Journal: Nature Communications

Article Title: Allelic effects on KLHL17 expression underlie a pancreatic cancer genome-wide association signal at chr1p36.33

doi: 10.1038/s41467-025-59109-2

Figure Lengend Snippet: Predicted TFs with allelic binding preferences for rs13303327 and rs13303160

Article Snippet: Recombinant ELF1 (TP760629), ELF2 (TP760288), ELF3 (TP300631), ELF4 (TP761826), JUNB (TP303595), JUND (TP316958 4), c-FOS (TP760257), FOS1L (TP302104), FOSB (TP762032), FOS2L (TP760114) proteins were purchased from Origene (Rockville, MD). c-JUN was purchased from Abcam (Waltham, MA) (ab84134).

Techniques: Binding Assay, Significance Assay

Journal: Nature Communications

Article Title: Allelic effects on KLHL17 expression underlie a pancreatic cancer genome-wide association signal at chr1p36.33

doi: 10.1038/s41467-025-59109-2

Figure Lengend Snippet: a in silico Transcription factor binding predictions; the risk (G) allele disrupts the motif. b Representative EMSA using TPA-stimulated nuclear HeLa extract and fluorescently labeled oligonucleotide ( n = 3 independent experiments). Arrow indicates the allele-preferential binding. c Luciferase reporter assay using DMSO and TPA stimulation and the rs13303160 sequence as an enhancer in the PANC-1 cell line; luciferase activity reported relative to the Empty Vector (EV, gray bars). Pink bars denote the risk allele, and blue bars represent the protective allele. Both alleles were tested in the forward (fwd) and reverse (rev) orientations. Unpaired, two-tailed t tests were performed on the relative luciferase activity of the A/G ratio compared to A/A; n = 6 biological replicates. d Representative EMSAs with increasing amounts of recombinant Fos proteins (from left to right: c-Fos ( n = 3 independent experiments); FosB ( n = 2); Fos1L ( n = 1); Fos2L ( n = 1)). e Representative EMSAs with increasing amounts of recombinant Jun proteins (from left to right: c-Jun ( n = 2 independent experiments), JunB ( n = 2), JunD ( n = 2)). Arrow indicates the allele-specific binding. f , g Representative supershift EMSA with antibodies against JunB and JunD ( n = 3 independent experiments each), respectively, using both TPA-stimulated nuclear lysate and recombinant protein; Arrows denote the shift in the bands. h ChIP-qPCR in SW1990 PDAC cells for JunB (denoted in blue, IgG in gray) ( n = 6 biological replicates) and JunD (denoted in blue, IgG in gray) ( n = 4 biological replicates) using 3 primer sets (PS) surrounding the SNP. Positive control (PC) is from a JunB ChIP-seq performed in the CFPAC1 PDAC cell line . Negative control (NC) is from a quiescent region on chr1p36.33; i TaqMan genotyping assay for rs13303160 using immunoprecipitated DNA from the ChIP. The ratio of A to G was determined relative to the quantity of A and G alleles in the input DNA (gray) ( n = 6 biological replicates for JunB; n = 5 biological replicates for JunD, blue bars). Red font denotes the risk allele in ( b – g ). For all graphs, error bars represent the SEM. Unpaired two-tailed t tests were performed. Source data are provided as a Source Data file.

Article Snippet: Recombinant ELF1 (TP760629), ELF2 (TP760288), ELF3 (TP300631), ELF4 (TP761826), JUNB (TP303595), JUND (TP316958 4), c-FOS (TP760257), FOS1L (TP302104), FOSB (TP762032), FOS2L (TP760114) proteins were purchased from Origene (Rockville, MD). c-JUN was purchased from Abcam (Waltham, MA) (ab84134).

Techniques: In Silico, Binding Assay, Labeling, Luciferase, Reporter Assay, Sequencing, Activity Assay, Plasmid Preparation, Two Tailed Test, Recombinant, ChIP-qPCR, Positive Control, ChIP-sequencing, Negative Control, Genotyping Assay, Immunoprecipitation

Journal: Journal of Experimental & Clinical Cancer Research : CR

Article Title: Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract

doi: 10.1186/1756-9966-28-62

Figure Lengend Snippet: Real-Time PCR Based Validation of Gene Expression Findings . To confirm the gene expression changes in biliary tract cancers identified on microarray analysis, selected genes were tested in tumor and control specimens by RT PCR and normalized to HRPT which is similarly expressed in tumors and normal biliary epithelia. Results are shown for (g) IL6 , (h) FOSB , (i) CDKN1C , (j) NR4A2 , and (k) DLC .

Article Snippet: 1 ug of total RNA was reverse-transcribed using the Thermoscript RT-PCR system (Invitrogen) at 52°C for 1 h. 20 ng of resultant cDNA was used in a Q-PCR reaction using an iCycler (Biorad, Hercules, California, USA) and pre-designed TaqMan ABI Gene expression Assays (Hs00270424_m1 for CCNB2 , Hs00938777_m1 for CDC2 , Hs00175938_m1 for CDKN1C , Hs01665258_m1 for DLC1 , Hs01547109_m1 for FOSB , Hs99999032_m1 for IL6 , s01118813_m1 for NR4A2 , Hs00971643_g1 for SRD5A1 , Hs01014001_m1 for STAT1 , Hs00426591_m1 for TYMS , Hs00197374_m1 for UBD ).

Techniques: Real-time Polymerase Chain Reaction, Biomarker Discovery, Gene Expression, Microarray, Control, Reverse Transcription Polymerase Chain Reaction

Journal: Cells

Article Title: Ethanol Induces Neuroinflammation in a Chronic Plus Binge Mouse Model of Alcohol Use Disorder via TLR4 and MyD88-Dependent Signaling

doi: 10.3390/cells12162109

Figure Lengend Snippet: TaqMan gene expression assays. 20X primer/probe sets (FAM-MGB) were purchased from Thermo Fisher Scientific, Cat. #4331182, and were used at a final concentration of 1X for qRT-PCR. Assays were selected to span an exon–exon junction where possible.

Article Snippet: Fosb , Mm00500403_m1.

Techniques: Gene Expression, Concentration Assay

Journal: Cells

Article Title: Ethanol Induces Neuroinflammation in a Chronic Plus Binge Mouse Model of Alcohol Use Disorder via TLR4 and MyD88-Dependent Signaling

doi: 10.3390/cells12162109

Figure Lengend Snippet: Two-way ANOVA for FosB and JunB in the cerebellum of wild-type, TLR4-, MyD88-, and TRIF-deficient mice. GraphPad Prism 9 was utilized to perform ordinary two-way analysis of variance (ANOVA) as described in the Methods. The main effects of treatment (control or ethanol) and genotype (wild-type or TLR4_KO, MyD88_KO, or TRIF_KO) and their interaction were evaluated. p values < 0.05 were considered significant. *** p < 0.001, ** p < 0.01, * p < 0.05, ns = not significant.

Article Snippet: Fosb , Mm00500403_m1.

Techniques: Control

Journal: Cells

Article Title: Ethanol Induces Neuroinflammation in a Chronic Plus Binge Mouse Model of Alcohol Use Disorder via TLR4 and MyD88-Dependent Signaling

doi: 10.3390/cells12162109

Figure Lengend Snippet: Effects of ethanol on FosB ( A ) and JunB ( B ) mRNA expression in the cerebellum of wild-type, TLR4-, MyD88-, and TRIF-deficient mice. Mice were given access to a control or ethanol liquid diet, as described in the Methods, and relative mRNA expression was measured using qRT-PCR. Results are expressed as ∆∆CT fold change relative to control for each genotype. Individual values for each sample were plotted and error bars denote mean +/− SEM. *** p < 0.001, ** p < 0.01, * p < 0.05, ns = not significant.

Article Snippet: Fosb , Mm00500403_m1.

Techniques: Expressing, Control, Quantitative RT-PCR