1
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Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BJM, Nakayasu ES, Qian WJ, Metz TO. Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. Trends Mol Med 2024:S1471-4914(24)00195-3. [PMID: 39152082 DOI: 10.1016/j.molmed.2024.07.009] [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: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yu Mi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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2
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Zhang R, Anguiano M, Aarrestad IK, Lin S, Chandra J, Vadde SS, Olson DE, Kim CK. Rapid, biochemical tagging of cellular activity history in vivo. Nat Methods 2024:10.1038/s41592-024-02375-7. [PMID: 39103446 DOI: 10.1038/s41592-024-02375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 06/21/2024] [Indexed: 08/07/2024]
Abstract
Intracellular calcium (Ca2+) is ubiquitous to cell signaling across biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated split-TurboID (CaST) labels activated cells within 10 min with an exogenously delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST readout can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
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Affiliation(s)
- Run Zhang
- Biomedical Engineering Graduate Group, University of California, Davis, Davis, CA, USA
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
| | - Maribel Anguiano
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Neuroscience Graduate Group, University of California, Davis, Davis, CA, USA
| | - Isak K Aarrestad
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Neuroscience Graduate Group, University of California, Davis, Davis, CA, USA
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA, USA
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | - Joshua Chandra
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Neuroscience Graduate Group, University of California, Davis, Davis, CA, USA
| | - Sruti S Vadde
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | - David E Olson
- Center for Neuroscience, University of California, Davis, Davis, CA, USA
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA, USA
| | - Christina K Kim
- Center for Neuroscience, University of California, Davis, Davis, CA, USA.
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA, USA.
- Department of Neurology, University of California, Davis, Sacramento, CA, USA.
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3
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Rietjens RG, Wang G, van den Berg BM, Rabelink TJ. Spatial metabolomics in tissue injury and regeneration. Curr Opin Genet Dev 2024; 87:102223. [PMID: 38901101 DOI: 10.1016/j.gde.2024.102223] [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: 02/09/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
Tissue homeostasis is intricately linked to cellular metabolism and metabolite exchange within the tissue microenvironment. The orchestration of adaptive cellular responses during injury and repair depends critically upon metabolic adaptation. This adaptation, in turn, shapes cell fate decisions required for the restoration of tissue homeostasis. Understanding the nuances of metabolic processes within the tissue context and comprehending the intricate communication between cells is therefore imperative for unraveling the complexity of tissue homeostasis and the processes of injury and repair. In this review, we focus on mass spectrometry imaging as an advanced platform with the potential to provide such comprehensive insights into the metabolic instruction governing tissue function. Recent advances in this technology allow to decipher the intricate metabolic networks that determine cellular behavior in the context of tissue resilience, injury, and repair. These insights not only advance our fundamental understanding of tissue biology but also hold implications for therapeutic interventions by targeting metabolic pathways critical for maintaining tissue homeostasis.
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Affiliation(s)
- Rosalie Gj Rietjens
- Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine & The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands. https://twitter.com/@RietjensRosalie
| | - Gangqi Wang
- Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine & The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands. https://twitter.com/@GangqiW
| | - Bernard M van den Berg
- Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine & The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Ton J Rabelink
- Department of Internal Medicine (Nephrology) & Einthoven Laboratory of Vascular and Regenerative Medicine & The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands.
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4
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Zhang H, Lu KH, Ebbini M, Huang P, Lu H, Li L. Mass spectrometry imaging for spatially resolved multi-omics molecular mapping. NPJ IMAGING 2024; 2:20. [PMID: 39036554 PMCID: PMC11254763 DOI: 10.1038/s44303-024-00025-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/21/2024] [Indexed: 07/23/2024]
Abstract
The recent upswing in the integration of spatial multi-omics for conducting multidimensional information measurements is opening a new chapter in biological research. Mapping the landscape of various biomolecules including metabolites, proteins, nucleic acids, etc., and even deciphering their functional interactions and pathways is believed to provide a more holistic and nuanced exploration of the molecular intricacies within living systems. Mass spectrometry imaging (MSI) stands as a forefront technique for spatially mapping the metabolome, lipidome, and proteome within diverse tissue and cell samples. In this review, we offer a systematic survey delineating different MSI techniques for spatially resolved multi-omics analysis, elucidating their principles, capabilities, and limitations. Particularly, we focus on the advancements in methodologies aimed at augmenting the molecular sensitivity and specificity of MSI; and depict the burgeoning integration of MSI-based spatial metabolomics, lipidomics, and proteomics, encompassing the synergy with other imaging modalities. Furthermore, we offer speculative insights into the potential trajectory of MSI technology in the future.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Kelly H. Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Malik Ebbini
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705 USA
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5
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Toyama Y, Nirasawa T, Morishima M, Saito Y, Irie K, Murayama S, Ikegawa M. Integrated Spatial Multi-Omics Study of Postmortem Brains of Alzheimer's Disease. Acta Histochem Cytochem 2024; 57:119-130. [PMID: 38988692 PMCID: PMC11231568 DOI: 10.1267/ahc.24-00025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 05/12/2024] [Indexed: 07/12/2024] Open
Abstract
Pathological hallmark of Alzheimer's disease (AD) is characterized by the accumulation and aggregation of amyloid β (Aβ) peptides into extracellular plaques of the brain. Clarification of the process of how soluble Aβ starts to assemble into amyloid fibrils is an essential step in elucidating the pathogenesis of AD. In our previous study, Aβ proteoforms including full-length Aβ40 and Aβ42/43 with N- and C-terminal truncated forms were visualized in postmortem brains from AD patients with matrix-assisted laser desorption/ionization-based mass spectrometry imaging (MALDI-MSI). In this study, Aβ proteoforms were consistently visualized by an updated protocol, and uncharacterized peptides such as Aβ1-29 and Aβ10-40 in AD brains were also visualized. To decipher neurotoxic effects of Aβ in patients' brains, here we integrate liquid chromatography tandem mass spectrometry (LC-MS/MS) based shotgun proteomics with laser microdissection (LMD) excised tissue samples as well as direct tissue imaging with MALDI-MSI. With this approach, we have highlighted dynamic alterations of microtubule associating proteins (MAPs) including MAP1A, MAP1B and MAP2 as well as AD dominant proteins including APP, UCHL1, SNCA, and APOE. Of note, as lipid dysregulation has been implicated with AD pathology, we have challenged to integrate proteomics and lipid imaging for AD and control brain tissue. Spatial multi-omics is also valid to uncover molecular pathology of white matter as well as grey matter and leptomeningeal area, for example, by visualizing heme in patients' postmortem brains.
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Affiliation(s)
- Yumiko Toyama
- Department of Life and Medical Systems, Doshisha University, Kyotanabe, Japan
| | | | - Maho Morishima
- The Brain Bank for Aging Research, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Yuko Saito
- The Brain Bank for Aging Research, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Kazuhiro Irie
- Department of Life and Medical Systems, Doshisha University, Kyotanabe, Japan
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Shigeo Murayama
- The Brain Bank for Aging Research, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
| | - Masaya Ikegawa
- Department of Life and Medical Systems, Doshisha University, Kyotanabe, Japan
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6
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Chan YH, Pathmasiri KC, Pierre-Jacques D, Hibbard MC, Tao N, Fischer JL, Yang E, Cologna SM, Gao R. Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. Nat Commun 2024; 15:5036. [PMID: 38866734 PMCID: PMC11169460 DOI: 10.1038/s41467-024-49384-w] [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: 09/10/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
A technique capable of label-free detection, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of native biomolecules in intact specimens. However, MSI has often been precluded from single-cell applications due to the spatial resolution limit set forth by the physical and instrumental constraints of the method. By taking advantage of the reversible interaction between the analytes and a superabsorbent hydrogel, we have developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome the spatial resolution limits of modern mass spectrometers. With GAMSI, we show that the spatial resolution of MALDI-MSI can be enhanced ~3-6-fold to the sub-micrometer level without changing the existing mass spectrometry hardware or analysis pipeline. This approach will vastly enhance the accessibility of MSI-based spatial analysis at the cellular scale.
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Affiliation(s)
- Yat Ho Chan
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | - Maddison C Hibbard
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | | | | | | | - Stephanie M Cologna
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA.
- Laboratory for Integrative Neuroscience, University of Illinois Chicago, Chicago, IL, USA.
- Department of Biological Sciences, University of Illinois Chicago, Chicago, IL, USA.
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7
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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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8
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Zhang R, Anguiano M, Aarrestad IK, Lin S, Chandra J, Vadde SS, Olson DE, Kim CK. Rapid, biochemical tagging of cellular activity history in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.06.556431. [PMID: 38798353 PMCID: PMC11118534 DOI: 10.1101/2023.09.06.556431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Intracellular calcium (Ca2+) is ubiquitous to cell signaling across all biology. While existing fluorescent sensors and reporters can detect activated cells with elevated Ca2+ levels, these approaches require implants to deliver light to deep tissue, precluding their noninvasive use in freely-behaving animals. Here we engineered an enzyme-catalyzed approach that rapidly and biochemically tags cells with elevated Ca2+ in vivo. Ca2+-activated Split-TurboID (CaST) labels activated cells within 10 minutes with an exogenously-delivered biotin molecule. The enzymatic signal increases with Ca2+ concentration and biotin labeling time, demonstrating that CaST is a time-gated integrator of total Ca2+ activity. Furthermore, the CaST read-out can be performed immediately after activity labeling, in contrast to transcriptional reporters that require hours to produce signal. These capabilities allowed us to apply CaST to tag prefrontal cortex neurons activated by psilocybin, and to correlate the CaST signal with psilocybin-induced head-twitch responses in untethered mice.
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Affiliation(s)
- Run Zhang
- Biomedical Engineering Graduate Group, University of California, Davis, Davis, CA 95616
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
| | - Maribel Anguiano
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
| | - Isak K. Aarrestad
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
| | - Sophia Lin
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
| | - Joshua Chandra
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Neuroscience Graduate Group, University of California, Davis, Davis, CA 95618
| | - Sruti S. Vadde
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
| | - David E. Olson
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
- Department of Chemistry, University of California, Davis, Davis, CA 95616
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Sacramento, CA 95817
| | - Christina K. Kim
- Center for Neuroscience, University of California, Davis, Davis, CA 95618
- Institute for Psychedelics and Neurotherapeutics, University of California, Davis, Davis, CA 95616
- Department of Neurology, University of California, Davis, Sacramento, CA 95817
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9
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Hartig J, Young LEA, Grimsley G, Mehta AS, Ippolito JE, Leach RJ, Angel PM, Drake RR. The glycosylation landscape of prostate cancer tissues and biofluids. Adv Cancer Res 2024; 161:1-30. [PMID: 39032948 DOI: 10.1016/bs.acr.2024.04.005] [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: 07/23/2024]
Abstract
An overview of the role of glycosylation in prostate cancer (PCa) development and progression is presented, focusing on recent advancements in defining the N-glycome through glycomic profiling and glycoproteomic methodologies. Glycosylation is a common post-translational modification typified by oligosaccharides attached N-linked to asparagine or O-linked to serine or threonine on carrier proteins. These attached sugars have crucial roles in protein folding and cellular recognition processes, such that altered glycosylation is a hallmark of cancer pathogenesis and progression. In the past decade, advancements in N-glycan profiling workflows using Matrix Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) technology have been applied to define the spatial distribution of glycans in PCa tissues. Multiple studies applying N-glycan MALDI-MSI to pathology-defined PCa tissues have identified significant alterations in N-glycan profiles associated with PCa progression. N-glycan compositions progressively increase in number, and structural complexity due to increased fucosylation and sialylation. Additionally, significant progress has been made in defining the glycan and glycopeptide compositions of prostatic-derived glycoproteins like prostate-specific antigen in tissues and biofluids. The glycosyltransferases involved in these changes are potential drug targets for PCa, and new approaches in this area are summarized. These advancements will be discussed in the context of the further development of clinical diagnostics and therapeutics targeting glycans and glycoproteins associated with PCa progression. Integration of large scale spatial glycomic data for PCa with other spatial-omic methodologies is now feasible at the tissue and single-cell levels.
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Affiliation(s)
- Jordan Hartig
- Medical University of South Carolina, Charleston, SC, United States
| | | | - Grace Grimsley
- Medical University of South Carolina, Charleston, SC, United States
| | - Anand S Mehta
- Medical University of South Carolina, Charleston, SC, United States
| | - Joseph E Ippolito
- Washington University School of Medicine in Saint Louis, St. Louis, MO, United States
| | - Robin J Leach
- University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Peggi M Angel
- Medical University of South Carolina, Charleston, SC, United States
| | - Richard R Drake
- Medical University of South Carolina, Charleston, SC, United States.
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10
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Zirem Y, Ledoux L, Roussel L, Maurage CA, Tirilly P, Le Rhun É, Meresse B, Yagnik G, Lim MJ, Rothschild KJ, Duhamel M, Salzet M, Fournier I. Real-time glioblastoma tumor microenvironment assessment by SpiderMass for improved patient management. Cell Rep Med 2024; 5:101482. [PMID: 38552622 PMCID: PMC11031375 DOI: 10.1016/j.xcrm.2024.101482] [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: 09/14/2023] [Revised: 01/15/2024] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Glioblastoma is a highly heterogeneous and infiltrative form of brain cancer associated with a poor outcome and limited therapeutic effectiveness. The extent of the surgery is related to survival. Reaching an accurate diagnosis and prognosis assessment by the time of the initial surgery is therefore paramount in the management of glioblastoma. To this end, we are studying the performance of SpiderMass, an ambient ionization mass spectrometry technology that can be used in vivo without invasiveness, coupled to our recently established artificial intelligence pipeline. We demonstrate that we can both stratify isocitrate dehydrogenase (IDH)-wild-type glioblastoma patients into molecular sub-groups and achieve an accurate diagnosis with over 90% accuracy after cross-validation. Interestingly, the developed method offers the same accuracy for prognosis. In addition, we are testing the potential of an immunoscoring strategy based on SpiderMass fingerprints, showing the association between prognosis and immune cell infiltration, to predict patient outcome.
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Affiliation(s)
- Yanis Zirem
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Léa Ledoux
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Lucas Roussel
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | | | - Pierre Tirilly
- Université de Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, 59000 Lille, France
| | - Émilie Le Rhun
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Departments of Neurosurgery and Neurology, Clinical Neuroscience Center, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Bertrand Meresse
- Université de Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, 59000 Lille, France
| | | | | | - Kenneth J Rothschild
- AmberGen, Inc., Billerica, MA, USA; Department of Physics and Photonics Center, Boston University, Boston, MA, USA
| | - Marie Duhamel
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Michel Salzet
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
| | - Isabelle Fournier
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
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11
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Duncan KD, Pětrošová H, Lum JJ, Goodlett DR. Mass spectrometry imaging methods for visualizing tumor heterogeneity. Curr Opin Biotechnol 2024; 86:103068. [PMID: 38310648 DOI: 10.1016/j.copbio.2024.103068] [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: 08/28/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
Profiling spatial distributions of lipids, metabolites, and proteins in tumors can reveal unique cellular microenvironments and provide molecular evidence for cancer cell dysfunction and proliferation. Mass spectrometry imaging (MSI) is a label-free technique that can be used to map biomolecules in tumors in situ. Here, we discuss current progress in applying MSI to uncover molecular heterogeneity in tumors. First, the analytical strategies to profile small molecules and proteins are outlined, and current methods for multimodal imaging to maximize biological information are highlighted. Second, we present and summarize biological insights obtained by MSI of tumor tissue. Finally, we discuss important considerations for designing MSI experiments and several current analytical challenges.
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Affiliation(s)
- Kyle D Duncan
- Department of Chemistry, Vancouver Island University, Nanaimo, British Columbia, Canada; Department of Chemistry, University of Victoria, Victoria, British Columbia, Canada.
| | - Helena Pětrošová
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, British Columbia, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| | - Julian J Lum
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada; Trev and Joyce Deeley Research Centre, BC Cancer, Victoria, British Columbia, Canada
| | - David R Goodlett
- University of Victoria Genome British Columbia Proteomics Center, University of Victoria, Victoria, British Columbia, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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12
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Holbrook JH, Kemper GE, Hummon AB. Quantitative mass spectrometry imaging: therapeutics & biomolecules. Chem Commun (Camb) 2024; 60:2137-2151. [PMID: 38284765 PMCID: PMC10878071 DOI: 10.1039/d3cc05988j] [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: 12/08/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024]
Abstract
Mass spectrometry imaging (MSI) has become increasingly utilized in the analysis of biological molecules. MSI grants the ability to spatially map thousands of molecules within one experimental run in a label-free manner. While MSI is considered by most to be a qualitative method, recent advancements in instrumentation, sample preparation, and development of standards has made quantitative MSI (qMSI) more common. In this feature article, we present a tailored review of recent advancements in qMSI of therapeutics and biomolecules such as lipids and peptides/proteins. We also provide detailed experimental considerations for conducting qMSI studies on biological samples, aiming to advance the methodology.
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Affiliation(s)
- Joseph H Holbrook
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Gabrielle E Kemper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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13
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Kim J, Dwivedi G, Boughton BA, Sharma A, Lee S. Advances in cellular and tissue-based imaging techniques for sarcoid granulomas. Am J Physiol Cell Physiol 2024; 326:C10-C26. [PMID: 37955119 DOI: 10.1152/ajpcell.00507.2023] [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: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Sarcoidosis embodies a complex inflammatory disorder spanning multiple systems, with its origin remaining elusive. It manifests as the infiltration of inflammatory cells that coalesce into distinctive noncaseous granulomas within afflicted organs. Unraveling this disease necessitates the utilization of cellular or tissue-based imaging methods to both visualize and characterize the biochemistry of these sarcoid granulomas. Although hematoxylin and eosin stain, standard in routine use alongside cytological stains have found utility in diagnosis within clinical contexts, special stains such as Masson's trichrome, reticulin, methenamine silver, and Ziehl-Neelsen provide additional varied perspectives of sarcoid granuloma imaging. Immunohistochemistry aids in pinpointing specific proteins and gene expressions further characterizing these granulomas. Finally, recent advances in spatial transcriptomics promise to divulge profound insights into their spatial orientation and three-dimensional (3-D) molecular mapping. This review focuses on a range of preexisting imaging methods employed for visualizing sarcoid granulomas at the cellular level while also exploring the potential of the latest cutting-edge approaches like spatial transcriptomics and matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI), with the overarching goal of shedding light on the trajectory of sarcoidosis research.
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Affiliation(s)
- Junwoo Kim
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Girish Dwivedi
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Berin A Boughton
- Australian National Phenome Centre, Murdoch University, Murdoch, Western Australia, Australia
| | - Ankur Sharma
- Onco-Fetal Ecosystem Laboratory, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Silvia Lee
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Curtin Medical School, Curtin University, Perth, Western Australia, Australia
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14
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Tinklepaugh J, Mamrak NE. Imaging in Type 1 Diabetes, Current Perspectives and Directions. Mol Imaging Biol 2023; 25:1142-1149. [PMID: 37934378 DOI: 10.1007/s11307-023-01873-y] [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: 07/31/2023] [Revised: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Type 1 diabetes (T1D) is characterized by the autoimmune-mediated attack of insulin-producing beta cells in the pancreas, leading to reliance on exogenous insulin to control a patient's blood glucose levels. As progress is being made in understanding the pathophysiology of the disease and how to better develop therapies to treat it, there is an increasing need for monitoring technologies to quantify beta cell mass and function throughout T1D progression and beta cell replacement therapy. Molecular imaging techniques offer a possible solution through both radiologic and non-radiologic means including positron emission tomography, magnetic resonance imaging, electron paramagnetic resonance imaging, and spatial omics. This commentary piece outlines the role of molecular imaging in T1D research and highlights the need for further applications of such methodologies in T1D.
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Affiliation(s)
- Jay Tinklepaugh
- Research Department, JDRF, 200 Vesey Street, New York, NY, USA
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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16
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Dunne J, Griner J, Romeo M, Macdonald J, Krieg C, Lim M, Yagnik G, Rothschild KJ, Drake RR, Mehta AS, Angel PM. Evaluation of antibody-based single cell type imaging techniques coupled to multiplexed imaging of N-glycans and collagen peptides by matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Bioanal Chem 2023; 415:7011-7024. [PMID: 37843548 PMCID: PMC10632234 DOI: 10.1007/s00216-023-04983-2] [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: 08/04/2023] [Revised: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/17/2023]
Abstract
The integration of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) with single cell spatial omics methods allows for a comprehensive investigation of single cell spatial information and matrisomal N-glycan and extracellular matrix protein imaging. Here, the performance of the antibody-directed single cell workflows coupled with MALDI-MSI are evaluated. Miralys™ photocleavable mass-tagged antibody probes (MALDI-IHC, AmberGen, Inc.), GeoMx DSP® (NanoString, Inc.), and Imaging Mass Cytometry (IMC, Standard BioTools Inc.) were used in series with MALDI-MSI of N-glycans and extracellular matrix peptides on formalin-fixed paraffin-embedded tissues. Single cell omics protocols were performed before and after MALDI-MSI. The data suggests that for each modality combination, there is an optimal order for performing both techniques on the same tissue section. An overall conclusion is that MALDI-MSI studies may be completed on the same tissue section as used for antibody-directed single cell modalities. This work increases access to combined cellular and extracellular information within the tissue microenvironment to enhance research on the pathological origins of disease.
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Affiliation(s)
- Jaclyn Dunne
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Jake Griner
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Martin Romeo
- Translational Science Laboratory, Hollings Cancer Center, Charleston, SC, 29425, USA
| | - Jade Macdonald
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Carsten Krieg
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Mark Lim
- AmberGen, Inc, 44 Manning Road, Billerica, MA, 01821, USA
| | - Gargey Yagnik
- AmberGen, Inc, 44 Manning Road, Billerica, MA, 01821, USA
| | - Kenneth J Rothschild
- AmberGen, Inc, 44 Manning Road, Billerica, MA, 01821, USA
- Department of Physics and Photonics Center, Boston University, Boston, MA, 02215, USA
| | - Richard R Drake
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Anand S Mehta
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA
| | - Peggi M Angel
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, 173 Ashley Avenue BSB 358, Charleston, SC, 29425, USA.
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Piga I, L'Imperio V, Capitoli G, Denti V, Smith A, Magni F, Pagni F. Paving the path toward multi-omics approaches in the diagnostic challenges faced in thyroid pathology. Expert Rev Proteomics 2023; 20:419-437. [PMID: 38000782 DOI: 10.1080/14789450.2023.2288222] [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: 09/12/2023] [Accepted: 11/22/2023] [Indexed: 11/26/2023]
Abstract
INTRODUCTION Despite advancements in diagnostic methods, the classification of indeterminate thyroid nodules still poses diagnostic challenges not only in pre-surgical evaluation but even after histological evaluation of surgical specimens. Proteomics, aided by mass spectrometry and integrated with artificial intelligence and machine learning algorithms, shows great promise in identifying diagnostic markers for thyroid lesions. AREAS COVERED This review provides in-depth exploration of how proteomics has contributed to the understanding of thyroid pathology. It discusses the technical advancements related to immunohistochemistry, genetic and proteomic techniques, such as mass spectrometry, which have greatly improved sensitivity and spatial resolution up to single-cell level. These improvements allowed the identification of specific protein signatures associated with different types of thyroid lesions. EXPERT COMMENTARY Among all the proteomics approaches, spatial proteomics stands out due to its unique ability to capture the spatial context of proteins in both cytological and tissue thyroid samples. The integration of multi-layers of molecular information combining spatial proteomics, genomics, immunohistochemistry or metabolomics and the implementation of artificial intelligence and machine learning approaches, represent hugely promising steps forward toward the possibility to uncover intricate relationships and interactions among various molecular components, providing a complete picture of the biological landscape whilst fostering thyroid nodule diagnosis.
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Affiliation(s)
- Isabella Piga
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
| | - Giulia Capitoli
- Department of Medicine and Surgery, Bicocca Bioinformatics Biostatistics and Bioimaging B4 Center, University of Milan - Bicocca (UNIMIB), Monza, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Andrew Smith
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fulvio Magni
- Department of Medicine and Surgery, Clinical Proteomics and Metabolomics Unit, University of Milano - Bicocca, Monza, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milan-Bicocca, Monza, Italy
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