Journal: International Journal of Molecular Sciences

Article Title: A Mixture of Cervus elaphus sibiricus and Glycine max (L.) Merrill Inhibits Ovariectomy-Induced Bone Loss Via Regulation of Osteogenic Molecules in a Mouse Model

doi: 10.3390/ijms24054876

Figure Lengend Snippet: Modulatory effects of BPX on bone formation and resorption markers in serum and modulation of BMP pathways in the femur. The levels of bone resorption markers, such as TRAP ( A ) and Ca ( B ), and bone formation markers, such as osteocalcin ( C ) and ALP ( D ), in serum were analyzed by ELISA. The mRNA expression of BMP-2, BSP-1, and OSX were assessed ( E ), and the protein levels of p -p38, p -smad 1/5/8, smad 4, and Runx2 were assessed by western blot ( F , G ) in the femurs of OVX-induced mice. All band intensities were quantified by Image J. The mice were divided into groups according to the treatment: the Sham, OVX, and BPX (OVX + BPX) groups. The data are expressed as the mean ± SD. # p < 0.05, ## p < 0.01 compared with the Sham group; * p < 0.05, ** p < 0.01 compared with the OVX group.

Article Snippet: Serum levels of bone turnover markers, that is, osteocalcin (OC) (E-EL-M0864, Elabscience, Houston, TX, USA), alkaline phosphatase (ALP), and tartrate-resistant acid phosphatase (TRAP) (MK301, Takara, Japan), and the biochemical marker calcium (E-BC-K103-M, Elabscience, Houston, TX, USA) were measured using an enzyme-linked immunosorbent assay (ELISA) kit.

Techniques: Enzyme-linked Immunosorbent Assay, Expressing, Western Blot

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: TCIRG1 expression in different tumors and their cancerous tissues. ( A ) TCIRG1 expression levels in TCGA tumor tissues and TCGA and GTEX normal tissues. ( B ) Comparison of TCIRG1 expression between TCGA tumor data and the corresponding TCGA normal data. ( C ) RNA expression levels of TCIRG1 in tumor and normal tissues in renal clear cell carcinoma (KIRC) samples from the UALCAN database. GEO database series, including TCIRG1 expression levels in GSE66272 ( D ) and GSE53757 ( E ), and GSE15641 ( F – H ) immunohistochemistry staining statistics results for normal kidney tissues and KIRC tissues. Scale bar: 50 μm. (* p < 0.05, ** p < 0.01, *** p < 0.001, ns indicates no statistical significance).

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing, Comparison, RNA Expression, Immunohistochemistry, Staining

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Correlation between the expression of TCIRG1 and tumor prognosis ( A , C , E ). Kaplan–Meier curves demonstrating OS, PFI, and DSS of patients in the high- and low-TCIRG1 expression groups in KIRC samples. Forest plots demonstrate the prognostic HR of TCIRG1 in different cancer subgroups in OS ( B ), PFI ( D ), and DSS ( F ).

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Correlation between high TCIRG1 expression and clinical traits. ( A ) Grade, ( B ) Stage, ( C ) T, ( D ) M, and ( E ) N correlation with TCIRG1 expression. ( F ) Heat map of correlation between clinical traits and TCIRG1 expression. ( G ) ROC curve to predict the diagnostic value of elevated TCIRG1. Nomogram for KIRC samples ( H ) and the calibration curve of the nomogram ( I ) for predicting OS at 1, 3, and 5 years. (* p < 0.05, ** p < 0.01, *** p < 0.001).

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing, Diagnostic Assay

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Analysis of OS using the Cox proportional hazards regression model.

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques:

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Molecular characterization of high- and low-TCIRG1 expression subgroups. ( A , B ) Distribution of the ten most commonly mutated genes in the high-TCIRG1 TCGA-KIRC subgroup. The top bar shows the TMB of each patient, and the right bar shows the different types of mutations. Differences in TCIRG1 expression between ( C ) wild-type and PBRM1 mutant subgroups and ( D ) BAP1 mutant subgroups. ( E ) Correlation analysis of TCIRG1 expression with TMB. ( F ) Relationship between TCIRG1 expression and DNA methylation. ( G ) Relationship between DNA methylation levels and OS. ( H,I ) Correlation analysis of TCIRG1 expression with cancer stemness DNAss and RNAss. ( J ) Correlation analysis of RNAss levels with OS.

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing, Mutagenesis, DNA Methylation Assay

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Enrichment analysis of co-expressed genes of TCIRG1 in TCGA-KIRC. ( A ) Volcano maps showing the co-expression of TCIRG1 genes (FDR < 0.01, COR > 0.4). ( B ) The top fifty genes with the strongest correlation are shown in the heat map. ( C ) GO pathway analysis of TCIRG1 co-expressed genes in KIRC. ( D ) KEGG pathway analysis of TCIRG1 co-expressed gene in KIRC.

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Correlation between TCIRG1 expression and tumor microenvironment score in KIRC. ( A ) BGN expression is associated with estimate score, Immunescore, and Stromalscore in renal cancer based on Pearson correlation analysis. ( B , C ) Relationship between OS of KIRC and Estimatedscore and Immunescore.(*** p < 0.001).

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: TIIC profile and correlation analysis in kidney cancer samples. Pie charts showing the estimated proportions of different types of TIICs in renal tumor samples predicted by ( A ) quanTIseq and ( B ) CIBERSOR. Pearson correlation matrix of the proportions of different TIICs in the microenvironment of renal cancer quantified by ( C ) quanTIseq and ( D ) CIBERSORT. The size of each bubble and the shading of each small colored box represents the corresponding correlation value between two cells. ( E , F ) Lollipop plots showing the correlation between TCIRG1 expression and different TIIC ratios analyzed by quanTIseq and CIBERSORT.

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: TCIRG1 and immune cell biomarkers in RCC were correlated using GEPIA2 and Timer2.0.

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques:

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: Division of subgroups according to TCIRG1 expression levels to predict potential immunotherapeutic responses in kidney cancer. ( A ) Immune checkpoint-associated genes are expressed in high- and low-TCIRG1 subpopulations. The Wilcoxon rank-sum test was used as a statistical significance test. ( B ) Tumor Immune Dysfunction and Exclusion (TIDE) score. ( C ) TCIRG1 expression differences between GSE67501-responding and non-responding groups. ( D – M ) IC50 differences between high- and low-TCIRG1 expression groups. (* p < 0.05, ** p < 0.01. *** p < 0.001).

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing

Journal: Cancers

Article Title: Integrative Analysis Identifies TCIRG1 as a Potential Prognostic and Immunotherapy-Relevant Biomarker Associated with Malignant Cell Migration in Clear Cell Renal Cell Carcinoma

doi: 10.3390/cancers14194583

Figure Lengend Snippet: ( A ) Expression of TCIRG1 in different kidney cancer cell lines. TCIRG1 promotes the migratory ability of RCC cells. ( B , C ) qPCR Western Blot and ( D ) Western blotting showed that the expression of TCIRG1 was silenced by siRNA in 769P and caki1, respectively. Scratch wound-healing ( E , F , I , J ) and ( G , H , K , L ) transwell migration healing assays demonstrated TCIRG1-regulated migration ability. The scale bar of (E and I) is 250 μm, and the scale bar of (G and K) is 100 μm (* p < 0.05, *** p < 0.001).

Article Snippet: Total proteins were then extracted, measured, and semi-dry transferred to PVDF (Millipore, Billerica, MA, USA) membranes after separation by 8–12% SDS-PAGE electrophoresis; PVDF membranes were first closed with TBS + Tween (TBST) solution containing 5% skim milk powder for 2 h, washed, and incubated with primary antibody at 4 °C overnight (TCIRG1, 12649-1-AP, Proteintech, 1:50); they were then rewashed and incubated for 2 h with a secondary antibody that was colored by horseradish peroxidase.

Techniques: Expressing, Western Blot, Migration

Journal: Cell reports

Article Title: Embryonic temporal–spatial delineation of excitatory spinal V3 interneuron diversity

doi: 10.1016/j.celrep.2023.113635

Figure Lengend Snippet: Key resources table

Article Snippet: Human ONECUT2/OC-2 Affinity Purified Polyclonal Ab , R and D Systems , RRID:AB_10640365.

Techniques: Recombinant, Affinity Purification, Produced, Virus, Plasmid Preparation, Labeling, Software

Journal: bioRxiv

Article Title: Multiparametric senescent cell phenotyping reveals CD24 osteolineage cells as targets of senolytic therapy in the aged murine skeleton

doi: 10.1101/2023.01.12.523760

Figure Lengend Snippet: Key Resources Table

Article Snippet: pCMV6-Bglap (Ocn) , Origene , MR226351.

Techniques: FACS, Recombinant, Red Blood Cell Lysis, Transfection, Lysis, Antibody Labeling, Staining, Software