non targeting scrambled shrna  (Addgene inc)

Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: UPK1B drives GC cell invasion and migration in a PI3K/AKT-dependent manner. (A) Gene set enrichment analysis indicated that genes upregulated in the UPK1B-high group were enriched in the PI3K/AKT pathway. (B) Protein levels of UPK1B in GC cell lines. (C) Knockdown of UPK1B reduced PI3K/AKT activation in MKN45 cells. Silencing UPK1B suppressed the (D) migration/invasion capacity and (E) wound closure rate of MKN45 cells. (F) Overexpression of UPK1B enhanced PI3K/AKT pathway activation in AGS cells, which was attenuated by the PI3K inhibitor LY294002. Inhibition of PI3K/AKT signaling reversed UPK1B-induced (G) migration/invasion capacity and (H) wound closure rate of AGS cells. UPK1B, uroplakin 1B; GC, gastric cancer; p-, phosphorylated; sh, short hairpin RNA; NC, negative control; OE, overexpression.

Article Snippet: Cells were also transfected with small interfering RNAs (siRNAs) targeting CDX2 or PIK3IP1 , with a universal non-targeting scrambled siRNA (si-NC) as the negative control , obtained from GeneChem, Inc. For UPK1B and CDX2 overexpression, the p-TSB-CMV-UPK1B and p-TSB-CMV-CDX2 expression vectors [Shanghai Genomeditech Co., Ltd.] and the corresponding empty p-TSB-CMV vector (negative control) were used.

Techniques: Migration, Knockdown, Activation Assay, Over Expression, Inhibition, shRNA, Negative Control

Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: CDX2 acts as a transcriptional repressor of UPK1B and its high expression is associated with favorable prognosis of patients with GC. (A) Venn diagram showing overlapping predicted transcriptional regulators of UPK1B from ChEA and ChEA3 databases. (B) Knockdown of CDX2 in AGS cells resulted in increased UPK1B (C) mRNA and (D) protein expression. (E) Overexpression of CDX2 in MKN45 cells reduced UPK1B protein levels. Data from (F) The Cancer Genome Atlas Stomach Adenocarcinoma cohort and (G) the Kaplan-Meier plotter database indicated that high CDX2 expression was associated with improved prognosis of patients with GC. UPK1B, uroplakin 1B; GC, gastric cancer; si, small interfering RNA; NC, negative control; OE, overexpression; HR, hazard ratio; CDX2, caudal-related homeobox transcription factor 2; ChEA, ChIP-X Enrichment Analysis.

Article Snippet: Cells were also transfected with small interfering RNAs (siRNAs) targeting CDX2 or PIK3IP1 , with a universal non-targeting scrambled siRNA (si-NC) as the negative control , obtained from GeneChem, Inc. For UPK1B and CDX2 overexpression, the p-TSB-CMV-UPK1B and p-TSB-CMV-CDX2 expression vectors [Shanghai Genomeditech Co., Ltd.] and the corresponding empty p-TSB-CMV vector (negative control) were used.

Techniques: Expressing, Knockdown, Over Expression, Small Interfering RNA, Negative Control

Journal: Experimental and Therapeutic Medicine

Article Title: CDX2-UPK1B-PIK3IP1-PI3K/AKT signaling axis regulates gastric cancer cell invasion and migration and influences patient prognosis

doi: 10.3892/etm.2026.13179

Figure Lengend Snippet: UPK1B activates PI3K/AKT signaling by antagonizing the inhibitory regulator PIK3IP1 in gastric cancer cells. (A) Venn diagram showing that PIK3IP1 was identified as a putative UPK1B-interacting partner based on BioGRID and HIPPIE protein-protein interaction databases. (B) UPK1B and PIK3IP1 co-localized in the cytoplasm and plasma membrane of MKN45 cells. (C) Interaction between UPK1B and PIK3IP1 in MKN45 cells. (D) Knockdown of PIK3IP1 in MKN45 cells. (E) Silencing PIK3IP1 in UPK1B-knockdown MKN45 cells restored PI3K/AKT pathway activation. Knockdown of PIK3IP1 reversed the decrease in (F) migration/invasion and (G) wound-healing capacity in UPK1B-silenced MKN45 cells. UPK1B, uroplakin 1B; p-, phosphorylated; si, small interfering RNA; sh, short hairpin RNA; NC, negative control; PIK3IP1, PI3K inhibitor interacting protein 1; HIPPIE, Human Integrated Protein-Protein Interaction Reference; IP, immunoprecipitation.

Article Snippet: Cells were also transfected with small interfering RNAs (siRNAs) targeting CDX2 or PIK3IP1 , with a universal non-targeting scrambled siRNA (si-NC) as the negative control , obtained from GeneChem, Inc. For UPK1B and CDX2 overexpression, the p-TSB-CMV-UPK1B and p-TSB-CMV-CDX2 expression vectors [Shanghai Genomeditech Co., Ltd.] and the corresponding empty p-TSB-CMV vector (negative control) were used.

Techniques: Clinical Proteomics, Membrane, Knockdown, Activation Assay, Migration, Small Interfering RNA, shRNA, Negative Control, Immunoprecipitation

Journal: Cell Death Discovery

Article Title: Inhibiting HSP27 activates the XBP1s/CerS1 interplay, which triggers DRP1-driven mitophagy, thereby protecting against cell death and promoting the KSHV lytic cycle in primary effusion lymphoma cells

doi: 10.1038/s41420-026-02979-2

Figure Lengend Snippet: BC3 and BCBL1 cell lines were treated or not with 10 and 20 μM J2 (HSP27 inhibitor). After 24 h ( A ) the cytotoxic effect of J2 was measured by trypan blue assay. The histograms represent the percentage of cell viability relative to the control. Data are shown as the mean plus S.D. of three experiments. p value * <0.05, as calculated by ANOVA test. B BiP and CHOP expression as evaluated by western blot analysis. Histone H3 (H3) was used as loading control. The histograms represent the densitometric analysis of the ratio of BiP/H3 and CHOP/H3. The data are represented as the mean plus S.D. of three different experiments. p value * <0.05, as calculated by ANOVA test. BC3 and BCBL1 cell lines treated or not with J2 (20 μM) for 4 h were analyzed by western blot for the expression of XBP1s ( C ) and after 24 h of treatment for cleaved PARP (clPARP) ( D ). GAPDH was used as loading control. The histograms represent the densitometric analysis of the ratio of XBP1s /GAPDH and clPARP/GAPDH. The data are represented as the mean plus S.D. of three different experiments. p value * <0.05, as calculated by Student’s t -test. BC3 and BCBL1 cell lines were knocked down for HSP27 (siHSP27) or scramble treated, using siRNA from different companies (Santa Cruz and Dharmacon respectively), for 24 h and the expression of BiP ( E ) and XBP1s was evaluated by western blot analysis while the effect on cell viability was evaluated by trypan blue assay ( F ). Histone H3 (H3) was used as loading control. The histograms represent the densitometric analysis of the ratio of HSP27/H3, BiP/H3 and XBP1s/H3. The data are represented as the mean plus S.D. of three different experiments. p value * <0.05, as calculated by Student’s t -test.

Article Snippet: For transfection 10 μl of INTERFERin reagent (Polyplus, Illkirch, France; cat. n. 101000016) in combination with 50 pmol of specific small interfering RNA (siRNA duplex) or with non-targeting (scramble) siRNA (Santa Cruz Biotechnology, Inc., Heidelberg, Germany cat. n. sc-29350) were diluted in 200 μl RPMI without serum and antibiotics, incubated for 10 minutes at RT then added to each well.

Techniques: Control, Expressing, Western Blot

Journal: bioRxiv

Article Title: Neurogranin enhances spontaneous activity and neuronal survival of hippocampal neurons

doi: 10.64898/2026.01.27.701932

Figure Lengend Snippet: Primary hippocampal neurons were infected with AAV-Ng at DIV7 or with AAV-shNg or scrambled shRNA (AAV-shScr) at DIV10 and analyzed at DIV15. (a) Ng protein levels were assessed by Western blot and normalized to GAPDH (upper panel; n = 4). The proportion of Ng-positive neurons was determined by fundingimmunofluorescence using DAPI to identify total cells (lower panel; n = 4). (b) Dendritic length per neuron, quantified for each field of view, increased following Ng expression. (c) Synaptic density was analyzed by co-localization of excitatory (vGluT1/PSD95) and inhibitory (GAD65/Gephyrin) pre- and postsynaptic markers. Data in histograms are total number of synapses per field of view (0.11 mm 2 ). Ng expression increased the number of excitatory and inhibitory synaptic contacts (yellow puncta; n = 52–58 images). (d) The axon initial segment (AIS) was labeled with anti-ankyrin G (AnkG). Total AIS length (left graph; n = 25 neurons per condition) and distances from soma to AIS onset, peak intensity, and distal end (right graph) were quantified using DAPI to locate the soma. Widefield images (a–c) were acquired on a Zeiss Axiovert 200M microscope with 10× (A, B) or 40× (c) objectives; AIS images (d) were obtained using a Zeiss LSM900 confocal microscope with a 63× objective.

Article Snippet: As a control, a non-targeting scrambled shRNA (gtgccaagacgggtagtca, Addgene #181875) was used.

Techniques: Infection, shRNA, Western Blot, Expressing, Labeling, Microscopy

Journal: bioRxiv

Article Title: Encephalitic Alphavirus Infection Induces PARP-1 Hyperactivation Mediated Energy Collapse in Motor Neurons

doi: 10.64898/2026.01.23.701280

Figure Lengend Snippet: ( A ) Representative western blot analysis of PAR accumulation and PARP-1 expression at 24 hpi with VEEV (MOI 1.0). NSC34 cells were transfected with either PARP1 siRNA (siPARP1; 20 pmol) or scrambled control siRNA (siCon; 20 pmol) 48 hours prior to infection. Pharmacological inhibition was achieved using ABT-888 (PARPi; 20µM) initiated 1 hour prior to infection and maintained throughout the experiment. ( B ) VEEV replication kinetics in NSC34 and diMN cells (MOI 1.0) following PARP-1 manipulation or nicotinamide riboside (NR; 500 µM) supplementation. To maintain effective concentrations, a 250µM NR spike was added to the infectious media at 12 hpi. Viral titers were quantified by plaque assay on Vero cells from supernatants collected between 6 and 48 hpi. Data represent mean ± SEM from at least three independent biological replicates. PARP-1 inhibition (siPARP1 and PARPi) resulted in an approximate one-log increase in viral titers between 12 and 24 hpi. (C–E) Metabolic and viability rescue at 24 hpi. (C) Intracellular NAD + (NAD/NADH-Glo) and (D)ATP levels (Luminescent ATP Detection) were quantified following treatment with siCon, siPARP1, PARPi, or NR as described above. All metabolic values were normalized to the number of viable cells in matched wells on the same plate to account for infection-induced cell loss. (E) Cell viability was assessed via Alamar Blue fluorescence. All values are expressed relative to mean of uninfected Mock controls. Statistical significance was determined by ordinary one-way ANOVA assuming a lognormal distribution; infected-treated groups were compared to the infected-untreated (or siCon) control via Dunnett’s multiple comparisons test. Mock and treatment-only controls are shown for reference. Data represent mean ± SEM., * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001

Article Snippet: A non-targeting scrambled siRNA (Santa Cruz, #sc-37007) served as a control.

Techniques: Western Blot, Expressing, Transfection, Control, Infection, Inhibition, Plaque Assay, Fluorescence