Journal: Journal of Translational Medicine

Article Title: Integration of single-cell and bulk RNA sequencing to identify a distinct tumor stem cells and construct a novel prognostic signature for evaluating prognosis and immunotherapy in LUAD

doi: 10.1186/s12967-025-06243-6

Figure Lengend Snippet: TAF10 plays oncogenic role in LUAD. A mRNA expression levels of the corresponding gene in human normal bronchial epithelial cells (16HBE) and LUAD cell lines. B TAF10 mRNA expression levels in various tumors and matched normal tissues from the TCGA and GTEx databases, analyzed using SangerBox platform. C The stemness features (RNA expression-based stemness scores) analyses of TAF10 across different types of tumors in the TCGA database, analyzed by SangerBox platform. (D-E) Disease-free survival (D) and overall survival (E) analyses of TAF10 in LUAD samples from the TCGA database, performed using the GEPIA2 platform. (F) Protein expression levels of TAF10 in 16HBE and LUAD cell lines. G Representative IHC analysis of TAF10 expression in paired adjacent and tumorous tissues from LUAD patients (n = 5 pairs, 10 tissues in total). Black scale bar: 50 μm; red scale bar: 20 μm. H TAF10 knockdown in LUAD cells was confirmed by Western blot analysis. I LUAD cell lines were stably transfected with either shCtl or shTAF10 for 24, 48, and 72 h, and cell viability was measured using a CCK-8 assay. (J) The effect of TAF10 knockdown on colony formation in LUAD cells was assessed using a colony formation assay. (K) Representative micrographs and quantification of tumor sphere formation by TAF10 - silenced cells (shTAF10) or vector control cells (shCtl). Scale bar, 100 μm. L – N GSEA plot of KEGG (L) , GOBP (M) , and Hallmark pathways (N) , grouped by TAF10 expression into TAF10-high and TAF10-low subgroups. NES represents the normalized enrichment score, and FDR represents the adjusted p-value

Article Snippet: Antibodies for TAF10 (Novus Cat# NBP1-80,706, RRID: AB_11006462) were purchased from NOVUS Biologicals, and GAPDH antibody (Sigma-Aldrich Cat# SAB5600208, RRID: AB_2920926) was purchased from Sigma as a loading control.

Techniques: Expressing, RNA Expression, Knockdown, Western Blot, Stable Transfection, Transfection, CCK-8 Assay, Colony Assay, Plasmid Preparation, Control

Journal: eLife

Article Title: TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells

doi: 10.7554/eLife.12534

Figure Lengend Snippet: ( A ) Immunoblot analysis from nuclear extracts was used to determine protein levels of TFIID subunits TBP, TAF1, TAF2, TAF4, TAF6, TAF10, TAF12 expressed in proliferating myoblasts (MB) and differentiated myotubes (MT). Myoblast-specific expression of Cyclin D1 and myotube-specific expression of muscle markers Myogenin, MHC and Actinin 3 are used as markers of C2C12 differentiation. Ponceau staining of proteins on the immunoblot membrane was used as a loading control. Representative experiment is show. ( B ) Immunoprecipitation of endogenous TBP from C2C12 nuclear extract results in co-immunoprecipitation of TAF4 and TAF6 subunits of TFIID in both myoblasts (MB) and myotubes (MT). ( C ) 10–55% glycerol gradient size fractionation assay monitors co-fractionation of TFIID subunits TBP, TAF4 and TAF6 in high molecular weight fractions with a signal peaking in fractions corresponding to 0.6–1 MDa in both myoblasts (lower panel) and myotubes (upper panel). DOI: http://dx.doi.org/10.7554/eLife.12534.007

Article Snippet: Antibodies used for immunoblot probing were as follows: anti-TBP (3TF1-3G3, mouse monoclonal) , anti-TAF1 (sc-17134, Santa Cruz), anti-TAF2 (3038, rabbit polyclonal) , anti-TAF4 (32TA-2B9, mouse monoclonal) , anti-TAF6 (25TA-2G7, mouse monoclonal) , anti-TAF10 (6TA-2B11, mouse monoclonal) , anti-TAF12 (22TA-2A1, mouse monoclonal) , anti-TBP2 (2TBP-2B12, mouse monoclonal) , anti-Actinin 3 (EP2531Y, Origene, Rockville, MD, USA), anti-Cyclin D1 (EP272Y, EMD Millipore), anti-Myogenin (clone F5D, Developmental Studies Hybridoma Bank), anti-Tubulin (clone DM1A, Sigma), anti-Actin (sc-8432, Santa Cruz), anti-Myosin Heavy Chain (MHC, clone MF20, Developmental Studies Hybridoma Bank).

Techniques: Western Blot, Expressing, Staining, Immunoprecipitation, Fractionation, Molecular Weight

Journal: eLife

Article Title: TBP/TFIID-dependent activation of MyoD target genes in skeletal muscle cells

doi: 10.7554/eLife.12534

Figure Lengend Snippet: Squences of the primers used in this study. DOI: http://dx.doi.org/10.7554/eLife.12534.010

Article Snippet: Antibodies used for immunoblot probing were as follows: anti-TBP (3TF1-3G3, mouse monoclonal) , anti-TAF1 (sc-17134, Santa Cruz), anti-TAF2 (3038, rabbit polyclonal) , anti-TAF4 (32TA-2B9, mouse monoclonal) , anti-TAF6 (25TA-2G7, mouse monoclonal) , anti-TAF10 (6TA-2B11, mouse monoclonal) , anti-TAF12 (22TA-2A1, mouse monoclonal) , anti-TBP2 (2TBP-2B12, mouse monoclonal) , anti-Actinin 3 (EP2531Y, Origene, Rockville, MD, USA), anti-Cyclin D1 (EP272Y, EMD Millipore), anti-Myogenin (clone F5D, Developmental Studies Hybridoma Bank), anti-Tubulin (clone DM1A, Sigma), anti-Actin (sc-8432, Santa Cruz), anti-Myosin Heavy Chain (MHC, clone MF20, Developmental Studies Hybridoma Bank).

Techniques:

Journal: Breast Cancer Research : BCR

Article Title: RHAMM regulates MMTV-PyMT-induced lung metastasis by connecting STING-dependent DNA damage sensing to interferon/STAT1 pro-apoptosis signaling

doi: 10.1186/s13058-023-01652-1

Figure Lengend Snippet: Rhamm -loss in MMTV-PyMT transgenic mice increases lung metastasis without affecting primary mammary tumor initiation, incidence or size. A Comparison of RHAMM mRNA expression in breast cancer subtypes (Breast Invasive Carcinoma, TCGA, PanCancer Atlas). RHAMM expression is significantly higher in basal and luminal B breast cancer subtypes than in luminal A comparators. B Rhamm- loss detected by the Mouse Diversity Genotyping Array (MDGA) genotyping was confirmed by ddPCR, which is the standard ultrasensitive method for verification of genotyping array-based CNV detection. Two additional ddPCR assays confirm another CNV deletion overlapping Ilk and Taf10 genes that is detected by MDGA CNV genotyping, confirming accuracy of the MDGA and consistency of the two detection methods. WT = Wildtype; Rh −/− = Rhamm −/− . C Western blot assays were performed using primary tumor lysates and RHAMM antibodies to the N-terminal sequence as described in Methods. Full-length RHAMM is expressed in Wildtype tumors (arrow) and is not detected in Rhamm −/− tumors. D Histology sections of primary tumors from 16-week-old mice. Tissue was paraffin-processed, stained for RHAMM protein and imaged with a Nikon confocal microscope as described in Methods. Results show heterogeneous RHAMM staining in primary tumors and also in the host microenvironment (arrows). The lack of staining in histology sections from Rhamm −/− tissue confirms the specificity of the anti-RHAMM antibody. E Whole mounts of mammary fat pads were prepared as described in Methods and show primary tumor initiation at 5 weeks in both Wildtype and Rhamm −/− mice. Detectable primary tumor masses of Wildtype and Rhamm −/− mice were measured weekly with calipers. Differences between genotypes are not statistically significant. Values are the Mean and S.E.M. n = 15 mice. F The lungs of Wildtype and Rhamm −/− mice were harvested and metastatic nodules identified in hematoxylin/eosin-stained histology sections. 100% of Rhamm −/− mice contain metastatic nodules in lungs in contrast to 58% of Wildtype mice, n = 11 mice/genotype. G Metastatic nodules were quantified from serial histology sections as described in Methods. Rhamm -loss significantly increases the number of metastatic colonies/lung compared to Wildtype. Values are the Mean and S.E.M. n = 15 mice. * p < 0.05

Article Snippet: Ilk / Rrp8, Taf10 genes (Mm00232271_cn), which overlap the same CNV region, were used for confirmation by ddPCR.

Techniques: Transgenic Assay, Comparison, Expressing, Western Blot, Sequencing, Staining, Microscopy