Project description:In this study we have sequenced the ctDNA of 28 Squamous Cell Carcinoma patients in the TP53 gene, each sample has been sequenced twice.
Project description:Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis due to the development of locoregional recurrences, distant metastases and second primary tumors. There is an urgent need for biomarkers that enable detection and monitoring of the disease to provide adequate therapeutic strategies. In this study we have investigated markers in peripheral blood cells (PBC) of 28 HNSCC patients who underwent surgery by means of expression profiling. Our hypothesis is that nucleated blood cells circulate continuously, also passing the tumor, and might change their expression profiles in response to tumor cell factors. For comparison, we enrolled a control group of 11 patients who underwent surgery in the head and neck region for non-HNSCC reasons. A set of 2,349 genes was found to be statistically different between the groups (p<0.05, false discovery rate-corrected) and the most prominently different pathways were EIF2 and mTOR signaling. These preliminary results are promising and warrant further studies on the definitive role of PBC gene expression as a biomarker for HNSCC detection and monitoring. Two-color experiment with each individual sample in a single channel. RNA of nucleated blood cells of humans was analysed. Case-control analysis, with 28 cases, patients with head and neck squamous cell carcinoma and 11 controls, without squamous cell carcinoma
Project description:Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (Squamous cell carcinoma), aC (AC) and large-cell carcinoma (Large cell carcinoma). The aim of this study was to gain a systems biology insight into the current clinical classification. Patients and Methods: Comparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC. Using integrated systems biology approches, we sought to find out if combining data types from different levels of biology would improve clinical assessment of NSCLC. Results: At both DNA, RNA and miRNA levels we could identify molecular markers that discriminated significantly between the various clinicopathological entities of NSCLC. Conclusions: We report proofs of distinct molecular profiles that contribute to distinguishing NSCLC tumor subtypes even in small biopsies. The246 miRNA experiments have been made in single color with Agilent Human Genome miRNA 15K arrays v3 (design 021827).
Project description:Tumor-adjacent tissues are very important for tumor research. This study aimed to identify hub genes in tumor-adjacent tissues of mice transplanted with 786-o renal cell carcinoma cells. 786-o cells were implanted in nude mice raised to 1 month of age, and normal tissues, tumor tissues, and adjacent tissues were obtained for RNA sequencing. All tissues were sequenced for transcriptome genes. This was the first systematic exploration of the hub genes in the tumor-adjacent tissues of mice transplanted with 786-o renal cell carcinoma cells, which provides a genetic basis for further in-depth study on the underlying regulatory mechanism of renal cell carcinoma.
Project description:To identify differentially expressed genes in tumor tissues, several human cancer tissues (hypopharyngeal squamous cell carcinoma, maxillary sinus squamous cell carcinoma, and renal cell carcinoma) were subjected to Agilent whole genome microarrays. A total of nine pairs of primary hypopharyngeal squamous cell carcinoma samples and adjacent normal mucosa were obtained from patients who underwent tumor resection at Chiba University Hospital (Chiba, Japan). A total of seven pairs of primary maxillary sinus squamous cell carcinoma samples and adjacent normal mucosa were obtained from patients who underwent tumor resection at Chiba University Hospital (Chiba, Japan). A total of five pairs of renal cell carcinoma samples and adjacent normal tissues were obtained from patients who underwent tumor resection at Kagoshima University Hospital (Kagoshima, Japan). The Ethics Committee of Chiba University and the Bioethics Committee of Kagoshima University approved our study, and informed consent was obtained from all patients for use of their tissue samples and clinical data. The tissue samples were immediately frozen in liquid nitrogen and stored at -80°C until use.
Project description:To better understand tumor microenvironment and tumor heterogeneity in head and neck squamous cell carcinoma, we profiled primary tumors from two treatment naive patients by single-cell sequencing.
Project description:CSMD1 gene, mapping to human chromosomal region 8p23, encodes a transmembrane protein with an extracellular region containing 14 CUB and 28 sushi domains, a transmembrane domain and a cytoplasmic domain with a putative tyrosine phosphorylation site.The loss of CSMD1 has been found to be associated with enhanced cell proliferation, migration and poor prognosis in head and neck squamous cell carcinoma (HNSCCs), lung squamous cell carcinoma (SCCs), melanoma, and breast cancer, suggesting its role as a tumor suppresser.However, its role in hypertrophic scar has not been uncovered. So we decided using fibroblasts to see its transcriptomes changing after CSMD1 knockdown.
Project description:RNA of tumor samples from 14 patients with head and neck squamous cell carcinoma treated anti-PD1 was analyzed on the nCounter system using the Pan cancer IO360 panel
Project description:Human hypopharygeal squamous cell carcinoma (HSCC) is a common head and neck cancer with a poor prognosis in advanced stages. Determining genes associated with transferring in HSCC could provide new targets and therapeutic strategies. We performed single-cell RNA sequencing of hypopharyngeal carcinoma and lymphoid metastases from five patients with hypopharyngeal squamous cell carcinoma.
