OBJECTIVETo screen and identify the new long non-coding RNAs from transcriptome of laryngeal squamous cell cancer using strand-specific RNA-Seq technology and bioinformatics tools, and to analyze the difference expression of these LncRNAs.

METHODSRNA was extracted from laryngeal squamous cell cancer tissues of 10 patients and the strand-specific libraries were constructed for high-throughput sequencing. The low-quality data were filtered and the high quality sequencing reads were mapped to the reference genome and assembled. The obtained transcripts were classified and annotated, the optimized LncRNA identification pipeline was used to discover novel LncRNA in these transcriptome, and the characteristics of LncRNA were analyzed.

RESULTSA more optimized pipeline were established and 134 new LncRNA transcripts were found, which was not included in the public database. The new LncRNA transcripts had some characteristics in length distribution, ORF length, and expression.

CONCLUSIONSome new LncRNA from the transcriptome of laryngeal carcinoma were identified, with different expression, and they may play an important role in laryngeal squamous cell cancer.

Carcinoma ; genetics ; Genome ; Humans ; Laryngeal Neoplasms ; genetics ; RNA ; RNA, Long Noncoding ; Transcriptome

OBJECTIVEBy collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient.

METHODSBased on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer.

RESULTSThe established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly.

CONCLUSIONThe database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

Databases, Genetic ; Genes, Neoplasm ; Humans ; Internet ; Laryngeal Neoplasms ; genetics ; MicroRNAs ; genetics

OBJECTIVEThe effects of lentivirus-mediated suppression of Cyclin Y (CCNY) expression on the proliferation of laryngeal cancer cells were investigated in vitro.

METHODSThe lentivirus vectors containing a small hairpin RNA (shRNA) to target CCNY were constructed.Hep-2 cells were divided into the following two experimental groups:the negative control group (control lentivirus infected cells) and CCNY knockdown group (CCNY shRNA-expressing lentivirus infected cells). After Hep-2 cells were infected, Real-time PCR was used to measure CCNY expression. The influence of CCNY on the proliferation of laryngeal cancer cells were assessed using MTT and colony formation experiments.Each experiment was performed in triplicate and repeated three times.

RESULTSLentiviruses expressing shRNA against CCNY were constructed and Hep-2 cells were infected with above mentioned lentivirus at MOI (Multiplicity of infection) of 120.Real-time PCR analysis showed that the mRNA expression of CCNY in Hep-2 cells in the knockdown group was significantly decreased (P < 0.05); the mRNA level of CCNY was 75.3% lower in the si-CCNY group than in the si-CTRL group. After 5 days of lentiviral infection, the cell viability was significantly lower in cells infected with the CCNY-shRNA lentivirus compared to cells infected with the control lentivirus following a 6-day incubation. The colony number was decreased by 60% in Hep-2 cells infected with the CCNY-shRNA-lentivirus infected cells following a 10-day incubation.

CONCLUSIONSThe results suggested that lentivirus-mediated downregulation of CCNY expression decreased the proliferation and growth potency of laryngeal cancer cells.Lentiviruses delivering shRNA against CCNY may be a promising tool for laryngeal cancer therapy.

Cell Line, Tumor ; Cell Proliferation ; Cyclins ; Humans ; Laryngeal Neoplasms ; metabolism ; Lentivirus ; genetics ; RNA, Small Interfering ; genetics

OBJECTIVE: To explore the association of XRCC3 gene polymorphisms and haplotypes with laryngeal. METHOD: We selected 4 tag SNPs (rs12432907, rs861536, rs861537, rs861531, rs861531) for the present study. 310 laryngeal patients and 310 healthy control subject were genotyping. The distribution of genotypes and haplotypes in these two group was compared. RESULT: The distributions of rs12432907 was significantly different between these two groups. The CCAG haplotype frequency was higher in laryngeal group than that in control group. But TCAG and TTAG haplotype frequency was were lower in the laryngeal patient than that those in the control subject. CONCLUSION XRCC3 gene polymorphism was associated with the risk of laryngeal patients.
Case-Control Studies ; DNA-Binding Proteins ; genetics ; Genotype ; Haplotypes ; Humans ; Laryngeal Neoplasms ; genetics ; Polymorphism, Single Nucleotide

OBJECTIVE: To observe expression of stathmin gene in laryngeal squamous cell carcinoma (LSCC) and relation between expression of stathmin gene and occurrence and development of LSCC. METHOD: The expression of the stathmin gene was determined in 35 LSCC of specimens and 18 normal laryngeal tissues (NLT) of specimens by in situ hybridization with Digoxigenin labeled probe of stathmin mRNA. RESULT: Expression of stathmin gene was observed in 35 cases of laryngeal squamous cell carcinoma tissue (positive rate, 69%) and positive signal was observed in both cytoplasm and nuclear. Among 18 cases of normal tissue, only 6 showed weak positive signal. There was significant difference in expression of stathmin gene between laryngeal squamous cell carcinoma tissue and normal tissue. CONCLUSION Expression of stathmin gene may play a key role in the pathogenesis and development of laryngeal squamous cell carcinoma. It may be a very important biotherapy target in the treatment of laryngeal squamous cell carcinoma.
Carcinoma, Squamous Cell ; genetics ; metabolism ; pathology ; Gene Expression ; Humans ; Laryngeal Neoplasms ; genetics ; metabolism ; pathology ; RNA, Messenger ; genetics ; Stathmin ; genetics ; metabolism

Carcinoma, Squamous Cell ; genetics ; Cell Division ; Chromosome Deletion ; Humans ; Laryngeal Neoplasms ; genetics ; Telomere ; genetics ; Tumor Cells, Cultured

OBJECTIVE: To study the impacts of RelA antisense oligonucleotides on proliferation in laryngeal carcinoma Hep-2 cell. METHOD: RelA antisense oligonucleotides was designed, which was transferred into laryngeal carcinoma Hep-2 cell. MTT was used to detect the growth-inhibiting ratio at different transferred timepoints. Hep-2 cell which was transferred 48 h was used to do colony assay, and expression of RelA was detected by Reverse Transcription PCR and Western blot. RESULT: MTT results showed that RelA antisense oligonucleotides could significantly suppress the proliferation of Hep-2 cell, and the suppression-ratio elevated with time. There were statistical difference compared with control groups. The number of cells colony was reduced in RelA antisense oligonucleotides group compared with control groups, which had statistic significance. RT-PCR and Western blot results demonstrated that RelA antisense oligonucleotides could significantly inhibit the expression of messenger RNA and protein in Hep-2 cell. CONCLUSION RelA antisense oligonucleotides can inhibit the expression of messenger RNA and protein, and induce the cell proliferation and increase the number of cells colony in Hep-2 cell.
Cell Line, Tumor ; Cell Proliferation ; drug effects ; Humans ; Laryngeal Neoplasms ; genetics ; pathology ; Oligonucleotides, Antisense ; genetics ; pharmacology ; Transcription Factor RelA ; genetics

OBJECTIVE: To detect the expression of microRNAs (miRNAs) in laryngeal carcinoma and adjacent normal tissue using microarray, and to discuss the relationship between miRNAs and laryngeal carcinoma. METHOD: miRNA were extracted from 8 cases of laryngeal cancer tissue and its adjacent normal tissue. miRNA identification were performed by microarray of miRNA hybridization and cluster analysis was used with Significance Analysis of Microarrays (SAM, version 2.1) and Cluster 3.0 software. miRNA were confirmed by real time quantification RT-PCR with RNA-tailing and primer extension. RESULT: Totally 47 different miRNAs were found expressed in laryngeal cancer, with 23 of miRNA expression were up-regulated and 24 of miRNA expression were down-regulated. The expression of miR-1, miR-486-5p, miR-206, miR-487a,miR-375, miR-422a, miR-144, miR-384, miR-378, miR-133a were down-regulated by 5 multiple and while expression of miR-93, miR-31, miR-20b were up-regulated by 3 multiple. There are 5 miRNA clusters with coexpression in laryngeal cancer tissue and located on chromosome 8, 13, 14, 18 and X. Moreover, RT-PCR analysis demonstrated that there was no significantly difference of miRNA expression between microarray and RT-PCR. CONCLUSION The different expression of miRNA may play an important role in the pathogenesis and development of laryngeal cancer.
Adult ; Female ; Gene Expression Profiling ; Humans ; Laryngeal Mucosa ; pathology ; Laryngeal Neoplasms ; genetics ; pathology ; Male ; MicroRNAs ; genetics ; Microarray Analysis ; Middle Aged ; Oligonucleotide Array Sequence Analysis

OBJECTIVETo search for characteristic chromosome changes in primary laryngeal squamous cell carcinoma (LSCC) and Hep-2 cell line and to realize the relationship between the cytogenetic abnormality and the pathogenetic mechanism in LSCC.

METHODSThe fresh resulted samples of LSCC were analyzed with an improved primary cell culture for chromosome preparation and G-banding technique. Hep-2 cell line was analyzed by high resolution banding technique. Molecular cytogenetics analysis was made by chromosome 6 painting probe.

RESULTSFour primary LSCC succeeded in primary cell culture and obtained metaphases, one was tetraploid, the other three were triploid. The chromosome mode of Hep-2 cell line was from 68 to 75 and fifteen marker chromosomes were found. The most structural abnormalities of chromosome in primary LSCC and HEP-2 cell line were unbalance translocation, terminal deletion and isochromosome. The complicate aberration in chromosome 6 was common in LSCC and Hep-2.

CONCLUSION6q-, I(5p), 17p-, 5q- are considered as characteristic chomosome changs in LSCC. Fluorescence in situ hybridization (FISH) may enhance the ability of detecting complicated chromosome rearrangements and marker chromosomes, which could provide more value data to verify the chromosome characteristic aberration in LSCC.

Cell Line, Tumor ; Chromosome Aberrations ; Humans ; In Situ Hybridization, Fluorescence ; Laryngeal Neoplasms ; genetics ; pathology ; Tumor Cells, Cultured

OBJECTIVES: Laryngeal cancer (LC) is a globally prevalent and highly lethal tumor. Despite extensive efforts, the underlying mechanisms of LC remain inadequately understood. This study aims to conduct an innovative bioinformatic analysis to identify hub genes that could potentially serve as biomarkers or therapeutic targets in LC. METHODS: We acquired a dataset consisting of 117 LC patient samples, 16 746 LC gene RNA sequencing data points, and 9 clinical features from the Cancer Genome Atlas (TCGA) database in the United States. We employed weighted gene co-expression network analysis (WGCNA) to construct multiple co-expression gene modules. Subsequently, we assessed the correlations between these co-expression modules and clinical features to validate their associations. We also explored the interplay between modules to identify pivotal genes within disease pathways. Finally, we used the Kaplan-Meier plotter to validate the correlation between enriched genes and LC prognosis. RESULTS: WGCNA analysis led to the creation of a total of 16 co-expression gene modules related to LC. Four of these modules (designated as the yellow, magenta, black, and brown modules) exhibited significant correlations with 3 clinical features: The age of initial pathological diagnosis, cancer status, and pathological N stage. Specifically, the yellow and magenta gene modules displayed negative correlations with the age of pathological diagnosis (r=-0.23, P<0.05; r=-0.33, P<0.05), while the black and brown gene modules demonstrated negative associations with cancer status (r=-0.39, P<0.05; r=-0.50, P<0.05). The brown gene module displayed a positive correlation with pathological N stage. Gene Ontology (GO) enrichment analysis identified 77 items, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified 30 related signaling pathways, including the calcium signaling pathway, cytokine-cytokine receptor interaction, neuro active ligand-receptor interaction, and regulation of lipolysis in adipocytes, etc. Consequently, central genes within these modules that were significantly linked to the overall survival rate of LC patients were identified. Central genes included CHRNB4, FOXL2, KCNG1, LOC440173, ADAMTS15, BMP2, FAP, and KIAA1644. CONCLUSIONS This study, utilizing WGCNA and subsequent validation, pinpointed 8 genes with potential as gene biomarkers for LC. These findings offer valuable references for the clinical diagnosis, prognosis, and treatment of LC.
Humans ; Laryngeal Neoplasms/genetics* ; Rosaniline Dyes ; Biomarkers ; Adipocytes ; Gene Regulatory Networks ; Gene Expression Profiling