Journal: Experimental Hematology & Oncology

Article Title: METTL3 modulates m6A modification of CDC25B and promotes head and neck squamous cell carcinoma malignant progression

doi: 10.1186/s40164-022-00256-3

Figure Lengend Snippet: METTL3 high expression is associated with poor prognosis of HNSCC patients. A Dot blot assay was conducted with mRNA extracted from HNSCC tissues and paired paracancerous normal tissues using an anti-m6A antibody, and MB (methylene blue) staining served as the loading control (representative images in left panel). The relative m6A contents on mRNA in HNSCC tissues and paired normal normal tissues were calculated (right panel, n = 7). B TCGA data showed that METTL3 expression was significantly upregulated in HNSCC (n = 520) than normal tissue (n = 44). C Disease-free survival (RFS) of HNSCC patients based on METTL3 expression obtained from GEPIA website ( http://gepia.cancer-pku.cn/ ). D The levels of METTL3 expression in HNSCC and paired normal tissues were measured by qRT-PCR (n = 10). E METTL3 protein levels were measured in HNSCC tissues and paired normal tissues by western blotting (n = 7). F METTL3 expression was significantly upregulated in HNSCC compared with the paired paracancerous normal tissue by IHC staining (n = 5, scale bars = 100 μm). G Kaplan–Meier OS analysis of HNSCC patients based on METTL3 expression measured by IHC of tissue microarray (n = 100). H Univariate Cox regression analysis was conducted in HNSCC patients (n = 100). All bars correspond to 95% confidence intervals. I Multivariate Cox regression analysis was conducted in HNSCC patients (n = 100). J The time-dependent receiver operating characteristic (ROC) analysis for the clinical risk score (TNM stage), the METTL3 risk score, and the combined METTL3 and clinical risk scores in HNSCC cohort

Article Snippet: After hybridizing these cRNAs onto a Arraystar Epitranscriptomic Microarray slide (8 × 60 K, Arraystar) and washing it, an Agilent Scanner G2505C was used to scan the array.

Techniques: Expressing, Dot Blot, Staining, Quantitative RT-PCR, Western Blot, Immunohistochemistry, Microarray

Journal: Experimental Hematology & Oncology

Article Title: METTL3 modulates m6A modification of CDC25B and promotes head and neck squamous cell carcinoma malignant progression

doi: 10.1186/s40164-022-00256-3

Figure Lengend Snippet: METTL3 mediates the m6A modification on CDC25B mRNA in HNSCC. A m6A-mRNA epitranscriptomic microarray showed signal pathways in which most differentially expressed gene enriched in METTL3 knockdown cells (SAS), DE represents differentially expressed. B m6A-mRNA epitranscriptomic microarray showed signal pathways in which most differentially methylated genes enriched in METTL3 knockdown cells (SAS), DM represents differentially methylated. C m6A-mRNA epitranscriptomic microarray showed an overlap of the total differentially expressed gene, total differentially methylated gene, and differentially expressed and methylated gene enriched in the cell cycle pathway. D Genes selected from the overlap were used for qRT-PCR in METTL3 knockdown and their corresponding control cells, and CDC25B was the most significantly downregulated gene upon knockdown of METTL3. E , F CDC25B mRNA expression was confirmed by qRT-PCR in METTL3 knockdown (FaDu) and METTL3 overexpression (Hep2) cells. G CDC25B protein level was measured by western blot assay in METTL3 knockdown SAS cells. H CDC25B protein level was measured by western blot assay in METTL3 knockdown FaDu cells. I CDC25B protein level was measured by western blot assay in METTL3 overexpressed Hep2 cells. J MeRIP-qPCR was conducted to detect the m6A level of CDC25B mRNA in METTL3 knockdown (SAS) cells. K MeRIP-qPCR was conducted to detect the m6A level of CDC25B mRNA in METTL3 knockdown (FaDu) cells. L , M The levels of CDC25B expression in METTL3 knockdown and their corresponding control cells treated with actinomycin D (5 μg/mL) at the indicated time points were detected by qRT-PCR. The data are the means ± SD of three independent experiments. */# p < 0.05; **/## p < 0.01; ***/### p < 0.001; ****/#### p < 0.0001

Article Snippet: After hybridizing these cRNAs onto a Arraystar Epitranscriptomic Microarray slide (8 × 60 K, Arraystar) and washing it, an Agilent Scanner G2505C was used to scan the array.

Techniques: Modification, Microarray, Methylation, Quantitative RT-PCR, Expressing, Over Expression, Western Blot

Journal: PLoS ONE

Article Title: Expression Profiling of RNA Transcripts during Neuronal Maturation and Ischemic Injury

doi: 10.1371/journal.pone.0103525

Figure Lengend Snippet: ( A ) Hierarchical clustering analyses of mRNAs in maturing cortical neurons. Clusters of highly down- and up-regulated mRNAs were identified. Bi) lncRNAs in maturing neurons. Clusters of highly down- and up-regulated lncRNAs with their orientation to the genome or proximal gene loci were identified. ( Bii ) Subgroup analyses of altered lncRNAs in relation to their nearby coding genes. ( C ) miRNAs in maturing cortical neurons. Clusters of highly down- and up-regulated miRNAs were identified. Total RNA from 4 separate experiments (n = 4) carried out in triplicates were pooled for each time points. The microarray analyses were carried out for each time point on the pooled RNA. The average signal intensities were 369.03, 501.12, 429.58 and 455.03 for the lncRNA and mRNA microarray for Day 2, Day 4, Day 6 and Day 8 respectively. For miRNA microarray, the average signal intensities were 1673.43, 1783.01, 1385.10 and 1698.38 for Day 2, Day 4, Day 6 and Day 8 respectively. Hierarchical clusters were constructed out using average linkage and Euclidean distance as the similarity measure. Green rectangle indicates downregulation and red, upregulation.

Article Snippet: Fifty μl of hybridization solution was dispensed into the gasket slide and assembled to the Mouse LncRNA Array v2.0 (8×60 K, Arraystar Inc., Rockville, USA) microarray slide.

Techniques: Microarray, Construct

Journal: PLoS ONE

Article Title: Expression Profiling of RNA Transcripts during Neuronal Maturation and Ischemic Injury

doi: 10.1371/journal.pone.0103525

Figure Lengend Snippet: mRNA expression of the gene is indicated followed by the expression of the associated lncRNA (S: sense overlap; AS: antisense overlap; B: bidirectional). Differentially expressed miRNAs that are predicted to target the gene (TargetScan and microRNA.org) are indicated. Validated miRNAs are underlined. Expression is indicated in SLR relative to Day 2. Red, indicates upregulation and green, downregulation.

Article Snippet: Fifty μl of hybridization solution was dispensed into the gasket slide and assembled to the Mouse LncRNA Array v2.0 (8×60 K, Arraystar Inc., Rockville, USA) microarray slide.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Expression Profiling of RNA Transcripts during Neuronal Maturation and Ischemic Injury

doi: 10.1371/journal.pone.0103525

Figure Lengend Snippet: ( A ) Ncam1 mRNA (NM_010875) and lncRNA (AK156022), ( B ) Negr1 mRNA (NM_001039094) and lncRNA (uc008rva.1), ( C ) Ncam1 and Negr1 mRNA-lncRNA pairs in neurons subjected to 2 hr OGD. ( D ) Stem-loop PCR quantification of miR-377 in maturing neurons. Expression of GAPDH was used as a control/housekeeping gene to normalize mRNA, lncRNA and miRNA expression. Statistically significant differences were tested using the Student’s t-test (* p<0.05 , ** p<0.01 ).

Article Snippet: Fifty μl of hybridization solution was dispensed into the gasket slide and assembled to the Mouse LncRNA Array v2.0 (8×60 K, Arraystar Inc., Rockville, USA) microarray slide.

Techniques: Expressing, Control

Journal: Oncology Letters

Article Title: Integrated analysis of transcriptome profiling predicts potential lncRNA and circRNA targets in human nasopharyngeal carcinoma

doi: 10.3892/ol.2020.11412

Figure Lengend Snippet: Validation of selected (A) lncRNAs, (B) mRNAs and (C) circRNAs based on microarray and RT-qPCR data. Column heights represent the fold changes (log2 transformed) between NPC and CNP tissues, determined using RT-qPCR and microarray data. The validation results indicated a positive association between the RT-qPCR and microarray data. **P<0.01 vs. microarray. lncRNA, long non-coding RNA; circRNA, circular RNA; RT-qPCR, reverse transcription-quantitative PCR; NPC, nasopharyngeal carcinoma; CNP, chronic nasopharyngitis.

Article Snippet: A total of 40 μl hybridization solution was dispensed into a gasket slide and placed into the Human LncRNA Array (version 3.0; 8×60 K; Arraystar, Inc.), which contained 30,586 lncRNAs and 26,109 mRNAs.

Techniques: Biomarker Discovery, Microarray, Quantitative RT-PCR, Transformation Assay, Reverse Transcription, Real-time Polymerase Chain Reaction