Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: (A) Schematic of the study design, showing tumor anatomical locations (top) and the ELMER approach for identifying Master Regulator Transcription Factors (MRTFs, bottom). (B) ELMER analysis was applied in each type of GIAC. A color is shown in each cell where the MRTF was identified (q < 0.05), and the color represents the p-value normalized for each GIAC (Z-score). (C) Scatter plots of top candidate MRTFs (HNF4A and HNF1A), showing the average DNA methylation level of predicted MRTF-binding regions (X axis) vs. the mRNA expression of the MRTF (Y axis) in each sample (dot). (D-E) Plots showing average WGBS methylation levels of predicted HNF4A binding sites, either averaged across all samples of the same subtype to show spatial pattern (left) or for each sample individually (right). (D) shows ELMER-predicted HNF4A binding sites, and (E) shows ESCA-specific ATAC-Seq peaks overlapping an HNF4A binding motif.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: DNA Methylation Assay, Binding Assay, Expressing, Methylation

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: (A) Expression of HNF4A in RNA-Seq data from TCGA Pan-Cancer samples. Each box represents a cancer type (TCGA abbreviations can be found at Supplemental Table 3. (B) HNF4A protein expression was interrogated using the IHC data from Human Protein Atlas project, and GIACs are highlighted in red. Representative IHC photos are shown as inserted panels. (C) IHC staining on 3 GIAC cohorts of internal samples. (D) Overall survival analyses of HNF4A expression in both EAC and COAD patients, from TCGA and other named studies.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: Expressing, RNA Sequencing Assay, Immunohistochemistry

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: (A) HNF4A gene amplification in SNP-array data from TCGA Pan-Cancer samples, with GIACs highlighted in red. (B) IGV (Integrative Genomics Viewer) plots of HNF4A -amplified GIACs samples. (C) mRNA level of HNF4A in GIAC samples with different HNF4A genomic status. Copy number gain refers to samples with between 2 and 4 copies of the HNF4A locus, and amplification refers to those with greater than 4 copies. (D) IGV plots showing HNF4A locus using both in-house WGBS samples (EAC=5, ESCC=12) and TCGA ATAC-Seq samples (EAC=6, COAD=38, STAD=21, ESCC=12, HNSCC=9). Arrows show several regions that are specifically accessible and demethylated in GIAC tumor types.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: Amplification

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: In EAC (Eso26), COAD (Colo205) and PAAD (Suit2) cell lines, HNF4A expression was silenced by three different shRNAs and followed by Western Blotting assay (A), cell proliferation assay (B), colony formation assay (C), and apoptosis assays (D). In (E), HNF4A was ectopically expressed and validated by Western Blotting in EAC (SKGT4 and OACM5.1), COAD (SNU398) and PAAD (ASPC-1) cells. HNF4A-overexpressing cells were subjected to cell proliferation (F) and colony formation (G) assays (OV-NC, overexpression control; OV-HNF4A, overexpression of HNF4A). Data is presented as Mean ± s.d. *, P<0.05; **, P<0.01. (H) High-throughput shRNA screen in a pan-cancer analysis of 500 cell lines from CCLE and DepMap. Scatter plot showing the HNF4A shRNA dependency score vs. the expression of HNF4A. (I) Scatter plot showing the mRNA expression of HNF4A and the methylation of its promoter. (J) Scatter plot showing the HNF4A dependency score vs. the methylation of HNF4A promoter. Each dot represents one cell line, and GIAC cells are highlighted.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: Expressing, Western Blot, Proliferation Assay, Colony Assay, Over Expression, High Throughput Screening Assay, shRNA, Methylation

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: (A) Western blotting assay (Left) validating the knockdown of HNF4A using Dox-inducible shRNA in Eso26 cells, which led to decreased cell proliferation in vitro (Right). (B) Tumor growth and (C) weight of the xenografts were significantly inhibited by HNF4A-silencing. (D) IHC staining of HNF4A and Ki-67 in xenograft samples. (E) qRT-PCR analysis (Left) and luciferase reporter assay (Right) validating the on-target effect of BI-6015. (F) Dose-response curves of GIAC and squamous cancer cell (SCC) lines treated with BI-6015 (72 hr). Data represent mean ± SD of three replicates. (G) Colony formation of Eso26 (EAC cell) and KYSE450 (SCC cell) treated with increasing dose of BI-6015. (H) Scatter plot showing the negative correlation between cell sensitivity (measured by IC50 of BI-6015) and HNF4A expression. Each dot represents one cell line. (I) Xenograft assay showed that BI-6015 inhibited the growth of GIAC tumors but did not affect the weight of the mice (J). Mean ± s.d. are shown. *, P<0.05; **, P<0.01.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: Western Blot, shRNA, In Vitro, Immunohistochemistry, Quantitative RT-PCR, Luciferase, Reporter Assay, Expressing, Xenograft Assay

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: (A) 4C-Seq assay showing the long-range interactions anchored on HNF4A promoter in Eso26 cells. Deeper red color indicates higher interaction frequency. (B) ChIP-Seq profiles for H3K27Ac and indicated MRTFs at HNF4A loci in Eso26 cells. (C) Zoom in view of ChIP-Seq signals. Connecting lines showing the most significant interactions detected by 4C. Shaded regions showing three enhancers (E1-E3) and one negative control (Ctrl) region which were separately cloned into the luciferase reporter vector. (D) Motif enrichment analysis of promoter and E1-E3 regions. (E) Enhancer activity measured by luciferase assays in Eso26 and KYSE450 cells. (F) Enhancer and promoter activity measured by luciferase assays in Eso26 cells upon silencing each of the 5 MRTFs. Mean ± s.d. are shown. *, P<0.05; **, P<0.01.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: ChIP-sequencing, Negative Control, Clone Assay, Luciferase, Plasmid Preparation, Activity Assay

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: (A) Western Blotting and (B) qRT-PCR assay upon each individual knockdown of indicated MRTFs in Eso26 cells. (C) Co-IP assay of GATA4, GATA6, and HNF4A in Eso26 cells. (D) Pathway enrichment analysis of the differentially expressed genes upon silencing of HNF4A in Eso26 cells. (E) HNF4A ChIP-Seq showing its binding peak at the enhancer of IL4R in Eso26 (EAC), Caco2 (COAD), GP5d (COAD) and LoVo (COAD) cells. (F) qRT-PCR analysis showed that knockdown of HNF4A decreased the expression level of the HNF4A targets of Interleukin signaling. (G) IL4R, LYN, ELK1 and IL6ST was silenced by individual siRNAs in Eso26 cells, and cell proliferation was measured. Mean ± s.d. are shown. *, P<0.05; **, P<0.01.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: Western Blot, Quantitative RT-PCR, Co-Immunoprecipitation Assay, ChIP-sequencing, Binding Assay, Expressing

Journal: bioRxiv

Article Title: Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

doi: 10.1101/812149

Figure Lengend Snippet: Proposed model of epigenomic and genomic activation of lineage-specific oncogene HNF4A which promotes GIAC cancers.

Article Snippet: HNF4A promoter luciferase reporter vector HNF4A-P2-2200 was purchased from Addgene (Addgene, 31062).

Techniques: Activation Assay