Journal: International journal of molecular sciences

Article Title: Cell Membrane-Integrated Neuroligin-1 Regulates the Anti-Inflammatory Effects of CRC Cell-Derived Exosomes.

doi: 10.3390/ijms26020503

Figure Lengend Snippet: Figure 6. M0 macrophages were treated with the exosomes of the NLG1 expressing (EXO) and NLG1 knock-downed (sh-EXO) CRC cells and the mRNA expression level (Log2 FC) of the CD206 and CD80 genes as phenotypical markers (a) and pro-inflammatory genes including IL8, IL6, IL1β, and TNFa as makers for the macrophage functionality (b), were analyzed using qRT-PCR. Data shown for qRT-PCR are the means ± standard deviation (SD).

Article Snippet: NLG1 silenced HuTu80 cell populations were generated by infection with lentiviral vectors targeting NLG1 from Origene: cat # TL3111634B (shNLGN1b) (pGFP-C-shLenti shRNA-29mer expression vector-ORIGENE, Rockville, MD, USA).

Techniques: Expressing, Quantitative RT-PCR, Standard Deviation

Journal: International journal of molecular sciences

Article Title: Cell Membrane-Integrated Neuroligin-1 Regulates the Anti-Inflammatory Effects of CRC Cell-Derived Exosomes.

doi: 10.3390/ijms26020503

Figure Lengend Snippet: Figure 5. M0 macrophages were treated with exosomes of NLG1-expressing CRC cells (HuTu80 cells), IL13+1L4 (M2-stimuli), LPS+INF-γ (M1-stimuli) for 48 h. The expression levels of CD206, and CD80 as makers for the macrophage phenotype (a), IL8, IL6, TNFa, and IL1β genes as makers for the macrophage functionality (b), were determined using qRT-PCR. Gene expression level (Log2 FC) was calculated relative to untreated M0 macrophages. Data shown are the means ± standard deviation (SD).

Article Snippet: NLG1 silenced HuTu80 cell populations were generated by infection with lentiviral vectors targeting NLG1 from Origene: cat # TL3111634B (shNLGN1b) (pGFP-C-shLenti shRNA-29mer expression vector-ORIGENE, Rockville, MD, USA).

Techniques: Expressing, Quantitative RT-PCR, Gene Expression, Standard Deviation

Journal: Nature Communications

Article Title: Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes

doi: 10.1038/s41467-023-37221-5

Figure Lengend Snippet: a IHC staining of the expression level of AARS1 from normal to advanced stage tissue. b Overrepresentation of AARS1 and PARP1 in tumor tissue is detected by western blot analysis ( n = 12 repeats per group) (two-sided Student’s t -test, mean ± SD). N = tumor-adjacent tissue, T = tumor tissue. The left panel shows western blot analysis of AARS1, TARS1, SARS1, PARP1, PARylation, actin, and lysine alanylation of PARP1 in tumor tissues and tumor-adjacent normal tissues. The bottom panel shows the quantified western blot results of 12 pairs of samples. The results of the other 6 pairs of samples are provided in Extended Data Fig. . c The impacts of AARS1 overexpression (OE) on Hutu80 cells and WDC-1 cells’ proliferation ( n = 5 repeats per group) (two-sided Student’s t -test, mean ± SD): vector (control), OE-AARS1, and OE-AARS1-alaninol. The value of OD450 and days are shown on the y - and x -axes, respectively. d The impacts of AARS1 knock-down (KO) on Hutu80 cells and WDC-1 cells’ proliferation ( n = 5 repeats per group) (two-sided Student’s t -test, mean ± SD): scrambled siRNA and AARS1 KO. e The effects of AARS1 OE (left)/KO (right) Hutu80 cells and WDC-1 cells invasion ( n = 5 repeats per group) (two-sided Student’s t -test, mean ± SD). f Gene Ontology enrichment analysis of AARS1-interacting proteins in biological processes. These proteins are identified by a proteomics survey using tandem affinity purification. g Co-immunoprecipitation assay showing that exogenous AARS1 and exogenous PARP1 interacted in cultured Hutu80 cells and WDC-1 cells. h The impacts of AARS1 on cellular PARylation level. i Activities of PARP1 immunoprecipitated from cells transfected with different aminoacyl-tRNA synthetases ( n = 5 repeats per group) (two-sided Student’s t -test, mean ± SD). **** p < 1.0E−4, *** p < 1.0E−3, ** p < 1.0E−2, * p < 0.05, ns. >0.05. Source data are provided as a Source data file.

Article Snippet: Human Hutu80 (ATCC, Catalog: CRL-7928; RRID: CVCL_1301) and WDC-1 (Cobioer, Catalog: CBP61181, RRID: CVCL_R803) cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA), 100 units/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen).

Techniques: Immunohistochemistry, Expressing, Western Blot, Over Expression, Plasmid Preparation, Control, Knockdown, Affinity Purification, Co-Immunoprecipitation Assay, Cell Culture, Immunoprecipitation, Transfection

Journal: Nature Communications

Article Title: Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes

doi: 10.1038/s41467-023-37221-5

Figure Lengend Snippet: a The impacts of AARS overexpressing (OE) in Hutu80 cells and WDC-1 cells apoptosis ( n = 5 repeats per group) (two-sided Student’s t -test, mean ± SD): OE-AARS1, OE-AARS1-alaninol, CPT, OE-AARS1-CPT, and OE-AARS1-CPT-alaninol. CPT camptothecins. b Immunofluorescence staining of γH2AX with various treatments: OE-AARS1 and OE-AARS1-CPT. The scale bar indicates 20 µm. c The effects of AARS1 and PARP1 on K-Ala levels. d The capacity of SIRT6 to dealanylate the synthetic PARP1 K621-Ala peptide. e K-Ala levels in cells with different treatments. f DNA binding affinities of PARP1 and PARP1 mutants ( n = 5 repeats per group, two-sided Student’s t -test, mean ± SD). K-Ala: lysine-alanylation. g PARP1 activities in PARP1 WT and PARP1 mutants. h The impacts of alaninol on cellular K-Ala and PARylation levels. i Tumor sizes of cell xenografts with different treatments in normal nude mice or alaninol-fed nude mice. n = 6 mice per group. **** p < 1.0E−4, *** p < 1.0E−3, ** p < 1.0E−2, * p < 0.05, ns. >0.05. Source data are provided as a Source data file.

Article Snippet: Human Hutu80 (ATCC, Catalog: CRL-7928; RRID: CVCL_1301) and WDC-1 (Cobioer, Catalog: CBP61181, RRID: CVCL_R803) cells were cultured in RPMI 1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA), 100 units/mL penicillin (Invitrogen), and 100 μg/mL streptomycin (Invitrogen).

Techniques: Immunofluorescence, Staining, Binding Assay