1
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Johann DJ, Shin IJ, Roberge A, Laun S, Peterson EA, Liu M, Steliga MA, Muesse J, Emmert-Buck MR, Tangrea MA. Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples. J Histochem Cytochem 2022; 70:643-658. [PMID: 36129255 PMCID: PMC9527476 DOI: 10.1369/00221554221124163] [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: 05/25/2021] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Immunohistochemical (IHC) staining is an established technique for visualizing proteins in tissue sections for research studies and clinical applications. IHC is increasingly used as a targeting strategy for procurement of labeled cells via tissue microdissection, including immunodissection, computer-aided laser dissection (CALD), expression microdissection (xMD), and other techniques. The initial antigen retrieval (AR) process increases epitope availability and improves staining characteristics; however, the procedure can damage DNA. To better understand the effects of AR on DNA quality and quantity in immunodissected samples, both clinical specimens (KRAS gene mutation positive cases) and model system samples (lung cancer patient-derived xenograft tissue) were subjected to commonly employed AR methods (heat induced epitope retrieval [HIER], protease digestion) and the effects on DNA were assessed by Qubit, fragment analysis, quantitative PCR, digital droplet PCR (ddPCR), library preparation, and targeted sequencing. The data showed that HIER resulted in optimal IHC staining characteristics, but induced significant damage to DNA, producing extensive fragmentation and decreased overall yields. However, neither of the AR methods combined with IHC prevented ddPCR amplification of small amplicons and gene mutations were successfully identified from immunodissected clinical samples. The results indicate for the first time that DNA recovered from immunostained slides after standard AR and IHC processing can be successfully employed for genomic mutation analysis via ddPCR and next-generation sequencing (NGS) short-read methods.
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Affiliation(s)
- Donald J. Johann
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Ik Jae Shin
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Sarah Laun
- Avoneaux Medical Institute, Baltimore,
Maryland
- Alvin & Lois Lapidus Cancer Institute,
Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, Maryland
| | - Erich A. Peterson
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Meei Liu
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Matthew A. Steliga
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jason Muesse
- Winthrop P. Rockefeller Cancer Institute,
University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Michael A. Tangrea
- Alvin & Lois Lapidus Cancer Institute,
Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, Maryland
- Biology Department, Loyola University
Maryland, Baltimore, Maryland
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2
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Baldelli E, Mandarano M, Bellezza G, Petricoin EF, Pierobon M. Analysis of neuroendocrine clones in NSCLCs using an immuno-guided laser-capture microdissection-based approach. CELL REPORTS METHODS 2022; 2:100271. [PMID: 36046628 PMCID: PMC9421534 DOI: 10.1016/j.crmeth.2022.100271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/03/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Clonal evolution and lineage plasticity are key contributors to tumor heterogeneity and response to treatment in cancer. However, capturing signal transduction events in coexisting clones remains challenging from a technical perspective. In this study, we developed and tested a signal-transduction-based workflow to isolate and profile coexisting clones within a complex cellular system like non-small cell lung cancers (NSCLCs). Cooccurring clones were isolated under immunohistochemical guidance using laser-capture microdissection, and cell signaling activation portraits were measured using the reverse-phase protein microarray. To increase the translational potential of this work and capture druggable vulnerabilities within different clones, we measured expression/activation of a panel of key drug targets and downstream substrates of FDA-approved or investigational agents. We isolated intermixed clones, including poorly represented ones (<5% of cells), within the tumor microecology and identified molecular characteristics uniquely attributable to cancer cells that undergo lineage plasticity and neuroendocrine transdifferentiation in NSCLCs.
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Affiliation(s)
- Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Martina Mandarano
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Guido Bellezza
- Department of Medicine and Surgery, Section of Anatomic Pathology and Histology, University of Perugia, Perugia, Italy
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
- School of Systems Biology, George Mason University, Manassas, VA, USA
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3
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Mazzarella G, Iacomino G, Luca PD, Iaquinto S, Fabiana C, Troncone R, Aufiero VR. Cell-type-specific gene expression profile by laser capture microdissection on mirror sections. J Immunol Methods 2022; 505:113276. [PMID: 35476945 DOI: 10.1016/j.jim.2022.113276] [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: 12/21/2021] [Revised: 03/29/2022] [Accepted: 04/20/2022] [Indexed: 11/27/2022]
Abstract
Immuno-laser capture microdissection (Immuno-LCM) has been used to analyze cell-specific gene expression profiles. However, the usefulness of such a technique is frequently limited by RNA degradation. We, therefore, developed a rapid protocol of LCM on mirror sections, which allows for preserving RNA integrity. With such a procedure, we investigated cell-type-specific gene expression of γδ intraepithelial lymphocytes (IELs) in untreated celiac disease (CD). An increase in TGF-β mRNA expression levels was observed in γδ + IELs compared to intestinal enterocytes (IEs), whereas anti-inflammatory IL-10 mRNA production from γδ + IELs was lower compared to IEs. In untreated CD patients, the production of anti-inflammatory cytokines by γδ + IELs is suggestive of a regulatory function, thus playing a critical role in limiting inflammation. This work underscores the importance of LCM on mirror sections as a valuable tool to perform cell-type-specific molecular analysis in tissue.
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Affiliation(s)
- Giuseppe Mazzarella
- Institute of Food Sciences, CNR, Avellino, Italy; Department of Translational Medical Science and E.L.F.I.D, University "Federico II" Napoli, Italy
| | | | - Pasquale De Luca
- Research Infrastructure for Marine Biological Resources Department, Stazione Zoologica Anton Dohrn, CAP80121 (NA) Villa Comunale, Italy
| | | | - Capuano Fabiana
- Gastroenterology Department, S. G. Moscati Hospital, Avellino, Italy
| | - Riccardo Troncone
- Department of Translational Medical Science and E.L.F.I.D, University "Federico II" Napoli, Italy
| | - Vera Rotondi Aufiero
- Institute of Food Sciences, CNR, Avellino, Italy; Department of Translational Medical Science and E.L.F.I.D, University "Federico II" Napoli, Italy.
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4
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Zhang X, Hu C, Huang C, Wei Y, Li X, Hu M, Li H, Wu J, Czajkowsky DM, Guo Y, Shao Z. Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection. Front Cell Dev Biol 2022; 10:853188. [PMID: 35399504 PMCID: PMC8990165 DOI: 10.3389/fcell.2022.853188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue, as local interactions precipitate intra-cellular events that often lead to changes in expression. However, our understanding of these processes in tissues, whether healthy or diseased, is limited at present owing to the difficulty in acquiring comprehensive transcriptional programs of spatially- and phenotypically-defined cells in situ. Here we present a robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved transcriptional programs with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues sufficient to resolve even isoforms. The protocol is optimized to protect the RNA with a small molecule inhibitor, the ribonucleoside vanadyl complex (RVC), which thereby enables the typical time-consuming immunostaining and laser capture steps of this procedure during which RNA is usually severely degraded in existing approaches. The efficacy of this approach is exemplified by the characterization of differentially expressed genes between the mouse small intestine lacteal cells at the tip versus the main capillary body, including those that function in sensing and responding to local environmental cues to stimulate intra-cellular signalling. With the extensive repertoire of specific antibodies that are presently available, our method provides an unprecedented capability for the analysis of transcriptional networks and signalling pathways during development, pathogenesis, and aging of specific cell types within native tissues.
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Affiliation(s)
- Xiaodan Zhang
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wei
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miaomiao Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M. Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Yan Guo
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
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5
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Zhang X, Wang Z, Zhang C, Li Y, Lu S, Steffens S, Mohanta S, Weber C, Habenicht A, Yin C. Laser Capture Microdissection-Based mRNA Expression Microarrays and Single-Cell RNA Sequencing in Atherosclerosis Research. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2419:715-726. [PMID: 35237997 DOI: 10.1007/978-1-0716-1924-7_43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A major goal of methodologies related to large scale gene expression analyses is to initiate comprehensive information on transcript signatures in single cells within the tissue's anatomy. Until now, this could be achieved in a stepwise experimental approach: (1) identify the majority of transcripts in a single cell (single cell transcriptome); (2) provide information on transcripts on multiple cell subtypes in a complex sample (cell heterogeneity); and (3) give information on each cell's spatial location within the tissue (zonation transcriptomics). Such genetic information will allow construction of functionally relevant gene expression maps of single cells of a given anatomically defined tissue compartment and thus pave the way for subsequent analyses, including their epigenetic modifications. Until today these aims have not been achieved in the area of cardiovascular disease research though steps toward these goals become apparent: laser capture microdissection (LCM)-based mRNA expression microarrays of atherosclerotic plaques were applied to gain information on local gene expression changes during disease progression, providing limited spatial resolution. Moreover, while LCM-derived tissue RNA extracts have been shown to be highly sensitive and covers a range of 10-16,000 genes per array/small amount of RNA, its original promise to isolate single cells from a tissue section turned out not to be practicable because of the inherent contamination of the cell's RNA of interest with RNA from neighboring cells. Many shortcomings of LCM-based analyses have been overcome using single-cell RNA sequencing (scRNA-seq) technologies though scRNA-seq also has several limitations including low numbers of transcripts/cell and the complete loss of spatial information. Here, we describe a protocol toward combining advantages of both techniques while avoiding their flaws.
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Affiliation(s)
- Xi Zhang
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany.
| | - Zhihua Wang
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Chuankai Zhang
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Yutao Li
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Shu Lu
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Sabine Steffens
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany
| | - Sarajo Mohanta
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany.,Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands.,Munich Cluster of Systems Neurology (SyNergy), Ludwig-Maximilians-University Munich, Munich, Germany
| | - Andreas Habenicht
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany
| | - Changjun Yin
- Institute for Cardiovascular Prevention (IPEK), Klinikum of the University of Munich (KUM), Ludwig-Maximilians-University (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany. .,Munich Cluster of Systems Neurology (SyNergy), Ludwig-Maximilians-University Munich, Munich, Germany.
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6
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Laser Capture Microdissection in the Spatial Analysis of Epigenetic Modifications in Skin: A Comprehensive Review. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4127238. [PMID: 35186184 PMCID: PMC8850045 DOI: 10.1155/2022/4127238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/29/2021] [Accepted: 12/24/2021] [Indexed: 12/15/2022]
Abstract
Each cell in the body contains an intricate regulation for the expression of its relevant DNA. While every cell in a multicellular organism contains identical DNA, each tissue-specific cell expresses a different set of active genes. This organizational property exists in a paradigm that is largely controlled by forces external to the DNA sequence via epigenetic regulation. DNA methylation and chromatin modifications represent some of the classical epigenetic modifications that control gene expression. Complex tissues like skin consist of heterogeneous cell types that are spatially distributed and mixed. Furthermore, each individual skin cell has a unique response to physiological and pathological cues. As such, it is difficult to classify skin tissue as homogenous across all cell types and across different environmental exposures. Therefore, it would be prudent to isolate targeted tissue elements prior to any molecular analysis to avoid a possibility of confounding the sample with unwanted cell types. Laser capture microdissection (LCM) is a powerful technique used to isolate a targeted cell group with extreme microscopic precision. LCM presents itself as a solution to tackling the problem of tissue heterogeneity in molecular analysis. This review will cover an overview of LCM technology, the principals surrounding its application, and benefits of its application to the newly defined field of epigenomics, in particular of cutaneous pathology. This presents a comprehensive review about LCM and its use in the spatial analysis of skin epigenetics. Within the realm of skin pathology, this ability to isolate tissues under specific environmental stresses, such as oxidative stress, allows a far more focused investigation.
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7
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Johann DJ, Laun S, Shin IJ, Weigman R, Stephens O, Roberge A, Liu M, Greisman V, Steliga M, Muesse J, Peterson E, Emmert-Buck MR, Tangrea MA. Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine. Methods Mol Biol 2022; 2394:93-107. [PMID: 35094324 DOI: 10.1007/978-1-0716-1811-0_7] [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: 06/14/2023]
Abstract
Improving the utilization of tumor tissue from diagnostic biopsies is an unmet medical need. This is especially relevant today in the rapidly evolving precision oncology field where tumor genotyping is often essential for the indication of many advanced and targeted therapies. National Comprehensive Cancer Network (NCCN) guidelines now mandate molecular testing for clinically actionable targets in certain malignancies. Utilizing advanced stage lung cancer as an example, an improved genotyping approach for solid tumors is possible. The strategy involves optimization of the microdissection process and analysis of a large number of identical target cells from formalin-fixed paraffin-embedded (FFPE) specimens sharing similar characteristics, in other words, single-cell subtype analysis. The shared characteristics can include immunostaining status, cell phenotype, and/or spatial location within a histological section. Synergy between microdissection and droplet digital PCR (ddPCR) enhances the molecular analysis. We demonstrate here a methodology that illustrates genotyping of a solid tumor from a small tissue biopsy sample in a time- and cost-efficient manner, using immunostain targeting as an example.
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Affiliation(s)
- Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah Laun
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Ik Jae Shin
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Robert Weigman
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Owen Stephens
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Adam Roberge
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
| | - Meeiyueh Liu
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Valerie Greisman
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA
- Biology Department, Loyola University Maryland, Baltimore, MD, USA
| | - Mathew Steliga
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jason Muesse
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Erich Peterson
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Michael A Tangrea
- Alvin & Lois Lapidus Cancer Institute, Sinai Hospital of Baltimore, LifeBridge Health, Baltimore, MD, USA.
- Biology Department, Loyola University Maryland, Baltimore, MD, USA.
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8
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Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G. Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Cancer Cell 2021; 39:1623-1642.e20. [PMID: 34739845 PMCID: PMC8861565 DOI: 10.1016/j.ccell.2021.10.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/06/2021] [Accepted: 10/15/2021] [Indexed: 12/15/2022]
Abstract
The mechanisms regulating exhaustion of tumor-infiltrating lymphocytes (TIL) and responsiveness to PD-1 blockade remain partly unknown. In human ovarian cancer, we show that tumor-specific CD8+ TIL accumulate in tumor islets, where they engage antigen and upregulate PD-1, which restrains their functions. Intraepithelial PD-1+CD8+ TIL can be, however, polyfunctional. PD-1+ TIL indeed exhibit a continuum of exhaustion states, with variable levels of CD28 costimulation, which is provided by antigen-presenting cells (APC) in intraepithelial tumor myeloid niches. CD28 costimulation is associated with improved effector fitness of exhausted CD8+ TIL and is required for their activation upon PD-1 blockade, which also requires tumor myeloid APC. Exhausted TIL lacking proper CD28 costimulation in situ fail to respond to PD-1 blockade, and their response may be rescued by local CTLA-4 blockade and tumor APC stimulation via CD40L.
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Affiliation(s)
- Jaikumar Duraiswamy
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Riccardo Turrini
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Aspram Minasyan
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - David Barras
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Isaac Crespo
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Alizée J Grimm
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Julia Casado
- Research Program of Systems Oncology, University of Helsinki, 00014 Helsinki, Finland
| | - Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Fabrizio Benedetti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Alexandre Wicky
- Center for Precision Oncology, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Kalliopi Ioannidou
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Wilson Castro
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Christopher Neal
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Amandine Moriot
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Stéphanie Renaud-Tissot
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Victor Anstett
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Noémie Fahr
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Janos L Tanyi
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monika A Eiva
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connor A Jacobson
- Harvard Ludwig Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Lana E Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Department of Oncology, UNIL, 1011 Lausanne, Switzerland
| | - Peter K Sorger
- Harvard Ludwig Center, Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Anniina Färkkilä
- Research Program of Systems Oncology, University of Helsinki, 00014 Helsinki, Finland; Department of Obstetrics and Gynecology, Helsinki University Hospital, 00014 Helsinki, Finland
| | - Olivier Michielin
- Center for Precision Oncology, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Santiago J Carmona
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Periklis G Foukas
- 2nd Department of Pathology, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Daniel J Powell
- Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sylvie Rusakiewicz
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, CHUV, 1011 Lausanne, Switzerland
| | - Marie-Agnès Doucey
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Denarda Dangaj Laniti
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland.
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9
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Armingol E, Officer A, Harismendy O, Lewis NE. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet 2021; 22:71-88. [PMID: 33168968 PMCID: PMC7649713 DOI: 10.1038/s41576-020-00292-x] [Citation(s) in RCA: 445] [Impact Index Per Article: 148.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 12/13/2022]
Abstract
Cell-cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein-protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand-receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell-cell interactions from transcriptomic data and review the methods and tools used in this context.
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Affiliation(s)
- Erick Armingol
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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10
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Eggeling F, Hoffmann F. Microdissection—An Essential Prerequisite for Spatial Cancer Omics. Proteomics 2020; 20:e2000077. [DOI: 10.1002/pmic.202000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ferdinand Eggeling
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
| | - Franziska Hoffmann
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
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11
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Ji Y, Yu C, Zhang H. contamDE-lm: linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples. Bioinformatics 2020; 36:2492-2499. [PMID: 31917401 DOI: 10.1093/bioinformatics/btaa006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 11/30/2019] [Accepted: 01/03/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Tumor and adjacent normal RNA samples are commonly used to screen differentially expressed genes between normal and tumor samples or among tumor subtypes. Such paired-sample design could avoid numerous confounders in differential expression (DE) analysis, but the cellular contamination of tumor samples can be an important noise and confounding factor, which can both inflate false-positive rate and deflate true-positive rate. The existing DE tools that use next-generation RNA-seq data either do not account for cellular contamination or are computationally extensive with increasingly large sample size. RESULTS A novel linear model was proposed to avoid the problem that could arise from tumor-normal correlation for paired samples. A statistically robust and computationally very fast DE analysis procedure, contamDE-lm, was developed based on the novel model to account for cellular contamination, boosting DE analysis power through the reduction in individual residual variances using gene-wise information. The desired advantages of contamDE-lm over some state-of-the-art methods (limma and DESeq2) were evaluated through the applications to simulated data, TCGA database and Gene Expression Omnibus (GEO) database. AVAILABILITY AND IMPLEMENTATION The proposed method contamDE-lm was implemented in an updated R package contamDE (version 2.0), which is freely available at https://github.com/zhanghfd/contamDE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yifan Ji
- Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China
| | - Chang Yu
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Hong Zhang
- Department of Statistics and Finance, School of Management, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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12
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Qin Y, Tang T, Li W, Liu Z, Yang X, Shi X, Sun G, Liu X, Wang M, Liang X, Cong P, Mo D, Liu X, Chen Y, He Z. Bone Morphogenetic Protein 15 Knockdown Inhibits Porcine Ovarian Follicular Development and Ovulation. Front Cell Dev Biol 2019; 7:286. [PMID: 31803742 PMCID: PMC6877722 DOI: 10.3389/fcell.2019.00286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/04/2019] [Indexed: 12/21/2022] Open
Abstract
Bone morphogenetic protein 15 (BMP15) is strongly associated with animal reproduction and woman reproductive disease. As a multifunctional oocyte-specific secret factor, BMP15 controls female fertility and follicular development in both species-specific and dosage-sensitive manners. Previous studies found that BMP15 played a critical role in follicular development and ovulation rate in mono-ovulatory mammalian species, especially in sheep and human, but study on knockout mouse model implied that BMP15 possibly has minimal impact on female fertility of poly-ovulatory species. However, this needs to be validated in other poly-ovulatory species. To investigate the regulatory role of BMP15 on porcine female fertility, we generated a BMP15-knockdown pig model through somatic nuclear transfer technology. The BMP15-knockdown gilts showed markedly reduced fertility accompanied by phenotype of dysplastic ovaries containing significantly declined number of follicles, increased number of abnormal follicles, and abnormally enlarged antral follicles resulting in disordered ovulation, which is remarkably different from the unchanged fertility observed in BMP15 knockout mice. Molecular and transcriptome analysis revealed that the knockdown of BMP15 significantly affected both granulosa cells (GCs) and oocytes development, including suppression of cell proliferation, differentiation, and follicle stimulating hormone receptor (Fshr) expression, leading to premature luteinization and reduced estradiol (E2) production in GCs, and simultaneously decreased quality and meiotic maturation of oocyte. Our results provide in vivo evidence of the essential role of BMP15 in porcine ovarian and follicular development, and new insight into the complicated regulatory function of BMP15 in female fertility of poly-ovulatory species.
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Affiliation(s)
- Yufeng Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tao Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhiguo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoliang Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Guanjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiqing Cong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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13
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Transcriptome variation in human populations and its potential application in forensics. J Appl Genet 2019; 60:319-328. [PMID: 31401728 PMCID: PMC6803616 DOI: 10.1007/s13353-019-00510-1] [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: 04/14/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 12/04/2022]
Abstract
This review presents the state-of-the-art in the forensic application of genetic methods driven by the research in population transcriptomics. In the first part of the review, the constraints of using classical genomic markers are shortly reviewed. In the second part, the developments in the field of inter-population diversity at the transcriptomic level are presented. Subsequently, a potential of population-specific transcriptomic markers in forensic science applications, including ascertaining population affiliation of human samples and cell mixtures separation, are presented.
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14
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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: 17] [Impact Index Per Article: 3.4] [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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15
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Singh S, Wang L, Schaff DL, Sutcliffe MD, Koeppel AF, Kim J, Onengut-Gumuscu S, Park KS, Zong H, Janes KA. In situ 10-cell RNA sequencing in tissue and tumor biopsy samples. Sci Rep 2019; 9:4836. [PMID: 30894605 PMCID: PMC6426952 DOI: 10.1038/s41598-019-41235-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 03/04/2019] [Indexed: 12/11/2022] Open
Abstract
Single-cell transcriptomic methods classify new and existing cell types very effectively, but alternative approaches are needed to quantify the individual regulatory states of cells in their native tissue context. We combined the tissue preservation and single-cell resolution of laser capture with an improved preamplification procedure enabling RNA sequencing of 10 microdissected cells. This in situ 10-cell RNA sequencing (10cRNA-seq) can exploit fluorescent reporters of cell type in genetically engineered mice and is compatible with freshly cryoembedded clinical biopsies from patients. Through recombinant RNA spike-ins, we estimate dropout-free technical reliability as low as ~250 copies and a 50% detection sensitivity of ~45 copies per 10-cell reaction. By using small pools of microdissected cells, 10cRNA-seq improves technical per-cell reliability and sensitivity beyond existing approaches for single-cell RNA sequencing (scRNA-seq). Detection of low-abundance transcripts by 10cRNA-seq is comparable to random 10-cell groups of scRNA-seq data, suggesting no loss of gene recovery when cells are isolated in situ. Combined with existing approaches to deconvolve small pools of cells, 10cRNA-seq offers a reliable, unbiased, and sensitive way to measure cell-state heterogeneity in tissues and tumors.
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Affiliation(s)
- Shambhavi Singh
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lixin Wang
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Dylan L Schaff
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Matthew D Sutcliffe
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Alex F Koeppel
- Bioinformatics Core, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jungeun Kim
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Kwon-Sik Park
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Hui Zong
- Department of Microbiology, Immunology & Cancer Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Kevin A Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, 22908, USA.
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16
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Himmel LE, Hackett TA, Moore JL, Adams WR, Thomas G, Novitskaya T, Caprioli RM, Zijlstra A, Mahadevan-Jansen A, Boyd KL. Beyond the H&E: Advanced Technologies for in situ Tissue Biomarker Imaging. ILAR J 2018; 59:51-65. [PMID: 30462242 PMCID: PMC6645175 DOI: 10.1093/ilar/ily004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/27/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023] Open
Abstract
For decades, histopathology with routine hematoxylin and eosin staining has been and remains the gold standard for reaching a morphologic diagnosis in tissue samples from humans and veterinary species. However, within the past decade, there has been exponential growth in advanced techniques for in situ tissue biomarker imaging that bridge the divide between anatomic and molecular pathology. It is now possible to simultaneously observe localization and expression magnitude of multiple protein, nucleic acid, and molecular targets in tissue sections and apply machine learning to synthesize vast, image-derived datasets. As these technologies become more sophisticated and widely available, a team-science approach involving subspecialists with medical, engineering, and physics backgrounds is critical to upholding quality and validity in studies generating these data. The purpose of this manuscript is to detail the scientific premise, tools and training, quality control, and data collection and analysis considerations needed for the most prominent advanced imaging technologies currently applied in tissue sections: immunofluorescence, in situ hybridization, laser capture microdissection, matrix-assisted laser desorption ionization imaging mass spectrometry, and spectroscopic/optical methods. We conclude with a brief overview of future directions for ex vivo and in vivo imaging techniques.
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Affiliation(s)
- Lauren E Himmel
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Troy A Hackett
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Jessica L Moore
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Wilson R Adams
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Giju Thomas
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Tatiana Novitskaya
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Richard M Caprioli
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Andries Zijlstra
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Anita Mahadevan-Jansen
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
| | - Kelli L Boyd
- Lauren E. Himmel, DVM, PhD, is an assistant professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee. Troy A. Hackett, PhD, is a professor in the Department of Hearing and Speech Sciences at Vanderbilt University Medical Center in Nashville, Tennessee. Jessica L. Moore, PhD, is a postdoctoral research fellow in the Mass Spectrometry Research Center at the Vanderbilt University School of Medicine in Nashville, Tennessee. Wilson R. Adams, BS, is graduate student in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Giju Thomas, PhD, is a post-doctoral researcher in the Biophotonics Center and Department of Biomedical Engineering at Vanderbilt University in Nashville, Tennessee. Tatiana Novitskaya, MD, PhD, is a staff scientist in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center. Richard M. Caprioli, PhD, is a professor in the Department of Chemistry at the Vanderbilt University School of Medicine in Nashville, Tennessee. Andries Zijlstra, PhD, is an associate professor in the Department of Pathology, Microbiology and Immunology at Vanderbilt University Medical Center in Nashville, Tennessee. Anita Mahadevan-Jansen, PhD, is a professor in the Department of Biomedical Engineering at the Vanderbilt University School of Engineering and Department of Neurosurgery at Vanderbilt University Medical Center in Nashville, Tennessee. Kelli L. Boyd, DVM, PhD, is a professor and veterinary pathologist in the Division of Comparative Medicine at Vanderbilt University Medical Center in Nashville, Tennessee
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Mo MS, Li GH, Sun CC, Huang SX, Wei L, Zhang LM, Zhou MM, Wu ZH, Guo WY, Yang XL, Chen CJ, Qu SG, He JX, Xu PY. Dopaminergic neurons show increased low-molecular-mass protein 7 activity induced by 6-hydroxydopamine in vitro and in vivo. Transl Neurodegener 2018; 7:19. [PMID: 30128145 PMCID: PMC6097308 DOI: 10.1186/s40035-018-0125-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/30/2018] [Indexed: 02/08/2023] Open
Abstract
Background Abnormal expression of major histocompatibility complex class I (MHC-I) is increased in dopaminergic (DA) neurons in the substantia nigra (SN) in Parkinson’s disease (PD). Low-molecular-mass protein 7 (β5i) is a proteolytic subunit of the immunoproteasome that regulates protein degradation and the MHC pathway in immune cells. Methods In this study, we investigated the role of β5i in DA neurons using a 6-hydroxydopamine (6-OHDA) model in vitro and vivo. Results We showed that 6-OHDA upregulated β5i expression in DA neurons in a concentration- and time-dependent manner. Inhibition and downregulation of β5i induced the expression of glucose-regulated protein (Bip) and exacerbated 6-OHDA neurotoxicity in DA neurons. The inhibition of β5i further promoted the activation of Caspase 3-related pathways induced by 6-OHDA. β5i also activated transporter associated with antigen processing 1 (TAP1) and promoted MHC-I expression on DA neurons. Conclusion Taken together, our data suggest that β5i is activated in DA neurons under 6-OHDA treatment and may play a neuroprotective role in PD. Electronic supplementary material The online version of this article (10.1186/s40035-018-0125-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-Shu Mo
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Gui-Hua Li
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Cong-Cong Sun
- 2Department of Neurology, Qilu Hospital of Shandong University, Jinan, 250012 Shandong China
| | - Shu-Xuan Huang
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Lei Wei
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Li-Min Zhang
- 3Department of Neurology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080 Guangdong China
| | - Miao-Miao Zhou
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Zhuo-Hua Wu
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Wen-Yuan Guo
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Xin-Ling Yang
- 4Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumchi, 830011 Xinjiang China
| | - Chao-Jun Chen
- Clinic Brain Center, Guangzhou Hospital of Integrated Traditional and Western Medicine, Guangzhou, 510800 Guangdong China
| | - Shao-Gang Qu
- 6Department of Blood Transfusion, Fifth Affiliated Hospital Southern Medical University, Guangzhou, 510900 Guangdong China
| | - Jian-Xing He
- 7Department of Thoracic Surgery, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China
| | - Ping-Yi Xu
- 1Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120 Guangdong China.,4Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumchi, 830011 Xinjiang China
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18
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Guo ZH, Zhang W, Jia YYS, Liu QX, Li ZF, Lin JS. An Insight into the Difficulties in the Discovery of Specific Biomarkers of Limbal Stem Cells. Int J Mol Sci 2018; 19:ijms19071982. [PMID: 29986467 PMCID: PMC6073450 DOI: 10.3390/ijms19071982] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
Keeping the integrity and transparency of the cornea is the most important issue to ensure normal vision. There are more than 10 million patients going blind due to the cornea diseases worldwide. One of the effective ways to cure corneal diseases is corneal transplantation. Currently, donations are the main source of corneas for transplantation, but immune rejection and a shortage of donor corneas are still serious problems. Graft rejection could cause transplanted cornea opacity to fail. Therefore, bioengineer-based corneas become a new source for corneal transplantation. Limbal stem cells (LSCs) are located at the basal layer in the epithelial palisades of Vogt, which serve a homeostatic function for the cornea epithelium and repair the damaged cornea. LSC-based transplantation is one of the hot topics currently. Clinical data showed that the ratio of LSCs to total candidate cells for a transplantation has a significant impact on the effectiveness of the transplantation. It indicates that it is very important to accurately identify the LSCs. To date, several putative biomarkers of LSCs have been widely reported, whereas their specificity is controversial. As reported, the identification of LSCs is based on the characteristics of stem cells, such as a nuclear-to-cytoplasm ratio (N/C) ≥ 0.7, label-retaining, and side population (SP) phenotype. Here, we review recently published data to provide an insight into the circumstances in the study of LSC biomarkers. The particularities of limbus anatomy and histochemistry, the limits of the current technology level for LSC isolation, the heterogeneity of LSCs and the influence of enzyme digestion are discussed. Practical approaches are proposed in order to overcome the difficulties in basic and applied research for LSC-specific biomarkers.
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Affiliation(s)
- Zhi Hou Guo
- School of Medicine, Huaqiao University, Quanzhou 362021, China.
| | - Wei Zhang
- School of Medicine, Huaqiao University, Quanzhou 362021, China.
| | | | - Qing Xiu Liu
- School of Medicine, Huaqiao University, Quanzhou 362021, China.
| | - Zhao Fa Li
- School of Medicine, Huaqiao University, Quanzhou 362021, China.
| | - Jun Sheng Lin
- School of Medicine, Huaqiao University, Quanzhou 362021, China.
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19
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Laser capture microdissection for transcriptomic profiles in human skin biopsies. BMC Mol Biol 2018; 19:7. [PMID: 29921228 PMCID: PMC6009967 DOI: 10.1186/s12867-018-0108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 06/11/2018] [Indexed: 01/08/2023] Open
Abstract
Background The acquisition of reliable tissue-specific RNA sequencing data from human skin biopsy represents a major advance in research. However, the complexity of the process of isolation of specific layers from fresh-frozen human specimen by laser capture microdissection, the abundant presence of skin nucleases and RNA instability remain relevant methodological challenges. We developed and optimized a protocol to extract RNA from layers of human skin biopsies and to provide satisfactory quality and amount of mRNA sequencing data. Results The protocol includes steps of collection, embedding, freezing, histological coloration and relative optimization to preserve RNA extracted from specific components of fresh-frozen human skin biopsy of 14 subjects. Optimization of the protocol includes a preservation step in RNALater® Solution, the control of specimen temperature, the use of RNase Inhibitors and the time reduction of the staining procedure. The quality of extracted RNA was measured using the percentage of fragments longer than 200 nucleotides (DV200), a more suitable measurement for successful library preparation than the RNA Integrity Number (RIN). RNA was then enriched using the TruSeq® RNA Access Library Prep Kit (Illumina®) and sequenced on HiSeq® 2500 platform (Illumina®). Quality control on RNA sequencing data was adequate to get reliable data for downstream analysis. Conclusions The described implemented and optimized protocol can be used for generating transcriptomics data on skin tissues, and it is potentially applicable to other tissues. It can be extended to multicenter studies, due to the introduction of an initial step of preservation of the specimen that allowed the shipment of biological samples. Electronic supplementary material The online version of this article (10.1186/s12867-018-0108-5) contains supplementary material, which is available to authorized users.
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20
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Goldstein NB, Koster MI, Hoaglin LG, Wright MJ, Robinson SE, Robinson WA, Roop DR, Norris DA, Birlea SA. Isolating RNA from precursor and mature melanocytes from human vitiligo and normal skin using laser capture microdissection. Exp Dermatol 2018; 25:805-11. [PMID: 27193292 DOI: 10.1111/exd.13072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2016] [Indexed: 12/14/2022]
Abstract
To characterize the gene expression profile of regenerated melanocytes in the narrow band UVB (NBUVB)-treated vitiligo epidermis and their precursors in the hair follicle, we present here a strategy of RNA isolation from in situ melanocytes using human frozen skin. We developed a rapid immunostaining protocol using the NKI-beteb antibody, which labels differentiated and precursor melanocytes, followed by fluorescent laser capture microdissection. This technique enabled the direct isolation, from melanocyte and adjacent keratinocyte populations, of satisfactory quality RNA that was successfully amplified and analysed by qRT-PCR. The melanocyte-specific gene transcripts TYR, DCT, TYRP1 and PMEL were significantly upregulated in our NBUVB-treated melanocyte samples as compared with the keratinocyte samples, while keratinocyte-specific genes (KRT5 and KRT14) were expressed significantly higher in the keratinocyte samples as compared with the melanocyte samples. Furthermore, in both NBUVB-treated vitiligo skin and normal skin, when bulge melanocytes were compared with epidermal melanocytes, we found significantly lower expression of melanocyte-specific genes and significantly higher expression of three melanocytic stem cell genes (SOX9, WIF1 and SFRP1), while ALCAM and ALDH1A1 transcripts did not show significant variation. We found significantly higher expression of melanocyte-specific genes in the epidermis of NBUVB-treated vitiligo, as compared to the normal skin. When comparing bulge melanocyte samples from untreated vitiligo, NBUVB-treated vitiligo and normal skin, we did not find significant differences in the expression of melanocyte-specific genes or melanocytic stem cell genes. These techniques offer valuable opportunities to study melanocytes and their precursors in vitiligo and other pigmentation disorders.
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Affiliation(s)
- Nathaniel B Goldstein
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Maranke I Koster
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Charles C. Gates Center for Regenerative Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Laura G Hoaglin
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Charles C. Gates Center for Regenerative Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michael J Wright
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Steven E Robinson
- Department of Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - William A Robinson
- Department of Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis R Roop
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Charles C. Gates Center for Regenerative Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David A Norris
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Charles C. Gates Center for Regenerative Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Stanca A Birlea
- Department of Dermatology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Abstract
Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 µm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue. The on-chip reaction was validated by mRNA fluorescence in situ hybridization (mFISH) from cells in the tissue section. The entire process, from tissue loading on microchip to results from RT-LAMP can be carried out in less than 2 h. We anticipate that this technique, with its ease of use, fast turnaround, and quantitative molecular outputs, would become an invaluable tissue analysis tool for researchers and clinicians in the biomedical arena. Spatial localization of genetic information is important for tissue heterogeneity but difficult to capture with current analytical techniques. Here the authors present “Pixelated RT-LAMP”, an approach that uses parallel on-chip reactions to provide the distribution of target sequences directly from tissue.
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22
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Laser Microdissection Workflow for Isolating Nucleic Acids from Fixed and Frozen Tissue Samples. Methods Mol Biol 2018; 1723:33-93. [PMID: 29344854 DOI: 10.1007/978-1-4939-7558-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Laser Capture Microdissection has earned a permanent place among modern techniques connecting histology and molecular biology. Laser Capture Microdissection has become an invaluable tool in medical research as a means for collection of specific cell populations isolated from their environment. Such genomic sample enrichment dramatically increases the sensitivity and precision of downstream molecular assays used for biomarker discovery, monitoring disease onset and progression, and in the development of personalized medicine. The diversity of research targets (cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, frozen tissues, archival repository slides, etc.) and scientific objectives present a challenge in establishing standard protocols for Laser Capture Microdissection. In the present chapter, we share our experiences in design and successful execution of numerous diverse microdissection projects, and provide considerations to be taken into account in planning a microdissection study. Our workflow and protocols are standardized for a wide range of animal and human tissues and adapted to downstream analysis platforms.
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23
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Bevilacqua C, Ducos B. Laser microdissection: A powerful tool for genomics at cell level. Mol Aspects Med 2017; 59:5-27. [PMID: 28927943 DOI: 10.1016/j.mam.2017.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022]
Abstract
Laser microdissection (LM) has become widely democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i.e. analysis of biomolecules at the cell level. In spite of the advances these rapidly developing methods have allowed, the workflow for sampling and collection by LM remains a critical step in insuring sample integrity in terms of histology (accurate cell identification) and biochemistry (reliable analyzes of biomolecules). In this review, we describe the sample processing as well as the strengths and limiting factors of LM applied to the specific selection of one or more cells of interest from a heterogeneous tissue. We will see how the latest developments in protocols and methods have made LM a powerful and sometimes essential tool for genomic and proteomic analyzes of tiny amounts of biomolecules extracted from few cells isolated from a complex tissue, in their physiological context, thus offering new opportunities for understanding fundamental physiological and/or patho-physiological processes.
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Affiliation(s)
- Claudia Bevilacqua
- GABI, Plateforme @BRIDGE, INRA, AgroParisTech, Université Paris-Saclay, Domaine de Vilvert, 78350 Jouy en Josas, France.
| | - Bertrand Ducos
- LPS-ENS, CNRS UMR 8550, UPMC, Université Denis Diderot, PSL Research University, 24 Rue Lhomond, 75005 Paris France; High Throughput qPCR Core Facility, IBENS, 46 Rue d'Ulm, 75005 Paris France; Laser Microdissection Facility of Montagne Sainte Geneviève, CIRB Collège de France, Place Marcellin Berthelot, 75005 Paris France.
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24
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Podgorny OV, Lazarev VN. Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts. J Microbiol Methods 2017; 138:82-92. [PMID: 26775287 DOI: 10.1016/j.mimet.2016.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/11/2015] [Accepted: 01/01/2016] [Indexed: 12/14/2022]
Abstract
Laser microdissection is a method that allows for the isolation of homogenous cell populations from their native niches in tissues for downstream molecular assays. This method is widely used for genomic analysis, gene expression profiling and proteomic and metabolite assays in various fields of biology, but it remains an uncommon approach in microbiological research. In spite of the limited number of publications, laser microdissection was shown to be an extremely useful method for studying host-microorganism interactions in animals and plants, investigating bacteria within biofilms, identifying uncultivated bacteria and performing single prokaryotic cell analysis. The current paper describes the methodological aspects of commercially available laser microdissection instruments and representative examples that demonstrate the advantages of this method for resolving a variety of issues in microbiology.
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Affiliation(s)
- Oleg V Podgorny
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str., Moscow 119435, Russia; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 26 Vavilov Str., Moscow 119334, Russia.
| | - Vassili N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 1a Malaya Pirogovskaya Str., Moscow 119435, Russia
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25
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Chen Gonzalez E, McGee JS. Research Techniques Made Simple: Laser Capture Microdissection in Cutaneous Research. J Invest Dermatol 2017; 136:e99-e103. [PMID: 27664715 DOI: 10.1016/j.jid.2016.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In cutaneous research, we aim to study the molecular signature of a diseased tissue. However, such a study is met with obstacles due to the inherent heterogeneous nature of tissues because multiple cell types reside within a tissue. Furthermore, there is cellular communication between the tissue and the neighboring extracellular matrix. Laser capture microdissection is a powerful technique that allows researchers to isolate cells of interest from any tissue using a laser source under microscopic visualization, thereby circumventing the issue of tissue heterogeneity. Target cells from fixed preparations can be extracted and examined without disturbing the tissue structure. In live cultures, a subpopulation of cells can be extracted in real time with minimal disturbance of cellular communication and molecular signatures. Here we describe the basic principles of the technique, the different types of laser capture microdissection, and the subsequent downstream analyses. This article will also discuss how the technique has been employed in cutaneous research, as well as future directions.
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Affiliation(s)
- Estela Chen Gonzalez
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jean Suh McGee
- Department of Dermatology, Boston University School of Medicine, Boston, Massachusetts, USA.
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26
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Stiehl DP, Tritto E, Chibout SD, Cordier A, Moulin P. The Utility of Gene Expression Profiling from Tissue Samples to Support Drug Safety Assessments. ILAR J 2017; 58:69-79. [DOI: 10.1093/ilar/ilx016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 04/12/2017] [Indexed: 12/17/2022] Open
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Verckist L, Lembrechts R, Thys S, Pintelon I, Timmermans JP, Brouns I, Adriaensen D. Selective gene expression analysis of the neuroepithelial body microenvironment in postnatal lungs with special interest for potential stem cell characteristics. Respir Res 2017; 18:87. [PMID: 28482837 PMCID: PMC5422937 DOI: 10.1186/s12931-017-0571-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/01/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The pulmonary neuroepithelial body (NEB) microenvironment (ME) consists of innervated cell clusters that occur sparsely distributed in the airway epithelium, an organization that has so far hampered reliable selective gene expression analysis. Although the NEB ME has been suggested to be important for airway epithelial repair after ablation, little is known about their potential stem cell characteristics in healthy postnatal lungs. Here we report on a large-scale selective gene expression analysis of the NEB ME. METHODS A GAD67-GFP mouse model was used that harbors GFP-fluorescent NEBs, allowing quick selection and pooling by laser microdissection (LMD) without further treatment. A panel of stem cell-related PCR arrays was used to selectively compare mRNA expression in the NEB ME to control airway epithelium (CAE). For genes that showed a higher expression in the NEB ME, a ranking was made based on the relative expression level. Single qPCR and immunohistochemistry were used to validate and quantify the PCR array data. RESULTS Careful optimization of all protocols appeared to be essential to finally obtain high-quality RNA from pooled LMD samples of NEB ME. About 30% of the more than 600 analyzed genes showed an at least two-fold higher expression compared to CAE. The gene that showed the highest relative expression in the NEB ME, Delta-like ligand 3 (Dll3), was investigated in more detail. Selective Dll3 gene expression in the NEB ME could be quantified via single qPCR experiments, and Dll3 protein expression could be localized specifically to NEB cell surface membranes. CONCLUSIONS This study emphasized the importance of good protocols and RNA quality controls because of the, often neglected, fast RNA degradation in postnatal lung samples. It was shown that sufficient amounts of high-quality RNA for reliable complex gene expression analysis can be obtained from pooled LMD-collected NEB ME samples of postnatal lungs. Dll3 expression, which has also been reported to be important in high-grade pulmonary tumor-initiating cells, was used as a proof-of-concept to confirm that the described methodology represents a promising tool for further unraveling the molecular basis of NEB ME physiology in general, and its postnatal stem cell capacities in particular.
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Affiliation(s)
- Line Verckist
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Robrecht Lembrechts
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Inge Brouns
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium
| | - Dirk Adriaensen
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, BE-2610, Antwerpen, Wilrijk, Belgium.
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28
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Mallard J, Papazian E, Soulas C, Nolan DJ, Salemi M, Williams KC. A method for obtaining simian immunodeficiency virus RNA sequences from laser capture microdissected and immune captured CD68+ and CD163+ macrophages from frozen tissue sections of bone marrow and brain. J Immunol Methods 2017; 442:59-63. [PMID: 28093272 DOI: 10.1016/j.jim.2017.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 01/30/2023]
Abstract
Laser capture microdissection (LCM) is used to extract cells or tissue regions for analysis of RNA, DNA or protein. Several methods of LCM are established for different applications, but a protocol for consistently obtaining lentiviral RNA from LCM captured immune cell populations is not described. Obtaining optimal viral RNA for analysis of viral genes from immune-captured cells using immunohistochemistry (IHC) and LCM is challenging. IHC protocols have long antibody incubation times that increase risk of RNA degradation. But, immune capture of specific cell populations like macrophages without staining for virus cannot result in obtaining only a fraction of cells which are productively lentivirally infected. In this study we sought to obtain simian immunodeficiency virus (SIV) RNA from SIV gp120+ and CD68+ monocyte/macrophages in bone marrow (BM) and CD163+ perivascular macrophages in brain of SIV-infected rhesus macaques. Here, we report an IHC protocol with RNase inhibitors that consistently results in optimal quantity and yield of lentiviral RNA from LCM-captured immune cells.
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Affiliation(s)
- Jaclyn Mallard
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Emily Papazian
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Caroline Soulas
- Department of Biology, Boston College, Chestnut Hill, MA, USA; Department of Research and Development, Innate Pharma, Marseille, France
| | - David J Nolan
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Pathology Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
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29
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Saturno G, Pesenti M, Cavazzoli C, Rossi A, Giusti AM, Gierke B, Pawlak M, Venturi M. Expression of Serine/Threonine Protein-Kinases and Related Factors in Normal Monkey and Human Retinas: The Mechanistic Understanding of a CDK2 Inhibitor Induced Retinal Toxicity. Toxicol Pathol 2016; 35:972-83. [DOI: 10.1080/01926230701748271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Protein-kinase inhibitors are among the most advanced compounds in development using the new drug discovery paradigm of developing small-molecule drugs against specific molecular targets in cancer. After treatment with a cyclin dependent kinase CDK2 inhibitor in monkey, histopathological analysis of the eye showed specific cellular damage in the photoreceptor layer. Since this CDK2 inhibitor showed activity also on other CDKs, in order to investigate the mechanism of toxicity of this compound, we isolated cones and rods from the retina of normal monkey and humans by Laser Capture Microdissection. Using Real-Time PCR we first measured the expression of cyclin dependent protein-kinases (CDK)1, 2, 4, 5, Glycogen synthase kinase 3β (GSK3β) and microtubule associated protein TAU. We additionally verified the presence of these proteins in monkey eye sections by immunohistochemistry and immunofluorescence analysis and afterwards quantified GSK3β , phospho-GSK3β and TAU by Reverse Phase Protein Microarrays. With this work we demonstrate how complementary gene expression and protein-based technologies constitute a powerful tool for the understanding of the molecular mechanism of a CDK2 inhibitor induced toxicity. Moreover, this investigative approach is helpful to better understand and characterize the mechanism of species-specific toxicities and further support a rational, molecular mechanism-based safety assessment in humans.
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Affiliation(s)
- Grazia Saturno
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Manuela Pesenti
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Cristiano Cavazzoli
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Anna Rossi
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Anna M. Giusti
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
| | - Berthold Gierke
- Natural and Medical Sciences Institute (NMI), at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Michael Pawlak
- Natural and Medical Sciences Institute (NMI), at the University of Tuebingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Miro Venturi
- Nerviano Medical Sciences (NMS), Accelera, v.le Pasteur 10, 20014 Nerviano MI, Italy
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Sethi S, Chourasia D, Parhar IS. Approaches for targeted proteomics and its potential applications in neuroscience. J Biosci 2016; 40:607-27. [PMID: 26333406 DOI: 10.1007/s12038-015-9537-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other 'omics' approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.
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Affiliation(s)
- Sumit Sethi
- Brain Research Institute, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor Darul Ehsan, Malaysia,
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31
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Laser capture microdissection tailored to type 1 diabetes mellitus research. Biotechniques 2016; 60:293-8. [PMID: 27286806 DOI: 10.2144/000114426] [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] [Received: 07/25/2015] [Accepted: 03/03/2016] [Indexed: 11/23/2022] Open
Abstract
RNA isolation from pancreatic islets poses unique challenges. Here, we present a reproducible means of obtaining high-quality RNA from juvenile rodent islets in sufficient quantities for use in ex vivo expression studies. Tissue was extracted from female non-obese diabetic (NOD) toll-like receptor 3 (TLR3)(+/+) and (TLR3)(-/-) mice in the pre-diabetic stage. Samples were frozen in liquid nitrogen, sectioned, fixed in a highly alcoholic solution, and stained with an alcoholic cresyl violet (CV) solution. Rehydration of the fixed sections was minimized. Islets were identified visually and isolated with the Leica LMD6000 laser capture microdissection (LCM) system to yield samples highly enriched in islet RNA. Real time qPCR was performed on the islet cDNA using probes for CXC chemokine ligand 10 (CXCL10), an inflammatory marker that plays a critical role in the pathogenesis of type 1 diabetes mellitus (TIDM). This method represents an improvement over currently described LCM techniques for rodent pancreatic islets and makes feasible expression studies using small amounts of starting tissue without the need for RNA pre-amplification. This has immediate implications for ongoing TIDM studies using the NOD mouse.
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Butler AE, Matveyenko AV, Kirakossian D, Park J, Gurlo T, Butler PC. Recovery of high-quality RNA from laser capture microdissected human and rodent pancreas. J Histotechnol 2016; 39:59-65. [PMID: 27231405 DOI: 10.1080/01478885.2015.1106073] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Laser capture microdissection (LCM) is a powerful method to isolate specific populations of cells for subsequent analysis such as gene expression profiling, for example, microarrays or ribonucleic (RNA)-Seq. This technique has been applied to frozen as well as formalin-fixed, paraffin-embedded (FFPE) specimens with variable outcomes regarding quality and quantity of extracted RNA. The goal of the study was to develop the methods to isolate high-quality RNA from islets of Langerhans and pancreatic duct glands (PDG) isolated by LCM. We report an optimized protocol for frozen sections to minimize RNA degradation and maximize recovery of expected transcripts from the samples using quantitative real-time polymerase chain reaction (RT-PCR) by adding RNase inhibitors at multiple steps during the experiment. This technique reproducibly delivered intact RNA (RIN values 6-7). Using quantitative RT-PCR, the expected profiles of insulin, glucagon, mucin6 (Muc6), and cytokeratin-19 (CK-19) mRNA in PDGs and pancreatic islets were detected. The described experimental protocol for frozen pancreas tissue might also be useful for other tissues with moderate to high levels of intrinsic ribonuclease (RNase) activity.
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Affiliation(s)
- Alexandra E Butler
- Larry L. Hillblom Islet Research Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Aleksey V Matveyenko
- Larry L. Hillblom Islet Research Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA ; Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| | - David Kirakossian
- Larry L. Hillblom Islet Research Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Johanna Park
- Larry L. Hillblom Islet Research Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Tatyana Gurlo
- Larry L. Hillblom Islet Research Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Peter C Butler
- Larry L. Hillblom Islet Research Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA ; Jonsson Comprehensive Cancer Center, University of California Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA
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Hoshino K, Chung H, Wu CH, Rajendran K, Huang YY, Chen P, Sokolov KV, Kim J, Zhang JXJ. An Immunofluorescence-Assisted Microfluidic Single Cell Quantitative Reverse Transcription Polymerase Chain Reaction Analysis of Tumour Cells Separated from Blood. J Circ Biomark 2015; 4:11. [PMID: 28936247 PMCID: PMC5572989 DOI: 10.5772/61822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/01/2015] [Indexed: 12/26/2022] Open
Abstract
Circulating tumour cells (CTCs) are important indicators of metastatic cancer and may provide critical information for individualized treatment. As CTCs are usually very rare, the techniques to obtain information from very small numbers of cells are crucial. Here, we propose a method to perform a single cell quantitative reverse transcription polymerase chain reaction (qPCR) analysis of rare tumour cells. We utilized a microfluidic immunomagnetic assay to separate cancer cells from blood. A combination of detailed immunofluorescence and laser microdissection enabled the precise selection of individual cells. Cancer cells that were spiked into blood were successfully separated and picked up for a single cell PCR analysis. The breast cancer cell lines MCF7, SKBR3 and MDAMB231 were tested with 10 different genes. The result of the single cell analysis matched the results from a few thousand cells. Some markers (e.g., ER, HER2) that are commonly used for cancer identification showed relatively large deviations in expression levels. However, others (e.g., GRB7) showed deviations that are small enough to supplement single cell disease profiling.
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Affiliation(s)
- Kazunori Hoshino
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA
| | - HaeWon Chung
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Chun-Hsien Wu
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Kaarthik Rajendran
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yu-Yen Huang
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Peng Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Konstantin V Sokolov
- Department of Imaging Physics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - John X J Zhang
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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Datta S, Malhotra L, Dickerson R, Chaffee S, Sen CK, Roy S. Laser capture microdissection: Big data from small samples. Histol Histopathol 2015; 30:1255-69. [PMID: 25892148 PMCID: PMC4665617 DOI: 10.14670/hh-11-622] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Any tissue is made up of a heterogeneous mix of spatially distributed cell types. In response to any (patho) physiological cue, responses of each cell type in any given tissue may be unique and cannot be homogenized across cell-types and spatial co-ordinates. For example, in response to myocardial infarction, on one hand myocytes and fibroblasts of the heart tissue respond differently. On the other hand, myocytes in the infarct core respond differently compared to those in the peri-infarct zone. Therefore, isolation of pure targeted cells is an important and essential step for the molecular analysis of cells involved in the progression of disease. Laser capture microdissection (LCM) is powerful to obtain a pure targeted cell subgroup, or even a single cell, quickly and precisely under the microscope, successfully tackling the problem of tissue heterogeneity in molecular analysis. This review presents an overview of LCM technology, the principles, advantages and limitations and its down-stream applications in the fields of proteomics, genomics and transcriptomics. With powerful technologies and appropriate applications, this technique provides unprecedented insights into cell biology from cells grown in their natural tissue habitat as opposed to those cultured in artificial petri dish conditions.
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Affiliation(s)
- Soma Datta
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Lavina Malhotra
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Ryan Dickerson
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Scott Chaffee
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Chandan K Sen
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Sashwati Roy
- Department of Surgery, Center for Regenerative Medicine and Cell Based Therapies and Comprehensive Wound Center, Laser Capture Molecular Core, The Ohio State University Wexner Medical Center, Columbus, Ohio, 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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Omar E. Future Imaging Alternatives: The Clinical Non-invasive Modalities in Diagnosis of Oral Squamous Cell Carcinoma (OSCC). Open Dent J 2015; 9:311-8. [PMID: 26464601 PMCID: PMC4598385 DOI: 10.2174/1874210601509010311] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 12/15/2014] [Accepted: 05/25/2015] [Indexed: 01/08/2023] Open
Abstract
Background : Oral squamous cell carcinoma (OSCC) has a remarkably high incidence worldwide, and a fairly serious prognosis. This is encouraging further research into advanced technologies for non-invasive methods of making early diagnoses, ideally in primary care settings. Method : In this article, the available objective Non-imaging methods for diagnosing OSCC have been reviewed. MEDLINE, EMBASE, the Cochrane Library, and CINAHL have been searched for advanced technologies of non-invasive methods in diagnosis of OSCC, including oral brush biopsy, optical biopsy, saliva-based oral cancer diagnosis and others. Results : Toluidine blue, one of the oldest non-invasive methods for diagnosing OSCC, is unreliable because of its subjectivity, as it is dependent on the experience of the examiner. The diagnosis of Oral carcinoma by Oral brush biopsy with exfoliative cytology based on nano-bio-chip sensor platform shows 97–100% sensitivity and 86% specificity. Another promising non-invasive technique for OSCC diagnosis is saliva-based oral cancer diagnosis, which is an alternative to serum testing. Optical biopsy, which uses the technology of spectroscopy, can be used to detect changes at a sub-cellular level; thus, it provides information that may not be available with conventional histology with reliable sensitivity and specificity. Conclusion : It is clearly evident that screening and early effective detection of cancer and pre-cancerous lesions have the potential to reduce the morbidity and mortality of this disease. The imaging technologies are subjective procedures since all of them require interpretation and significantly affected by the examiner experience. These make further research for advanced objective procedures. Saliva-based oral cancer diagnosis and optical biopsy are promising objective non-invasive methods for diagnosing OSCC. They are easy to perform clinically at primary care set. They show promising pathways for future development of more effective method for the diagnosis of OSCC.
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Affiliation(s)
- Esam Omar
- Department of Oral & Maxillofacial Surgery, College of Dentistry, Taibah University, Saudi Arabia
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Benner S, Kakeyama M, Endo T, Yoshioka W, Tohyama C. Application of NeuroTrace staining in the fresh frozen brain samples to laser microdissection combined with quantitative RT-PCR analysis. BMC Res Notes 2015; 8:252. [PMID: 26092293 PMCID: PMC4473849 DOI: 10.1186/s13104-015-1222-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 06/04/2015] [Indexed: 12/27/2022] Open
Abstract
Background The heterogeneity of the brain requires appropriate molecular biological approaches to account for its morphological complexity. Laser-assisted microdissection followed by transcript profiling by quantitative determination has been reported to be an optimal methodology. Nevertheless, not all brain regions can be identified easily without staining, restricting the accuracy and efficiency in sampling. The aim of the present study was to validate whether fixation and staining treatments are suitable for quantitative transcript expression analysis in laser microdissection (LMD) samples. Quantitative RT-PCR was used to determine the absolute transcript expression levels and profiles of samples obtained from the hippocampal dentate gyrus from fresh frozen mice brain sections that had been fixed with ethanol and stained with NeuroTrace. The results were compared with those obtained from unfixed and unstained samples. Results We found that the quantitative relationship of transcript expression levels between various housekeeping genes and immediate early genes was preserved, although the preparation compromised the yield of the transcripts. In addition, histological and molecular integrities of the fixed and stained specimens were preserved for at least a week at room temperature. Based on the lobe specific profiles of transcripts in the anterior and posterior lobes of the pituitary, we confirmed that no cross-contamination on transcription expressions occurred as a result of the fixation and staining. Conclusions We have provided detailed information of the procedures on ethanol fixation followed by NeuroTrace staining on the absolute quantitative RT-PCR analysis using microdissected fresh frozen mouse brain tissues. The present study demonstrated that quantitative transcript expression analysis can be conducted reliably on stained tissues. This method is suitable for applications in basic and clinical studies on particular transcript expressions in various regions of the brain. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1222-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seico Benner
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masaki Kakeyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Dept. Neurobiol. and Behav. Grad. Sch. Biomed. Sci, Nagasaki University, Nagasaki, Japan.
| | - Toshihiro Endo
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Wataru Yoshioka
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Department of Pathophysiology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan.
| | - Chiharu Tohyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Environmental Biology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
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Oh SY, Lee HT. Efficiency of EGFR mutation analysis for small microdissected cytological specimens using multitech DNA extraction solution. Cancer Cytopathol 2015; 123:401-12. [PMID: 25964184 DOI: 10.1002/cncy.21550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/23/2015] [Accepted: 03/31/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND The microdissection method has greatly facilitated the isolation of pure cell populations for accurate analysis of mutations. However, the absence of coverslips in these preparations leads to poor resolution of cellular morphological features. In the current study, the authors developed the MultiTech DNA extraction solution to improve the visualization of cell morphology for microdissection and tested it for the preservation of morphological properties of cells, quality of DNA, and ability to detect mutations. METHODS A total of 121 cytological samples, including fine-needle aspirates, sputum, pleural fluid, and bronchial washings, were selected from hospital archives. DNA extracted from microdissected cells was evaluated by epidermal growth factor receptor (EGFR) mutation analysis using pyrosequencing, Sanger sequencing, and peptide nucleic acid (PNA)-mediated real-time polymerase chain reaction clamping. Morphological features of cells as well as DNA quality and quantity were analyzed in several cytological samples to assess the performance of the MultiTech DNA extraction solution. The results were compared with previous EGFR mutation tests. RESULTS The MultiTech DNA extraction solution improved the morphology of archived stained cells before microdissection and provided a higher DNA yield than the commercial QIAamp DNA Mini Kit in samples containing a minimal number of cells (25-50 cells). The authors were able to detect identical EGFR mutations by using different analysis platforms and consistently identified these mutations in samples comprising as few as 25 microdissected cells. CONCLUSIONS The MultiTech DNA extraction solution is a reliable medium that improves the resolution of cell morphology during microdissection. It was particularly useful in EGFR mutations of samples containing a small number of cells.
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Affiliation(s)
- Seo Young Oh
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea
| | - Hoon Taek Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Konkuk University, Seoul, Korea
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Li Y, Li W, Ying Z, Tian H, Zhu X, Li J, Li M. Metastatic heterogeneity of breast cancer cells is associated with expression of a heterogeneous TGFβ-activating miR424-503 gene cluster. Cancer Res 2014; 74:6107-18. [PMID: 25164015 DOI: 10.1158/0008-5472.can-14-0389] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
TGFβ signaling is known to drive metastasis in human cancer. Under physiologic conditions, the level of TGFβ activity is tightly controlled by a regulatory network involving multiple negative regulators. At metastasis, however, these inhibitory mechanisms are usually overridden so that oncogenic TGFβ signaling can be overactivated and sustained. To better understand how the TGFβ inhibitors are suppressed in metastatic breast cancer cells, we compared miRNA expression profiles between breast cancers with or without metastasis and found that the miR424-503 cluster was markedly overexpressed in metastatic breast cancer. Mechanistic studies revealed that miR424 and miR503 simultaneously suppressed Smad7 and Smurf2, two key inhibitory factors of TGFβ signaling, leading to enhanced TGFβ signaling and metastatic capability of breast cancer cells. Moreover, antagonizing miR424-503 in breast cancer cells suppressed metastasis in vivo and increased overall host survival. Interestingly, our study also found that heterogeneous expression of the miR424-503 cluster contributed to the heterogeneity of TGFβ activity levels in, and metastatic potential of, breast cancer cell subsets. Overall, our findings demonstrate a novel mechanism, mediated by elevated expression of the miR424-503 cluster, underlying TGFβ activation and metastasis of human breast cancer.
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Affiliation(s)
- Yun Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China
| | - Wei Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China
| | - Zhe Ying
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China
| | - Han Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China
| | - Xun Zhu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China
| | - Jun Li
- Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China. Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Mengfeng Li
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China. Key Laboratory of Tropical Disease Control (Sun Yat-Sen University), Chinese Ministry of Education, Guangzhou, Guangdong, China.
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MARIS: method for analyzing RNA following intracellular sorting. PLoS One 2014; 9:e89459. [PMID: 24594682 PMCID: PMC3940959 DOI: 10.1371/journal.pone.0089459] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/22/2014] [Indexed: 11/21/2022] Open
Abstract
Transcriptional profiling is a key technique in the study of cell biology that is limited by the availability of reagents to uniquely identify specific cell types and isolate high quality RNA from them. We report a Method for Analyzing RNA following Intracellular Sorting (MARIS) that generates high quality RNA for transcriptome profiling following cellular fixation, intracellular immunofluorescent staining and FACS. MARIS can therefore be used to isolate high quality RNA from many otherwise inaccessible cell types simply based on immunofluorescent tagging of unique intracellular proteins. As proof of principle, we isolate RNA from sorted human embryonic stem cell-derived insulin-expressing cells as well as adult human β cells. MARIS is a basic molecular biology technique that could be used across several biological disciplines.
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Torres Mena JE, Sánchez Rodríguez R, Quintanar Jurado V, Mojica Espinosa R, Del Pozo Yauner L, Meléndez Zajgla J, Villa Treviño S, Pérez Carreón JI. Laser capture microdissection after γ-glutamyl transferase histochemistry: An optimization for gene expression analysis. Anal Biochem 2014; 447:126-32. [DOI: 10.1016/j.ab.2013.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/08/2013] [Accepted: 11/11/2013] [Indexed: 11/16/2022]
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Legres LG, Janin A, Masselon C, Bertheau P. Beyond laser microdissection technology: follow the yellow brick road for cancer research. Am J Cancer Res 2014; 4:1-28. [PMID: 24482735 PMCID: PMC3902229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/25/2013] [Indexed: 06/03/2023] Open
Abstract
Normal biological tissues harbour different populations of cells with intricate spacial distribution patterns resulting in heterogeneity of their overall cellular composition. Laser microdissection involving direct viewing and expertise by a pathologist, enables access to defined cell populations or specific region on any type of tissue sample, thus selecting near-pure populations of targeted cells. It opens the way for molecular methods directed towards well-defined populations, and provides also a powerful tool in studies focused on a limited number of cells. Laser microdissection has wide applications in oncology (diagnosis and research), cellular and molecular biology, biochemistry and forensics for tissue selection, but other areas have been gradually opened up to these new methodological approaches, such as cell cultures and cytogenetics. In clinical oncology trials, molecular profiling of microdissected samples can yield global "omics" information which, together, with the morphological analysis of cells, can provide the basis for diagnosis, prognosis and patient-tailored treatments. This remarkable technology has brought new insights in the understanding of DNA, RNA, and the biological functions and regulation of proteins to identify molecular disease signatures. We review herein the different applications of laser microdissection in a variety of fields, and we particularly focus attention on the pre-analytical steps that are crucial to successfully perform molecular-level investigations.
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Affiliation(s)
- Luc G Legres
- Inserm UMR_S1165, Institut Universitaire d’HématologieParis
- Université Paris-DiderotParis
| | - Anne Janin
- Inserm UMR_S1165, Institut Universitaire d’HématologieParis
- Université Paris-DiderotParis
- AP-HP, Hôpital Saint-Louis, Service de PathologieParis
| | - Christophe Masselon
- CEA, iRTSV/Laboratoire de Biologie à Grande EchelleGrenoble
- Inserm UMR_S 1038Grenoble
| | - Philippe Bertheau
- Inserm UMR_S1165, Institut Universitaire d’HématologieParis
- Université Paris-DiderotParis
- AP-HP, Hôpital Saint-Louis, Service de PathologieParis
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Hashimoto A, Matsui T, Tanaka S, Ishikawa A, Endo H, Hirohata S, Kondo H, Neumann E, Tarner IH, Müller-Ladner U. Laser-mediated microdissection for analysis of gene expression in synovial tissue. Mod Rheumatol 2014. [DOI: 10.3109/s10165-007-0564-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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The Outline of Prognosis and New Advances in Diagnosis of Oral Squamous Cell Carcinoma (OSCC): Review of the Literature. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/519312] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Objective. Oral squamous cell carcinoma (OSCC) has a remarkable incidence over the world and a fairly strenuous prognosis, encouraging further research on the prognostic factors and new techniques for diagnosis that might modify disease outcome. Data Sources. A web-based search for all types of articles published was initiated using Medline/Pub Med, with the key words such as oral cancer, prognostic factors of oral cancer, diagnostic method of oral cancer, and imaging techniques for diagnosis of oral cancer. The search was restricted to articles published in English, with no publication date restriction (last update April, 2013). Review Methods. In this paper, I approach the factors of prognosis of OSCC and the new advances in diagnostic technologies as well. I also reviewed available studies of the tissue fluorescence spectroscopy and other noninvasive diagnostic aids for OSCC. Results. The outcome is greatly influenced by the stage of the disease (especially TNM). Prognosis also depends or varies with tumour primary site, nodal involvement, tumour thickness, and the status of the surgical margins. Conclusion. Tumour diameter is not the most accurate when compared to tumour thickness or depth of invasion, which can be related directly to prognosis. There is a wide agreement on using ultrasound guided fine needle aspiration biopsies in the evaluation of lymph node metastasis.
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Priem EKV, Maeyer JHD, Vandewoestyne M, Deforce D, Lefebvre RA. Predominant mucosal expression of 5-HT4(+h) receptor splice variants in pig stomach and colon. World J Gastroenterol 2013; 19:3747-3760. [PMID: 23840113 PMCID: PMC3699052 DOI: 10.3748/wjg.v19.i24.3747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/21/2012] [Accepted: 12/17/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate cellular 5-HT4(-h/+h) receptor distribution, particularly in the epithelial layer, by laser microdissection and polymerase chain reaction (PCR) in porcine gastrointestinal (GI) tissues.
METHODS: A stepwise approach was used to evaluate RNA quality and to study cell-specific 5-HT4 receptor mRNA expression in the porcine gastric fundus and colon descendens. After freezing, staining and laser microdissection and pressure catapulting (LMPC), RNA quality was evaluated by the Experion automated electrophoresis system. 5-HT4 receptor and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) expressions were examined by endpoint reverse transcription (RT)-PCR in mucosal and muscle-myenteric plexus (MMP) tissue fractions, in mucosal and MMP parts of hematoxylin and eosin (HE) stained tissue sections and in microdissected patches of the epithelial and circular smooth muscle cell layer in these sections. Pig gastric fundus tissue sections were also stained immunohistochemically (IHC) for enterochromaffin cells (EC cells; MAB352); these cells were isolated by LMPC and examined by endpoint RT-PCR.
RESULTS: After HE staining, the epithelial and circular smooth muscle cell layer of pig colon descendens and the epithelial cell layer of gastric fundus were identified morphologically and isolated by LMPC. EC cells of pig gastric fundus were successfully stained by IHC and isolated by LMPC. Freezing, HE and IHC staining, and LMPC had no influence on RNA quality. 5-HT4 receptor and GAPDH mRNA expressions were detected in mucosa and MMP tissue fractions, and in mucosal and MMP parts of HE stained tissue sections of pig colon descendens and gastric fundus. In the mucosa tissue fractions of both GI regions, the expression of h-exon containing receptor [5-HT4(+h) receptor] mRNA was significantly higher (P < 0.01) compared to 5-HT4(-h) receptor expression, and a similar trend was obtained in the mucosal part of HE stained tissue sections. Large microdissected patches of the epithelial and circular smooth muscle cell layer of pig colon descendens and of the epithelial cell layer of pig gastric fundus, also showed 5-HT4 receptor and GAPDH mRNA expression. No 5-HT4 receptor mRNA expression was detected in gastric LMPC-isolated EC cells from IHC stained tissues, which cells were positive for GAPDH.
CONCLUSION: Porcine GI mucosa predominantly expresses 5-HT4(+h) receptor splice variants, suggesting their contribution to the 5-HT4 receptor-mediated mucosal effects of 5-HT.
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Santoro M, Masciullo M, Bonvissuto D, Bianchi MLE, Michetti F, Silvestri G. Alternative splicing of human insulin receptor gene (INSR) in type I and type II skeletal muscle fibers of patients with myotonic dystrophy type 1 and type 2. Mol Cell Biochem 2013; 380:259-65. [PMID: 23666741 DOI: 10.1007/s11010-013-1681-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/02/2013] [Indexed: 12/20/2022]
Abstract
INSR, one of those genes aberrantly expressed in myotonic dystrophy type 1 (DM1) and type 2 (DM2) due to a toxic RNA effect, encodes for the insulin receptor (IR). Its expression is regulated by alternative splicing generating two isoforms: IR-A, which predominates in embryonic tissue, and IR-B, which is highly expressed in adult, insulin-responsive tissues (skeletal muscle, liver, and adipose tissue). The aberrant INSR expression detected in DM1 and DM2 muscles tissues, characterized by a relative increase of IR-A versus IR-B, was pathogenically related to the insulin resistance occurring in DM patients. To assess if differences in the aberrant splicing of INSR could underlie the distinct fiber type involvement observed in DM1 and DM2 muscle tissues, we have used laser capture microdissection (LCM) and RT-PCR, comparing the alternative splicing of INSR in type I and type II muscle fibers isolated from muscle biopsies of DM1, DM2 patients and controls. In the controls, the relative amounts of IR-A and IR-B showed no obvious differences between type I and type II fibers, as in the whole muscle tissue. In DM1 and DM2 patients, both fiber types showed a similar, relative increase of IR-A versus IR-B, as also evident in the whole muscle tissue. Our data suggest that the distinct fiber type involvement in DM1 and DM2 muscle tissues would not be related to qualitative differences in the expression of INSR. LCM can represent a powerful tool to give a better understanding of the pathogenesis of myotonic dystrophies, as well as other myopathies.
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Boone DR, Sell SL, Hellmich HL. Laser capture microdissection of enriched populations of neurons or single neurons for gene expression analysis after traumatic brain injury. J Vis Exp 2013. [PMID: 23603738 PMCID: PMC3653564 DOI: 10.3791/50308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Long-term cognitive disability after TBI is associated with injury-induced neurodegeneration in the hippocampus-a region in the medial temporal lobe that is critical for learning, memory and executive function.1,2 Hence our studies focus on gene expression analysis of specific neuronal populations in distinct subregions of the hippocampus. The technique of laser capture microdissection (LCM), introduced in 1996 by Emmert-Buck, et al.,3 has allowed for significant advances in gene expression analysis of single cells and enriched populations of cells from heterogeneous tissues such as the mammalian brain that contains thousands of functional cell types.4 We use LCM and a well established rat model of traumatic brain injury (TBI) to investigate the molecular mechanisms that underlie the pathogenesis of TBI. Following fluid-percussion TBI, brains are removed at pre-determined times post-injury, immediately frozen on dry ice, and prepared for sectioning in a cryostat. The rat brains can be embedded in OCT and sectioned immediately, or stored several months at -80 °C before sectioning for laser capture microdissection. Additionally, we use LCM to study the effects of TBI on circadian rhythms. For this, we capture neurons from the suprachiasmatic nuclei that contain the master clock of the mammalian brain. Here, we demonstrate the use of LCM to obtain single identified neurons (injured and degenerating, Fluoro-Jade-positive, or uninjured, Fluoro-Jade-negative) and enriched populations of hippocampal neurons for subsequent gene expression analysis by real time PCR and/or whole-genome microarrays. These LCM-enabled studies have revealed that the selective vulnerability of anatomically distinct regions of the rat hippocampus are reflected in the different gene expression profiles of different populations of neurons obtained by LCM from these distinct regions. The results from our single-cell studies, where we compare the transcriptional profiles of dying and adjacent surviving hippocampal neurons, suggest the existence of a cell survival rheostat that regulates cell death and survival after TBI.
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Affiliation(s)
- Deborah R Boone
- Department of Anesthesiology, University of Texas Medical Branch, USA
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Levenson RM, Fornari A, Loda M. Multispectral imaging and pathology: seeing and doing more. ACTA ACUST UNITED AC 2013; 2:1067-81. [PMID: 23495926 DOI: 10.1517/17530059.2.9.1067] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The current appreciation of the biological complexity of disease has led to increasing demands on pathologists to provide clinically relevant, quantitative morphological and molecular information while preserving cellular and tissue context. This can be technically challenging, especially when signals of interest are colocalized. With fluorescence-based methods, sensitivity and quantitative reliability may be compromised by spectral cross-talk between labels and by autofluorescence. In brightfield microscopy, overlapping chromogenic signals pose similar imaging difficulties. APPROACH These challenges can be addressed using commercially available multispectral imaging technologies attached to standard microscope platforms, or alternatively, integrated into whole-slide scanning instruments. ASSESSMENT Multispectral techniques, along with other developments in digital analysis, will allow pathologists to deliver appropriate quantitative and multiplexed analyses in a reproducible and timely manner. Caveats apply - as the complexity of the sample preparation and analysis components increases, commensurate attention must be paid to the use of appropriate controls for all stages of the process.
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Affiliation(s)
- Richard M Levenson
- CRI, 35B Cabot Road, Woburn, MA 01801, USA +1 781 935 9099, ext. 204 ; +1 781 935 3388 ;
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Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells. Nat Protoc 2013; 8:282-301. [PMID: 23306461 DOI: 10.1038/nprot.2012.158] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Single-cell variations in gene and protein expression are important during development and disease. Such cell-to-cell heterogeneities can be directly inspected one cell at a time, but global methods are usually not sensitive enough to work with the starting material of a single cell. Here we provide a detailed protocol for stochastic profiling, a method that infers single-cell regulatory heterogeneities by repeatedly sampling small collections of cells selected at random. Repeated stochastic sampling is performed by laser-capture microdissection or limiting dilution, followed by careful exponential cDNA amplification, hybridization to microarrays and statistical analysis. Stochastic profiling surveys the transcriptome for programs that are heterogeneously regulated among cellular subpopulations in their native tissue context. The protocol is readily optimized for specific biological applications and takes about 1 week to complete.
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Rodriguez-Canales J, Hanson JC, Hipp JD, Balis UJ, Tangrea MA, Emmert-Buck MR, Bova GS. Optimal molecular profiling of tissue and tissue components: defining the best processing and microdissection methods for biomedical applications. Methods Mol Biol 2013; 980:61-120. [PMID: 23359150 DOI: 10.1007/978-1-62703-287-2_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Isolation of well-preserved pure cell populations is a prerequisite for sound studies of the molecular basis of any tissue-based biological phenomenon. This updated chapter reviews current methods for obtaining anatomically specific signals from molecules isolated from tissues, a basic requirement for productive linking of phenotype and genotype. The quality of samples isolated from tissue and used for molecular analysis is often glossed over or omitted from publications, making interpretation and replication of data difficult or impossible. Fortunately, recently developed techniques allow life scientists to better document and control the quality of samples used for a given assay, creating a foundation for improvement in this area. Tissue processing for molecular studies usually involves some or all of the following steps: tissue collection, gross dissection/identification, fixation, processing/embedding, storage/archiving, sectioning, staining, microdissection/annotation, and pure analyte labeling/identification and quantification. We provide a detailed comparison of some current tissue microdissection technologies and provide detailed example protocols for tissue component handling upstream and downstream from microdissection. We also discuss some of the physical and chemical issues related to optimal tissue processing and include methods specific to cytology specimens. We encourage each laboratory to use these as a starting point for optimization of their overall process of moving from collected tissue to high-quality, appropriately anatomically tagged scientific results. Improvement in this area will significantly increase life science quality and productivity. The chapter is divided into introduction, materials, protocols, and notes subheadings. Because many protocols are covered in each of these sections, information relating to a single protocol is not contiguous. To get the greatest benefit from this chapter, readers are advised to read through the entire chapter first, identify protocols appropriate to their laboratory for each step in their workflow, and then reread entries in each section pertaining to each of these single protocols.
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Affiliation(s)
- Jaime Rodriguez-Canales
- Laser Capture Microdissection (LCM) Core, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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