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Stillger MN, Li MJ, Hönscheid P, von Neubeck C, Föll MC. Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma. Proteomics 2024; 24:e2300001. [PMID: 38402423 DOI: 10.1002/pmic.202300001] [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: 06/08/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
MALDI mass spectrometry imaging (MALDI imaging) uniquely advances cancer research, by measuring spatial distribution of endogenous and exogenous molecules directly from tissue sections. These molecular maps provide valuable insights into basic and translational cancer research, including tumor biology, tumor microenvironment, biomarker identification, drug treatment, and patient stratification. Despite its advantages, MALDI imaging is underutilized in studying rare cancers. Sarcomas, a group of malignant mesenchymal tumors, pose unique challenges in medical research due to their complex heterogeneity and low incidence, resulting in understudied subtypes with suboptimal management and outcomes. In this review, we explore the applicability of MALDI imaging in sarcoma research, showcasing its value in understanding this highly heterogeneous and challenging rare cancer. We summarize all MALDI imaging studies in sarcoma to date, highlight their impact on key research fields, including molecular signatures, cancer heterogeneity, and drug studies. We address specific challenges encountered when employing MALDI imaging for sarcomas, and propose solutions, such as using formalin-fixed paraffin-embedded tissues, and multiplexed experiments, and considerations for multi-site studies and digital data sharing practices. Through this review, we aim to spark collaboration between MALDI imaging researchers and clinical colleagues, to deploy the unique capabilities of MALDI imaging in the context of sarcoma.
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Affiliation(s)
- Maren Nicole Stillger
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center, Freiburg, Germany
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Mujia Jenny Li
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center, Freiburg, Germany
- Institute for Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Pia Hönscheid
- Institute of Pathology, Faculty of Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- National Center for Tumor Diseases, Partner Site Dresden, German Cancer Research Center Heidelberg, Dresden, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cläre von Neubeck
- Department of Particle Therapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Melanie Christine Föll
- Institute for Surgical Pathology, Faculty of Medicine, University Medical Center, Freiburg, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Khoury College of Computer Sciences, Northeastern University, Boston, USA
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Van Assche CXL, Krüger DN, Flinders B, Vandenbosch M, Franssen C, Guns PJD, Heeren RMA, Cillero-Pastor B. Improved on-tissue detection of the anti-cancer agent doxorubicin by quantitative matrix-assisted laser desorption/ionization mass spectrometry imaging. Talanta 2024; 271:125667. [PMID: 38245959 DOI: 10.1016/j.talanta.2024.125667] [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: 07/01/2023] [Revised: 12/18/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Doxorubicin (dox) is an affordable, and highly effective chemotherapeutic agent used in cancer treatment, yet its application is known to cause cumulative cardiac and renal toxicity. In this study, we employed matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to evaluate the distribution of dox in mouse heart and kidney after in vivo treatment. To this end, we performed absolute quantification using an isotopically labeled form (13C d3-dox) as an internal standard. Unfortunately, ion suppression often leads to loss of sensitivity in compound detection and can result in hampered drug quantification. To overcome this issue, we developed an on-tissue chemical derivatization (OTCD) method using Girard's reagent T (GirT). With the developed method, dox signal was increased by two orders of magnitude. This optimized sample preparation enabled a sensible gain in dox detection, making it possible to study its distribution and abundance (up to 0.11 pmol/mm2 in the heart and 0.33 pmol/mm2 in the kidney medulla). The optimized approach for on-tissue derivatization and subsequent quantification creates a powerful tool to better understand the relationship between dox exposure (at clinically relevant concentrations) and its biological detrimental effects in various tissues. Overall, this work is a showcase of the added value of MALDI-MSI for pharmaceutical studies to better understand heterogeneity in drug exposure between and within organs.
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Affiliation(s)
- Charles X L Van Assche
- Maastricht Multimodal Molecular Imaging institute (M4i), Maastricht University, Maastricht, Netherlands
| | - Dustin N Krüger
- Laboratory of Physiopharmacology, Faculty of Medicine and Health Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Antwerp B-2610, Belgium
| | - Bryn Flinders
- Maastricht Multimodal Molecular Imaging institute (M4i), Maastricht University, Maastricht, Netherlands
| | - Michiel Vandenbosch
- Maastricht Multimodal Molecular Imaging institute (M4i), Maastricht University, Maastricht, Netherlands
| | - Constantijn Franssen
- Research Group Cardiovascular Diseases, GENCOR, University of Antwerp, B-2610 Antwerp, Belgium; Department of Cardiology, Antwerp University Hospital (UZA), Drie Eikenstraat 655, Edegem, Belgium
| | - Pieter-Jan D Guns
- Laboratory of Physiopharmacology, Faculty of Medicine and Health Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Antwerp B-2610, Belgium
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging institute (M4i), Maastricht University, Maastricht, Netherlands
| | - Berta Cillero-Pastor
- Maastricht Multimodal Molecular Imaging institute (M4i), Maastricht University, Maastricht, Netherlands; Institute for Technology-Inspired Regenerative Medicine (MERLN), Department of Cell Biology-Inspired Tissue Engineering, Maastricht University, Maastricht, Netherlands.
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Truong JXM, Rao SR, Ryan FJ, Lynn DJ, Snel MF, Butler LM, Trim PJ. Spatial MS multiomics on clinical prostate cancer tissues. Anal Bioanal Chem 2024; 416:1745-1757. [PMID: 38324070 DOI: 10.1007/s00216-024-05178-z] [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: 12/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/08/2024]
Abstract
Mass spectrometry (MS) and MS imaging (MSI) are used extensively for both the spatial and bulk characterization of samples in lipidomics and proteomics workflows. These datasets are typically generated independently due to different requirements for sample preparation. However, modern omics technologies now provide higher sample throughput and deeper molecular coverage, which, in combination with more sophisticated bioinformatic and statistical pipelines, make generating multiomics data from a single sample a reality. In this workflow, we use spatial lipidomics data generated by matrix-assisted laser desorption/ionization MSI (MALDI-MSI) on prostate cancer (PCa) radical prostatectomy cores to guide the definition of tumor and benign tissue regions for laser capture microdissection (LCM) and bottom-up proteomics all on the same sample and using the same mass spectrometer. Accurate region of interest (ROI) mapping was facilitated by the SCiLS region mapper software and dissected regions were analyzed using a dia-PASEF workflow. A total of 5525 unique protein groups were identified from all dissected regions. Lysophosphatidylcholine acyltransferase 1 (LPCAT1), a lipid remodelling enzyme, was significantly enriched in the dissected regions of cancerous epithelium (CE) compared to benign epithelium (BE). The increased abundance of this protein was reflected in the lipidomics data with an increased ion intensity ratio for pairs of phosphatidylcholines (PC) and lysophosphatidylcholines (LPC) in CE compared to BE.
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Affiliation(s)
- Jacob X M Truong
- The University of Adelaide, North Terrace, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia
- Freemasons Centre for Male Health and Wellbeing, University of Adelaide, North Terrace, Adelaide, South Australia, 5000, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), North Terrace, Adelaide, South Australia, 5000, Australia
| | - Sushma R Rao
- The University of Adelaide, North Terrace, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia
| | - Feargal J Ryan
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - David J Lynn
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Marten F Snel
- The University of Adelaide, North Terrace, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia
| | - Lisa M Butler
- The University of Adelaide, North Terrace, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia
- Freemasons Centre for Male Health and Wellbeing, University of Adelaide, North Terrace, Adelaide, South Australia, 5000, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), North Terrace, Adelaide, South Australia, 5000, Australia
| | - Paul J Trim
- The University of Adelaide, North Terrace, Adelaide, SA, 5000, Australia.
- South Australian Health and Medical Research Institute (SAHMRI), North Terrace, Adelaide, South Australia, 5000, Australia.
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Mallikarjun V, Yin B, Caggiano LR, Blimbaum S, Pavelec CM, Holmes JW, Ewald SE. Automated spatially targeted optical micro proteomics identifies fibroblast- and macrophage-specific regulation of myocardial infarction scar maturation in rats. J Mol Cell Cardiol 2024; 186:1-15. [PMID: 37951204 DOI: 10.1016/j.yjmcc.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/13/2023]
Abstract
Myocardial infarction (MI) results from occlusion of blood supply to the heart muscle causing death of cardiac muscle cells. Following myocardial infarction (MI), extracellular matrix deposition and scar formation mechanically stabilize the injured heart as damaged myocytes undergo necrosis and removal. Fibroblasts and macrophages are key drivers of post-MI scar formation, maturation, and ongoing long-term remodelling; however, their individual contributions are difficult to assess from bulk analyses of infarct scar. Here, we employ state-of-the-art automated spatially targeted optical micro proteomics (autoSTOMP) to photochemically tag and isolate proteomes associated with subpopulations of fibroblasts (SMA+) and macrophages (CD68+) in the context of the native, MI tissue environment. Over a time course of 6-weeks post-MI, we captured dynamic changes in the whole-infarct proteome and determined that some of these protein composition signatures were differentially localized near SMA+ fibroblasts or CD68+ macrophages within the scar region. These results link specific cell populations to within-infarct protein remodelling and illustrate the distinct metabolic and structural processes underlying the observed physiology of each cell type.
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Affiliation(s)
- Venkatesh Mallikarjun
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Bocheng Yin
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Laura R Caggiano
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Sydney Blimbaum
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Caitlin M Pavelec
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Jeffrey W Holmes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA; School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Sarah E Ewald
- Department of Microbiology, Immunology and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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Broadwin M, Aghagoli G, Sabe SA, Harris DD, Wallace J, Lawson J, Ragayendran A, Fedulov AV, Sellke FW. Extracellular vesicle treatment partially reverts epigenetic alterations in chronically ischemic porcine myocardium. VESSEL PLUS 2023; 7:25. [PMID: 37982029 PMCID: PMC10656099 DOI: 10.20517/2574-1209.2023.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Introduction Research has shown epigenetic change via alternation of the methylation profile of human skeletal muscle DNA after Cardio-Pulmonary Bypass (CPB). In this study, we investigated the change in epigenome-wide DNA methylation profiles of porcine myocardium after ischemic insult in the setting of treatment with extracellular vesicle (EV) therapy in normal vs. high-fat diet (HFD) pigs. Methods Four groups of three pigs underwent ameroid constrictor placement to the left circumflex artery (LCx) and were assigned to the following groups: (1) normal diet saline injection; (2) normal diet EV injection; (3) HFD saline injection; and (4) HFD EV injection. DNA methylation was profiled via reduced-representation bisulfite sequencing (RRBS) and compared using a custom bioinformatic pipeline. Results After initial analysis, 441 loci had a nominal P value < 0.05 when examining the effect of ischemia vs. normal heart tissue on a normal diet in the absence of treatment. 426 loci at P value threshold < 0.05 were identified when comparing the ischemic vs. normal tissue from high-fat diet animals. When examining the effect of EV treatment in ischemic tissue in subjects on a normal diet, there were 574 loci with nominal P value < 0.05 with two loci Fructosamine 3 kinase related protein [(FN3KRP) (P < 0.001)] and SNTG1 (P = 0.03) significant after Bonferroni correction. When examining the effect of EV treatment in ischemic tissue in HFD, there were 511 loci with nominal P values < 0.05. After Bonferroni correction, two loci had P values less than 0.05, betacellulin [(BTC) (P = 0.008)] and [proprotein convertase subtilisin/kexin type 7 (PCSK7) (P = 0.01)]. Conclusions Alterations in DNA methylation were identified in pig myocardium after ischemic insult, change in diet, and treatment with EVs. Hundreds of differentially methylated loci were detected, but the magnitude of the effects was low. These changes represent significant alterations in DNA methylation and merit further investigation.
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Affiliation(s)
- Mark Broadwin
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02909, USA
| | - Ghazal Aghagoli
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02909, USA
| | - Sharif A. Sabe
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02909, USA
| | - Dwight D. Harris
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02909, USA
| | - Joselynn Wallace
- Center for Computation and Visualization, Brown University, Providence, RI 02912, USA
| | - Jordan Lawson
- Center for Computation and Visualization, Brown University, Providence, RI 02912, USA
| | - Ashok Ragayendran
- Center for Computational Biology of Human Disease, Brown University, Providence, RI 02912, USA
| | - Alexey V. Fedulov
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02909, USA
| | - Frank W. Sellke
- Division of Cardiothoracic Surgery, Department of Surgery, Cardiovascular Research Center, Rhode Island Hospital, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02909, USA
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Chen TY, You L, Hardillo JAU, Chien MP. Spatial Transcriptomic Technologies. Cells 2023; 12:2042. [PMID: 37626852 PMCID: PMC10453065 DOI: 10.3390/cells12162042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Spatial transcriptomic technologies enable measurement of expression levels of genes systematically throughout tissue space, deepening our understanding of cellular organizations and interactions within tissues as well as illuminating biological insights in neuroscience, developmental biology and a range of diseases, including cancer. A variety of spatial technologies have been developed and/or commercialized, differing in spatial resolution, sensitivity, multiplexing capability, throughput and coverage. In this paper, we review key enabling spatial transcriptomic technologies and their applications as well as the perspective of the techniques and new emerging technologies that are developed to address current limitations of spatial methodologies. In addition, we describe how spatial transcriptomics data can be integrated with other omics modalities, complementing other methods in deciphering cellar interactions and phenotypes within tissues as well as providing novel insight into tissue organization.
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Affiliation(s)
- Tsai-Ying Chen
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (T.-Y.C.); (L.Y.)
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Li You
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (T.-Y.C.); (L.Y.)
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Jose Angelito U. Hardillo
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Department of Otorhinolaryngology, Head and Neck Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands; (T.-Y.C.); (L.Y.)
- Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Department of Otorhinolaryngology, Head and Neck Surgery, Erasmus University Medical Center, 3015 GD Rotterdam, The Netherlands
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