Journal: Clinics

Article Title: RNA-binding protein with serine-rich domain 1 regulates microsatellite instability of uterine corpus endometrial adenocarcinoma

doi: 10.6061/clinics/2021/e3318

Figure Lengend Snippet: (A) GSEA of the correlation between RNPS1 and Notch or Notch4 signaling pathway in UCEC. (B) Western blot assay for the analysis of the RNPS1, MSH1, MSH2, MSH6, and PMS2 expression levels in vivo . (B) Quantitation of RNPS1, MSH1, MSH2, MSH6, and PMS2 expression levels. (n=6, * p <0.05: sh-RNPS1 vs. Con; # p <0.05: IMR-1A+sh-RNPS1 vs. sh-RNPS1).

Article Snippet: The secondary antibodies used were anti-rabbit IgG (AS014) and anti-mouse IgG (H+L) (AS003), both from ABclonal (Wuhan, China), and IMR-1A (HY-100431A; MedChemExpress, Dallas, TX, USA).

Techniques: Western Blot, Expressing, In Vivo, Quantitation Assay

Journal: Genome Research

Article Title: Reorganization of the host epigenome by a viral oncogene

doi: 10.1101/gr.132308.111

Figure Lengend Snippet: Small e1a causes global deacetylation and redistribution of H3K18ac. ( A ) Venn diagram showing the overlap between significant peaks of H3K18ac in mock- (dark blue) and dl 1500-infected cells (light blue). ( B ) Venn diagram showing the overlap between significant peaks of H3K9ac in mock- (dark orange) and dl 1500-infected cells (yellow). ( C ) Patterns of H3K18ac and H3K9ac in the intergenic region between COPS8 and COL6A3 genes in mock-, dl 1500-infected, and asynchronous IMR90 cells. ( D ) Quantitative PCR (% of input) for EP300 and CREBBP in mock- and dl 1500-infected cells for the COL6A3 intergenic region, and CCNE2 and POLD3 promoters are shown as bar plots. Patterns of H3K18ac in mock- and dl 1500-infected cells at CCNE2 and POLD3 loci are also shown. For each histone modification, the y -axis indicates the number of input-normalized ChIP-seq reads across the locus ( x -axis). (Light blue arrows) New peaks of acetylation in e1a-expressing cells. (Dark arrows) Direction of transcription. ( E , F ) Overview of distribution of H3K18ac and H3K9ac peaks in mock- and dl 1500-infected cells in relation to gene structure are shown as pie charts. ( G ) Distribution of significant peaks of H3K18ac with respect to TSS in mock- (dark blue) and dl 1500-infected (light blue) cells. ( H ) Distribution of significant peaks of H3K9ac with respect to TSS in mock- (dark orange) and dl 1500-infected (yellow) cells.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO 2 .

Techniques: Infection, Real-time Polymerase Chain Reaction, Modification, ChIP-sequencing, Expressing

Journal: Genome Research

Article Title: Reorganization of the host epigenome by a viral oncogene

doi: 10.1101/gr.132308.111

Figure Lengend Snippet: Analyses of RB-family protein genome-wide binding in contact-inhibited IMR90 fibroblasts. ( A ) Overview of RB1, RBL2, and RBL1 peak distributions in mock-infected cells in relation to gene structure are shown as pie charts. ( B ) Average binding profiles (significant counts) of the indicated RB-family members across the TSS regions of their respective target genes. ( C ) A 600-bp region around the peaks of RB1, RBL2, and RBL1 in mock-infected cells were analyzed for TF binding motifs using sitepro (Galaxy). Top three significant motifs for each family member are shown. All P -values are less than 1 × 10 −10 . ( D ) The distributions of the RB-family proteins across ±5 kb of TSS for genes with at least one RB-family member bound are shown as heat maps. The seven clusters are based on combinatorial binding patterns of the three proteins. ( E ) Relative gene expression changes of each of the seven clusters after e1a expression at 24 h p.i. are shown as box plots.

Article Snippet: IMR90 human primary lung embryo fibroblasts (ATCC) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 10% fetal bovine serum (FBS) at 37°C in 5% CO 2 .

Techniques: Genome Wide, Binding Assay, Infection, Gene Expression, Expressing

Journal: Nature Aging

Article Title: Modulating IL-11-dependent matrix stiffness to delay ovarian aging

doi: 10.1038/s43587-026-01159-2

Figure Lengend Snippet: a , Immunofluorescent staining of COL1A1 and TGFβ1. L and H represent regions with low and high coexpression of COL1A1 and TGFβ1, respectively. b , Measurement of ovarian matrix stiffness in COL1A1 lo TGFβ1 lo or COL1A1 hi TGFβ1 hi regions. Data are presented as the mean ± s.d. (Welch’s two-sided t -test). n = 20 per group. c , Schematic of RNA-seq of primary human ovarian fibroblasts (pHOFs) after in vitro TGFβ1 treatment (10 ng ml −1 , 24 h). d , IL11 RNA expression is upregulated in pHOFs stimulated with TGFβ1. Differential expression was assessed using a two-sided Wald test, with P values adjusted for multiple comparisons through the Benjamini–Hochberg method ( n = 3 per group). e , IL-11 protein abundance in human, mouse and rat ovaries across different age groups. f , Representative images of IL-11 immunohistochemical staining in ovaries from individuals of different ages or with ovarian dysfunction due to various diseases. g , Representative images of pHOFs immunostained for COL1A1 and ACTA2 after 24 h of incubation without stimulus (control), TGFβ1 (10 ng ml −1 ) or IL-11 (10 ng ml −1 ) or with TGFβ1 (10 ng ml −1 ) and an anti-IL-11 neutralizing antibody (2 μg ml −1 ). h , GO and KEGG enrichment analysis of differentially expressed genes in pHOFs incubated without stimulus (control) or IL-11 (10 ng ml −1 ) for 24 h. Red labels highlight GO terms enriched in pathways related to the ECM and its receptor. The analyses were performed using the hypergeometric test. P values were adjusted for multiple comparisons using the Benjamini–Hochberg FDR method. n = 3 per group. i , COL1A1 mRNA expression in pHOFs treated with IL-11 or IL-11 and NOTCH pathway inhibitor (PF-3084014, IMR-1), PI3K–AKT pathway inhibitor (PI3K/AKT-IN-1, BYL-719), cGMP–PKG pathway inhibitor (KT5823, MBP146-78), p38 MAPK pathway inhibitor (p38 MAPK-IN-1, SB 203580), ERK1/2 pathway inhibitor (ravoxertinib, SCH772984), JNK pathway inhibitor (JNK-IN-7, SP600125) or mTOR pathway inhibitor (rapamycin, everolimus). Red box highlighting indicates the ERK1/2 inhibitor group, which showed the most significant reduction in IL‑11‑induced COL1A1 upregulation. Data are presented as mean ± s.d., n = 3 for each group (unpaired two-tailed t -test or Welch’s two-tailed t -test). j , k , Human phospho-kinase array of pHOFs treated with 10 ng ml −1 IL-11 or vehicle control for 24 h. Numbers 1–8 on the blot ( j ) and the corresponding bars ( k ) indicate the following: 1) CREB at serine 133; 2) ERK1/2 at threonine 202 and tyrosine 204; 3) GSK3β at serine 9; 4) WNK1 at threonine 60; 5) β‑Catenin; 6) RSK1/2 at serine 221 and serine 227; 7) RSK1/2/3 at serine 380, serine 386 and serine 377; 8) STAT3 at tyrosine 705. Data are presented as the mean ± s.d., n = 3 for each group (unpaired two-tailed t -test). l , Western blot analysis of COL1A1 and ACTA2 expression in pHOFs treated with IL-11, with or without the ERK1/2 inhibitor SCH772984. m , Representative immunofluorescence images and quantification of COL1A1 and ACTA2 in pHOFs treated with IL-11 or IL-11 + SCH772984. int., integrated intensity. Data are presented as the mean ± s.d., n = 5 per group (one-way ANOVA).

Article Snippet: Experiments were carried out at low cell passages (≤ passage 3) and HOFs were treated with TGFβ1 (10 ng ml −1 ) or IL-11 (10 ng ml −1 ) in serum-free DMEM for 24 h. For pathway screening studies, HOFs were stimulated with IL-11 in the presence of PF-3084014 (10 μM, MedChemExpress), IMR-1 (10 μM, MedChemExpress), PI3K/AKT-IN-1 (5 μM, MedChemExpress), BYL-719 (250 nM, MedChemExpress), KT5823 (5 μM, MedChemExpress), MBP146-78 (150 nM, MedChemExpress), p38 MAPK-IN-1 (50 nM, MedChemExpress), SB 203580 (50 nM, MedChemExpress), ravoxertinib (5 nM, MedChemExpress), SCH772984 (5 nM, MedChemExpress), JNK-IN-7 (5 nM, MedChemExpress), SP600125 (100 nM, MedChemExpress), rapamycin (50 nM, MedChemExpress) or everolimus (10 nM, MedChemExpress) for 24 h. The anti-IL-11 antibody (R&D Systems, cat. no. MAB218, human) was used to neutralize IL-11 activity, and the Neutralization Dose (ND50) was 80 μg ml −1 in the presence of 10 ng ml −1 recombinant human IL-11.

Techniques: Staining, RNA Sequencing, In Vitro, RNA Expression, Quantitative Proteomics, Immunohistochemical staining, Incubation, Control, Expressing, Two Tailed Test, Western Blot, Immunofluorescence