Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Microarray analysis was applied to detect the lncRNAs and mRNAs in glioma compared to normal peritumoral tissue. A – Differentially expressed lncRNAs were detected in gliomas. A, B – Differentially expressed mRNAs were detected in gliomas. C – Clustering data of lncRNAs in gliomas were analyzed. D – Clustering data of mRNAs in gliomas were analyzed

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Microarray

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Summary of data from microarray for three pairs of glioma and adjacent normal tissues

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Microarray, RNA Expression

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: LncRNA-mRNA co-expression network: nodes with red cycle represent lncRNAs, nodes without cycle represent mRNAs, straight lines represent interactions between genes, purple represents increased expression, and blue represents decreased expression. The size of the node represents the degree; the higher the degree, the more genes interact with the particular node in the network

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Expressing

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Degree was used to assess interactions in the lncRNA/mRNA network. This table is a collection of a series of key lncRNA/mRNAs

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques:

Journal: Archives of Medical Science : AMS

Article Title: Aberrant expression of long non-coding RNAs (lncRNAs) is involved in brain glioma development

doi: 10.5114/aoms.2020.91290

Figure Lengend Snippet: Comparison of microarray data and qPCR results. A – qPCR was used to verify expression of lncRNAs ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc003qmb.2. B – Distribution of lncRNA expression levels were provided. All six lncRNAs of ak125809, ak098473, uc002ehu.1, bc043564, NR_027322, and uc- 003qmb.2 were validated by qPCR analysis in the 40 paired glioma and peritumoral tissues. Each histogram represents the average fold change (T/N) with logarithmic conversion. Error bars are indicative of standard deviation. Distribution of lncRNA expression

Article Snippet: The synthesized cDNAs were labeled and hybridized to Arraystar Human lncRNA Microarray V2.0 (Arraystar, Rockville, MD) containing probes for 33,045 lncRNAs and 30,215 mRNAs identified from both publications and authoritative databases, such as RefSeq, UCSC Knowngenes, and Ensembl.

Techniques: Comparison, Microarray, Expressing, Standard Deviation

Journal: Acta Pharmaceutica Sinica. B

Article Title: Sulfation of chondroitin and bile acids converges to antagonize Wnt/ β -catenin signaling and inhibit APC deficiency-induced gut tumorigenesis

doi: 10.1016/j.apsb.2023.12.006

Figure Lengend Snippet: Decreased expression of PAPSS2 correlates with poor survival of colon cancer patients. (A, B) Bioinformatic analyses of scRNA-seq dataset derived from normal human gut. Shown are scaled expression of PAPSS2 in different cell lineages and clustering of different cell lineages in small intestine (A) and colon (B). (C) Analysis of PAPSS2 gene expression in paired tumor adjacent normal tissues and primary tumors in TCGA cohorts of cancers. BLCA, bladder urothelial carcinoma; BRCA, breast invasive carcinoma; CHOL, cholangiocarcinoma; COAD, colon adenocarcinoma (red box); ESCA, esophageal carcinoma; HNSC, head and neck squamous cell carcinoma; KICH, kidney chromophobe; KIRC, kidney renal clear cell carcinoma; KIRP, kidney renal papillary cell carcinoma; LIHC, liver hepatocellular carcinoma; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; PAAD, pancreatic adenocarcinoma; PRAD, prostate adenocarcinoma; READ, rectum adenocarcinoma; STAD, stomach adenocarcinoma; THCA, thyroid carcinoma; UCEC, uterine corpus endometrial carcinoma. (D) Representative H&E and IHC staining of PAPSS2 on human normal colon and different stages of colon cancer tissue array. Shown on the right is the quantifications of PAPSS2 positive area. Scale bars: 100 μm. (E) Receiver operating characteristic (ROC) curve analysis for PAPSS2 as a predictor of patients with colon cancer. (F) Parsing of human COAD patient survival curves in different stages based on the PAPSS2 expression. One-way ANOVA with Tukey's test was used for multiple comparisons. Survival curves were plotted using the Kaplan–Meier method, and the log-rank test was utilized to determine statistical differences. Data are presented as the mean ± SEM. ns means no significant difference; ∗ P < 0.05; ∗∗ P < 0.01; ∗∗∗ P < 0.001.

Article Snippet: Human normal colon and colon tumor tissues array were purchased from US Biomax (Derwood, MD) and used for H&E and immunohistochemical staining.

Techniques: Expressing, Derivative Assay, Immunohistochemistry

Journal: Acta Pharmaceutica Sinica. B

Article Title: Sulfation of chondroitin and bile acids converges to antagonize Wnt/ β -catenin signaling and inhibit APC deficiency-induced gut tumorigenesis

doi: 10.1016/j.apsb.2023.12.006

Figure Lengend Snippet: Sensitization of gut tumorigenesis by intestinal Papss2 ablation is accompanied by the activation of Wnt/ β -catenin and suppression of Wnt repressor TLE3. (A, B) Top 20 hallmark pathways (A) and GSEA (B) of RNA-seq data from the intestinal tumor of Apc Δgut -Het and Apc Δgut -Het Papss2 Δgut mice. (C) Relative mRNA expression of Wnt target genes. (D) Protein expression of β -catenin and TLE3 in the ileum by Western blotting. (E) Representative β -catenin immunostaining (green) of tumor sections with the quantifications of the nuclear-to-cytoplasmic ratio of β -catenin fluorescence shown on the right. n = 5, scale bars: 200 μm. (F) Protein expression of β -catenin and TLE3 in the colon of AOM-treated Papss2 fl/fl and Papss2 Δgut mice by Western blotting. (G) Representative β -catenin immunostaining (green) of colonic tumor with the quantifications of the nuclear-to-cytoplasmic ratio of β -catenin fluorescence shown on the right. n = 5, scale bars: 200 μm. (H) Representative TLE3 immunostaining in the tumor (T) or nontumor (N) regions of Apc Δgut -Het and Apc Δgut -Het Papss2 Δgut mice. Scale bars: 100 μm. (I) Representative H&E and IHC staining of TLE3 on human normal colon and different stages of colon cancer tissue array. Shown on the right is the quantifications of TLE3 positive area. Scale bars: 100 μm. (J) Correlations between the immunohistochemical intensity of PAPSS2 and TLE3 in the same cohort of samples shown in (I). (K–M) Correlations between the expression of PAPSS2 and TLE3 (K), Wnt target genes (L) and β -catenin target genes (M) in human COAD patient cohorts from TCGA using Gene Expression Profiling Interactive Analyses. (N) Luciferase reporter gene assay in HCT116 cells transfected with the TCF/TEF-luciferase reporter and treated with sulfation inhibitor NaClO 3 (left panel), or co-transfected with pCDNA-PAPSS2 expression plasmid (right panel). n = 4–5. (O) Protein expression of β -Catenin and TLE3 in the HCT116 cells transfected with pCDNA3.1 vector or pCDNA-PAPSS2. Shown on the right are the quantifications of protein expressions. n = 3–4. Statistical significance between two groups was assessed by two-tailed Student's t -test. One-way ANOVA with Tukey's test was used for multiple comparisons. The gene expression correlation analysis was performed using the Pearson correlation coefficient. Data are presented as the mean ± SEM or box plots. ∗ P < 0.05; ∗∗ P < 0.01; ∗∗∗ P < 0.001.

Article Snippet: Human normal colon and colon tumor tissues array were purchased from US Biomax (Derwood, MD) and used for H&E and immunohistochemical staining.

Techniques: Activation Assay, RNA Sequencing Assay, Expressing, Western Blot, Immunostaining, Fluorescence, Immunohistochemistry, Immunohistochemical staining, Luciferase, Reporter Gene Assay, Transfection, Plasmid Preparation, Two Tailed Test