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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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Bemis KA, Föll MC, Guo D, Lakkimsetty SS, Vitek O. Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis. Nat Methods 2023; 20:1883-1886. [PMID: 37996752 DOI: 10.1038/s41592-023-02070-z] [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: 03/06/2023] [Accepted: 10/06/2023] [Indexed: 11/25/2023]
Abstract
Cardinal v.3 is an open-source software for reproducible analysis of mass spectrometry imaging experiments. A major update from its previous versions, Cardinal v.3 supports most mass spectrometry imaging workflows. Its analytical capabilities include advanced data processing such as mass recalibration, advanced statistical analyses such as single-ion segmentation and rough annotation-based classification, and memory-efficient analyses of large-scale multitissue experiments.
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Affiliation(s)
- Kylie Ariel Bemis
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Melanie Christine Föll
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
- Institute of Surgical Pathology, Medical Center, University of Freiburg, Faculty of Medicine, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dan Guo
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | | | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
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徐 晨, 王 寅, 魏 东, 李 文, 钱 晔, 潘 新, 雷 大. [Advances of spatial omics in the individualized diagnosis and treatment of head and neck cancer]. LIN CHUANG ER BI YAN HOU TOU JING WAI KE ZA ZHI = JOURNAL OF CLINICAL OTORHINOLARYNGOLOGY, HEAD, AND NECK SURGERY 2023; 37:729-733;739. [PMID: 37830120 PMCID: PMC10722126 DOI: 10.13201/j.issn.2096-7993.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 10/14/2023]
Abstract
Spatialomics is another research hotspot of biotechnology after single-cell sequencing technology, which can make up for the defect that single-cell sequencing technology can not obtain cell spatial distribution information. Spatialomics mainly studies the relative position of cells in tissue samples to reveal the effect of cell spatial distribution on diseases. In recent years, spatialomics has made new progress in the pathogenesis, target exploration, drug development and many other aspects of head and neck tumors. This paper summarizes the latest progress of spatialomics in the diagnosis and treatment of head and neck cancer.
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Affiliation(s)
- 晨阳 徐
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 寅 王
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 东敏 魏
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 文明 李
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 晔 钱
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 新良 潘
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
| | - 大鹏 雷
- 山东大学齐鲁医院耳鼻咽喉科,国家卫生健康委员会耳鼻喉科学重点实验室(山东大学)(济南,250012)Department of Otorhinolaryngology, Qilu Hospital of Shandong University, National Health Commission Key Laboratory of Otorhinolaryngology[Shandong University], Jinan, 250012, China
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Šebela M. The use of matrix-assisted laser desorption/ionization mass spectrometry in enzyme activity assays and its position in the context of other available methods. MASS SPECTROMETRY REVIEWS 2023; 42:1008-1031. [PMID: 34549449 DOI: 10.1002/mas.21733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Activity assays are indispensable for studying biochemical properties of enzymes. The purposes of measuring activity are wide ranging from a simple detection of the presence of an enzyme to kinetic experiments evaluating the substrate specificity, reaction mechanisms, and susceptibility to inhibitors. Common activity assay methods include spectroscopy, electrochemical sensors, or liquid chromatography coupled with various detection techniques. This review focuses on the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a growing and modern alternative, which offers high speed of analysis, sensitivity, versatility, possibility of automation, and cost-effectiveness. It may reveal reaction intermediates, side products or measure more enzymes at once. The addition of an internal standard or calculating the ratios of the substrate and product peak intensities and areas overcome the inherent inhomogeneous distribution of analyte and matrix in the sample spot, which otherwise results in a poor reproducibility. Examples of the application of MALDI-TOF MS for assaying hydrolases (including peptidases and β-lactamases for antibiotic resistance tests) and other enzymes are provided. Concluding remarks summarize advantages and challenges coming from the present experience, and draw future perspectives such as a screening of large libraries of chemical compounds for their substrate or inhibitory properties towards enzymes.
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Affiliation(s)
- Marek Šebela
- Department of Biochemistry, Faculty of Science, and CATRIN, Palacký University, Olomouc, Czech Republic
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Hu H, Laskin J. Emerging Computational Methods in Mass Spectrometry Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203339. [PMID: 36253139 PMCID: PMC9731724 DOI: 10.1002/advs.202203339] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/17/2022] [Indexed: 05/10/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high-spatial resolution and high-throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation-driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods.
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Affiliation(s)
- Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
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Device-Controlled Microcondensation for Spatially Confined On-Tissue Digests in MALDI Imaging of N-Glycans. Pharmaceuticals (Basel) 2022; 15:ph15111356. [PMID: 36355528 PMCID: PMC9698097 DOI: 10.3390/ph15111356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
On-tissue enzymatic digestion is a prerequisite for MALDI mass spectrometry imaging (MSI) and spatialomic analysis of tissue proteins and their N-glycan conjugates. Despite the more widely accepted importance of N-glycans as diagnostic and prognostic biomarkers of many diseases and their potential as pharmacodynamic markers, the crucial sample preparation step, namely on-tissue digestion with enzymes like PNGaseF, is currently mainly carried out by specialized laboratories using home-built incubation arrangements, e.g., petri dishes placed in an incubator. Standardized spatially confined enzyme digests, however, require precise control and possible regulation of humidity and temperature, as high humidity increases the risk of analyte dislocation and low humidity compromises enzyme function. Here, a digestion device that controls humidity by cyclic ventilation and heating of the slide holder and the chamber lid was designed to enable controlled micro-condensation on the slide and to stabilize and monitor the digestion process. The device presented here may help with standardization in MSI. Using sagittal mouse brain sections and xenografted human U87 glioblastoma cells in CD1 nu/nu mouse brain, a device-controlled workflow for MALDI MSI of N-glycans was developed.
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Ikuta S, Shinohara N, Fukusaki E, Shimma S. Mass spectrometry imaging enables visualization of the localization of glutamate decarboxylase activity in germinating legume seeds. J Biosci Bioeng 2022; 134:356-361. [PMID: 36008275 DOI: 10.1016/j.jbiosc.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022]
Abstract
Visualizing the distribution of enzymes is vital for understanding physiological phenomena. Enzyme histochemistry is a technique used to investigate the localization of enzyme activity. However, the target is restricted to enzymes with easy-to-design artificial substrates that can develop color through reactions. Mass spectrometry imaging (MSI)-based enzyme histochemistry has been developed as a novel method to visualize enzyme localization. It can be applied to enzyme histochemistry as it detects products from the supplied substrate using enzymes present on the tissue sections. However, enzyme histochemistry using MSI has not been applied to plant tissue samples yet. Glutamate decarboxylase (GAD, EC: 4.1.1.15) is an enzyme that catalyzes the decarboxylation reaction of l-glutamic acid to produce γ-aminobutyric acid (GABA). GABA biosynthesis is important both in the field of food chemistry and plant physiology. This study focused on GAD during the legume germination process and successfully visualized GAD activity in legume seeds using MSI for the first time. Furthermore, the localization of GAD activity in the embryonic axis of germinated soybean seeds and alfalfa seeds could be visualized.
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Affiliation(s)
- Soichiro Ikuta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Naho Shinohara
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Urbiola-Salvador V, Miroszewska D, Jabłońska A, Qureshi T, Chen Z. Proteomics approaches to characterize the immune responses in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119266. [PMID: 35390423 DOI: 10.1016/j.bbamcr.2022.119266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/01/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Despite the dynamic development of cancer research, annually millions of people die of cancer. The human immune system is the major 'guard' against tumor development. Unfortunately, cancer cells have the ability to evade the immune system and continue to grow. The proper understanding of the intricate immune response in tumorigenesis remains the holy grail of cancer immunology and designing effective immunotherapy. To decode the immune responses in cancer, in recent years, proteomics studies have received considerable attention. Proteomics studies focus on the detection and quantification of proteins, which are the effectors of biological functions, and as such, are proven to reflect the cell state more accurately, in comparison to genomic or transcriptomic studies. In this review, we discuss the proteomics studies applied to characterize the immune responses in cancer and tumor immune microenvironment heterogeneity. Further, we describe emerging single-cell proteomics approaches that have the potential to be applied in cancer immunity studies.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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Dong Y, Aharoni A. Image to insight: exploring natural products through mass spectrometry imaging. Nat Prod Rep 2022; 39:1510-1530. [PMID: 35735199 DOI: 10.1039/d2np00011c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: 2017 to 2022Mass spectrometry imaging (MSI) has become a mature molecular imaging technique that is well-matched for natural product (NP) discovery. Here we present a brief overview of MSI, followed by a thorough discussion of different MSI applications in NP research. This review will mainly focus on the recent progress of MSI in plants and microorganisms as they are the main producers of NPs. Specifically, the opportunity and potential of combining MSI with other imaging modalities and stable isotope labeling are discussed. Throughout, we focus on both the strengths and weaknesses of MSI, with an eye on future improvements that are necessary for the progression of MSI toward routine NP studies. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
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Affiliation(s)
- Yonghui Dong
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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Wisman AP, Minami M, Tamada Y, Hirohata S, Gomi K, Fukusaki E, Shimma S. Visualization of dipeptidyl peptidase B enzymatic reaction in rice koji using mass spectrometry imaging. J Biosci Bioeng 2022; 134:133-137. [PMID: 35643851 DOI: 10.1016/j.jbiosc.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 10/18/2022]
Abstract
Enzyme histochemistry via mass spectrometry imaging (MSI) has garnered attention as a straightforward approach for visualizing enzymatic reactions. While several studies in the medical and physiological fields have shown its promising application potential, its applicability to agricultural or food studies has not yet been demonstrated. Rice koji, known as an enzyme source for various fermented products, is a suitable model for demonstrating the applicability of this method to food-related materials. In this study, the enzymatic reaction of dipeptidyl peptidase B (DppB) in rice koji was visualized using MSI for the first time. The method was optimized and applied to investigate the effects of rice variety, polishing ratio, and cultivation time on the location of the DppB reaction. The DppB enzymatic reaction was found to occur in different locations in each of the two rice varieties, Yamadanishiki and Hakutsurunishiki. The polishing ratio also affected the distribution of the DppB enzymatic reactions. Furthermore, a time-course investigation of rice koji cultivation revealed that while the location of the reaction was largely associated with mycelial penetration, the structure and features of the rice grain may also affect the location of the enzymatic reaction. In summary, these results demonstrate the applicability of enzyme histochemistry by MSI to food-related materials.
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Affiliation(s)
- Adinda Putri Wisman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan
| | - Makiho Minami
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan
| | - Yoshihiro Tamada
- Hakutsuru Sake Brewing Co., Ltd., 4-5-5 Sumiyoshi Minamimachi, Higashinada-ku, Kobe, Hyogo 6580041, Japan
| | - Shuji Hirohata
- Hakutsuru Sake Brewing Co., Ltd., 4-5-5 Sumiyoshi Minamimachi, Higashinada-ku, Kobe, Hyogo 6580041, Japan
| | - Katsuya Gomi
- Department of Bioindustrial Informatics and Genomics, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 9808572, Japan; Laboratory of Fermentation Microbiology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 9808572, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Osaka University Shimadzu Omics Innovation Research Laboratory, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 5650871, Japan.
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DeLaney K, Phetsanthad A, Li L. ADVANCES IN HIGH-RESOLUTION MALDI MASS SPECTROMETRY FOR NEUROBIOLOGY. MASS SPECTROMETRY REVIEWS 2022; 41:194-214. [PMID: 33165982 PMCID: PMC8106695 DOI: 10.1002/mas.21661] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 09/13/2020] [Indexed: 05/08/2023]
Abstract
Research in the field of neurobiology and neurochemistry has seen a rapid expansion in the last several years due to advances in technologies and instrumentation, facilitating the detection of biomolecules critical to the complex signaling of neurons. Part of this growth has been due to the development and implementation of high-resolution Fourier transform (FT) mass spectrometry (MS), as is offered by FT ion cyclotron resonance (FTICR) and Orbitrap mass analyzers, which improves the accuracy of measurements and helps resolve the complex biological mixtures often analyzed in the nervous system. The coupling of matrix-assisted laser desorption/ionization (MALDI) with high-resolution MS has drastically expanded the information that can be obtained with these complex samples. This review discusses notable technical developments in MALDI-FTICR and MALDI-Orbitrap platforms and their applications toward molecules in the nervous system, including sequence elucidation and profiling with de novo sequencing, analysis of post-translational modifications, in situ analysis, key advances in sample preparation and handling, quantitation, and imaging. Notable novel applications are also discussed to highlight key developments critical to advancing our understanding of neurobiology and providing insight into the exciting future of this field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
- To whom correspondence should be addressed. , Phone: (608) 265-8491, Fax: (608) 262-5345., Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53706
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Li H, Wu R, Hu Q, Chen X, Dominic Chan TW. A Matrix Sublimation Device with an Integrated Solvent Nebulizer for MALDI-MSI. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:11-16. [PMID: 34939792 DOI: 10.1021/jasms.1c00335] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The current matrix deposition methods in MALDI-mass spectrometry imaging (MALDI-MSI) face technical problems related to the inhomogeneous distribution of crystals and the low analyte extraction and cocrystallization efficiency. In this work, an integrated matrix sublimation device with synchronous solvent nebulization was developed for MALDI-MSI. Droplets of solvents were directly introduced into the chamber of the sublimator by using a miniaturized ultrasonic nebulizer unit. The synchronous and asynchronous working modes of solvent nebulization and matrix sublimation were systematically investigated. Imaging of both protein and small metabolite distributions in mouse brain tissue sections was successfully performed using the developed matrix deposition device. The sensitivity and quality of the images were clearly improved in synchronous mode compared with those of the conventional spray and sublimation methods. These results demonstrate that the integrated device with both solvent nebulization and matrix sublimation is a useful tool in MALDI-MSI applications.
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Affiliation(s)
- Huizhi Li
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Sciences), 19th Keyuan Road, Jinan, Shandong 250014, P.R. China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
| | - Qiongzheng Hu
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Sciences), 19th Keyuan Road, Jinan, Shandong 250014, P.R. China
| | - Xiangfeng Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Centre, Qilu University of Technology (Shandong Academy of Sciences), 19th Keyuan Road, Jinan, Shandong 250014, P.R. China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, P.R. China
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13
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Abe C, Zhang Y, Takao K, Sasaki K, Ochiai K, Matsui T. Visualization Analysis of Glyceollin Production in Germinating Soybeans by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Imaging Technique. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7057-7063. [PMID: 34152141 DOI: 10.1021/acs.jafc.1c02261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Apart from the physiological functions of soybean phytoalexins, the production sites in soybeans remain unknown. In this study, the dynamic production of phytoalexins, glyceollins, in germinating soybeans inoculated with Aspergillus oryzae was visually investigated using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging. During a 3-day sensitization using a fungus, glyceollins I-III were produced in germinating soybeans (from 0.03 mg/g for glyceollin III to 0.96 mg/g for glyceollin I). Imaging analysis provided visual evidence that glyceollins were produced only in the regions of seed coat and germinated root of the soybeans, while no production was observed in other regions, including the cotyledons. In contrast, their precursor, isoflavone, was distributed throughout the soybean. The evidence that the inoculation of the inactivated fungi also caused glyceollin production at the seed coat led us to speculate that glyceollins could be produced in the region of soybean attached to the fungus body.
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Affiliation(s)
- Chizumi Abe
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Ye Zhang
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazuhiro Takao
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kuni Sasaki
- DAIZ Inc., 3-14-3 Minami-kumamoto, Chuo-ku, Kumamoto 860-0812, Japan
| | - Koji Ochiai
- DAIZ Inc., 3-14-3 Minami-kumamoto, Chuo-ku, Kumamoto 860-0812, Japan
| | - Toshiro Matsui
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School of Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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14
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Takeo E, Sugiura Y, Ohnishi Y, Kishima H, Fukusaki E, Shimma S. Mass Spectrometric Enzyme Histochemistry for Choline Acetyltransferase Reveals De Novo Acetylcholine Synthesis in Rodent Brain and Spinal Cord. ACS Chem Neurosci 2021; 12:2079-2087. [PMID: 34078081 DOI: 10.1021/acschemneuro.0c00720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Choline acetyltransferase (ChAT), responsible for the synthesis of acetylcholine, plays an important role in neurotransmission. However, no method to visualize the ChAT activity in tissues has been reported to date. In this study, mass spectrometry imaging (MSI) was used to visualize ChAT activity in situ, which is difficult with conventional enzyme histochemistry. By using choline chloride-trimethyl-d9 (choline-d9) as a substrate and simultaneously supplying an inhibitor of cholinesterase to tissues, we succeeded in directly visualizing the ChAT activity in the rodent brain and spinal cord. The findings revealed heterogeneous ChAT activity in the striatum of the mouse brain and in the spinal lower motor neurons that connect the anterior horn to the ventral root. Furthermore, extending the developed method to spinal cord injury (SCI) model mice revealed the site-specific effect of primary and secondary injury on ChAT activity. This study shows that the MSI-based enzyme histochemistry of ChAT could be a useful tool for studying cholinergic neurons.
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Affiliation(s)
- Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yuichiro Ohnishi
- Department of Neurosurgery, Graduate school of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate school of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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15
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Wang N, Li X, Wang R, Ding Z. Spatial transcriptomics and proteomics technologies for deconvoluting the tumor microenvironment. Biotechnol J 2021; 16:e2100041. [PMID: 34125481 DOI: 10.1002/biot.202100041] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022]
Abstract
The tumor microenvironment (TME) harbors heterogeneous contents and plays critical roles in tumorigenesis, metastasis, and drug resistance. Therefore, the deconvolution of the TME becomes increasingly essential to every aspect of cancer research and treatment. Novel spatially-resolved high-plex molecular profiling technologies have been emerging rapidly as powerful tools to obtain in-depth understanding from TME perspectives due to their capacity to allow high-plex protein and RNA profiling while keeping valuable spatial information. Based on our practical experience, we review a variety of available spatial proteogenomic technologies, including 10X Visium, GeoMx Digital Spatial Profiler (DSP), cyclic immunofluorescence-based CODEX and Multi-Omyx, mass spectrometry (MS)-based imaging mass spectrometry (IMS) and multiplex ion-beam imaging (MIBI). We also discuss FISSEQ, MERFISH, Slide-seq, and HDST, some of which may become commercially available in the near future. In particular, with our experience, we elaborate on DSP for spatial proteogenomic profiling and discuss its unique features designed for immuno-oncology and propose anticipation towards its future direction. The emerging spatially technologies are rapidly reshaping the magnitude of our understanding of the TME.
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Affiliation(s)
- Nan Wang
- Fynn Biotechnologies Ltd., Mills Institute for Personalized Cancer Care, Jinan City, Shandong Province, P. R. China
| | - Xia Li
- Fynn Biotechnologies Ltd., Mills Institute for Personalized Cancer Care, Jinan City, Shandong Province, P. R. China
| | - Rongshui Wang
- Fynn Biotechnologies Ltd., Mills Institute for Personalized Cancer Care, Jinan City, Shandong Province, P. R. China
| | - Zhiyong Ding
- Fynn Biotechnologies Ltd., Mills Institute for Personalized Cancer Care, Jinan City, Shandong Province, P. R. China
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16
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Xie H, Wu R, Hung YLW, Chen X, Chan TWD. Development of a Matrix Sublimation Device with Controllable Crystallization Temperature for MALDI Mass Spectrometry Imaging. Anal Chem 2021; 93:6342-6347. [PMID: 33852267 DOI: 10.1021/acs.analchem.1c00260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The size and distribution of matrix crystals deposited on the surface of a tissue section play a key role in the performance of MALDI mass spectrometry imaging (MALDI-MSI). In this study, uniform distribution and a restricted size of matrix crystals were achieved via a homemade matrix sublimation device with controllable crystallization temperature. The crystallization temperature was stably controlled at a subzero temperature, and homogeneous matrix crystals with diameters <0.2 μm were generated on the sample surface. Typical MALDI-MSI experiments of endogenous and exogenous components in the tissues of strawberries, kidneys, and mussels were conducted to examine the performance of the sublimator. Good reproducibility of MALDI-MSI was achieved, and the quality of ion images was significantly improved. These results demonstrate that the developed sublimator should have potential in matrix deposition for further high resolution MALDI-MSI application.
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Affiliation(s)
- Hanyi Xie
- School of Pharmaceutical sciences, Qilu University of Technology (Shandong Academy of Sciences), 19th Keyuan Road, Jinan, Shandong 250014, People's Republic of China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, People's Republic of China
| | - Y L Winnie Hung
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, People's Republic of China
| | - Xiangfeng Chen
- School of Pharmaceutical sciences, Qilu University of Technology (Shandong Academy of Sciences), 19th Keyuan Road, Jinan, Shandong 250014, People's Republic of China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, People's Republic of China
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17
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Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13051097. [PMID: 33806447 PMCID: PMC7961698 DOI: 10.3390/cancers13051097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/28/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Different types of cells with tumor-initiating cell (TIC) activity contribute to colorectal cancer (CRC) progression and resistance to anti-cancer treatment. In this study, we aimed to understand whether different cell types exist within a patient-derived tumor culture, distinguishable by different patterns of their gene expression. By mRNA sequencing of patient-derived CRC cultures at the single-cell level, we defined expression programs that closely resemble differentiated cell populations of the normal intestine. Here, cell type-associated subpopulations showed differences in functional properties such as cell growth and energy metabolism. Subsequent functional analyses in vitro and in vivo demonstrated that metabolic states are linked to TIC activity in primary CRC cultures. We also show that TIC activity is dependent on oxidative phosphorylation, which may therefore represent a target for novel therapies. Abstract Intra-tumor heterogeneity of tumor-initiating cell (TIC) activity drives colorectal cancer (CRC) progression and therapy resistance. Here, we used single-cell RNA-sequencing of patient-derived CRC models to decipher distinct cell subpopulations based on their transcriptional profiles. Cell type-specific expression modules of stem-like, transit amplifying-like, and differentiated CRC cells resemble differentiation states of normal intestinal epithelial cells. Strikingly, identified subpopulations differ in proliferative activity and metabolic state. In summary, we here show at single-cell resolution that transcriptional heterogeneity identifies functional states during TIC differentiation. Furthermore, identified expression signatures are linked to patient prognosis. Targeting transcriptional states associated to cancer cell differentiation might unravel novel vulnerabilities in human CRC.
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Klein O, Haeckel A, Reimer U, Nebrich G, Schellenberger E. Multiplex enzyme activity imaging by MALDI-IMS of substrate library conversions. Sci Rep 2020; 10:15522. [PMID: 32968143 PMCID: PMC7511933 DOI: 10.1038/s41598-020-72436-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Enzymes are fundamental to biological processes and involved in most pathologies. Here we demonstrate the concept of simultaneously mapping multiple enzyme activities (EA) by applying enzyme substrate libraries to tissue sections and analyzing their conversion by matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS). To that end, we spray-applied a solution of 20 naturally derived peptides that are known substrates for proteases, kinases, and phosphatases to zinc-fixed paraffin tissue sections of mouse kidneys. After enzyme conversion for 5 to 120 min at 37 °C and matrix application, the tissue sections were imaged by MALDI-IMS. We could image incubation time-dependently 16 of the applied substrates with differing signal intensities and 12 masses of expected products. Utilizing inherent enzyme amplification, EA-IMS can become a powerful tool to locally study multiple, potentially even lowly expressed, enzyme activities, networks, and their pharmaceutical modulation. Differences in the substrate detectability highlight the need for future optimizations.
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Affiliation(s)
- Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Akvile Haeckel
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstraße 5, 12489, Berlin, Germany
| | - Grit Nebrich
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Eyk Schellenberger
- Department of Radiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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19
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Takeo E, Fukusaki E, Shimma S. Mass Spectrometric Enzyme Histochemistry Method Developed for Visualizing In Situ Cholinesterase Activity in Mus musculus and Drosophila melanogaster. Anal Chem 2020; 92:12379-12386. [DOI: 10.1021/acs.analchem.0c02106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emi Takeo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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20
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Burian A, Lujber L, Gerlinger I, Jarai T, Orosz E, Turiak L, Acs A, Hegedus Z, Peter AK, Tornoczki T, Gombos K, Mark L. Label-Free Semiquantitative Liquid Chromatography-Tandem Mass Spectrometry Proteomics Analysis of Laryngeal/Hypopharyngeal Squamous Cell Carcinoma on Formalin-Fixed, Paraffin-Embedded Tissue Samples - a Pilot Study. Pathol Oncol Res 2020; 26:2801-2807. [PMID: 32564264 PMCID: PMC7471140 DOI: 10.1007/s12253-020-00849-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 06/11/2020] [Indexed: 11/30/2022]
Abstract
Squamous cell carcinoma (SCC) of the head and neck region is the sixth most frequent malignancy with high mortality rate. Due to its poor prognosis it is considered a growing public health problem worldwide inspite of existing treatment modalities. Thus, early diagnosis of new diseases and recurrences is emerging on one hand, but on the other hand troublesome in the lack of reliable tumor markers in this field. The rapid development of proteomics has opened new perspectives in tumor marker discovery. Liquid chromatography/mass spectrometry (LC/MS) as the gold standard in proteomics enables the semi-quantitative analysis of proteins within various tissues. Abundance differences between tumor and normal tissue also can be interpreted as tumor specific changes. The aim of this study was to identify potential tumor markers of laryngeal/hypopharyngeal SCC by revealing abundance changes between cancerous and the surrounding phenotypically healthy tissue. After separating the phenotypically cancerous and healthy parts of formalin-fixed paraffin-embedded tissues, each sample underwent protein recovery process and tryptic digestion for label-free semi-quantitative LC/MS analysis. Eight proteins showed significantly higher abundance in tumor including tenascin, transmembrane emp24 domain-containing protein 2, cytoplasmic dynein light chain 1, coactosin-like protein, small proline-rich protein 2D, nucleolin, U5 small nuclear RNP 200-kDa helicase and fatty aldehyde dehydrogenase. Desmoglein-1 and keratin type I cytoskeletal 9 were down-regulated in tumor. Using Ingenuity Pathway Analysis we mapped the signaling pathways these proteins play role in regarding other tumors. Based on these findings these proteins may serve as promising biomarkers in the fight against laryngeal/hypopharyngeal SCCs.
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Affiliation(s)
- Andras Burian
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Laszlo Lujber
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Imre Gerlinger
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Tamas Jarai
- Tolna County Balassa Janos Hospital, Beri Balogh Adam Str 5-7, Szekszard, H-7100, Hungary
| | - Eva Orosz
- Clinical Centre, Department of Otorhinolaryngology and Head and Neck Surgery, University of Pecs, Munkacsy M Str 2, Pecs, H-7621, Hungary
| | - Lilla Turiak
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok Blvd 2, Budapest, H-1117, Hungary
| | - Andras Acs
- MS Proteomics Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudosok Blvd 2, Budapest, H-1117, Hungary.,Ph.D. School of Pharmaceutical Sciences, Semmelweis University, Ulloi Str 26, Budapest, H-1085, Hungary
| | - Zoltan Hegedus
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Temesvari Blvd 62, Szeged, H-6726, Hungary.,Medical School, Institute of Biochemistry and Medical Chemistry, University of Pecs, Szigeti Str 12, Pecs, H-7624, Hungary
| | - Aniko Konigne Peter
- Medical School, Institute of Bioanalysis, University of Pecs, Honved Str 1, Pecs, H-7624, Hungary
| | - Tamas Tornoczki
- Medical School, Institute of Pathology, University of Pecs, Szigeti Str 12, Pecs, H-7624, Hungary
| | - Katalin Gombos
- Clinical Centre, Department of Laboratory Medicine, University of Pecs, Ifjusag Str 13, Pecs, H-7624, Hungary
| | - Laszlo Mark
- Medical School, Institute of Biochemistry and Medical Chemistry, University of Pecs, Szigeti Str 12, Pecs, H-7624, Hungary. .,MTA-PTE Human Reproduction Research Group, Edesanyak str. 1, Pecs, H-7624, Hungary.
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21
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Müller T, Kalxdorf M, Longuespée R, Kazdal DN, Stenzinger A, Krijgsveld J. Automated sample preparation with SP3 for low-input clinical proteomics. Mol Syst Biol 2020; 16:e9111. [PMID: 32129943 PMCID: PMC6966100 DOI: 10.15252/msb.20199111] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh-frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directly analyzed by LCMS, thereby significantly reducing hands-on time, reducing variability in protein quantification, and improving longitudinal reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1,000 proteins from 100 to 1,000 cells. Furthermore, we applied this approach to a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples and recapitulated their separation into known histological growth patterns. Finally, we integrated autoSP3 with AFA ultrasonication for the automated end-to-end sample preparation and LCMS analysis of 96 intact tissue samples. Collectively, this constitutes a generic, scalable, and cost-effective workflow with minimal manual intervention, enabling reproducible tissue proteomics in a broad range of clinical and non-clinical applications.
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Affiliation(s)
- Torsten Müller
- German Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
| | - Mathias Kalxdorf
- German Cancer Research Center (DKFZ)HeidelbergGermany
- EMBLHeidelbergGermany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and PharmacoepidemiologyHeidelberg UniversityHeidelbergGermany
| | - Daniel N Kazdal
- Institute of PathologyHeidelberg UniversityHeidelbergGermany
| | | | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
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22
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Ahmed M, Broeckx G, Baggerman G, Schildermans K, Pauwels P, Van Craenenbroeck AH, Dendooven A. Next-generation protein analysis in the pathology department. J Clin Pathol 2019; 73:1-6. [DOI: 10.1136/jclinpath-2019-205864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/12/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
Abstract
Traditionally, immunohistochemistry (IHC) is used by pathologists to localise specific proteins or peptides in tissue slides. In the era of personalised medicine, however, molecular tissue analysis becomes indispensable for correct diagnosis, prognosis and therapeutic decision, not only on the DNA or mRNA level but also on the protein level. Combining molecular information with imaging presents many advantages. Therefore, matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) is a promising technique to be added to the armamentarium of the pathologist. Here, we focus on the workflow, advantages and drawbacks of both MALDI IMS and IHC. We also briefly discuss a few other protein imaging modalities and give examples of applications.
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