Journal: International Journal of Biological Sciences

Article Title: Cdh1 functions as an oncogene by inducing self-renewal of lung cancer stem-like cells via oncogenic pathways

doi: 10.7150/ijbs.38672

Figure Lengend Snippet: Primers for RT-qPCR

Article Snippet: The following primary antibodies were used: anti-E-cadherin (Proteintech, USA), anti-PI3K, anti-Akt, anti-mTOR, anti-S6K, anti-Eif4e, anti-Erk1/2, anti-p-Mek1/2, anti-p-Erk1/2, anti-p-Akt, anti-p-mTOR, anti-p-S6k (Cell Signaling Technology, USA), anti-Mek1 (Upstate, USA) and anti-GAPDH (Proteintech, USA).

Techniques:

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Spatio-temporal expression profiles of ( A ) ACTB, ( B ) ACTN4, ( C ) INF2, and ( D ) MYL6 retrieved from BrainSpan. The darker the blue color, the higher the protein expression level in the brain region.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques: Expressing

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Validity verification of DEDRGs. ( A ) Validation of DEDRGs by Western blotting. ( B ) Statistical plots of SLC7A11, ACTB, ACTN4, INF2, and MYL6. Compared with the saline group, ns = no significance, * p < 0.05, ** p < 0.01. n = 3. ( C ) Location of ACTN4 and INF2 proteins in cells from the HPA database: green represents the target protein, red represents microtubules, yellow represents the endoplasmic reticulum, and blue represents the nucleus (scale bar, 20 µm).

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques: Biomarker Discovery, Western Blot, Saline

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Box plot of differential expression of DEDRGs between normal and tumor samples. ( A ) The differential expression of ACTB in pan-cancer. ( B ) The differential expression of ACTN4 in pan-cancer. ( C ) The differential expression of INF2 in pan-cancer. ( D ) The differential expression of MYL6 in pan-cancer. Compared with the normal samples, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques: Quantitative Proteomics

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Pan-cancer prognostic analysis of DEDRGs using univariate Cox regression, including ( A ) ACTB, ( B ) ACTN4, ( C ) INF2, and ( D ) MYL6.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques:

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Survival analysis of DEDRG expression in pan-cancer. ( A – H ) Survival curves of ACTB in GBMLGG, LGG, MESO, KIRC, UVM, HNSC, LIHC, LUAD. ( I – N ) Survival curves of ACTN4 in GBMLGG, LGG, MESO, PAAD, LUAD, KIRC. ( O – R ) Survival curves of INF2 in LIHC, HNSC, GBM, LAML. ( S – X ) Survival curves of MYL6 in GBMLGG, LGG, ACC, UVM, LAML, SARC.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques: Expressing

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Pan-cancer immune infiltration analysis: ( A ) Immunoinfiltration analysis of ACTB in GBMLGG, LGG, MESO, KIRC, UVM, HNSC, LIHC, LUAD, and GBM. ( B ) Immunoinfiltration analysis of ACTN4 in GBMLGG, LGG, MESO, PAAD, LUAD, and KIRC. ( C ) Immunoinfiltration analysis of INF2 in LIHC, HNSC, GBM, and LAML. ( D ) Immunoinfiltration analysis of MYL6 in GBMLGG, ACC, LGG, UVM, LAML, and SARC. The correlation coefficient being positive indicates a positive correlation between two variables; a negative correlation coefficient indicates a negative correlation between two variables. The absolute value of the correlation coefficient represents the degree of correlation: 0–0.3 indicates weak or no correlation; 0.3–0.5 indicates weak correlation; 0.5–0.8 indicates moderate correlation; 0.8–1 indicates strong correlation. * p < 0.05, ** p < 0.01, *** p < 0.001.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques:

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Single-cell type analysis of DEDRGs, including ACTB, ACTN4, INF2, and MYL6, mainly from glandular epithelial cells, squamous epithelial cells, specialized epithelial cells, endocrine cells, neuronal cells, glial cells, germ cells, trophoblast cells, endothelial cells, muscle cells, adipocytes, pigment cells, mesenchymal cells, undifferentiated cells, and blood and immune cells.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques:

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Gene mutation analysis of DEDRGs. ( A ) The pan-cancer mutation status of ACTB was determined using the cBioPortal tool. ( B ) ACTB base mutation frequency. ( C ) The pan-cancer mutation status of ACTN4 was determined using the cBioPortal tool. ( D ) ACTN4 base mutation frequency. ( E ) The pan-cancer mutation status of INF2 was determined using the cBioPortal tool. ( F ) INF2 base mutation frequency. ( G ) The pan-cancer mutation status of MYL6 was determined using the cBioPortal tool. ( H ) MYL6 base mutation frequency.

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques: Mutagenesis

Journal: Current Issues in Molecular Biology

Article Title: Disulfidptosis: A New Target for Parkinson’s Disease and Cancer

doi: 10.3390/cimb46090600

Figure Lengend Snippet: Tumor pathological staining of ACTB in glioma, renal cancer, head and neck cancer, liver cancer, and lung cancer; ACTN4 in glioma, pancreatic cancer, lung cancer, and renal cancer; INF2 in liver cancer, head and neck cancer, and glioma; MYL6 in glioma (scale bar, 20 µm).

Article Snippet: The membrane was blocked with 5% nonfat milk in TBST for 1 h at room temperature and probed overnight at 4 °C with primary antibodies: beta Actin (1:3000, AF7018, Affinity, Melbourne, Australia), ACTN4 (1:1000, DF8000, Affinity, Melbourne, Australia), INF2 (1:1500, 20466-1-AP, Proteintech, Chicago, IL, USA), MYL6 (1:1000, DF4718, Affinity, Melbourne, Australia), and GAPDH (1:3000, Affinity, Melbourne, Australia) in TBST containing 1% nonfat milk.

Techniques: Staining

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development

doi: 10.1186/s13018-024-04573-7

Figure Lengend Snippet: qRT-PCR primer sequence and cycling conditions

Article Snippet: Primary antibodies against ADAMTS4 (1:500 dilution, Proteintech, 11865-1-AP), ADAMTS5 (1:1000 dilution, Abcam, ab41037)), MMP3 (1:500 dilution, Proteintech, 17873-1-AP), MMP13 (1:500 dilution, Proteintech, 18165-1-AP), SOX9 (1:1000 dilution, Cell Signaling Technology, 82630), COL2A1 (1:1000 dilution, Abcam, ab34712), HOXD11 (1:500 dilution, Proteintech, 18734-1-AP), and GAPDH (1:1000 dilution, Proteintech, 60004-1-Ig) were diluted at appropriate concentration and incubated with membranes at 4 °C overnight.

Techniques: Sequencing, Amplification

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development

doi: 10.1186/s13018-024-04573-7

Figure Lengend Snippet: The DEGs

Article Snippet: Primary antibodies against ADAMTS4 (1:500 dilution, Proteintech, 11865-1-AP), ADAMTS5 (1:1000 dilution, Abcam, ab41037)), MMP3 (1:500 dilution, Proteintech, 17873-1-AP), MMP13 (1:500 dilution, Proteintech, 18165-1-AP), SOX9 (1:1000 dilution, Cell Signaling Technology, 82630), COL2A1 (1:1000 dilution, Abcam, ab34712), HOXD11 (1:500 dilution, Proteintech, 18734-1-AP), and GAPDH (1:1000 dilution, Proteintech, 60004-1-Ig) were diluted at appropriate concentration and incubated with membranes at 4 °C overnight.

Techniques:

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development

doi: 10.1186/s13018-024-04573-7

Figure Lengend Snippet: Expression of HOXD11 in OA cells and normal chondrocytes. a qRT-PCR was conducted to quantify 5′-HOXD mRNA levels ( HOXD9 , HOXD10 , HOXD11 , HOXD12 , and HOXD13) . b WB was conducted to quantify HOXD11 protein levels in OA cells and normal chondrocytes. * P < 0.05 and ** P < 0.01 as relative with control

Article Snippet: Primary antibodies against ADAMTS4 (1:500 dilution, Proteintech, 11865-1-AP), ADAMTS5 (1:1000 dilution, Abcam, ab41037)), MMP3 (1:500 dilution, Proteintech, 17873-1-AP), MMP13 (1:500 dilution, Proteintech, 18165-1-AP), SOX9 (1:1000 dilution, Cell Signaling Technology, 82630), COL2A1 (1:1000 dilution, Abcam, ab34712), HOXD11 (1:500 dilution, Proteintech, 18734-1-AP), and GAPDH (1:1000 dilution, Proteintech, 60004-1-Ig) were diluted at appropriate concentration and incubated with membranes at 4 °C overnight.

Techniques: Expressing, Quantitative RT-PCR, Control

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development

doi: 10.1186/s13018-024-04573-7

Figure Lengend Snippet: Overexpression of HOXD11 in OA cells reverses the effects. a The cultivated chondrocyte cells in 60 mm plates (magnification, × 100). Scale bars: 200 μM. b qRT-PCR was performed to evaluate HOXD11 mRNA expression. c CCK-8 was conducted to evaluate proliferation. d Flow cytometry was performed to evaluate cell apoptosis. e WB was performed to evaluate expression of SOX9 and COL2A1. f qRT-PCR was conducted to evaluate SOX9 and COL2A1 mRNA levels. g WB was used to quantify MMP13 and ADAMTS5 expression. h qRT-PCR was utilized to quantify MMP13 and ADAMTS5 mRNA levels. * P < 0.05, ** P < 0.01 versus control or OA + vector

Article Snippet: Primary antibodies against ADAMTS4 (1:500 dilution, Proteintech, 11865-1-AP), ADAMTS5 (1:1000 dilution, Abcam, ab41037)), MMP3 (1:500 dilution, Proteintech, 17873-1-AP), MMP13 (1:500 dilution, Proteintech, 18165-1-AP), SOX9 (1:1000 dilution, Cell Signaling Technology, 82630), COL2A1 (1:1000 dilution, Abcam, ab34712), HOXD11 (1:500 dilution, Proteintech, 18734-1-AP), and GAPDH (1:1000 dilution, Proteintech, 60004-1-Ig) were diluted at appropriate concentration and incubated with membranes at 4 °C overnight.

Techniques: Over Expression, Quantitative RT-PCR, Expressing, CCK-8 Assay, Flow Cytometry, Control, Plasmid Preparation

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development

doi: 10.1186/s13018-024-04573-7

Figure Lengend Snippet: Cartilage staining and immunohistochemistry assay of SOX9 and HOXD11 expression. a and b H&E and SOFG were used to stain the cartilage and assess the cartilage damage (original magnification × 40). Scale bars: 500 μM. c and d Immunohistochemistry of SOX9 and HOXD11 in human normal and OA knee joint cartilage (original magnification × 400). Scale bars: 50 μM. e OARSI histological score of OA severity in normal and OA knee joint cartilage. f Quantification of proteoglycan loss in normal and OA knee joint cartilage. g and h SOX9, HOXD11 -positive cells were quantified in normal and OA knee joint cartilage. * P < 0.05, ** P < 0.01 versus control

Article Snippet: Primary antibodies against ADAMTS4 (1:500 dilution, Proteintech, 11865-1-AP), ADAMTS5 (1:1000 dilution, Abcam, ab41037)), MMP3 (1:500 dilution, Proteintech, 17873-1-AP), MMP13 (1:500 dilution, Proteintech, 18165-1-AP), SOX9 (1:1000 dilution, Cell Signaling Technology, 82630), COL2A1 (1:1000 dilution, Abcam, ab34712), HOXD11 (1:500 dilution, Proteintech, 18734-1-AP), and GAPDH (1:1000 dilution, Proteintech, 60004-1-Ig) were diluted at appropriate concentration and incubated with membranes at 4 °C overnight.

Techniques: Staining, Immunohistochemistry, Expressing, Control

Journal: Journal of Orthopaedic Surgery and Research

Article Title: Inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development

doi: 10.1186/s13018-024-04573-7

Figure Lengend Snippet: Model for inhibition of HOXD11 promotes cartilage degradation and induces osteoarthritis development (red arrow). In OA chondrocytes, the decreased expression of HOXD11 inhibits cell proliferation and enhances apoptosis. HOXD11 downregulates SOX9 via inducing catabolism and restraining anabolism, leading to the upregulation of MMP13 and ADAMTS5, which downregulates COL2A1, ultimately promoting cartilage degradation and inducing osteoarthritis development. Lentivirus-mediated HOXD11 overexpression reverses these effects (green arrow)

Article Snippet: Primary antibodies against ADAMTS4 (1:500 dilution, Proteintech, 11865-1-AP), ADAMTS5 (1:1000 dilution, Abcam, ab41037)), MMP3 (1:500 dilution, Proteintech, 17873-1-AP), MMP13 (1:500 dilution, Proteintech, 18165-1-AP), SOX9 (1:1000 dilution, Cell Signaling Technology, 82630), COL2A1 (1:1000 dilution, Abcam, ab34712), HOXD11 (1:500 dilution, Proteintech, 18734-1-AP), and GAPDH (1:1000 dilution, Proteintech, 60004-1-Ig) were diluted at appropriate concentration and incubated with membranes at 4 °C overnight.

Techniques: Inhibition, Expressing, Over Expression

Journal: EMBO Reports

Article Title: Muskelin is a substrate adaptor of the highly regulated Drosophila embryonic CTLH E3 ligase

doi: 10.1038/s44319-025-00397-6

Figure Lengend Snippet: Reagents and tools table

Article Snippet: Rabbit anti-eIF4E (Boster) was used at 1:10000.

Techniques: SYBR Green Assay, Imaging, Recombinant, Sequencing, Software, Microscopy, Ion-Mobility Spectrometry, Mass Spectrometry