Journal: Brain Pathology

Article Title: Galectin‐1 Is Implicated in the Protein Kinase C ε/Vimentin‐Controlled Trafficking of Integrin‐β1 in Glioblastoma Cells

doi: 10.1111/j.1750-3639.2008.00227.x

Figure Lengend Snippet: Transient transfection of galectin‐1 using targeted small interfering RNA (siRNA) decreases intracellular galectin‐1 protein. WB analysis of galectin‐1 expression levels at days 5, 7 and 9 post‐transfection in control (ctrl), scramble‐transfected (scr), and galectin‐1‐transfected (siGal1) U87 ( A ) and Hs683 ( C ) cells. Immunofluorescence (IF) analysis of galectin‐1 expression levels in U87 day 7 post‐transfection ( B ) and Hs683 day 5 post‐transfection ( D ) using scrambled or anti‐galectin‐1 siRNA. Top rows are the corresponding bright fields to the IF images.

Article Snippet: The Hs683 [American Type Culture Collection (ATCC) code HTB‐138], U87 (ATCC code HTB‐14), U373 (ATCC code HTB‐17) and T98G (ATCC code CRL‐1690) human GBM cell lines were obtained from the ATCC (Manassas, VA, USA) and maintained in our laboratory as detailed previously , , , .

Techniques: Transfection, Small Interfering RNA, Expressing, Control, Immunofluorescence

Journal: Brain Pathology

Article Title: Galectin‐1 Is Implicated in the Protein Kinase C ε/Vimentin‐Controlled Trafficking of Integrin‐β1 in Glioblastoma Cells

doi: 10.1111/j.1750-3639.2008.00227.x

Figure Lengend Snippet: Integrin‐α9 versus integrin‐β1 expression . A. Integrin‐α9, integrin‐β1 and actin expression across eight glioma cell lines by reverse transcription‐polymerase chain reaction (RT‐PCR) analysis. B. Quantitative RT‐PCR analysis of integrin‐α9 versus integrin‐β1 expression in glioma cell lines Hs683, U87 and U373. C. Hs683 expression levels of integrin‐α9 and integrin‐β1 under control (ctrl), scramble‐transfected (scr) or galectin‐1 siRNA‐transfected (siGal1) conditions obtained through microarray analysis using the Affymetrix Human Genome U133 set Plus 2.0.

Article Snippet: The Hs683 [American Type Culture Collection (ATCC) code HTB‐138], U87 (ATCC code HTB‐14), U373 (ATCC code HTB‐17) and T98G (ATCC code CRL‐1690) human GBM cell lines were obtained from the ATCC (Manassas, VA, USA) and maintained in our laboratory as detailed previously , , , .

Techniques: Expressing, Reverse Transcription, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Control, Transfection, Microarray

Journal: Brain Pathology

Article Title: Galectin‐1 Is Implicated in the Protein Kinase C ε/Vimentin‐Controlled Trafficking of Integrin‐β1 in Glioblastoma Cells

doi: 10.1111/j.1750-3639.2008.00227.x

Figure Lengend Snippet: Galectin‐1‐targeted siRNA induces both a decrease of integrin‐β1 at the edges of the cell membrane and an increase in the intracellular accumulation of integrin‐β1 . A. U87 control wild‐type cells ( Aa,Ab ) and U87 cells containing stably transfected antisense galectin‐1 vectors ( Ac ) were co‐stained under non‐permeabilized conditions for integrin‐β1 [the red staining at the tip of actin stress fibers (in green fluorescence)], fibrillar actin (green) and globular actin (red staining inside the cells). Ab. Higher magnification of the control wild‐type ( Aa ) image. B. U87 control wild‐type cells ( Ba ) and U87 cells containing stably transfected antisense galectin‐1 vectors ( Bb ) were stained under permeabilized conditions for integrin‐β1 only (in green), without any staining to reveal actin ( Ba,Bb ). C. U87 and Hs683 cells were transiently transfected with either scrambled siRNA (scr) or siRNA targeted against galectin‐1 (siGal1). Cells were stained for integrin‐β1 (in red) under both permeablized and non‐permeabilized conditions on either day 5 post‐transfection (Hs683) or day 7 post‐transfection (U87).

Article Snippet: The Hs683 [American Type Culture Collection (ATCC) code HTB‐138], U87 (ATCC code HTB‐14), U373 (ATCC code HTB‐17) and T98G (ATCC code CRL‐1690) human GBM cell lines were obtained from the ATCC (Manassas, VA, USA) and maintained in our laboratory as detailed previously , , , .

Techniques: Membrane, Control, Stable Transfection, Transfection, Staining, Fluorescence

Journal: Brain Pathology

Article Title: Galectin‐1 Is Implicated in the Protein Kinase C ε/Vimentin‐Controlled Trafficking of Integrin‐β1 in Glioblastoma Cells

doi: 10.1111/j.1750-3639.2008.00227.x

Figure Lengend Snippet: Western blot (WB) and immunofluorescence (IF) analysis of vimentin and protein kinase C epsilon (PKCε) protein expression levels; galectin‐1‐targeted siRNA increases only vimentin protein levels in Hs683, induces increased perinulear amassment of both PKCε and vimentin, and diminishes the diffuse cytoplasmic staining of PKCε . WB analysis of PKCε and vimentin protein expression levels in U87 ( A ) or Hs683 ( B ) cells untreated (ctrl), scramble‐transfected (scr) or galectin‐1 siRNA‐transfected (siGal1) at days 5, 7 and 9 post‐transfection. IF analysis of PKCε localization in U87 ( C ) or Hs683 ( D ) scr or siGal1 at either day 5 (Hs683) or day 7 (U87) post‐transfection. IF analysis of vimentin localization in U87 ( E ) or Hs683 ( F ) cells scr or galectin‐1 siRNA‐transfected (siGal1) at either day 5 (Hs683) or day 7 (U87) post‐transfection. In all IF figures right columns represent the corresponding bright field images.

Article Snippet: The Hs683 [American Type Culture Collection (ATCC) code HTB‐138], U87 (ATCC code HTB‐14), U373 (ATCC code HTB‐17) and T98G (ATCC code CRL‐1690) human GBM cell lines were obtained from the ATCC (Manassas, VA, USA) and maintained in our laboratory as detailed previously , , , .

Techniques: Western Blot, Immunofluorescence, Expressing, Staining, Transfection

Journal: Brain Pathology

Article Title: Galectin‐1 Is Implicated in the Protein Kinase C ε/Vimentin‐Controlled Trafficking of Integrin‐β1 in Glioblastoma Cells

doi: 10.1111/j.1750-3639.2008.00227.x

Figure Lengend Snippet: Integrin‐α9 versus integrin‐β1 expression . A. Integrin‐α9, integrin‐β1 and actin expression across eight glioma cell lines by reverse transcription‐polymerase chain reaction (RT‐PCR) analysis. B. Quantitative RT‐PCR analysis of integrin‐α9 versus integrin‐β1 expression in glioma cell lines Hs683, U87 and U373. C. Hs683 expression levels of integrin‐α9 and integrin‐β1 under control (ctrl), scramble‐transfected (scr) or galectin‐1 siRNA‐transfected (siGal1) conditions obtained through microarray analysis using the Affymetrix Human Genome U133 set Plus 2.0.

Article Snippet: The Hs683 [American Type Culture Collection (ATCC) code HTB‐138], U87 (ATCC code HTB‐14), U373 (ATCC code HTB‐17) and T98G (ATCC code CRL‐1690) human GBM cell lines were obtained from the ATCC (Manassas, VA, USA) and maintained in our laboratory as detailed previously , , , .

Techniques: Expressing, Reverse Transcription, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Control, Transfection, Microarray

Journal: Translational Cancer Research

Article Title: Functional analysis of long-chain non-coding RNA in oral squamous cell carcinoma

doi: 10.21037/tcr.2019.12.67

Figure Lengend Snippet: Clustered panels of differentially expressed lncRNAs (A) and mRNAs (B). Each column represents a sample; each row represents the degree of expression of a gene in different samples, the red refers to relatively high expression, and the green refers to the relatively low expression; the color in the upper left bar represents the fold change of gene expression; the top sample tree represents the clustering of similarity; the top color block represents the expected grouping of samples before the clustering analysis, and the samples with the same color are expected to be in the same group. LncRNA, long-chain non-coding RNA.

Article Snippet: The differentially expressed lncRNA and mRNAs were examined in 5 pairs of tissues with the 4×180 K lncRNA + mRNA Human Gene Expression Microarray V4.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing, Gene Expression, Blocking Assay

Journal: Translational Cancer Research

Article Title: Functional analysis of long-chain non-coding RNA in oral squamous cell carcinoma

doi: 10.21037/tcr.2019.12.67

Figure Lengend Snippet: Scatter plot of mRNA (A) and lncRNA (B). The number of genes with up-regulated and down-regulated expression was described in the upper left and lower right corners, respectively. The red line X2 is the threshold line of the up-regulated expression, the green line X(−2) is the threshold line of the down-regulated expression, and the middle gray line is the fitted line of the overall expression. The equations in the figure are the fitted line equations, and R represents the correlation coefficient. LncRNA, long-chain non-coding RNA.

Article Snippet: The differentially expressed lncRNA and mRNAs were examined in 5 pairs of tissues with the 4×180 K lncRNA + mRNA Human Gene Expression Microarray V4.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing

Journal: Translational Cancer Research

Article Title: Functional analysis of long-chain non-coding RNA in oral squamous cell carcinoma

doi: 10.21037/tcr.2019.12.67

Figure Lengend Snippet: Volcano plot of mRNA (A) and lncRNA (B). The horizontal ordinate is the log2 (P values) and the longitudinal ordinate is the log2 (fold change). The red refers to the up-regulated genes, the green refers to the down-regulated genes, and the black refers to genes without significant difference in the expression. Volcanoplot can intuitively reflect the number, significance, and reliability of differentially expressed genes. The closer to the right upper or left upper corner, the more significant the difference in the expression is between two groups. LncRNA, long-chain non-coding RNA.

Article Snippet: The differentially expressed lncRNA and mRNAs were examined in 5 pairs of tissues with the 4×180 K lncRNA + mRNA Human Gene Expression Microarray V4.0 (CapitalBio Technology, Beijing, China).

Techniques: Expressing

Journal: Translational Cancer Research

Article Title: Functional analysis of long-chain non-coding RNA in oral squamous cell carcinoma

doi: 10.21037/tcr.2019.12.67

Figure Lengend Snippet: Disease enrichment analysis of differentially expressed mRNA (top 30 terms). As shown in the figure, the diseases with the most enrichment of mRNAs included immune system diseases, primary immunodeficiency, muscular diseases, allergies and autoimmune diseases, skin and soft tissue diseases, skin diseases, musculoskeletal diseases, celiac diseases, cardiac diseases, inflammatory bowel disease, dilated cardiomyopathy, Graves’ disease, cardiovascular diseases, systemic sclerosis, systemic lupus erythematosus, vitiligo and rheumatoid arthritis.

Article Snippet: The differentially expressed lncRNA and mRNAs were examined in 5 pairs of tissues with the 4×180 K lncRNA + mRNA Human Gene Expression Microarray V4.0 (CapitalBio Technology, Beijing, China).

Techniques:

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: ATM-dependent regulation of lncRNA expression in response to DNA damage. (A) Experimental layout to identify ATM-dependent lncRNAs. Atm+/+ and Atm−/− mouse embryonic fibroblasts (MEFs) were treated with NCS (200 ng/ml) and harvested at indicated time points for microarray analyses. (B) The number of ATM-dependent lncRNAs upon DNA damage. (C) A representative group of ATM-dependent and DNA damage-induced lncRNAs. Green or red colour on the heat map indicates a decrease or an increase in the lncRNA level and colour intensities correspond to relative signal levels on a logarithmic scale. (D) Quantitative PCR validation of representative lncRNAs. Data represent the mean of three experimental replicates, with error bars depicting s.d.

Article Snippet: LncRNA in situ hybridization Breast cancer tissue microarray (no. {"type":"entrez-nucleotide","attrs":{"text":"BC081115","term_id":"51703523","term_text":"BC081115"}} BC081115 ) was purchased from Biomax, including 100 breast tumour samples and 10 control breast tissue samples.

Techniques: Expressing, Microarray, Real-time Polymerase Chain Reaction, Biomarker Discovery

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: LncRNA-JADE is induced after DNA damage. (A) Schematic illustration showing Jade1 and lncRNA-JADE genes in mouse and human. (B) Mouse and human lncRNA-JADE are induced in an ATM-dependent manner after DNA damage. (C) DNA damage positively regulates lncRNA-JADE promoter activity in an ATM-dependent manner. ATM-IN: ATM inhibitor. (D) Schematic illustration showing the NF-κB binding elements in the Jade1 promoter. DNA damage induces the activity of lncRNA-JADE promoter in an NF-κB-dependent manner. NF-κB-IN: NF-κB inhibitor. (E) Expression of LncRNA-JADE is regulated by ATM and NF-κB after DNA damage. IRF-1 (interferon response factor-1) is served as a positive control in the NF-κB signalling. Graphic data in this figure present the mean of three experimental replicates and error bars depict s.d.

Article Snippet: LncRNA in situ hybridization Breast cancer tissue microarray (no. {"type":"entrez-nucleotide","attrs":{"text":"BC081115","term_id":"51703523","term_text":"BC081115"}} BC081115 ) was purchased from Biomax, including 100 breast tumour samples and 10 control breast tissue samples.

Techniques: Activity Assay, Binding Assay, Expressing, Positive Control

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: LncRNA-JADE positively regulates histone H4 acetylation through Jade1. (A) H4 acetylation is induced after DNA damage. MCF7 cells were treated with NCS (500 ng/ml). H4Ac: total histone H4 acetylation; K5, K8, K12: Histone H4 acetylation at lysine 5, 8, or 12. (B) Jade1 knockdown abolishes the induction of H4 acetylation after DNA damage. (C) LncRNA-JADE positively regulates H4 acetylation and Jade1. Overexpression of lncRNA-JADE enhanced the induction of H4 acetylation and Jade1, and knockdown of lncRNA-JADE abolished the induction of H4 acetylation and Jade1. Semi-quantification of proteins is shown at the bottom.

Article Snippet: LncRNA in situ hybridization Breast cancer tissue microarray (no. {"type":"entrez-nucleotide","attrs":{"text":"BC081115","term_id":"51703523","term_text":"BC081115"}} BC081115 ) was purchased from Biomax, including 100 breast tumour samples and 10 control breast tissue samples.

Techniques: Knockdown, Over Expression

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: Brca1 binds lncRNA-JADE and mediates Jade1 induction in the DNA damage response via p300-containing transcription complex. (A) Schematic illustration showing the p300/CBP binding elements in the Jade1 promoter. (B) p300 physically interacts with the promoter region of Jade1 gene. Control or lncRNA-JADE knockdown MCF7 cells were treated with or without NCS (200 ng/ml) and cell lysates were immunoprecipitated with control IgG or p300 antibodies. The p300-binding activity of Jade1 promoter DNA was quantified by qPCR. (C) Brca1 interacts with p300 and this interaction is increased after DNA damage. (D) Jade1 promoter activity is induced in a Brca1-dependent manner after DNA damage. MCF-7 cells were infected with lentiviruses expressing control or Brca1 shRNA. The cells were transfected with pGL3-control vector (SV40 promoter) or Jade1 promoter-driven firefly luciferase expression vector and Renilla luciferase expression vector 2 days post infection. They were treated with NCS (500 ng/ml) 24 h after transfection and then harvested 16 h after treatment. Firefly luciferase activity was measured and normalized to the activity of Renilla luciferase. (E) LncRNA-JADE physically interacts with Brca1. 5′- and 3′-deletion mutants of lncRNA-JADE were generated as indicated. Two pairs of primers were used to detect the Brca1-binding sequences of lncRNA-JADE in RIP assays. Graphic data in this figure present the mean of three experimental replicates and error bars depict s.d.

Article Snippet: LncRNA in situ hybridization Breast cancer tissue microarray (no. {"type":"entrez-nucleotide","attrs":{"text":"BC081115","term_id":"51703523","term_text":"BC081115"}} BC081115 ) was purchased from Biomax, including 100 breast tumour samples and 10 control breast tissue samples.

Techniques: Binding Assay, Control, Knockdown, Immunoprecipitation, Activity Assay, Infection, Expressing, shRNA, Transfection, Plasmid Preparation, Luciferase, Generated

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: Biological functions of lncRNA-JADE in human MCF7 cells. (A) LncRNA-JADE positively regulates MCF7 cell proliferation. (B) Altering lncRNA-JADE expression affects DNA damage-induced cell-cycle arrest. Cell-cycle profiles were analysed by flow cytometry using propidium iodide-stained cells. (C) Knockdown of lncRNA-JADE increases cell apoptosis in the control and NCS-treated cells. The percentage of TUNEL-positive cells was summarized in the graph. (D) Knockdown of lncRNA-JADE increases the cell sensitivity to DNA damaging drugs NCS, Etopside, and Bleomycin. MCF7 cells were treated with DNA damaging agents as indicated and cultured for 48 h and cell viability was measured. Graphic data in this figure present the mean of three biological replicates and error bars depict s.d.

Article Snippet: LncRNA in situ hybridization Breast cancer tissue microarray (no. {"type":"entrez-nucleotide","attrs":{"text":"BC081115","term_id":"51703523","term_text":"BC081115"}} BC081115 ) was purchased from Biomax, including 100 breast tumour samples and 10 control breast tissue samples.

Techniques: Expressing, Flow Cytometry, Staining, Knockdown, Control, TUNEL Assay, Cell Culture

Journal: The EMBO Journal

Article Title: A novel non-coding RNA lncRNA-JADE connects DNA damage signalling to histone H4 acetylation

doi: 10.1038/emboj.2013.221

Figure Lengend Snippet: Knockdown of lncRNA-JADE inhibits mammary tumour growth in vivo. (A) Higher levels of lncRNA-JADE in human breast cancer tissues in comparison with normal breast tissues. In situ hybridization of lncRNA-JADE was performed on tissue microarray comprised of human normal breast and breast cancer tissues. (B) Correlation between lncRNA-JADE and Jade1 up-expression in breast cancer tissue cDNA array. The level of lncRNA-JADE and Jade1 was measured by RT–PCR. The lncRNA-JADE expression demonstrated a significant correlation with the Jade1 expression according to the Spearman correlation coefficient (r=0.6983 and P=0.0294). (C) Comparison of survival curves between patients with Jade1 overexpression and patients with normal Jade1 expression using TCGA data in breast invasive carcinomas. (D) Knockdown of lncRNA-JADE inhibits xenografted 4T1 tumour growth in vivo. One million luciferase expressing 4T1 cells stably expressing control or lncRNA-JADE shRNA were injected into the mammary fat pad of each Balb/cSCID mouse. Two weeks after injection, luciferase activity was measured and quantified by an IVIS device (left panel and upper right panel). Breast tumour size was measured in the mice for 24 days (bottom right panel). Graphic data present the mean of five mice and error bars depict s.d.

Article Snippet: LncRNA in situ hybridization Breast cancer tissue microarray (no. {"type":"entrez-nucleotide","attrs":{"text":"BC081115","term_id":"51703523","term_text":"BC081115"}} BC081115 ) was purchased from Biomax, including 100 breast tumour samples and 10 control breast tissue samples.

Techniques: Knockdown, In Vivo, Comparison, In Situ Hybridization, Microarray, Expressing, Reverse Transcription Polymerase Chain Reaction, Over Expression, Luciferase, Stable Transfection, Control, shRNA, Injection, Activity Assay