Journal: Journal of Liver Cancer

Article Title: Synergistic effects of L-arginine and argininosuccinate synthetase 1 in inducing apoptosis in hepatocellular carcinoma

doi: 10.17998/jlc.2024.12.27

Figure Lengend Snippet: ASS1 expression increases the sensitivity of HCC cell lines to cisplatin. (A) Endogenous ASS1 expression levels in HCC cell lines. The protein lanes are as follows: 1) F2N, 2) Huh6, 3) Huh7, 4) Hep3B, 5) SK-Hep1, 6) PLC/PRF/5, 7) SNU398, 8) SNU449, 9) SNU475, 10) AMCH1, 11) AMC-H2. (B) Endogenous ASS1 mRNA expression levels in HCC cell lines. The mRNA lanes are as follows: 1) HepG2, 2) Hep3B, 3) Huh7, 4) PLC/PRF/5, 5) SNU398, 6) SNU449, 7) SNU475, 8) AMC-H1, 9) AMC-H2, 10) A431. A431 was used as a positive control. (C) Higher en-dogenous ASS1 expression increases sensitivity to cisplatin. Cell viability in response to cisplatin was evaluated by overexpressing ASS1 in Huh7 and SNU475 cells or silencing its expression in Hep3B and PLC/PRF/5 cells using siRNA. Data are presented as mean± SEM. ASS1, argininosuccinate synthetase; GADPH, glyceraldehyde-3-phosphate dehydrogenase; CON, control; siRNA, small interfering RNA; HCC, hepatocellular carcinoma; SEM, standard error of the mean. ** P <0.01 and *** P <0.001.

Article Snippet: After seeding 5×105 cells in a 10 cm dish, siRNA targeting ASS1 was purchased from L-004819-00-0005 (Dharmacon, Lafayette, CO, USA), SMARTpool ON-TARGETplus ASS1 siRNA (Horizon Discovery, Waterbeach, UK), siRNA ID 445-1, 445-2, and 445-3 (BIONEER), and sc-45810 (Santa Cruz Biotechnology, Dallas, TX, USA). siRNA was transfected into HCC cell lines using Lipofectamine RNAiMAX (Invitrogen) reagent with Opti-MEM, and the cells were incubated at 37°C for 48 hours.

Techniques: Expressing, Positive Control, Control, Small Interfering RNA

Journal: bioRxiv

Article Title: FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism

doi: 10.1101/2024.01.15.575789

Figure Lengend Snippet: Mouse embryonic fibroblasts (MEFs) were transfected with non-targeting control siRNA or siRNAs targeting FAK and p130Cas, synchronized to G0, and plated on fibronectin-coated soft or stiff substrates for 1 h. (A) Immunoblots of total cell lysates showing protein levels of FAK and p130Cas with GAPDH as the loading control. (B) Graphs present mean + SD, normalized to GAPDH abundance, and plotted relative to the signal on the soft hydrogels, n = 3. *p < 0.05, **p < 0.01, ***p < 0.001; ns, not significant. Correlation heat map (C) and principal-component analysis plot (D) for the entire transcriptome list. (E) Volcano plot illustrates the distribution of differentially expressed genes (DEGs) in response to stiffer ECM; significance determined by adjusted p value of <0.05; log2(fold-change) <−0.32 or >0.32; and baseMean > 500. Bubble plots depict the top 20 significantly enriched biological processes (F) and cellular components (G) among DEGs in response to stiff versus soft substrate.

Article Snippet: FAK and p130Cas siRNAs were obtained from Ambion: FAK siRNA #1 (ID: 157448): CCUAGCAGACUUUAACCAAtt; FAK siRNA #2 (ID: 61352): GGCAUGGAGAUGCUACUGAtt; p130Cas siRNA #1 (ID: 161328): GCCAAUCGGCAUCUUCCUUtt; p130Cas siRNA #2 (ID: 161329): GCUGAAACAGUUUGAGCGAtt.

Techniques: Transfection, Western Blot

Journal: bioRxiv

Article Title: FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism

doi: 10.1101/2024.01.15.575789

Figure Lengend Snippet: Volcano plot (A) and heat map (B) to visualize the distribution and expression patterns, respectively, of differentially expressed genes (DEGs) in response to FAK knockdown. Bubble plots show the top 20 enriched biological processes for significantly downregulated (C) and upregulated (D) DEGs comparing FAK siRNA to control siRNA in cells on stiff hydrogels. (E) Top 20 enriched KEGG pathways for DEGs with FAK siRNA versus control siRNA in cells on stiff hydrogels. (F) Histogram represents significantly and differentially activated or inhibited [absolute activation z score ≥ 2; −log10(p value) ≥ 2)] canonical pathways in response to FAK knockdown.

Article Snippet: FAK and p130Cas siRNAs were obtained from Ambion: FAK siRNA #1 (ID: 157448): CCUAGCAGACUUUAACCAAtt; FAK siRNA #2 (ID: 61352): GGCAUGGAGAUGCUACUGAtt; p130Cas siRNA #1 (ID: 161328): GCCAAUCGGCAUCUUCCUUtt; p130Cas siRNA #2 (ID: 161329): GCUGAAACAGUUUGAGCGAtt.

Techniques: Expressing, Activation Assay

Journal: bioRxiv

Article Title: FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism

doi: 10.1101/2024.01.15.575789

Figure Lengend Snippet: Volcano plot (A) and heat map (B) to visualize the distribution and expression patterns, respectively, of differentially expressed genes (DEGs) in response to p130Cas knockdown. Bubble plots show the top 20 enriched biological processes for significantly downregulated (C) and upregulated (D) DEGs comparing p130Cas siRNA to control siRNA in cells on stiff hydrogels. (E) Top 20 enriched KEGG pathways for DEGs with p130Cas siRNA versus control siRNA in cells on stiff hydrogels. (F) Histogram represents significantly and differentially activated or inhibited [absolute activation z score ≥ 2; −log10(p value) ≥ 2)] canonical pathways in response to p130Cas knockdown.

Article Snippet: FAK and p130Cas siRNAs were obtained from Ambion: FAK siRNA #1 (ID: 157448): CCUAGCAGACUUUAACCAAtt; FAK siRNA #2 (ID: 61352): GGCAUGGAGAUGCUACUGAtt; p130Cas siRNA #1 (ID: 161328): GCCAAUCGGCAUCUUCCUUtt; p130Cas siRNA #2 (ID: 161329): GCUGAAACAGUUUGAGCGAtt.

Techniques: Expressing, Activation Assay

Journal: bioRxiv

Article Title: FAK and p130Cas modulate stiffness-mediated early transcription and cellular metabolism

doi: 10.1101/2024.01.15.575789

Figure Lengend Snippet: Venn diagrams show commonly downregulated (A) and upregulated (B) differentially expressed genes (DEGs) in cells on stiff hydrogels with FAK siRNA or p130Cas siRNA. (C) Gene ontology (GO) analysis identifies a network of significantly connected and grouped biological processes (p < 0.0001 by two-sided hypergeometric test with Benjamini–Hochberg correction; global network specificity) among common DEGs of FAK-p130Cas signaling. (D) Dendrogram shows hierarchical clustering of significantly enriched (p < 0.05) RNA-binding protein motifs identified by the Transite set motif analysis tool in 3′ and 5′ untranslated regions of common DEGs. (E) STRING enrichment analysis shows a protein–protein interaction network (21 nodes and 67 edges) of all enriched RNA-binding proteins and their associated biological processes.

Article Snippet: FAK and p130Cas siRNAs were obtained from Ambion: FAK siRNA #1 (ID: 157448): CCUAGCAGACUUUAACCAAtt; FAK siRNA #2 (ID: 61352): GGCAUGGAGAUGCUACUGAtt; p130Cas siRNA #1 (ID: 161328): GCCAAUCGGCAUCUUCCUUtt; p130Cas siRNA #2 (ID: 161329): GCUGAAACAGUUUGAGCGAtt.

Techniques: RNA Binding Assay