silencing sirt7  (Vector Biolabs)

Journal: bioRxiv

Article Title: Loss of piR-hsa-7221 regulation drives the expression of the LINE1-derived oncogenic lncRNA CASC9 in testicular cancer

doi: 10.64898/2026.02.14.705912

Figure Lengend Snippet: Mapping of piRNAs, LINE1 and lncRNA sequences. A. Schematic of piRNAs mapping to lncRNAs transcribed from LINE1 antisense promoters with volcano plot of differentially expressed piRNAs in SEM. IDs of low expressed piRNAs mapping lncRNAs are indicated. B. Overlap of LINE1-derived lncRNAs with highly expressed lncRNA in TCGA SEM samples. Expression of overlapping lncRNAs is shown with a cut-off expression of RPKM ≥2 (dotted line). C. Western blotting and immunostaining showing expression of LINE1 ORF1 protein (LORF1p) in TCam-2 cells. Expression of ACTB was used as a loading control (LORF1p red, cell cytoskeleton green, nucleus blue). D. Bisulfite sequencing of the proximal and distal promoter region of the CASC9-LIPA5 sequence. Ten independent sequence clones are shown with white and black circles representing unmethylated and methylated CG residues, respectively. E. PiR-hsa-7221 expression in TCam-2 cells (top; *P < 0.05, Student’s t-test) and in SEM (bottom; TGCA, n= 58; *FDR < 0.05) compared to normal testis. F. Expression of PIWIL1, PIWIL2 and PIWIL4 in TCam-2 cells (left; n=3, *P < 0.05, Student’s t-test) and in the TCGA SEM samples (right; n=58, *FDR < 0.05). G. CASC9 expression in TCam-2 cells (top; *P < 0.05, Student’s t-test) and in SEM (bottom; TGCA, n= 58; *FDR < 0.05) compared to normal testis.

Article Snippet: For CASC9 silencing, a mixture (1:1) of the Silencer® Select CASC9 siRNAs (assays # n544070 and n544071; ThermoFisher) was transfected at a final concentration of 25 nM with the TransIT-X2® transfection reagent (Mirus).

Techniques: Derivative Assay, Expressing, Western Blot, Immunostaining, Control, Methylation Sequencing, Sequencing, Clone Assay, Methylation

Journal: bioRxiv

Article Title: Loss of piR-hsa-7221 regulation drives the expression of the LINE1-derived oncogenic lncRNA CASC9 in testicular cancer

doi: 10.64898/2026.02.14.705912

Figure Lengend Snippet: Regulation of LINE1 activity in TGCTs. A. Validation of the expression of piR-hsa-7221 after transfection in the presence or absence of PIWI proteins (n = 3) (*P < 0.05, Two-way Anova followed by Tukey’s multiple comparisons test). B. Gain of function expression of PIWI proteins in TCam-2 cells. A. Validation of the expression of PIWIL1, PIWIL2, and PIWIL4 after transfection (n = 3) (*P < 0.05, Student’s t-test). C. Luciferase assay demonstrating the binding of piR-hsa-7221 to the complementary LINE1 sequence in the presence or absence of co-transfected PIWI proteins. D. Regulation of CASC9 expression by piR-hsa-7221 and PIWI proteins (n=3, *P<0.05 compared to piR-hsa-7221, Two-way Anova followed by Tukey’s multiple comparisons test).

Article Snippet: For CASC9 silencing, a mixture (1:1) of the Silencer® Select CASC9 siRNAs (assays # n544070 and n544071; ThermoFisher) was transfected at a final concentration of 25 nM with the TransIT-X2® transfection reagent (Mirus).

Techniques: Activity Assay, Biomarker Discovery, Expressing, Transfection, Luciferase, Binding Assay, Sequencing

Journal: bioRxiv

Article Title: Loss of piR-hsa-7221 regulation drives the expression of the LINE1-derived oncogenic lncRNA CASC9 in testicular cancer

doi: 10.64898/2026.02.14.705912

Figure Lengend Snippet: Regulation of CASC9 expression and associated cancer phenotypes. A. CASC9 expression after siRNA silencing (n=3, *P < 0.05, Student’s t-test compared to scrambled). B. Effect of CASC9 silencing on cell proliferation and cell viability (n = 3; *P < 0.05 compared to scrambled, Two-way Anova followed by Tukey’s multiple comparisons test). Viable cells are stained in purple. C. Effect of CASC9 silencing on cell invasion (n = 3, 10 fields of view; *P < 0.05 compared to scrambled, Mann Whitney test), scale = 500 μm; D. Effect of CASC9 silencing on cell sensitivity to cisplatin (n = 3; *P < 0.05 compared to scrambled, Two-way Anova followed by Tukey’s multiple comparisons test).

Article Snippet: For CASC9 silencing, a mixture (1:1) of the Silencer® Select CASC9 siRNAs (assays # n544070 and n544071; ThermoFisher) was transfected at a final concentration of 25 nM with the TransIT-X2® transfection reagent (Mirus).

Techniques: Expressing, Staining, MANN-WHITNEY

Journal: bioRxiv

Article Title: Loss of piR-hsa-7221 regulation drives the expression of the LINE1-derived oncogenic lncRNA CASC9 in testicular cancer

doi: 10.64898/2026.02.14.705912

Figure Lengend Snippet: Gene expression signatures enriched in CASC9 knockdown cells (FDR < 0.05, compared to scrambled). A. Volcan plot of differentially expressed genes after CASC9 silencing. Green dots represent downregulated genes; red dots represent upregulated genes. B. Gene ontology analysis of differentially expressed genes (BP indicates biological process, CC indicates cellular location and MF indicates molecular function). C. Enriched pathways. D. Enriched GSEA signatures. E. Enriched functional protein networks. F. WNT signalling protein network cluster and expression fold changes of genes associated with the WNT pathway (FDR<0.05).

Article Snippet: For CASC9 silencing, a mixture (1:1) of the Silencer® Select CASC9 siRNAs (assays # n544070 and n544071; ThermoFisher) was transfected at a final concentration of 25 nM with the TransIT-X2® transfection reagent (Mirus).

Techniques: Gene Expression, Knockdown, Functional Assay, Expressing

Journal: Journal of Translational Medicine

Article Title: Eriocitrin inhibits sodium iodate-induced cuproptosis and barrier function impairment in retinal pigment epithelium via SIRT7/YAP/ATP7A pathway

doi: 10.1186/s12967-025-07451-w

Figure Lengend Snippet: Eriocitrin inhibited cuproptosis by targeting SIRT7 to regulate the YAP/ATP7A pathway. ( A ) qPCR analysis of cuproptosis-related gene expression ( n = 8). ( B ) WB detection of protein expression after siRNA gene silencing of SIRT7 ( n = 3). ( C - D ) WB analysis of YAP/ATP7A axis ( n = 3). ( E ) qPCR analysis of cuproptosis-related gene expression ( n = 8). ( F ) WB detection of YAP expression after addition of Verteporfin ( n = 3). ( G ) WB analysis of SIRT7, ATP7A expression ( n = 3). ( H ) WB detection of protein expression after siRNA gene silencing of ATP7A ( n = 3). ( I ) WB analysis of YAP, FDX1, DLAT ( n = 3). ( J ) WB analysis of FDX1, DLAT ( n = 3). si-RNA, siRNA negative control. Verteporfin, YAP inhibitor. Data were normalized to β-actin. Data were presented as mean ± SD ( n ≥ 3 independent biological replicates). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

Article Snippet: Silencing SIRT7 in mice using SIRT7 shRNA-containing adeno-associated virus (AAV), purchased from Vector Biolabs (shAAV-272012).

Techniques: Gene Expression, Expressing, Negative Control

Journal: Journal of Translational Medicine

Article Title: Eriocitrin inhibits sodium iodate-induced cuproptosis and barrier function impairment in retinal pigment epithelium via SIRT7/YAP/ATP7A pathway

doi: 10.1186/s12967-025-07451-w

Figure Lengend Snippet: SIRT7 deficiency significantly impaired the protective effect of eriocitrin in alleviating NaIO₃-induced retinal barrier dysfunction and cuproptosis. ( A - B ) Western blot analysis of SIRT7 expression in mouse retinal tissue ( n = 3). ( C ) Retinal copper ion levels ( n = 7). ( D - E ) Immunofluorescence images of RPE65 in mouse retinal tissue and quantitative analysis ( n = 5). ( F - G ) Western blot analysis and quantification of YAP, ATP7A, FDX1, and DLAT protein expression ( n = 3). ( H ) qRT-PCR analysis of cuproptosis-related genes including FDX1 and DLAT ( n = 9). ( I - J ) Western blot analysis of barrier function proteins in retinal tissues ( n = 3). Scramble group: non-specific shRNA. Er: eriocitrin. Data were normalized to β-actin. Scale bar: 50 μm. Data were presented as mean ± SD ( n ≥ 3 independent biological replicates). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001

Article Snippet: Silencing SIRT7 in mice using SIRT7 shRNA-containing adeno-associated virus (AAV), purchased from Vector Biolabs (shAAV-272012).

Techniques: Western Blot, Expressing, Immunofluorescence, Quantitative RT-PCR, shRNA

Journal: Bioactive Materials

Article Title: Extracellular vesicles derived from salivary gland stem cells cultured on microwell scaffolds loaded with WNT3A promote the recovery of salivary gland function damaged by radiation via the YWHAZ-PI3K-AKT pathway

doi: 10.1016/j.bioactmat.2025.06.024

Figure Lengend Snippet: Functional validation of YWHAZ as a key effector in 3D WNT -EV-mediated restoration of irradiated mouse SGOs. (A) Representative bright-field, H&E, and PAS images of SGOs under five conditions: untreated (Control), irradiated + PBS (PBS), irradiated + 3D WNT -EVs derived from sgEpSCs transfected with YWHAZ siRNA (YWHAZ siRNA-EVs), irradiated + 3D WNT -EVs derived from sgEpSCs transfected with scrambled siRNA (scrambled siRNA-EVs), and irradiated + 3D WNT -EVs (3D WNT -EVs). SGOs treated with PBS or YWHAZ siRNA-EVs exhibited smaller size and cystic morphology, while those treated with scrambled siRNA-EVs or 3D WNT -EVs showed regenerative end-bud structures. H&E staining showed keratin pearl-like structures in the PBS group, while PAS staining revealed mucin recovery in all EV-treated groups, with greater intensity in scrambled and 3D WNT -EV conditions. Scale bars, 100 μm. (B) Representative immunofluorescence images of phosphorylated AKT (p-AKT) in SGOs under each treatment condition. SGOs treated with 3D WNT -EVs or scrambled siRNA-EVs showed elevated p-AKT levels compared to the PBS and YWHAZ siRNA-EVs groups. DAPI was used for nuclear counterstaining. Scale bars, 100 μm. (C) Cell viability, size of mouse SGOs and mucin area in EV-treated groups compared with the control and PBS groups. (D) Quantification of p-AKT + in SGOs shown in (B). Individual data points represent biological or technical replicates, per group ranging from 3 to 9. Error bars indicate SD. Statistical significance was determined using one-way ANOVA followed by Tukey's post hoc test. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001.

Article Snippet: RNA interference (RNAi) was performed in human salivary gland–derived epithelial stem cells (sgEpSCs) using a Silencer® Pre-designed siRNA targeting human YWHAZ (ID: 107095, Ref: AM16708, Lot: ASO2NMXZ) and a non-targeting negative control siRNA (Ref: AM4611, Lot: ASO2NAC8), both purchased from Invitrogen (Thermo Fisher Scientific, USA).

Techniques: Functional Assay, Biomarker Discovery, Irradiation, Control, Derivative Assay, Transfection, Staining, Immunofluorescence

Journal: Cellular and Molecular Life Sciences: CMLS

Article Title: Macrophage migration inhibitory factor mediates joint capsule fibrosis via facilitating phospholipid metabolite PGE2 production in fibroblasts

doi: 10.1007/s00018-025-05800-y

Figure Lengend Snippet: Effects of CREB on the MIF-induced COX2 expression and PGE2 production. A , Western blot analysis of p-CREB following joint capsule fibroblasts treated with 2 µg/mL MIF for 0, 15, 30, 60, and 120 min. B , Quantitative results of A. C , Western blot analysis of p-CREB in joint capsule fibroblasts following siRNA2 knockdown of CD74 for 48 h and 2 µg/mL MIF stimulation for 15 min. D , Quantitative results of C. E , Evaluation of CREB knockdown efficiency using qRT-PCR after transfection for 48 h and siRNA1 was selected for subsequent experiments. F–H , Following siRNA1 knockdown of CREB for 48 h and 2 μg/ml MIF stimulation for 24 h, COX2 expression in joint capsule fibroblasts was assessed by qRT-PCR ( F ) and Western blot ( G ). Quantitative results of G as shown in ( H ). I and J , PGE2 production in supernatant ( I ) and lysate ( J ) of joint capsule fibroblasts were tested by ELISA accordingly. Each experiment was conducted three times. Error bars denote standard deviation. * P < 0.05 compared with Control group or 0 min group

Article Snippet: CREB gene silencing (RiboBio, Guangzhou, China) was similarly performed using different siRNA sequences (siRNA1, siRNA2, siRNA3) following the same procedures.

Techniques: Expressing, Western Blot, Knockdown, Quantitative RT-PCR, Transfection, Enzyme-linked Immunosorbent Assay, Standard Deviation, Control