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: 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: Molecular Medicine Reports

Article Title: N‑methyladenosine reader YTHDF2‑mediated AC026691.1 degradation promotes gastric cancer cell proliferation, migration and M2 macrophage polarization

doi: 10.3892/mmr.2025.13485

Figure Lengend Snippet: Downregulation of lncRNA AC026691.1 in gastric cancer cells. Reverse transcription-quantitative polymerase chain reaction analysis of the expression levels of lncRNA AC026691.1 in normal gastric epithelial cells (GES-1) and human gastric cancer cells (AGS and MKN-45), **P<0.01 vs. GES-1. lncRNA, long non-coding RNA.

Article Snippet: Subsequently, 1,000 ng extracted RNA was reverse transcribed into cDNA using the lnRcute lncRNA First-Strand cDNA Kit (cat. no. KR202; Tiangen Biotech Co., Ltd.) and FastKing cDNA First-Strand Synthesis Kit (cat. no. KR116; Tiangen Biotech Co., Ltd.) according to the manufacturer's instructions, prior to qPCR.

Techniques: Reverse Transcription, Real-time Polymerase Chain Reaction, Expressing

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: Cell Death Discovery

Article Title: LINC317.5 as a novel biomarker for hypertriglyceridemia in normal glucose metabolism

doi: 10.1038/s41420-024-01968-7

Figure Lengend Snippet: A The TG level of si-lncRNA and si-NC in the HepG2-IR model. B The effect of knockdown of LINC317.5 on the activity of HepG2-IR models with CCK-8. C The effect of knockdown of LINC317.5 on apoptosis of HepG2-IR model with flow cytometry ( a ) si-NC; ( b ) si-lncRNA; ( c ) Relative apoptosis rate. D The TKFC relative expression after knockdown of LINC317.5 in the HepG2-IR model; ( a ) for gene expression by qRT-PCR and ( b ) for protein expression by western blot. E The effect of knockdown of LINC317.5 on transcription factors of HepG2-IR model with qRT-PCR. The housekeeping gene which was used to establish the relative expression of the analyzed genes was β-actin. F The lipid metabolism-related protein expression of knockdown of LINC317.5 in the HepG2-IR (ACADM, CPT1A, FAS, ACC1). Western blot experiments have been repeated three times (The relative expression was calculated based on the target gene expression levels in the si-NC group. The relative proliferation was calculated based on the proliferation level in the si-NC group. The relative apoptotic rate was calculated based on the apoptotic rate in the si-NC group. * P < 0.05, ** P < 0.01, *** P < 0.001) (TG: triglyceride).

Article Snippet: The cDNA was then analyzed by qRT-PCR using lnRcute lncRNA qPCR Kit (FP402, TIANGEN) on QuantStudio 3 system (Applied Biosystems).

Techniques: Knockdown, Activity Assay, CCK-8 Assay, Flow Cytometry, Expressing, Gene Expression, Quantitative RT-PCR, Western Blot, Targeted Gene Expression

Journal: Cell Death Discovery

Article Title: LINC317.5 as a novel biomarker for hypertriglyceridemia in normal glucose metabolism

doi: 10.1038/s41420-024-01968-7

Figure Lengend Snippet: A The TG level of O-lncRNA and O-Control in the HepG2-IR model. B The effect of overexpression the LINC317.5 on the activity of HepG2-IR models with CCK-8. C The effect of overexpression the LINC317.5 on apoptosis of HepG2-IR model with flow cytometry ( a ) O-Control; ( b ) O-lncRNA; ( c ) Relative apoptosis rate. D The TKFC relative expression after overexpression the LINC317.5 in the HepG2-IR model; ( a ) for gene expression by qRT-PCR and ( b ) for protein expression by western blot. E The effect of overexpression the LINC317.5 on transcription factors of HepG2-IR model with qRT-PCR. The housekeeping gene which was used to establish the relative expression of the analyzed genes was β-actin. F The lipid metabolism-related protein expression of overexpression the LINC317.5 in the HepG2-IR (ACADM, CPT1A, FAS, ACC1). Western blot experiments have been repeated three times (The relative expression was calculated based on the expression level in the O-Control group. The relative proliferation was calculated based on the proliferation level in the O-Control group. The relative apoptotic rate was calculated based on the apoptotic rate in the O-Control group. * P < 0.05, ** P < 0.01, *** P < 0.001) (TG: triglyceride).

Article Snippet: The cDNA was then analyzed by qRT-PCR using lnRcute lncRNA qPCR Kit (FP402, TIANGEN) on QuantStudio 3 system (Applied Biosystems).

Techniques: Control, Over Expression, Activity Assay, CCK-8 Assay, Flow Cytometry, Expressing, Gene Expression, Quantitative RT-PCR, Western Blot

Journal: Cell Death Discovery

Article Title: LINC317.5 as a novel biomarker for hypertriglyceridemia in normal glucose metabolism

doi: 10.1038/s41420-024-01968-7

Figure Lengend Snippet: A The TG level of knockdown of LINC317.5 binding to TKFC in the HepG2-IR model. B The effect of knockdown of LINC317.5 binding to TKFC on the activity of HepG2-IR models with CCK-8. C The effect of knockdown of LINC317.5 binding to TKFC on apoptosis of HepG2-IR model with flow cytometry ( a ) lncRNA-NC+mR-NC; ( b ) lncRNA-NC+si-mR; ( c ) si-lncRNA+mR-NC; ( d ) si-lncRNA+si-mR; ( e ) Relative apoptosis rate. D The TKFC relative expression after LINC317.5 binding to TKFC in the HepG2-IR model; ( a ) for gene expression by qRT-PCR and ( b ) for protein expression by western blot. E The effect of knockdown of LINC317.5 binding to TKFC on transcription factors of HepG2-IR model with qRT-PCR. The housekeeping gene which was used to establish the relative expression of the analyzed genes was β-actin. F The lipid metabolism-related protein expression of knockdown of LINC317.5 binding to TKFC in the HepG2-IR (ACADM, CPT1A, FAS, ACC1). Western blot experiments have been repeated three times (The relative expression was calculated based on the expression level in the lncRNA-NC + mRNA-NC group. The relative proliferation was calculated based on the proliferation level in the lncRNA-NC + mRNA-NC group. The relative apoptotic rate was calculated based on the apoptotic rate in the lncRNA-NC + mRNA-NC group. * P < 0.05, ** P < 0.01, *** P < 0.001) (TG: triglyceride).

Article Snippet: The cDNA was then analyzed by qRT-PCR using lnRcute lncRNA qPCR Kit (FP402, TIANGEN) on QuantStudio 3 system (Applied Biosystems).

Techniques: Knockdown, Binding Assay, Activity Assay, CCK-8 Assay, Flow Cytometry, Expressing, Gene Expression, Quantitative RT-PCR, Western Blot