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Molecular Characterization of Laser Microdissected Circumventricular Organs and Third Ventricle Ependyma in the Adult Rat by Microarray Analysis.

ABSTRACT: We used LCM and microarrays to analyze the transcriptomes of three CVOs, the SCO, the subfornical organ (SFO), and the PG, and the third ventricle ependyma in the adult rat in order to better characterize these organs at the molecular level.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE35089 | GEO | 2012/05/24

SECONDARY ACCESSION(S): PRJNA150925

REPOSITORIES: GEO

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Molecular Characterization of Laser Microdissected Circumventricular Organs and Third Ventricle Ependyma in the Adult Rat by Microarray Analysis.

Project description:We used LCM and microarrays to analyze the transcriptomes of three CVOs, the SCO, the subfornical organ (SFO), and the PG, and the third ventricle ependyma in the adult rat in order to better characterize these organs at the molecular level. Gene expression was performed on laser microdissection of rat Pineal Gland (n=2), Subcommisural Organ (pool of 2), Subfornical Organ (pool of 2) and Third Ventricle Ependyma (pool of 2). Pool of rat total normal brains was used as reference.

2012-05-23 | E-GEOD-35089 | biostudies-arrayexpress

Laser-capture microdissected invasive micropapillary carcinomas of the breast

Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs).

2011-04-25 | GSE28821 | GEO

Gene expression anlaysis of laser-capture microdissected tumor and stroma from triple negative breast cancer

Project description:LCM was perfomed on adjacent tumor and stromal cells to identify differentially expressed genes in triple negative breast cancer.

2016-07-01 | GSE81838 | GEO

Expression Profiles of Rats Treated with Clofibric Acid: Comparison of Whole and Laser Capture Microdissected Liver

Project description:This is an evaluation of the impact of the successive steps of LCM procedure on gene expression profiling by comparing profiles from LCM samples to those obtained with non-microdissected liver samples collected after a one month CLO treatment in the rat. We showed that the H&E staining used for identifying PP-foci and the laser microdissection itself do not impact on RNA quality. Keywords = Microdissection Keywords = Clofibric Acid Keywords: other

2003-12-03 | GSE691 | GEO

Laser-capture microdissected invasive micropapillary carcinomas of the breast

Project description:The purpose of this study was to identify differentially expressed genes in laser-capture microdissected (LCM) invasive mammary carcinomas (IMCs). Invasive mammary carcinoma of the breast surgical resection specimens were laser capture microdissected for RNA extraction and hybridization to Affymetrix microarrays.

2011-04-25 | E-GEOD-28821 | biostudies-arrayexpress

Transcriptomic Analysis of Laser Capture Microdissected Tumors of Pancreatic Ductal Adenocarcinoma

Project description:In this study, we performed laser capture microdissection (LCM) of PDAC samples to define their cancer- and stroma-specific molecular subtypes and identify a prognostic gene expression signature for short-term and long-term survival. LCM and RNA-seq analysis of cancer and adjacent stroma of 19 treatment-naïve PDAC tumors were performed. Gene expression signatures were tested for their robustness in a large independent validation set. An RNA in situ hybridization (RNA-ISH) assay with pooled probes for genes associated with disease-free survival (DFS) was developed to probe 111 PDAC tumor samples. Gene expression profiling identified four subtypes of cancer cells (C1-C4) and three subtypes of cancer-adjacent stroma (S1-S3). These stroma-specific subtypes were associated with DFS (p=5.55E-07), with S1 associated with better prognoses when paired with C1 and C2. Thirteen genes were found to be predominantly expressed in cancer cells and corresponded with DFS in a validation using existing RNA-seq datasets. A second validation on an independent cohort of patients using RNA-ISH probes to six of these prognostic genes demonstrated significant association with overall survival (median 17 versus 25 months; p<0.02). Our results identified specific signatures from the epithelial and the stroma components of PDAC, which add clarity to the nature of PDAC molecular subtypes and may help predict survival.

2021-06-30 | GSE164665 | GEO

Proteomics on formalin-fixed and stained laser-capure microdissected human lung sections

Project description:A broad range of tissues have been examined by microscopy following a process of formalin fixation, paraffin embedment, sectioning and staining. Haematoxylin and eosin (H&E) – which respectively stain nuclei blue and other cellular and stromal material pink – are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterisation can be achieved by coupling spatially resolved methods to mass spectrometry (MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing, embedding and staining tissues for histological analysis is poorly compatible with standard sample preparation methods for mass spectrometry, resulting in a reduction in the number of proteins identified. Here we describe a microproteomics technique optimised to analyse H&E-stained, formalin-fixed paraffin-embedded (FFPE) sections of human lung tissue. Laser capture microdissection (LCM) was used to isolate sections of morphologically normal alveoli and blood vessels from tissue-banked specimens of human idiopathic pulmonary fibrosis (IPF). Following sample digestion and clean-up, MS was able to identify 1252 differentially expressed proteins. This work provides an optimised pipeline for the analysis of FFPE tissue sections by LCM-MS. Furthermore, it offers proof of principal that MS can identify distinct, characteristic proteomic compositions of anatomical features within complex tissues.

2021-09-08 | PXD014762 | Pride

Proteomic profiling of stromal reprogramming in canine simple mammary carcinomas using laser-capture microdissected FFPE tissue

Project description:Cancer-associated stroma (CAS) profoundly influences development and progression of tumours including mammary carcinoma (mCA). Spontaneous canine simple mCA represent relevant models of human mCA, notably also with respect to CAS reprogramming. While transcriptomic changes in CAS of mCA are well described, it remains unclear to what extent these differences translate to the protein level. Therefore, we sought to gain insight into the proteomic changes in CAS and compare them with transcriptomic changes in the same tissue. To this end, we analysed CAS and matched normal stroma isolated by laser-capture microdissection (LCM) by LC-MS/MS in a cohort of 14 Formalin-fixed paraffin embedded (FFPE) canine mCAs that we had previously characterized using LCM-RNAseq. Our results reveal clear differences in protein abundance between CAS and normal stroma, which are characterised by changes in the extracellular matrix, the cytoskeleton, and cytokines such as TNF. While the proteomics-based analysis of LCM-FFPE tissue detects fewer targets than RNAseq, the protein and RNA levels show a decent degree of correlation, especially for the most deregulated targets. Moreover, the results from both approaches reveal a comparable picture with regards to pathway activation. Finally, we validate transcriptomic upregulation of LTBP2, IGFBP2, COL6A5, POSTN, FN1, COL4A1, COL12A1, PLOD2, COL4A2, and IGFBP7 in CAS on the protein level and demonstrate their adverse prognostic value for human breast cancer. Given the relevance of canine mCA as model for the human disease, our analysis substantiates these targets as disease-promoting stromal components with implications for breast cancer in both humans and dogs.

2021-03-30 | PXD023023 | Pride

Transcription profiling of rat glomeruli: conventionally-isolated and laser capture microdissected glomeruli

Project description:We compared the gene expression analysis of 2 different glomerular isolation techniques (laser capture microdissection with 2 rounds of RNA amplification and unamplified glomerular RNA after iron perfusion with glomerular sieving) and obtained different results depending on the glomerular isolation technique that was used Experiment Overall Design: Paired kidneys from Lewis-Hsd rat kidneys were collected. The glomeruli of one kidney was obtained by LCM with 2 rounds of RNA amplification while the unamplified glomerular RNA of the contralateral kidney was obtained after perfusion with iron oxide and isolated by magnetic purification and a glomerular sieving technique. The RNA was analyzed using the Affymetrix Rat 230A microarrays.

2008-06-17 | E-GEOD-8998 | biostudies-arrayexpress

Gene expression anlaysis of laser-capture microdissected tumor and stroma from triple negative breast cancer

Project description:LCM was perfomed on adjacent tumor and stromal cells to identify differentially expressed genes in triple negative breast cancer. To determine differences in tumor and adjacent stromal tissue, laser-capture microdissction was perfomed on 10 triple negative breast cancer specimans to isolate tumor and stromal cells for gene expression analysis. RNA was isolated from captured cells and hybridized to affymetrix gene expression microarrays.

2016-07-01 | E-GEOD-81838 | biostudies-arrayexpress

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