sirt3  (Sino Biological)

Journal: bioRxiv

Article Title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

doi: 10.64898/2026.03.13.711520

Figure Lengend Snippet: RT-qPCR and WB of SIRT3 in scramble (SCR) and si SIRT3 conditions (A). Representative images of SCR and si SIRT3 in hNE cell cultures (B). SIRT3 silencing effects on SIRT family mRNA abundance in hNECs (C). RT-qPCR and WB of empty vector (EV) and SIRT3 overexpression (OE) conditions (D). Representative images of EV and SIRT3 OE in hNE cell cultures (E). SIRT3 OE effects on SIRT family mRNA abundance in hNECs (F). Data are presented as mean±SEM . *P<0.05 vs. control group (a.u: arbitrary units).

Article Snippet: Briefly, 1 μg of either SIRT3 (HG13033-UT, Sino Biological) or control GFP (CV026, Sino Biological) plasmid DNA was mixed with Lipofectamine 3000 (Fisher, Waltham, MA, USA, L3000015) at a 1:2 ratio in DMEM and incubated for 15 min at room temperature.

Techniques: Quantitative RT-PCR, Plasmid Preparation, Over Expression, Control

Journal: bioRxiv

Article Title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

doi: 10.64898/2026.03.13.711520

Figure Lengend Snippet: Overlap between down- and up-regulated DEGs (A) and DPPs (B) from SIRT3 silencing and overexpression conditions. Functional analysis of DEGs, DEPs and DPPs from SIRT3 silencing (si) (C) and overexpression (OE) (D).

Article Snippet: Briefly, 1 μg of either SIRT3 (HG13033-UT, Sino Biological) or control GFP (CV026, Sino Biological) plasmid DNA was mixed with Lipofectamine 3000 (Fisher, Waltham, MA, USA, L3000015) at a 1:2 ratio in DMEM and incubated for 15 min at room temperature.

Techniques: Over Expression, Functional Assay

Journal: bioRxiv

Article Title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

doi: 10.64898/2026.03.13.711520

Figure Lengend Snippet: Functional mapping of deregulated genes (DEGs), proteins (DEPs) and phosphoproteins (DPPs) upon SIRT3 silencing conditions in hNECs.

Article Snippet: Briefly, 1 μg of either SIRT3 (HG13033-UT, Sino Biological) or control GFP (CV026, Sino Biological) plasmid DNA was mixed with Lipofectamine 3000 (Fisher, Waltham, MA, USA, L3000015) at a 1:2 ratio in DMEM and incubated for 15 min at room temperature.

Techniques: Functional Assay

Journal: bioRxiv

Article Title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

doi: 10.64898/2026.03.13.711520

Figure Lengend Snippet: Functional mapping of deregulated genes (DEGs), proteins (DEPs) and phosphoproteins (DPPs) upon SIRT3 overexpressing conditions in hNECs.

Article Snippet: Briefly, 1 μg of either SIRT3 (HG13033-UT, Sino Biological) or control GFP (CV026, Sino Biological) plasmid DNA was mixed with Lipofectamine 3000 (Fisher, Waltham, MA, USA, L3000015) at a 1:2 ratio in DMEM and incubated for 15 min at room temperature.

Techniques: Functional Assay

Journal: bioRxiv

Article Title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

doi: 10.64898/2026.03.13.711520

Figure Lengend Snippet: Steady state protein levels of SIRT 1-3 were measured by Western blotting (WB) at 8-24-48 hours post-treatment (A). * p<0.05 respect to untreated-hNEC control cells. Overlap between down- and up-regulated DPPs from SIRT3 silencing and overexpression upon Aβ oligomer protein stimulation in hNECs (B). Selected differentially phosphorylated proteins affected by SIRT3 modulation in Aβ-treated cells (C). Functional analysis of DPPs from SIRT3 silencing (si) and overexpression (OE) (D).

Article Snippet: Briefly, 1 μg of either SIRT3 (HG13033-UT, Sino Biological) or control GFP (CV026, Sino Biological) plasmid DNA was mixed with Lipofectamine 3000 (Fisher, Waltham, MA, USA, L3000015) at a 1:2 ratio in DMEM and incubated for 15 min at room temperature.

Techniques: Western Blot, Control, Over Expression, Functional Assay

Journal: bioRxiv

Article Title: Multi-omics characterization of SIRT3 metabolism and its adaptation to the presence of amyloid-beta oligomers in nasal epithelial cells

doi: 10.64898/2026.03.13.711520

Figure Lengend Snippet: Predictive activation profile of pathways, biofunctions and upstream regulators at the level of SIRT3 silencing and/or overexpression upon Aβ oligomer considering APP as main hub. Positive z-scores indicate potential activated pathways, whereas negative z-scores refer to predicted inhibited pathways. Based on SIRT3 silencing and overexpression datasets (A). Activation prediction of significantly altered pathways and neuronal functions (B). Systems Biology analysis were performed through the Ingenuity Pathway Analysis software .

Article Snippet: Briefly, 1 μg of either SIRT3 (HG13033-UT, Sino Biological) or control GFP (CV026, Sino Biological) plasmid DNA was mixed with Lipofectamine 3000 (Fisher, Waltham, MA, USA, L3000015) at a 1:2 ratio in DMEM and incubated for 15 min at room temperature.

Techniques: Activation Assay, Over Expression, Software

Journal: bioRxiv

Article Title: CXCR6⁺ natural killer cell immunotherapy preserves CD4⁺ T helper cells in humanized mice

doi: 10.64898/2026.05.28.728486

Figure Lengend Snippet: A) Expansion kinetics of sorted CXCR6⁻ and CXCR6⁺ NK cells from independent peripheral blood NK-cell donors during 15 days of ex vivo culture with CXCL16-expressing feeder cells, irradiated allogeneic PBMC feeders, and cytokine supplementation. B) Representative post-expansion flow cytometry plots showing maintenance of CXCR6-defined NK-cell phenotypes following expansion. C) Representative intracellular HIV-Gag flow cytometry plots from the indicated culture conditions. Activated primary CD4⁺ T cells from a single peripheral blood donor were infected with HIV-1 Q23.17 at an MOI of 0.01 and cultured alone or co-cultured for 3 days with day 14-expanded CXCR6⁺ or CXCR6⁻ NK cells at a 1:1 effector-to-target ratio. HIV infection was quantified by intracellular HIV-Gag staining and flow cytometry. D) Quantification of HIV suppression assay results. CXCR6⁺ and CXCR6⁻ NK cells were tested using NK cells from five independent genetically unrelated donors, with the same HIV-infected CD4⁺ T-cell target donor used across all NK donor and subset conditions. For each NK donor and condition, the CD4 + T cell-frequency was determined by flow cytometry, triplicate technical wells per donor were averaged before statistical analysis, and the five NK donors were analyzed as biological replicates. Donor-level paired comparisons were analyzed using two-sided paired tests with Holm correction for multiple comparisons. CXCR6⁺ NK cells significantly reduced the frequency of HIV-Gag⁺ CD4⁺ T cells compared with HIV-only cultures, p = 0.000064. CXCR6⁻ NK cells also significantly reduced HIV-Gag⁺ CD4⁺ T cells compared with HIV-only cultures, p = 0.004059. CXCR6⁺ NK cells suppressed HIV significantly more effectively than paired CXCR6⁻ NK cells, p = 0.009637. Data are presented as mean ± SD, with each color representing an independent NK-cell donor. **p < 0.01, ****p < 0.0001.

Article Snippet: RPMI 8866 cells were transduced with lentiviral particles (pLenti C mGFP, Origene) carrying CXCL16 transcript variant 1 (TV1, NM_022059) or variant 2 (TV2, NM_001100812).

Techniques: Ex Vivo, Expressing, Irradiation, Flow Cytometry, Infection, Cell Culture, Staining, HIV Inhibition Assay

Journal: Molecular Therapy Oncology

Article Title: Survivin/BIRC5-derived peptide disrupts survivin dimerization and cell division and induces multifaceted anti-cancer effects

doi: 10.1016/j.omton.2025.201123

Figure Lengend Snippet: Cell death induction by 1H13-survivin/BIRC5-derived peptides targeted to the cytoplasm, mitochondria, or nucleus (A) The sequences added to the 1H13-BIRC5 peptide to target it to the: (1) cytoplasm, (2) mitochondria, or (3) nucleus. The underlined sequence represents the 1H13 peptide; in red, amino acids indicate D-amino acid substitutions. (B) A549 cells were incubated for 90 min with 5 μM FITC-labeled, nucleus-targeted peptide IH13-Nuc, and were also IF-stained with anti--SMAC, anti-IP3R or anti-GM130 antibodies, and stained with DAPI to visualize the mitochondria, ER, Golgi, and nucleus, respectively. Confocal microscope images are shown, with white arrows indicating peptide co-localization with the mitochondria (SMAC). Orange and yellow arrows indicate peptide presence in the nucleus and cytosol, respectively. (C) A549 cells were incubated with the mitochondria- or nucleus-targeted 1H13-BIRC5-derived peptide for 24 h in serum-free medium, followed by a cell proliferation assay using the SRB method. (D and E) Apoptotic cell death as induced in A549 cells following incubation for 24 h with the nucleus-targeted peptide (2/3D-1H13-Nuc) in the presence or absence of the indicated concentrations of the peptides in serum-free medium and subjected to FITC–annexin V/PI staining, followed by a flow cytometry analysis. Representative histograms for control and selected peptide concentration (D) and analysis of early and late apoptotic stages are shown (E). (F and G) Cell death as induced by 2/3D-1H13-Nuc in different cell lines, A549, SH-SY5Y, U-87MG, PC-3, and HUV-EC-C (F) or Jurkat, K562, and KMH2-LC (G) were treated with the indicated concentrations of the peptide for 24 h, then subjected to cell death analysis using propidium iodide (PI) staining and flow cytometry. (H and I) A549 cells were seeded at a density of 2 × 10 5 cells per well in a 12-well plate. After 24 h, the cells were transfected with 2 μg of a pCMV3-survivin expression plasmid (HG10356-UT, Sino Biological, China) or with an empty pCMV3 plasmid (control) using JetPrime transfection reagent (Polyplus, France), following the manufacturer’s instructions. Twenty-four hours post-transfection, the cells were re-seeded at 1 × 10 5 cells per well in a 12-well plate. After another 24 h, the culture medium was replaced with serum-free medium, and the cells were treated with the indicated concentrations of the 2/3D-1H13-Nuc peptide. Survivin overexpression levels were assessed by immunoblotting (H), and cell death was analyzed by propidium iodide (PI) staining followed by FACS analysis (I). Results represent the means ± SEM ( n = 3).

Article Snippet: After 24 h, the cells were transfected with 2 μg of a pCMV3-survivin expression plasmid (HG10356-UT, Sino Biological, China) or with an empty pCMV3 plasmid (control) using JetPrime transfection reagent (Polyplus, France), following the manufacturer’s instructions.

Techniques: Derivative Assay, Sequencing, Incubation, Labeling, Staining, Microscopy, Proliferation Assay, Flow Cytometry, Control, Concentration Assay, Transfection, Expressing, Plasmid Preparation, Over Expression, Western Blot

Journal: bioRxiv

Article Title: Matrix metalloproteinases proteolyze RAB proteins and contribute to cisplatin-induced ototoxicity

doi: 10.64898/2026.02.28.708770

Figure Lengend Snippet: Gelatin zymography (A, C, E) and corresponding quantitative analysis (B, D, F, G) of MMP-2 and MMP-9 activities in the conditioned media of HEI-OC1 cells following 6 h (A, B) and 48 h (C, D) of exposure to 20 μM cisplatin. Cytosolic MMP-2 and MMP-9 activities were measured following 4 h and 6 h of treatment with 20 μM cisplatin (E-G). Standard (Std) derives from conditioned medium from HT-1080 cells. H) mRNA expression of Ifit-1 was measured using RT-qPCR following a 24h exposure to 20 μM cisplatin in the presence or absence of ARP-100 (5 μM), compared to the untreated control (nil), and normalized to B2M expression. The data are represented as the mean ± SD of three independent experiments. Statistical significance was determined using one-way ANOVA followed by Dunnett’s post-hoc test (* p < 0.05 and ** p <0.01).

Article Snippet: For overexpression studies, the pCMV3-C-FLAG vector encoding human MMP-2 ORF (HG10082-CF, Sino Biological) was transfected into HEI-OC1 using jetPRIME Reagent (Polyplus) according to the manufacturer’s protocol.

Techniques: Zymography, Expressing, Quantitative RT-PCR, Control

Journal: bioRxiv

Article Title: Matrix metalloproteinases proteolyze RAB proteins and contribute to cisplatin-induced ototoxicity

doi: 10.64898/2026.02.28.708770

Figure Lengend Snippet: mRNA expression of N-terminal truncated (NTT)- Mmp-2 (A), full-length (FL)- Mmp-2 (B), and Mmp-9 (C) was measured using RT-qPCR following exposure to 20 μM cisplatin for various timepoints, compared to the untreated control (0), and normalized to B2M expression. D) Immunofluorescence staining of HEI-OC1 cells treated with 20 μM cisplatin for 6 h or untreated cells. Staining was performed using an antibody specific to MMP-2, followed by detection with a secondary antibody conjugated to Alexa Fluor 647 (red). The zoomed-in boxes indicate nuclei with an increased red signal (magenta). The data are represented as the mean ± SD of three independent experiments. Statistical significance was determined using one-way ANOVA followed by Dunnett’s post-hoc test (* p < 0.05).

Article Snippet: For overexpression studies, the pCMV3-C-FLAG vector encoding human MMP-2 ORF (HG10082-CF, Sino Biological) was transfected into HEI-OC1 using jetPRIME Reagent (Polyplus) according to the manufacturer’s protocol.

Techniques: Expressing, Quantitative RT-PCR, Control, Immunofluorescence, Staining

Journal: bioRxiv

Article Title: Matrix metalloproteinases proteolyze RAB proteins and contribute to cisplatin-induced ototoxicity

doi: 10.64898/2026.02.28.708770

Figure Lengend Snippet: (A) IL-6 secretion in cells transfected with either an empty vector (EV) or an Mmp-2 -expressing vector and treated with 100 μM cisplatin or left untreated (nil) for 24 h. (B, C) IL-6 secretion in cells pre-treated for 2 h with the vehicle or 5 μM ARP-100 (B) or ONO-4817 (C), followed by treatment with 20 μM cisplatin for 24 h. (D) IL-6 secretion in cells transfected with non-targeting siRNA ( siNT ), Mmp-9 -targeting siRNA ( siMmp-9 ), and exposed to 20 μM cisplatin for 24 h. The data are represented as the mean ± SD of three independent experiments. Statistical significance was determined using one-way ANOVA followed by Dunnett’s post-hoc test (* p < 0.05).

Article Snippet: For overexpression studies, the pCMV3-C-FLAG vector encoding human MMP-2 ORF (HG10082-CF, Sino Biological) was transfected into HEI-OC1 using jetPRIME Reagent (Polyplus) according to the manufacturer’s protocol.

Techniques: Transfection, Plasmid Preparation, Expressing

Journal: bioRxiv

Article Title: Matrix metalloproteinases proteolyze RAB proteins and contribute to cisplatin-induced ototoxicity

doi: 10.64898/2026.02.28.708770

Figure Lengend Snippet: A, B) Immunoblot of in vitro time course proteolysis of recombinant RAB9A at 37 °C with 100 ng MMP-2 (A) or for 30 minutes in the presence or absence of MMP-2-preferring inhibitors (B). C) In silico analysis of the top 10 MMP-2 cleavage sites in the structure of mouse RAB9A according to ProsperousPlus. D) Crystal structure of mouse RAB9A showing the predicted cleavage sites (green balls).

Article Snippet: For overexpression studies, the pCMV3-C-FLAG vector encoding human MMP-2 ORF (HG10082-CF, Sino Biological) was transfected into HEI-OC1 using jetPRIME Reagent (Polyplus) according to the manufacturer’s protocol.

Techniques: Western Blot, In Vitro, Recombinant, In Silico

Journal: Nature Communications

Article Title: A common 19 bp APOE enhancer deletion is protective against Alzheimer’s disease in African Americans

doi: 10.1038/s41467-026-68808-3

Figure Lengend Snippet: a Alignment of phased long-read alleles. b gnomAD minor allele frequency of the 19 bp SNP. c Relative frequency of the deletion in 1000 Genomes Project populations ordered by relative abundance. * = African Ancestry in Southwest US. d Number of alleles with the deletion in APOE-ε4 homozygous individuals from the 1000 Genomes Project populations. e UCSC genome browser track showing the location of the deletion allele relative to APOE and transcription factor binding sites on the GRCh37 build. f Presence of the deletion and strong (red) and modest (orange) predicted SPI1 binding sites along with sequence conservation in the mouse genome.

Article Snippet: Briefly, the SPI1 expression plasmid containing the human SPI1 transcript variant 1 driven by a CMV promoter was obtained from Origene (RC217488).

Techniques: Binding Assay, Sequencing

Journal: Nature Communications

Article Title: A common 19 bp APOE enhancer deletion is protective against Alzheimer’s disease in African Americans

doi: 10.1038/s41467-026-68808-3

Figure Lengend Snippet: a Schematic of the luciferase experimental design and constructs. The APOE 3′UTR ( APOE 3′UTR only) plus ~400 bp of downstream DNA containing the 19 bp deletion region and SPI1 binding site were cloned into a psiCheck2.2 dual luciferase reporter construct. b Renilla:Firefly luciferase expression data in HMC3 cells after delivery of APOE SPI1 WT sequence ( p = 0.0016 relative to the APOE 3′UTR only) or delivery of the 19 bp deletion [ p = 0.8252; one-way ANOVA, n = 12 samples/group (3 biological replicates, 4 technical replicates), ± SD]. c –e HMC3 gene expression following SPI1 overexpression. c Effect of SPI1 overexpression on c APOE expression ( p = 0.3831, F = 1.789, unpaired two-tailed t-test, n = 12 control and 12 SPI1 biological replicates derived from the average of 4 technical replicates/sample, ± SEM), d APOC1 expression ( p = <0.0001, F = 2.987, unpaired two-tailed t-test, n = 11 control and 12 SPI1 biological replicates derived from the average of 4 technical replicates/sample, ± SEM), and e lncRNA ENSG00000280087 expression ( p = 0.0170, F = 5.414, unpaired two-tailed t-test, n = 12 control and 10 SPI1 biological replicates derived from the average of 4 technical replicates/sample, ± SEM). f – h HMC3 gene expression following Aβ 1:42 treatment. f Effect of Aβ 1:42 treatment on APOE expression ( p = 0.2098, F = 1.243, unpaired two-tailed t-test, n = 12 control and 12 Aβ biological replicates derived from the average of 4 technical replicates/sample, ± SEM), g APOC1 expression ( p = 0.0015, F = 4.657, unpaired two-tailed t-test, n = 11 control and 12 Aβ biological replicates derived from the average of 4 technical replicates/sample, ± SEM) and h, lncRNA ENSG00000280087 expression ( p = 0.0255, F = 2.502, unpaired two-tailed t-test, n = 12 control and 12 Aβ biological replicates derived from the average of 4 technical replicates/sample, ± SEM) in HMC3 cells.

Article Snippet: Briefly, the SPI1 expression plasmid containing the human SPI1 transcript variant 1 driven by a CMV promoter was obtained from Origene (RC217488).

Techniques: Luciferase, Construct, Binding Assay, Clone Assay, Expressing, Sequencing, Gene Expression, Over Expression, Two Tailed Test, Control, Derivative Assay