1
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Wang X, Peng J, Cai P, Xia Y, Yi C, Shang A, Akanyibah FA, Mao F. The emerging role of the gut microbiota and its application in inflammatory bowel disease. Biomed Pharmacother 2024; 179:117302. [PMID: 39163678 DOI: 10.1016/j.biopha.2024.117302] [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: 06/19/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 08/22/2024] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a complex disorder with an unknown cause. However, the dysbiosis of the gut microbiome has been found to play a role in IBD etiology, including exacerbated immune responses and defective intestinal barrier integrity. The gut microbiome can also be a potential biomarker for several diseases, including IBD. Currently, conventional treatments targeting pro-inflammatory cytokines and pathways in IBD-associated dysbiosis do not yield effective results. Other therapies that directly target the dysbiotic microbiome for effective outcomes are emerging. We review the role of the gut microbiome in health and IBD and its potential as a diagnostic, prognostic, and therapeutic target for IBD. This review also explores emerging therapeutic advancements that target gut microbiome-associated alterations in IBD, such as nanoparticle or encapsulation delivery, fecal microbiota transplantation, nutritional therapies, microbiome/probiotic engineering, phage therapy, mesenchymal stem cells (MSCs), gut proteins, and herbal formulas.
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Affiliation(s)
- Xiu Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, China
| | - Jianhua Peng
- The People's Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu 212300, China
| | - Peipei Cai
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yuxuan Xia
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chengxue Yi
- School of Medical Technology, Zhenjiang College, Zhenjiang 212028, China
| | - Anquan Shang
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, China
| | - Francis Atim Akanyibah
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu 222006, China.
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2
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Zhou Y, Qi T, Yang Y, Li Z, Hou Z, Zhao X, Ge Q, Lu Z. Effect of Different Staining Methods on Brain Cryosections. ACS Chem Neurosci 2024; 15:2243-2252. [PMID: 38779816 DOI: 10.1021/acschemneuro.4c00069] [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: 05/25/2024] Open
Abstract
Staining frozen sections is often required to distinguish cell types for spatial transcriptomic studies of the brain. The impact of the staining methods on the RNA integrity of the cells becomes one of the limitations of spatial transcriptome technology with microdissection. However, there is a lack of systematic comparisons of different staining modalities for the pretreatment of frozen sections of brain tissue as well as their effects on transcriptome sequencing results. In this study, four different staining methods were analyzed for their effect on RNA integrity in frozen sections of brain tissue. Subsequently, differences in RNA quality in frozen sections under different staining conditions and their impact on transcriptome sequencing results were assessed by RNA-seq. As one of the most commonly used methods for staining pathological sections, HE staining seriously affects the RNA quality of frozen sections of brain tissue. In contrast, the homemade cresyl violet staining method developed in this study has the advantages of short staining time, low cost, and less RNA degradation. The homemade cresyl violet staining proposed in this study can be applied instead of HE staining as an advance staining step for transcriptome studies in frozen sections of brain tissue. In the future, this staining method may be suitable for wide application in brain-related studies of frozen tissue sections. Moreover, it is expected to become a routine step for staining cells before sampling in brain science.
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Affiliation(s)
- Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuwei Yang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhihui Li
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhuoran Hou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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3
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Romanens L, Chaskar P, Marcone R, Ryser S, Tille JC, Genolet R, Heimgartner-Hu K, Heimgartner K, Moore JS, Liaudet N, Kaya G, Pittet MJ, Dietrich PY, Delorenzi M, Speiser DE, Harari A, Tsantoulis P, Labidi-Galy SI. Clonal expansion of intra-epithelial T cells in breast cancer revealed by spatial transcriptomics. Int J Cancer 2023; 153:1568-1578. [PMID: 37306359 DOI: 10.1002/ijc.34620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 06/13/2023]
Abstract
The spatial distribution of tumor-infiltrating lymphocytes (TIL) predicts breast cancer outcome and response to systemic therapy, highlighting the importance of an intact tissue structure for characterizing tumors. Here, we present ST-FFPE, a spatial transcriptomics method for the analysis of formalin-fixed paraffin-embedded samples, which opens the possibility of interrogating archival tissue. The method involves extraction, exome capture and sequencing of RNA from different tumor compartments microdissected by laser-capture, and can be used to study the cellular composition of tumor microenvironment. Focusing on triple-negative breast cancer (TNBC), we characterized T cells, B cells, dendritic cells, fibroblasts and endothelial cells in both stromal and intra-epithelial compartments. We found a highly variable spatial distribution of immune cell subsets among tumors. This analysis revealed that the immune repertoires of intra-epithelial T and B cells were consistently less diverse and more clonal than those of stromal T and B cells. T-cell receptor (TCR) sequencing confirmed a reduced diversity and higher clonality of intra-epithelial T cells relative to the corresponding stromal T cells. Analysis of the top 10 dominant clonotypes in the two compartments showed a majority of shared but also some unique clonotypes both in stromal and intra-epithelial T cells. Hyperexpanded clonotypes were more abundant among intra-epithelial than stromal T cells. These findings validate the ST-FFPE method and suggest an accumulation of antigen-specific T cells within tumor core. Because ST-FFPE is applicable for analysis of previously collected tissue samples, it could be useful for rapid assessment of intratumoral cellular heterogeneity in multiple disease and treatment settings.
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Affiliation(s)
- Lou Romanens
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
| | - Prasad Chaskar
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
- Department of Oncology, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Rachel Marcone
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephan Ryser
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
| | - Jean-Christophe Tille
- Department of Diagnosis, Division of Clinical Pathology, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Raphael Genolet
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Ketty Heimgartner-Hu
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
| | - Killian Heimgartner
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
| | - Jonathan S Moore
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
| | - Nicolas Liaudet
- Bioimaging Core Facility, Faculty of Medicine, University of Geneva, Genève, Switzerland
| | - Gürkan Kaya
- Department of Diagnosis, Division of Clinical Pathology, Hôpitaux Universitaires de Genève, Genève, Switzerland
- Department of Medicine, Division of Dermatology, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Mikael J Pittet
- Department of Oncology, Hôpitaux Universitaires de Genève, Genève, Switzerland
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Genève, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- AGORA Cancer Center, Lausanne, Switzerland
| | - Pierre-Yves Dietrich
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
- Department of Oncology, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Daniel E Speiser
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Swiss Cancer Center Leman, Lausanne, Switzerland
- AGORA Cancer Center, Lausanne, Switzerland
| | - Petros Tsantoulis
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
- Department of Oncology, Hôpitaux Universitaires de Genève, Genève, Switzerland
| | - Sana Intidhar Labidi-Galy
- Faculty of Medicine, Department of Medicine and Center of Translational Research in Onco-Hematology, University of Geneva, Swiss Cancer Center Leman, Genève, Switzerland
- Department of Oncology, Hôpitaux Universitaires de Genève, Genève, Switzerland
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4
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Almeida D, Turecki G. Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. Methods 2022; 207:3-10. [PMID: 36064002 DOI: 10.1016/j.ymeth.2022.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.
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Affiliation(s)
- Daniel Almeida
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3; Department of Psychiatry, McGill University, Montreal, QC, Canada, H3A 1A1.
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5
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May-Zhang AA, Benthal JT, Southard-Smith EM. Hybridization Chain Reaction for mRNA Localization in Single Cells from Mouse and Human Cryosections. Curr Protoc 2022; 2:e439. [PMID: 35612422 PMCID: PMC9202517 DOI: 10.1002/cpz1.439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In situ hybridization has been a robust method for detection of mRNA expression in whole-mount samples or tissue sections for more than 50 years. Recent technical advances for in situ hybridization have incorporated oligo-based probes that attain greater tissue penetration and signal amplification steps with restricted localization for visualization of specific mRNAs within single cells. One such method is third-generation in situ hybridization chain reaction (V3HCR). Here, we report an optimized protocol for V3HCR detection of gene expression using sectioned frozen tissues from mouse and human on microscope slides. Our methods and modifications for cryosectioning, tissue fixation, and processing over a three-day V3HCR protocol are detailed along with recommendations for aliquoting and storing V3HCR single-stranded DNA probes and hairpin amplifiers. In addition, we describe a method for blocking background signal from lipofuscin, a highly autofluorescent material that is widespread in human neurons and often complicates imaging efforts. After testing multiple strategies for reduction of lipofuscin, we determined that application of a lipofuscin quencher dye is compatible with V3HCR, in contrast to other methods like cupric sulfate quenching or Sudan Black B blocking that cause V3HCR signal loss. This adaptation enables application of V3HCR for in situ detection of gene expression in human neuronal populations that are otherwise problematic due to lipofuscin autofluorescence. © 2022 Wiley Periodicals LLC. Basic Protocol: Mouse and human fresh-frozen tissue in situ hybridization chain reaction on microscope slides Support Protocol: Aliquoting of HCR probes and hairpins.
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Affiliation(s)
- Aaron A. May-Zhang
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Joseph T. Benthal
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - E. Michelle Southard-Smith
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN 37232.,Corresponding Author:
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6
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Smajić S, Prada-Medina CA, Landoulsi Z, Ghelfi J, Delcambre S, Dietrich C, Jarazo J, Henck J, Balachandran S, Pachchek S, Morris CM, Antony P, Timmermann B, Sauer S, Pereira SL, Schwamborn JC, May P, Grünewald A, Spielmann M. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain 2022; 145:964-978. [PMID: 34919646 PMCID: PMC9050543 DOI: 10.1093/brain/awab446] [Citation(s) in RCA: 169] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/21/2021] [Accepted: 11/18/2021] [Indexed: 11/29/2022] Open
Abstract
Idiopathic Parkinson's disease is characterized by a progressive loss of dopaminergic neurons, but the exact disease aetiology remains largely unknown. To date, Parkinson's disease research has mainly focused on nigral dopaminergic neurons, although recent studies suggest disease-related changes also in non-neuronal cells and in midbrain regions beyond the substantia nigra. While there is some evidence for glial involvement in Parkinson's disease, the molecular mechanisms remain poorly understood. The aim of this study was to characterize the contribution of all cell types of the midbrain to Parkinson's disease pathology by single-nuclei RNA sequencing and to assess the cell type-specific risk for Parkinson's disease using the latest genome-wide association study. We profiled >41 000 single-nuclei transcriptomes of post-mortem midbrain from six idiopathic Parkinson's disease patients and five age-/sex-matched controls. To validate our findings in a spatial context, we utilized immunolabelling of the same tissues. Moreover, we analysed Parkinson's disease-associated risk enrichment in genes with cell type-specific expression patterns. We discovered a neuronal cell cluster characterized by CADPS2 overexpression and low TH levels, which was exclusively present in idiopathic Parkinson's disease midbrains. Validation analyses in laser-microdissected neurons suggest that this cluster represents dysfunctional dopaminergic neurons. With regard to glial cells, we observed an increase in nigral microglia in Parkinson's disease patients. Moreover, nigral idiopathic Parkinson's disease microglia were more amoeboid, indicating an activated state. We also discovered a reduction in idiopathic Parkinson's disease oligodendrocyte numbers with the remaining cells being characterized by a stress-induced upregulation of S100B. Parkinson's disease risk variants were associated with glia- and neuron-specific gene expression patterns in idiopathic Parkinson's disease cases. Furthermore, astrocytes and microglia presented idiopathic Parkinson's disease-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signalling. While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson's disease microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B, GPNMB and HSP90AA1. Taken together, we generated the first single-nuclei RNA sequencing dataset from the idiopathic Parkinson's disease midbrain, which highlights a disease-specific neuronal cell cluster as well as 'pan-glial' activation as a central mechanism in the pathology of the movement disorder. This finding warrants further research into inflammatory signalling and immunomodulatory treatments in Parkinson's disease.
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Affiliation(s)
- Semra Smajić
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | | | - Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jenny Ghelfi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carola Dietrich
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Javier Jarazo
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jana Henck
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | | | - Sinthuja Pachchek
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Christopher M. Morris
- Newcastle Brain Tissue Resource, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
| | - Sascha Sauer
- Max-Delbrück-Centrum für Molekulare Medizin, Genomics Group, D-13125 Berlin, Germany
| | - Sandro L. Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Jens C. Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, D-23562 Lübeck, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany
- Institute of Human Genetics, Kiel University, D-42118 Kiel, Germany
- Institute of Human Genetics, University of Lübeck, D-23562 Lübeck, Germany
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7
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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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8
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Khan UW, Newmark PA. Somatic regulation of female germ cell regeneration and development in planarians. Cell Rep 2022; 38:110525. [PMID: 35294875 PMCID: PMC8994625 DOI: 10.1016/j.celrep.2022.110525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 12/23/2022] Open
Abstract
Female germ cells develop into oocytes, with the capacity for totipotency. In most animals, these remarkable cells are specified during development and cannot be regenerated. By contrast, planarians, known for their regenerative prowess, can regenerate germ cells. To uncover mechanisms required for female germ cell development and regeneration, we generated gonad-specific transcriptomes and identified genes whose expression defines progressive stages of female germ cell development. Strikingly, early female germ cells share molecular signatures with the pluripotent stem cells driving planarian regeneration. We observe spatial heterogeneity within somatic ovarian cells and find that a regionally enriched foxL homolog is required for oocyte differentiation, but not specification, suggestive of functionally distinct somatic compartments. Unexpectedly, a neurotransmitter-biosynthetic enzyme, aromatic L-amino acid decarboxylase (AADC), is also expressed in somatic gonadal cells, and plays opposing roles in female and male germ cell development. Thus, somatic gonadal cells deploy conserved factors to regulate germ cell development and regeneration in planarians.
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Affiliation(s)
- Umair W Khan
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, WI, USA; Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Phillip A Newmark
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA; Howard Hughes Medical Institute, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA.
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9
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Lavoie NS, Truong V, Malone D, Pengo T, Patil N, Dutton JR, Parr AM. Human induced pluripotent stem cells integrate, create synapses and extend long axons after spinal cord injury. J Cell Mol Med 2022; 26:1932-1942. [PMID: 35257489 PMCID: PMC8980929 DOI: 10.1111/jcmm.17217] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 12/17/2021] [Accepted: 01/08/2022] [Indexed: 12/26/2022] Open
Abstract
Numerous interventions have been explored in animal models using cells differentiated from human induced pluripotent stem cells (iPSCs) in the context of neural injury with some success. Our work seeks to transplant cells that are generated from hiPSCs into regionally specific spinal neural progenitor cells (sNPCs) utilizing a novel accelerated differentiation protocol designed for clinical translation. We chose a xenotransplantation model because our laboratory is focused on the behaviour of human cells in order to bring this potential therapy to translation. Cells were transplanted into adult immunodeficient rats after moderate contusion spinal cord injury (SCI). Twelve weeks later, cells derived from the transplanted sNPCs survived and differentiated into neurons and glia that filled the lesion cavity and produced a thoracic spinal cord transcriptional program in vivo. Furthermore, neurogenesis and ionic channel expression were promoted within the adjacent host spinal cord tissue. Transplanted cells displayed robust integration properties including synapse formation and myelination by host oligodendrocytes. Axons from transplanted hiPSC sNPC‐derived cells extended both rostrally and caudally from the SCI transplant site, rostrally approximately 6 cm into supraspinal structures. Thus, iPSC‐derived sNPCs may provide a patient‐specific cell source for patients with SCI that could provide a relay system across the site of injury.
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Affiliation(s)
- Nicolas Stoflet Lavoie
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vincent Truong
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Dane Malone
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Thomas Pengo
- University of Minnesota Imaging Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Nandadevi Patil
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - James R Dutton
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ann M Parr
- Stem Cell Institute, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA
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10
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Blaskovic S, Donati Y, Ruchonnet-Metrailler I, Avila Y, Schittny D, Schlepütz CM, Schittny JC, Barazzone-Argiroffo C. Early life exposure to nicotine modifies lung gene response after elastase-induced emphysema. Respir Res 2022; 23:44. [PMID: 35241086 PMCID: PMC8895880 DOI: 10.1186/s12931-022-01956-4] [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: 04/29/2021] [Accepted: 02/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is among the top 5 causes of mortality in the world and can develop as a consequence of genetic and/or environmental factors. Current efforts are focused on identifying early life insults and how these contribute to COPD development. In line with this, our study focuses on the influence of early life nicotine exposure and its potential impact on (a) lung pulmonary functions, and (b) elastase-induced emphysema in adulthood.
Methods To address this hypothesis, we developed a model of 2 hits, delivered at different time points: mouse pups were first exposed to nicotine/placebo in utero and during lactation, and then subsequently received elastase/placebo at the age of 11 weeks. The effect of nicotine pretreatment and elastase instillation was assessed by (a) measurement of pulmonary function at post-elastase day (ped) 21, and (b) transcriptomic profiling at ped3 and 21, and complementary protein determination. Statistical significance was determined by 3- and 2-way ANOVA for pulmonary functions, and RNAseq results were analyzed using the R project.
Results We did not observe any impact of nicotine pre- and early post-natal exposure compared to control samples on lung pulmonary functions in adulthood, as measured by FLEXIVENT technology. After elastase instillation, substantial lung damage was detected by x-ray tomography and was accompanied by loss in body weight at ped3 as well as an increase in cell numbers, inflammatory markers in BAL and lung volume at ped21. Lung functions showed a decrease in elastance and an increase in deep inflation volume and pressure volume (pv) loop area in animals with emphysema at ped21. Nicotine had no effect on elastance and deep inflation volume, but did affect the pv loop area in animals with emphysema at ped21. Extensive transcriptomic changes were induced by elastase at ped3 both in the nicotine-pretreated and the control samples, with several pathways common to both groups, such as for cell cycle, DNA adhesion and DNA damage. Nicotine pretreatment affected the number of lymphocytes present in BAL after elastase instillation and some of the complement pathway related proteins, arguing for a slight modification of the immune response, as well as changes related to general body metabolism. The majority of elastase-induced transcriptomic changes detected at ped3 had disappeared at ped21. In addition, transcriptomic profiling singled out a common gene pool that was independently activated by nicotine and elastase. Conclusions Our study reports a broad spectrum of transient transcriptomic changes in mouse emphysema and identifies nicotine as influencing the emphysema-associated immune system response. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-01956-4.
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Affiliation(s)
- Sanja Blaskovic
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University of Geneva, 4 rue Gabrielle-Perret-Gentil, 1211, Genève 14, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Institute of Anatomy, University of Bern, Bern, Switzerland
| | - Yves Donati
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University of Geneva, 4 rue Gabrielle-Perret-Gentil, 1211, Genève 14, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Isabelle Ruchonnet-Metrailler
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University of Geneva, 4 rue Gabrielle-Perret-Gentil, 1211, Genève 14, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Yannick Avila
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University of Geneva, 4 rue Gabrielle-Perret-Gentil, 1211, Genève 14, Switzerland.,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | | | | | - Constance Barazzone-Argiroffo
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University of Geneva, 4 rue Gabrielle-Perret-Gentil, 1211, Genève 14, Switzerland. .,Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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11
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Shibuya Y, Hokugo A, Okawa H, Kondo T, Khalil D, Wang L, Roca Y, Clements A, Sasaki H, Berry E, Nishimura I, Jarrahy R. Therapeutic downregulation of neuronal PAS domain 2 ( Npas2) promotes surgical skin wound healing. eLife 2022; 11:e71074. [PMID: 35040776 PMCID: PMC8789286 DOI: 10.7554/elife.71074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Attempts to minimize scarring remain among the most difficult challenges facing surgeons, despite the use of optimal wound closure techniques. Previously, we reported improved healing of dermal excisional wounds in circadian clock neuronal PAS domain 2 (Npas2)-null mice. In this study, we performed high-throughput drug screening to identify a compound that downregulates Npas2 activity. The hit compound (Dwn1) suppressed circadian Npas2 expression, increased murine dermal fibroblast cell migration, and decreased collagen synthesis in vitro. Based on the in vitro results, Dwn1 was topically applied to iatrogenic full-thickness dorsal cutaneous wounds in a murine model. The Dwn1-treated dermal wounds healed faster with favorable mechanical strength and developed less granulation tissue than the controls. The expression of type I collagen, Tgfβ1, and α-smooth muscle actin was significantly decreased in Dwn1-treated wounds, suggesting that hypertrophic scarring and myofibroblast differentiation are attenuated by Dwn1 treatment. NPAS2 may represent an important target for therapeutic approaches to optimal surgical wound management.
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Affiliation(s)
- Yoichiro Shibuya
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
- Department of Plastic and Reconstructive Surgery, Faculty of Medicine, University of TsukubaTsukubaJapan
| | - Akishige Hokugo
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
| | - Hiroko Okawa
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of DentistryMiyagiJapan
| | - Takeru Kondo
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of DentistryMiyagiJapan
| | - Daniel Khalil
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Lixin Wang
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Yvonne Roca
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Adam Clements
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Hodaka Sasaki
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
| | - Ella Berry
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Ichiro Nishimura
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
| | - Reza Jarrahy
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
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12
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Jia E, Zhou Y, Shi H, Pan M, Zhao X, Ge Q. Effects of brain tissue section processing and storage time on gene expression. Anal Chim Acta 2021; 1142:38-47. [PMID: 33280702 DOI: 10.1016/j.aca.2020.10.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022]
Abstract
The pre-processing of samples is important factors that affect the results of the RNA-sequencing (RNA-seq) data. However, the effects of frozen sections storage conditions on the integrity of RNA and sequencing results haven't been reported. The study of frozen section protection schemes can provide reliable experimental results for single-cell and spatial transcriptome sequencing. In this study, RNA was isolated to be studied for RNA from brain section at different temperatures (RT: room temperature, -20 °C) and storage time (0 h, 2 h, 4 h, 8 h, 12 h, 16 h, 24 h, 7day, 3week, 6month). The stability of reference genes was validated using reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that the storage at room temperature significantly affected RNA integrity number (RIN), and the RIN value was lower with the prolongation of storage, while the storage at -20 °C exerted less effect on the RIN value. Cresyl violet staining for brain tissue sections had little effect on RNA integrity. 1925, 899 and 3390 differential expression genes (DEGs) were screened at 2 h, 4 h and 8 h at room temperature, respectively. A total of 892, 478 and 619 genes were shown to be differentially expressed at -20 °C for 7d, 3w and 6 m, respectively. Among them, the expression of glycoprotein m6a (Gpm6a), calmodulin 1 (Calm1), calmodulin 1 (Calm2), thymosin, beta 4, X chromosome (Tmsb4x), ribosomal protein S21 (Rps21) and so on were correlated with RNA quality. According to the expression stability of 4 reference genes (Actb: beta-actin; Gapdh: glyceraldehyde-3-phosphate dehydrogenase; 18S: 18S ribosomal; Hprt1: hypoxanthine phosphoribosyltransferase 1), 18S is the most stable reference gene in the brain. In conclusion, the storage temperature and time of frozen sections have significant effects on RNA integrity and sequencing results. But there are still some genes that are stable and not affected by worsening of overall RNA integrity ie the decrease of RIN value. In addition, 1% cresyl violet staining can protect RNA.
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Affiliation(s)
- Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ying Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing, 210097, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China.
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13
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Mentges M, Glasenapp A, Boenisch M, Malz S, Henrissat B, Frandsen RJ, Güldener U, Münsterkötter M, Bormann J, Lebrun M, Schäfer W, Martinez‐Rocha AL. Infection cushions of Fusarium graminearum are fungal arsenals for wheat infection. MOLECULAR PLANT PATHOLOGY 2020; 21:1070-1087. [PMID: 32573086 PMCID: PMC7368127 DOI: 10.1111/mpp.12960] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/07/2020] [Accepted: 05/09/2020] [Indexed: 05/22/2023]
Abstract
Fusarium graminearum is one of the most destructive plant pathogens worldwide, causing fusarium head blight (FHB) on cereals. F. graminearum colonizes wheat plant surfaces with specialized unbranched hyphae called runner hyphae (RH), which develop multicelled complex appressoria called infection cushions (IC). IC generate multiple penetration sites, allowing the fungus to enter the plant cuticle. Complex infection structures are typical for several economically important plant pathogens, yet with unknown molecular basis. In this study, RH and IC formed on the surface of wheat paleae were isolated by laser capture microdissection. RNA-Seq-based transcriptomic analyses were performed on RH and IC and compared to mycelium grown in complete medium (MY). Both RH and IC displayed a high number of infection up-regulated genes (982), encoding, among others, carbohydrate-active enzymes (CAZymes: 140), putative effectors (PE: 88), or secondary metabolism gene clusters (SMC: 12 of 67 clusters). RH specifically up-regulated one SMC corresponding to aurofusarin biosynthesis, a broad activity antibiotic. IC specifically up-regulated 248 genes encoding mostly putative virulence factors such as 7 SMC, including the mycotoxin deoxynivalenol and the newly identified fusaoctaxin A, 33 PE, and 42 CAZymes. Furthermore, we studied selected candidate virulence factors using cellular biology and reverse genetics. Hence, our results demonstrate that IC accumulate an arsenal of proven and putative virulence factors to facilitate the invasion of epidermal cells.
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Affiliation(s)
- Michael Mentges
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
| | - Anika Glasenapp
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
| | - Marike Boenisch
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
| | - Sascha Malz
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
| | | | - Rasmus J.N. Frandsen
- Department of Biotechnology and BiomedicineTechnical University of DenmarkKgs. LyngbyDenmark
| | - Ulrich Güldener
- Department of BioinformaticsTechnical University of MunichTUM School of Life Sciences WeihenstephanFreisingGermany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems BiologyMünchenGermany
- Present address:
Functional Genomics and BioinformaticsSopron UniversitySopronHungary
| | - Jörg Bormann
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
| | | | - Wilhelm Schäfer
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
| | - Ana Lilia Martinez‐Rocha
- Molekulare PhytopathologieInstitut für Pflanzenwissenschaften und MikrobiologieUniversität HamburgHamburgGermany
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14
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Pote A, Boghenco O, Marques-Ramos A. Molecular analysis of H&E- and Papanicolau-stained samples-systematic review. Histochem Cell Biol 2020; 154:7-20. [PMID: 32372108 DOI: 10.1007/s00418-020-01882-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2020] [Indexed: 12/12/2022]
Abstract
Molecular pathology allows the identification of causative agents in infectious diseases and detection of biomarkers important for prediction of disease susceptibility, diagnosis and personalized therapy. Accordingly, nucleic acid-based methods have gained a special role in clinical laboratories particularly to evaluate solid and hematological tumors. Extraction of nucleic acids is commonly performed in microdissected formalin-fixed paraffin-embedded (FFPE) or cytological samples that had been previously evaluated through the use of hematoxylin and eosin (H&E) or Papanicolau (Pap) stains, respectively. Although the effect of both stains on nucleic acids integrity has been explored by several authors, the results are not consistent and require further examination. Accordingly, the goal of this review was to assess the influence of H&E and Pap stains on DNA and RNA integrity and to address the mechanism by which each staining compromises molecular based-analysis. The analyzed studies demonstrate that H&E- and Pap-staining result in low DNA recovery and some degree of DNA fragmentation. Additionally, it is concluded that hemalum inhibits PCR by interfering with DNA extraction, preventing DNA polymerase attachment and possibly by rescuing divalent cations. Accordingly, proper sample purification and adjustment of PCR conditions are of key importance to achieve satisfactory results by PCR in H&E- and Pap-stained samples. Furthermore, although H&E results in RNA fragmentation, it is possible to perform expression analysis in H&E-stained frozen sections, using RNase-free conditions, low amounts of hematoxylin and a rapid protocol from sample collection to RNA analysis. It The effect of Pap-staining on RNA integrity remains to be determined.
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Affiliation(s)
- Alexandra Pote
- ESTeSL, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096, Lisboa, Portugal
| | - Otília Boghenco
- ESTeSL, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096, Lisboa, Portugal
| | - Ana Marques-Ramos
- ESTeSL, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096, Lisboa, Portugal.
- H&TRC, Health and Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisboa, Portugal.
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15
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Comba A, Dunn PJ, Kish PE, Kadiyala P, Kahana A, Castro MG, Lowenstein PR. Laser Capture Microdissection of Glioma Subregions for Spatial and Molecular Characterization of Intratumoral Heterogeneity, Oncostreams, and Invasion. J Vis Exp 2020. [PMID: 32338655 DOI: 10.3791/60939] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Gliomas are primary brain tumors characterized by their invasiveness and heterogeneity. Specific histological patterns such as pseudopalisades, microvascular proliferation, mesenchymal transformation and necrosis characterize the histological heterogeneity of high-grade gliomas. Our laboratory has demonstrated that the presence of high densities of mesenchymal cells, named oncostreams, correlate with tumor malignancy. We have developed a unique approach to understand the mechanisms that underlie glioma's growth and invasion. Here, we describe a comprehensive protocol that utilizes laser capture microdissection (LMD) and RNA sequencing to analyze differential mRNA expression of intra-tumoral heterogeneous multicellular structures (i.e., mesenchymal areas or areas of tumor invasion). This method maintains good tissue histology and RNA integrity. Perfusion, freezing, embedding, sectioning, and staining were optimized to preserve morphology and obtain high-quality laser microdissection samples. The results indicate that perfusion of glioma bearing mice using 30% sucrose provides good morphology and RNA quality. In addition, staining tumor sections with 4% Cresyl violet and 0.5% eosin results in good nuclear and cellular staining, while preserving RNA integrity. The method described is sensitive and highly reproducible and it can be utilized to study tumor morphology in various tumor models. In summary, we describe a complete method to perform LMD that preserves morphology and RNA quality for sequencing to study the molecular features of heterogeneous multicellular structures within solid tumors.
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Affiliation(s)
- Andrea Comba
- Dept. of Neurosurgery, University of Michigan Medical School; Dept. of Cell and Developmental Biology, University of Michigan Medical School; Rogel Cancer Center, University of Michigan Medical School
| | - Patrick J Dunn
- Dept. of Neurosurgery, University of Michigan Medical School; Dept. of Cell and Developmental Biology, University of Michigan Medical School; Rogel Cancer Center, University of Michigan Medical School
| | - Phillip E Kish
- Dept. of Neurosurgery, University of Michigan Medical School; Dept. of Ophthalmology & Visual Science, University of Michigan Medical School
| | - Padma Kadiyala
- Dept. of Neurosurgery, University of Michigan Medical School; Dept. of Cell and Developmental Biology, University of Michigan Medical School; Rogel Cancer Center, University of Michigan Medical School
| | - Alon Kahana
- Dept. of Ophthalmology & Visual Science, University of Michigan Medical School
| | - Maria G Castro
- Dept. of Neurosurgery, University of Michigan Medical School; Dept. of Cell and Developmental Biology, University of Michigan Medical School; Rogel Cancer Center, University of Michigan Medical School
| | - Pedro R Lowenstein
- Dept. of Neurosurgery, University of Michigan Medical School; Dept. of Cell and Developmental Biology, University of Michigan Medical School; Rogel Cancer Center, University of Michigan Medical School;
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16
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An Optimised Protocol Harnessing Laser Capture Microdissection for Transcriptomic Analysis on Matched Primary and Metastatic Colorectal Tumours. Sci Rep 2020; 10:682. [PMID: 31959771 PMCID: PMC6971024 DOI: 10.1038/s41598-019-55146-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/23/2019] [Indexed: 11/08/2022] Open
Abstract
Generation of large amounts of genomic data is now feasible and cost-effective with improvements in next generation sequencing (NGS) technology. Ribonucleic acid sequencing (RNA-Seq) is becoming the preferred method for comprehensively characterising global transcriptome activity. Unique to cytoreductive surgery (CRS), multiple spatially discrete tumour specimens could be systematically harvested for genomic analysis. To facilitate such downstream analyses, laser capture microdissection (LCM) could be utilized to obtain pure cell populations. The aim of this protocol study was to develop a methodology to obtain high-quality expression data from matched primary tumours and metastases by utilizing LCM to isolate pure cellular populations. We demonstrate an optimized LCM protocol which reproducibly delivered intact RNA used for RNA sequencing and quantitative polymerase chain reaction (qPCR). After pathologic annotation of normal epithelial, tumour and stromal components, LCM coupled with cDNA library generation provided for successful RNA sequencing. To illustrate our framework's potential to identify targets that would otherwise be missed with conventional bulk tumour sequencing, we performed qPCR and immunohistochemical technical validation to show that the genes identified were truly expressed only in certain sub-components. This study suggests that the combination of matched tissue specimens with tissue microdissection and NGS provides a viable platform to unmask hidden biomarkers and provides insight into tumour biology at a higher resolution.
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17
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Reynolds RH, Hardy J, Ryten M, Gagliano Taliun SA. Informing disease modelling with brain-relevant functional genomic annotations. Brain 2019; 142:3694-3712. [PMID: 31603214 PMCID: PMC6885670 DOI: 10.1093/brain/awz295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/05/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
The past decade has seen a surge in the number of disease/trait-associated variants, largely because of the union of studies to share genetic data and the availability of electronic health records from large cohorts for research use. Variant discovery for neurological and neuropsychiatric genome-wide association studies, including schizophrenia, Parkinson's disease and Alzheimer's disease, has greatly benefitted; however, the translation of these genetic association results to interpretable biological mechanisms and models is lagging. Interpreting disease-associated variants requires knowledge of gene regulatory mechanisms and computational tools that permit integration of this knowledge with genome-wide association study results. Here, we summarize key conceptual advances in the generation of brain-relevant functional genomic annotations and amongst tools that allow integration of these annotations with association summary statistics, which together provide a new and exciting opportunity to identify disease-relevant genes, pathways and cell types in silico. We discuss the opportunities and challenges associated with these developments and conclude with our perspective on future advances in annotation generation, tool development and the union of the two.
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Affiliation(s)
- Regina H Reynolds
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - John Hardy
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
- UK Dementia Research Institute at University College London (UCL), London, UK
| | - Mina Ryten
- Department of Neurodegenerative Disease, University College London (UCL) Institute of Neurology, London, UK
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
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18
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Basudan AM, Yang Y. Optimizing Laser Capture Microdissection Protocol for Isolating Zone-Specific Cell Populations from Mandibular Condylar Cartilage. Int J Dent 2019; 2019:5427326. [PMID: 31885587 PMCID: PMC6914897 DOI: 10.1155/2019/5427326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/24/2019] [Accepted: 11/02/2019] [Indexed: 01/06/2023] Open
Abstract
Mandibular condylar cartilage (MCC) is a multizonal heterogeneous fibrocartilage consisting of fibrous (FZ), proliferative (PZ), mature (MZ), and hypertrophic (HZ) zones. Gross sampling of the whole tissue may conceal some important information and compromise the validity of the molecular analysis. Laser capture microdissection (LCM) technology allows isolating zonal (homogenous) cell populations and consequently generating more accurate molecular and genetic data, but the challenges during tissue preparation and microdissection procedures are to obtain acceptable tissue section morphology that allows histological identification of the desirable cell type and to minimize RNA degradation. Therefore, our aim is to optimize an LCM protocol for isolating four homogenous zone-specific cell populations from their respective MCC zones while preserving the quality of RNA recovered. MCC and FCC (femoral condylar cartilage) specimens were harvested from 5-week-old Sprague-Dawley male rats. Formalin-fixed and frozen unfixed tissue sections were prepared and compared histologically. Additional specimens were microdissected to prepare LCM samples from FCC and each MCC zone individually. Then, to evaluate LCM-RNA integrity, 3'/m ratios of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-Actin) using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) were calculated. Both fixed and unfixed tissue sections allowed reliable identification of MCC zones. The improved morphology of the frozen sections of our protocol has extended the range of cell types to be isolated. Under the empirically set LCM parameters, four homogeneous cell populations were efficiently isolated from their respective zones. The 3'/m ratio means of GAPDH and β-Actin ranged between 1.11-1.56 and 1.41-2.12, respectively. These values are in line with the reported quality control requirements. The present study shows that the optimized LCM protocol could allow isolation of four homogenous zone-specific cell populations from MCC, meanwhile preserving RNA integrity to meet the high quality requirements for subsequent molecular analyses. Thereby, accurate molecular and genetic data could be generated.
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Affiliation(s)
- Aisha M. Basudan
- Division of Orthodontics, Dental Services Department, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- College of Dentistry King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Yanqi Yang
- Department of Orthodontics, Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong
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19
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Validation of Laser Capture Microdissection Protocol in Endometriosis Studies. ACTA ACUST UNITED AC 2019; 55:medicina55090520. [PMID: 31443551 PMCID: PMC6780092 DOI: 10.3390/medicina55090520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/10/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022]
Abstract
Background and Objectives: The presence of endometrial-like tissue outside the uterine cavity is a key feature of endometriosis. Although endometriotic lesions appear to be histologically quite similar to the eutopic endometrium, detailed studies comparing both tissues are required because their inner and surrounding cellular arrangement is distinct. Thus, comparison between tissues might require methods, such as laser capture microdissection (LCM), that allow for precise selection of an area and its specific cell populations. However, it is known that the efficient use of LCM depends on the type of studied tissue and on the choice of an adequate protocol. Recent studies have reported the use of LCM in endometriosis studies. The main objective of the present study is to establish a standardized protocol to obtain good-quality microdissected material from eutopic or ectopic endometrium. Materials and Methods: The main methodological steps involved in the processing of the lesion samples for LCM were standardized to yield material of good quality to be further used in molecular techniques. Results: We obtained satisfactory results regarding the yields and integrity of RNA and protein obtained from LCM-processed endometriosis tissues. Conclusion: LCM can provide more precise analysis of endometriosis biopsies, provided that key steps of the methodology are followed.
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Hayden EY, Putman J, Nunez S, Shin WS, Oberoi M, Charreton M, Dutta S, Li Z, Komuro Y, Joy MT, Bitan G, MacKenzie-Graham A, Jiang L, Hinman JD. Ischemic axonal injury up-regulates MARK4 in cortical neurons and primes tau phosphorylation and aggregation. Acta Neuropathol Commun 2019; 7:135. [PMID: 31429800 PMCID: PMC6700776 DOI: 10.1186/s40478-019-0783-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Ischemic injury to white matter tracts is increasingly recognized to play a key role in age-related cognitive decline, vascular dementia, and Alzheimer’s disease. Knowledge of the effects of ischemic axonal injury on cortical neurons is limited yet critical to identifying molecular pathways that link neurodegeneration and ischemia. Using a mouse model of subcortical white matter ischemic injury coupled with retrograde neuronal tracing, we employed magnetic affinity cell sorting with fluorescence-activated cell sorting to capture layer-specific cortical neurons and performed RNA-sequencing. With this approach, we identified a role for microtubule reorganization within stroke-injured neurons acting through the regulation of tau. We find that subcortical stroke-injured Layer 5 cortical neurons up-regulate the microtubule affinity-regulating kinase, Mark4, in response to axonal injury. Stroke-induced up-regulation of Mark4 is associated with selective remodeling of the apical dendrite after stroke and the phosphorylation of tau in vivo. In a cell-based tau biosensor assay, Mark4 promotes the aggregation of human tau in vitro. Increased expression of Mark4 after ischemic axonal injury in deep layer cortical neurons provides new evidence for synergism between axonal and neurodegenerative pathologies by priming of tau phosphorylation and aggregation.
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21
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A Talip B, Snelling WJ, Sleator RD, Lowery C, Dooley JSG. A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides. BMC Microbiol 2018; 18:196. [PMID: 30477427 PMCID: PMC6260770 DOI: 10.1186/s12866-018-1335-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/12/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM coupled with PCR amplification of a suitable target. RESULTS Mycobacterium smegmatis was used as a model organism to provide a proof of principle for a method to recover bacteria from a stained sample on a glass slide using a laser capture system. Ziehl-Neelsen (ZN) stained cells were excised and catapulted into tubes. Recovered cells were subjected to DNA extraction and pre-amplified with multiple displacement amplification (MDA). This system allowed a minimum of 30 catapulted cells to be detected following a nested real-time PCR assay, using rpoB specific primers. The combination of MDA and nested real-time PCR resulted in a 30-fold increase in sensitivity for the detection of low numbers of cells isolated using LCM. CONCLUSIONS This study highlights the potential of LCM coupled with MDA as a tool to improve the recovery of amplifiable nucleic acids from archived glass slides. The inclusion of the MDA step was essential to enable downstream amplification. This platform should be broadly applicable to a variety of diagnostic applications and we have used it as a proof of principle with a Mycobacterium sp. model system.
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Affiliation(s)
- Balkis A Talip
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84000 Pagoh, Muar, Johor, Malaysia
| | - William J Snelling
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Colm Lowery
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland
| | - James S G Dooley
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland.
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22
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May-Zhang AA, Deal KK, Southard-Smith EM. Optimization of Laser-Capture Microdissection for the Isolation of Enteric Ganglia from Fresh-Frozen Human Tissue. J Vis Exp 2018. [PMID: 29985370 DOI: 10.3791/57762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The purpose of this method is to obtain high-integrity RNA samples from enteric ganglia collected from unfixed, freshly-resected human intestinal tissue using laser capture microdissection (LCM). We have identified five steps in the workflow that are crucial for obtaining RNA isolates from enteric ganglia with sufficiently high quality and quantity for RNA-seq. First, when preparing intestinal tissue, each sample must have all excess liquid removed by blotting prior to flattening the serosa as much as possible across the bottom of large base molds. Samples are then quickly frozen atop a slurry of dry ice and 2-methylbutane. Second, when sectioning the tissue, it is important to position cryomolds so that intestinal sections parallel the full plane of the myenteric plexus, thereby yielding the greatest surface area of enteric ganglia per slide. Third, during LCM, polyethylene napthalate (PEN)-membrane slides offer the greatest speed and flexibility in outlining the non-uniform shapes of enteric ganglia when collecting enteric ganglia. Fourth, for distinct visualization of enteric ganglia within sections, ethanol-compatible dyes, like Cresyl Violet, offer excellent preservation of RNA integrity relative to aqueous dyes. Finally, for the extraction of RNA from captured ganglia, we observed differences between commercial RNA extraction kits that yielded superior RNA quantity and quality, while eliminating DNA contamination. Optimization of these factors in the current protocol greatly accelerates the workflow and yields enteric ganglia samples with exceptional RNA quality and quantity.
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Braun A, Martinez C, Schmitteckert S, Röth R, Lasitschka F, Niesler B. Site-specific gene expression analysis from archived human intestine samples combining laser-capture microdissection and multiplexed color-coded probes. Neurogastroenterol Motil 2018; 30:e13261. [PMID: 29193461 DOI: 10.1111/nmo.13261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/07/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Alterations of site-specific gene expression profiles in disease-relevant networks within the different layers of the intestinal wall may contribute to the onset and clinical course of gastrointestinal disorders. To date, no systematic analysis has assessed and compared sub-regional gene expression patterns in all distinct layers of the gut using fresh frozen human samples. Our aim was to establish an optimized protocol for site-specific RNA isolation in order to achieve maximum RNA quality and amount for subsequent gene expression analysis combining laser-capture microdissection (LCM) with a probe-based technology, the NanoString nCounter Analysis system. METHODS Four full-thickness colon samples from patients who underwent surgery due to pathological conditions were processed and separated into epithelium, lamina propria, myenteric plexus, submucosa, and tunica muscularis by LCM. Site-specific marker expression by nCounter technology was performed on total RNA from each sub-region, respectively. KEY RESULTS Collecting ~10 mm² (~100 000-250 000 cells) of tissue from the epithelial layer, lamina propria, and myenteric plexus provided sufficient amounts of RNA of appropriate quality for subsequent analyses. In contrast, ~40 mm² (~250 000-650 000 cells) of tissue were dissected from the less cell-rich submucosal and tunica muscularis layer. nCounter analysis revealed a site-specific expression pattern of marker genes in the different layers of the colonic wall which were highly correlating (r > .9). CONCLUSIONS AND INFERENCES LCM in combination with nCounter expression analysis enables site-specific, sensitive, reliable detection, and quantification of mRNA from histologically heterogeneous tissues.
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Affiliation(s)
- A Braun
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - C Martinez
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,Digestive System Research Unit, Department of Gastroenterology, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Departamento de Medicina), Barcelona, Spain.,COST Action BM1106 Genes in Irritable Bowel Syndrome Research Network Europe (GENIEUR), Heidelberg, Germany
| | - S Schmitteckert
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,COST Action BM1106 Genes in Irritable Bowel Syndrome Research Network Europe (GENIEUR), Heidelberg, Germany
| | - R Röth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - F Lasitschka
- Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - B Niesler
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.,COST Action BM1106 Genes in Irritable Bowel Syndrome Research Network Europe (GENIEUR), Heidelberg, Germany.,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
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24
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Cummings M, Mappa G, Orsi NM. Laser Capture Microdissection and Isolation of High-Quality RNA from Frozen Endometrial Tissue. Methods Mol Biol 2018; 1723:155-166. [PMID: 29344859 DOI: 10.1007/978-1-4939-7558-7_8] [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: 04/21/2023]
Abstract
Laser capture microdissection (LCM) allows expression profiling of specific cell populations within tissues. However, isolation of high-quality RNA from laser capture microdissected frozen tissue is beset by problems arising from intrinsic tissue RNase activity. Herein, we describe an optimized staining/LCM/RNA extraction protocol developed for the isolation of epithelial RNA from frozen tissue sections using human endometrial cancer as a model tissue. This method combines excellent, reproducible visualization of tissue morphology with the isolation of high-integrity RNA suitable for downstream applications such as expression microarray analysis. We present quantitative and qualitative RNA data obtained from >200 endometrial epithelial samples (normal, hyperplastic, and cancerous), where 92% of samples had RIN values of 7 and above and highlight common pitfalls faced by investigators. This method should also be broadly applicable to a range of other tissue types.
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Affiliation(s)
- Michele Cummings
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Georgia Mappa
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Nicolas M Orsi
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK.
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25
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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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26
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Kooliyottil R, Dandurand LM, Kuhl JC, Caplan A, Xiao F. Microaspiration of Solanum tuberosum root cells at early stages of infection by Globodera pallida. PLANT METHODS 2017; 13:68. [PMID: 28855955 PMCID: PMC5571573 DOI: 10.1186/s13007-017-0219-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/16/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Sedentary endoparasitic cyst nematodes form a feeding structure in plant roots, called a syncytium. Syncytium formation involves extensive transcriptional modifications, which leads to cell modifications such as increased cytoplasmic streaming, enlarged nuclei, increased numbers of organelles, and replacement of a central vacuole by many small vacuoles. When whole root RNA is isolated and analyzed, transcript changes manifested in the infected plant cells are overshadowed by gene expression from cells of the entire root system. Use of microaspiration allows isolation of the content of nematode infected cells from a heterogeneous cell population. However, one challenge with this method is identifying the nematode infected cells under the microscope at early stages of infection. This problem was addressed by staining nematode juveniles with a fluorescent dye prior to infection so that the infected cells could be located and microaspirated. RESULTS In the present study, we used the fluorescent vital stain PKH26 coupled with a micro-rhizosphere chamber to locate the infected nematode Globodera pallida in Solanum tuberosum root cells. This enabled microaspiration of nematode-infected root cells during the early stages of parasitism. To study the transcriptional events occurring in these cells, an RNA isolation method from microaspirated samples was optimized, and subsequently the RNA was purified using magnetic beads. With this method, we obtained an RNA quality number of 7.8. For transcriptome studies, cDNA was synthesized from the isolated RNA and assessed by successfully amplifying several pathogenesis related protein coding genes. CONCLUSION The use of PKH26 stained nematode juveniles enabled early detection of nematode infected cells for microaspiration. To investigate transcriptional changes in low yielding RNA samples, bead-based RNA extraction procedures minimized RNA degradation and provided high quality RNA. This protocol provides a robust procedure to analyze gene expression in nematode-infected cells.
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Affiliation(s)
- Rinu Kooliyottil
- Department of Plant Soil and Entomological Sciences, University of Idaho, Moscow, ID 83844 USA
| | - Louise-Marie Dandurand
- Department of Plant Soil and Entomological Sciences, University of Idaho, Moscow, ID 83844 USA
| | - Joseph C. Kuhl
- Department of Plant Soil and Entomological Sciences, University of Idaho, Moscow, ID 83844 USA
| | - Allan Caplan
- Department of Plant Soil and Entomological Sciences, University of Idaho, Moscow, ID 83844 USA
| | - Fangming Xiao
- Department of Plant Soil and Entomological Sciences, University of Idaho, Moscow, ID 83844 USA
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27
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Jumper N, Hodgkinson T, Paus R, Bayat A. Site-specific gene expression profiling as a novel strategy for unravelling keloid disease pathobiology. PLoS One 2017; 12:e0172955. [PMID: 28257480 PMCID: PMC5336271 DOI: 10.1371/journal.pone.0172955] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 02/13/2017] [Indexed: 12/13/2022] Open
Abstract
Keloid disease (KD) is a fibroproliferative cutaneous tumour characterised by heterogeneity, excess collagen deposition and aggressive local invasion. Lack of a validated animal model and resistance to a multitude of current therapies has resulted in unsatisfactory clinical outcomes of KD management. In order to address KD from a new perspective, we applied for the first time a site-specific in situ microdissection and gene expression profiling approach, through combined laser capture microdissection and transcriptomic array. The aim here was to analyse the utility of this approach compared with established methods of investigation, including whole tissue biopsy and monolayer cell culture techniques. This study was designed to approach KD from a hypothesis-free and compartment-specific angle, using state-of-the-art microdissection and gene expression profiling technology. We sought to characterise expression differences between specific keloid lesional sites and elucidate potential contributions of significantly dysregulated genes to mechanisms underlying keloid pathobiology, thus informing future explorative research into KD. Here, we highlight the advantages of our in situ microdissection strategy in generating expression data with improved sensitivity and accuracy over traditional methods. This methodological approach supports an active role for the epidermis in the pathogenesis of KD through identification of genes and upstream regulators implicated in epithelial-mesenchymal transition, inflammation and immune modulation. We describe dermal expression patterns crucial to collagen deposition that are associated with TGFβ-mediated signalling, which have not previously been examined in KD. Additionally, this study supports the previously proposed presence of a cancer-like stem cell population in KD and explores the possible contribution of gene dysregulation to the resistance of KD to conventional therapy. Through this innovative in situ microdissection gene profiling approach, we provide better-defined gene signatures of distinct KD regions, thereby addressing KD heterogeneity, facilitating differential diagnosis with other cutaneous fibroses via transcriptional fingerprinting, and highlighting key areas for future KD research.
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Affiliation(s)
- N. Jumper
- Plastic and Reconstructive Surgery Research, University of Manchester, Oxford Rd, Manchester, United Kingdom
| | - T. Hodgkinson
- Plastic and Reconstructive Surgery Research, University of Manchester, Oxford Rd, Manchester, United Kingdom
- Centre for Tissue Injury and Repair, University of Manchester, and MAHSC, Manchester, United Kingdom
| | - R. Paus
- Centre for Dermatology Research, University of Manchester, and MAHSC, Manchester, United Kingdom
| | - A. Bayat
- Plastic and Reconstructive Surgery Research, University of Manchester, Oxford Rd, Manchester, United Kingdom
- Centre for Dermatology Research, University of Manchester, and MAHSC, Manchester, United Kingdom
- * E-mail:
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28
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Chen J, Suo S, Tam PP, Han JDJ, Peng G, Jing N. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nat Protoc 2017; 12:566-580. [PMID: 28207000 DOI: 10.1038/nprot.2017.003] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cannot be identified. Here, we describe how to use Geo-seq, a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology. The combination of these two methods enables the elucidation of cellular heterogeneity and spatial variance simultaneously. The Geo-seq protocol allows the profiling of transcriptome information from only a small number cells and retains their native spatial information. This protocol has wide potential applications to address biological and pathological questions of cellular properties such as prospective cell fates, biological function and the gene regulatory network. Geo-seq has been applied to investigate the spatial transcriptome of mouse early embryo, mouse brain, and pathological liver and sperm tissues. The entire protocol from tissue collection and microdissection to sequencing requires ∼5 d, Data analysis takes another 1 or 2 weeks, depending on the amount of data and the speed of the processor.
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Affiliation(s)
- Jun Chen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Shengbao Suo
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Patrick Pl Tam
- Embryology Unit, Children's Medical Research Institute and School of MedicalSciences, Sydney Medical School, University of Sydney, Sydney, Australia
| | - Jing-Dong J Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guangdun Peng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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Laser microdissection of tomato fruit cell and tissue types for transcriptome profiling. Nat Protoc 2016; 11:2376-2388. [PMID: 27809311 DOI: 10.1038/nprot.2016.146] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This protocol enables transcriptome profiling of specific cell or tissue types that are isolated from tomato using laser microdissection (LM). To prepare tissue for LM, fruit samples are first fixed in optimal cutting temperature (OCT) medium and frozen in molds. The tissue is then sectioned using a cryostat before being dissected using an LM instrument. The RNAs contained in the harvested cells are purified and subjected to two rounds of amplification to yield sufficient quantities of RNA to generate cDNA libraries. Unlike several other techniques that are used to isolate specific cell types, LM has the advantage of being readily applied to any plant species without having to generate transgenic plants. Using the protocols described here, LM-mediated cell-type transcriptomic analysis of two samples requires ∼8 d from tissue harvest to RNA sequencing (RNA-seq), whereas each additional sample, up to a total of 12 samples, requires ∼1 additional day for the LM step. RNA obtained using this method has been successfully used for deep-coverage transcriptome profiling, which is a particularly effective strategy for identifying genes that are differentially expressed between cell or tissue types.
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30
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Thennavan A, Sharma M, Chandrashekar C, Hunter K, Radhakrishnan R. Exploring the potential of laser capture microdissection technology in integrated oral biosciences. Oral Dis 2016; 23:737-748. [DOI: 10.1111/odi.12578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 12/19/2022]
Affiliation(s)
- A Thennavan
- Department of Oral Pathology; Manipal College of Dental Sciences; Manipal Karnataka India
| | - M Sharma
- Pacific Academy of Higher Education and Research (PAHER) University; Udaipur Rajasthan India
- Department of Oral Pathology; ITS Dental College; Hospital and Research Center; Greater Noida India
| | - C Chandrashekar
- Department of Oral Pathology; Manipal College of Dental Sciences; Manipal Karnataka India
| | - K Hunter
- School of Clinical Dentistry; The University of Sheffield; Sheffield UK
| | - R Radhakrishnan
- Department of Oral Pathology; Manipal College of Dental Sciences; Manipal Karnataka India
- School of Clinical Dentistry; The University of Sheffield; Sheffield UK
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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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32
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Castro NP, Merchant AS, Saylor KL, Anver MR, Salomon DS, Golubeva YG. Adaptation of Laser Microdissection Technique for the Study of a Spontaneous Metastatic Mammary Carcinoma Mouse Model by NanoString Technologies. PLoS One 2016; 11:e0153270. [PMID: 27077656 PMCID: PMC4831786 DOI: 10.1371/journal.pone.0153270] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/25/2016] [Indexed: 02/07/2023] Open
Abstract
Laser capture microdissection (LCM) of tissue is an established tool in medical research for collection of distinguished cell populations under direct microscopic visualization for molecular analysis. LCM samples have been successfully analyzed in a number of genomic and proteomic downstream molecular applications. However, LCM sample collection and preparation procedure has to be adapted to each downstream analysis platform. In this present manuscript we describe in detail the adaptation of LCM methodology for the collection and preparation of fresh frozen samples for NanoString analysis based on a study of a model of mouse mammary gland carcinoma and its lung metastasis. Our adaptation of LCM sample preparation and workflow to the requirements of the NanoString platform allowed acquiring samples with high RNA quality. The NanoString analysis of such samples provided sensitive detection of genes of interest and their associated molecular pathways. NanoString is a reliable gene expression analysis platform that can be effectively coupled with LCM.
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Affiliation(s)
- Nadia P. Castro
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Anand S. Merchant
- CCRIFX Bioinformatics Core, National Cancer Institute, Bethesda, MD, 20892, United States of America
| | - Karen L. Saylor
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Miriam R. Anver
- Pathology-Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
| | - David S. Salomon
- Tumor Growth Factor Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, 21702, United States of America
| | - Yelena G. Golubeva
- Pathology-Histotechnology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States of America
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33
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Bari MF, Ngo S, Bastie CC, Sheppard AM, Vatish M. Gestational diabetic transcriptomic profiling of microdissected human trophoblast. J Endocrinol 2016; 229:47-59. [PMID: 26869332 DOI: 10.1530/joe-15-0424] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/11/2016] [Indexed: 12/16/2022]
Abstract
Gestational diabetes mellitus (GDM), the most common metabolic complication of pregnancy, is influenced by the placenta, and its prevalence directly increases with obesity. Therefore, to define the aetiology of GDM requires that the confounding influence of obesity and the heterogeneous nature of the placenta impairing accurate quantitative studies be accounted for. Using laser capture microdissection (LCM), we optimized RNA extraction from human placental trophoblast, the metabolic cellular interface between mother and foetus. This allowed specific transcriptomic profiling of trophoblast isolated from GDM, and obese and normal human placentae. Genome-wide gene expression analysis was performed on the RNA extracted from the trophoblast of GDM and obese and normal placentae. Forty-five differentially expressed genes (DEGs) specifically discriminated GDM from matched obese subjects. Two genes previously linked with GDM, pregnancy specific beta-1 glycoprotein 6 (PSG6) and placental system A sodium-dependent transporter system (SLC38A1), were significantly increased in GDM. A number of these DEGs (8 ubiquitin-conjugating enzymes (UBE) splice variants (UBE2D3 variants 1, 3, 4, 5, 6, 7, and 9) and UBE2V1 variant 4)) were involved in RNA processing and splicing, and a significant number of the DEGs, including the UBE variants, were associated with increased maternal fasting plasma glucose.It is concluded that DEGs discriminating GDM from obese subjects were pinpointed. Our data indicate a biological link between genes involved in RNA processing and splicing, ubiquitination, and fasting plasma glucose in GDM taking into account obesity as the confounder.
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Affiliation(s)
| | - Sherry Ngo
- Liggins InstituteUniversity of Auckland, Auckland, New Zealand
| | - Claire C Bastie
- Division of Biomedical SciencesWarwick Medical School, Coventry, UK
| | | | - Manu Vatish
- Nuffield Department of Obstetrics and GynaecologyUniversity of Oxford, John Radcliffe Hospital, Oxford, UK
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Kolijn K, van Leenders GJLH. Comparison of RNA extraction kits and histological stains for laser capture microdissected prostate tissue. BMC Res Notes 2016; 9:17. [PMID: 26744212 PMCID: PMC4705748 DOI: 10.1186/s13104-015-1813-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 12/17/2015] [Indexed: 12/02/2022] Open
Abstract
Background Laser capture microdissection offers unique possibilities for the isolation of specific cell populations or histological structures. However, isolation of RNA from microdissected tissue is challenging due to degradation and minimal yield of RNA during laser capture microdissection (LCM). Our aim was to optimize the isolation of high-quality RNA from laser capture microdissected fresh frozen prostate tissue on the level of staining and RNA extraction. Results Cresyl violet and haematoxylin were compared as histological stains for LCM. While RNA quality was similar for cresyl violet (median RIN 7.4) and haematoxylin (median RIN 7.6), tissue morphology was more detailed with cresyl violet as compared to haematoxylin. RNA quality from the following kits was compared: RNeasy® Micro (median RIN 7.2), miRNeasy Mini (median RIN 6.6), Picopure® (median RIN 6.0), mirVana™ miRNA (median RIN 6.5) and RNAqueous®-Micro (median RIN 6.3). RNA quality from microdissected samples with either the RNeasy Micro or miRNeasy Mini kit, was comparable to RNA isolated directly from whole tissue slices (median RIN 7.5, p = 0.09). Isolated RNA from benign and prostate cancer microdissected tissue demonstrated that RNA quality can vary between regions from the same clinical sample. Additionally, RNA quality (r = 0.89), but not quantity (r = 0.69) could be precisely measured with the Agilent Bioanalyzer. Conclusions We demonstrate that staining with cresyl violet results in the isolation of high quality RNA from laser capture microdissected tissue with high discriminative morphology. The RNeasy Micro and miRNeasy Mini RNA extraction kits generated the highest quality RNA compared to Picopure, mirVana and RNAqueous with minimal loss of RNA quality during LCM. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1813-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kimberley Kolijn
- Department of Pathology, Erasmus MC, Rotterdam, The Netherlands.
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Bergau N, Navarette Santos A, Henning A, Balcke GU, Tissier A. Autofluorescence as a Signal to Sort Developing Glandular Trichomes by Flow Cytometry. FRONTIERS IN PLANT SCIENCE 2016; 7:949. [PMID: 27446176 PMCID: PMC4923063 DOI: 10.3389/fpls.2016.00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/14/2016] [Indexed: 05/04/2023]
Abstract
The industrial relevance of a number of metabolites produced in plant glandular trichomes (GTs) has spurred research on these specialized organs for a number of years. Most of the research, however, has focused on the elucidation of secondary metabolite pathways and comparatively little has been undertaken on the development and differentiation of GTs. One way to gain insight into these developmental processes is to generate stage-specific transcriptome and metabolome data. The difficulty for this resides in the isolation of early stages of development of the GTs. Here we describe a method for the separation and isolation of intact young and mature type VI trichomes from the wild tomato species Solanum habrochaites. The final and key step of the method uses cell sorting based on distinct autofluorescence signals of the young and mature trichomes. We demonstrate that sorting by flow cytometry allows recovering pure fractions of young and mature trichomes. Furthermore, we show that the sorted trichomes can be used for transcript and metabolite analyses. Because many plant tissues or cells have distinct autofluorescence components, the principles of this method can be generally applicable for the isolation of specific cell types without prior labeling.
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Affiliation(s)
- Nick Bergau
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | | | - Anja Henning
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Gerd U. Balcke
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz-Institute of Plant BiochemistryHalle, Germany
- *Correspondence: Alain Tissier,
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Enrichment of single neurons and defined brain regions from human brain tissue samples for subsequent proteome analysis. J Neural Transm (Vienna) 2015; 122:993-1005. [PMID: 26123835 DOI: 10.1007/s00702-015-1414-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/11/2015] [Indexed: 12/11/2022]
Abstract
Brain function in normal aging and neurological diseases has long been a subject of interest. With current technology, it is possible to go beyond descriptive analyses to characterize brain cell populations at the molecular level. However, the brain comprises over 100 billion highly specialized cells, and it is a challenge to discriminate different cell groups for analyses. Isolating intact neurons is not feasible with traditional methods, such as tissue homogenization techniques. The advent of laser microdissection techniques promises to overcome previous limitations in the isolation of specific cells. Here, we provide a detailed protocol for isolating and analyzing neurons from postmortem human brain tissue samples. We describe a workflow for successfully freezing, sectioning and staining tissue for laser microdissection. This protocol was validated by mass spectrometric analysis. Isolated neurons can also be employed for western blotting or PCR. This protocol will enable further examinations of brain cell-specific molecular pathways and aid in elucidating distinct brain functions.
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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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Winslow S, Leandersson K, Edsjö A, Larsson C. Prognostic stromal gene signatures in breast cancer. Breast Cancer Res 2015; 17:23. [PMID: 25848820 PMCID: PMC4360948 DOI: 10.1186/s13058-015-0530-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 02/02/2015] [Indexed: 12/21/2022] Open
Abstract
Introduction Global gene expression analysis of tumor samples has been a valuable tool to subgroup tumors and has the potential to be of prognostic and predictive value. However, tumors are heterogeneous, and homogenates will consist of several different cell types. This study was designed to obtain more refined expression data representing different compartments of the tumor. Methods Formalin-fixed paraffin-embedded stroma-rich triple-negative breast cancer tumors were laser-microdissected, and RNA was extracted and processed to enable microarray hybridization. Genes enriched in stroma were identified and used to generate signatures by identifying correlating genes in publicly available data sets. The prognostic implications of the signature were analyzed. Results Comparison of the expression pattern from stromal and cancer cell compartments from three tumors revealed a number of genes that were essentially specifically expressed in the respective compartments. The stroma-specific genes indicated contribution from fibroblasts, endothelial cells, and immune/inflammatory cells. The gene set was expanded by identifying correlating mRNAs using breast cancer mRNA expression data from The Cancer Genome Atlas. By iterative analyses, 16 gene signatures of highly correlating genes were characterized. Based on the gene composition, they seem to represent different cell types. In multivariate Cox proportional hazard models, two immune/inflammatory signatures had opposing hazard ratios for breast cancer recurrence also after adjusting for clinicopathological variables and molecular subgroup. The signature associated with poor prognosis consisted mainly of C1Q genes and the one associated with good prognosis contained HLA genes. This association with prognosis was seen for other cancers as well as in other breast cancer data sets. Conclusions Our data indicate that the molecular composition of the immune response in a tumor may be a powerful predictor of cancer prognosis. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0530-2) contains supplementary material, which is available to authorized users.
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Gu J, Lei Y, Huang Y, Zhao Y, Li J, Huang T, Zhang J, Wang J, Deng X, Chen Z, Korteweg C, Deng R, Yan M, Xu Q, Dong S, Cai M, Luo L, Huang G, Wang Y, Li Q, Lin C, Su M, Yang C, Zhuang Z. Fab fragment glycosylated IgG may play a central role in placental immune evasion. Hum Reprod 2015; 30:380-91. [PMID: 25505012 PMCID: PMC4303772 DOI: 10.1093/humrep/deu323] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 10/10/2014] [Accepted: 10/30/2014] [Indexed: 02/05/2023] Open
Abstract
STUDY QUESTION How does the placenta protect the fetus from immune rejection by the mother? SUMMARY ANSWER The placenta can produce IgG that is glycosylated at one of its Fab arms (asymmetric IgG; aIgG) which can interact with other antibodies and certain leukocytes to affect local immune reactions at the junction between the two genetically distinct entities. WHAT IS KNOWN ALREADY The placenta can protect the semi-allogenic fetus from immune rejection by the immune potent mother. aIgG in serum is increased during pregnancy and returns to the normal range after giving birth. aIgG can react to antigens to form immune complexes which do not cause a subsequent immune effector reaction, including fixing complements, inducing cytotoxicity and phagocytosis, and therefore has been called 'blocking antibody'. STUDY DESIGN, SIZE, DURATION Eighty-eight human placentas, four trophoblast cell lines (TEV-1, JAR, JEG and BeWo), primary culture of human placental trophoblasts and a gene knock-out mouse model were investigated in this study. PARTICIPANTS/MATERIALS, SETTING, METHODS The general approach included the techniques of cell culture, immunohistochemistry, in situ hybridization, immuno-electron microscopy, western blot, quantitative PCR, protein isolation, glycosylation analysis, enzyme digestion, gene sequencing, mass spectrophotometry, laser-guided microdissection, enzyme-linked immunosorbent assay, pulse chase assay, double and multiple staining to analyze protein and DNA and RNA analysis at the cellular and molecular levels. MAIN RESULTS AND THE ROLE OF CHANCE Three major discoveries were made: (i) placental trophoblasts and endothelial cells are capable of producing IgG, a significant portion of which is aberrantly glycosylated at one of its Fab arms to form aIgG; (ii) the asymmetrically glycosylated IgG produced by trophoblasts and endothelial cells can react to immunoglobulin molecules of human, rat, mouse, goat and rabbit at the Fc portion; (iii) asymmetrically glycosylated IgG can react to certain leukocytes in the membrane and cytoplasm, while symmetric IgG from the placenta does not have this property. LIMITATIONS, REASONS FOR CAUTION Most of the experiments were performed in vitro. The proposed mechanism calls for verification in normal and abnormal pregnancy. WIDER IMPLICATIONS OF THE FINDINGS This study identified a number of new phenomena suggesting that aIgG produced by the placenta would be able to react to detrimental antibodies and leukocytes and interfere with their immune reactions against the placenta and the fetus. This opens a new dimension for further studies on pregnancy physiology and immunology. Should the mechanism proposed here be confirmed, it will have a direct impact on our understanding of the physiology and pathology of human reproduction and offer new possibilities for the treatment of many diseases including spontaneous abortion, infertility and pre-eclampsia. It also sheds light on the mechanism of immune evasion in general including that of cancer.
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Affiliation(s)
- Jiang Gu
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China Department of Pathology, Beijing University Health Science Center, Beijing 100083, China Translational Medicine Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Yu Lei
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yuanping Huang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yingying Zhao
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China Department of Pathology, Beijing University Health Science Center, Beijing 100083, China
| | - Jing Li
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Tao Huang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Junjun Zhang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Juping Wang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xiaodong Deng
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhengshan Chen
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Christine Korteweg
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Ruishu Deng
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China Department of Pathology, Beijing University Health Science Center, Beijing 100083, China
| | - Meiling Yan
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Qian Xu
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Shengnan Dong
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Monghong Cai
- Translational Medicine Center, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Lili Luo
- Department of Gynecology and Obstetrician, First Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Guowei Huang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yun Wang
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Qian Li
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Changmei Lin
- Department of Fertility, Haidian Maternal and Child Health Hospital, Beijing 100080, China
| | - Meng Su
- Department of Pathology and Provincial Key Laboratory of Infectious Diseases and Immunopathology, Shantou University Medical College, Shantou, Guangdong 515041, China Department of Pathology, Beijing University Health Science Center, Beijing 100083, China
| | - Chunzhang Yang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Building 10, Room 5D 37, 10 Center Drive, Bethesda, MD 20892, USA
| | - Zhengping Zhuang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Building 10, Room 5D 37, 10 Center Drive, Bethesda, MD 20892, USA
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Cai J, Li T, Huang B, Cheng H, Ding H, Dong W, Xiao M, Liu L, Wang Z. The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples. PLoS One 2014; 9:e95974. [PMID: 24776823 PMCID: PMC4002476 DOI: 10.1371/journal.pone.0095974] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/01/2014] [Indexed: 11/19/2022] Open
Abstract
Quantitative real-time PCR (qPCR) is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M) were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD), an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA) and nonparametric (Kruskal-Wallis) tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP) and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.
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Affiliation(s)
- Jing Cai
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Li
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bangxing Huang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Henghui Cheng
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Ding
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weihong Dong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Man Xiao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ling Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zehua Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail:
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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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Bari MF, Brown H, Nicholson AG, Kerr KM, Gosney JR, Wallace WA, Soomro I, Muller S, Peat D, Moore JD, Ward LA, Freidin MB, Lim E, Vatish M, Snead DRJ. BAI3, CDX2 and VIL1: a panel of three antibodies to distinguish small cell from large cell neuroendocrine lung carcinomas. Histopathology 2013; 64:547-56. [PMID: 24266897 DOI: 10.1111/his.12278] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/04/2013] [Indexed: 11/29/2022]
Abstract
AIMS Discriminating small-cell lung carcinoma (SCLC) from large-cell neuroendocrine carcinoma (LCNEC) rests on morphological criteria, and reproducibility has been shown to be poor. We aimed to identify immunohistochemical markers to assist this diagnosis. METHODS AND RESULTS Gene expression profiling on laser captured frozen tumour samples from eight SCLC and eight LCNEC tumours identified a total of 888 differentially expressed genes (DEGs), 23 of which were validated by qRT-PCR. Antibodies to four selected gene products were then evaluated as immunohistochemical markers on a cohort of 173 formalin-fixed paraffin-embedded (FFPE) SCLC/LCNEC tumour samples, including 26 indeterminate tumours without a consensus diagnosis. Three markers, CDX2, VIL1 and BAI3, gave significantly different results in the two tumour types (P < 0.0001): CDX2 and VIL1 in combination (either marker positive) showed sensitivity and specificity of 81% for LCNEC while BAI3 showed 89% sensitivity and 75% specificity for SCLC. Of the 26 indeterminate tumours 15 (58%) showed an immunophenotype suggesting either SCLC or LCNEC, eight (31%) showed staining of both tumour types, and three (11%) were negative for all markers. CONCLUSION A panel of three markers, BAI3, CDX2 and VIL1, is a useful adjunct in the diagnosis of these tumour types.
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Affiliation(s)
- Muhammad F Bari
- Department of Pathology, Dow International Medical College, Karachi, Pakistan; Department of Pathology, University Hospitals Coventry and Warwickshire NHS Trust, Coventry, UK; Divisions of Reproduction and Metabolic and Vascular Health, Warwick Medical School, Coventry, UK
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Harries MJ, Meyer K, Chaudhry I, E Kloepper J, Poblet E, Griffiths CE, Paus R. Lichen planopilaris is characterized by immune privilege collapse of the hair follicle's epithelial stem cell niche. J Pathol 2013; 231:236-47. [PMID: 23788005 DOI: 10.1002/path.4233] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/01/2013] [Accepted: 06/07/2013] [Indexed: 12/16/2022]
Abstract
Lichen planopilaris (LPP) is a chronic inflammatory disease of unknown pathogenesis that leads to permanent hair loss. Whilst destruction of epithelial hair follicle stem cells (eHFSCs) that reside in an immunologically protected niche of the HF epithelium, the bulge, is a likely key event in LPP pathogenesis, this remains to be demonstrated. We have tested the hypotheses that bulge immune privilege (IP) collapse and inflammation-induced eHFSC death are key components in the pathogenesis of LPP. Biopsies of lesional and non-lesional scalp skin from adult LPP patients (n = 42) were analysed by quantitative (immuno)histomorphometry, real-time quantitative polymerase chain reaction (qRT-PCR), laser capture microdissection and microarray analysis, or skin organ culture. At both the protein and transcriptional level, lesional LPP HFs showed evidence for bulge IP collapse (ie increased expression of MHC class I and II, β2microglobulin; reduced TGFβ2 and CD200 expression). This was accompanied by a Th1-biased cytotoxic T cell response (ie increased CD8(+) GranzymeB(+) T cells and CD123(+) plasmacytoid dendritic cells, with increased CXCR3 expression) and increased expression of interferon-inducible chemokines (CXCL9/10/11). Interestingly, lesional LPP eHFSCs showed both increased proliferation and apoptosis in situ. Microarray analysis revealed a loss of eHFSC signatures and increased expression of T cell activation/binding markers in active LPP, while bulge PPARγ transcription was unaltered compared to non-lesional LPP HFs. In organ culture of non-lesional LPP skin, interferon-γ (IFNγ) induced bulge IP collapse. LPP is an excellent model disease for studying and preventing immune destruction of human epithelial stem cells in situ. These novel findings raise the possibility that LPP represents an autoimmune disease in whose pathogenesis IFNγ-induced bulge IP collapse plays an important role. Therapeutically, bulge IP protection/restoration may help to better manage this highly treatment-resistant cicatricial alopecia.
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Affiliation(s)
- Matthew J Harries
- Dermatology Centre, Salford Royal NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, UK
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45
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Huang G, Wang S. Establishment of a new method to detect gene expression by laser capture microdissection-assisted single-cell real time RT-PCR without RNA purification. Mol Biol 2013. [DOI: 10.1134/s0026893313040055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vandewoestyne M, Goossens K, Burvenich C, Van Soom A, Peelman L, Deforce D. Laser capture microdissection: Should an ultraviolet or infrared laser be used? Anal Biochem 2013; 439:88-98. [DOI: 10.1016/j.ab.2013.04.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 11/28/2022]
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47
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Golubeva YG, Smith RM, Sternberg LR. Optimizing Frozen Sample Preparation for Laser Microdissection: Assessment of CryoJane Tape-Transfer System®. PLoS One 2013; 8:e66854. [PMID: 23805281 PMCID: PMC3689705 DOI: 10.1371/journal.pone.0066854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 05/10/2013] [Indexed: 01/26/2023] Open
Abstract
Laser microdissection is an invaluable tool in medical research that facilitates collecting specific cell populations for molecular analysis. Diversity of research targets (e.g., cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, etc.) and varied scientific objectives, however, present challenges toward establishing standard laser microdissection protocols. Sample preparation is crucial for quality RNA, DNA and protein retrieval, where it often determines the feasibility of a laser microdissection project. The majority of microdissection studies in clinical and animal model research are conducted on frozen tissues containing native nucleic acids, unmodified by fixation. However, the variable morphological quality of frozen sections from tissues containing fat, collagen or delicate cell structures can limit or prevent successful harvest of the desired cell population via laser dissection. The CryoJane Tape-Transfer System®, a commercial device that improves cryosectioning outcomes on glass slides has been reported superior for slide preparation and isolation of high quality osteocyte RNA (frozen bone) during laser dissection. Considering the reported advantages of CryoJane for laser dissection on glass slides, we asked whether the system could also work with the plastic membrane slides used by UV laser based microdissection instruments, as these are better suited for collection of larger target areas. In an attempt to optimize laser microdissection slide preparation for tissues of different RNA stability and cryosectioning difficulty, we evaluated the CryoJane system for use with both glass (laser capture microdissection) and membrane (laser cutting microdissection) slides. We have established a sample preparation protocol for glass and membrane slides including manual coating of membrane slides with CryoJane solutions, cryosectioning, slide staining and dissection procedure, lysis and RNA extraction that facilitated efficient dissection and high quality RNA retrieval from CryoJane preparations. CryoJane technology therefore has the potential to facilitate standardization of laser microdissection slide preparation from frozen tissues.
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Affiliation(s)
- Yelena G. Golubeva
- Pathology-Histotechnology Laboratory, Science Applications International Corporation-Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Roberta M. Smith
- Pathology-Histotechnology Laboratory, Science Applications International Corporation-Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lawrence R. Sternberg
- Pathology-Histotechnology Laboratory, Science Applications International Corporation-Frederick, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
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Russ AE, Peters JS, McNabb WC, Barnett MPG, Anderson RC, Park Z, Zhu S, Maclean P, Young W, Reynolds GW, Roy NC. Gene expression changes in the colon epithelium are similar to those of intact colon during late inflammation in interleukin-10 gene deficient mice. PLoS One 2013; 8:e63251. [PMID: 23700416 PMCID: PMC3659096 DOI: 10.1371/journal.pone.0063251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/01/2013] [Indexed: 01/08/2023] Open
Abstract
In addition to their role in absorption and secretion, epithelial cells play an important role in the protection of the colon mucosa from the resident microbiota and are important for the maintenance of homeostasis. Microarray analysis of intact colon samples is widely used to gain an overview of the cellular pathways and processes that are active in the colon during inflammation. Laser microdissection of colon epithelial cells allows a more targeted analysis of molecular pathways in the mucosa, preceding and during inflammation, with potentially increased sensitivity to changes in specific cell populations. The aim of this study was to investigate the molecular changes that occur in early and late inflammation stages in colon epithelium of a mouse model of inflammatory bowel diseases. Microarray analysis of intact colon samples and microdissected colon epithelial cell samples from interleukin-10 gene deficient and control mice at 6 and 12 weeks of age was undertaken. Results of gene set enrichment analysis showed that more immune-related pathways were identified between interleukin-10 gene deficient and control mice at 6 weeks of age in epithelial cells than intact colon. This suggests that targeting epithelial cells could increase sensitivity for detecting immune changes that occur early in the inflammatory process. However, in the later stages of inflammation, microarray analyses of intact colon and epithelium both provide a similar overview of gene expression changes in the colon mucosa at the pathway level.
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Affiliation(s)
- Anna E. Russ
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
- Institute of Food Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| | - Jason S. Peters
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
| | - Warren C. McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
- AgResearch Grasslands, Palmerston North, New Zealand
| | - Matthew P. G. Barnett
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
| | - Rachel C. Anderson
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
| | - Zaneta Park
- Bioinformatics & Statistics, AgResearch, Hamilton, New Zealand
| | - Shuotun Zhu
- Discipline of Nutrition, Faculty of Medicine and Health Sciences, The University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Paul Maclean
- Bioinformatics & Statistics, AgResearch, Hamilton, New Zealand
| | - Wayne Young
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
| | - Gordon W. Reynolds
- Institute of Food Nutrition and Human Health, Massey University, Palmerston North, New Zealand
| | - Nicole C. Roy
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Grasslands, Palmerston North, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- * E-mail:
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Orsi W, Biddle JF, Edgcomb V. Deep sequencing of subseafloor eukaryotic rRNA reveals active Fungi across marine subsurface provinces. PLoS One 2013; 8:e56335. [PMID: 23418556 PMCID: PMC3572030 DOI: 10.1371/journal.pone.0056335] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/08/2013] [Indexed: 02/01/2023] Open
Abstract
The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface.
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Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America.
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Grover PK, Cummins AG, Price TJ, Roberts-Thomson IC, Hardingham JE. A simple, cost-effective and flexible method for processing of snap-frozen tissue to prepare large amounts of intact RNA using laser microdissection. Biochimie 2012; 94:2491-7. [PMID: 22796379 DOI: 10.1016/j.biochi.2012.06.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 06/22/2012] [Indexed: 12/16/2022]
Abstract
Understanding the molecular basis of disease requires gene expression profiling of normal and pathological tissue. Although the advent of laser microdissection (LMD) has greatly facilitated the procurement of specific cell populations, often only small amounts of low quality RNA is recovered. This precludes the use of global approaches of gene expression profiling which require sizable amounts of high quality RNA. Here we report a method for processing of snap-frozen tissue to prepare large amounts of intact RNA using LMD. Portions of small intestine from piglets (n = 6) were snap-frozen in Optimum Cutting Temperature compound (experimental) and in RNAlater (control). A randomly selected sample was laser microdissected using the developed protocol in multiple sessions totalling 4 h each day on four consecutive days. RNAs were extracted from these samples and its control and their quality (RIN) determined. RINs of the experimental samples were independent of time (p = 0.12) and day (p = 0.56) of the microdissection thereby suggesting that their RNA quality remained unaltered. These samples exhibited high quality (RIN ≥ 8) with good recovery (81.2%) and excellent yield (1539 ng/1.2 × 10(7) μm(2)). Their overall RIN, 8.029 ± 0.116, was not significantly different from 8.2 (p = 0.123), the value obtained from the control, non-laser microdissected, sample. This indicated that the RNA quality from the laser microdissected and non-microdissected samples was comparable. The method allowed LMD for up to 4 h each day for a total of four days. The microdissected samples can be pooled thereby increasing amount of RNA at least by ten-fold. The procedure did not require any expensive limited-shelf life RNase inhibitors, RNA protectors, staining kits or toxic chemicals. Furthermore, it was flexible and enabled the processing without affecting routine laboratory workflow. The method developed was simple, inexpensive and provided substantial amounts of high quality RNA suitable for gene expression profiling and other cellular and molecular analyses for biology and molecular medicine.
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Affiliation(s)
- Phulwinder K Grover
- Department of Surgery, Basil Hetzel Institute for Translational Health Research, The Queen Elizabeth Hospital and Discipline of Medicine, University of Adelaide, 28 Woodville Road, Woodville South, South Australia 5011, Australia.
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