Journal: Frontiers in Oncology

Article Title: SNHG9, a Papillary Thyroid Cancer Cell Exosome-Enriched lncRNA, Inhibits Cell Autophagy and Promotes Cell Apoptosis of Normal Thyroid Epithelial Cell Nthy-ori-3 Through YBOX3/P21 Pathway

doi: 10.3389/fonc.2021.647034

Figure Lengend Snippet: Identification and expression of PTC cell exosome-enriched lncRNA SNHG9. (A) High-throughput screening identification of PTC associated exosome lncRNAs. SNHG9 is PTC cell exosome-enriched lncRNA in TPC-1 and K-1 cells compared with Nthy-ori-3 cell. (B, C) Validation of SNHG9 overexpression in both TPC-1 and K-1 cells and their respective exosomes compared with Nthy-ori-3 cell and its exosome by qPCR. (D) Coregulation network of SNHG9 with mRNA/miRNA. SNHG9 had an interaction with autophagy related molecules. (E) Gene ontology enrichment analysis showed the highest regulation scores in autophagy and apoptosis. (F) KEGG-pathway-weighted analysis showed SNHG9 mainly targeted apoptosis and autophagy pathways. (G) SNHG9 in the PTC cell supernatant mainly derived from cell exosomes. QPCR showed significantly lower SNHG9 expression level in supernatant treated with Rnase and Triton compared with supernatant treated with only Rnase and control group. (H) QPCR confirmed no SNHG9 expression in cell supernatants after exosome extraction. (I) SNHG9 expression level between tumor and normal tissues in 70 PTC patients from FUSCC. The results were normalized to β-actin mRNA level. (J) Waterfall plot showed the distribution of SNHG9 expression level in each PTC patients from FUSCC. ***P < 0.001, data were pooled from three independent experiments. FUSCC, Fudan University Shanghai Cancer Center; PTC, papillary thyroid cancer.

Article Snippet: Next, we used the Arraystar Human LncRNA Array v2.0 gene chip to compare expression profile data of lncRNAs in Nthy-ori-3, TPC-1 and K-1 cells and their respective exosomes.

Techniques: Expressing, High Throughput Screening Assay, Biomarker Discovery, Over Expression, Derivative Assay, Control, Extraction

Journal: Oncotarget

Article Title: AB209630, a long non-coding RNA decreased expression in hypopharyngeal squamous cell carcinoma, influences proliferation, invasion, metastasis, and survival

doi: 10.18632/oncotarget.7403

Figure Lengend Snippet: A. The proliferation assay was performed on parental (CON), lentiviral vector control (NC), and overexpression lncRNA-AB209630 (OE) FaDU cells. The absorbance was measured on days 1, 2, 3, 4, and 5 according to the MTT method. B. The Gimsa-stained colonies were observed and measured under a microscope (×200). A bar graph shows the differences in colony formation among the three groups. The data are presented as the mean ± SD for three independent experiments (* P <0.01, compared with NC). C. Colonies were photographed. D. The diameter of OE sarcospheres was much smaller than that of CON and NC sarcospheres. E. Sarcospheres were photographed under a fluorescent microscope (×200).

Article Snippet: In the present study, we used the Arraystar LncRNA Gene Chip technology to identify two lncRNA transcripts with significant differences in expression: AB209630 and AB019562.

Techniques: Proliferation Assay, Plasmid Preparation, Control, Over Expression, Staining, Microscopy

Journal: Oncotarget

Article Title: AB209630, a long non-coding RNA decreased expression in hypopharyngeal squamous cell carcinoma, influences proliferation, invasion, metastasis, and survival

doi: 10.18632/oncotarget.7403

Figure Lengend Snippet: Kaplan-Meier overall survival curve stratified by lncRNA AB209630 expression

Article Snippet: In the present study, we used the Arraystar LncRNA Gene Chip technology to identify two lncRNA transcripts with significant differences in expression: AB209630 and AB019562.

Techniques: Expressing

Journal: Hypertension

Article Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING RNAS IN RAT MODELS OF CARDIOVASCULAR AND RENAL DISEASE

doi: 10.1161/HYPERTENSIONAHA.114.04498

Figure Lengend Snippet: LncRNA expression in Dahl S, Dahl R and SHR. Raw fragments per kilobase of exon per million fragments mapped (FPKM) sequence count was used to identify the total number of LncRNAs expressed in each strain and unique LncRNAs in each strain (indicated by + and − symbols for strains that detected a particular lncRNA or not, respectively). Individual LncRNA location data and FPKM values are given in Supplementary Table S1.

Article Snippet: ArrayStar designed the lncRNA ChIP (GEO platform accession number: {"type":"entrez-geo","attrs":{"text":"GPL15690","term_id":"15690"}} GPL15690 ), taking into account not only the transcripts already in the database, but also with the aim of predicting new transcripts.

Techniques: Expressing, Sequencing

Journal: Hypertension

Article Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING RNAS IN RAT MODELS OF CARDIOVASCULAR AND RENAL DISEASE

doi: 10.1161/HYPERTENSIONAHA.114.04498

Figure Lengend Snippet: Box plots (whiskers: 10– 90 percentile) show the distribution of mean expression levels as fragments per kilobase of exon per million fragments mapped (FPKM) for each strain. Raw sequence count FPKM data was normalized by dividing each value by the sample mean, and then taking the square root. Median expression is marked with a line. Mean expression is marked with a + symbol. Mean values for protein coding transcripts were 0.5753 (Dahl S), 0.5616 (Dahl R) and 0.5642 (SHR). For lncRNA the mean values were 0.4756 (Dahl S), 0.4801(Dahl R), and 0.4853 (SHR). Outlier peaks show expression as high as 34.09 for protein coding genes and 26.9 for LncRNAs.

Article Snippet: ArrayStar designed the lncRNA ChIP (GEO platform accession number: {"type":"entrez-geo","attrs":{"text":"GPL15690","term_id":"15690"}} GPL15690 ), taking into account not only the transcripts already in the database, but also with the aim of predicting new transcripts.

Techniques: Expressing, Sequencing

Journal: Hypertension

Article Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING RNAS IN RAT MODELS OF CARDIOVASCULAR AND RENAL DISEASE

doi: 10.1161/HYPERTENSIONAHA.114.04498

Figure Lengend Snippet: Color coded heat maps for the differentially expressed lncRNAs and mRNAs (Dahl S v Dahl R). The normalized intensities for each differentially expressed (1.5 fold up/ down, p < 0.05) lncRNA from the array for each animal were used to create the heat map using CIMminer (one matrix) and clustering was done by Euclidean Distance method and average linkage cluster algorithm. Panel A: From the all differentially expressed lncRNA set, a first subset was created by extracting any differentially expressed lncRNA have neighboring genes. Panel B: A second subset created by extracting lncRNA differentially expressed along with mRNA genes in cis (labeled as target genes) that were also differentially expressed (1.5 fold up/ down, P<0.05). Panel C: Expanded view of Panel B with selected lncRNAs and their cis mRNAs; Panel D: Fold change of lncRNAs and their corresponding cis mRNA (labeled as associated gene) expression.

Article Snippet: ArrayStar designed the lncRNA ChIP (GEO platform accession number: {"type":"entrez-geo","attrs":{"text":"GPL15690","term_id":"15690"}} GPL15690 ), taking into account not only the transcripts already in the database, but also with the aim of predicting new transcripts.

Techniques: Labeling, Gene Expression

Journal: Hypertension

Article Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING RNAS IN RAT MODELS OF CARDIOVASCULAR AND RENAL DISEASE

doi: 10.1161/HYPERTENSIONAHA.114.04498

Figure Lengend Snippet: Color coded heat maps for the differentially expressed lncRNAs and mRNAs (Dahl S v SHR). The normalized intensities for each differentially expressed (1.5 fold up/ down, p < 0.05) lncRNA from the array for each animal were used to create the heat map using CIMminer (one matrix) and clustering was done by Euclidean Distance method and average linkage cluster algorithm. Panel A: From the all differentially expressed lncRNA set, a first subset was created by extracting any differentially expressed lncRNA have neighboring genes. Panel B: A second subset created by extracting lncRNA differentially expressed along with mRNA genes in cis (labeled as target genes) that were also differentially expressed (1.5 fold up/ down, P<0.05). Panel C: Expanded view of Panel B with selected lncRNAs and their cis mRNAs; Panel D: Fold change of lncRNAs and their corresponding cis mRNA (labeled as associated gene) expression.

Article Snippet: ArrayStar designed the lncRNA ChIP (GEO platform accession number: {"type":"entrez-geo","attrs":{"text":"GPL15690","term_id":"15690"}} GPL15690 ), taking into account not only the transcripts already in the database, but also with the aim of predicting new transcripts.

Techniques: Labeling, Gene Expression

Journal: Hypertension

Article Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING RNAS IN RAT MODELS OF CARDIOVASCULAR AND RENAL DISEASE

doi: 10.1161/HYPERTENSIONAHA.114.04498

Figure Lengend Snippet: Protein expression analysis of select cis genes associated with differentially expressed lncRNAs. Whole-kidney lysates from Dahl S (n=3) and Dahl R (n=3) were probed with antibodies against each of the select proteins by immunoblotting. Fold change for each protein is shown on the right along with corresponding lncRNA and the expression level of each gene at the mRNA level from the array (**p<0.01 *** p<0.001 and NS-not significant).

Article Snippet: ArrayStar designed the lncRNA ChIP (GEO platform accession number: {"type":"entrez-geo","attrs":{"text":"GPL15690","term_id":"15690"}} GPL15690 ), taking into account not only the transcripts already in the database, but also with the aim of predicting new transcripts.

Techniques: Expressing, Western Blot

Journal: Hypertension

Article Title: GENOME-WIDE IDENTIFICATION OF LONG NON-CODING RNAS IN RAT MODELS OF CARDIOVASCULAR AND RENAL DISEASE

doi: 10.1161/HYPERTENSIONAHA.114.04498

Figure Lengend Snippet: Web based gene set enrichment analysis of differentially expressed lncRNA associated genes. The LncRNA associated cis mRNA genes from each of the strain comparisons (provided in Supplementary Table S3) were used for differential gene enrichment analysis to detect alterations in physiological/pathological pathways. The top ten pathways with high enrichment value and significant hypergeometric p value are presented.

Article Snippet: ArrayStar designed the lncRNA ChIP (GEO platform accession number: {"type":"entrez-geo","attrs":{"text":"GPL15690","term_id":"15690"}} GPL15690 ), taking into account not only the transcripts already in the database, but also with the aim of predicting new transcripts.

Techniques:

Journal: eLife

Article Title: Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs

doi: 10.7554/eLife.77357

Figure Lengend Snippet: ( A ) Density plots showing the distribution of proliferation-inducing and -suppressing lncRNA levels in cells treated with doxorubicin (Dox), 5-fluorouracil (5-FU), or ionizing radiation (IR) in seven bulk RNA-seq data and seven bulk RNA-seq data of cells treated with Nutlin-3. ( B ) Density plots as in ( A ) from 24 single-cell RNA-seq data from cells treated with Nutlin-3 (7 p53 WT and 17 p53 MUT cell lines). ( C ) Heatmap showing fold change of predicted proliferation-inducing and -suppressing lncRNAs across 14 RNA-seq datasets, indicated in ( A ). n is the number of consistently upregulated lncRNAs across the RNA-seq datasets with statistical significance (Benjamini–Hochberg [BH] adjusted *p<0.05) calculated by the meta-analysis tool RobustRankAggreg; a subset of the top proliferation suppressors are highlighted in the box. ( D ) The number of ChIP-seq datasets showing p53-binding sites near the transcription start site of the 13 meta-analyses-derived significantly upregulated lncRNAs, indicated in ( C ), or background lncRNAs. For ( A , B , D ), p-values were calculated from two-tailed Wilcoxon rank-sum tests. ( E ) The expression fold change of two poorly characterized top predicted proliferation-suppressing lncRNAs in cells treated with p53-activating agents (see A ) compared to control cells. The X-axis indicates the accession number of the 14 RNA-seq datasets present in the Gene Expression Omnibus database. ( F ) Two lung adenocarcinoma (LUAD) cell lines treated with 10 µM of Nutlin (NUT), etoposide (ETO), or cisplatin (CIS) or received 5 Gy of gamma-radiation (IR) were harvested at intervals. qRT-PCR (triplicate) for specific lncRNA was performed. BAX and AchR mRNA are positive and negative controls, respectively. RNA levels were normalized to β-ACTIN, and values are presented as 2 -ΔΔCt , with vehicle control-treated cells set at 1 (black line); data are mean ± SEM. For A549, PSLR-1 *p<6.86 × 10 –4 , PSLR-2 *p<1.17 × 10 –2 , BAX *p<4.93 × 10 –6 ; for H460, PSLR-1 *p<6.95 × 10 –6 , PSLR-2 *p<5.69 × 10 –3 , and BAX *p<3.99 × 10 –4 ; two-tailed t -tests. Figure 3—source data 1. qRT-PCR for .

Article Snippet: Transfected construct ( Homo sapiens ) , PSLR-1 , VectorBuilder , FAM198B-AS1 VB200405-4575kbk , Lentiviral construct to express the lncRNA.

Techniques: RNA Sequencing, ChIP-sequencing, Binding Assay, Derivative Assay, Two Tailed Test, Expressing, Control, Gene Expression, Quantitative RT-PCR

Journal: eLife

Article Title: Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs

doi: 10.7554/eLife.77357

Figure Lengend Snippet: ( A ) Expression of PSLR-1 and -2 was measured by qRT-PCR (triplicate) in normal human lung tissue (n = 5) and LUAD patient samples (n = 10). RNA levels were normalized to β-ACTIN and values are presented as 2 -ΔCt ; data are mean ± SEM. PSLR-1, *p=7.75 × 10 –9 ; PSLR-2, *p=2.77 × 10 –8 ; two-tailed t -tests. ( B–D ) RNA-sequencing of A549 LUAD cell line after expression of each of the two long noncoding RNAs (lncRNAs) or vector control (quadruplicate). ( B ) Genes that have significant (adjusted regression p<10 –3 ) positive or negative associations with the indicated lncRNA in TCGA LUAD data were selected. Empirical cumulative distribution of expression fold changes of these genes in A549 cells expressing the indicated lncRNA compared with vector control. ( C ) Empirical cumulative distribution of expression changes of curated tumor-suppressor genes and oncogenes in A549 cells expressing the indicated lncRNA compared with vector control. For ( B , C ), x-axis indicates the expression fold changes of genes, y-axis estimates the percentage of genes at a log2 fold-change value indicated on the x-axis, and p-values were from two-tailed Wilcoxon rank-sum tests. ( D ) Gene Set Enrichment Analysis (GSEA) demonstrated top up- and downregulated Hallmark genesets after expression of the indicated lncRNA in A549 cells compared with vector control. Positive and negative normalized enrichment scores (NES) indicate up- and downregulation, respectively. Significantly enriched (false discovery rate [FDR] < 0.05) proliferation-associated pathways/gene signatures indicated. ( E ) Enrichr-calculated combined score indicates transcription factor (TF) enrichment of genes altered upon expression of the indicated lncRNA in A549 LUAD cells. ( F ) HOMER-calculated promoter motif enrichment of downregulated genes upon indicated lncRNA expression in LUAD cells. CHR motif elements are shown (right). Figure 4—source data 1. qRT-PCR for .

Article Snippet: Transfected construct ( Homo sapiens ) , PSLR-1 , VectorBuilder , FAM198B-AS1 VB200405-4575kbk , Lentiviral construct to express the lncRNA.

Techniques: Expressing, Quantitative RT-PCR, Two Tailed Test, RNA Sequencing, Plasmid Preparation, Control

Journal: eLife

Article Title: Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs

doi: 10.7554/eLife.77357

Figure Lengend Snippet: The lncRNAs PSLR-1 , PSLR-2 , or MALAT1 or vector control were expressed (lentivirus) in LUAD cell lines. ( A ) MTT assays (quadruplicate) performed at 24 hr intervals. Each assay performed 2–4 independent times for both cell lines and one representative experiment is shown ± SD; A549 *p=1.11 × 10 –4 and **p<3.03 × 10 –4 , H460 *p=2.04 × 10 –5 and **p<2.28 × 10 –4 ; two-tailed t -tests. ( B ) Colonies from colony formation assays were counted 14 days after lncRNA expression. Assays (triplicate) performed 2–3 independent times and a representative experiment ± SEM and images (no magnification) shown; A549 *p=1.49 × 10 –2 and **p<2.09 × 10 –4 , H460 *p=3.42 × 10 –2 and **p<1.16 × 10 –3 ; two-tailed t -tests. ( C ) Live cell number determined by Trypan Blue dye exclusion 48 hr after placing cells in 6-well plates. Mean of four independent experiments for both cell lines ± SD is graphed; A549 *p=5.77 × 10 –4 and **p<2.68 × 10 –5 , H460 *p=2.90 × 10 –5 and **p<3.63 × 10 –6 ; two-tailed t -tests. ( D ) Cell cycle evaluated at intervals following propidium iodide staining and flow cytometry; representative histograms from one experiment shown (left). Graphs of the cell cycle phases represent the mean of four independent experiments for both cell lines at 48 hr ± SEM; A549 *p=8.82 × 10 –3 and **p<1.73 × 10 –2 , H460 *p=4.00 × 10 –3 and **p<1.35 × 10 –3 ; two-tailed t -tests. Figure 5—source data 1. MTT for . Figure 5—source data 2. Colony number for . Figure 5—source data 3. Live cell number for . Figure 5—source data 4. Cell cycle for .

Article Snippet: Transfected construct ( Homo sapiens ) , PSLR-1 , VectorBuilder , FAM198B-AS1 VB200405-4575kbk , Lentiviral construct to express the lncRNA.

Techniques: Plasmid Preparation, Control, Two Tailed Test, Expressing, Staining, Flow Cytometry

Journal: eLife

Article Title: Systematic lncRNA mapping to genome-wide co-essential modules uncovers cancer dependency on uncharacterized lncRNAs

doi: 10.7554/eLife.77357

Figure Lengend Snippet:

Article Snippet: Transfected construct ( Homo sapiens ) , PSLR-1 , VectorBuilder , FAM198B-AS1 VB200405-4575kbk , Lentiviral construct to express the lncRNA.

Techniques: Transfection, Construct, Plasmid Preparation, Control, Staining, Sequencing, SYBR Green Assay, cDNA Synthesis, Isolation, Proliferation Assay, Colony Assay, Cell Cycle Assay, Positive Control, Software