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Sample Preparation and Analysis of Single Cells Using High Performance MALDI FTICR Mass Spectrometry.
Yang B, Tsui T, Caprioli RM, Norris JL
(2020) Methods Mol Biol 2064: 125-134
MeSH Terms: Animals, Equipment Design, Lipid Metabolism, Lipids, Metabolome, Metabolomics, Mice, RAW 264.7 Cells, Single-Cell Analysis, Specimen Handling, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Show Abstract · Added October 15, 2019
Imaging mass spectrometry is a powerful technology that combines the molecular measurements of mass spectrometry with the spatial information inherent to microscopy. This unique combination of capabilities is ideally suited for the analysis of metabolites and lipids from single cells. This chapter describes a methodology for the sample preparation and analysis of single cells using high performance MALDI FTICR MS. Using this approach, we are able to generate profiles of lipid and metabolite expression from single cells that characterize cellular heterogeneity. This approach also enables the detection of variations in the expression profiles of lipids and metabolites induced by chemical stimulation of the cells. These results demonstrate that MALDI IMS provides an insightful view of lipid and metabolite expression useful in the characterization of a number of biological systems at the single cell level.
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11 MeSH Terms
A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry.
Judd AM, Gutierrez DB, Moore JL, Patterson NH, Yang J, Romer CE, Norris JL, Caprioli RM
(2019) J Mass Spectrom 54: 716-727
MeSH Terms: Formaldehyde, Humans, Paraffin Embedding, Proteins, Proteolysis, Specimen Handling, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tissue Array Analysis, Tissue Fixation, Trypsin
Show Abstract · Added October 15, 2019
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a molecular imaging technology uniquely capable of untargeted measurement of proteins, lipids, and metabolites while retaining spatial information about their location in situ. This powerful combination of capabilities has the potential to bring a wealth of knowledge to the field of molecular histology. Translation of this innovative research tool into clinical laboratories requires the development of reliable sample preparation protocols for the analysis of proteins from formalin-fixed paraffin-embedded (FFPE) tissues, the standard preservation process in clinical pathology. Although ideal for stained tissue analysis by microscopy, the FFPE process cross-links, disrupts, or can remove proteins from the tissue, making analysis of the protein content challenging. To date, reported approaches differ widely in process and efficacy. This tutorial presents a strategy derived from systematic testing and optimization of key parameters, for reproducible in situ tryptic digestion of proteins in FFPE tissue and subsequent MALDI IMS analysis. The approach describes a generalized method for FFPE tissues originating from virtually any source.
© 2019 John Wiley & Sons, Ltd.
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Protein identification strategies in MALDI imaging mass spectrometry: a brief review.
Ryan DJ, Spraggins JM, Caprioli RM
(2019) Curr Opin Chem Biol 48: 64-72
MeSH Terms: Animals, Equipment Design, Humans, Molecular Imaging, Proteins, Specimen Handling, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Workflow
Show Abstract · Added March 26, 2019
Matrix assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful technology used to investigate the spatial distributions of thousands of molecules throughout a tissue section from a single experiment. As proteins represent an important group of functional molecules in tissue and cells, the imaging of proteins has been an important point of focus in the development of IMS technologies and methods. Protein identification is crucial for the biological contextualization of molecular imaging data. However, gas-phase fragmentation efficiency of MALDI generated proteins presents significant challenges, making protein identification directly from tissue difficult. This review highlights methods and technologies specifically related to protein identification that have been developed to overcome these challenges in MALDI IMS experiments.
Copyright © 2018 Elsevier Ltd. All rights reserved.
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8 MeSH Terms
P2X7R antagonism after subfailure overstretch injury of blood vessels reverses vasomotor dysfunction and prevents apoptosis.
Luo W, Feldman D, McCallister R, Brophy C, Cheung-Flynn J
(2017) Purinergic Signal 13: 579-590
MeSH Terms: Animals, Aorta, Apoptosis, Coronary Artery Bypass, Female, Humans, Male, Purinergic P2X Receptor Antagonists, Rats, Rats, Sprague-Dawley, Receptors, Purinergic P2X7, Saphenous Vein, Specimen Handling
Show Abstract · Added May 22, 2018
Human saphenous vein (HSV) is harvested and prepared prior to implantation as an arterial bypass graft. Injury and the response to injury from surgical harvest and preparation trigger cascades of molecular events and contribute to graft remodeling and intimal hyperplasia. Apoptosis is an early response after implantation that contributes the development of neointimal lesions. Here, we showed that surgical harvest and preparation of HSV leads to vasomotor dysfunction, increased apoptosis and downregulation of the phosphorylation of the anti-apoptotic protein, Niban. A model of subfailure overstretch injury in rat aorta (RA) was used to demonstrate impaired vasomotor function, increased extracellular ATP (eATP) release, and increased apoptosis following pathological vascular injury. The subfailure overstretch injury was associated with activation of p38 MAPK stress pathway and decreases in the phosphorylation of the anti-apoptotic protein Niban. Treatment of RA after overstretch injury with antagonists to purinergic P2X7 receptor (P2X7R) antagonists or P2X7R/pannexin (PanX1) complex, but not PanX1 alone, restored vasomotor function. Inhibitors to P2X7R and PanX1 reduced stretch-induced eATP release. P2X7R/PanX1 antagonism led to decrease in p38 MAPK phosphorylation, restoration of Niban phosphorylation and increases in the phosphorylation of the anti-apoptotic protein Akt in RA and reduced TNFα-stimulated caspase 3/7 activity in cultured rat vascular smooth muscle cells. In conclusion, inhibition of P2X7R after overstretch injury restored vasomotor function and inhibited apoptosis. Treatment with P2X7R/PanX1 complex inhibitors after harvest and preparation injury of blood vessels used for bypass conduits may prevent the subsequent response to injury that lead to apoptosis and represents a novel therapeutic approach to prevent graft failure.
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13 MeSH Terms
Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.
Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V
(2015) Nat Protoc 10: 1860-1896
MeSH Terms: Animals, Detergents, Histocytochemistry, Lipids, Mice, Optical Imaging, Pathology, Rats, Specimen Handling, Staining and Labeling, Time Factors, Tissue Embedding, Tissue Fixation
Show Abstract · Added July 20, 2016
To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.
1 Communities
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13 MeSH Terms
Histology-guided protein digestion/extraction from formalin-fixed and paraffin-embedded pressure ulcer biopsies.
Taverna D, Pollins AC, Nanney LB, Sindona G, Caprioli RM
(2016) Exp Dermatol 25: 143-6
MeSH Terms: Biopsy, Chromatography, Liquid, Eosine Yellowish-(YS), Formaldehyde, Hematoxylin, Humans, Hydrogels, Paraffin Embedding, Pressure Ulcer, Proteins, Proteomics, Specimen Handling, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Staining and Labeling, Tandem Mass Spectrometry, Tissue Fixation, Trypsin
Show Abstract · Added October 15, 2015
Herein we present a simple, reproducible and versatile approach for in situ protein digestion and identification on formalin-fixed and paraffin-embedded (FFPE) tissues. This adaptation is based on the use of an enzyme delivery platform (hydrogel discs) that can be positioned on the surface of a tissue section. By simultaneous deposition of multiple hydrogels over select regions of interest within the same tissue section, multiple peptide extracts can be obtained from discrete histological areas. After enzymatic digestion, the hydrogel extracts are submitted for LC-MS/MS analysis followed by database inquiry for protein identification. Further, imaging mass spectrometry (IMS) is used to reveal the spatial distribution of the identified peptides within a serial tissue section. Optimization was achieved using cutaneous tissue from surgically excised pressure ulcers that were subdivided into two prime regions of interest: the wound bed and the adjacent dermal area. The robust display of tryptic peptides within these spectral analyses of histologically defined tissue regions suggests that LC-MS/MS in combination with IMS can serve as useful exploratory tools.
© 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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17 MeSH Terms
RePORT International: Advancing Tuberculosis Biomarker Research Through Global Collaboration.
Hamilton CD, Swaminathan S, Christopher DJ, Ellner J, Gupta A, Sterling TR, Rolla V, Srinivasan S, Karyana M, Siddiqui S, Stoszek SK, Kim P
(2015) Clin Infect Dis 61Suppl 3: S155-9
MeSH Terms: Biological Specimen Banks, Biomarkers, Biomedical Research, Brazil, Humans, India, Indonesia, International Cooperation, Prospective Studies, Specimen Handling, Tuberculosis
Show Abstract · Added February 17, 2016
Progress in tuberculosis clinical research is hampered by a lack of reliable biomarkers that predict progression from latent to active tuberculosis, and subsequent cure, relapse, or failure. Regional Prospective Observational Research in Tuberculosis (RePORT) International represents a consortium of regional cohorts (RePORT India, RePORT Brazil, and RePORT Indonesia) that are linked through the implementation of a Common Protocol for data and specimen collection, and are poised to address this critical research need. Each RePORT network is designed to support local, in-country tuberculosis-specific data and specimen biorepositories, and associated research. Taken together, the expected results include greater global clinical research capacity in high-burden settings, and increased local access to quality data and specimens for members of each network and their domestic and international collaborators. Additional networks are expected to be added, helping to spur tuberculosis treatment and prevention research around the world.
© The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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11 MeSH Terms
Image-Guided Percutaneous Abdominal Mass Biopsy: Technical and Clinical Considerations.
Lipnik AJ, Brown DB
(2015) Radiol Clin North Am 53: 1049-59
MeSH Terms: Biopsy, Needle, Blood Coagulation Tests, Conscious Sedation, Contraindications, Humans, Image-Guided Biopsy, Kidney Diseases, Liver Diseases, Magnetic Resonance Imaging, Interventional, Neoplasm Seeding, Patient Positioning, Radiography, Interventional, Specimen Handling, Ultrasonography, Interventional
Show Abstract · Added September 18, 2015
Image-guided percutaneous biopsy of abdominal masses is a safe, minimally invasive procedure with a high diagnostic yield for a variety of pathologic processes. This article describes the basic technique of percutaneous biopsy, including the different modalities available for imaging guidance. Patient selection and preparation for safe performance of the procedure is emphasized, and the periprocedural management of coagulation status as well as basic indications and contraindications of the procedure are briefly discussed. In particular, the role of biopsy in the diagnosis of liver and renal masses is highlighted.
Copyright © 2015 Elsevier Inc. All rights reserved.
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14 MeSH Terms
An Optimized Preparation Technique for Saphenous Vein Graft.
Wise ES, Hocking KM, Feldman D, Komalavilas P, Cheung-Flynn J, Brophy CM
(2015) Am Surg 81: E274-6
MeSH Terms: Humans, Saphenous Vein, Specimen Handling, Tissue and Organ Harvesting
Added March 3, 2020
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Human islet preparations distributed for research exhibit a variety of insulin-secretory profiles.
Kayton NS, Poffenberger G, Henske J, Dai C, Thompson C, Aramandla R, Shostak A, Nicholson W, Brissova M, Bush WS, Powers AC
(2015) Am J Physiol Endocrinol Metab 308: E592-602
MeSH Terms: Adolescent, Adult, Aged, Child, Female, Humans, Insulin, Insulin Secretion, Islets of Langerhans, Male, Middle Aged, Research, Specimen Handling, Tissue Donors, Tissue and Organ Procurement, Young Adult
Show Abstract · Added July 28, 2015
Human islet research is providing new insights into human islet biology and diabetes, using islets isolated at multiple US centers from donors with varying characteristics. This creates challenges for understanding, interpreting, and integrating research findings from the many laboratories that use these islets. In what is, to our knowledge, the first standardized assessment of human islet preparations from multiple isolation centers, we measured insulin secretion from 202 preparations isolated at 15 centers over 11 years and noted five distinct patterns of insulin secretion. Approximately three quarters were appropriately responsive to stimuli, but one quarter were dysfunctional, with unstable basal insulin secretion and/or an impairment in stimulated insulin secretion. Importantly, the patterns of insulin secretion by responsive human islet preparations (stable Baseline and Fold stimulation of insulin secretion) isolated at different centers were similar and improved slightly over the years studied. When all preparations studied were considered, basal and stimulated insulin secretion did not correlate with isolation center, biological differences of the islet donor, or differences in isolation, such as Cold Ischemia Time. Dysfunctional islet preparations could not be predicted from the information provided by the isolation center and had altered expression of genes encoding components of the glucose-sensing pathway, but not of insulin production or cell death. These results indicate that insulin secretion by most preparations from multiple centers is similar but that in vitro responsiveness of human islets cannot be predicted, necessitating preexperimental human islet assessment. These results should be considered when one is designing, interpreting, and integrating experiments using human islets.
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16 MeSH Terms