Project description:Our preliminary data from unbiased analyses of both ESCC patient samples and cell lines identified interferon-γ (IFN-γ) signaling pathway as the most significantly enriched pathways suppressed by TP63. To validate the activation of IFN pathways and the immune responses upon silencing of TP63, we utilized immune-competent mice to conduct allograft experiments. To analyze the effect of TP63 on ESCC tumor microenvironment, resected tumors were then collected to perform scRNA-seq.
Project description:Genomics studies have detected numerous genetic alterations in esophageal squamous-cell carcinoma (ESCC), a highly malignant and leading mortal cancer. However, the functions of these mutations in the formation and progression of ESCC largely remain elusive, partially due to lack of feasible animal models. Here, we report a convenient platform with normal esophageal organoids, CRISPR/cas9-mediated introduction of ESCC-associated genetic alterations, and orthotopic transplantation to generate a serial of primary ESCC models in mice. With this platform, we validated that multiple frequently mutated genes, including FAT1/2/4, NOTCH2, KMT2D, EP300, and TGFBR2, as bona fide tumor suppressor genes in ESCC. Among them, TGFBR2 loss dramatically promoted tumorigenesis and multi-organ metastasis. Paradoxically, TGFBR2 deficiency led to Smad3 activation and disruption of Smad3 could partially restrain the progression of Tgfbr2 mutated tumors. Drug screening with tumor organoids revealed that pinaverium bromide, a calcium channel blocker used for irritable bowel syndrome, could repress Smad3 activity and restrain Tgfbr2 deficient ESCC in vitro and in vivo. Our studies provide a highly efficient platform to investigate the in vivo functional of ESCC-associated mutations and develop potential treatment for this miserable malignancy.
Project description:Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC should improve identification of risk factors in molecular subtypes and provide potential targets for early detection and therapy. To better characterize molecular changes in ESCC, we followed up a previous cDNA array study with additional discovery and confirmatory studies in new ESCC cases using alternative methods. We profiled global gene expression (Affymetrix U133A/B chip) for discovery and confirmation, and validated selected dysregulated genes with additional RNA (qRT-PCR, N=51) or protein studies (immunohistochemistry [IHC] of tumor tissue microarray [TMA], N=275).We also found genes associated with survival. The dysregulated genes should aid in identifying risk factors in ESCC, as well as potential targets for early detection, and outcome prediction and therapy. 53 ESCC samples and 53 matched normal samples were analyzed (samples AE43 and AE45 were not run on HG-U133B due to not having enough material). Contributors have chosen not to include the clinical phenotypes in their GEO submission.
Project description:Protein identification in esophageal squamous cell carcinoma(ESCC) was performed,we explored the proteomic landscape in ESCC and attempted to perform clinical-related patient classification based on ESCC proteome.
Project description:To understand the difference of protein expression between paired esophageal squamous cell carcinoma (ESCC) and adjacent normal tissues, we collected 10 paired ESCC and normal tissues from surgical resected specimems for high-throughput proteomic experiments. From comparative analysis, the dysregulated signaling pathways in ESCC could be uncovered.
Project description:To discover ESCC related proteins, we used SWATH to quantify the protein abundance between ESCC and adjacent tissues. Briefly, we pooled 10 ESCCtissues and their corresponding adjacent tissues for SWATH acquisition with three replicates.Three DDA repeats were also acquired with the pooled 10-paired ESCC tissue.The trypsin digested peptide mixture was analyzed by AB SCIEX 5600 (AB SCIEX).The database searching procedure was achieved using ProteinPilot v4.5 (AB Sciex). The database is IPI_homo_sapiens_V3.87.
Project description:Genomic and proteomic studies have advanced our understanding of esophageal squamous cell carcinoma (ESCC) biology and pathogenesisGenomic and proteomic studies of esophageal squamous cell carcinoma (ESCC) have advanced our understanding of the biology and pathogenesis of the disease. However, the histone modification landscape inprofile of ESCC remains poorly characterized, especially from human clinical samplesunderstood. Here, we performed comprehensive histone modification profiling of paired samples from 122 ESCC patients, identifying numerous aberrantly expressed histone modification sitesand identified a number of modification sites that are aberrantly expressed in ESCC. Most of these alterations correlate with patient survivalMost of these differentially expressed histone modification sites are associated with survival in ESCC patients. In particular, H3K27ac is aberrantly expressed in tumor tissue and stroma and its high expression is significantly correlated with poor prognosis of ESCC patients. We analyzed the H3K27ac ChIP-seq data for primary ESCC tumor tissues and ESCC cell lines and identified hundreds of altered putative super-enhancers (SEs) in ESCC tissues respectively relative to ESCC cell lines. Moreover, these differential SEs contribute to the transcriptomic aberrations in ESCC tissues. Genes regulated by ESCC tissue- gained SEs are highly expressed in ESCC tissues compared to ESCCthan in cell lines and are mostly enriched in microenvironment-related pathways. We definerefer to these SEs as tumor microenvironment-acquired super-enhancers (TMEA-SEs). Through integrative analysis of ChIP-seq, RNA-seq, scRNA-seq and ATAC-seq data, we identified a TMEA-SE activated in cancer-associated fibroblasts (CAFs) and found that IL1R1 is directly regulated by this TMEA-SE. We demonstrated that IL1R1 activation can affect CAFs to promotes ESCC cells migration and invasion via CAFs. Collectively, our findings these observations reveal that a critical oncogenic mechanism in ESCC whereby TMEA-SE drive malignancy by activating IL1R1 in CAFs.
Project description:Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC should improve identification of risk factors in molecular subtypes and provide potential targets for early detection and therapy. To better characterize molecular changes in ESCC, we followed up a previous cDNA array study with additional discovery and confirmatory studies in new ESCC cases using alternative methods. We profiled global gene expression (Affymetrix U133A/B chip) for discovery and confirmation, and validated selected dysregulated genes with additional RNA (qRT-PCR, N=51) or protein studies (immunohistochemistry [IHC] of tumor tissue microarray [TMA], N=275).We also found genes associated with survival. The dysregulated genes should aid in identifying risk factors in ESCC, as well as potential targets for early detection, and outcome prediction and therapy.
Project description:Purpose: To identify TP63 expression regulated pathways in HNSCC Methods: A recombinant lentivirus encoding either NS shRNA or TP63 shRNA was introduced into a HNSCC cell line, FaDu. SCCs were gene generated by implanting either FaDu-NS shRNA (n=3) or FaDu-TP63 shRNA into the tongue of athymic nude mice. Tongue SCCs harvested at the end of study were used for transcriptome analysis