williams
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lisa M. Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
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7
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Lang X, Guo W, Fang Z, Xie G, Mei G, Duan Z, Liu D, Zhai Y, Lu X. Crystalline-Amorphous Interfaces Engineering of CoO-InO x for Highly Efficient CO 2 Electroreduction to CO. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311694. [PMID: 38363062 DOI: 10.1002/smll.202311694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/30/2024] [Indexed: 02/17/2024]
Abstract
As a fundamental product of CO2 conversion through two-electron transfer, CO is used to produce numerous chemicals and fuels with high efficiency, which has broad application prospects. In this work, it has successfully optimized catalytic activity by fabricating an electrocatalyst featuring crystalline-amorphous CoO-InOx interfaces, thereby significantly expediting CO production. The 1.21%CoO-InOx consists of randomly dispersed CoO crystalline particles among amorphous InOx nanoribbons. In contrast to the same-phase structure, the unique CoO-InOx heterostructure provides plentiful reactive crystalline-amorphous interfacial sites. The Faradaic efficiency of CO (FECO) can reach up to 95.67% with a current density of 61.72 mA cm-2 in a typical H-cell using MeCN containing 0.5 M 1-Butyl-3-methylimidazolium hexafluorophosphate ([Bmim]PF6) as the electrolyte. Comprehensive experiments indicate that CoO-InOx interfaces with optimization of charge transfer enhance the double-layer capacitance and CO2 adsorption capacity. Theoretical calculations further reveal that the regulating of the electronic structure at interfacial sites not only optimizes the Gibbs free energy of *COOH intermediate formation but also inhibits HER, resulting in high selectivity toward CO.
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Affiliation(s)
- Xianzhen Lang
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Weiwei Guo
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Zijian Fang
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Guixian Xie
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Guoliang Mei
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Zongxia Duan
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Doudou Liu
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Yanling Zhai
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
| | - Xiaoquan Lu
- Institute of Molecular Metrology, College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266071, P. R. China
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8
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Chandran RR, Vijayaraj P, Garcia-Milian R, King J, Castillo K, Chen L, Kwon Y, William S, Rickabaugh TM, Langerman J, Choi W, Sen C, Lever JEP, Li Q, Pavelkova N, Plosa EJ, Rowe SM, Plath K, Clair G, Gomperts BN. Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599411. [PMID: 38948715 PMCID: PMC11212876 DOI: 10.1101/2024.06.17.599411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The distal bronchioles in Idiopathic Pulmonary Fibrosis (IPF) exhibit histopathological abnormalities such as bronchiolization, peribronchiolar fibrosis and honeycomb cysts that contribute to the overall architectural remodeling of lung tissue seen in the disease. Here we describe an additional histopathologic finding of epithelial desquamation in patients with IPF, wherein epithelial cells detach from the basement membrane of the distal bronchioles. To understand the mechanism driving this pathology, we performed spatial transcriptomics of the epithelial cells and spatial proteomics of the basement membrane of the distal bronchioles from IPF patients and patients with no prior history of lung disease. Our findings reveal a downregulation of cell junctional components, upregulation of epithelial-mesenchymal transition signatures and dysregulated basement membrane matrix in IPF distal bronchioles, facilitating epithelial desquamation. Further, functional assays identified regulation between Collagen IV in the matrix, and the junctional genes JUP and PLEC , that is crucial for maintaining distal bronchiolar homeostasis. In IPF, this balanced regulation between matrix and cell-junctions is disrupted, leading to loss of epithelial adhesion, peribronchiolar fibrosis and epithelial desquamation. Overall, our study suggests that in IPF the interplay between the loss of cell junctions and a dysregulated matrix results in desquamation of distal bronchiolar epithelium and lung remodeling, exacerbating the disease. One Sentence Summary Two-way regulation of cell junctional proteins and matrix proteins drives cellular desquamation and fibrosis in the distal bronchioles of patients with Idiopathic Pulmonary Fibrosis.
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9
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Hu S, Habib A, Xiong W, Chen L, Bi L, Wen L. Mass Spectrometry Imaging Techniques: Non-Ambient and Ambient Ionization Approaches. Crit Rev Anal Chem 2024:1-54. [PMID: 38889072 DOI: 10.1080/10408347.2024.2362703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Molecular information can be acquired from sample surfaces in real time using a revolutionary molecular imaging technique called mass spectrometry imaging (MSI). The technique can concurrently provide high spatial resolution information on the spatial distribution and relative proportion of many different compounds. Thus, many scientists have been drawn to the innovative capabilities of the MSI approach, leading to significant focus in various fields during the past few decades. This review describes the sampling protocol, working principle and applications of a few non-ambient and ambient ionization mass spectrometry imaging techniques. The non-ambient techniques include secondary ionization mass spectrometry and matrix-assisted laser desorption ionization, while the ambient techniques include desorption electrospray ionization, laser ablation electrospray ionization, probe electro-spray ionization, desorption atmospheric pressure photo-ionization and femtosecond laser desorption ionization. The review additionally addresses the advantages and disadvantages of ambient and non-ambient MSI techniques in relation to their suitability, particularly for biological samples used in tissue diagnostics. Last but not least, suggestions and conclusions are made regarding the challenges and future prospects of MSI.
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Affiliation(s)
- Shundi Hu
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Wei Xiong
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - La Chen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Lei Bi
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Luhong Wen
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
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10
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Meldrum KL, Swansiger AK, Daniels MM, Hale WA, Kirmiz Cody C, Qiu X, Knierman M, Sausen J, Prell JS. Gábor Transform-Based Signal Isolation, Rapid Deconvolution, and Quantitation of Intact Protein Ions with Mass Spectrometry. Anal Chem 2024; 96:9512-9523. [PMID: 38788216 DOI: 10.1021/acs.analchem.4c00978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
High-resolution mass spectrometry (HRMS) is a powerful technique for the characterization and quantitation of complex biological mixtures, with several applications including clinical monitoring and tissue imaging. However, these medical and pharmaceutical applications are pushing the analytical limits of modern HRMS techniques, requiring either further development in instrumentation or data processing methods. Here, we demonstrate new developments in the interactive Fourier-transform analysis for mass spectrometry (iFAMS) software including the first application of Gábor transform (GT) to protein quantitation. Newly added automation tools detect signals from minimal user input and apply thresholds for signal selection, deconvolution, and baseline correction to improve the objectivity and reproducibility of deconvolution. Additional tools were added to improve the deconvolution of highly complex or congested mass spectra and are demonstrated here for the first time. The "Gábor Slicer" enables the user to explore trends in the Gábor spectrogram with instantaneous ion mass estimates accurate to 10 Da. The charge adjuster allows for easy visual confirmation of accurate charge state assignments and quick adjustment if necessary. Deconvolution refinement utilizes a second GT of isotopically resolved data to remove common deconvolution artifacts. To assess the quality of deconvolution from iFAMS, several comparisons are made to deconvolutions using other algorithms such as UniDec and an implementation of MaxEnt in Agilent MassHunter BioConfirm. Lastly, the newly added batch processing and quantitation capabilities of iFAMS are demonstrated and compared to a common extracted ion chromatogram approach.
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Affiliation(s)
- Kayd L Meldrum
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Andrew K Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Meghan M Daniels
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Wendi A Hale
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Crystal Kirmiz Cody
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Xi Qiu
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - Michael Knierman
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - John Sausen
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, California 95051, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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11
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Faktor J, Kote S, Bienkowski M, Hupp TR, Marek-Trzonkowska N. Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker. Commun Biol 2024; 7:708. [PMID: 38851810 PMCID: PMC11162451 DOI: 10.1038/s42003-024-06354-8] [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] [Received: 01/20/2023] [Accepted: 05/20/2024] [Indexed: 06/10/2024] Open
Abstract
Robotically assisted proteomics provides insights into the regulation of multiple proteins achieving excellent spatial resolution. However, developing an effective method for spatially resolved quantitative proteomics of formalin fixed paraffin embedded tissue (FFPE) in an accessible and economical manner remains challenging. We introduce non-robotic In-insert FFPE proteomics approach, combining glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). In-insert approach identifies 450 proteins from a 5 µm thick breast FFPE tissue voxel with 50 µm lateral dimensions covering several tens of cells. Furthermore, In-insert approach associated a keratin series and moesin (MOES) with prolactin-induced protein (PIP) indicating their prolactin and/or estrogen regulation. Our data suggest that PIP is a spatial biomarker for hormonally triggered cytoskeletal remodeling, potentially useful for screening hormonally affected hotspots in breast tissue. In-insert proteomics represents an alternative FFPE processing method, requiring minimal laboratory equipment and skills to generate spatial proteotype repositories from FFPE tissue.
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Affiliation(s)
- Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Michal Bienkowski
- Medical University of Gdansk, University of Gdansk, Mariana Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
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12
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Wang H, Aslam MK, Nie Z, Yang K, Li X, Chen S, Li Q, Chao D, Duan J. Dual-Anion Regulation for Reversible and Energetic Aqueous Zn-CO 2 Batteries. SMALL METHODS 2024; 8:e2300867. [PMID: 37904326 DOI: 10.1002/smtd.202300867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/01/2023] [Indexed: 11/01/2023]
Abstract
Aqueous Zn-CO2 batteries can not only convert CO2 into high-value chemicals but also store/output electric energy for external use. However, their performance is limited by sluggish and complicated CO2 electroreduction at the cathode. Herein, a dual-anion regulated Bi electrocatalyst is developed to selectively reduce CO2 to formate with a Faradaic efficiency of up to 97% at a large current density of 250 mA cm-2. With O and/or F, the rate-determine step of CO2 electroreduction has been manipulated (from the first hydrogenation to *HCOOH desorption step) with a reduced energy barrier. Significantly, the fabricated Zn-CO2 battery exhibits a high discharge voltage of 1.2 V, optimal power density of 4.51 mW cm-2, remarkable energy density of 802 Wh kg-1, and energy-conversion efficiency of 70.74%, stability up to 200 cycles and 68 h. This study provides possible strategies to fabricate reversible and energetic aqueous Zn-CO2 batteries by addressing cathodic problems.
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Affiliation(s)
- Herui Wang
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Muhammad Kashif Aslam
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Zhihao Nie
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Kang Yang
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Xinran Li
- Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials College of Chemistry and Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Sheng Chen
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Qiang Li
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Dongliang Chao
- Laboratory of Advanced Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials College of Chemistry and Materials, Fudan University, Shanghai, 200433, P. R. China
| | - Jingjing Duan
- School of Energy and Power Engineering, MIIT Key Laboratory of Thermal Control of Electronic Equipment, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
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13
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Zhang Y, Lee RY, Tan CW, Guo X, Yim WWY, Lim JC, Wee FY, Yang WU, Kharbanda M, Lee JYJ, Ngo NT, Leow WQ, Loo LH, Lim TK, Sobota RM, Lau MC, Davis MJ, Yeong J. Spatial omics techniques and data analysis for cancer immunotherapy applications. Curr Opin Biotechnol 2024; 87:103111. [PMID: 38520821 DOI: 10.1016/j.copbio.2024.103111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/25/2024]
Abstract
In-depth profiling of cancer cells/tissues is expanding our understanding of the genomic, epigenomic, transcriptomic, and proteomic landscape of cancer. However, the complexity of the cancer microenvironment, particularly its immune regulation, has made it difficult to exploit the potential of cancer immunotherapy. High-throughput spatial omics technologies and analysis pipelines have emerged as powerful tools for tackling this challenge. As a result, a potential revolution in cancer diagnosis, prognosis, and treatment is on the horizon. In this review, we discuss the technological advances in spatial profiling of cancer around and beyond the central dogma to harness the full benefits of immunotherapy. We also discuss the promise and challenges of spatial data analysis and interpretation and provide an outlook for the future.
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Affiliation(s)
- Yue Zhang
- Duke-NUS Medical School, Singapore 169856, Singapore
| | - Ren Yuan Lee
- Yong Loo Lin School of Medicine, National University of Singapore, 169856 Singapore; Singapore Thong Chai Medical Institution, Singapore 169874, Singapore
| | - Chin Wee Tan
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia
| | - Xue Guo
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Willa W-Y Yim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Jeffrey Ct Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Felicia Yt Wee
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - W U Yang
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Malvika Kharbanda
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jia-Ying J Lee
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Nye Thane Ngo
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Wei Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore
| | - Tony Kh Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore
| | - Mai Chan Lau
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A⁎STAR), Singapore 138648, Singapore
| | - Melissa J Davis
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia; Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland 4102, Australia; immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joe Yeong
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A⁎STAR), Singapore 169856, Singapore; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A⁎STAR), Singapore 138671, Singapore.
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14
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Zhang L, Xiong Z, Xiao M. A Review of the Application of Spatial Transcriptomics in Neuroscience. Interdiscip Sci 2024; 16:243-260. [PMID: 38374297 DOI: 10.1007/s12539-024-00603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024]
Abstract
Since spatial transcriptomics can locate and distinguish the gene expression of functional genes in special regions and tissue, it is important for us to investigate the brain development, the development mechanism of brain diseases, and the relationship between brain structure and function in Neuroscience (or Brain science). While previous studies have introduced the crucial spatial transcriptomic techniques and data analysis methods, there are few studies to comprehensively overview the key methods, data resources, and technological applications of spatial transcriptomics in Neuroscience. For these reasons, we first investigate several common spatial transcriptomic data analysis approaches and data resources. Second, we introduce the applications of the spatial transcriptomic data analysis approaches in Neuroscience. Third, we summarize the integrating spatial transcriptomics with other technologies in Neuroscience. Finally, we discuss the challenges and future research directions of spatial transcriptomics in Neuroscience.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Zhenqi Xiong
- College of Computer Science, Sichuan University, Chengdu, 610065, China
| | - Ming Xiao
- College of Computer Science, Sichuan University, Chengdu, 610065, China.
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15
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Kuan CH, Tai KY, Lu SC, Wu YF, Wu PS, Kwang N, Wang WH, Mai-Yi Fan S, Wang SH, Chien HF, Lai HS, Lin MH, Plikus MV, Lin SJ. Delayed Collagen Production without Myofibroblast Formation Contributes to Reduced Scarring in Adult Skin Microwounds. J Invest Dermatol 2024; 144:1124-1133.e7. [PMID: 38036291 DOI: 10.1016/j.jid.2023.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/02/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
In adult mammals, wound healing predominantly follows a fibrotic pathway, culminating in scar formation. However, cutaneous microwounds generated through fractional photothermolysis, a modality that produces a constellation of microthermal zones, exhibit a markedly different healing trajectory. Our study delineates the cellular attributes of these microthermal zones, underscoring a temporally limited, subclinical inflammatory milieu concomitant with rapid re-epithelialization within 24 hours. This wound closure is facilitated by the activation of genes associated with keratinocyte migration and differentiation. In contrast to macrothermal wounds, which predominantly heal through a robust myofibroblast-mediated collagen deposition, microthermal zones are characterized by absence of wound contraction and feature delayed collagen remodeling, initiating 5-6 weeks after injury. This distinct wound healing is characterized by a rapid re-epithelialization process and a muted inflammatory response, which collectively serve to mitigate excessive myofibroblast activation. Furthermore, we identify an initial reparative phase characterized by a heterogeneous extracellular matrix protein composition, which precedes the delayed collagen remodeling. These findings extend our understanding of cutaneous wound healing and may have significant implications for the optimization of therapeutic strategies aimed at mitigating scar formation.
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Affiliation(s)
- Chen-Hsiang Kuan
- Graduate Institute of Clinical Research, College of Medicine, National Taiwan University, Taipei, Taiwan; Division of Plastic Surgery, Department of Surgery, National Taiwan University Hospital, College of Medicine, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Kang-Yu Tai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Shao-Chi Lu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Yueh-Feng Wu
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Pei-Shan Wu
- Department of Ophthalmology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Nellie Kwang
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA
| | - Wei-Hung Wang
- Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan
| | - Sabrina Mai-Yi Fan
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Shiou-Han Wang
- Department of Dermatology, National Taiwan University Hospital, College of Medicine, Taipei, Taiwan
| | - Hsiung-Fei Chien
- Division of Plastic Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan; TMU Center for Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hong-Shiee Lai
- Department of Surgery, National Taiwan University Hospital, College of Medicine, Taipei, Taiwan; Department of Surgery, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
| | - Miao-Hsia Lin
- Graduate Institute and Department of Microbiology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Sung-Jan Lin
- Graduate Institute of Clinical Research, College of Medicine, National Taiwan University, Taipei, Taiwan; Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan; Department of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan; Center for Frontier Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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16
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Huber RE, Babbitt C, Peyton SR. Heterogeneity of brain extracellular matrix and astrocyte activation. J Neurosci Res 2024; 102:e25356. [PMID: 38773875 DOI: 10.1002/jnr.25356] [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: 08/30/2023] [Revised: 04/01/2024] [Accepted: 05/05/2024] [Indexed: 05/24/2024]
Abstract
From the blood brain barrier to the synaptic space, astrocytes provide structural, metabolic, ionic, and extracellular matrix (ECM) support across the brain. Astrocytes include a vast array of subtypes, their phenotypes and functions varying both regionally and temporally. Astrocytes' metabolic and regulatory functions poise them to be quick and sensitive responders to injury and disease in the brain as revealed by single cell sequencing. Far less is known about the influence of the local healthy and aging microenvironments on these astrocyte activation states. In this forward-looking review, we describe the known relationship between astrocytes and their local microenvironment, the remodeling of the microenvironment during disease and injury, and postulate how they may drive astrocyte activation. We suggest technology development to better understand the dynamic diversity of astrocyte activation states, and how basal and activation states depend on the ECM microenvironment. A deeper understanding of astrocyte response to stimuli in ECM-specific contexts (brain region, age, and sex of individual), paves the way to revolutionize how the field considers astrocyte-ECM interactions in brain injury and disease and opens routes to return astrocytes to a healthy quiescent state.
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Affiliation(s)
- Rebecca E Huber
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Courtney Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Shelly R Peyton
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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17
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Makhmut A, Qin D, Hartlmayr D, Seth A, Coscia F. An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics. Mol Cell Proteomics 2024; 23:100750. [PMID: 38513891 PMCID: PMC11067455 DOI: 10.1016/j.mcpro.2024.100750] [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: 12/08/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
Spatial tissue proteomics integrating whole-slide imaging, laser microdissection, and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE robotic system, which has the capacity to process 192 samples in 3 h. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking, and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows 'on-the-fly' sample clean-up, particularly pertinent for laser microdissection workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell, and epithelial microregions of 4000 μm2 to a depth of ∼2000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.
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Affiliation(s)
- Anuar Makhmut
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Di Qin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | | | | | - Fabian Coscia
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
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18
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Berrell N, Sadeghirad H, Blick T, Bidgood C, Leggatt GR, O'Byrne K, Kulasinghe A. Metabolomics at the tumor microenvironment interface: Decoding cellular conversations. Med Res Rev 2024; 44:1121-1146. [PMID: 38146814 DOI: 10.1002/med.22010] [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: 09/21/2023] [Revised: 11/08/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
Cancer heterogeneity remains a significant challenge for effective cancer treatments. Altered energetics is one of the hallmarks of cancer and influences tumor growth and drug resistance. Studies have shown that heterogeneity exists within the metabolic profile of tumors, and personalized-combination therapy with relevant metabolic interventions could improve patient response. Metabolomic studies are identifying novel biomarkers and therapeutic targets that have improved treatment response. The spatial location of elements in the tumor microenvironment are becoming increasingly important for understanding disease progression. The evolution of spatial metabolomics analysis now allows scientists to deeply understand how metabolite distribution contributes to cancer biology. Recently, these techniques have spatially resolved metabolite distribution to a subcellular level. It has been proposed that metabolite mapping could improve patient outcomes by improving precision medicine, enabling earlier diagnosis and intraoperatively identifying tumor margins. This review will discuss how altered metabolic pathways contribute to cancer progression and drug resistance and will explore the current capabilities of spatial metabolomics technologies and how these could be integrated into clinical practice to improve patient outcomes.
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Affiliation(s)
- Naomi Berrell
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Habib Sadeghirad
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Tony Blick
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Charles Bidgood
- APCRC-Q, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Graham R Leggatt
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Ken O'Byrne
- Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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19
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Xue Q, Song J, Lu F, Ma J, Cao D. Optical system design of a femi-class ultra-high-resolution spectrometer based on the quaternary dispersion of a middle echelon grating. APPLIED OPTICS 2024; 63:3029-3038. [PMID: 38856446 DOI: 10.1364/ao.521955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/17/2024] [Indexed: 06/11/2024]
Abstract
In order to meet the needs of the femi-ultra-high spectral resolution test, an optical system of the femi-ultra-high spectral resolution spectrometer in the spectral range of 190-800 nm is designed based on the quaternary dispersion of the middle echelon grating under the condition that the volume and weight of the spectrometer do not increase sharply. After the optimization design, the spectral resolution can reach 51.149 fm in the full field of view of 0.5 mm; at the wavelength of 191 nm, the spectral resolution in the whole spectral range is better than 150 fm, and the maximum distortion of the system is 0.2288%, which can provide a feasible reference for the subsequent design of the spectrometer optical system to realize the simultaneous detection of a wide band and high spectral resolution.
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20
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Hughes JW, Sisley EK, Hale OJ, Cooper HJ. Laser capture microdissection and native mass spectrometry for spatially-resolved analysis of intact protein assemblies in tissue. Chem Sci 2024; 15:5723-5729. [PMID: 38638209 PMCID: PMC11023061 DOI: 10.1039/d3sc04933g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/03/2024] [Indexed: 04/20/2024] Open
Abstract
Previously, we have shown that native ambient mass spectrometry imaging allows the spatial mapping of folded proteins and their complexes in thin tissue sections. Subsequent top-down native ambient mass spectrometry of adjacent tissue section enables protein identification. The challenges associated with protein identification by this approach are (i) the low abundance of proteins in tissue and associated long data acquisition timescales and (ii) irregular spatial distributions which hamper targeted sampling of the relevant tissue location. Here, we demonstrate that these challenges may be overcome through integration of laser capture microdissection in the workflow. We show identification of intact protein assemblies in rat liver tissue and apply the approach to identification of proteins in the granular layer of rat cerebellum.
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Affiliation(s)
- James W Hughes
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Emma K Sisley
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Oliver J Hale
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK
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21
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Noro J, Vilaça-Faria H, Reis RL, Pirraco RP. Extracellular matrix-derived materials for tissue engineering and regenerative medicine: A journey from isolation to characterization and application. Bioact Mater 2024; 34:494-519. [PMID: 38298755 PMCID: PMC10827697 DOI: 10.1016/j.bioactmat.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024] Open
Abstract
Biomaterial choice is an essential step during the development tissue engineering and regenerative medicine (TERM) applications. The selected biomaterial must present properties allowing the physiological-like recapitulation of several processes that lead to the reestablishment of homeostatic tissue or organ function. Biomaterials derived from the extracellular matrix (ECM) present many such properties and their use in the field has been steadily increasing. Considering this growing importance, it becomes imperative to provide a comprehensive overview of ECM biomaterials, encompassing their sourcing, processing, and integration into TERM applications. This review compiles the main strategies used to isolate and process ECM-derived biomaterials as well as different techniques used for its characterization, namely biochemical and chemical, physical, morphological, and biological. Lastly, some of their applications in the TERM field are explored and discussed.
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Affiliation(s)
- Jennifer Noro
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Helena Vilaça-Faria
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L. Reis
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rogério P. Pirraco
- 3B's Research Group, I3Bs – Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
- ICVS/3B's – PT Government Associate Laboratory, Braga, Guimarães, Portugal
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22
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Ma X, Fernández FM. Advances in mass spectrometry imaging for spatial cancer metabolomics. MASS SPECTROMETRY REVIEWS 2024; 43:235-268. [PMID: 36065601 PMCID: PMC9986357 DOI: 10.1002/mas.21804] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 05/09/2023]
Abstract
Mass spectrometry (MS) has become a central technique in cancer research. The ability to analyze various types of biomolecules in complex biological matrices makes it well suited for understanding biochemical alterations associated with disease progression. Different biological samples, including serum, urine, saliva, and tissues have been successfully analyzed using mass spectrometry. In particular, spatial metabolomics using MS imaging (MSI) allows the direct visualization of metabolite distributions in tissues, thus enabling in-depth understanding of cancer-associated biochemical changes within specific structures. In recent years, MSI studies have been increasingly used to uncover metabolic reprogramming associated with cancer development, enabling the discovery of key biomarkers with potential for cancer diagnostics. In this review, we aim to cover the basic principles of MSI experiments for the nonspecialists, including fundamentals, the sample preparation process, the evolution of the mass spectrometry techniques used, and data analysis strategies. We also review MSI advances associated with cancer research in the last 5 years, including spatial lipidomics and glycomics, the adoption of three-dimensional and multimodal imaging MSI approaches, and the implementation of artificial intelligence/machine learning in MSI-based cancer studies. The adoption of MSI in clinical research and for single-cell metabolomics is also discussed. Spatially resolved studies on other small molecule metabolites such as amino acids, polyamines, and nucleotides/nucleosides will not be discussed in the context.
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Affiliation(s)
- Xin Ma
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, USA
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23
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Xie YR, Castro DC, Rubakhin SS, Trinklein TJ, Sweedler JV, Lam F. Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry. Nat Methods 2024; 21:521-530. [PMID: 38366241 PMCID: PMC10927565 DOI: 10.1038/s41592-024-02171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
Spatial omics technologies can reveal the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive biochemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping using MEISTER, an integrative experimental and computational mass spectrometry (MS) framework. Our framework integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating three-dimensional (3D) molecular distributions and a data integration method fitting cell-specific mass spectra to 3D datasets. We imaged detailed lipid profiles in tissues with millions of pixels and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future development of multiscale technologies for biochemical characterization of the brain.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Daniel C Castro
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stanislav S Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Timothy J Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Fan Lam
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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24
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Fan X, Sun AR, Young RSE, Afara IO, Hamilton BR, Ong LJY, Crawford R, Prasadam I. Spatial analysis of the osteoarthritis microenvironment: techniques, insights, and applications. Bone Res 2024; 12:7. [PMID: 38311627 PMCID: PMC10838951 DOI: 10.1038/s41413-023-00304-6] [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: 09/05/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 02/06/2024] Open
Abstract
Osteoarthritis (OA) is a debilitating degenerative disease affecting multiple joint tissues, including cartilage, bone, synovium, and adipose tissues. OA presents diverse clinical phenotypes and distinct molecular endotypes, including inflammatory, metabolic, mechanical, genetic, and synovial variants. Consequently, innovative technologies are needed to support the development of effective diagnostic and precision therapeutic approaches. Traditional analysis of bulk OA tissue extracts has limitations due to technical constraints, causing challenges in the differentiation between various physiological and pathological phenotypes in joint tissues. This issue has led to standardization difficulties and hindered the success of clinical trials. Gaining insights into the spatial variations of the cellular and molecular structures in OA tissues, encompassing DNA, RNA, metabolites, and proteins, as well as their chemical properties, elemental composition, and mechanical attributes, can contribute to a more comprehensive understanding of the disease subtypes. Spatially resolved biology enables biologists to investigate cells within the context of their tissue microenvironment, providing a more holistic view of cellular function. Recent advances in innovative spatial biology techniques now allow intact tissue sections to be examined using various -omics lenses, such as genomics, transcriptomics, proteomics, and metabolomics, with spatial data. This fusion of approaches provides researchers with critical insights into the molecular composition and functions of the cells and tissues at precise spatial coordinates. Furthermore, advanced imaging techniques, including high-resolution microscopy, hyperspectral imaging, and mass spectrometry imaging, enable the visualization and analysis of the spatial distribution of biomolecules, cells, and tissues. Linking these molecular imaging outputs to conventional tissue histology can facilitate a more comprehensive characterization of disease phenotypes. This review summarizes the recent advancements in the molecular imaging modalities and methodologies for in-depth spatial analysis. It explores their applications, challenges, and potential opportunities in the field of OA. Additionally, this review provides a perspective on the potential research directions for these contemporary approaches that can meet the requirements of clinical diagnoses and the establishment of therapeutic targets for OA.
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Affiliation(s)
- Xiwei Fan
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Antonia Rujia Sun
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Reuben S E Young
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, QLD, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, Australia
| | - Isaac O Afara
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, QLD, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, QLD, Australia
| | - Louis Jun Ye Ong
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Ross Crawford
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia
- The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Indira Prasadam
- Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, QLD, Australia.
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, Brisbane, QLD, Australia.
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25
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Yang N, Yue G, Zhang Y, Qin X, Gao Z, Mi B, Fan Q, Qian Y. Reproducible and High-Performance WOLEDs Based on Independent High-Efficiency Triplet Harvesting of Yellow Hot-Exciton ESIPT and Blue TADF Emitters. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304615. [PMID: 37822169 DOI: 10.1002/smll.202304615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/04/2023] [Indexed: 10/13/2023]
Abstract
Hot exciton organic light-emitting diode (OLED) emitters can balance the high performance of a device and reduce efficiency roll-off by fast reverse intersystem crossing from high-lying triplets (hRISC). In this study, an excited-state intramolecular proton transfer (ESIPT) fluorophore of 2-(benzo[d]thiazol-2-yl)-4-(pyren-1-yl)phenol (PyHBT) with the typical characteristic properties of a hot exciton is developed. With high efficiency of utilization of the exciton (91%), its yellow OLED exhibited high external quantum efficiency (EQE) of 5.6%, current efficiency (CE) of 16.8 cd A-1 , and power efficiency (PE) of 17.3 lm W-1 . The performance of the yellow emissive "hot exciton" ESIPT fluorophores is among the highest recorded. Due to the large Stokes shift of the ESIPT emitter, non-energy-transferred high-performance white OLEDs (WOLEDs) are developed, which are reproducible and highly efficient. This is possible because of the independent harvesting of most of the triplets in both complementary-color emitters without the interference of energy transfer. The PyHBT-based WOLEDs exhibit a maximum EQE of 14.3% and CE of 41.1 cd A-1 , which facilitates the high-yield mass production of inexpensive WOLEDs.
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Affiliation(s)
- Ningjing Yang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Guochang Yue
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Yong Zhang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Xiaoyu Qin
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Zhiqiang Gao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Baoxiu Mi
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Quli Fan
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Yan Qian
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
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26
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Chen G, Xu W, Long Z, Chong Y, Lin B, Jie Y. Single-cell Technologies Provide Novel Insights into Liver Physiology and Pathology. J Clin Transl Hepatol 2024; 12:79-90. [PMID: 38250462 PMCID: PMC10794276 DOI: 10.14218/jcth.2023.00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 01/23/2024] Open
Abstract
The liver is the largest glandular organ in the body and has a unique distribution of cells and biomolecules. However, the treatment outcome of end-stage liver disease is extremely poor. Single-cell sequencing is a new advanced and powerful technique for identifying rare cell populations and biomolecules by analyzing the characteristics of gene expression between individual cells. These cells and biomolecules might be used as potential targets for immunotherapy of liver diseases and contribute to the development of precise individualized treatment. Compared to whole-tissue RNA sequencing, single-cell RNA sequencing (scRNA-seq) or other single-cell histological techniques have solved the problem of cell population heterogeneity and characterize molecular changes associated with liver diseases with higher accuracy and resolution. In this review, we comprehensively summarized single-cell approaches including transcriptomic, spatial transcriptomic, immunomic, proteomic, epigenomic, and multiomic technologies, and described their application in liver physiology and pathology. We also discussed advanced techniques and recent studies in the field of single-cell; our review might provide new insights into the pathophysiological mechanisms of the liver to achieve precise and individualized treatment of liver diseases.
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Affiliation(s)
| | | | - Zhicong Long
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yutian Chong
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bingliang Lin
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yusheng Jie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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27
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [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: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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28
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Bi S, Wang M, Pu Q, Yang J, Jiang N, Zhao X, Qiu S, Liu R, Xu R, Li X, Hu C, Yang L, Gu J, Du D. Multi-MSIProcessor: Data Visualizing and Analysis Software for Spatial Metabolomics Research. Anal Chem 2024; 96:339-346. [PMID: 38102989 DOI: 10.1021/acs.analchem.3c04192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Mass spectrometry imaging (MSI) has emerged as a revolutionary analytical strategy in biomedical research for molecular visualization. By linking the characterization of functional metabolites with tissue architecture, it is now possible to reveal unknown biological functions of tissues. However, due to the complexity and high dimensionality of MSI data, mining bioinformatics-related peaks from batch MSI data sets and achieving complete spatially resolved metabolomics analysis remain a great challenge. Here, we propose novel MSI data processing software, Multi-MSIProcessor (MMP), which integrates the data read-in, MSI visualization, processed data preservation, and biomarker discovery functions. The MMP focuses on the AFADESI-MSI data platform but also supports mzXML and imzmL data input formats for compatibility with data generated by other MSI platforms such as MALDI/SIMS-MSI. MMP enables deep mining of batch MSI data and has flexible adaptability with the source code opened that welcomes new functions and personalized analysis strategies. Using multiple clinical biosamples with complex heterogeneity, we demonstrated that MMP can rapidly establish complete MSI analysis workflows, assess batch sample data quality, screen and annotate differential MS peaks, and obtain abnormal metabolic pathways. MMP provides a novel platform for spatial metabolomics analysis of multiple samples that could meet the diverse analysis requirements of scholars.
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Affiliation(s)
- Siwei Bi
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Manjiangcuo Wang
- Advanced Mass Spectrometry Center, Research Core Facility, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
| | - Qianlun Pu
- Advanced Mass Spectrometry Center, Research Core Facility, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
| | - Jinxi Yang
- West China Centre of Excellence for Pancreatitis, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital/West China Medical School, Sichuan University, Chengdu 610041, China
| | - Na Jiang
- Advanced Mass Spectrometry Center, Research Core Facility, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
| | - Xueshan Zhao
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Siyuan Qiu
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu,Sichuan 610041, China
| | - Ruiqi Liu
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Renjie Xu
- Department of Respiratory Health West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xia Li
- West China School of Nursing, Sichuan University, Chengdu, Sichuan 610041, China
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chenggong Hu
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lie Yang
- Division of Gastrointestinal Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu,Sichuan 610041, China
| | - Jun Gu
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dan Du
- Advanced Mass Spectrometry Center, Research Core Facility, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610213, China
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29
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Truong T, Sanchez-Avila X, Webber KGI, Johnston SM, Kelly RT. Efficient and Sensitive Sample Preparation, Separations, and Data Acquisition for Label-Free Single-Cell Proteomics. Methods Mol Biol 2024; 2817:67-84. [PMID: 38907148 DOI: 10.1007/978-1-0716-3934-4_7] [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: 06/23/2024]
Abstract
We describe a sensitive and efficient workflow for label-free single-cell proteomics that spans sample preparation, liquid chromatography separations, and mass spectrometry data acquisition. The Tecan Uno Single Cell Dispenser provides rapid cell isolation and nanoliter-volume reagent dispensing within 384-well PCR plates. A newly developed sample processing workflow achieves cell lysis, protein denaturation, and digestion in 1 h with a single reagent dispensing step. Low-flow liquid chromatography coupled with wide-window data-dependent acquisition results in the quantification of nearly 3000 proteins per cell using an Orbitrap Exploris 480 mass spectrometer. This approach greatly broadens accessibility to sensitive single-cell proteome profiling for nonspecialist laboratories.
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Affiliation(s)
- Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Ximena Sanchez-Avila
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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30
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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31
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Xiang P, Liyu A, Kwon Y, Hu D, Williams SM, Veličković D, Markillie LM, Chrisler WB, Paša-Tolić L, Zhu Y. Spatial Proteomics toward Subcellular Resolution by Coupling Deep Ultraviolet Laser Ablation with Nanodroplet Sample Preparation. ACS MEASUREMENT SCIENCE AU 2023; 3:459-468. [PMID: 38145026 PMCID: PMC10740121 DOI: 10.1021/acsmeasuresciau.3c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 12/26/2023]
Abstract
Multiplexed molecular profiling of tissue microenvironments, or spatial omics, can provide critical insights into cellular functions and disease pathology. The coupling of laser microdissection with mass spectrometry-based proteomics has enabled deep and unbiased mapping of >1000 proteins. However, the throughput of laser microdissection is often limited due to tedious two-step procedures, sequential laser cutting, and sample collection. The two-step procedure also hinders the further improvement of spatial resolution to <10 μm as needed for subcellular proteomics. Herein, we developed a high-throughput and high-resolution spatial proteomics platform by seamlessly coupling deep ultraviolet (DUV) laser ablation (LA) with nanoPOTS (Nanodroplet Processing in One pot for Trace Samples)-based sample preparation. We demonstrated the DUV-LA system can quickly isolate and collect tissue samples at a throughput of ∼30 spots/min and a spatial resolution down to 2 μm from a 10 μm thick human pancreas tissue section. To improve sample recovery, we developed a proximity aerosol collection approach by placing DMSO droplets close to LA spots. We demonstrated the DUV-LA-nanoPOTS platform can detect an average of 1312, 1533, and 1966 proteins from ablation spots with diameters of 7, 13, and 19 μm, respectively. In a proof-of-concept study, we isolated and profiled two distinct subcellular regions of the pancreas tissue revealed by hematoxylin and eosin (H&E) staining. Quantitative proteomics revealed proteins specifically enriched to subcellular compartments.
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Affiliation(s)
- Piliang Xiang
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Andrey Liyu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Yumi Kwon
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dehong Hu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Sarah M. Williams
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Lye Meng Markillie
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Department
of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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32
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Wang H, Zhang X, Liu Y, Zhou S. A nicking enzyme-assisted allosteric strategy for self-resetting DNA switching circuits. Analyst 2023; 149:169-179. [PMID: 37999719 DOI: 10.1039/d3an01677c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
The self-regulation of biochemical reaction networks is crucial for maintaining balance, stability, and adaptability within biological systems. DNA switching circuits, serving as basic units, play essential roles in regulating pathways, facilitating signal transduction, and processing biochemical reaction networks. However, the non-reusability of DNA switching circuits hinders its application in current complex information processing. Herein, we proposed a nicking enzyme-assisted allosteric strategy for constructing self-resetting DNA switching circuits to realize complex information processing. This strategy utilizes the unique cleavage ability of the nicking enzyme to achieve the automatic restoration of states. Based on this strategy, we implemented a self-resetting DNA switch. By leveraging the reusability of the DNA switch, we constructed a DNA switching circuit with selective activation characteristics and further extended its functionality to include fan-out and fan-in processes by expanding the number of functional modules and connection modes. Furthermore, we demonstrated the complex information processing capabilities of these switching circuits by integrating recognition, translation, and decision functional modules, which could analyze and transmit multiple input signals and realize parallel logic operations. This strategy simplifies the design of switching circuits and promotes the future development of biosensing, molecular computing, and nanomachines.
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Affiliation(s)
- Haoliang Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China.
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China.
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China.
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33
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Bender K, Wang Y, Zhai CY, Saenz Z, Wang A, Neumann EK. Sample Preparation Method for MALDI Mass Spectrometry Imaging of Fresh-Frozen Spines. Anal Chem 2023; 95:17337-17346. [PMID: 37886878 PMCID: PMC10688227 DOI: 10.1021/acs.analchem.3c03672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
Technologies assessing the lipidomics, genomics, epigenomics, transcriptomics, and proteomics of tissue samples at single-cell resolution have deepened our understanding of physiology and pathophysiology at an unprecedented level of detail. However, the study of single-cell spatial metabolomics in undecalcified bones faces several significant challenges, such as the fragility of bone, which often requires decalcification or fixation leading to the degradation or removal of lipids and other molecules. As such, we describe a method for performing mass spectrometry imaging on undecalcified spine that is compatible with other spatial omics measurements. In brief, we use fresh-frozen rat spines and a system of carboxyl methylcellulose embedding, cryofilm, and polytetrafluoroethylene rollers to maintain tissue integrity while avoiding signal loss from variations in laser focus and artifacts from traditional tissue processing. This reveals various tissue types and lipidomic profiles of spinal regions at 10 μm spatial resolutions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We expect this method to be adapted and applied to the analysis of the spinal cord, shedding light on the mechanistic aspects of cellular heterogeneity, development, and disease pathogenesis underlying different bone-related conditions and diseases. This study furthers the methodology for high spatial metabolomics of spines and adds to the collective efforts to achieve a holistic understanding of diseases via single-cell spatial multiomics.
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Affiliation(s)
- Kayle
J. Bender
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Yongheng Wang
- Department
of Biomedical Engineering, University of
California, Davis, Davis, California 95616, United States
| | - Chuo Ying Zhai
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Zoe Saenz
- Department
of Surgery, School of Medicine, University
of California, Davis, Sacramento, California 95817, United States
| | - Aijun Wang
- Center
for Surgical Bioengineering, Department of Surgery, School of Medicine, University of California, Davis, Sacramento, California 95817, United States
- Institute
for Pediatric Regenerative Medicine, Shriners
Hospital for Children Northern California, UC Davis School of Medicine, Sacramento, California 96817, United States
| | - Elizabeth K. Neumann
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
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Davis S, Scott C, Oetjen J, Charles PD, Kessler BM, Ansorge O, Fischer R. Deep topographic proteomics of a human brain tumour. Nat Commun 2023; 14:7710. [PMID: 38001067 PMCID: PMC10673928 DOI: 10.1038/s41467-023-43520-8] [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] [Received: 03/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour at three spatial resolutions, the highest being 40 µm, to reveal distinct abundance patterns of thousands of proteins. We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns and correlate proteins in the context of tissue heterogeneity and cellular features such as extracellular matrix or proximity to blood vessels. We identify PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, we demonstrate spatially-aware deep proteo-phenotyping of tissue heterogeneity, to re-define understanding tissue biology and pathology at the molecular level.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Connor Scott
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Janina Oetjen
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Philip D Charles
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Olaf Ansorge
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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Huang CF, Su P, Fisher TD, Levitsky J, Kelleher NL, Forte E. Mass spectrometry-based proteomics for advancing solid organ transplantation research. FRONTIERS IN TRANSPLANTATION 2023; 2:1286881. [PMID: 38993855 PMCID: PMC11235370 DOI: 10.3389/frtra.2023.1286881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/13/2023] [Indexed: 07/13/2024]
Abstract
Scarcity of high-quality organs, suboptimal organ quality assessment, unsatisfactory pre-implantation procedures, and poor long-term organ and patient survival are the main challenges currently faced by the solid organ transplant (SOT) field. New biomarkers for assessing graft quality pre-implantation, detecting, and predicting graft injury, rejection, dysfunction, and survival are critical to provide clinicians with invaluable prediction tools and guidance for personalized patients' treatment. Additionally, new therapeutic targets are also needed to reduce injury and rejection and improve transplant outcomes. Proteins, which underlie phenotypes, are ideal candidate biomarkers of health and disease statuses and therapeutic targets. A protein can exist in different molecular forms, called proteoforms. As the function of a protein depends on its exact composition, proteoforms can offer a more accurate basis for connection to complex phenotypes than protein from which they derive. Mass spectrometry-based proteomics has been largely used in SOT research for identification of candidate biomarkers and therapeutic intervention targets by so-called "bottom-up" proteomics (BUP). However, such BUP approaches analyze small peptides in lieu of intact proteins and provide incomplete information on the exact molecular composition of the proteins of interest. In contrast, "Top-down" proteomics (TDP), which analyze intact proteins retaining proteoform-level information, have been only recently adopted in transplantation studies and already led to the identification of promising proteoforms as biomarkers for organ rejection and dysfunction. We anticipate that the use of top-down strategies in combination with new technological advancements in single-cell and spatial proteomics could drive future breakthroughs in biomarker and therapeutic target discovery in SOT.
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Affiliation(s)
- Che-Fan Huang
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Pei Su
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Troy D. Fisher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Josh Levitsky
- Division of Gastroenterology and Hepatology, Comprehensive Transplant Center Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Chemistry, Northwestern University, Evanston, IL, United States
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
| | - Eleonora Forte
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
- Department of Surgery, Feinberg School of Medicine, Comprehensive Transplant Center, Northwestern University, Chicago, IL, United States
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36
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Xie YR, Castro DC, Rubakhin SS, Trinklein TJ, Sweedler JV, Lam F. Integrative Multiscale Biochemical Mapping of the Brain via Deep-Learning-Enhanced High-Throughput Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543144. [PMID: 37398021 PMCID: PMC10312594 DOI: 10.1101/2023.05.31.543144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Elucidating the spatial-biochemical organization of the brain across different scales produces invaluable insight into the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive chemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping via MEISTER, an integrative experimental and computational mass spectrometry framework. MEISTER integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating 3D molecular distributions, and a data integration method fitting cell-specific mass spectra to 3D data sets. We imaged detailed lipid profiles in tissues with data sets containing millions of pixels, and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents, and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future developments of multiscale technologies for biochemical characterization of the brain.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Daniel C. Castro
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Stanislav S. Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Timothy J. Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Jonathan V. Sweedler
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carl R. Woese Institute for Genomic Biology. University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Fan Lam
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carl R. Woese Institute for Genomic Biology. University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
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37
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Makhmut A, Qin D, Fritzsche S, Nimo J, König J, Coscia F. A framework for ultra-low-input spatial tissue proteomics. Cell Syst 2023; 14:1002-1014.e5. [PMID: 37909047 DOI: 10.1016/j.cels.2023.10.003] [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: 06/01/2023] [Revised: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
Abstract
Spatial proteomics combining microscopy-based cell phenotyping with ultrasensitive mass-spectrometry-based proteomics is an emerging and powerful concept to study cell function and heterogeneity in (patho)physiology. However, optimized workflows that preserve morphological information for phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected tissue are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low-input archival material. Benchmarking in murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions. Applied to human tonsil, we profiled 146 microregions including T and B lymphocyte niches and quantified cell-type-specific markers, cytokines, and transcription factors. These data also highlighted proteome dynamics within activated germinal centers, illuminating sites undergoing B cell proliferation and somatic hypermutation. This approach has broad implications in biomedicine, including early disease profiling and drug target and biomarker discovery. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Anuar Makhmut
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Di Qin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Sonja Fritzsche
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Jose Nimo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Janett König
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Fabian Coscia
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
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38
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Petrosius V, Aragon-Fernandez P, Üresin N, Kovacs G, Phlairaharn T, Furtwängler B, Op De Beeck J, Skovbakke SL, Goletz S, Thomsen SF, Keller UAD, Natarajan KN, Porse BT, Schoof EM. Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition. Nat Commun 2023; 14:5910. [PMID: 37737208 PMCID: PMC10517177 DOI: 10.1038/s41467-023-41602-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-state heterogeneity and distinct cellular signaling patterns that remain obscured with population-based techniques. The limited amount of material encapsulated in a single cell however, raises significant technical challenges to molecular profiling. Due to extensive optimization efforts, single-cell proteomics by Mass Spectrometry (scp-MS) has emerged as a powerful tool to facilitate proteome profiling from ultra-low amounts of input, although further development is needed to realize its full potential. To this end, we carry out comprehensive analysis of orbitrap-based data-independent acquisition (DIA) for limited material proteomics. Notably, we find a fundamental difference between optimal DIA methods for high- and low-load samples. We further improve our low-input DIA method by relying on high-resolution MS1 quantification, thus enhancing sensitivity by more efficiently utilizing available mass analyzer time. With our ultra-low input tailored DIA method, we are able to accommodate long injection times and high resolution, while keeping the scan cycle time low enough to ensure robust quantification. Finally, we demonstrate the capability of our approach by profiling mouse embryonic stem cell culture conditions, showcasing heterogeneity in global proteomes and highlighting distinct differences in key metabolic enzyme expression in distinct cell subclusters.
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Affiliation(s)
- Valdemaras Petrosius
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Pedro Aragon-Fernandez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Nil Üresin
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Gergo Kovacs
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Teeradon Phlairaharn
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, 82152, Germany
- MaxPlanck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Benjamin Furtwängler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Jeff Op De Beeck
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, B-9052, Gent, Belgium
| | - Sarah L Skovbakke
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Simon Francis Thomsen
- Department of Dermatology, Bispebjerg Hospital and Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Kedar N Natarajan
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Erwin M Schoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 224 2800 Kgs, Lyngby, Denmark.
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Meah A, Vedarethinam V, Bronstein R, Gujarati N, Jain T, Mallipattu SK, Li Y, Wang J. Single-Cell Spatial MIST for Versatile, Scalable Detection of Protein Markers. BIOSENSORS 2023; 13:852. [PMID: 37754086 PMCID: PMC10526469 DOI: 10.3390/bios13090852] [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: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023]
Abstract
High-multiplex detection of protein biomarkers across tissue regions has been an attractive spatial biology approach due to significant advantages over traditional immunohistochemistry (IHC) methods. Different from most methods, spatial multiplex in situ tagging (MIST) transfers the spatial protein expression information to an ultrahigh-density, large-scale MIST array. This technique has been optimized to reach single-cell resolution by adoption of smaller array units and 30% 8-arm PEG polymer as transfer medium. Tissue cell nuclei stained with lamin B have been clearly visualized on the MIST arrays and are colocalized with detection of nine mouse brain markers. Pseudocells defined at 10 μm in size have been used to fully profile tissue regions including cells and the intercellular space. We showcased the versatility of our technology by successfully detecting 20 marker proteins in kidney samples with the addition of five minutes atop the duration of standard immunohistochemistry protocols. Spatial MIST is amenable to iterative staining and detection on the same tissue samples. When 25 proteins were co-detected on 1 mouse brain section for each round and 5 rounds were executed, an ultrahigh multiplexity of 125 proteins was obtained for each pseudocell. With its unique abilities, this single-cell spatial MIST technology has the potential to become an important method in advanced diagnosis of complex diseases.
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Affiliation(s)
- Arafat Meah
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Vadanasundari Vedarethinam
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Robert Bronstein
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
| | - Nehaben Gujarati
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
| | - Sandeep K. Mallipattu
- Division of Nephrology and Hypertension, Department of Medicine, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
- Renal Section, Northport VA Medical Center, Northport, NY 11768, USA
| | - Yueming Li
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Programs of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065, USA
- Programs of Pharmacology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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40
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Bender KJ, Wang Y, Zhai CY, Saenz Z, Wang A, Neumann EK. Spatial lipidomics of fresh-frozen spines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554488. [PMID: 37662353 PMCID: PMC10473750 DOI: 10.1101/2023.08.23.554488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Technologies assessing the lipidomics, genomics, epigenomics, transcriptomics, and proteomics of tissue samples at single-cell resolution have deepened our understanding of physiology and pathophysiology at an unprecedented level of detail. However, the study of single-cell spatial metabolomics in undecalcified bones faces several significant challenges, such as the fragility of bone which often requires decalcification or fixation leading to the degradation or removal of lipids and other molecules and. As such, we describe a method for performing mass spectrometry imaging on undecalcified spine that is compatible with other spatial omics measurements. In brief, we use fresh-freeze rat spines and a system of carboxyl methylcellulose embedding, cryofilm, and polytetrafluoroethylene rollers to maintain tissue integrity, while avoiding signal loss from variations in laser focus and artifacts from traditional tissue processing. This reveals various tissue types and lipidomic profiles of spinal regions at 10 μm spatial resolutions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We expect this method to be adapted and applied to the analysis of spinal cord, shedding light on the mechanistic aspects of cellular heterogeneity, development, and disease pathogenesis underlying different bone-related conditions and diseases. This study furthers the methodology for high spatial metabolomics of spines, as well as adds to the collective efforts to achieve a holistic understanding of diseases via single-cell spatial multi-omics.
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Affiliation(s)
- Kayle J. Bender
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Yongheng Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, United States
| | - Chuo Ying Zhai
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Zoe Saenz
- Department of Surgery, University of California, Davis, School of Medicine, Sacramento, CA 95817, United States
| | - Aijun Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, United States
- Department of Surgery, University of California, Davis, School of Medicine, Sacramento, CA 95817, United States
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, UC Davis School of Medicine, Sacramento, CA 96817, United States
| | - Elizabeth K. Neumann
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
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41
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Gosline SJC, Veličković M, Pino JC, Day LZ, Attah IK, Swensen AC, Danna V, Posso C, Rodland KD, Chen J, Matthews CE, Campbell-Thompson M, Laskin J, Burnum-Johnson K, Zhu Y, Piehowski PD. Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. Mol Cell Proteomics 2023; 22:100592. [PMID: 37328065 PMCID: PMC10460696 DOI: 10.1016/j.mcpro.2023.100592] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/24/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023] Open
Abstract
The need for a clinically accessible method with the ability to match protein activity within heterogeneous tissues is currently unmet by existing technologies. Our proteomics sample preparation platform, named microPOTS (Microdroplet Processing in One pot for Trace Samples), can be used to measure relative protein abundance in micron-scale samples alongside the spatial location of each measurement, thereby tying biologically interesting proteins and pathways to distinct regions. However, given the smaller pixel/voxel number and amount of tissue measured, standard mass spectrometric analysis pipelines have proven inadequate. Here we describe how existing computational approaches can be adapted to focus on the specific biological questions asked in spatial proteomics experiments. We apply this approach to present an unbiased characterization of the human islet microenvironment comprising the entire complex array of cell types involved while maintaining spatial information and the degree of the islet's sphere of influence. We identify specific functional activity unique to the pancreatic islet cells and demonstrate how far their signature can be detected in the adjacent tissue. Our results show that we can distinguish pancreatic islet cells from the neighboring exocrine tissue environment, recapitulate known biological functions of islet cells, and identify a spatial gradient in the expression of RNA processing proteins within the islet microenvironment.
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Affiliation(s)
- Sara J C Gosline
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | | | - James C Pino
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Le Z Day
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Isaac K Attah
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Adam C Swensen
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Vincent Danna
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Camilo Posso
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Karin D Rodland
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Clayton E Matthews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Ying Zhu
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Paul D Piehowski
- Pacific Northwest National Laboratories, Richland, Washington, USA.
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42
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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43
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Pierobon M, Petricoin EF. Functional proteomic analysis, a missing piece for understanding clonal evolution and cooperation in the tissue microecology. Expert Rev Mol Diagn 2023; 23:1057-1059. [PMID: 37902050 DOI: 10.1080/14737159.2023.2277371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023]
Affiliation(s)
- Mariaelena Pierobon
- School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- School of Systems Biology, Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
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44
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Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler AR, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. CELL REPORTS METHODS 2023; 3:100511. [PMID: 37426761 PMCID: PMC10326451 DOI: 10.1016/j.crmeth.2023.100511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.
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Affiliation(s)
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Zhaoguan Wu
- CHU Sainte Justine Research Center, Montreal, QC, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Department of Chemistry, University of Montreal, Montreal, QC, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Etienne Caron
- CHU Sainte Justine Research Center, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, QC, Canada
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45
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Guo X, Wang X, Tian C, Dai J, Zhao Z, Duan Y. Development of mass spectrometry imaging techniques and its latest applications. Talanta 2023; 264:124721. [PMID: 37271004 DOI: 10.1016/j.talanta.2023.124721] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Mass spectrometry imaging (MSI) is a novel molecular imaging technology that collects molecular information from the surface of samples in situ. The spatial distribution and relative content of various compounds can be visualized simultaneously with high spatial resolution. The prominent advantages of MSI promote the active development of ionization technology and its broader applications in diverse fields. This article first gives a brief introduction to the vital parts of the processes during MSI. On this basis, provides a comprehensive overview of the most relevant MS-based imaging techniques from their mechanisms, pros and cons, and applications. In addition, a critical issue in MSI, matrix effects is also discussed. Then, the representative applications of MSI in biological, forensic, and environmental fields in the past 5 years have been summarized, with a focus on various types of analytes (e.g., proteins, lipids, polymers, etc.) Finally, the challenges and further perspectives of MSI are proposed and concluded.
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Affiliation(s)
- Xing Guo
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China
| | - Xin Wang
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China
| | - Caiyan Tian
- College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Jianxiong Dai
- Aliben Science and Technology Company Limited, Chengdu, 610064, PR China
| | | | - Yixiang Duan
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China; Research Center of Analytical Instrumentation, Sichuan University, Chengdu, 610064, PR China.
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46
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Sharman K, Patterson NH, Weiss A, Neumann EK, Guiberson ER, Ryan DJ, Gutierrez DB, Spraggins JM, Van de Plas R, Skaar EP, Caprioli RM. Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. J Proteome Res 2023; 22:1394-1405. [PMID: 35849531 PMCID: PMC9845430 DOI: 10.1021/acs.jproteome.2c00206] [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: 01/21/2023]
Abstract
Spatially targeted proteomics analyzes the proteome of specific cell types and functional regions within tissue. While spatial context is often essential to understanding biological processes, interpreting sub-region-specific protein profiles can pose a challenge due to the high-dimensional nature of the data. Here, we develop a multivariate approach for rapid exploration of differential protein profiles acquired from distinct tissue regions and apply it to analyze a published spatially targeted proteomics data set collected from Staphylococcus aureus-infected murine kidney, 4 and 10 days postinfection. The data analysis process rapidly filters high-dimensional proteomic data to reveal relevant differentiating species among hundreds to thousands of measured molecules. We employ principal component analysis (PCA) for dimensionality reduction of protein profiles measured by microliquid extraction surface analysis mass spectrometry. Subsequently, k-means clustering of the PCA-processed data groups samples by chemical similarity. Cluster center interpretation revealed a subset of proteins that differentiate between spatial regions of infection over two time points. These proteins appear involved in tricarboxylic acid metabolomic pathways, calcium-dependent processes, and cytoskeletal organization. Gene ontology analysis further uncovered relationships to tissue damage/repair and calcium-related defense mechanisms. Applying our analysis in infectious disease highlighted differential proteomic changes across abscess regions over time, reflecting the dynamic nature of host-pathogen interactions.
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Affiliation(s)
- Kavya Sharman
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Program in Chemical & Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andy Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
| | - Elizabeth K Neumann
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Emma R Guiberson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Daniel J Ryan
- Pfizer Inc., Chesterfield, Missouri 63017, United States
| | - Danielle B Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Raf Van de Plas
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Delft Center for Systems and Control, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232, United States
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47
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Ye W, Wang Y, Cao T, Meng H, Wang C, Hu B, Gao Z, Wang C. Respiration-Responsive Colorful Room-Temperature Phosphorescent Materials and Assembly-Induced Phosphorescence Enhancement Strategies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207403. [PMID: 36775952 DOI: 10.1002/smll.202207403] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/30/2022] [Indexed: 05/04/2023]
Abstract
It is still very challenging to obtain colorful and long-afterglow room-temperature phosphorescent (RTP) materials from pure organic polymers. Herein, it is found that chitosan (CS), a natural polymer, not only has its own RTP, but also reacts with different phosphorescent molecules to obtain a multicolor, long-afterglow RTP material. CS can emit RTP with a lifetime of 48 ms. In addition, CS is rich in amino groups, and grafting different phosphorescent molecules onto CS by an amidation reaction can modulate it to emit different colors of phosphorescence and obtain a series of colorful CS derivatives. The obtained polymer films also have ultra-long RTP due to the good film-forming ability. In addition, one of the CS derivatives selected with α-cyclodextrin is used to construct RTP materials with lifetimes of up to seconds. The host-guest interactions are used to suppress nonradiative relaxation and build crystalline domains, thus synergistically enhancing the RTP. Interestingly, the RTP properties of the CS derivative films are extremely sensitive to water and heat stimuli, because water broke the hydrogen bonds between adjacent CS molecules and thus altered the rigid environment in the material. Finally, they can be used as a stimuli-responsive ink and for monitoring environmental humidity.
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Affiliation(s)
- Wenyan Ye
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yandong Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tengyang Cao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Meng
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunlei Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingxuan Hu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zeyu Gao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caiqi Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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48
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Geier B, Gil-Mansilla E, Liutkevičiūtė Z, Hellinger R, Vanden Broeck J, Oetjen J, Liebeke M, Gruber CW. Multiplexed neuropeptide mapping in ant brains integrating microtomography and three-dimensional mass spectrometry imaging. PNAS NEXUS 2023; 2:pgad144. [PMID: 37215633 PMCID: PMC10194420 DOI: 10.1093/pnasnexus/pgad144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
Neuropeptides are important regulators of animal physiology and behavior. Hitherto the gold standard for the localization of neuropeptides have been immunohistochemical methods that require the synthesis of antibody panels, while another limiting factor has been the brain's opacity for subsequent in situ light or fluorescence microscopy. To address these limitations, we explored the integration of high-resolution mass spectrometry imaging (MSI) with microtomography for a multiplexed mapping of neuropeptides in two evolutionary distant ant species, Atta sexdens and Lasius niger. For analyzing the spatial distribution of chemically diverse peptide molecules across the brain in each species, the acquisition of serial mass spectrometry images was essential. As a result, we have comparatively mapped the three-dimensional (3D) distributions of eight conserved neuropeptides throughout the brain microanatomy. We demonstrate that integrating the 3D MSI data into high-resolution anatomy models can be critical for studying organs with high plasticity such as brains of social insects. Several peptides, like the tachykinin-related peptides (TK) 1 and 4, were widely distributed in many brain areas of both ant species, whereas others, for instance myosuppressin, were restricted to specific regions only. Also, we detected differences at the species level; many peptides were identified in the optic lobe of L. niger, but only one peptide (ITG-like) was found in this region in A. sexdens. Building upon MS imaging studies on neuropeptides in invertebrate model systems, our approach leverages correlative MSI and computed microtomography for investigating fundamental neurobiological processes by visualizing the unbiased 3D neurochemistry in its complex anatomic environment.
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Affiliation(s)
| | | | - Zita Liutkevičiūtė
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna 1090, Austria
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction Group, Zoological Institute, KU Leuven, Leuven 3000, Belgium
| | - Janina Oetjen
- To whom correspondence should be addressed: (J.O.); (M.L.); (C.W.G.)
| | - Manuel Liebeke
- To whom correspondence should be addressed: (J.O.); (M.L.); (C.W.G.)
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49
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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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50
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Yang M, Unsihuay D, Hu H, Nguele Meke F, Qu Z, Zhang ZY, Laskin J. Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. Anal Chem 2023; 95:5214-5222. [PMID: 36917636 DOI: 10.1021/acs.analchem.2c04795] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful tool for label-free mapping of the spatial distribution of proteins in biological tissues. We have previously demonstrated imaging of individual proteoforms in biological tissues using nanospray desorption electrospray ionization (nano-DESI), an ambient liquid extraction-based MSI technique. Nano-DESI MSI generates multiply charged protein ions, which is advantageous for their identification using top-down proteomics analysis. In this study, we demonstrate proteoform mapping in biological tissues with a spatial resolution down to 7 μm using nano-DESI MSI. A substantial decrease in protein signals observed in high-spatial-resolution MSI makes these experiments challenging. We have enhanced the sensitivity of nano-DESI MSI experiments by optimizing the design of the capillary-based probe and the thickness of the tissue section. In addition, we demonstrate that oversampling may be used to further improve spatial resolution at little or no expense to sensitivity. These developments represent a new step in MSI-based spatial proteomics, which complements targeted imaging modalities widely used for studying biological systems.
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Affiliation(s)
- Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Daisy Unsihuay
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hang Hu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Frederick Nguele Meke
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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