Journal: bioRxiv

Article Title: The CX3CL1 oligomerization is required for efficient CX3CR1-specific cell adherence

doi: 10.1101/865998

Figure Lengend Snippet: A.Cell lysate of L CX3CL1 cells stably transfected with CX3CL1-EYFP was analyzed by SDS-PAGE and Western blot. B.Cell lysate of L CX3CL1 was analyzed by native electrophoresis using Nu-Page gel in the presence of 1% DDM (dodecylmaltoside) and Western blot. C. The affinity-purified CX3CL1 from L CX3CL1 membranes was analyzed by native PAGE. CXCL3 was solubilized using CALX173ACE and affinity purified (CXCL1 antibody). Mini-proteon TGX gel electrophoresis (Biorad) were used for Native PAGE.

Article Snippet: The immunodetection of CX3CL1 was performed by using the SNAP i.d. system ( Millipore ) with primary antibody (R&D system, MAB3651) against CX3CL1 (1/500 dilution) and revealed using a mouse HRP secondary antibody (Santa Cruz, 3/10,000 dilution).

Techniques: Stable Transfection, Transfection, SDS Page, Western Blot, Electrophoresis, Affinity Purification, Clear Native PAGE, Nucleic Acid Electrophoresis

Journal: bioRxiv

Article Title: The CX3CL1 oligomerization is required for efficient CX3CR1-specific cell adherence

doi: 10.1101/865998

Figure Lengend Snippet: A. Fluorescence of the membrane preparation of L CX3CL1 diluted in DOPC analyzed by TIRF. Bar 10µm B. Examples of the fluorescence of two particles tracked during two minutes C. Distribution of the number of elementary fluorescence units per particle calculated after analysis of the fluorescence kinetic of 126 different particles. The Gaussian curve fits the data with an amplitude of 27.5, a mean of 4.3 and a standard deviation of 1.8.

Article Snippet: The immunodetection of CX3CL1 was performed by using the SNAP i.d. system ( Millipore ) with primary antibody (R&D system, MAB3651) against CX3CL1 (1/500 dilution) and revealed using a mouse HRP secondary antibody (Santa Cruz, 3/10,000 dilution).

Techniques: Fluorescence, Membrane, Standard Deviation

Journal: bioRxiv

Article Title: The CX3CL1 oligomerization is required for efficient CX3CR1-specific cell adherence

doi: 10.1101/865998

Figure Lengend Snippet: The lateral diffusion rate of the CX3CL1-EYFP protein was assayed after transient expression in COS-7 cell line after 15 min preincubation in the presence or not of 3 or 10 µM of TM24 or SCR24 peptides. Each point is the mean of triplicates±SD.

Article Snippet: The immunodetection of CX3CL1 was performed by using the SNAP i.d. system ( Millipore ) with primary antibody (R&D system, MAB3651) against CX3CL1 (1/500 dilution) and revealed using a mouse HRP secondary antibody (Santa Cruz, 3/10,000 dilution).

Techniques: Diffusion-based Assay, Expressing

Journal: bioRxiv

Article Title: The CX3CL1 oligomerization is required for efficient CX3CR1-specific cell adherence

doi: 10.1101/865998

Figure Lengend Snippet: A. Real time adherence of CHO CX3CR1 cells to L 929 (dashed traces) or L CX3CL1 cells (solid traces) as assayed by the LigandTracer™ technique, in the presence of 5µM TM24 (red traces), 5µM SCR24 (blue traces) or none (black traces). The data were normalized using the control trace with L CX3CL1 cells in the absence of peptide (100% after 60 minutes). The curves are the mean of three independent experiments. B. Specific adherence of CHO CX3CR1 cells to L CX3CL1 cells using data of . The data obtained with L CX3CL1 cells were subtracted from data obtained with L 929 and normalized at 100% at the 60 minutes time. The bars in the right of the Fig shows the specific adherence after 60 minutes (mean of triplicates±SD) in the presence of 5µM TM24 (red) and 5µM SCR24 (blue). C. Real time binding of 100nM of fluorescent CX3CL1 to coated CHO CX3CR1 cells using the LigandTracer™ technique, in the presence of 5µM TM24 (red trace), 1µM unstained CX3CL1 (dashed trace) or none (black trace). The data were normalized using the control trace without peptide (100% after 60 minutes). D. Specific adherence of CHO CX3CR1 cells to L CX3CL1 cells after 60 minutes in the presence of various TM24 peptide concentrations and in the presence (filled squares) or in absence (empty squares) of 1µg/ml of anti-CX3CL1 antibody. The data were calculated and normalized as in . Experiments are performed in duplicate except for the 1µM TM24 concentration done in triplicates (mean±SD).

Article Snippet: The immunodetection of CX3CL1 was performed by using the SNAP i.d. system ( Millipore ) with primary antibody (R&D system, MAB3651) against CX3CL1 (1/500 dilution) and revealed using a mouse HRP secondary antibody (Santa Cruz, 3/10,000 dilution).

Techniques: Control, Binding Assay, Concentration Assay

Journal: Nature Communications

Article Title: Targeting tRNA-dependent tyrosine usage unveils a metabolic vulnerability in hepatocellular carcinoma

doi: 10.1038/s41467-026-70112-z

Figure Lengend Snippet: a – d The graphs representing gene levels detected by transcriptomics and translatomics ( a ), transcriptomics and proteomics ( c ) or translatomics and proteomics ( d ) of SNU398 tyrosine-restricted cells compared to control cells. A heat map ( b ) representing amino acids and codon enrichment analysis in genes translating downregulated compared to the genes translating upregulated. e The frequency of tyrosine and tyrosine cognate TAC codon in coding sequence is sorted from high to low. f The graph representing significantly altered signatures in proteomics and metabolomics data upon tyrosine restriction. g Ribosome-protected fragment and total RNA tracks at SCD1 , NDUFB8 , and NDUFB1 gene loci are shown. h A graphic illustration of the indicated reporter with a different tyrosine codon frequency. Quantification of luciferase activities normalised to Renilla luciferase activities in SNU398 cells. ( n = 3 independent experiments). i , j Native-PAGE analysis (left) and SDS-PAGE analysis (right) of SNU398 cells ( i ) ( n = 3 independent experiments) or the livers from Myc/Alb-cre mice ( j ) ( n = 6 mice). k , l The activity of mitochondrial complex I-V of SNU398 cells ( k ) ( n = 3 independent experiments) or the livers of Myc/Alb-cre mice ( l ) ( n = 6 mice). m Seahorse assays showing the oxygen consumption rate (OCR) (left) in SNU398 cells. Quantification of maximal respiration (right). ( n = 4 independent experiments). n Representative TEM images of SNU398 cells (top) ( n = 3 independent experiments) or the livers from Myc/Alb-cre mice (bottom) ( n = 6 mice). Morphometric analysis of maximal cristae width of cells or livers. o Representative Ki-67, TUNEL, and 4-HNE staining images and quantification statistics of liver sections. ( n = 6 mice). i , j The samples are derived from the same experiment, and all gels/blots are processed in parallel under identical conditions. Source data are provided as a Source Data file. Data are representative of three independent experiments ( h , i , k , m , n ). Data are presented as means ± SD, two-tailed Student’s t test ( b , h , k – o ), two-sided Wald test with Benjamini-Hochberg adjustments ( a , c , d , f ).

Article Snippet: One-step TUNEL apoptosis assay kit (Beyotime, Cat# C1088) was used to detect apoptotic cells in the liver sections from the mouse according to the manufacturer’s protocol.

Techniques: Transcriptomics, Control, Sequencing, Luciferase, Clear Native PAGE, SDS Page, Activity Assay, TUNEL Assay, Staining, Derivative Assay, Two Tailed Test

Journal: Nature Communications

Article Title: Targeting tRNA-dependent tyrosine usage unveils a metabolic vulnerability in hepatocellular carcinoma

doi: 10.1038/s41467-026-70112-z

Figure Lengend Snippet: a A diagram depicting the reaction mechanism of tyrosine and phenylalanine degradation by TAL/PAL. b Purified FjTAL protein directly binds tyrosine but does not bind to phenylalanine, in ITC binding affinity analysis. c IC50 curve of FjTAL in HCC cell lines. ( n = 3 independent experiments). d The activities of mitochondrial complex I-V of SNU398 cells upon FjTAL treatment. ( n = 3 independent experiments). e OCR and maximal respiration of SNU398 cells with FjTAL treatment. ( n = 4 independent experiments). f , g BODIPY493/503 staining ( f ) in HCC cell lines treated with FjTAL or vehicle and quantification of lipid peroxidation ( g ). ( n = 3 independent experiments). h – k Graphic illustration ( h ), representative images of livers ( i ), the plots of the body weight excluding liver weight, liver to body weight ratio, tumour number and maximum tumour diameter ( j ) ( n = 4 mice), and survival curves ( k ) ( n = 6 mice) of Myc/Alb-cre mice with the indicated treatment are shown. l Native-PAGE analysis (left) and SDS-PAGE analysis (right) of livers from Myc/Alb-cre mice treated with FjTAL or vehicle. ( n = 4 mice). m Representative TEM images of livers from Myc/Alb-cre mice treated with FjTAL or vehicle (left). Morphometric analysis of maximal cristae width of cells in 15 randomly selected mitochondria (right). n , o Representative Ki-67, TUNEL and 4-HNE staining of liver sections from Myc/Alb-cre mice treated with FjTAL or vehicle ( n ). Quantification of staining intensities and positive cells is shown ( o ). ( n = 4 mice). l The samples are derived from the same experiment, and all gels/blots are processed in parallel under identical conditions. Data are representative of three independent experiments ( c – g ). Source data are provided as a Source Data file. Data are presented as means ± SD, two-tailed Student’s t test ( d , e , g , m , o ), one-way ANOVA followed by multiple comparisons ( j ), two-sided log-rank test ( k ).

Article Snippet: One-step TUNEL apoptosis assay kit (Beyotime, Cat# C1088) was used to detect apoptotic cells in the liver sections from the mouse according to the manufacturer’s protocol.

Techniques: Purification, Binding Assay, Staining, Clear Native PAGE, SDS Page, TUNEL Assay, Derivative Assay, Two Tailed Test

Journal: Nature Communications

Article Title: Targeting tRNA-dependent tyrosine usage unveils a metabolic vulnerability in hepatocellular carcinoma

doi: 10.1038/s41467-026-70112-z

Figure Lengend Snippet: a The chemical structure of tyrosine and tyrosinol. b ITC assay of YARS1 binding to tyrosine and tyrosinol. c Relative luciferase activities in SNU398 cells with the indicated treatments. ( n = 3 independent experiments). d RT-qPCR after ribosomal immunoprecipitation in SNU398 cells transfected with Flag-RPL22 and treated with tyrosinol. ( n = 3 independent experiments). e The activities of mitochondrial complex I-V of SNU398 cells treated with tyrosinol or vehicle. ( n = 3 independent experiments). f OCR (left) and maximal respiration (right) of SNU398 cells with tyrosinol treatment. ( n = 3 independent experiments). g BODIPY493/503 staining in HCC cell lines treated with tyrosinol or vehicle (left). Quantification of lipid peroxidation (right). ( n = 3 independent experiments). h – j Representative images of livers ( h ), the plots of the body weight excluding liver weight, liver to body weight ratio, tumour number and maximum tumour diameter ( i ) ( n = 6 mice), and survival curves ( j ) ( n = 10 mice) of Myc/Alb-cre mice with the indicated treatment are shown. k The activities of mitochondrial complex I-V of livers from Myc/Alb-cre mice treated with tyrosinol or vehicle. ( n = 6 mice). l Representative electron micrographs of livers from Myc/Alb-cre mice treated with tyrosinol or vehicle (left). Morphometric analysis of maximal cristae width of cells in 15 randomly selected mitochondria (right). m , n Representative Ki-67, TUNEL and 4-HNE staining of liver sections from Myc/Alb-cre mice treated with tyrosinol or vehicle ( m ). Quantification of staining intensities and positive cells is shown ( n ). ( n = 6 mice). Source data are provided as a Source Data file. Data are representative of three independent experiments ( c – g ). Data are presented as means ± SD, two-tailed Student’s t -test ( c – g , k , l , n ), one-way ANOVA followed by multiple comparisons ( i ), two-sided log-rank test ( j ).

Article Snippet: One-step TUNEL apoptosis assay kit (Beyotime, Cat# C1088) was used to detect apoptotic cells in the liver sections from the mouse according to the manufacturer’s protocol.

Techniques: Isothermal Titration Calorimetry, Binding Assay, Luciferase, Quantitative RT-PCR, Immunoprecipitation, Transfection, Staining, TUNEL Assay, Two Tailed Test