bap1-short hairpin rna (shrna)  (Santa Cruz Biotechnology)

Journal: Oncology Reports

Article Title: High expression of eIF4A1 promotes angiogenesis through the NF-κB/VEGFA pathway and predicts poor prognosis in gastric cancer

doi: 10.3892/or.2025.8951

Figure Lengend Snippet: eIF4A1 is upregulated in gastric cancer tissues. (A) Pan-cancer analysis of eIF4A1 expression was performed using UALCAN. (B) Expression of eIF4A1 in gastric cancer tissues and in peripheral normal tissues from patients with gastric cancer was assessed using Home For Researchers database. (C) Expression of eIF4A1 in late-stage GC tissues, early-stage GC tissues and in peripheral normal tissues. (D) Statistics of eIF4A1 expression in different types of gastric tissues. (E) eIF4A1 protein in GC tissues and normal gastric tissues: (a) Well-differentiated adenocarcinoma, (b) papillary adenocarcinoma, (c) poorly-differentiated adenocarcinoma, (d) mucinous adenocarcinoma, (e) CG, (f) pericarcinomatous mucosa tissue, (g) IM and (h) HGIN. *P<0.05, ***P<0.001, ****P<0.0001. CG, chronic gastritis; eIF4A1, eukaryotic translation initiation factor 4A; HGIN, high-grade intraepithelial neoplasia; IM, intestinal metaplasia; LGIN, low-grade intraepithelial neoplasia.

Article Snippet: Lentiviruses containing eIF4A1 cDNA (pLV3-CMV-eIF4A1-CopGFP-Puro) or short hairpin (sh)RNA against eIF4A1 (pLV3-U6-eIF4A1-shRNA-CopGFP-Puro) were produced by GeneCopoeia, Inc, as well as their controls (NC and shNC).

Techniques: Expressing

Journal: Oncology Reports

Article Title: High expression of eIF4A1 promotes angiogenesis through the NF-κB/VEGFA pathway and predicts poor prognosis in gastric cancer

doi: 10.3892/or.2025.8951

Figure Lengend Snippet: Survival curves confirming the prognostic value of eIF4A1 and TNM stage in GC. (A) High eIF4A1 expression was associated with overall survival in patients with GC. (B) TNM stage was associated with the overall survival of patients with GC. GC, gastric cancer; TNM, Tumor-Node-Metastasis.

Article Snippet: Lentiviruses containing eIF4A1 cDNA (pLV3-CMV-eIF4A1-CopGFP-Puro) or short hairpin (sh)RNA against eIF4A1 (pLV3-U6-eIF4A1-shRNA-CopGFP-Puro) were produced by GeneCopoeia, Inc, as well as their controls (NC and shNC).

Techniques: Expressing

Journal: Oncology Reports

Article Title: High expression of eIF4A1 promotes angiogenesis through the NF-κB/VEGFA pathway and predicts poor prognosis in gastric cancer

doi: 10.3892/or.2025.8951

Figure Lengend Snippet: Dysregulation of eIF4A1 affects the angiogenic activity of gastric cancer cells. (A) Western blotting detected the expression of eIF4A1 in cells after lentivirus infection. (B) Cell Counting Kit 8 assay assessed the proliferation of HUVECs treated with CM derived from specific cells. The optical density at 0 h was set at 100%. (C) Representative images (left) and quantification (right) of wound healing assay of HUVECs treated with CM derived from specific cells. (D) Representative images (left) and quantification (right) of Transwell assay of HUVECs treated with CM derived from specific cells. (E) Representative images (left) and quantification (right) of angiogenesis assay of HUVECs treated with CM derived from specific cells. (F) Representative image of the tumors. (G) Growth curves of the tumors and (H) weight of the tumors. (I) Representative images (left) and quantification (right) of CD31 staining in tissues from a subcutaneous xenograft tumor model. # P<0.05 vs. NC; & P<0.05 vs. shNC; *P<0.05. CM, conditioned media; eIF4A1, eukaryotic translation initiation factor 4A; HUVECs, human umbilical cord endothelial cells; MVD, microvessel density; NC, negative control; sh, short hairpin.

Article Snippet: Lentiviruses containing eIF4A1 cDNA (pLV3-CMV-eIF4A1-CopGFP-Puro) or short hairpin (sh)RNA against eIF4A1 (pLV3-U6-eIF4A1-shRNA-CopGFP-Puro) were produced by GeneCopoeia, Inc, as well as their controls (NC and shNC).

Techniques: Activity Assay, Western Blot, Expressing, Infection, Cell Counting, Derivative Assay, Wound Healing Assay, Transwell Assay, Angiogenesis Assay, Staining, Negative Control

Journal: Oncology Reports

Article Title: High expression of eIF4A1 promotes angiogenesis through the NF-κB/VEGFA pathway and predicts poor prognosis in gastric cancer

doi: 10.3892/or.2025.8951

Figure Lengend Snippet: eIF4A1 affects regulation of the TME and angiogenesis. Association between eIF4A1 expression and various component cells in the TME was detected using R package (4.3.3) in (A) GSE62254 , (B) GSE15459 and (C) GSE84426 . Part of the left panel was enlarged and presented in the right panel. (D) Correlations between eIF4A1 expression and CD31, VEGFA, NFKB1 and NFKB2. (E) mRNA levels of VEGF family genes were detected by reverse transcription-quantitative polymerase chain reaction. (F) Changes in VEGEF and NF-κB expression after eIF4A1 overexpression and knockdown were detected by western blotting. *P<0.05. eIF4A1, eukaryotic translation initiation factor 4A; NC, negative control; sh, short hairpin; TME, tumor microenvironment. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.

Article Snippet: Lentiviruses containing eIF4A1 cDNA (pLV3-CMV-eIF4A1-CopGFP-Puro) or short hairpin (sh)RNA against eIF4A1 (pLV3-U6-eIF4A1-shRNA-CopGFP-Puro) were produced by GeneCopoeia, Inc, as well as their controls (NC and shNC).

Techniques: Expressing, Reverse Transcription, Real-time Polymerase Chain Reaction, Over Expression, Knockdown, Western Blot, Negative Control

Journal: bioRxiv

Article Title: sTelomere replication stress-induced DNA damage response triggers inflammatory signaling via canonical and non-canonical STING pathways

doi: 10.1101/2025.07.11.664434

Figure Lengend Snippet: Activation of the NFκB/IL6 and IRF3/IFNβ pathways is STING-dependent in TRF1-deficient MEFs. (A) Western blot analysis confirming STING knockdown. MEFs were transfected with either non-targeting shRNA control (shNT) or Sting shRNA lentivirus for 72 hours. (B) shRNA-mediated STING knockdown MEFs were treated with mock or OHT for the indicated times, and knockdown efficiency was assessed by RT-qPCR. (C) Whole cell lysates harvested at 96 hours were analyzed by Western blot with the indicated antibodies. Black dashes on the left denote the position of the protein of interest. (D) MEFs were treated with OHT for 96 hours in the presence (+) or absence (–) of the STING inhibitor H-151. H-151 was administered 24 hours post-initiation of OHT treatment. Cell lysates were analyzed by Western blot with the indicated antibodies. (E–F) IFNβ and IL6 protein levels were measured by cytokine array in both cell pellets and culture medium from OHT-treated MEFs for indicated times. H-151 was administered 24 hours post-initiation of OHT treatment. Values were normalized to total protein concentration in the cell pellet. P values were calculated using two-way ANOVA for multiple comparisons. Data are presented as mean ± SD from a representative experiment out of three independent experiments.

Article Snippet: STING small hairpin RNA (shRNA) lentiviral plasmids (Millipore Sigma, SHCLNG-TRCN0000346266, SHCLNG-TRCN0000346319, SHCLNG-TRCN0000346320), along with the packaging plasmid (pCMV Δ8.2) and envelope plasmid (pCMV VSVG), were used to generate lentivirus in 293T cells.

Techniques: Activation Assay, Western Blot, Knockdown, Transfection, shRNA, Control, Quantitative RT-PCR, Protein Concentration

Journal: bioRxiv

Article Title: sTelomere replication stress-induced DNA damage response triggers inflammatory signaling via canonical and non-canonical STING pathways

doi: 10.1101/2025.07.11.664434

Figure Lengend Snippet: STING is essential for the activation of the inflammatory response in TRF1-deficient MEFs. (A) Western blot analysis confirming STING knockdown in MEFs transfected with either non-targeting control or STING siRNA for 72 hours. (B) MEFs were treated with OHT for 24 hours, followed by STING siRNA transfection for 48–72 hours. Sting mRNA levels were measured by RT-qPCR. (C–E) Expression levels of Il6 and Cxcl10 mRNA were analyzed at various time points following treatment with Sting siRNA (C), Sting shRNA (D), or STING inhibitor (E), in the presence or absence of OHT. (F) TNFα, IL1β, and IFNγ protein levels were measured by cytokine array in cell pellets from OHT-treated MEFs for indicated times and normalized to total protein concentration in the cell pellet. H-151 was administered 24 hours post-initiation of OHT treatment. P values were calculated using two-way ANOVA for multiple comparisons. Data are presented as mean ± SD from a representative experiment out of three independent experiments.

Article Snippet: STING small hairpin RNA (shRNA) lentiviral plasmids (Millipore Sigma, SHCLNG-TRCN0000346266, SHCLNG-TRCN0000346319, SHCLNG-TRCN0000346320), along with the packaging plasmid (pCMV Δ8.2) and envelope plasmid (pCMV VSVG), were used to generate lentivirus in 293T cells.

Techniques: Activation Assay, Western Blot, Knockdown, Transfection, Control, Quantitative RT-PCR, Expressing, shRNA, Protein Concentration

Journal: Discover Oncology

Article Title: SLC3A2 as a key anoikis−related gene for prognosis and tumor microenvironment remodeling in melanoma

doi: 10.1007/s12672-025-03125-7

Figure Lengend Snippet: Composition of genes within the anoikis-related prognostic model.The weight coefficients of genes included in the final model, with SLC3A2 displaying the strongest positive association with risk score

Article Snippet: To knock down SLC3A2 expression, specific short hairpin RNAs (shRNAs) targeting human SLC3A2 were designed and synthesized by GenePharma (Shanghai, China)(Supplemental Table 1).

Techniques:

Journal: Discover Oncology

Article Title: SLC3A2 as a key anoikis−related gene for prognosis and tumor microenvironment remodeling in melanoma

doi: 10.1007/s12672-025-03125-7

Figure Lengend Snippet: Expression, clinical significance, and biological implications of SLC3A2 in melanoma.( A–E ) SLC3A2 expression profiles across tumor and normal tissues, T stages, and treatment response groups. (F–J) Kaplan–Meier survival curves indicating the association between high SLC3A2 expression and worse prognosis in multiple datasets. ( K ) Forest plot of multivariate Cox regression analysis confirming SLC3A2 as an independent risk factor. ( L–O ) Gene set enrichment analysis (GSEA) identifying biological pathways significantly enriched in high SLC3A2 expression. ( P ) Drug sensitivity analysis highlighting potential compounds related to SLC3A2-mediated drug response

Article Snippet: To knock down SLC3A2 expression, specific short hairpin RNAs (shRNAs) targeting human SLC3A2 were designed and synthesized by GenePharma (Shanghai, China)(Supplemental Table 1).

Techniques: Expressing

Journal: Discover Oncology

Article Title: SLC3A2 as a key anoikis−related gene for prognosis and tumor microenvironment remodeling in melanoma

doi: 10.1007/s12672-025-03125-7

Figure Lengend Snippet: Functional validation of SLC3A2 in melanoma cell lines. ( A–B ) Wound healing and transwell migration assays showing impaired cell migration after SLC3A2 knockdown in A375 cells. ( C ) Colony formation assay demonstrating reduced proliferative capacity following SLC3A2 silencing

Article Snippet: To knock down SLC3A2 expression, specific short hairpin RNAs (shRNAs) targeting human SLC3A2 were designed and synthesized by GenePharma (Shanghai, China)(Supplemental Table 1).

Techniques: Functional Assay, Biomarker Discovery, Migration, Knockdown, Colony Assay