Journal: bioRxiv

Article Title: Lysosome-Dependent Sphingolipid Regulation as a potential therapeutic Target for Cohen Syndrome

doi: 10.1101/2025.09.04.674037

Figure Lengend Snippet: A) Abundance of indicated lipid classes in VPS13B KO cells (clone 2D9) treated with the indicated compounds (10 µM, 24 hours), relative to untreated cells. DLZ (dilazep); AZL (azelastine); RLX (raloxifene); TFPZ (trifluoperazine); CBZP (cyclobenzaprine); SER (sertraline). (*q<0.05, **q<0.01. multiple paired t-tests with Benjamini-Hochberg correction; N=4) B) Volcano plot illustrating relatives changes in individual lipid species in compound treated VPS13B KO cells (clone 2D9) ( upper panel , AZL; lower panel , TFPZ) relative to WT. Cells at 10 µM for 24 hours. sphingomyelin (green); ceramides (magenta) are highlighted. (AZL (N=12); TFPZ (N=6). C) Relative amounts of SM 36:1 (calculated as a fraction of total SM) in VPS12B KO cells treated with the indicated compounds for 6 or 24 hours (10 µM). (*p<0.05, **p<0.01. one-way ANOVA with Šidák correction; N=4) D) Relative amounts of total SM, total CER, SM 36:1 (calculated as a fraction of total SM) and CER 36:1 (calculated as a fraction of total CER) in light (LM) or Heavy (HM) membranes prepared from VPS12B KO cells treated (TFPZ) with not (UT) with TFPZ 10 µM for 24 hours. (*p<0.05, **p<0.01. paired t-test, 2-tails; N=2). E) Relative amounts of SM 36:1 and CER 36:1 (calculated as a fraction of the respective lipid class) in cells treated (AZL) or not (UT) with 10µM AZL for 6 hours in combination with 20 µM fumonisin B1 (FB1) or 5 µM HPA-12. (*p<0.05, **p<0.01. paired t-test, 2-tails; N=3).

Article Snippet: Compounds used in further follow-up experiments were purchased separately: azelastine hydrochloride (MedChemExpress, cat. HY-B0462 for HeLa cells experiments; Sigma-Aldrich, cat. A7611 for brain organoid experiments); brefeldin A (Merck, cat. B6542) cyclobenzaprine hydrochloride (Merck, cat. T8516); dilazep dihydrochloride (MedChemExpress, cat. HY-100957); fumonisin B1 ((Merck, cat. F1147); HPA-12 (MedChemExpress, cat. HY-132182); lovastatin (MedChemExpress, cat. HY-N0504); nocodazole (Apex Bio, cat. A8487); raloxifene (MedChemExpress, cat. HY-13738 for HeLa cells experiments; Sigma-Aldrich, cat. PHR1852 for brain organoid experiments); sertraline hydrochloride (Merck, cat. S6319); trifluoperazine dihydrochloride (Merck, cat. C4542); U18666A (Merck, cat. U3633).

Techniques:

Journal: bioRxiv

Article Title: Lysosome-Dependent Sphingolipid Regulation as a potential therapeutic Target for Cohen Syndrome

doi: 10.1101/2025.09.04.674037

Figure Lengend Snippet: Relative amounts of total SM and total CER in cells treated (AZL) or not (UT) with 10µM AZL for 6 hours in combination with 20 µM fumonisin B1 (FB1) or 5 µM HPA-12. (*p<0.05, **p<0.01. one-way ANOVA with Šidák correction (N=3).

Article Snippet: Compounds used in further follow-up experiments were purchased separately: azelastine hydrochloride (MedChemExpress, cat. HY-B0462 for HeLa cells experiments; Sigma-Aldrich, cat. A7611 for brain organoid experiments); brefeldin A (Merck, cat. B6542) cyclobenzaprine hydrochloride (Merck, cat. T8516); dilazep dihydrochloride (MedChemExpress, cat. HY-100957); fumonisin B1 ((Merck, cat. F1147); HPA-12 (MedChemExpress, cat. HY-132182); lovastatin (MedChemExpress, cat. HY-N0504); nocodazole (Apex Bio, cat. A8487); raloxifene (MedChemExpress, cat. HY-13738 for HeLa cells experiments; Sigma-Aldrich, cat. PHR1852 for brain organoid experiments); sertraline hydrochloride (Merck, cat. S6319); trifluoperazine dihydrochloride (Merck, cat. C4542); U18666A (Merck, cat. U3633).

Techniques:

Journal: BMC Complementary Medicine and Therapies

Article Title: Synergistic overcoming of cisplatin resistance in ovarian cancer by combined Astragalus Membranaceus and cisplatin treatment: network pharmacology and experimental validation

doi: 10.1186/s12906-025-05066-8

Figure Lengend Snippet: Impact of potential therapeutic targets on the prognosis of OC patients. A - I Kaplan-Meier survival curves for the nine candidate targets (IL1B, IL1A, PLAU, SERPINE1, CAV1, ITGA2, NT5E, AXL, PTGES) significantly associated with the prognosis of OC patients, showing PFS (left) and OS (right). J Correlation analysis between these targets and immune infiltration in OC, with color indicating the strength of correlation: blue for negative correlation, red for positive correlation

Article Snippet: Membranes were blocked with 5% non-fat milk in TBST (Tris-buffered saline with 0.1% Tween 20) for 1 h at room temperature, followed by overnight incubation at 4 °C with primary antibodies: IL-1α (30 kDa; Wuhan Sanying Biotechnology, China; 16765-1-AP,), IL-1β (30 kDa; Abcam, USA; Ab254360 ), SERPINE1 (45 kDa; Wuhan Sanying Biotechnology, China; 13801-1-AP), ITGA2 (150 kDa; ABclonal, China; A19068), and AXL (140 kDa; Wuhan Sanying Biotechnology, China; 13196-1-AP).

Techniques: Biomarker Discovery

Journal: BMC Complementary Medicine and Therapies

Article Title: Synergistic overcoming of cisplatin resistance in ovarian cancer by combined Astragalus Membranaceus and cisplatin treatment: network pharmacology and experimental validation

doi: 10.1186/s12906-025-05066-8

Figure Lengend Snippet: Molecular docking of AS’ active compounds with potential DDP resistance targets. A - J show the binding modes and affinities of AS’ active compounds (quercetin, FA, and kaempferol) with potential DDP resistance targets (IL1B, IL1A, PLAU, SERPINE1, CAV1, ITGA2, NT5E, AXL, and PTGES). The left panel illustrates the overall view of the binding, while the right panel provides detailed binding interactions. The receptor and ligand used in molecular docking and the binding energy (ΔG; kJ/mol) are indicated in the top left corner. Active compounds (green) and amino acid residues of the potential targets (blue) are represented as stick structures, with hydrogen bonds depicted as yellow dashed lines. Bond energies are annotated in white numbers beside the interactions

Article Snippet: Membranes were blocked with 5% non-fat milk in TBST (Tris-buffered saline with 0.1% Tween 20) for 1 h at room temperature, followed by overnight incubation at 4 °C with primary antibodies: IL-1α (30 kDa; Wuhan Sanying Biotechnology, China; 16765-1-AP,), IL-1β (30 kDa; Abcam, USA; Ab254360 ), SERPINE1 (45 kDa; Wuhan Sanying Biotechnology, China; 13801-1-AP), ITGA2 (150 kDa; ABclonal, China; A19068), and AXL (140 kDa; Wuhan Sanying Biotechnology, China; 13196-1-AP).

Techniques: Binding Assay

Journal: BMC Complementary Medicine and Therapies

Article Title: Synergistic overcoming of cisplatin resistance in ovarian cancer by combined Astragalus Membranaceus and cisplatin treatment: network pharmacology and experimental validation

doi: 10.1186/s12906-025-05066-8

Figure Lengend Snippet: Western blot analysis of key proteins in DDP-resistant cell lines under different treatments. Western blot analysis of SKOV3-DDP and A2780-DDP cell lines treated with AS, DDP, or a combination of both ( A ), showing the expression levels of ( B ) ITGA2, ( C ) SERPINE1, ( D ) IL1A, ( E ) AXL, and ( F ) IL1B. Protein expression levels were quantified using GAPDH as a loading control and normalized to the untreated group

Article Snippet: Membranes were blocked with 5% non-fat milk in TBST (Tris-buffered saline with 0.1% Tween 20) for 1 h at room temperature, followed by overnight incubation at 4 °C with primary antibodies: IL-1α (30 kDa; Wuhan Sanying Biotechnology, China; 16765-1-AP,), IL-1β (30 kDa; Abcam, USA; Ab254360 ), SERPINE1 (45 kDa; Wuhan Sanying Biotechnology, China; 13801-1-AP), ITGA2 (150 kDa; ABclonal, China; A19068), and AXL (140 kDa; Wuhan Sanying Biotechnology, China; 13196-1-AP).

Techniques: Western Blot, Expressing, Control

Journal: Oncotarget

Article Title: CD49b inhibits osteogenic differentiation and plays an important role in osteosarcoma progression

doi: 10.18632/oncotarget.21254

Figure Lengend Snippet: (A) Western blot assay was performed to detect the expression of CD49b protein, (B) Densitometric assays were performed and data were presented as mean ± standard deviation of three independent experiments. *** means they were significantly different when compared to MSC at day 0 with p < 0.001.

Article Snippet: Lenti cDNA clone of human CD49b (RC212617L1) and Lenti-Vpak lentiviral Packaging Kit (TR30022) were purchased from Origene (Rockville, MD).

Techniques: Western Blot, Expressing, Standard Deviation

Journal: Oncotarget

Article Title: CD49b inhibits osteogenic differentiation and plays an important role in osteosarcoma progression

doi: 10.18632/oncotarget.21254

Figure Lengend Snippet: (A) Stable knock down of CD49b in osteosarcoma cell lines HOS and MG63. (B) Down regulation of CD49b in HOS and MG63 inhibits their migration and invasion capacity in vitro . Data are presented as the mean ± standard deviation of 3 independent experiments. * and ** means they were significantly different when compared to the control group with p < 0.05 and p < 0.01, respectively.

Article Snippet: Lenti cDNA clone of human CD49b (RC212617L1) and Lenti-Vpak lentiviral Packaging Kit (TR30022) were purchased from Origene (Rockville, MD).

Techniques: Knockdown, Migration, In Vitro, Standard Deviation, Control

Journal: Oncotarget

Article Title: CD49b inhibits osteogenic differentiation and plays an important role in osteosarcoma progression

doi: 10.18632/oncotarget.21254

Figure Lengend Snippet: (a) H&E staining is shown the osteosarcoma cells in osteosarcoma TMA (Magnification, ×100). (b) Negative staining of CD49b in osteosarcoma TMA (Magnification, ×100). (c) and (d) Positive staining of CD49b in osteosarcoma TMA (Magnification, ×100 and ×400, respectively). Brown staining in the membrane of osteosarcoma cells indicates CD49b expression.

Article Snippet: Lenti cDNA clone of human CD49b (RC212617L1) and Lenti-Vpak lentiviral Packaging Kit (TR30022) were purchased from Origene (Rockville, MD).

Techniques: Staining, Negative Staining, Membrane, Expressing

Journal: Oncotarget

Article Title: CD49b inhibits osteogenic differentiation and plays an important role in osteosarcoma progression

doi: 10.18632/oncotarget.21254

Figure Lengend Snippet: The relationship between CD49b expression and clinicopathological variables of osteosarcoma

Article Snippet: Lenti cDNA clone of human CD49b (RC212617L1) and Lenti-Vpak lentiviral Packaging Kit (TR30022) were purchased from Origene (Rockville, MD).

Techniques: Expressing

Journal: Oncotarget

Article Title: CD49b inhibits osteogenic differentiation and plays an important role in osteosarcoma progression

doi: 10.18632/oncotarget.21254

Figure Lengend Snippet: Kaplan-Meier curves for overall survival in 57 osteosarcoma patients with or without positive CD49b staining, showing that patients with CD49b–positive tumors had significantly worse overall survival (p=0.026) than patients with CD49b–negative tumors

Article Snippet: Lenti cDNA clone of human CD49b (RC212617L1) and Lenti-Vpak lentiviral Packaging Kit (TR30022) were purchased from Origene (Rockville, MD).

Techniques: Staining

Journal: Thyroid Research

Article Title: A preliminary study developing a scoring model incorporating fibrinogen-like protein 2 for predicting glucocorticoid resistance in thyroid eye disease

doi: 10.1186/s13044-026-00293-8

Figure Lengend Snippet: Proteomics analysis comparing responders with non-responders in TED. ( A ) Volcano plot showing differential protein abundance between ivGC responders and non-responders. The y-axis represents -log10 unadjusted p-values. Multiple testing correction was performed using the Benjamini-Hochberg method; however, no proteins remained significant after FDR correction (q < 0.05). Therefore, unadjusted P values are shown for hypothesis-generating visualization. Candidate biomarkers are highlighted with circles. ( B ) PPI network analysis centered on TGF-β. Interactions were analyzed using the STRING database, illustrating the key regulatory nodes and connections among the DAPs. The network showed significant enrichment of protein-protein interactions (PPI enrichment p = 4.48 × 10 − 7 ). ARPC5, actin-related protein 2/3 complex subunit 5; CAH1, carbonic anhydrase 1; CAH2, carbonic anhydrase 2; CMGA, chromogranin A; DAPs, differentially abundant proteins; DIA, data-independent acquisition; FGL2, fibrinogen-like protein 2; PGN, progranulin; HPA, heparanase; INHBE, inhibin beta E chain; MBL2, mannose-binding lectin 2; MGAT1, alpha-1,3-mannosyl-glycoprotein; PPI, protein–protein interaction; PRDX6, peroxiredoxin 6; TED, thyroid eye disease; TGF-β, transforming growth factor beta; UROM, uromodulin; VTN, vitronectin

Article Snippet: Serum fibrinogen-like protein 2 (FGL2), transforming growth factor beta (TGF-β), and heparanase were measured using commercially available ELISA kits, as follows: FGL2 (LEGEND MAXTM Human sFGL2 ELISA kit, Cat. No. 381558, BioLegend, San Diego, California, USA; intra-assay coefficient of variation [CoV] 5.9%–8.4%, inter-assay CoV 8.7%–10.8%, standard range 0.25–16 ng/mL), TGF-β (Human TGF-β1 Sandwich ELISA kit, Cat. No. KE00002, Proteintech; intra-assay CoV 4.5%–4.9%, inter-assay CoV 2.0%–9.4%, standard range 15.6–1000 pg/mL), and heparanase (Human Heparanase ELISA kit, Cat. No. CSB-E09899h, CUSABIO; intra-assay CoV < 8%, inter-assay CoV < 10%, standard range 0.156–10 ng/mL).

Techniques: Quantitative Proteomics, Protein-Protein interactions, Data-independent acquisition, Binding Assay

Journal: Thyroid Research

Article Title: A preliminary study developing a scoring model incorporating fibrinogen-like protein 2 for predicting glucocorticoid resistance in thyroid eye disease

doi: 10.1186/s13044-026-00293-8

Figure Lengend Snippet: Comparison of protein abundance among the four groups in the DIA proteomics analysis of the 12 candidate biomarker proteins based on the criteria described in the Methods. TGF-β, FGL2, and heparanase, which also showed significant differences between responders and non-responders with TED in the four-group comparison, were selected as final candidate biomarkers. Statistical significance was assessed by the Kruskal–Wallis test. * P < 0.05; ** P < 0.01. DIA, data-independent acquisition; FGL2, fibrinogen-like protein 2; TED, thyroid eye disease; TGF-β, transforming growth factor beta

Article Snippet: Serum fibrinogen-like protein 2 (FGL2), transforming growth factor beta (TGF-β), and heparanase were measured using commercially available ELISA kits, as follows: FGL2 (LEGEND MAXTM Human sFGL2 ELISA kit, Cat. No. 381558, BioLegend, San Diego, California, USA; intra-assay coefficient of variation [CoV] 5.9%–8.4%, inter-assay CoV 8.7%–10.8%, standard range 0.25–16 ng/mL), TGF-β (Human TGF-β1 Sandwich ELISA kit, Cat. No. KE00002, Proteintech; intra-assay CoV 4.5%–4.9%, inter-assay CoV 2.0%–9.4%, standard range 15.6–1000 pg/mL), and heparanase (Human Heparanase ELISA kit, Cat. No. CSB-E09899h, CUSABIO; intra-assay CoV < 8%, inter-assay CoV < 10%, standard range 0.156–10 ng/mL).

Techniques: Comparison, Quantitative Proteomics, Biomarker Discovery, Data-independent acquisition