Journal: Frontiers in genetics

Article Title: A novel hypoxia-driven gene signature that can predict the prognosis and drug resistance of gliomas.

doi: 10.3389/fgene.2022.976356

Figure Lengend Snippet: FIGURE 4 Examination of the risk model in the TCGA training cohort. (A) Glioma samples in the TCGA were divided into low-risk and high-risk groups. (B) Kaplan–Meier plot analysis of the overall survival rates of low-risk or high-risk patients with glioma in the TCGA. (C–E) Receiver operating characteristic (ROC) curves showing the diagnostic value of the risk model for the 1-year, 3-year and 5-year survival rates of patients with gliomas in the TCGA. (F) Survival time and status of each glioma patient in the TCGA cohort. (G) Expression levels of MYOD1, MMP9, SHOX2, WT1, HOXC6 and HOXA2 in glioma tissues from patients with high-risk or low-risk scores in the TCGA.

Article Snippet: Antigen retrieval (10× Citrate Buffer, pH 6.0, Sigma-Aldrich, United States) was performed for specimens and peroxidase blocking (Servicebio, Wuhan, China)) was carried out, followed by incubation overnight at 4°C with primary antibodies including hypoxyprobe pimonidazole (combined with Mab; 1:200; Cat no. HP1-100 kit; Hypoxyprobe, Inc., United States), HOXC6 (1:8000; Cat no. PA5-41479, Thermo Fisher Scientific, United States), MMP9 (1:500; Cat No. 10375-2-AP, Proteintech, Wuhan, China), WT1 (1:200; Cat No. A16319, Abconal, Wuhan, China), SHOX2 (1:200; Cat No. ab229851, Abcam, United States), MYOD1 (1:500; Cat No. 18943-1-AP, Proteintech, Wuhan, China) and HOXA2 (1:200; Cat No. ab229960, Abcam, United States).

Techniques: Diagnostic Assay, Expressing

Journal: Frontiers in genetics

Article Title: A novel hypoxia-driven gene signature that can predict the prognosis and drug resistance of gliomas.

doi: 10.3389/fgene.2022.976356

Figure Lengend Snippet: FIGURE 5 Examination of the risk model in the CGGA training cohort. (A) Glioma samples in the CGGA were divided into low-risk or high-risk groups. (B) Kaplan-Meier plot analysis of the overall survival rate in low-risk and in high-risk patients with glioma in the CGGA. (C–E) Receiver operating characteristic (ROC) curves showing the diagnostic value of the risk model for the 1-year, 3-year and 5-year survival rates of patients with gliomas in the CGGA. (F) Survival time and status of each glioma patient in the CGGA cohort. (G) Expression levels of MYOD1, MMP9, SHOX2, WT1, HOXC6 and HOXA2 in glioma tissues from patients with high-risk or low-risk scores in the CGGA.

Article Snippet: Antigen retrieval (10× Citrate Buffer, pH 6.0, Sigma-Aldrich, United States) was performed for specimens and peroxidase blocking (Servicebio, Wuhan, China)) was carried out, followed by incubation overnight at 4°C with primary antibodies including hypoxyprobe pimonidazole (combined with Mab; 1:200; Cat no. HP1-100 kit; Hypoxyprobe, Inc., United States), HOXC6 (1:8000; Cat no. PA5-41479, Thermo Fisher Scientific, United States), MMP9 (1:500; Cat No. 10375-2-AP, Proteintech, Wuhan, China), WT1 (1:200; Cat No. A16319, Abconal, Wuhan, China), SHOX2 (1:200; Cat No. ab229851, Abcam, United States), MYOD1 (1:500; Cat No. 18943-1-AP, Proteintech, Wuhan, China) and HOXA2 (1:200; Cat No. ab229960, Abcam, United States).

Techniques: Diagnostic Assay, Expressing

Journal: Frontiers in genetics

Article Title: A novel hypoxia-driven gene signature that can predict the prognosis and drug resistance of gliomas.

doi: 10.3389/fgene.2022.976356

Figure Lengend Snippet: FIGURE 6 Verification of the expression levels of MYOD1, MMP9, SHOX2, WT1, HOXC6 and HOXA2 in glioma tissues. (A) Expression of hypoxyprobe, HOXC6, MMP9, WT1, SHOX2, MYOD1 and HOXA2 in each glioma tissue (n = 60). (B) Representative IHC stained images of Hypoxyprobe, HOXC6, MMP9, SHOX2 and MYOD1 in primary and/or recurrent glioma tissues (compared to primary glioma tissues, red gene names in recurrent tissues indicate high expression and blue gene names indicate reduced expression). (C) Co-expressed score of Hypoxyprobe, HOXC6, MMP9, WT1, SHOX2, MYOD1 and HOXA2 in gliomas.

Article Snippet: Antigen retrieval (10× Citrate Buffer, pH 6.0, Sigma-Aldrich, United States) was performed for specimens and peroxidase blocking (Servicebio, Wuhan, China)) was carried out, followed by incubation overnight at 4°C with primary antibodies including hypoxyprobe pimonidazole (combined with Mab; 1:200; Cat no. HP1-100 kit; Hypoxyprobe, Inc., United States), HOXC6 (1:8000; Cat no. PA5-41479, Thermo Fisher Scientific, United States), MMP9 (1:500; Cat No. 10375-2-AP, Proteintech, Wuhan, China), WT1 (1:200; Cat No. A16319, Abconal, Wuhan, China), SHOX2 (1:200; Cat No. ab229851, Abcam, United States), MYOD1 (1:500; Cat No. 18943-1-AP, Proteintech, Wuhan, China) and HOXA2 (1:200; Cat No. ab229960, Abcam, United States).

Techniques: Expressing, Staining

Journal: The Journal of Biological Chemistry

Article Title: TFPI2 suppresses the interaction of TGF-β2 pathway regulators to promote endothelial–mesenchymal transition in diabetic nephropathy

doi: 10.1016/j.jbc.2022.101725

Figure Lengend Snippet: Knockdown of TFPI2 attenuates renal fibrosis and EndMT. A and B, immunostaining for TFPI2 and Masson staining for fibrosis in renal cortex using consecutive tissues. C and H, the expression of VE-cadherin, α-SMA, desmin, and FSP-1 in renal cortex was detected by Western blot. Semiquantitative analysis of ( D and I ) VE-cadherin, ( E and J ) α-SMA, ( F and K ) desmin, and ( G and L ) FSP-1. Data are shown as the mean ± SD (n = 8). ∗∗ p < 0.01, ∗∗∗ p < 0.001. EndMT, endothelial–mesenchymal transition; TFP12, tissue factor pathway inhibitor 2.

Article Snippet: The primary antibodies were as following: anti-TFPI2 (#A03697-1; Boster, Wuhan, China), anti-SMAD4 (#A19116; ABclonal), anti-SMURF2 (#DF7683; Affinity Biosciences, Jiangsu, China), anti-pro/cleaved caspase 3 (#A19654; ABclonal), anti-pro/cleaved caspase 7 (#12827; Cell Signaling Technology), anti-VE-cadherin (#AF6265, Affinity), anti- α-SMA (#ab7817; Abcam), anti-desmin (#A3736, ABclonal), anti-FSP-1 (#A1631, ABclonal), anti-SMAD7 (#AF5147, Affinity), anti-TGFBR1 (#AF5347, Affinity), anti-TGFBR2 (#AF5449, Affinity), anti-SMAD2 (#AF6449, Affinity), anti-p-SMAD2 (#AF3449, Affinity), anti-SMAD3 (#AF6362, Affinity), anti-p-SMAD3 (#AF8315, Affinity), anti-ubiquitin (#A19686, ABclonal) and anti-β-actin (#60008-1-Ig; Proteintech Group, Rosemont, IL, USA). β-actin served as an internal reference gene.

Techniques: Immunostaining, Staining, Expressing, Western Blot

Journal: The Journal of Biological Chemistry

Article Title: TFPI2 suppresses the interaction of TGF-β2 pathway regulators to promote endothelial–mesenchymal transition in diabetic nephropathy

doi: 10.1016/j.jbc.2022.101725

Figure Lengend Snippet: TFPI2 promotes TGF-β2-induced EndMT in vitro . TGF-β2 is considered as a potent inducer of EndMT. Human renal glomerular endothelial cells (hRGECs) were treated with 5 ng/ml TGF-β2 for 48 h to induce EndMT. A, Western blotting analysis revealed TGF-β2-induced TFPI2 expression as well as adenovirus-mediated TFPI2 knockdown (TFPI2 shRNA) and TFPI2 overexpression (TFPI2 OE) in vitro . B, immunofluorescent staining for α-SMA in hRGECs. C, Western blotting and semiquantitative analysis of ( D ) VE-cadherin, ( E ) α-SMA, ( F ) desmin, and ( G ) FSP-1 expression. Data are shown as the mean ± SD (n = 3). ∗ p < 0.5, ∗∗ p < 0.01, ∗∗∗ p < 0.001. EndMT, endothelial–mesenchymal transition; hRGEC, human renal glomerular endothelial cell; TFP12, tissue factor pathway inhibitor 2.

Article Snippet: The primary antibodies were as following: anti-TFPI2 (#A03697-1; Boster, Wuhan, China), anti-SMAD4 (#A19116; ABclonal), anti-SMURF2 (#DF7683; Affinity Biosciences, Jiangsu, China), anti-pro/cleaved caspase 3 (#A19654; ABclonal), anti-pro/cleaved caspase 7 (#12827; Cell Signaling Technology), anti-VE-cadherin (#AF6265, Affinity), anti- α-SMA (#ab7817; Abcam), anti-desmin (#A3736, ABclonal), anti-FSP-1 (#A1631, ABclonal), anti-SMAD7 (#AF5147, Affinity), anti-TGFBR1 (#AF5347, Affinity), anti-TGFBR2 (#AF5449, Affinity), anti-SMAD2 (#AF6449, Affinity), anti-p-SMAD2 (#AF3449, Affinity), anti-SMAD3 (#AF6362, Affinity), anti-p-SMAD3 (#AF8315, Affinity), anti-ubiquitin (#A19686, ABclonal) and anti-β-actin (#60008-1-Ig; Proteintech Group, Rosemont, IL, USA). β-actin served as an internal reference gene.

Techniques: In Vitro, Western Blot, Expressing, shRNA, Over Expression, Staining

Journal: Journal of Animal Science and Biotechnology

Article Title: Proteo-transcriptomic profiles reveal key regulatory pathways and functions of LDHA in the ovulation of domestic chickens ( Gallus gallus )

doi: 10.1186/s40104-024-01019-2

Figure Lengend Snippet: Proteomic profiling of CL_F1 vs. IL_F1. A Comparison of peptides and proteins in data-independent acquisition strategies. B Volcano plot of differentially abundant proteins (DAPs) in the CL_F1 vs. IL_F1 group. DAPs with P < 0.05 and quantitative fold change > 1.5 are marked in red; DAPs with P < 0.05 and quantitative ratio < 0.67 marked in blue. C Heatmap of DAPs between CL_F1 vs. IL_F1. D , E Protein expression levels of PTDSS1, FMOD, LDHA, and ALDOB in CL_F1 and IL_F1 groups. * P < 0.05, ** P < 0.01

Article Snippet: The membranes were then further incubated with a secondary antibody (Solarbio, Beijing, China) conjugated to horseradish peroxidase at room temperature (25 ± 2 °C) for 1 h. The primary antibodies of α-Tubulin (Absin, abs131993), ALDOB (Abclonal, A3728), LDHA (Abclonal, A16394), FMOD (Abclonal, A6375), and PTDSS1 (Abclonal, A13065) were diluted to a ratio of 1:1,000 according to the manufacturer's instructions.

Techniques: Comparison, Expressing