Methods in molecular biology
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Mass spectrometry-based proteomics analysis could categorize proteins and study their interactions in large scale in human cancers. By this method, many proteins are upregulated or downregulated in esophageal squamous cell carcinoma (ESCC) when compared to nonneoplastic esophageal mucosae. ⋯ Different biological matrices such as pathological tissue, body fluids, and cancer cell lines-based proteomics have widely been used. Herein, we described cell line-based label-free shotgun proteomics (in-solution tryptic digestion) to identify the protein biomarkers differently expressed in ESCC.
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Early detection of cancer and the monitoring of cancer recurrence in treated patients are significant challenges in esophageal squamous cell carcinoma (ESCC). Liquid biopsy is the identification of tumor biomarkers from minimally invasive samples of biological fluids, including urine, blood, stool, saliva, or cerebrospinal fluid. ⋯ These sources of information have the potential to significantly improve the management of patients with ESCC. In this chapter, we detail a method for the isolation of cell-free DNA from blood plasma and DNA associated with exosomes in blood from patients with esophageal squamous cell carcinomas.
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Pathological assessment of frozen sections of tissues is important in the clinical management (intraoperative consultation) and research in patients with esophageal squamous cell carcinoma. Frozen sections may be used in the assessment of status of resection margins, extent of cancer metastasis (pathological staging), confirmation of the pathology, and increased volume of cancer cells for tissue banking. However, the applications of frozen sections have many technical limitations. Thus, interpretation of frozen sections needs expertise, collaborations, and attention to proper technical skills in the sectioning.
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The simple applicability and facile target programming of the CRISPR/Cas9-system abolish the major boundaries of previous genome editing tools, making it the tool of choice for generating site-specific genome alterations. Its versatility and efficacy have been demonstrated in various organisms; however, accurately predicting guide RNA efficiencies remains an organism-independent challenge. Thus, designing optimal guide RNAs is essential to maximize the experimental outcome. Here, we summarize the current knowledge for guide RNA design and highlight discrepancies between different experimental systems.
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MicroRNAs (miRNAs) are 20-22 nucleotides long single-stranded noncoding RNAs. They regulate gene expression posttranscriptionally by base pairing with the complementary sequences in the 3'-untranslated region of their targeted mRNA. Aberrant expression of miRNAs leads to alterations in the expression of oncogenes and tumor suppressors, thereby affecting cellular growth, proliferation, apoptosis, motility, and invasion capacity of gastrointestinal cells, including cells of esophageal squamous cell carcinoma (ESCC). ⋯ Consequently, expression profiles of miRNAs could be useful as diagnostic, prognostic, and prediction biomarkers in ESCC. Herein, we describe the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and microarray methods for detection and quantitate miRNAs in ESCC. In addition, we summarize the roles of miRNAs in ESCC pathogenesis, progression, and prognosis.