Journal: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

Article Title: Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method

doi: 10.1093/dnares/dsn010

Figure Lengend Snippet: Long-sized full-length cDNA clones with >7 kb insert

Article Snippet: Probes and primers designed by TaqMan Gene Expression Assays (Applied Biosystems) were used for the assays of ACTB (Hs99999903_m1), CFL1 (Hs00830568_g1), FLNA (Hs99999905_m1), FLNB (Hs00181698_m1), GAPDH (Hs99999905_m1), GUK1 (Hs00176133_m1), MYH9 (Hs00159522_m1), and RAI14 (Hs00210238_m1).

Techniques: Clone Assay, Binding Assay, Control, Translocation Assay, Membrane

Journal: Journal of Lipid Research

Article Title: Sphinganine as a potentially relevant metabolite in pulmonary involvement of primary Sjögren’s syndrome

doi: 10.1016/j.jlr.2025.100961

Figure Lengend Snippet: Identification of Myh9 as a direct binding target of Sa and evaluation of complex stability. A: Schematic representation of the chemoproteomic workflow using a biotin-labeled Sa probe in NIH3T3 cells. B: Coomassie blue-stained SDS-PAGE gel showing differential protein bands between treatment groups. The band marked by a dashed box was excised for LC-MS/MS analysis. C: Molecular docking model displaying the binding conformation of Sa with Myh9 and key interacting residues. D: Two-dimensional interaction diagram illustrating hydrogen bonds and hydrophobic interactions between Sa and Myh9. E–G: Molecular dynamics simulation of the Sa–Myh9 complex: (E) RMSD, (F) RMSF of chain D, and (G) Rg plots, reflecting structural stability, residue flexibility, and compactness over 100 ns. H–K: CETSA evaluating Myh9 thermal stability in A253 (H and J) and NIH3T3 (I and K) cells treated with Sa (10 μg/ml). Melting curves derived from CETSA illustrate increased thermal stability of Myh9. Data are presented as mean ± SD. P < 0.05, P < 0.01 versus control group. CETSA, cellular thermal shift assay; RMSD, root mean square deviation; RMSF, root mean square fluctuation; Rg, radius of gyration.

Article Snippet: For the Myh9 inhibition assay, cells were pretreated with 2 μM Blebbistatin (TargetMol, Shanghai, China) for 4 h in serum-free medium.

Techniques: Binding Assay, Labeling, Staining, SDS Page, Liquid Chromatography with Mass Spectroscopy, Residue, Derivative Assay, Control, Thermal Shift Assay

Journal: Journal of Lipid Research

Article Title: Sphinganine as a potentially relevant metabolite in pulmonary involvement of primary Sjögren’s syndrome

doi: 10.1016/j.jlr.2025.100961

Figure Lengend Snippet: Functional role of Myh9 in Sa-induced epithelial injury and fibroblast activation. A: Relative mRNA expression of Myh9 in submandibular gland tissues as measured by qRT-PCR. B: Immunohistochemical staining analysis and (C) quantitative analysis of the expression of Myh9 in lung tissues. D and E: Western blot analysis (D) and corresponding quantification (E) of Myh9 protein expression in A253 cells treated with increasing concentrations of Sa. F and G: Western blot (F) and densitometric analysis (G) of Myh9 expression in NIH3T3 cells treated with Sa or TGF-β1 (positive control). H and I: Western blot (H) and quantification (I) of AQP5 expression in A253 cells treated with Sa, with or without the Myh9 inhibitor blebbistatin. J and K: Western blot (J) and quantification (K) of fibronectin and α-SMA protein levels in NIH3T3 cells treated with Sa, with or without blebbistatin. Data are presented as mean ± SD. ∗ P < 0.05, ∗∗ P < 0.01, ∗∗∗ P < 0.001, ∗∗∗∗ P < 0.0001; ns, not significant. # P < 0.05, ## P < 0.01 Sa group with 4-PBA treatment. α-SMA, alpha-smooth muscle actin; 4-PBA, 4-phenylbutyric acid; AQP5, aquaporin-5

Article Snippet: For the Myh9 inhibition assay, cells were pretreated with 2 μM Blebbistatin (TargetMol, Shanghai, China) for 4 h in serum-free medium.

Techniques: Functional Assay, Activation Assay, Expressing, Quantitative RT-PCR, Immunohistochemical staining, Staining, Western Blot, Positive Control

Journal: Journal of Lipid Research

Article Title: Sphinganine as a potentially relevant metabolite in pulmonary involvement of primary Sjögren’s syndrome

doi: 10.1016/j.jlr.2025.100961

Figure Lengend Snippet: Molecular mechanism of Sa induces salivary hyposecretion and pulmonary fibrosis in pSS through the ATF6–Myh9 signaling pathway. Sa, sphinganine; pSS, primary Sjögren’s syndrome.

Article Snippet: For the Myh9 inhibition assay, cells were pretreated with 2 μM Blebbistatin (TargetMol, Shanghai, China) for 4 h in serum-free medium.

Techniques:

Journal: Communications Biology

Article Title: Compressive stress triggers fibroblasts spreading over cancer cells to generate carcinoma in situ organization

doi: 10.1038/s42003-024-05883-6

Figure Lengend Snippet: a Western blot showing N-cadherin expression level in Control fibroblasts (Ctrl, transfected with scrambled shRNA) and fibroblast depleted from N-cadherin (shN-cadh). GAPDH is used as a loading control. b Frequency of capsules in which fibroblasts enveloped cancer cells. Capsules contain cancer cells with control or N-cadherin-depleted fibroblasts. t = 0 corresponds to the confluent stage. n ≥ 30 capsules per condition. c . Western blot showing Fibronectin expression level in Control fibroblasts (shCtrl, transfected with scrambled shRNA) and fibroblast depleted from fibronectin (shFN) using five different shRNA probes. GAPDH is used as a loading control. d Frequency of capsules in which fibroblasts enveloped cancer cells. Capsules contain fibroblasts showing different degrees of fibronectin depletion. t = 0 corresponds to the confluent stage. n = 40 capsules. e Confocal images of co-culture at day 5, which corresponds to the early stage, before confluency (two upper rows) and 10 days, which corresponds to the final stage with fully spread fibroblasts (two bottom rows). Both cell types are labeled with phalloidin (F-actin, red), fibroblasts express GFP (green), fibronectin is labeled with antibodies (magenta). Scale bar: 100 μm. f Confocal images of co-culture at the onset of fibroblasts spreading. Fibroblasts expressed GFP (green), cancer cells are unstained, and fibronectin is labeled with antibodies (magenta). Insets, higher magnification of boxed regions. Scale bars: 20 μm.

Article Snippet: HT29 cells and NIH3T3 were infected with MyH9 shRNA lentiviral particles (aYAP, Gift), control shRNA Lentiviral Particles (Santa Cruz Biotechnology, sc-108080), N-cadherin shRNA lentiviral particles (Santa Cruz Biotechnology sc-35999-V) and Fibronectin shRNA lentiviral particles (SHCLNG, MERCK) and shCtrl (SHC002, MERCK).

Techniques: Western Blot, Expressing, Control, Transfection, shRNA, Capsules, Co-Culture Assay, Labeling

Journal: Communications Biology

Article Title: Compressive stress triggers fibroblasts spreading over cancer cells to generate carcinoma in situ organization

doi: 10.1038/s42003-024-05883-6

Figure Lengend Snippet: a Measurement of surface tension using the micropipette aspiration assay. First row: Phase contrast and epifluorescent image showing micropipette aspiration of HT29 cancer cell side; second row: Phase contrast and epifluorescent image showing micropipette aspiration of GFP expressing NIH3T3 fibroblasts side. Scale bar, 50 μm. b Individual (dots) surface tension measurements on cancer cell spheroids (red) and fibroblast spheroids (green) growing without confinement and co-cultures after the onset of fibroblast spreading. N = 3 runs of encapsulation, n = 82 capsules. One-way ANOVA test was performed (*** p < 0.001). Three independent experiments were performed. n = 82 capsules. c Measurement of a spheroid using microplates assay. Scale bars: 25 μm. d Evolution of force as a function of time in a microplate assay. e Individual (dots) surface tension measurements on cancer cell spheroids (red) and fibroblast spheroids (green) growing without confinement. One-way ANOVA test (*** p < 0.001). n = 40 spheroids from three independent experiments. f Western blot showing myosin IIA expression level in control HT29 cancer cells (Ctrl, transfected with scrambled shRNA) and myosin II-depleted cancer cells (shMyosinIIa). GAPDH is used as a loading control. g Individual (dots) surface tension measurements on cancer cell spheroids made of control and myosin IIa-depleted cancer cells growing without confinement. One-way ANOVA test was performed (** p < 0.01). Three independent experiments were performed. n = 59 capsules, from N = 3 experiments. h Frequency of capsules in which fibroblasts enveloped cancer cells. Capsules contain fibroblasts and control or myosin IIa-depleted cancer cells. t = 0 corresponds to the confluent stage. n ≥ 40 capsules per condition.

Article Snippet: HT29 cells and NIH3T3 were infected with MyH9 shRNA lentiviral particles (aYAP, Gift), control shRNA Lentiviral Particles (Santa Cruz Biotechnology, sc-108080), N-cadherin shRNA lentiviral particles (Santa Cruz Biotechnology sc-35999-V) and Fibronectin shRNA lentiviral particles (SHCLNG, MERCK) and shCtrl (SHC002, MERCK).

Techniques: Expressing, Encapsulation, Capsules, Western Blot, Control, Transfection, shRNA

Journal: International Journal of Oncology

Article Title: Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

doi: 10.3892/ijo.2014.2287

Figure Lengend Snippet: The Applied Biosystems assays.

Article Snippet: MYH9 , Myosin; heavy chain 9; non-muscle , Hs01066369_m1 , NM_002473.4 , 23–24 , 1.96.

Techniques:

Journal: International Journal of Oncology

Article Title: Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

doi: 10.3892/ijo.2014.2287

Figure Lengend Snippet: Significantly regulated motility genes: FC ≤-2 or FC ≥2 and FDR ≤0.05.

Article Snippet: MYH9 , Myosin; heavy chain 9; non-muscle , Hs01066369_m1 , NM_002473.4 , 23–24 , 1.96.

Techniques:

Journal: International Journal of Oncology

Article Title: Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

doi: 10.3892/ijo.2014.2287

Figure Lengend Snippet: Microarray data of motility genes selected for RT-qPCR confirmation.

Article Snippet: MYH9 , Myosin; heavy chain 9; non-muscle , Hs01066369_m1 , NM_002473.4 , 23–24 , 1.96.

Techniques: Microarray

Journal: International Journal of Oncology

Article Title: Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

doi: 10.3892/ijo.2014.2287

Figure Lengend Snippet: Relative gene expression changes of six selected motility genes 8 h after carbon ion or X-irradiation. Log 2 (ratio) of the expression of (A) MYH9 , s(B) ROCK1 , (C) NEXN , (D) FN1 , (E) MYH10 and (F) CCDC88A is presented. Significantly altered gene expression compared to CTRL samples ( * P≤0.05) based on one-tailed Mann-Whitney tests. RT-qPCR results confirm the downregulation observed by microarray analysis after radiation which was more pronounced after carbon ion radiation when compared to X-rays.

Article Snippet: MYH9 , Myosin; heavy chain 9; non-muscle , Hs01066369_m1 , NM_002473.4 , 23–24 , 1.96.

Techniques: Gene Expression, Irradiation, Expressing, One-tailed Test, MANN-WHITNEY, Quantitative RT-PCR, Microarray

Journal: International Journal of Oncology

Article Title: Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

doi: 10.3892/ijo.2014.2287

Figure Lengend Snippet: Kaplan-Meier survival analysis of (A) CCDC88A , (B) FN1 , (C) MYH9 , (D) MYH10 , (E) NEXN and (F) ROCK1 gene expression performed on the data set of Taylor et al . Tumor samples were divided into three groups based on whether the gene expression value was high (♦, dark grey); intermediate (▴, light grey); or low (•, black). Differences in survival were found to be significant for CCDC88A , FN1 , NEXN and ROCK1 when log-rank P≤0.05.

Article Snippet: MYH9 , Myosin; heavy chain 9; non-muscle , Hs01066369_m1 , NM_002473.4 , 23–24 , 1.96.

Techniques: Gene Expression

Journal: International Journal of Oncology

Article Title: Carbon ion irradiation of the human prostate cancer cell line PC3: A whole genome microarray study

doi: 10.3892/ijo.2014.2287

Figure Lengend Snippet: Kaplan-Meier survival analysis of (A) CCDC88A , (B) FN1 , (C) MYH9 , (D) MYH10 , (E) NEXN and (F) ROCK1 gene expression performed on the data set of Gulzar et al . Tumor samples were divided into three groups based on whether the gene expression value was high (♦, dark grey); intermediate (▴, light grey); or low (•, black). Differences in survival were found to be significant for FN1 (log-rank P=0.0257).

Article Snippet: MYH9 , Myosin; heavy chain 9; non-muscle , Hs01066369_m1 , NM_002473.4 , 23–24 , 1.96.

Techniques: Gene Expression