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Retinal Layer Separation (ReLayS) method enables the molecular analysis of photoreceptor segments and cell bodies, as well as the inner retina. Sci Rep 2022; 12:20195. [PMID: 36424523 PMCID: PMC9691741 DOI: 10.1038/s41598-022-24586-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding the physiology of the retina, and especially of the highly polarized photoreceptors, is essential not only to broaden our knowledge of the processes required for normal vision, but also to develop effective therapies to prevent or slow retinal degenerative diseases. However, the molecular analysis of photoreceptors is a challenge due to the heterogeneity of the retinal tissue and the lack of easy and reliable methods for cell separation. Here we present the ReLayS method-a simple technique for the separation of photoreceptor segments (PS) containing both inner and outer segments, outer nuclear layer (ONL), and inner retina (InR) that contains the remaining retinal layers. The layer-specific material isolated from a mouse half-retina with the ReLayS method was sufficient for protein isolation and Western blotting or RNA isolation and real-time PCR studies. The separation of PS, ONL, and InR was successfully validated by Western blotting and real-time PCR using proteins and genes with known expression profiles within the retina. Furthermore, the separation of the PS from the ONL enabled the detection of light-driven translocation of transducin from the PS to the soma. ReLayS is a simple and useful method to address protein and possibly metabolites distribution in photoreceptor compartments in various situations including development, ageing, and degenerative diseases.
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2
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Application of Label-Free Proteomics for Quantitative Analysis of Urothelial Carcinoma and Cystitis Tissue. Methods Mol Biol 2021; 2228:283-292. [PMID: 33950498 DOI: 10.1007/978-1-0716-1024-4_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A label-free approach based on a highly reproducible and stable workflow allows for quantitative proteome analysis . Due to advantages compared to labeling methods, the label-free approach has the potential to measure unlimited samples from clinical specimen monitoring and comparing thousands of proteins. The presented label-free workflow includes a new sample preparation technique depending on automatic annotation and tissue isolation via FTIR-guided laser microdissection, in-solution digestion, LC-MS/MS analyses, data evaluation by means of Proteome Discoverer and Progenesis software, and verification of differential proteins. We successfully applied this workflow in a proteomics study analyzing human cystitis and high-grade urothelial carcinoma tissue regarding the identification of a diagnostic tissue biomarker. The differential analysis of only 1 mm2 of isolated tissue cells led to 74 significantly differentially abundant proteins.
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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4
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MacDonald ML, Favo D, Garver M, Sun Z, Arion D, Ding Y, Yates N, Sweet RA, Lewis DA. Laser capture microdissection-targeted mass spectrometry: a method for multiplexed protein quantification within individual layers of the cerebral cortex. Neuropsychopharmacology 2019; 44:743-748. [PMID: 30390066 PMCID: PMC6372704 DOI: 10.1038/s41386-018-0260-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/17/2018] [Indexed: 11/09/2022]
Abstract
The mammalian neocortex is organized into layers distinguished by the size, packing density, and connectivity of their constituent neurons. Many neuropsychiatric illnesses are complex trait disorders with etiologic factors converging on neuronal protein networks. Cortical pathology of neuropsychiatric diseases, such as schizophrenia, is often restricted to, or more pronounced in, certain cortical layers, suggesting that genetic vulnerabilities manifest with laminar specificity. Thus, the ability to investigate cortical layer-specific protein levels in human postmortem brain is highly desirable. Here, we developed and validated a laser capture microdissection-mass spectrometry (LCM-MS) approach to quantify over 200 proteins in cortical layers 3 and 5 of two cohorts of human subjects as well as a monkey model of postmortem interval. LCM-MS was readily implementable and reliably identified protein patterns that differed between cortical layers 3 and 5. Our findings suggest that LCM-MS facilitates the precise quantification of proteins within individual cortical layers from human postmortem brain tissue, providing a powerful tool in the study of neuropsychiatric disease.
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Affiliation(s)
- Matthew L MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Daley Favo
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Megan Garver
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sun
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dominique Arion
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathan Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
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5
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Protocol for the Analysis of Laser Capture Microdissected Fresh-Frozen Tissue Homogenates by Silver-Stained 1D SDS-PAGE. Methods Mol Biol 2018; 1723:95-110. [PMID: 29344855 DOI: 10.1007/978-1-4939-7558-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The heterogeneity present in solid tumors adds significant difficulty to scientific analysis and improved understanding. Fundamentally, solid tumor formation consists of cancer cells proper along with stromal elements. The burgeoning malignant process is dependent upon modified stromal elements. Collectively, the stroma forms an essential microenvironment, which is indispensable for the survival and growth of the malignant neoplasm. This cellular heterogeneity makes molecular profiling of solid tumors via mass spectrometry (MS)-based proteomics a daunting task. Laser capture microdissection (LCM) is commonly used to obtain distinct histological cell types (e.g., tumor parenchymal cells, stromal cells) from tumor tissue and attempt to address the tumor heterogeneity interference with downstream liquid chromatography (LC) MS analysis. To provide optimal LC-MS analysis of micro-scale and/or nano-scale tissue sections, we modified and optimized a silver-stained one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) protocol for the LC-MS analysis of LCM-procured fresh-frozen tissue specimens. Presented is a detailed in-gel digestion protocol adjusted specifically to maximize the proteome coverage of amount-limited LCM samples, and facilitate in-depth molecular profiling. Following LCM, targeted tissue sections are further fractionated using silver-stained 1D-SDS-PAGE to resolve and visualize tissue proteins prior to in-gel digestion and subsequent LC-MS analysis.
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Combine Phage Antibody Display Library Selection on Patient Tissue Specimens with Laser Capture Microdissection to Identify Novel Human Antibodies Targeting Clinically Relevant Tumor Antigens. Methods Mol Biol 2018; 1701:331-347. [PMID: 29116514 DOI: 10.1007/978-1-4939-7447-4_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A functional approach to generate tumor-targeting human monoclonal antibodies is through selection of phage antibody display libraries directly on tumor cells. Although technically convenient, the use of cancer cell lines for the selection has limitations as those cell lines often undergo genetic and epigenetic changes during prolonged in vitro culture and alter their cell surface antigen expression profile. The key is to develop a technology that allows selection of phage antibody display libraries on tumor cells in situ residing in their natural tissue microenvironment. Laser capture microdissection (LCM) permits the precise procurement of tumor cells from human cancer patient tissue sections. Here, we describe a LCM-based method for selecting phage antibodies against tumor cells in situ using both fresh frozen and paraffin-embedded tissues. To restrict the selection to antibodies that bind internalizing epitopes, the method utilizes a polyclonal phage population pre-enriched for internalizing phage antibodies. The ability to recognize tumor cells in situ residing in their natural tissue microenvironment and to deliver payload intracellularly makes these LCM-selected antibodies attractive candidates for the development of targeted cancer therapeutics.
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Aring L, Steinbach S, Marcus K, May C. Isolation of Distinct Types of Neurons from Fresh Brain Tissue Using Laser Microdissection in Combination with High-Performance Liquid Chromatography-Mass Spectrometry. Methods Mol Biol 2018; 1723:247-260. [PMID: 29344865 DOI: 10.1007/978-1-4939-7558-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Humans age and the ageing process affects cells in all areas of the human body, including nerve cells within the brain. With advancing age there is also a rise in the probability of developing a neurodegenerative disorder such as, e.g., amyotrophic lateral sclerosis, Huntington's disease, Parkinson's disease, or Alzheimer's disease. In all these age-related neurodegenerative disorders, distinct neuron populations within specific brain regions are primarily affected. For example, Parkinson's disease is characterized by a slowly progressive degeneration of dopaminergic neurons in the substantia nigra whereas the entorhinal cortex is first affected in Alzheimer's disease. In patients suffering from Huntington's disease, neurons in both striatum and cortex undergo substantial cell loss and in amyotrophic lateral sclerosis the neurodegeneration arises from the spinal cord and the motor cortex. For the investigation of the differences in neuronal vulnerability, it is important to examine the protein expression pattern in these specific neural populations. By this, conclusions about the origination process of these diseases can be achieved. In order to obtain this objective, specific isolation of distinct neurons from the surrounding brain tissue is indispensable. However, discrimination as well as isolation of distinct types of neurons can be challenging, due to the brain tissue's complexity. With traditional methods such as the homogenization of tissue samples, a specific isolation of single neuron populations is not feasible because homogenization results into a mixture containing all cell types. Laser microdissection can overcome this technical limitation. First, this method enables visualization of tissues via a microscopic unit and therefore an enhanced discrimination of different brain cells. Second, a laser device guarantees a contact-free and consequently a contamination-free separation of distinct neurons from the surrounding brain tissue. In the following, we present a detailed protocol that includes a workflow for the isolation and analysis of neurons from freshly frozen post mortem human brain tissue samples. During this procedure, the brain tissue is sectioned, stained, laser microdissected, and ultimately analyzed by high-performance liquid chromatography-mass spectrometry.
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Affiliation(s)
- Luisa Aring
- Zentrum für Klinische Forschung I, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Simone Steinbach
- Zentrum für Klinische Forschung I, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Katrin Marcus
- Zentrum für Klinische Forschung I, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
| | - Caroline May
- Zentrum für Klinische Forschung I, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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Cabral T, Toral MA, Velez G, DiCarlo JE, Gore AM, Mahajan M, Tsang SH, Bassuk AG, Mahajan VB. Dissection of Human Retina and RPE-Choroid for Proteomic Analysis. J Vis Exp 2017. [PMID: 29155757 DOI: 10.3791/56203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The human retina is composed of the sensory neuroretina and the underlying retinal pigmented epithelium (RPE), which is firmly complexed to the vascular choroid layer. Different regions of the retina are anatomically and molecularly distinct, facilitating unique functions and demonstrating differential susceptibility to disease. Proteomic analysis of each of these regions and layers can provide vital insights into the molecular process of many diseases, including Age-Related Macular Degeneration (AMD), diabetes mellitus, and glaucoma. However, separation of retinal regions and layers is essential before quantitative proteomic analysis can be accomplished. Here, we describe a method for dissection and collection of the foveal, macular, and peripheral retinal regions and underlying RPE-choroid complex, involving regional punch biopsies and manual removal of tissue layers from a human eye.One-dimensional SDS-PAGE as well as downstream proteomic analysis, such as liquid chromatography-tandem mass spectrometry (LC-MS/MS), can be used to identify proteins in each dissected retinal layer, revealing molecular biomarkers for retinal disease.
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Affiliation(s)
- Thiago Cabral
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital; Department of Ophthalmology, Federal University of Sao Paulo (UNIFESP); Department of Ophthalmology, Federal University of EspÍrito Santo (UFES)
| | - Marcus A Toral
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University; Medical Scientist Training Program, University of Iowa
| | - Gabriel Velez
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University; Medical Scientist Training Program, University of Iowa
| | - James E DiCarlo
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital
| | - Anuradha M Gore
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University
| | - MaryAnn Mahajan
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University
| | - Stephen H Tsang
- Barbara & Donald Jonas Stem Cell Laboratory, and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Pathology & Cell Biology, Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University; Edward S. Harkness Eye Institute, New York-Presbyterian Hospital
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa; Department of Neurology, University of Iowa
| | - Vinit B Mahajan
- Omics Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University; Palo Alto Veterans Administration, Palo Alto, CA;
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Taverna D, Mignogna C, Gabriele C, Santise G, Donato G, Cuda G, Gaspari M. An optimized procedure for on-tissue localized protein digestion and quantification using hydrogel discs and isobaric mass tags: analysis of cardiac myxoma. Anal Bioanal Chem 2017; 409:2919-2930. [PMID: 28190108 DOI: 10.1007/s00216-017-0237-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/20/2017] [Accepted: 01/31/2017] [Indexed: 01/22/2023]
Abstract
An optimized workflow for multiplexed and spatially localized on-tissue quantitative protein analysis is here presented. The method is based on the use of an enzyme delivery platform, a polymeric hydrogel disc, allowing for a localized digestion directly onto the tissue surface coupled with an isobaric mass tag strategy for peptide labeling and relative quantification. The digestion occurs within such hydrogels, followed by peptide solvent extraction and identification by liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS). Since this is a histology-directed on-tissue analysis, multiple hydrogels were placed onto morphologically and spatially different regions of interest (ROIs) within the tissue surface, e.g., cardiac myxoma tumor vascularized region and the adjacent hypocellular area. After a microwave digestion step (2 min), enzymatically cleaved peptides were labeled using TMT reagents with isobaric mass tags, enabling analysis of multiple samples per experiment. Thus, N = 8 hydrogel-digested samples from cardiac myxoma serial tissue sections (N = 4 from the vascularized ROIs and N = 4 from the adjacent hypocellular areas) were processed and then combined before a single LC-MS/MS analysis. Regulated proteins from both cardiac myxoma regions were assayed in a single experiment. Graphical abstract The workflow for histology-guided on-tissue localized protein digestion followed by isobaric mass tagging and LC-MS/MS analysis for proteins quantification is here summarized.
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Affiliation(s)
- Domenico Taverna
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy.
| | - Chiara Mignogna
- Department of Health Science, Magna Graecia University of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Caterina Gabriele
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Gianluca Santise
- Cardiothoracic Surgery Unit, Sant'Anna Hospital, Via Pio X, 111, 88100, Catanzaro, Italy
| | - Giuseppe Donato
- Department of Health Science, Magna Graecia University of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Giovanni Cuda
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
| | - Marco Gaspari
- Research Center for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus "S. Venuta", Viale Europa, Loc. Germaneto, 88100, Catanzaro, Italy
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Cho WJ, Oliveira DSM, Najy AJ, Mainetti LE, Aoun HD, Cher ML, Heath E, Kim HRC, Bonfil RD. Gene expression analysis of bone metastasis and circulating tumor cells from metastatic castrate-resistant prostate cancer patients. J Transl Med 2016; 14:72. [PMID: 26975354 PMCID: PMC4791970 DOI: 10.1186/s12967-016-0829-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/05/2016] [Indexed: 01/15/2023] Open
Abstract
Background Characterization of genes linked to bone metastasis is critical for identification of novel prognostic or predictive biomarkers and potential therapeutic targets in metastatic castrate-resistant prostate cancer (mCRPC). Although bone marrow core biopsies (BMBx) can be obtained for gene profiling, the procedure itself is invasive and uncommon practice in mCRPC patients. Conversely, circulating tumor cells (CTCs), which are likely to stem from bone metastases, can be isolated from blood. The goals of this exploratory study were to establish a sensitive methodology to analyze gene expression in BMBx and CTCs, and to determine whether the presence or absence of detectable gene expression is concordant in matching samples from mCRPC patients. Methods The CellSearch® platform was used to enrich and enumerate CTCs. Low numbers of PC3 prostate cancer (PCa) cells were spiked into normal blood to assess cell recovery rate. RNA extracted from recovered PC3 cells was amplified using an Eberwine-based procedure to obtain antisense mRNA (aRNA), and assess the linearity of the RNA amplification method. In this pilot study, RNAs extracted from CTCs and PCa cells microdissected from formalin-fixed paraffin-embedded BMBx, were amplified to obtain aRNA and assess the expression of eight genes functionally relevant to PCa bone metastasis using RT-PCR. Results RNAs were successfully extracted from as few as 1–5 PCa cells in blood samples. The relative expression levels of reference genes were maintained after RNA amplification. The integrity of the amplified RNA was also demonstrated by RT-PCR analysis using primer sets that target the 5′-end, middle, and 3′-end of reference mRNA. We found that in 21 out of 28 comparisons, the presence or absence of detectable gene expression in CTCs and PCa cells microdissected from single bone lesions of the same patients was concordant. Conclusions This exploratory analysis suggests that aRNA amplification through in vitro transcription may be useful as a method to detect gene expression in small numbers of CTCs and tumor cells microdissected from bone metastatic lesions. In some cases, gene expression in CTCs and BMBxs was not concordant, raising questions about using CTC gene expression to make clinical decisions. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0829-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Won Jin Cho
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA
| | - Daniel S M Oliveira
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA
| | - Abdo J Najy
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Leandro E Mainetti
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA
| | - Hussein D Aoun
- Department of Radiology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Michael L Cher
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA.,Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Elisabeth Heath
- Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - Hyeong-Reh C Kim
- Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA
| | - R Daniel Bonfil
- Department of Urology, Wayne State University School of Medicine and Karmanos Cancer Institute, 540 E. Canfield, Scott Hall # 9105, Detroit, MI, 4820, USA. .,Department of Pathology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA. .,Department of Oncology, Wayne State University School of Medicine and Karmanos Cancer Institute, Detroit, MI, USA.
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11
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Stuart CA, Stone WL, Howell MEA, Brannon MF, Hall HK, Gibson AL, Stone MH. Myosin content of individual human muscle fibers isolated by laser capture microdissection. Am J Physiol Cell Physiol 2015; 310:C381-9. [PMID: 26676053 DOI: 10.1152/ajpcell.00317.2015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/10/2015] [Indexed: 12/12/2022]
Abstract
Muscle fiber composition correlates with insulin resistance, and exercise training can increase slow-twitch (type I) fibers and, thereby, mitigate diabetes risk. Human skeletal muscle is made up of three distinct fiber types, but muscle contains many more isoforms of myosin heavy and light chains, which are coded by 15 and 11 different genes, respectively. Laser capture microdissection techniques allow assessment of mRNA and protein content in individual fibers. We found that specific human fiber types contain different mixtures of myosin heavy and light chains. Fast-twitch (type IIx) fibers consistently contained myosin heavy chains 1, 2, and 4 and myosin light chain 1. Type I fibers always contained myosin heavy chains 6 and 7 (MYH6 and MYH7) and myosin light chain 3 (MYL3), whereas MYH6, MYH7, and MYL3 were nearly absent from type IIx fibers. In contrast to cardiomyocytes, where MYH6 (also known as α-myosin heavy chain) is seen solely in fast-twitch cells, only slow-twitch fibers of skeletal muscle contained MYH6. Classical fast myosin heavy chains (MHC1, MHC2, and MHC4) were present in variable proportions in all fiber types, but significant MYH6 and MYH7 expression indicated slow-twitch phenotype, and the absence of these two isoforms determined a fast-twitch phenotype. The mixed myosin heavy and light chain content of type IIa fibers was consistent with its role as a transition between fast and slow phenotypes. These new observations suggest that the presence or absence of MYH6 and MYH7 proteins dictates the slow- or fast-twitch phenotype in skeletal muscle.
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Affiliation(s)
- Charles A Stuart
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee;
| | - William L Stone
- Department of Pediatrics, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; and
| | - Mary E A Howell
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee
| | - Marianne F Brannon
- Department of Pediatrics, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; and
| | - H Kenton Hall
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee
| | - Andrew L Gibson
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee
| | - Michael H Stone
- Department of Exercise and Sport Science, Clemmer College of Education, East Tennessee State University, Johnson City, Tennessee
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12
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Taverna D, Pollins AC, Nanney LB, Sindona G, Caprioli RM. Histology-guided protein digestion/extraction from formalin-fixed and paraffin-embedded pressure ulcer biopsies. Exp Dermatol 2015; 25:143-6. [PMID: 26440596 DOI: 10.1111/exd.12870] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2015] [Indexed: 12/24/2022]
Abstract
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.
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Affiliation(s)
- Domenico Taverna
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata di Rende, Italy.,Mass Spectrometry Research Center, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Alonda C Pollins
- Department of Plastic Surgery, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Lillian B Nanney
- Department of Plastic Surgery, Vanderbilt School of Medicine, Nashville, TN, USA.,Department of Cell & Developmental Biology, Vanderbilt School of Medicine, Nashville, TN, USA
| | - Giovanni Sindona
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Arcavacata di Rende, Italy
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt School of Medicine, Nashville, TN, USA.,Department of Biochemistry, Vanderbilt School of Medicine, Nashville, TN, USA
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Frost AR, Eltoum I, Siegal GP, Emmert‐Buck MR, Tangrea MA. Laser Microdissection. ACTA ACUST UNITED AC 2015; 112:25A.1.1-25A.1.30. [DOI: 10.1002/0471142727.mb25a01s112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andra R. Frost
- Department of Pathology, University of Alabama at Birmingham Birmingham Alabama
| | - Isam‐Eldin Eltoum
- Department of Pathology, University of Alabama at Birmingham Birmingham Alabama
| | - Gene P. Siegal
- Department of Pathology, University of Alabama at Birmingham Birmingham Alabama
| | | | - Michael A. Tangrea
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital Baltimore Maryland
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Abstract
Reverse phase protein array (RPPA) technology evolved from the advent of miniaturized immunoassays and gene microarray technology. Reverse phase protein arrays provide either a low throughput or high throughput methodology for quantifying proteins and their post-translationally modified forms in both cellular and non-cellular samples. As the demand for patient tailored therapies increases so does the need for precise and sensitive technology to accurately profile the molecular circuitry driving an individual patient's disease. RPPAs are currently utilized in clinical trials for profiling and comparing the functional state of protein signaling pathways, either temporally within tumors, between patients, or within the same patients before/after treatment. RPPAs are generally employed for quantifying large numbers of samples on one array, under identical experimental conditions. However, the goal of personalized cancer medicine is to design therapies based on the molecular portrait of a patient's tumor, which in turn result in more efficacious treatments with less toxicity. Therefore, RPPAs are also being validated for low throughput assays of individual patient samples. This review explores RPPA technology in the cancer research field, concentrating on its role as a fundamental tool for deciphering protein signaling networks and its emerging role in personalized medicine.
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Cantor DI, Nice EC, Baker MS. Recent findings from the human proteome project: opening the mass spectrometry toolbox to advance cancer diagnosis, surveillance and treatment. Expert Rev Proteomics 2015; 12:279-93. [DOI: 10.1586/14789450.2015.1040770] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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16
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Unger C, Kramer N, Walzl A, Scherzer M, Hengstschläger M, Dolznig H. Modeling human carcinomas: physiologically relevant 3D models to improve anti-cancer drug development. Adv Drug Deliv Rev 2014; 79-80:50-67. [PMID: 25453261 DOI: 10.1016/j.addr.2014.10.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/02/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022]
Abstract
Anti-cancer drug development is inefficient, mostly due to lack of efficacy in human patients. The high fail rate is partly due to the lack of predictive models or the inadequate use of existing preclinical test systems. However, progress has been made and preclinical models were improved or newly developed, which all account for basic features of solid cancers, three-dimensionality and heterotypic cell interaction. Here we give an overview of available in vivo and in vitro models of cancer, which meet the criteria of being 3D and mirroring human tumor-stroma interactions. We only focus on drug response models without touching models for pharmacokinetic and dynamic, toxicity or delivery aspects.
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Taverna D, Norris JL, Caprioli RM. Histology-directed microwave assisted enzymatic protein digestion for MALDI MS analysis of mammalian tissue. Anal Chem 2014; 87:670-6. [PMID: 25427280 PMCID: PMC4287167 DOI: 10.1021/ac503479a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
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This study presents on-tissue proteolytic
digestion using a microwave
irradiation and peptide extraction method for in situ analysis of proteins from spatially defined regions of a tissue
section. The methodology utilizes hydrogel discs (1 mm diameter) embedded
with trypsin solution. The enzyme-laced hydrogel discs are applied
to a tissue section, directing enzymatic digestion to a spatially
confined area of the tissue. By applying microwave radiation, protein
digestion is performed in 2 min on-tissue, and the extracted peptides
are then analyzed by matrix assisted laser desorption/ionization mass
spectrometry (MALDI MS) and liquid chromatography tandem mass spectrometry
(LC-MS/MS). The reliability and reproducibility of the microwave assisted
hydrogel mediated on-tissue digestion is demonstrated by the comparison
with other on-tissue digestion strategies, including comparisons with
conventional heating and in-solution digestion. LC-MS/MS data were
evaluated considering the number of identified proteins as well as
the number of protein groups and distinct peptides. The results of
this study demonstrate that rapid and reliable protein digestion can
be performed on a single thin tissue section while preserving the
relationship between the molecular information obtained and the tissue
architecture, and the resulting peptides can be extracted in sufficient
abundance to permit analysis using LC-MS/MS. This approach will be
most useful for samples that have limited availability but are needed
for multiple analyses, especially for the correlation of proteomics
data with histology and immunohistochemistry.
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Affiliation(s)
- Domenico Taverna
- Department of Chemistry and Technological Chemistry, University of Calabria , Arcavacata di Rende, Cosenza 87036, Italy
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18
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Harris RA. Spatial, Temporal, and Functional Aspects of Macrophages during "The Good, the Bad, and the Ugly" Phases of Inflammation. Front Immunol 2014; 5:612. [PMID: 25520719 PMCID: PMC4253962 DOI: 10.3389/fimmu.2014.00612] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 11/13/2014] [Indexed: 12/14/2022] Open
Affiliation(s)
- Robert A Harris
- Applied Immunology and Immunotherapy, Department of Clinical Neurosciences, Karolinska Institutet, Karolinska Hospital , Stockholm , Sweden
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19
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Mateos J, Pernas PF, Labora JF, Blanco F, Arufe MDC. Proteomic Applications in the Study of Human Mesenchymal Stem Cells. Proteomes 2014; 2:53-71. [PMID: 28250369 PMCID: PMC5302726 DOI: 10.3390/proteomes2010053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/15/2014] [Accepted: 01/26/2014] [Indexed: 02/05/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are undifferentiated cells with an unlimited capacity for self-renewal and able to differentiate towards specific lineages under appropriate conditions. MSCs are, a priori, a good target for cell therapy and clinical trials as an alternative to embryonic stem cells, avoiding ethical problems and the chance for malignant transformation in the host. However, regarding MSCs, several biological implications must be solved before their application in cell therapy, such as safe ex vivo expansion and manipulation to obtain an extensive cell quantity amplification number for use in the host without risk accumulation of genetic and epigenetic abnormalities. Cell surface markers for direct characterization of MSCs remain unknown, and the precise molecular mechanisms whereby growth factors stimulate their differentiation are still missing. In the last decade, quantitative proteomics has emerged as a promising set of techniques to address these questions, the answers to which will determine whether MSCs retain their potential for use in cell therapy. Proteomics provides tools to globally analyze cellular activity at the protein level. This proteomic profiling allows the elucidation of connections between broad cellular pathways and molecules that were previously impossible to determine using only traditional biochemical analysis. However; thus far, the results obtained must be orthogonally validated with other approaches. This review will focus on how these techniques have been applied in the evaluation of MSCs for their future applications in safe therapies.
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Affiliation(s)
- Jesús Mateos
- Rheumatology Division, ProteoRed/ISCIII, INIBIC-Hospital Universitario A Coruña, A Coruña 15006, Spain.
| | - Pablo Fernández Pernas
- CIBER-BBN, INIBIC-Hospital Universitario A Coruña, A Coruña 15006, Spain.
- Department of Medicine, University of A Coruña, A Coruña 15006, Spain.
| | - Juan Fafián Labora
- CIBER-BBN, INIBIC-Hospital Universitario A Coruña, A Coruña 15006, Spain.
- Department of Medicine, University of A Coruña, A Coruña 15006, Spain.
| | - Francisco Blanco
- Rheumatology Division, ProteoRed/ISCIII, INIBIC-Hospital Universitario A Coruña, A Coruña 15006, Spain.
- CIBER-BBN, INIBIC-Hospital Universitario A Coruña, A Coruña 15006, Spain.
- Department of Medicine, University of Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - María Del Carmen Arufe
- CIBER-BBN, INIBIC-Hospital Universitario A Coruña, A Coruña 15006, Spain.
- Department of Medicine, University of A Coruña, A Coruña 15006, Spain.
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