Journal: bioRxiv

Article Title: Fibrillarin shapes oncogenic protein pools and ribosomal composition in triple-negative breast cancer

doi: 10.1101/2025.03.21.644506

Figure Lengend Snippet: ( A ) Violin plot illustrating the distribution of proteins detected in total proteomics based on the Log 2 (FC) compared to control for both KDs after 48 and 96 h of FBL depletion. ( B ) Venn diagram displaying the overlap of downregulated proteins at 48 h and 96 h in both FBL KDs. ( C ) Common enriched biological processes associated with downregulated proteins upon FBL KDs. ( D ) Venn diagram of the overlap between the commonly downregulated proteins, and the transcripts with downregulated translation efficiency. Highlighted in red are proteins with an already described role in breast cancer. ( E - G ) mRNA percentage distribution among the 14 fractions collected by polysome profiling for ( E ) MTA1 , ( F ) IRAK1 , and ( G ) TMSB10 in control and FBL-depleted cells. Ribosomal subunits and 80S fractions are highlighted in light grey, and polysome fractions are highlighted in blue. ( H ) Representative Western Blot images displaying the expression of FBL, MTA1, IRAK1, and TMSB10 in control and FBL-depleted (KD1 and KD2) MDA-MB-231 cells. β-ACTIN serves as a loading control. ( I ) RT-qPCR analysis of MTA1 , IRAK1, and TMSB10 levels from control and FBL-depleted (KD1 and KD2) MDA-MB-231 cells. mRNA expression levels were normalized to GAPDH and are presented relative to the control. ( J ) Representative Western Blot images displaying the expression of FBL, MTA1, IRAK1, and TMSB10 in control and FBL-depleted (KD1 and KD2) hTERT-HME1 cells. β-ACTIN serves as a loading control. Statistical analysis: All data are presented as the mean ± SD, n = 3. ( A ) Welch’s two-tailed t-test; **** P < 0.0001.( I ) Unpaired two-tailed t-test, * P < 0.05, ** P < 0.01, **** P < 0.0001. The cut-off applied to proteomic data analysis was Log 2 (FC) ± 0.585, adj P < 0.05.

Article Snippet: The following antibodies were used at the indicated concentrations: anti-FBL (A303-891A, Bethyl Laboratories, 1:2,500 dilution), anti-β-actin (A5441, Sigma, 1:10,000 dilution), anti-metastasis-associated 1 gene (MTA1) (A300-911A-T, Bethyl Laboratories, 1:2,000), anti-interleukin 1 receptor-associated kinase 1 (IRAK1) (ab302554, Abcam, 1:2,000 dilution), anti-thymosin B10 (sc-514309, Santa Cruz Biotechnology, 1:1,000 dilution), anti-RPS28 (14796-1-AP, Proteintech, 1:2,000 dilution), and anti-RPL22 (25002-1-AP, Proteintech, 1:2,000).

Techniques: Control, Western Blot, Expressing, Quantitative RT-PCR, Two Tailed Test

Journal: bioRxiv

Article Title: Fibrillarin shapes oncogenic protein pools and ribosomal composition in triple-negative breast cancer

doi: 10.1101/2025.03.21.644506

Figure Lengend Snippet: ( A ) MTT assay of control and RPS28-depleted (KD1 and KD2) cells over a 3-day period (24, 48, and 72 h) upon puromycin selection. ( B ) Crystal violet staining of control and RPS28-depleted (KD1 and KD2) cells, performed 10 days after puromycin selection. ( C ) Representative images from the wound-healing assay showing the wound-healing capacity of control and FBL-depleted (KD1 and KD2) cells upon scratch generation at 0 and 24 h. ( D ) Quantification of wound-healing capacity in RPS28-depleted (KD1 and KD2) cells relative to control. Scale bar: 100 µm. ( E ) Representative images showing cells that migrated through the trans-well in Scr and RPS28-depleted (KD1 and KD2) conditions. Scale bar: 100 µm. ( F ) Quantification of the migration capacity of RPS28-depleted (KD1 and KD2) cells relative to control. ( G ) Polysome profiling for control and RPS28-depleted (KD1 and KD2) cells in a 15-45% sucrose gradient. Peaks for 40S, 60S, 80S, and polysomes are highlighted and correspond to absorbance measurements at 260 nm. ( H - J ) mRNA percentage distribution among the 14 fractions collected by polysome profiling for ( H ) MTA1 , ( I ) IRAK1 , and ( J ) TMSB10 in control and RPS28-depleted cells. The fractions were combined as sub-polysomal (1 to 6) and polysomal (7 to 14). ( K ) Representative Western Blot showing RPS28, MTA1, IRAK1, TMSB10 protein expression in Scr control and RPS28-depleted (KD1 and KD2) MDA-MB-231 cells. β-ACTIN serves as a loading control. ( L) H-score quantification of RPS28 in TNBCs from SCAN-B project. Q1 and Q4, first and fourth quartiles, respectively. ( M ) Representative IHC images showing RPS28, IRAK1 and TMSB10 protein levels (low and high, respectively) in the same patient sample. Scale bar: 40µm. ( N and O ). Violin plots displaying the correlation of RPS28 and ( N ) IRAK1 and ( O ) TMSB10 H-scores in TNBC tumors from the SCAN-B project. ( P and Q ) Violin plots displaying the correlation of RPS28 H-score and ( P ) IRAK1 and ( Q ) TMSB10 mRNAs. Statistical analysis: All experimental data are presented as the mean ± SD, n = 3. ( A, D, and F ) Unpaired two-tailed t-test, * P < 0.05, ** P < 0.01, **** P < 0.0001. ( H-J ) Two-way ANOVA with Dunnett’s multiple comparisons test * adj P < 0.05, ** adj P < 0.01, ns = non-significant. ( N-Q ). Unpaired two-tailed t-test corrected with the BH method for multiple comparisons, * adj P < 0.05, ** adj P < 0.01, *** adj P < 0.001, **** adj P < 0.0001, ns adj P > 0.05.

Article Snippet: The following antibodies were used at the indicated concentrations: anti-FBL (A303-891A, Bethyl Laboratories, 1:2,500 dilution), anti-β-actin (A5441, Sigma, 1:10,000 dilution), anti-metastasis-associated 1 gene (MTA1) (A300-911A-T, Bethyl Laboratories, 1:2,000), anti-interleukin 1 receptor-associated kinase 1 (IRAK1) (ab302554, Abcam, 1:2,000 dilution), anti-thymosin B10 (sc-514309, Santa Cruz Biotechnology, 1:1,000 dilution), anti-RPS28 (14796-1-AP, Proteintech, 1:2,000 dilution), and anti-RPL22 (25002-1-AP, Proteintech, 1:2,000).

Techniques: MTT Assay, Control, Selection, Staining, Wound Healing Assay, Migration, Western Blot, Expressing, Two Tailed Test

Journal: Frontiers in Genetics

Article Title: Chrysin Modulates Aberrant Epigenetic Variations and Hampers Migratory Behavior of Human Cervical (HeLa) Cells

doi: 10.3389/fgene.2021.768130

Figure Lengend Snippet: Relative expression of TSGs and genes related to migration and metastasis. The values are taken as mean of three experiments ±SD ( p ≤ 0.05).

Article Snippet: MTA1 , Hs00183042_m1 , Metastasis associated 1 , 0.26 , 0.14.

Techniques: Expressing, Migration