1
|
Rosales RS, Risco D, García-Nicolás O, Pallarés FJ, Ramírez AS, Poveda JB, Nicholas RAJ, Salguero FJ. Differential Gene Expression in Porcine Lung Compartments after Experimental Infection with Mycoplasma hyopneumoniae. Animals (Basel) 2024; 14:1290. [PMID: 38731294 PMCID: PMC11083927 DOI: 10.3390/ani14091290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/20/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Mycoplasma hyopneumoniae (Mhyo) is the causative agent of porcine enzootic pneumonia (EP), as well as one of the main pathogens involved in the porcine respiratory disease complex. The host-pathogen interaction between Mhyo and infected pigs is complex and not completely understood; however, improving the understanding of these intricacies is essential for the development of effective control strategies of EP. In order to improve our knowledge about this interaction, laser-capture microdissection was used to collect bronchi, bronchi-associated lymphoid tissue, and lung parenchyma from animals infected with different strains of Mhyo, and mRNA expression levels of different molecules involved in Mhyo infection (ICAM1, IL-8, IL-10, IL-23, IFN-α, IFN-γ, TGF-β, and TNF-α) were analyzed by qPCR. In addition, the quantification of Mhyo load in the different lung compartments and the scoring of macroscopic and microscopic lung lesions were also performed. Strain-associated differences in virulence were observed, as well as the presence of significant differences in expression levels of cytokines among lung compartments. IL-8 and IL-10 presented the highest upregulation, with limited differences between strains and lung compartments. IFN-α was strongly downregulated in BALT, implying a relevant role for this cytokine in the immunomodulation associated with Mhyo infections. IL-23 was also upregulated in all lung compartments, suggesting the potential involvement of a Th17-mediated immune response in Mhyo infections. Our findings highlight the relevance of Th1 and Th2 immune response in cases of EP, shedding light on the gene expression levels of key cytokines in the lung of pigs at a microscopic level.
Collapse
Affiliation(s)
- Rubén S. Rosales
- Instituto Universitario de Sanidad Animal y Seguridad Alimentaria (IUSA), Veterinary Faculty, University of Las Palmas de Gran Canaria, Trasmontaña s/n, 35416 Arucas, Spain; (R.S.R.); (A.S.R.); (J.B.P.)
| | - David Risco
- Unidad de Histología y Anatomía Patológica, Departamento de Medicina Animal, Veterinary Faculty, University of Extremadura, Avenida de la Universidad, s/n, 10003 Cáceres, Spain
| | - Obdulio García-Nicolás
- Institute of Virology and Immunology (IVI), Sensemattstrasse 293, 3147 Mittelhäusern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Francisco J. Pallarés
- Pathology and Immunology Group (UCO-PIG), Department of Anatomy and Comparative Pathology and Toxicology, UIC Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, International Excellence Agrifood Campus “CeiA3”, 14001 Córdoba, Spain;
| | - Ana S. Ramírez
- Instituto Universitario de Sanidad Animal y Seguridad Alimentaria (IUSA), Veterinary Faculty, University of Las Palmas de Gran Canaria, Trasmontaña s/n, 35416 Arucas, Spain; (R.S.R.); (A.S.R.); (J.B.P.)
| | - José B. Poveda
- Instituto Universitario de Sanidad Animal y Seguridad Alimentaria (IUSA), Veterinary Faculty, University of Las Palmas de Gran Canaria, Trasmontaña s/n, 35416 Arucas, Spain; (R.S.R.); (A.S.R.); (J.B.P.)
| | | | - Francisco J. Salguero
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Rd, Guildford GU2 7AL, UK;
| |
Collapse
|
2
|
Machado JPD, de Almeida V, Zuardi AW, Hallak JEC, Crippa JA, Vieira AS. Cannabidiol modulates hippocampal genes involved in mitochondrial function, ribosome biogenesis, synapse organization, and chromatin modifications. Acta Neuropsychiatr 2024:1-7. [PMID: 38528655 DOI: 10.1017/neu.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
BACKGROUND Cannabidiol (CBD) is one of the main cannabinoids present in Cannabis sativa female flowers. Previous investigation has already provided insights into the CBD molecular mechanism; however, there is no transcriptome data for CBD effects on hippocampal subfields. Here, we investigate transcriptomic changes in dorsal and ventral CA1 of adult mice hippocampus after 100 mg/kg of CBD administration (i.p.) for one or seven consecutive days. METHODS C57BL/6JUnib mice were treated with either vehicle or CBD for 1 or 7 days. The collected brains were sectioned, and the hippocampal sub-regions were laser microdissected for RNA-Seq analysis. RESULTS The transcriptome analysis following 7 days of CBD administration indicates the differential expression of 1559 genes in dCA1 and 2924 genes in vCA1. Furthermore, GO/KEGG analysis identified 88 significantly enriched biological process and 26 significantly enriched pathways for dCBD7, whereas vCBD7 revealed 128 enriched BPs and 24 pathways. CONCLUSION This dataset indicates a widespread decrease of electron transport chain and ribosome biogenesis transcripts in CA1, while chromatin modifications and synapse organization transcripts were increased following CBD administration for 7 days.
Collapse
Affiliation(s)
- João P D Machado
- Laboratory of Electrophysiology, Neurobiology and Behaviour, Dept Functional and Structural Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Valéria de Almeida
- Laboratory of Neuroproteomics,, Dept Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinsas, São Paulo, Brazil
| | - Antonio W Zuardi
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute for Science and Technology - Translational Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jaime E C Hallak
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute for Science and Technology - Translational Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José A Crippa
- Department of Neuroscience and Behavior, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- National Institute for Science and Technology - Translational Medicine, Rio de Janeiro, Rio de Janeiro, Brazil
| | - André S Vieira
- Laboratory of Electrophysiology, Neurobiology and Behaviour, Dept Functional and Structural Biology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| |
Collapse
|
3
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
4
|
Whitehill JGA, Yuen MMS, Chiang A, Ritland CE, Bohlmann J. Transcriptome features of stone cell development in weevil-resistant and susceptible Sitka spruce. New Phytol 2023; 239:2138-2152. [PMID: 37403300 DOI: 10.1111/nph.19103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
Stone cells are a specialized, highly lignified cell type found in both angiosperms and gymnosperms. In conifers, abundance of stone cells in the cortex provides a robust constitutive physical defense against stem feeding insects. Stone cells are a major insect-resistance trait in Sitka spruce (Picea sitchensis), occurring in dense clusters in apical shoots of trees resistant (R) to spruce weevil (Pissodes strobi) but being rare in susceptible (S) trees. To learn more about molecular mechanisms of stone cell formation in conifers, we used laser microdissection and RNA sequencing to develop cell-type-specific transcriptomes of developing stone cells from R and S trees. Using light, immunohistochemical, and fluorescence microscopy, we also visualized the deposition of cellulose, xylan, and lignin associated with stone cell development. A total of 1293 genes were differentially expressed at higher levels in developing stone cells relative to cortical parenchyma. Genes with potential roles in stone cell secondary cell wall formation (SCW) were identified and their expression evaluated over a time course of stone cell formation in R and S trees. The expression of several transcriptional regulators was associated with stone cell formation, including a NAC family transcription factor and several genes annotated as MYB transcription factors with known roles in SCW formation.
Collapse
Affiliation(s)
- Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Forest Improvement and Research Management Branch, British Columbia Ministry of Forests, Lands, and Natural Resource Operations and Rural Development, 7380 Puckle Road, Saanichton, BC, V8M 1W4, Canada
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Angela Chiang
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Carol E Ritland
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| |
Collapse
|
5
|
Zhao LL, Zhang T, Huang WX, Guo TT, Gu XS. Transcriptional regulatory network during axonal regeneration of dorsal root ganglion neurons: laser-capture microdissection and deep sequencing. Neural Regen Res 2023; 18:2056-2066. [PMID: 36926732 DOI: 10.4103/1673-5374.366494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
The key regulators and regeneration-associated genes involved in axonal regeneration of neurons after injury have not been clarified. In high-throughput sequencing, various factors influence the final sequencing results, including the number and size of cells, the depth of sequencing, and the method of cell separation. There is still a lack of research on the detailed molecular expression profile during the regeneration of dorsal root ganglion neuron axon. In this study, we performed laser-capture microdissection coupled with RNA sequencing on dorsal root ganglion neurons at 0, 3, 6, and 12 hours and 1, 3, and 7 days after sciatic nerve crush in rats. We identified three stages after dorsal root ganglion injury: early (3-12 hours), pre-regeneration (1 day), and regeneration (3-7 days). Gene expression patterns and related function enrichment results showed that one module of genes was highly related to axonal regeneration. We verified the up-regulation of activating transcription factor 3 (Atf3), Kruppel like factor 6 (Klf6), AT-rich interaction domain 5A (Arid5a), CAMP responsive element modulator (Crem), and FOS like 1, AP-1 transcription factor Subunit (Fosl1) in dorsal root ganglion neurons after injury. Suppressing these transcription factors (Crem, Arid5a, Fosl1 and Klf6) reduced axonal regrowth in vitro. As the hub transcription factor, Atf3 showed higher expression and activity at the pre-regeneration and regeneration stages. G protein-coupled estrogen receptor 1 (Gper1), interleukin 12a (Il12a), estrogen receptor 1 (ESR1), and interleukin 6 (IL6) may be upstream factors that trigger the activation of Atf3 during the repair of axon injury in the early stage. Our study presents the detailed molecular expression profile during axonal regeneration of dorsal root ganglion neurons after peripheral nerve injury. These findings may provide reference for the clinical screening of molecular targets for the treatment of peripheral nerve injury.
Collapse
Affiliation(s)
- Li-Li Zhao
- Model Animal Research Center and MOE Key Laboratory of Animal Models of Disease, Nanjing University, Nanjing; Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Tao Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong; School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Wei-Xiao Huang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong; School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Ting-Ting Guo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Song Gu
- Model Animal Research Center and MOE Key Laboratory of Animal Models of Disease, Nanjing University, Nanjing; Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| |
Collapse
|
6
|
Rumpler É, Göcz B, Skrapits K, Sárvári M, Takács S, Farkas I, Póliska S, Papp M, Solymosi N, Hrabovszky E. Development of a versatile LCM-Seq method for spatial transcriptomics of fluorescently tagged cholinergic neuron populations. J Biol Chem 2023; 299:105121. [PMID: 37536628 PMCID: PMC10477691 DOI: 10.1016/j.jbc.2023.105121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/29/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
Single-cell transcriptomics are powerful tools to define neuronal cell types based on co-expressed gene clusters. Limited RNA input in these technologies necessarily compromises transcriptome coverage and accuracy of differential expression analysis. We propose that bulk RNA-Seq of neuronal pools defined by spatial position offers an alternative strategy to overcome these technical limitations. We report a laser-capture microdissection (LCM)-Seq method which allows deep transcriptome profiling of fluorescently tagged neuron populations isolated with LCM from histological sections of transgenic mice. Mild formaldehyde fixation of ZsGreen marker protein, LCM sampling of ∼300 pooled neurons, followed by RNA isolation, library preparation and RNA-Seq with methods optimized for nanogram amounts of moderately degraded RNA enabled us to detect ∼15,000 different transcripts in fluorescently labeled cholinergic neuron populations. The LCM-Seq approach showed excellent accuracy in quantitative studies, allowing us to detect 2891 transcripts expressed differentially between the spatially defined and clinically relevant cholinergic neuron populations of the dorsal caudate-putamen and medial septum. In summary, the LCM-Seq method we report in this study is a versatile, sensitive, and accurate bulk sequencing approach to study the transcriptome profile and differential gene expression of fluorescently tagged neuronal populations isolated from transgenic mice with high spatial precision.
Collapse
Affiliation(s)
- Éva Rumpler
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary.
| | - Balázs Göcz
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary; János Szentágothai Doctoral School of Neurosciences, Semmelweis University, Budapest, Hungary.
| | - Katalin Skrapits
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Miklós Sárvári
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Szabolcs Takács
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Imre Farkas
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary
| | - Szilárd Póliska
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine, Budapest, Hungary; Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Erik Hrabovszky
- Laboratory of Reproductive Neurobiology, Institute of Experimental Medicine, Budapest, Hungary.
| |
Collapse
|
7
|
Riemens RJM, Kenis G, Nolz J, Susano Chaves SC, Duroux D, Pishva E, Mastroeni D, Van Steen K, Haaf T, van den Hove DLA. Targeted Methylation Profiling of Single Laser-Capture Microdissected Post-Mortem Brain Cells by Adapted Limiting Dilution Bisulfite Pyrosequencing (LDBSP). Int J Mol Sci 2022; 23. [PMID: 36555213 DOI: 10.3390/ijms232415571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022] Open
Abstract
A reoccurring issue in neuroepigenomic studies, especially in the context of neurodegenerative disease, is the use of (heterogeneous) bulk tissue, which generates noise during epigenetic profiling. A workable solution to this issue is to quantify epigenetic patterns in individually isolated neuronal cells using laser capture microdissection (LCM). For this purpose, we established a novel approach for targeted DNA methylation profiling of individual genes that relies on a combination of LCM and limiting dilution bisulfite pyrosequencing (LDBSP). Using this approach, we determined cytosine-phosphate-guanine (CpG) methylation rates of single alleles derived from 50 neurons that were isolated from unfixed post-mortem brain tissue. In the present manuscript, we describe the general workflow and, as a showcase, demonstrate how targeted methylation analysis of various genes, in this case, RHBDF2, OXT, TNXB, DNAJB13, PGLYRP1, C3, and LMX1B, can be performed simultaneously. By doing so, we describe an adapted data analysis pipeline for LDBSP, allowing one to include and correct CpG methylation rates derived from multi-allele reactions. In addition, we show that the efficiency of LDBSP on DNA derived from LCM neurons is similar to the efficiency obtained in previously published studies using this technique on other cell types. Overall, the method described here provides the user with a more accurate estimation of the DNA methylation status of each target gene in the analyzed cell pools, thereby adding further validity to this approach.
Collapse
|
8
|
Babovskaya AA, Trifonova EA, Serebrova VN, Svarovskaya MG, Zarubin AA, Zhilyakova OV, Gabidulina TV, Poltanova AA, Rychkova LV, Stepanov VA. [Protocol of Transcriptome Analysis of Decidual Placenta Cells]. Mol Biol (Mosk) 2022; 56:325-333. [PMID: 35403625 DOI: 10.31857/s0026898422020045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/13/2021] [Indexed: 06/14/2023]
Abstract
The advent of high-throughput sequencing technologies has expanded our understanding of the biological significance of non-coding regions of the genome. In recent years, more and more studies have been devoted to studying the role of noncoding RNAs in the development of diseases, as well as their participation in various cellular processes. Until now, all transcriptome studies of native placental tissue with the description of the noncoding RNA region were carried out without isolating individual cell populations. This approach, due to the high cellular heterogeneity of the placental tissue, significantly complicates the ability to determine the molecular-biological functions of individual cells and their role in the molecular pathogenesis of reproductive disorders. In this work, we propose a technique for obtaining total RNA from single decidual cells of frozen placental tissue obtained by laser-capture microdissection technology for transcriptome sequencing, including a cluster of noncoding RNAs. This technique can be successfully used to study the full-genome expression profile of other placental cell populations. The high accuracy of results on the transcriptome profiling of decidual cells obtained using the developed technique was additionally confirmed by an integrative analysis with the results of a 10x Genomics experiment.
Collapse
Affiliation(s)
- A A Babovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| | - E A Trifonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
- Siberian State Medical University, Tomsk, 634050 Russia
| | - V N Serebrova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| | - M G Svarovskaya
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
- Siberian State Medical University, Tomsk, 634050 Russia
| | - A A Zarubin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| | | | | | - A A Poltanova
- Siberian State Medical University, Tomsk, 634050 Russia
| | - L V Rychkova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, 664003 Russia
| | - V A Stepanov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, 634050 Russia
| |
Collapse
|
9
|
Walczak-Jędrzejowska R, Forma E, Oszukowska E, Bryś M, Marchlewska K, Kula K, Słowikowska-Hilczer J. Expression of G-Protein-Coupled Estrogen Receptor ( GPER) in Whole Testicular Tissue and Laser-Capture Microdissected Testicular Compartments of Men with Normal and Aberrant Spermatogenesis. Biology (Basel) 2022; 11:biology11030373. [PMID: 35336747 PMCID: PMC8945034 DOI: 10.3390/biology11030373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 01/23/2023]
Abstract
Simple Summary Nowadays, there is no doubt that estrogens play an important role in male reproduction, affecting testicular cell differentiation, proliferation, apoptosis and metabolism. It is also widely believed that intratesticular balance of androgens and estrogens is crucial for the testicular development and function and that the increased testicular estrogen production may be associated with spermatogenic failure. There is also growing epidemiological evidence that the exposure of men to endocrine disruptors demonstrating estrogenic activity (xenoestrogens) may lead to impairment of male fertility via interference with estrogen signaling pathways. Besides the two classical nuclear estrogen receptors, the membrane-bound G protein-coupled estrogen receptor (GPER) was described in human testicular tissue. However, there are little data on its expression in testes with disturbed spermatogenesis. In this study, we investigated the GPER expression pattern in biopsies of azoospermic men with complete and aberrant spermatogenesis. Our results showed an increased expression of the GPER in testes with impaired spermatogenesis. Moreover, they indicate a possible involvement of estrogen signaling through GPER in disturbed function of Sertoli cells—the cells that support spermatogenic process. Abstract In this study, we retrospectively investigated GPER expression in biopsies of azoospermic men with complete (obstructive azoospermia—OA) and aberrant spermatogenesis (nonobstructive azoospermia—NOA). Each biopsy was histologically evaluated with morphometry. The testicular GPER expression was analyzed by the immunohistochemistry and RT-PCR technique in the whole testicular tissue and in seminiferous tubules and Leydig cells after laser-capture microdissection. In laser-microdissected compartments, we also analyzed transcriptional expression of selected Leydig (CYP17A1, HSD17B3, StAR) and Sertoli cell (AMH, SCF, BMP4) function markers. Immunohistochemical staining revealed expression of GPER in the cytoplasm of Leydig and Sertoli cells. Its stronger intensity was observed in Sertoli cells of NOA biopsies. The RT-PCR analysis of the GPER mRNA level unequivocally showed its increased expression in seminiferous tubules (i.e., Sertoli cells), not Leydig cells in NOA biopsies. This increased expression correlated positively with the transcriptional level of AMH—a marker of Sertoli cell immaturity, as well as FSH serum level in NOA but not in the OA group. Our results clearly demonstrate altered GPER expression in testes with primary spermatogenic impairment that might be related to Sertoli cell maturity/function.
Collapse
Affiliation(s)
- Renata Walczak-Jędrzejowska
- Department of Andrology and Reproductive Endocrinology, Medical University of Lodz, Pomorska Str. 251, 92-213 Lodz, Poland; (K.M.); (K.K.); (J.S.-H.)
- Correspondence: ; Tel.: +48-42-272-53-91
| | - Ewa Forma
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236 Lodz, Poland; (E.F.); (M.B.)
| | - Elżbieta Oszukowska
- II Clinic of Urology, Medical University of Lodz, Pabianicka Str. 62, 93-513 Lodz, Poland;
| | - Magdalena Bryś
- Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska Str. 141/143, 90-236 Lodz, Poland; (E.F.); (M.B.)
| | - Katarzyna Marchlewska
- Department of Andrology and Reproductive Endocrinology, Medical University of Lodz, Pomorska Str. 251, 92-213 Lodz, Poland; (K.M.); (K.K.); (J.S.-H.)
| | - Krzysztof Kula
- Department of Andrology and Reproductive Endocrinology, Medical University of Lodz, Pomorska Str. 251, 92-213 Lodz, Poland; (K.M.); (K.K.); (J.S.-H.)
| | - Jolanta Słowikowska-Hilczer
- Department of Andrology and Reproductive Endocrinology, Medical University of Lodz, Pomorska Str. 251, 92-213 Lodz, Poland; (K.M.); (K.K.); (J.S.-H.)
| |
Collapse
|
10
|
Jhu MY, Farhi M, Wang L, Zumstein K, Sinha NR. Investigating Host and Parasitic Plant Interaction by Tissue-Specific Gene Analyses on Tomato and Cuscuta campestris Interface at Three Haustorial Developmental Stages. Front Plant Sci 2022; 12:764843. [PMID: 35222447 PMCID: PMC8866705 DOI: 10.3389/fpls.2021.764843] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/28/2021] [Indexed: 05/26/2023]
Abstract
Parasitic weeds cause billions of dollars in agricultural losses each year worldwide. Cuscuta campestris (C. campestris), one of the most widespread and destructive parasitic plants in the United States, severely reduces yield in tomato plants. Reducing the spread of parasitic weeds requires understanding the interaction between parasites and hosts. Several studies have identified factors needed for parasitic plant germination and haustorium induction, and genes involved in host defense responses. However, knowledge of the mechanisms underlying the interactions between host and parasitic plants, specifically at the interface between the two organisms, is relatively limited. A detailed investigation of the crosstalk between the host and parasite at the tissue-specific level would enable development of effective parasite control strategies. To focus on the haustorial interface, we used laser-capture microdissection (LCM) with RNA-seq on early, intermediate and mature haustorial stages. In addition, the tomato host tissue that immediately surround the haustoria was collected to obtain tissue- resolution RNA-Seq profiles for C. campestris and tomato at the parasitism interface. After conducting RNA-Seq analysis and constructing gene coexpression networks (GCNs), we identified CcHB7, CcPMEI, and CcERF1 as putative key regulators involved in C. campestris haustorium organogenesis, and three potential regulators, SlPR1, SlCuRe1-like, and SlNLR, in tomatoes that are involved in perceiving signals from the parasite. We used host-induced gene silencing (HIGS) transgenic tomatoes to knock-down the candidate genes in C. campestris and produced CRISPR transgenic tomatoes to knock out candidate genes in tomatoes. The interactions of C. campestris with these transgenic lines were tested and compared with that in wild-type tomatoes. The results of this study reveal the tissue-resolution gene regulatory mechanisms at the parasitic plant-host interface and provide the potential of developing a parasite-resistant system in tomatoes.
Collapse
Affiliation(s)
- Min-Yao Jhu
- Department of Plant Biology, University of California, Davis, CA, United States
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Moran Farhi
- Department of Plant Biology, University of California, Davis, CA, United States
- The Better Meat Co., West Sacramento, CA, United States
| | - Li Wang
- Department of Plant Biology, University of California, Davis, CA, United States
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kristina Zumstein
- Department of Plant Biology, University of California, Davis, CA, United States
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, CA, United States
| |
Collapse
|
11
|
MacCuaig WM, Thomas A, Carlos-Sorto JC, Gomez-Gutierrez JG, Alexander AC, Wellberg EA, Grizzle WE, McNally LR. Differential expression of microRNA between triple negative breast cancer patients of African American and European American descent. Biotech Histochem 2022; 97:1-10. [PMID: 34979848 PMCID: PMC9047185 DOI: 10.1080/10520295.2021.2005147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
There are racial disparities in the outcome of triple negative breast cancer (TNBC) patients between women of African ancestry and women of European ancestry, even after accounting for lifestyle, socioeconomic and clinical factors. MicroRNA (miRNA) are non-coding molecules whose level of expression is associated with cancer suppression, proliferation and drug resistance; therefore, these have potential for biomarker applications in cancers including TNBC. Historically, miRNAs up-regulated in African American (AA) patients have received less attention than for patients of European ancestry. Using laser capture microdissection (LCM) to acquire ultrapure tumor cell samples, miRNA expression was evaluated in 15 AA and 15 European American (EA) TNBC patients. Tumor sections were evaluated using RNA extraction followed by miRNA analysis and profiling. Results were compared based on ethnicity and method of tissue fixation. miRNAs that showed high differential expression in AA TNBC patients compared to EA included: miR-19a, miR-192, miR-302a, miR-302b, miR-302c, miR-335, miR-520b, miR-520f and miR-645. LCM is a useful technique for isolation of tumor cells. We found a greater abundance of RNA in frozen samples compared to formalin fixed, paraffin embedded samples. miRNA appears to be a useful biomarker for TNBC to improve diagnosis and treatment.
Collapse
Affiliation(s)
- William M. MacCuaig
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma
| | - Alexandra Thomas
- Department of Hematology Oncology, Wake Forest Baptist Health, Winston-Salem, North Carolina
| | - Juan C. Carlos-Sorto
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Surgery, University of Oklahoma, Oklahoma City, Oklahoma
| | | | - Adam C. Alexander
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Family and Preventive Medicine, University of Oklahoma, Oklahoma City, Oklahoma
| | - Elizabeth A. Wellberg
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Pathology, University of Oklahoma, Oklahoma City, Oklahoma
| | - William E. Grizzle
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lacey R. McNally
- Stephenson Cancer Center, University of Oklahoma, Oklahoma City, Oklahoma,Department of Surgery, University of Oklahoma, Oklahoma City, Oklahoma
| |
Collapse
|
12
|
Koppolu A, Maksym RB, Paskal W, Machnicki M, Rak B, Pępek M, Garbicz F, Pełka K, Kuśmierczyk Z, Jacko J, Rydzanicz M, Banach-Orłowska M, Stokłosa T, Płoski R, Malejczyk J, Włodarski PK. Epithelial Cells of Deep Infiltrating Endometriosis Harbor Mutations in Cancer Driver Genes. Cells 2021; 10:749. [PMID: 33805315 PMCID: PMC8065889 DOI: 10.3390/cells10040749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
Endometriosis is an inflammatory condition manifested by the presence of endometrial-like tissue outside of the uterine cavity. The most common clinical presentations of endometriosis are dysmenorrhea, infertility, and severe pelvic pain. Few hypotheses attempt to explain the pathogenesis of endometriosis; however, none of the theories have been fully confirmed or considered universal. We examined somatic mutations in eutopic endometrium samples, deep endometriotic nodules and peripheral blood from 13 women with deep endometriosis of the rectovaginal space. Somatic variants were identified in laser microdissected samples using next-generation sequencing. A custom panel of 1296 cancer-related genes was employed, and selected genes representing cancer drivers and non-drivers for endometrial and ovarian cancer were thoroughly investigated. All 59 detected somatic variants were of low mutated allele frequency (<10%). In deep ectopic lesions, detected variants were significantly more often located in cancer driver genes, whereas in eutopic endometrium, there was no such distribution. Our results converge with other reports, where cancer-related mutations were found in endometriosis without cancer, particularly recurrent KRAS mutations. Genetic alterations located in ectopic endometriotic nodules could contribute to their formation; nevertheless, to better understand the pathogenesis of this disease, more research in this area must be performed.
Collapse
Affiliation(s)
- Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (A.K.); (M.R.); (R.P.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
| | - Radosław B. Maksym
- Department of Reproductive Health, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland
| | - Wiktor Paskal
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Marcin Machnicki
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.M.); (T.S.)
| | - Beata Rak
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
| | - Monika Pępek
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.M.); (T.S.)
| | - Filip Garbicz
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland; (B.R.); (M.P.); (F.G.)
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, 02-781 Warsaw, Poland
| | - Kacper Pełka
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Zofia Kuśmierczyk
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Joanna Jacko
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (A.K.); (M.R.); (R.P.)
| | - Magdalena Banach-Orłowska
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
| | - Tomasz Stokłosa
- Department of Tumor Biology and Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (M.M.); (T.S.)
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland; (A.K.); (M.R.); (R.P.)
| | - Jacek Malejczyk
- Laboratory of Centre for Preclinical Research, Department of Histology and Embryology, Medical University of Warsaw, 02-091 Warsaw, Poland; (M.B.-O.); (J.M.)
- Laboratory for Experimental Immunology, Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
| | - Paweł K. Włodarski
- Centre for Preclinical Research, Department of Methodology, Medical University of Warsaw, 02-091 Warsaw, Poland; (W.P.); (K.P.); (Z.K.); (J.J.)
| |
Collapse
|
13
|
Tam WY, Wang X, Cheng ASK, Cheung KK. In Search of Molecular Markers for Cerebellar Neurons. Int J Mol Sci 2021; 22:1850. [PMID: 33673348 DOI: 10.3390/ijms22041850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
The cerebellum, the region of the brain primarily responsible for motor coordination and balance, also contributes to non-motor functions, such as cognition, speech, and language comprehension. Maldevelopment and dysfunction of the cerebellum lead to cerebellar ataxia and may even be associated with autism, depression, and cognitive deficits. Hence, normal development of the cerebellum and its neuronal circuitry is critical for the cerebellum to function properly. Although nine major types of cerebellar neurons have been identified in the cerebellar cortex to date, the exact functions of each type are not fully understood due to a lack of cell-specific markers in neurons that renders cell-specific labeling and functional study by genetic manipulation unfeasible. The availability of cell-specific markers is thus vital for understanding the role of each neuronal type in the cerebellum and for elucidating the interactions between cell types within both the developing and mature cerebellum. This review discusses various technical approaches and recent progress in the search for cell-specific markers for cerebellar neurons.
Collapse
|
14
|
Canto AM, Matos AHB, Godoi AB, Vieira AS, Aoyama BB, Rocha CS, Henning B, Carvalho BS, Pascoal VDB, Veiga DFT, Gilioli R, Cendes F, Lopes-Cendes I. Multi-omics analysis suggests enhanced epileptogenesis in the Cornu Ammonis 3 of the pilocarpine model of mesial temporal lobe epilepsy. Hippocampus 2020; 31:122-139. [PMID: 33037862 DOI: 10.1002/hipo.23268] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/04/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Mesial temporal lobe epilepsy (MTLE) is a chronic neurological disorder characterized by the occurrence of seizures, and histopathological abnormalities in the mesial temporal lobe structures, mainly hippocampal sclerosis (HS). We used a multi-omics approach to determine the profile of transcript and protein expression in the dorsal and ventral hippocampal dentate gyrus (DG) and Cornu Ammonis 3 (CA3) in an animal model of MTLE induced by pilocarpine. We performed label-free proteomics and RNAseq from laser-microdissected tissue isolated from pilocarpine-induced Wistar rats. We divided the DG and CA3 into dorsal and ventral areas and analyzed them separately. We performed a data integration analysis and evaluated enriched signaling pathways, as well as the integrated networks generated based on the gene ontology processes. Our results indicate differences in the transcriptomic and proteomic profiles among the DG and the CA3 subfields of the hippocampus. Moreover, our data suggest that epileptogenesis is enhanced in the CA3 region when compared to the DG, with most abnormalities in transcript and protein levels occurring in the CA3. Furthermore, our results show that the epileptogenesis in the pilocarpine model involves predominantly abnormal regulation of excitatory neuronal mechanisms mediated by N-methyl D-aspartate (NMDA) receptors, changes in the serotonin signaling, and neuronal activity controlled by calcium/calmodulin-dependent protein kinase (CaMK) regulation and leucine-rich repeat kinase 2 (LRRK2)/WNT signaling pathways.
Collapse
Affiliation(s)
- Amanda M Canto
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Alexandre H B Matos
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Alexandre B Godoi
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - André S Vieira
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil.,Department of Structural and Functional Biology, Institute of Biology. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Beatriz B Aoyama
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil.,Department of Structural and Functional Biology, Institute of Biology. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Cristiane S Rocha
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Barbara Henning
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| | - Benilton S Carvalho
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil.,Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Vinicius D B Pascoal
- Department of Basic Sciences, Fluminense Federal University (UFF), Nova Friburgo, Rio de Janeiroz, Brazil
| | - Diogo F T Veiga
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Rovilson Gilioli
- Laboratory of Animal Quality Control, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fernando Cendes
- Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil.,Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, School of Medical Sciences. University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.,Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, São Paulo, Brazil
| |
Collapse
|
15
|
Meyer M, Paquet A, Arguel MJ, Peyre L, Gomes-Pereira LC, Lebrigand K, Mograbi B, Brest P, Waldmann R, Barbry P, Hofman P, Roux J. Profiling the Non-genetic Origins of Cancer Drug Resistance with a Single-Cell Functional Genomics Approach Using Predictive Cell Dynamics. Cell Syst 2020; 11:367-374.e5. [PMID: 33099406 DOI: 10.1016/j.cels.2020.08.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/12/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Non-genetic heterogeneity observed in clonal cell populations is an immediate cause of drug resistance that remains challenging to profile because of its transient nature. Here, we coupled three single-cell technologies to link the predicted drug response of a cell to its own genome-wide transcriptomic profile. As a proof of principle, we analyzed the response to tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL) in HeLa cells to demonstrate that cell dynamics can discriminate the transient transcriptional states at the origin of cell decisions such as sensitivity and resistance. Our same-cell approach, named fate-seq, can reveal the molecular factors regulating the efficacy of a drug in clonal cells, providing therapeutic targets of non-genetic drug resistance otherwise confounded in gene expression noise. A record of this paper's transparent peer review process is included in the Supplemental Information.
Collapse
Affiliation(s)
- Mickael Meyer
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Marie-Jeanne Arguel
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Ludovic Peyre
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Luis C Gomes-Pereira
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, 06560 Nice, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Baharia Mograbi
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Patrick Brest
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS UMR 7275, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, 06560 Nice, France
| | - Paul Hofman
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France
| | - Jérémie Roux
- Université Côte d'Azur, CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, 06107 Nice, France.
| |
Collapse
|
16
|
Martínez C, Lasitschka F, Thöni C, Wohlfarth C, Braun A, Granzow M, Röth R, Dizdar V, Rappold GA, Hausken T, Langeland N, Hanevik K, Niesler B. Comparative expression profiling in the intestine of patients with Giardia-induced postinfectious functional gastrointestinal disorders. Neurogastroenterol Motil 2020; 32:e13868. [PMID: 32391639 DOI: 10.1111/nmo.13868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/13/2020] [Accepted: 04/07/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND A Giardia outbreak in Bergen, Norway, caused postinfectious functional gastrointestinal disorders (PI-FGIDs). Despite the devastating effects of this outbreak, it presented a unique chance to investigate the implication on the dysregulation of genetic pathways in PI-FGID. METHODS We performed the first comparative expression profiling of miRNAs and their potential target genes in microdissected rectal biopsies from 20 Giardia-induced PI-FGID patients vs 18 healthy controls by nCounter analysis. Subsequently, candidates were validated on protein level by immunostaining. KEY RESULTS miRNA profiling on rectal biopsy samples from 5 diarrhea-predominant PI-IBS cases compared to 10 healthy controls revealed differential expression in the epithelial layer. The top five regulated miRNAs were implicated in GI disease, inflammatory response, and immunological disease. Subsequently, these miRNAs and 100 potential mRNA targets were examined in 20 PI-FGID cases and 18 healthy controls in both the mucosal epithelium and the lamina propria. Although deregulation of the selected miRNAs could not be verified in the larger sample set, mRNAs involved in barrier function were downregulated in the epithelium. Pro-inflammatory genes and genes implicated in epigenetic modifications were upregulated in the lamina propria. Immunostaining for selected candidates on 17 PI-FGID cases and 16 healthy controls revealed increased tryptase levels as well as a decreased and aberrant subcellular expression of occludin. CONCLUSIONS AND INFERENCES Genes relevant to immune and barrier function as well as stress response and epigenetic modulation are differentially expressed in PI-FGIDs and may contribute to disease manifestation.
Collapse
Affiliation(s)
- Cristina Martínez
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,Lleida Institute for Biomedical Research Dr. Pifarré Foundation (IRBLleida), Lleida, Spain.,Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
| | - Cornelia Thöni
- Institute of Pathology, Heidelberg University, Heidelberg, Germany
| | - Carolin Wohlfarth
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Alexander Braun
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ralph Röth
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,nCounter Core Facility Heidelberg, Institute of Human Genetics, Heidelberg, Germany
| | - Vernesa Dizdar
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,nCounter Core Facility Heidelberg, Institute of Human Genetics, Heidelberg, Germany
| | - Trygve Hausken
- Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Nina Langeland
- Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kurt Hanevik
- Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, National Advisory Center for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway
| | - Beate Niesler
- Department of Human Molecular Genetics, Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.,Genes in Irritable Bowel Syndrome (GENIEUR) Research Network Europe, Heidelberg, Germany.,nCounter Core Facility Heidelberg, Institute of Human Genetics, Heidelberg, Germany
| |
Collapse
|
17
|
Griesser E, Wyatt H, Ten Have S, Stierstorfer B, Lenter M, Lamond AI. Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue. Mol Cell Proteomics 2020; 19:839-851. [PMID: 32132230 PMCID: PMC7196589 DOI: 10.1074/mcp.ra119.001889] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/19/2020] [Indexed: 11/10/2022] Open
Abstract
Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (∼3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.
Collapse
Affiliation(s)
- Eva Griesser
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom; Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Hannah Wyatt
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sara Ten Have
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Birgit Stierstorfer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Martin Lenter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom.
| |
Collapse
|
18
|
Oishi N, Inoue T, Odate T, Mochizuki K, Ohashi K, Kirito K, Kondo T. Composite monoclonal B-cell lymphocytosis and MYD88 L265P-positive lymphoplasmacytic lymphoma in a patient with IgM light chain amyloidosis: Case report. Pathol Int 2020; 70:458-462. [PMID: 32323419 DOI: 10.1111/pin.12937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/23/2020] [Accepted: 04/06/2020] [Indexed: 11/29/2022]
Abstract
Monoclonal B-cell lymphocytosis (MBL) is an early or precursor asymptomatic proliferation of chronic lymphocytic lymphoma (CLL)-like B-cells. Lymphoplasmacytic lymphoma (LPL), often clinically associated with Waldenström macroglobulinemia, is a B-cell neoplasm characterized by frequent MYD88 L265P mutation. Here, we report a rare composite MBL and LPL in a patient with IgM light chain (AL) amyloidosis. A 74-year-old male with a known IgM monoclonal protein developed proteinuria. No lymphocytosis was detected. Renal biopsy showed deposition of AL λ amyloid in the glomeruli and vessels. Subsequent bone marrow biopsy revealed nodular atypical CLL-like small B-cell proliferation and scattered peripheral LPL. Immunohistochemistry and/or flow cytometry revealed that the atypical CLL-like population expressed CD19, CD20, CD5, weak CD23, LEF-1 and diminished surface Igκ. The LPL was positive for CD19, CD20 and surface Igλ. Using laser-capture microdissection and allele-specific polymerase chain reaction, we confirmed that MYD88 L265P was detectable in the LPL but not in the atypical CLL-like population. Thus, we demonstrated that these two populations were clonally independent, and made the diagnosis of composite MBL and LPL. An integrated clinical, pathological, immunophenotypic and genetic assessment is essential in such complicated cases, and especially 'clone-specific' MYD88 genotyping may facilitate the differential diagnoses of low-grade B-cell lymphomas.
Collapse
Affiliation(s)
- Naoki Oishi
- Department of Pathology, University of Yamanashi, Yamanashi, Japan
| | - Tomohiro Inoue
- Department of Pathology, University of Yamanashi, Yamanashi, Japan
| | - Toru Odate
- Department of Pathology, University of Yamanashi, Yamanashi, Japan
| | - Kunio Mochizuki
- Department of Pathology, University of Yamanashi, Yamanashi, Japan
| | - Kenichi Ohashi
- Department of Pathology, Yokohama City University, Kanagawa, Japan
| | - Keita Kirito
- Department of Hematology, University of Yamanashi, Yamanashi, Japan
| | - Tetsuo Kondo
- Department of Pathology, University of Yamanashi, Yamanashi, Japan
| |
Collapse
|
19
|
Forsthoefel DJ, Cejda NI, Khan UW, Newmark PA. Cell-type diversity and regionalized gene expression in the planarian intestine. eLife 2020; 9:e52613. [PMID: 32240093 PMCID: PMC7117911 DOI: 10.7554/elife.52613] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.
Collapse
Affiliation(s)
- David J Forsthoefel
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Nicholas I Cejda
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
| | - Umair W Khan
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| |
Collapse
|
20
|
Markkanen E. Know Thy Model: Charting Molecular Homology in Stromal Reprogramming Between Canine and Human Mammary Tumors. Front Cell Dev Biol 2019; 7:348. [PMID: 31921858 PMCID: PMC6927989 DOI: 10.3389/fcell.2019.00348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/03/2019] [Indexed: 12/24/2022] Open
Abstract
Spontaneous canine simple mammary tumors (CMTs) are often viewed as models of human breast cancer. Cancer-associated stroma (CAS) is central for initiation and progression of human cancer, and is likely to play a key role in canine tumors as well. Until recently, however, canine CAS in general, and in CMT in particular, lacked detailed characterization and it remained unclear how canine and human CAS compare. This void in knowledge regarding canine CAS and the resulting lack of unbiased cross-species analysis of molecular homologies and differences undermined the validity of the canine model for human disease. To assess stromal reprogramming in canine breast tumors, we have recently established a protocol to specifically isolate and analyze CAS and matched normal stroma from archival, formalin-fixed paraffin embedded (FFPE) clinical tumor samples using laser-capture microdissection followed by next-generation RNA-sequencing. Using this approach, we have analyzed stromal reprogramming in both malignant canine mammary carcinomas (mCAs) as well as benign canine mammary adenomas in a series of studies. Our results demonstrate strong stromal reprogramming in CMTs and identify high-grade molecular homology between human and canine CAS. Here, I aim to give a short background on the value of comparative oncology in general, and spontaneous CMT in particular. This will be followed by a concise review of the current knowledge of stromal reprogramming in both malignant canine mCA and benign adenoma. Finally, I will conclude with insights on highly conserved aspects of stromal reprogramming between CMT and human breast cancer that accentuate the relevance of CAS in CMT as a model for the human disease.
Collapse
Affiliation(s)
- Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| |
Collapse
|
21
|
Recchia GH, Konzen ER, Cassieri F, Caldas DGG, Tsai SM. Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean. Front Microbiol 2018; 9:1339. [PMID: 30013521 PMCID: PMC6036286 DOI: 10.3389/fmicb.2018.01339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/31/2018] [Indexed: 11/13/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) colonization in plants promotes both local and systemic changes in the gene expression profiles of the host that might be relevant for drought-stress perception and response. Drought-tolerant common bean plants (cv. BAT 477), colonized by a mixture of AMF (Glomus clarum, Acaulospora scrobiculata, and Gigaspora rosea), were exposed to a water deprivation regime of 96 h during pre-flowering. Root transcriptomes were accessed through RNA-Seq revealing a set of 9,965 transcripts with significant differential regulation in inoculated plants during a water deficit event, and 10,569 in non-inoculated. These data include 1,589 transcripts that are exclusively regulated by AMF-inoculation, and 2,313 under non-inoculation conditions. Relative gene expression analyses of nine aquaporin-related transcripts were performed in roots and leaves of plants harvested at initial stages of treatment. Significant shifts in gene expression were detected in AM water deficit-treated roots, in relation to non-inoculated, between 48 and 72 h. Leaves also showed significant mycorrhizal influence in gene expression, especially after 96 h. Root cortical cells, harboring or not arbuscules, were collected from both inoculation treatments through a laser microdissection-based technique. This allowed the identification of transcripts, such as the aquaporin PvPIP2;3 and Glucan 1,3 β-Glucosidase, that are unique to arbuscule-containing cells. During the water deficit treatment, AMF colonization exerted a fine-tune regulation in the expression of genes in the host. That seemed to initiate in arbuscule-containing cells and, as the stressful condition persisted, propagated to the whole-plant through secondary signaling events. Collectively, these results demonstrate that arbuscular mycorrhization leads to shifts in common bean's transcriptome that could potentially impact its adaptation capacity during water deficit events.
Collapse
Affiliation(s)
- Gustavo H. Recchia
- Laboratory of Molecular and Cellular Biology, Center of Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | | | | | | |
Collapse
|
22
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
23
|
Shimizu N, Doyal MF, Goins WF, Kadekawa K, Wada N, Kanai AJ, de Groat WC, Hirayama A, Uemura H, Glorioso JC, Yoshimura N. Morphological changes in different populations of bladder afferent neurons detected by herpes simplex virus (HSV) vectors with cell-type-specific promoters in mice with spinal cord injury. Neuroscience 2017; 364:190-201. [PMID: 28942324 DOI: 10.1016/j.neuroscience.2017.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 01/06/2023]
Abstract
Functional and morphological changes in C-fiber bladder afferent pathways are reportedly involved in neurogenic detrusor overactivity (NDO) after spinal cord injury (SCI). This study examined the morphological changes in different populations of bladder afferent neurons after SCI using replication-defective herpes simplex virus (HSV) vectors encoding the mCherry reporter driven by neuronal cell-type-specific promoters. Spinal intact (SI) and SCI mice were injected into the bladder wall with HSV mCherry vectors driven by the cytomegalovirus (CMV) promoter, CGRP promoter, TRPV1 promoter or neurofilament 200 (NF200) promoter. Two weeks after vector inoculation into the bladder wall, L1 and L6 dorsal root ganglia (DRG) were removed bilaterally for immunofluorescent staining using anti-mCherry antibody. The number of CMV promoter vector-labeled neurons was not altered after SCI. The number of CGRP and TRPV1 promoter vector-labeled neurons was significantly increased whereas the number of NF200 vector-labeled neurons was decreased in L6 DRG after SCI. The median size of CGRP promoter-labeled C-fiber neurons was increased from 247.0 in SI mice to 271.3μm2 in SCI mice whereas the median cell size of TRPV1 promoter vector-labeled neurons was decreased from 245.2 in SI mice to 216.5μm2 in SCI mice. CGRP and TRPV1 mRNA levels of laser-captured bladder afferent neurons labeled with Fast Blue were significantly increased in SCI mice compared to SI mice. Thus, using a novel HSV vector-mediated neuronal labeling technique, we found that SCI induces expansion of the CGRP- and TRPV1-expressing C-fiber cell population, which could contribute to C-fiber afferent hyperexcitability and NDO after SCI.
Collapse
Affiliation(s)
- Nobutaka Shimizu
- Department of Urology, University of Pittsburgh, Pittsburgh, PA 15213, United States; Department of Urology, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Mark F Doyal
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - William F Goins
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - Katsumi Kadekawa
- Department of Urology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Naoki Wada
- Department of Urology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Anthony J Kanai
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, United States
| | - William C de Groat
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Akihide Hirayama
- Department of Urology, Faculty of Medicine, Kindai University Nara Hospital, Nara, Japan
| | - Hirotsugu Uemura
- Department of Urology, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Joseph C Glorioso
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, United States
| | - Naoki Yoshimura
- Department of Urology, University of Pittsburgh, Pittsburgh, PA 15213, United States; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, United States.
| |
Collapse
|
24
|
Farris S, Wang Y, Ward JM, Dudek SM. Optimized Method for Robust Transcriptome Profiling of Minute Tissues Using Laser Capture Microdissection and Low-Input RNA-Seq. Front Mol Neurosci 2017; 10:185. [PMID: 28659759 PMCID: PMC5468370 DOI: 10.3389/fnmol.2017.00185] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/26/2017] [Indexed: 01/10/2023] Open
Abstract
Obtaining high quality RNA from complex biological tissues, such as the brain, is needed for establishing high-fidelity cell-type specific transcriptomes. Although combining genetic labeling techniques with laser capture microdissection (LCM) is generally sufficient, concerns over RNA degradation and limited yields call into question results of many sequencing studies. Here we set out to address both of these issues by: (1) developing a fluorescence-assisted LCM protocol that yields high quality RNA from fresh-frozen tissues; and (2) determining a suitable RNA-Seq library generation method for limited amounts of RNA (1–5 ng total RNA). The latter focused on comparing commercially available kits able to produce libraries of sufficient concentration and complexity while limiting PCR amplification biases. We find that high quality RNA (RNA integrity number, RIN, >9) of sufficient concentration can be isolated from laser-captured material from thinly-sectioned tissues when digestion time and temperature are minimized. Furthermore, we found that library generation approaches that retain ribosomal RNA (rRNA) through cDNA library generation required fewer cycles of PCR, minimizing bias in the resulting libraries. Lastly, end stage depletion of rRNA prior to sequencing enriches for target RNAs, thereby increasing read depth and level of gene detection while decreasing sequencing costs. Here we describe our protocol for generating robust RNA-Seq libraries from laser-captured tissue and demonstrate that with this method, we obtain samples with RNA quality superior to the current standard in the LCM field, and show that low-input RNA-Seq kits that minimize PCR bias produce high fidelity sequencing metrics with less variability compared to current practices.
Collapse
Affiliation(s)
- Shannon Farris
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle Park, NC, United States
| | - Yu Wang
- Cellular and Molecular Pathology, National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle Park, NC, United States
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle Park, NC, United States
| | - Serena M Dudek
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of HealthResearch Triangle Park, NC, United States
| |
Collapse
|
25
|
Schmidt F, Efferth T. Tumor Heterogeneity, Single-Cell Sequencing, and Drug Resistance. Pharmaceuticals (Basel) 2016; 9:E33. [PMID: 27322289 DOI: 10.3390/ph9020033] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 01/10/2023] Open
Abstract
Tumor heterogeneity has been compared with Darwinian evolution and survival of the fittest. The evolutionary ecosystem of tumors consisting of heterogeneous tumor cell populations represents a considerable challenge to tumor therapy, since all genetically and phenotypically different subpopulations have to be efficiently killed by therapy. Otherwise, even small surviving subpopulations may cause repopulation and refractory tumors. Single-cell sequencing allows for a better understanding of the genomic principles of tumor heterogeneity and represents the basis for more successful tumor treatments. The isolation and sequencing of single tumor cells still represents a considerable technical challenge and consists of three major steps: (1) single cell isolation (e.g., by laser-capture microdissection), fluorescence-activated cell sorting, micromanipulation, whole genome amplification (e.g., with the help of Phi29 DNA polymerase), and transcriptome-wide next generation sequencing technologies (e.g., 454 pyrosequencing, Illumina sequencing, and other systems). Data demonstrating the feasibility of single-cell sequencing for monitoring the emergence of drug-resistant cell clones in patient samples are discussed herein. It is envisioned that single-cell sequencing will be a valuable asset to assist the design of regimens for personalized tumor therapies based on tumor subpopulation-specific genetic alterations in individual patients.
Collapse
|
26
|
Molijn A, Jenkins D, Chen W, Zhang X, Pirog E, Enqi W, Liu B, Schmidt J, Cui J, Qiao Y, Quint W. The complex relationship between human papillomavirus and cervical adenocarcinoma. Int J Cancer 2015; 138:409-16. [PMID: 26334557 DOI: 10.1002/ijc.29722] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/17/2015] [Indexed: 02/01/2023]
Abstract
Human Papillomavirus (HPV) is reported in 60-100% of cervical adenocarcinoma (CADC) globally. We investigated this relationship in a hospital-based survey in China. 718 CADC samples from nine Chinese regions were analysed. Expert pathologists reviewed cases with p16 and progesterone receptor immunostaining. Cases were tested for HPV using whole-tissue sections (WTS) and laser-capture microdissection. All cases were HPV-tested by L1 based broad-spectrum SPF10 -DEIA-LiPA25 PCR. Negative cases were tested for DNA adequacy and with E6 oncogene, type-specific HPV PCRs. Using WTS-PCR CADC showed overall 75% HPV-positivity (33-100% for different histological types). LCM-PCR showed that none of minimal deviation or serous CADC, and <10% of all clear cell and endometrioid CADC were HPV-positive in tumour cells. Usual and adenosquamous CADC showed a single HPV genotype in 60 and 78% cases. In some cases, HPV was found in adjacent cervix but not in tumour. HPV 16, 18 and 45 accounted for 90% of HPV in tumour cells. Patients with HPV-positive tumours were on average 6 years younger and presented at a lower clinicopathological stage as compared to patients with HPV-negative cancers. CADC is diverse pathologically and in HPV status. Special histopathological tumor subtypes may develop through different cellular and molecular pathways. Between 20 and 40% usual and adenosquamous types, in particular these diagnosed in older women and at advanced FIGO stages, are not driven by oncogenic HPV. In these cases HPV may not be involved in carcinogenisis or maybe lost during tumour progression.
Collapse
Affiliation(s)
- Anco Molijn
- DDL Diagnostic Laboratory, Visseringlaan 25, 2288 ER, Rijswijk, The Netherlands
| | - David Jenkins
- DDL Diagnostic Laboratory, Visseringlaan 25, 2288 ER, Rijswijk, The Netherlands
| | - Wen Chen
- Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xun Zhang
- Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Edyta Pirog
- MINZU University of China, Haidian District, Beijing, China
| | - Wu Enqi
- Weill Medical College of Cornell University, 525 E 68th Street, New York, NY
| | - Bin Liu
- Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | | | - Jiangfeng Cui
- Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Youlin Qiao
- Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Wim Quint
- DDL Diagnostic Laboratory, Visseringlaan 25, 2288 ER, Rijswijk, The Netherlands
| | | |
Collapse
|
27
|
Watanabe T, Kato A, Terashima H, Matsubara K, Chen YJ, Adachi K, Mizuno H, Suzuki M. The PFA-AMeX method achieves a good balance between the morphology of tissues and the quality of RNA content in DNA microarray analysis with laser-capture microdissection samples. J Toxicol Pathol 2015; 28:43-9. [PMID: 26023261 PMCID: PMC4337499 DOI: 10.1293/tox.2014-0045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/14/2014] [Indexed: 01/18/2023] Open
Abstract
Recently, large-scale gene expression profiling is often performed using RNA extracted from unfixed frozen or formalin-fixed paraffin embedded (FFPE) samples. However, both types of samples have drawbacks in terms of the morphological preservation and RNA quality. In the present study, we investigated 30 human prostate tissues using the PFA-AMeX method (fixation using paraformaldehyde (PFA) followed by embedding in paraffin by AMeX) with a DNA microarray combined with laser-capture microdissection. Morphologically, in contrast to the case of atypical adenomatous hyperplasia, loss of basal cells in prostate adenocarcinomas was as obvious in PFA-AMeX samples as in FFPE samples. As for quality, the loss of rRNA peaks 18S and 28S on the capillary electropherograms from both FFPE and PFA-AMeX samples showed that the RNA was degraded equally during processing. However, qRT-PCR with 3' and 5' primer sets designed against human beta-actin revealed that, although RNA degradation occurred in both methods, it occurred more mildly in the PFA-AMeX samples. In conclusion, the PFA-AMeX method is good with respect to morphology and RNA quality, which makes it a promising tool for DNA microarrays combined with laser-capture microdissection, and if the appropriate RNA quality criteria are used, the capture of credible GeneChip data is well over 80% efficient, at least in human prostate specimens.
Collapse
Affiliation(s)
- Takeshi Watanabe
- Chugai Research Institute for Medical Science Inc., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Atsuhiko Kato
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Hiromichi Terashima
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Koichi Matsubara
- PharmaLogicals Research, Pte. Ltd., 11 Biopolis Way, #05-08/09 Helios, 138667, Singapore
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #04-11 to 17 Synapse, 138623, Singapore
| | - Yu Jau Chen
- PharmaLogicals Research, Pte. Ltd., 11 Biopolis Way, #05-08/09 Helios, 138667, Singapore
- Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #04-11 to 17 Synapse, 138623, Singapore
| | - Kenji Adachi
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Hideaki Mizuno
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| | - Masami Suzuki
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba-shi, Shizuoka 412-8513, Japan
| |
Collapse
|
28
|
Bongiovanni M, Molinari F, Eszlinger M, Paschke R, Barizzi J, Merlo E, Giovanella L, Fasolini F, Cattaneo F, Ramelli F, Mazzucchelli L, Frattini M. Laser capture microdissection is a valuable tool in the preoperative molecular screening of follicular lesions of the thyroid: an institutional experience. Cytopathology 2014; 26:288-96. [PMID: 25487739 DOI: 10.1111/cyt.12226] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2014] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The application of molecular tests to thyroid fine needle aspiration (FNA) has been shown to be a valuable tool to better refine the pre-operative malignant risk of patients with indeterminate cytology results. In this study, we investigated the feasibility of using the laser capture microdissection (LCM) technique to obtain DNA and RNA for molecular tests in routine thyroid FNA smears. METHODS Nine coupled FNA and histological retrospective cases and 31 prospective FNA cases with a follicular neoplasm/suspicious for a follicular neoplasm (FN/SFN) diagnosis were included in this study. Both cytological and histological specimens were investigated by direct sequencing and reverse transcription-polymerase chain reaction (RT-PCR) for BRAF and RAS mutations and for PAX8/PPARG and RET/PTC rearrangements, respectively. RESULTS LCM yielded good DNA and RNA quality in all cases (100%) in both series, irrespective of the staining used (Giemsa, Papanicolaou, immunostain for thyroglobulin) and the cytology technique (conventional or liquid-based preparations). Total mutations found in the FNA and in the corresponding histological specimen in both series were: one PAX8/PPARG rearrangement in a follicular carcinoma (FC), four NRAS mutations [in two FCs, one papillary carcinoma and one follicular adenoma (FA)] and one HRAS mutation in one FA. The sensitivity was 67% and the specificity was 91%. CONCLUSIONS LCM is a valuable tool to obtain good quality DNA and RNA for molecular tests in cytological material from thyroid FNA, and can be a useful option in the management of patients with an FN/SFN FNA diagnosis.
Collapse
Affiliation(s)
| | - F Molinari
- Institute of Pathology, Locarno, Switzerland
| | - M Eszlinger
- Division of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - R Paschke
- Division of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - J Barizzi
- Institute of Pathology, Locarno, Switzerland
| | - E Merlo
- Institute of Pathology, Locarno, Switzerland
| | - L Giovanella
- Department of Nuclear Medicine and Thyroid Centre, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - F Fasolini
- Department of Surgery, Ente Ospedaliero Cantonale, Mendrisio, Switzerland
| | - F Cattaneo
- Private Practice Endocrinologist, Lugano, Switzerland
| | - F Ramelli
- Private Practice Endocrinologist, Locarno, Switzerland
| | | | - M Frattini
- Institute of Pathology, Locarno, Switzerland
| |
Collapse
|
29
|
Solga AC, Pong WW, Walker J, Wylie T, Magrini V, Apicelli AJ, Griffith M, Griffith OL, Kohsaka S, Wu GF, Brody DL, Mardis ER, Gutmann DH. RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease. Glia 2014; 63:531-548. [PMID: 25258010 DOI: 10.1002/glia.22754] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 08/19/2014] [Accepted: 09/09/2014] [Indexed: 01/03/2023]
Abstract
Expression profiling of distinct central nervous system (CNS) cell populations has been employed to facilitate disease classification and to provide insights into the molecular basis of brain pathology. One important cell type implicated in a wide variety of CNS disease states is the resident brain macrophage (microglia). In these studies, microglia are often isolated from dissociated brain tissue by flow sorting procedures [fluorescence-activated cell sorting (FACS)] or from postnatal glial cultures by mechanic isolation. Given the highly dynamic and state-dependent functions of these cells, the use of FACS or short-term culture methods may not accurately capture the biology of brain microglia. In the current study, we performed RNA-sequencing using Cx3cr1(+/GFP) labeled microglia isolated from the brainstem of 6-week-old mice to compare the transcriptomes of FACS-sorted versus laser capture microdissection (LCM). While both isolation techniques resulted in a large number of shared (common) transcripts, we identified transcripts unique to FACS-isolated and LCM-captured microglia. In particular, ∼50% of these LCM-isolated microglial transcripts represented genes typically associated with neurons and glia. While these transcripts clearly localized to microglia using complementary methods, they were not translated into protein. Following the induction of murine experimental autoimmune encephalomyelitis, increased oligodendrocyte and neuronal transcripts were detected in microglia, while only the myelin basic protein oligodendrocyte transcript was increased in microglia after traumatic brain injury. Collectively, these findings have implications for the design and interpretation of microglia transcriptome-based investigations.
Collapse
Affiliation(s)
- Anne C Solga
- Department of Neurology, Washington University School of Medicine, St. Louis MO
| | - Winnie W Pong
- Department of Neurology, Washington University School of Medicine, St. Louis MO
| | - Jason Walker
- The Genome Institute, Washington University School of Medicine
| | - Todd Wylie
- The Genome Institute, Washington University School of Medicine
| | - Vincent Magrini
- The Genome Institute, Washington University School of Medicine
| | - Anthony J Apicelli
- Department of Neurology, Washington University School of Medicine, St. Louis MO
| | | | - Obi L Griffith
- The Genome Institute, Washington University School of Medicine
| | - Shinichi Kohsaka
- Department of Neurochemistry, National Institute of Neuroscience, Kodaira, Tokyo, Japan
| | - Gregory F Wu
- Department of Neurology, Washington University School of Medicine, St. Louis MO
| | - David L Brody
- Department of Neurology, Washington University School of Medicine, St. Louis MO
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis MO
| |
Collapse
|
30
|
Xiao X, Prasadan K, Guo P, El-Gohary Y, Fischbach S, Wiersch J, Gaffar I, Shiota C, Gittes GK. Pancreatic duct cells as a source of VEGF in mice. Diabetologia 2014; 57:991-1000. [PMID: 24535231 PMCID: PMC3986695 DOI: 10.1007/s00125-014-3179-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/16/2014] [Indexed: 12/25/2022]
Abstract
AIMS/HYPOTHESIS Vascular endothelial growth factor (VEGF) is essential for proper pancreatic development, islet vascularisation and insulin secretion. In the adult pancreas, VEGF is thought to be predominantly secreted by beta cells. Although human duct cells have previously been shown to secrete VEGF at angiogenic levels in culture, an analysis of the kinetics of VEGF synthesis and secretion, as well as elucidation of an in vivo role for this ductal VEGF in affecting islet function and physiology, has been lacking. METHODS We analysed purified duct cells independently prepared by flow cytometry, surgical isolation or laser-capture microdissection. We infected duct cells in vivo with Vegf (also known as Vegfa) short hairpin RNA (shRNA) in an intrapancreatic ductal infusion system and examined the effect of VEGF knockdown in duct cells in vitro and in vivo. RESULTS Pancreatic duct cells express high levels of Vegf mRNA. Compared with beta cells, duct cells had a much higher ratio of secreted to intracellular VEGF. As a bioassay, formation of tubular structures by human umbilical vein endothelial cells was essentially undetectable when cultured alone and was substantially increased when co-cultured with pancreatic duct cells but significantly reduced when co-cultured with duct cells pretreated with Vegf shRNA. Compared with islets transplanted alone, improved vascularisation and function was detected in the islets co-transplanted with duct cells but not in islets co-transplanted with duct cells pretreated with Vegf shRNA. CONCLUSIONS/INTERPRETATION Human islet preparations for transplantation typically contain some contaminating duct cells and our findings suggest that the presence of duct cells in the islet preparation may improve transplantation outcomes.
Collapse
Affiliation(s)
- Xiangwei Xiao
- Division of Pediatric Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, 4401 Penn Ave, Pittsburgh, PA, 15224, USA,
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Asi YT, Simpson JE, Heath PR, Wharton SB, Lees AJ, Revesz T, Houlden H, Holton JL. Alpha-synuclein mRNA expression in oligodendrocytes in MSA. Glia 2014; 62:964-70. [PMID: 24590631 PMCID: PMC4238782 DOI: 10.1002/glia.22653] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/25/2014] [Accepted: 02/10/2014] [Indexed: 01/14/2023]
Abstract
Multiple system atrophy (MSA) is a progressive neurodegenerative disease presenting clinically with parkinsonian, cerebellar, and autonomic features. α-Synuclein (αsyn), encoded by the gene SNCA, is the main constituent of glial cytoplasmic inclusion (GCI) found in oligodendrocytes in MSA, but the methods of its accumulation have not been established. The aim of this study is to investigate alterations in regional and cellular SNCA mRNA expression in MSA as a possible substrate for GCI formation. Quantitative reverse transcription polymerase chain reaction (qPCR) was performed on postmortem brain samples from 15 MSA, 5 IPD, and 5 control cases to investigate regional expression in the frontal and occipital regions, dorsal putamen, pontine base, and cerebellum. For cellular expression analysis, neurons and oligodendrocytes were isolated by laser-capture microdissection from five MSA and five control cases. SNCA mRNA expression was not significantly different between the MSA, IPD and control cases in all regions (multilevel model, P = 0.14). After adjusting for group effect, the highest expression was found in the occipital cortex while the lowest was in the putamen (multilevel model, P < 0.0001). At the cellular level, MSA oligodendrocytes expressed more SNCA than control oligodendrocytes and expression in MSA neurons was slightly lower than that in controls, however, these results did not reach statistical significance. We have demonstrated regional variations in SNCA expression, which is higher in cortical than subcortical regions. This study is the first to demonstrate SNCA mRNA expression by oligodendrocytes in human postmortem tissue using qPCR and, although not statistically significant, could suggest that this may be increased in MSA compared to controls.
Collapse
Affiliation(s)
- Yasmine T Asi
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Pietersen CY, Mauney SA, Kim SS, Lim MP, Rooney RJ, Goldstein JM, Petryshen TL, Seidman LJ, Shenton ME, McCarley RW, Sonntag KC, Woo TUW. Molecular profiles of pyramidal neurons in the superior temporal cortex in schizophrenia. J Neurogenet 2014; 28:53-69. [PMID: 24702465 PMCID: PMC4196521 DOI: 10.3109/01677063.2014.882918] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 01/09/2014] [Indexed: 12/22/2022]
Abstract
Disrupted synchronized oscillatory firing of pyramidal neuronal networks in the cerebral cortex in the gamma frequency band (i.e., 30-100 Hz) mediates many of the cognitive deficits and symptoms of schizophrenia. In fact, the density of dendritic spines and the average somal area of pyramidal neurons in layer 3 of the cerebral cortex, which mediate both long-range (associational) and local (intrinsic) corticocortical connections, are decreased in subjects with this illness. To explore the molecular pathophysiology of pyramidal neuronal dysfunction, we extracted ribonucleic acid (RNA) from laser-captured pyramidal neurons from layer 3 of Brodmann's area 42 of the superior temporal gyrus (STG) from postmortem brains from schizophrenia and normal control subjects. We then profiled the messenger RNA (mRNA) expression of these neurons, using microarray technology. We identified 1331 mRNAs that were differentially expressed in schizophrenia, including genes that belong to the transforming growth factor beta (TGF-β) and the bone morphogenetic proteins (BMPs) signaling pathways. Disturbances of these signaling mechanisms may in part contribute to the altered expression of other genes found to be differentially expressed in this study, such as those that regulate extracellular matrix (ECM), apoptosis, and cytoskeletal and synaptic plasticity. In addition, we identified 10 microRNAs (miRNAs) that were differentially expressed in schizophrenia; enrichment analysis of their predicted gene targets revealed signaling pathways and gene networks that were found by microarray to be dysregulated, raising an interesting possibility that dysfunction of pyramidal neurons in schizophrenia may in part be mediated by a concerted dysregulation of gene network functions as a result of the altered expression of a relatively small number of miRNAs. Taken together, findings of this study provide a neurobiological framework within which specific hypotheses about the molecular mechanisms of pyramidal cell dysfunction in schizophrenia can be formulated.
Collapse
Affiliation(s)
- Charmaine Y. Pietersen
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah A. Mauney
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
| | - Susie S. Kim
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
| | - Maribel P. Lim
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
| | | | - Jill M. Goldstein
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Tracey L. Petryshen
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Larry J. Seidman
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Martha E. Shenton
- Department of Psychiatry, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Robert W. McCarley
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Psychiatry, Veterans Affairs Boston Healthcare System, Brockton, Massachusetts, USA
| | - Kai-C. Sonntag
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, McLean Hospital, Belmont, Massachusetts, USA
| | - Tsung-Ung W. Woo
- Laboratory of Cellular Neuropathology, McLean Hospital, Belmont, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| |
Collapse
|
33
|
KANDATHIL ABRAHAMJ, GRAW FREDERIK, QUINN JEFFREY, HWANG HYONS, TORBENSON MICHAEL, PERELSON ALANS, RAY STUARTC, THOMAS DAVIDL, RIBEIRO RUYM, BALAGOPAL ASHWIN. Use of laser capture microdissection to map hepatitis C virus-positive hepatocytes in human liver. Gastroenterology 2013; 145:1404-13.e1-10. [PMID: 23973767 PMCID: PMC4005338 DOI: 10.1053/j.gastro.2013.08.034] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 08/10/2013] [Accepted: 08/14/2013] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) predominantly infects hepatocytes, but many hepatocytes are not infected; studies have shown that HCV antigens cluster within the liver. We investigated spatial distribution and determinants of HCV replication in human liver samples. METHODS We analyzed liver samples from 4 patients with chronic HCV infection (genotype 1, Metavir scores 0-1) to estimate the proportion of infected hepatocytes and the amount of HCV viral RNA (vRNA) per cell. Single-cell laser capture microdissection was used to capture more than 1000 hepatocytes in grids, to preserve geometric relationships. HCV vRNA and interferon-induced transmembrane protein 3 (IFITM3) messenger RNA (the transcript of an interferon-stimulated gene) were measured in the same hepatocytes by quantitative polymerase chain reaction and assembled in maps to identify areas of high and low HCV replication. RESULTS Patients' serum levels of HCV RNA ranged from 6.87 to 7.40 log10 IU/mL; the proportion of HCV-infected hepatocytes per person ranged from 21% to 45%, and the level of vRNA ranged from 1 to 50 IU/hepatocyte. Infection was not random; we identified clustering of HCV-positive hepatocytes using infected-neighbor analysis (P < .0005) and distance to the kth nearest neighbor compared with random distributions, obtained by bootstrap simulations (P < .02). Hepatocytes that expressed IFITM3 did not appear to cluster and were largely HCV negative. CONCLUSIONS We used single-cell laser capture and high-resolution analysis to show that in human liver HCV infects hepatocytes in nonrandom clusters, whereas expression of antiviral molecules is scattered among hepatocytes. These findings show that quantitative single-cell RNA measurements can be used to estimate the abundance of HCV vRNA per infected human hepatocyte and are consistent with cell-cell propagation of infection in the absence of clustered IFITM3.
Collapse
Affiliation(s)
| | - FREDERIK GRAW
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico
| | - JEFFREY QUINN
- Department of Medicine, Johns Hopkins University Baltimore, Maryland
| | - HYON S. HWANG
- Department of Medicine, Johns Hopkins University Baltimore, Maryland
| | - MICHAEL TORBENSON
- Department of Pathology, Johns Hopkins University Baltimore, Maryland
| | - ALAN S. PERELSON
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico
| | - STUART C. RAY
- Department of Medicine, Johns Hopkins University Baltimore, Maryland
| | - DAVID L. THOMAS
- Department of Medicine, Johns Hopkins University Baltimore, Maryland
| | - RUY M. RIBEIRO
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico
| | - ASHWIN BALAGOPAL
- Department of Medicine, Johns Hopkins University Baltimore, Maryland
| |
Collapse
|
34
|
Ji H, Gheysen G, Denil S, Lindsey K, Topping JF, Nahar K, Haegeman A, De Vos WH, Trooskens G, Van Criekinge W, De Meyer T, Kyndt T. Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots. J Exp Bot 2013; 64:3885-98. [PMID: 23881398 PMCID: PMC3745741 DOI: 10.1093/jxb/ert219] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
One of the reasons for the progressive yield decline observed in aerobic rice production is the rapid build-up of populations of the rice root knot nematode Meloidogyne graminicola. These nematodes induce specialized feeding cells inside root tissue, called giant cells. By injecting effectors in and sipping metabolites out of these cells, they reprogramme normal cell development and deprive the plant of its nutrients. In this research we have studied the transcriptome of giant cells in rice, after isolation of these cells by laser-capture microdissection. The expression profiles revealed a general induction of primary metabolism inside the giant cells. Although the roots were shielded from light induction, we detected a remarkable induction of genes involved in chloroplast biogenesis and tetrapyrrole synthesis. The presence of chloroplast-like structures inside these dark-grown cells was confirmed by confocal microscopy. On the other hand, genes involved in secondary metabolism and more specifically, the majority of defence-related genes were strongly suppressed in the giant cells. In addition, significant induction of transcripts involved in epigenetic processes was detected inside these cells 7 days after infection.
Collapse
Affiliation(s)
- Hongli Ji
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Godelieve Gheysen
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- * To whom correspondence should be addressed. E-mail:
| | - Simon Denil
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Keith Lindsey
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Jennifer F. Topping
- School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Kamrun Nahar
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Annelies Haegeman
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Winnok H. De Vos
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Geert Trooskens
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
- NXTGNT, Ghent University, Medical Research Building, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Tim De Meyer
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Tina Kyndt
- Department of Molecular Biotechnology, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| |
Collapse
|
35
|
Sodhi MS, Simmons M, McCullumsmith R, Haroutunian V, Meador-Woodruff JH. Glutamatergic gene expression is specifically reduced in thalamocortical projecting relay neurons in schizophrenia. Biol Psychiatry 2011; 70:646-54. [PMID: 21549355 PMCID: PMC3176961 DOI: 10.1016/j.biopsych.2011.02.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 01/28/2011] [Accepted: 02/22/2011] [Indexed: 11/28/2022]
Abstract
BACKGROUND Impairment of glutamate neurons that relay sensory and cognitive information from the medial dorsal thalamus to the dorsolateral prefrontal cortex and other cortical regions may contribute to the pathophysiology of schizophrenia. In this study, we have assessed the cell-specific expression of glutamatergic transcripts in the medial dorsal thalamus. METHODS We used laser capture microdissection to harvest two populations of medial dorsal thalamic cells, one enriched with glutamatergic relay neurons and the other with gamma-aminobutyric acidergic neurons and astroglia, from postmortem brains of subjects with schizophrenia (n = 14) and a comparison group (n = 20). Quantitative polymerase chain reaction of extracted RNA was used to assay gene expression in the different cell populations. RESULTS The transcripts encoding the ionotropic glutamate receptor subunits NR2D, GluR3, GluR6, GluR7, and the intracellular proteins GRIP1 and SynGAP1 were significantly decreased in relay neurons but not in the mixed glial and interneuron population in schizophrenia. CONCLUSIONS Our data suggest that reduced ionotropic glutamatergic expression occurs selectively in neurons, which give rise to the cortical projections of the medial dorsal thalamus in schizophrenia, rather than in thalamic cells that function locally. Our findings indicate that glutamatergic innervation is dysfunctional in the circuitry between the medial dorsal thalamus and cortex.
Collapse
Affiliation(s)
- Monsheel S. Sodhi
- Dept. Psychiatry and Behavioral Neurobiology, UAB, 1720 7 Avenue Sth. Birmingham, Alabama 35294-0019, USA,Dept. Pharmacy Practice and Center for Pharmaceutical Biotechnology, College of Pharmacy, 900 S Ashland Ave, Chicago, Illinois 60607-4067, USA,Correspondence should be addressed to: Monsheel Sodhi Ph.D., 900 S. Ashland Ave. Chicago IL 60607-4067, USA, Tel: +1-312-355-5949, Fax: +1-312-413-9303,
| | - Micah Simmons
- Dept. Psychiatry and Behavioral Neurobiology, UAB, 1720 7 Avenue Sth. Birmingham, Alabama 35294-0019, USA
| | - Robert McCullumsmith
- Dept. Psychiatry and Behavioral Neurobiology, UAB, 1720 7 Avenue Sth. Birmingham, Alabama 35294-0019, USA
| | - Vahram Haroutunian
- Dept. Psychiatry, The Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029-6574, USA
| | - James H. Meador-Woodruff
- Dept. Psychiatry and Behavioral Neurobiology, UAB, 1720 7 Avenue Sth. Birmingham, Alabama 35294-0019, USA
| |
Collapse
|
36
|
Bernard R, Kerman IA, Thompson RC, Jones EG, Bunney WE, Barchas JD, Schatzberg AF, Myers RM, Akil H, Watson SJ. Altered expression of glutamate signaling, growth factor, and glia genes in the locus coeruleus of patients with major depression. Mol Psychiatry 2011; 16:634-46. [PMID: 20386568 DOI: 10.1038/mp.2010.44] [Citation(s) in RCA: 247] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Several studies have proposed that brain glutamate signaling abnormalities and glial pathology have a role in the etiology of major depressive disorder (MDD). These conclusions were primarily drawn from post-mortem studies in which forebrain brain regions were examined. The locus coeruleus (LC) is the primary source of extensive noradrenergic innervation of the forebrain and as such exerts a powerful regulatory role over cognitive and affective functions, which are dysregulated in MDD. Furthermore, altered noradrenergic neurotransmission is associated with depressive symptoms and is thought to have a role in the pathophysiology of MDD. In the present study we used laser-capture microdissection (LCM) to selectively harvest LC tissue from post-mortem brains of MDD patients, patients with bipolar disorder (BPD) and from psychiatrically normal subjects. Using microarray technology we examined global patterns of gene expression. Differential mRNA expression of select candidate genes was then interrogated using quantitative real-time PCR (qPCR) and in situ hybridization (ISH). Our findings reveal multiple signaling pathway alterations in the LC of MDD but not BPD subjects. These include glutamate signaling genes, SLC1A2, SLC1A3 and GLUL, growth factor genes FGFR3 and TrkB, and several genes exclusively expressed in astroglia. Our data extend previous findings of altered glutamate, astroglial and growth factor functions in MDD for the first time to the brainstem. These findings indicate that such alterations: (1) are unique to MDD and distinguishable from BPD, and (2) affect multiple brain regions, suggesting a whole-brain dysregulation of such functions.
Collapse
|