Journal: Diagnostics

Article Title: A Pilot Study of Exploring miRNA–Protein Interaction Networks in Pancreatic Ductal Adenocarcinoma Patients: Implications for Diagnosis and Prognosis

doi: 10.3390/diagnostics15192479

Figure Lengend Snippet: The distribution of levels of the target proteins between PDAC patients and healthy individuals. ( a ) ESR1, ( b ) HCFC1, ( c ) KCNA1, ( d ) CACNG3, and ( e ) EPC1. Differences between the groups were analyzed using the Mann–Whitney U test. Bars represent mean protein concentration, and error bars indicate standard deviation (mean ± SD). * p < 0.05 was considered statistically significant.

Article Snippet: Quantitative analysis of ESR1 (Human Estrogen Receptor Alpha, ESR1 ELISA Kit, E7871Hu), HCFC1 (Human Host Cell Factor C1, HCFC1 ELISA Kit, E0307Hu), KCNA1 (Human Voltage-Gated Potassium Channel Subunit Alpha-1, KCNA1 ELISA Kit, E1757Hu), EPC1 (Human Enhancer of Polycomb Homolog 1, EPC1 ELISA Kit, E1137529Hu), and CACNG3 (Human Voltage-Dependent Calcium Channel Subunit Gamma-3, CACNG3 ELISA Kit, E4572Hu) proteins in the serum samples of PDAC patients was performed using sandwich-format ELISA kits (BT Lab, Bioassay Technology Laboratory, Shanghai, China).

Techniques: MANN-WHITNEY, Protein Concentration, Standard Deviation

Journal: Diagnostics

Article Title: A Pilot Study of Exploring miRNA–Protein Interaction Networks in Pancreatic Ductal Adenocarcinoma Patients: Implications for Diagnosis and Prognosis

doi: 10.3390/diagnostics15192479

Figure Lengend Snippet: Scatter plot matrix demonstrating the pairwise correlations among protein serum concentration levels of ESR1, HCFC1, KCNA1, CACNG3, and EPC1. The upper triangle of the matrix displays Pearson correlation coefficients (r) with corresponding p -values. Significant positive correlations were observed for each miRNA. * p < 0.05 and ** p < 0.001 were considered statistically significant.

Article Snippet: Quantitative analysis of ESR1 (Human Estrogen Receptor Alpha, ESR1 ELISA Kit, E7871Hu), HCFC1 (Human Host Cell Factor C1, HCFC1 ELISA Kit, E0307Hu), KCNA1 (Human Voltage-Gated Potassium Channel Subunit Alpha-1, KCNA1 ELISA Kit, E1757Hu), EPC1 (Human Enhancer of Polycomb Homolog 1, EPC1 ELISA Kit, E1137529Hu), and CACNG3 (Human Voltage-Dependent Calcium Channel Subunit Gamma-3, CACNG3 ELISA Kit, E4572Hu) proteins in the serum samples of PDAC patients was performed using sandwich-format ELISA kits (BT Lab, Bioassay Technology Laboratory, Shanghai, China).

Techniques: Concentration Assay

Journal: Diagnostics

Article Title: A Pilot Study of Exploring miRNA–Protein Interaction Networks in Pancreatic Ductal Adenocarcinoma Patients: Implications for Diagnosis and Prognosis

doi: 10.3390/diagnostics15192479

Figure Lengend Snippet: Kaplan–Meier survival curves showing overall survival durations of patients based on the expression levels of target proteins. ( a ) ESR1, ( b ) HCFC1, ( c ) KCNA1, ( d ) CACNG3, and ( e ) EPC1.

Article Snippet: Quantitative analysis of ESR1 (Human Estrogen Receptor Alpha, ESR1 ELISA Kit, E7871Hu), HCFC1 (Human Host Cell Factor C1, HCFC1 ELISA Kit, E0307Hu), KCNA1 (Human Voltage-Gated Potassium Channel Subunit Alpha-1, KCNA1 ELISA Kit, E1757Hu), EPC1 (Human Enhancer of Polycomb Homolog 1, EPC1 ELISA Kit, E1137529Hu), and CACNG3 (Human Voltage-Dependent Calcium Channel Subunit Gamma-3, CACNG3 ELISA Kit, E4572Hu) proteins in the serum samples of PDAC patients was performed using sandwich-format ELISA kits (BT Lab, Bioassay Technology Laboratory, Shanghai, China).

Techniques: Expressing

Journal: Cancer Research

Article Title: DLGAP1-AS2–Mediated Phosphatidic Acid Synthesis Activates YAP Signaling and Confers Chemoresistance in Squamous Cell Carcinoma

doi: 10.1158/0008-5472.can-22-0717

Figure Lengend Snippet: Figure 4. D-AS2 reduces H3K27ac enrichment at the FAM3D enhancer region. A, FISH detection of D-AS2 localization in KYSE30 and NCI-H1703 cells. Scale bar, 30 mm. B, qRT-PCR measurement of the D-AS2 level in precipitates from RIP assays performed using IgG or specific antibodies. The data are presented as the mean SD values; n ¼ 3 technical replicates. C, Western blot analyses of histones in precipitates from RNA pulldown assays performed using antisense or sense sequences of D-AS2. Representative results of at least three biological replicates are shown. D, Numbers of genes that exhibited shared or unique peaks identified by ATAC-seq in D-AS2–silenced and control NCI-H1703 cells. E, Numbers of genes with significant differences in the number of peaks in the gene collections that exhibited shared peaks. F, Unique peak identified by ATAC-seq in D-AS2–silenced NCI-H1703 cells. Four independent qPCR primer sets were designed within 1,000 bp upstream/downstream (blue bar) of the ATAC-seq peak (red bar). G–I, CUT&RUN assay of the FAM3D enhancer region in D-AS2–depleted and D-AS2–overexpressing SCC cells with antibodies against H3K27ac. The data are presented as the mean SD values; two-tailed t test; , P < 0.01; , P < 0.001; n ¼ 3 technical replicates.

Article Snippet: To determine the mRNA expression levels, qRT-PCR was performed using a StepOnePlus Real-Time PCR system (Applied Biosystems) and PowerUp SYBR Green Master Mix (A25918; Applied Biosystems). lncRNAs were reverse transcribed into cDNA using a lnRcute lncRNA First-Strand cDNA Kit (4992908; Tiangen Biotech), and lncRNA expression was quantified using a lnRcute lncRNA qPCR Kit (4992886; Tiangen Biotech).

Techniques: Quantitative RT-PCR, Western Blot, Control, Two Tailed Test

Journal: bioRxiv

Article Title: CRlSPR/Cas9 screening revealed BlRC6-AS1 /BlRC6 mediates abiraterone resistance via NHEJ pathway-dependent A20 degradation in prostate cancer

doi: 10.1101/2025.10.01.679907

Figure Lengend Snippet: ( A ) Schematic of CRISPR-Cas9 screens: A lentiviral sgRNA library was transduced into PC3-Cas9 cells, which were then treated with DMSO or Abiraterone, respectively. After 28 days, sgRNAs were extracted for NGS. ( B ) Box plots displaying sgRNA distribution in the experimental groups from lncRNA CRISPR-Cas9 library: D0-DMSO (baseline), D28-DMSO (vehicle control), and D28-Abiraterone (treatment). ( C and D ) Volcano plots showing depleted (red; RRA Score ≤ 0.05, -log□FC ≥ 2) and enriched (blue; RRA Score ≤ 0.05, log□FC ≥ 2) genes. Screening analysis was performed with MaGeCK RRA. ( C ) Negative selection identified 523 abiraterone resistance-associated LncRNAs and 553 essential LncRNAs. ( D ) Positive selection revealed 717 LncRNAs associated with abiraterone sensitivity and 169 essential LncRNAs. ( E ) Venn diagram showed negatively selected genes from two comparisons: Abiraterone vs Control and Control vs D0. ( F ) MAGeCK analysis results displayed a ranking of genes based on their RRA scores. ( G ) Frequency distribution of log2 fold change for all sgRNAs (top) and log2 fold change of individual sgRNAs for representative candidates (bottom). Enriched and depleted sgRNA hits were indicated by red and blue vertical bars, respectively. ( H ) The RRA score distribution plot revealed the top 10 candidate LncRNAs associated with abiraterone resistance. ( I-N ) Cell viability assays in PC3 ( I-K ) and DU145 ( L-N ) cells treated with 0-70 μM abiraterone for 48h, following transduction with either control sgRNAs or sgRNAs targeting candidate lncRNAs: RP11-1079K10.3 ( I and L ), WWTR1-AS1 ( J and M ), and RP11-49K24.4 ( K and N ). Data are shown as the mean ± SD (n = 4 biological replicates). Data were analyzed by two-way analysis of variance (ANOVA) with Dunnett’s multiple comparisons test ( I-N ).

Article Snippet: PC3-Cas9 cells (4×10 ) were transduced with either the Splicing-targeting CRISPR-Cas9 library for human lncRNAs (Addgene, Cat# 119977) or the Human genome-wide lentiviral CRISPR gRNA library version 1 (Addgene, Cat# 67989) at a multiplicity of infection (MOI) of 0.3, ensuring single gRNA integration per cell.

Techniques: CRISPR, Control, Selection, Transduction

Journal: Translational psychiatry

Article Title: Integrative analysis of long noncoding RNAs dysregulation and synapse-associated ceRNA regulatory axes in autism.

doi: 10.1038/s41398-023-02662-5

Figure Lengend Snippet: Fig. 4 lncRNA and mRNA co-expression modules dysregulated in postmortem ASD cortex. A Pearson’s correlation analysis between module eigengenes and different covariates (upper part). Correlation coefficients and p-values are shown at p < 0.05. The right side is named according to the BP of each module. The module enrichment analysis (Fisher’s exact test, FDR < 0.05) is shown on the lower part. Enrichment OR and FDR-corrected p-values are shown for enrichment with FDR < 0.05. B–F PPI network construction for five modules (M1, M3, M4, M8, and M10) was correlated with the disease status. ND neurodevelopment, BP biological process, PPI protein-protein interaction.

Article Snippet: Quantitative reverse transcription polymerase chain reaction The RNA was extracted using the Tiangen RNAsimple Total RNA Kit (Tiangen, DP419, Beijing, China) and reverse-transcribed using a FastKing reverse transcriptase kit (Tiangen, KR116-02, Beijing, China), TransGen TransScript miRNA First-Strand cDNA Synthesis SuperMIX (TransGen, Beijing, China), and lnRcute lncRNA First Strand cDNA Synthesis Kit (Tiangen, KR202-02, Beijing, China). qRT-PCR was performed on a LightCycler 96 (Roche, Switzerland).

Techniques: Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: PD-L1 Is a Tumor Suppressor in Aggressive Endometrial Cancer Cells and Its Expression Is Regulated by miR-216a and lncRNA MEG3

doi: 10.3389/fcell.2020.598205

Figure Lengend Snippet: MEG3 Acts as an Upstream Regulator of MiR-216a and PD-L1. (A) MEG3 expression in TCGA EC tissues and normal tissues (ENCORI database). (B) qRT-PCR analysis of MEG3 expression in HEC-50, SPAC-1-L and EM cells. (C) MEG3 levels in HEC-50 cells transfected with MEG3 siRNA (or control siRNA), and in SPAC-1-L cells transfected with MEG3 expression vector (or control vector). (D) miR-216a expression was measured in HEC-50 cells transfected with MEG3 siRNA (or control siRNA), and in SPAC-1-L cells transfected with MEG3 expression vector (or control vector). (E) Wound-healing and invasion assays in HEC-50 cells transfected as indicated. (F) Wound-healing and invasion assays in SPAC-1-L cells transfected as indicated. (G) Examination of PD-L1 expression in HEC-50 cells following knockdown of MEG3, and in SPAC-1-L cells following overexpression of MEG3, using western blotting assays. (H,I) The mRNA expression of the indicated genes in HEC-50 cells following knockdown of MEG3, and in SPAC-1-L cells following overexpression of MEG3. VIM: Vimentin. ∗ P < 0.05.

Article Snippet: The PD-L1 cDNA expresion vector pCMV6-PD-L1 (PD-L1-vec, RC213071), the MCL-1 cDNA expression vector pCMV6-MCL-1 (MCL-1-vec, RC200521), the MEG3 expression vector pCMV6-MEG3 (MEG3-vec, SC105816) and the pCMV6 control vector (Ctr-vec, PS100001) were purchased from OriGene (Rockville, MD, United States).

Techniques: Expressing, Quantitative RT-PCR, Transfection, Control, Plasmid Preparation, Knockdown, Over Expression, Western Blot

Journal: Frontiers in Cell and Developmental Biology

Article Title: PD-L1 Is a Tumor Suppressor in Aggressive Endometrial Cancer Cells and Its Expression Is Regulated by miR-216a and lncRNA MEG3

doi: 10.3389/fcell.2020.598205

Figure Lengend Snippet: Model Summarizing the Role of MEG3, MiR-216a, PD-L1, and MCL-1 in Controlling the Proliferative and Invasive Potential of aggressive EC cells. The downregulation of MEG3 causes an elevation of miR-216a expression. By targeting the 3′-UTR of PD-L1 mRNA, miR-216a suppresses PD-L1 expression. PD-L1 serves as a tumor-suppressor to inhibit the proliferation, EMT and invasive potential of aggressive EC cells via repressing MCL-1 expression.

Article Snippet: The PD-L1 cDNA expresion vector pCMV6-PD-L1 (PD-L1-vec, RC213071), the MCL-1 cDNA expression vector pCMV6-MCL-1 (MCL-1-vec, RC200521), the MEG3 expression vector pCMV6-MEG3 (MEG3-vec, SC105816) and the pCMV6 control vector (Ctr-vec, PS100001) were purchased from OriGene (Rockville, MD, United States).

Techniques: Expressing