Identification of biomarkers in laryngeal cancer by weighted gene co-expression network analysis / 中南大学学报(医学版)

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.

Genetic polymorphisms in the Cytochrome P450 family and squamous cell carcinoma of the oral cavity, pharynx and larynx / Polimorfismos genéticos da família Citocromo P450 e carcinoma de células escamosas de cavidade oral, faringe e laringe

Objective: To analyze the genetic polymorphisms of the cytochrome P450 family and their relationship with squamous cell carcinoma of the oral cavity, pharynx and larynx. Methods: We present a narrative literature review, conducted in Pubmed, Lilacs and Cochrane Databases of articles published in the last five years correlating genetic polymorphisms of the cytochrome P450 family and cancer risk in different populations worldwide. Results: We initially found 65 articles and, after selection criteria, 20 case-control studies with various populations worldwide were eligible. The most studied polymorphisms were those of CYP2E1 and CYP1A1 subfamilies. There is little about the other subfamilies. The association found between polymorphisms and cancer risk amounted to a countless number of variables, amongst them: population, selection methods, racial factors and different modes of exposure to carcinogens, genotyping methods, and nomenclature of the polymorphisms. Conclusion: so far, there is no proven link between genetic polymorphisms of cytochrome P450 family and squamous cell carcinoma of the oral cavity, pharynx and larynx relationship. .

Objetivo: analisar os polimorfismos genéticos da família Citocromo P450 e sua relação com o carcinoma de células escamosas de cavidade oral, faringe e laringe. Métodos: por meio de uma Revisão Narrativa de literatura, realizada nas principais bases de dados Pubmed, Lilacs, e Cochrane Database, de artigos publicados nos últimos cinco anos, correlacionando polimorfismos genéticos da família citocromo P450 e risco de câncer nas diversas populações mundiais. Resultados: foram encontrados inicialmente 65 artigos, que, após critérios de seleção, tornaram elegíveis 20 artigos do tipo caso-controle em diversas populações mundiais. Os polimorfismos mais estudados foram os das subfamílias CYP1A1 e CYP2E1. Pouco existe sobre as demais subfamílias. A associação entre os polimorfismos encontrados e risco de câncer sofreu um incontável número de variáveis, entre elas, população estudada, métodos de seleção, fatores raciais e diferentes modos de exposição aos carcinógenos, métodos de genotipagem, e nomenclatura dos polimorfismos. Conclusão: até o momento, não existe relação comprovada entre os polimorfismos genéticos da família Citocromo P450 e o carcinoma de células escamosas de cavidade oral, faringe e laringe. .

Identification of microRNAs and mRNAs associated with multidrug resistance of human laryngeal cancer Hep-2 cells

Multidrug resistance (MDR) poses a serious impediment to the success of chemotherapy for laryngeal cancer. To identify microRNAs and mRNAs associated with MDR of human laryngeal cancer Hep-2 cells, we developed a multidrug-resistant human laryngeal cancer subline, designated Hep-2/v, by exposing Hep-2 cells to stepwise increasing concentrations of vincristine (0.02-0.96'µM). Microarray assays were performed to compare the microRNA and mRNA expression profiles of Hep-2 and Hep-2/v cells. Compared to Hep-2 cells, Hep-2/v cells were more resistant to chemotherapy drugs (∼45-fold more resistant to vincristine, 5.1-fold more resistant to cisplatin, and 5.6-fold more resistant to 5-fluorouracil) and had a longer doubling time (42.33±1.76 vs 28.75±1.12'h, P<0.05), higher percentage of cells in G0/G1 phase (80.98±0.52 vs 69.14±0.89, P<0.05), increased efflux of rhodamine 123 (95.97±0.56 vs 12.40±0.44%, P<0.01), and up-regulated MDR1 expression. A total of 7 microRNAs and 605 mRNAs were differentially expressed between the two cell types. Of the differentially expressed mRNAs identified, regulator of G-protein signaling 10, high-temperature requirement protein A1, and nuclear protein 1 were found to be the putative targets of the differentially expressed microRNAs identified. These findings may open a new avenue for clarifying the mechanisms responsible for MDR in laryngeal cancer.

Frecuencia de los polimorfismos CYP1A1*2A y deleción del gen GSTM1 en pacientes con carcinoma de células escamosas de laringe en relación al hábito tabáquico: estudio piloto en Chile / Frequency of CYP1A1*2A and GSTM1 gene polymorphisms in Chilean patients with squamous cell carcinoma of the larynx in relation to smoking habit: a pilot study

Introducción: Entre los factores de riesgo para cáncer laríngeo (CL) son relevantes el consumo de tabaco y alcohol. Estos xenobióticos son metabolizados por un grupo de enzimas, entre las cuales están CYP1A1 y GSTM1, cuyas variantes polimórficas se postulan como factores de riesgo para esta enfermedad. Objetivos: Describir la frecuencia de las variantes de los polimorfismos de CYP1A1 y GSTM1 en un grupo de pacientes diagnosticados con CL. Analizar la posible correlación entre las variantes genéticas de ambas enzimas y la presencia de CL. Evaluar la influencia del hábito tabáquico en el riesgo de aparición de cáncer escamoso de laringe en pacientes con genotipos de riesgo. Material y método: Se seleccionaron 35 pacientes con CL entre los años 2000 y 2010 en Servicio de Otorrinolaringología del HBLT y 124 controles reclutados en el Centro de Investigaciones Farmacológicas y Toxicológicas (IFT). A todos los individuos se les registraron datos demográficos y extrajo una muestra de sangre para analizar las variantes polimórficas de CYP1A1 y GSTM1, mediante PCR-RFLP. Resultados: De un total de 35pacientes 54,3% presentan el genotipo GSTM1 (-/-) y 17,1% el genotipo CYP1A1*2A C/C. En el grupo control (n =140) estas frecuencias fueron de 19,35°% y 10,48%o, respectivamente. Se observó una correlación entre GSTM1 y el CL, estratificado por el hábito tabáquico y alcohólico. No se encontraron relaciones estadísticamente significativas con el hábito alcohólico y/o tabáquico. No se observaron asociaciones entre la patología y la combinación de genotipos o entre genotipos y el hábito tabáquico o alcohólico. Conclusiones: Los resultados muestran una asociación estadísticamente significativa entre la deleción de GSTM1 (-/-) y el riesgo de presentar CL, lo que refleja el importante papel que juega esta enzima en la desintoxicación de compuestos cancerígenos. Sin embargo, se requiere incrementar el número de pacientes para establecer apropiadamente la relación genético-ambiental que permite adjudicar un papel relevante a estos biomarcadores.

Introduction: Tobacco and alcohol consumption are recognized risk factors for squamous cell carcinoma of the larynx. These xenobiotics are metabolized by numerous enzymes, among which, CYP1A1 and GSTM1 gene polymorphisms have been identified as risk factors for developing tobacco related cancers as lung and laryngeal carcinomas. Nevertheless, these polymorphisms have not been studied in Chilean patients with squamous cell carcinoma of the larynx. Aim: To describe, for the first time, the frequency of CYP1A1 and GSTM1 gene polymorphisms in Chilean patients with squamous cell carcinoma of the larynx. Material and method: We conducted a case-control study. The case group consisted of 35 Chilean patients with squamous cell carcinoma of the larynx; the control group was formed by 124 Chilean subjects without cancer diagnosis. Demographic data as age, sex and quantification of tobacco smoking and alcohol consumption were recorded in all individuals. CYP1A1 and GSTM1 gene polymorphisms were evaluated by polymerase chain reaction and restriction enzymes (PCR-RFLP). Results: The frequency of CYP1A1*2A C/C genotype was 54, 3°% among laryngeal cancerpatients and 17,1%% among control subjects. The frequency ofGSTM1 (-/-) genotype was 19,35 %% among laryngeal cancer patients and 10,48%% among control subjects. There were no statistically significant relationships between this gene polymorphisms and tobacco smoking or alcohol consumption. There were no associations between the presence of both gene polymorphisms in the same individual and the presence of laryngeal cancer. Interestingly we found an OR of 8.69 (CI 2.90 to 26.01) for GSTM1 (-/-) polymorphism and laryngeal cancer, stratified by tobacco smoking and alcohol consumption. Conclusions: Our work shows that the deletion of GSTM1 could be an important risk factor for squamous cell carcinoma of the larynx in Chilean patients. This finding reflects the important role that detoxification of carcinogenic compounds plays in Chilean population. However, it is necessary to increase the number of studied patients to properly establish the genetic-environmental relationship ascribed to these biomarkers.

Perfil genômico do carcinoma de células escamosas de laringe e seu fronte de invasão / Genomic profiling of squamous cell carcinoma of the larynx and its invasive front

Câncer de laringe ocorre em 25 dos carcinomas de cabeça e pescoço e compreende 2 de todas as doenças malignas. É comum o aparecimento de segundos tumores primários e, aproximadamente, 5 dos pacientes apresentam cânceres sincrônicos. Há várias evidências indicando que a população celular presente no fronte de invasão possui características moleculares diferentes das áreas tumorais superficiais, tornando esta região importante para avaliação prognóstica. Neste estudo foram investigadas por CGH cromossômico de alta resolução (HR-CGH) as alterações genômicas na área superficial e no fronte de invasão de carcinomas de laringe e selecionadas regiões específicas para serem avaliadas por outras metodologias para a confirmação dos resultados. O componente superficial e o fronte de invasão de 33 carcinomas de laringe fixados em formalina e em blocos de parafina foram avaliados por HR-CGH. Foram detectadas alterações comuns aos dois componentes assim como alterações exclusivas a cada um deles. Adicionalmente, foi investigada e confirmada a expressão aumentada da proteína ciclina D1 o gene CCND1 esta mapeada em 11q13) por análise de expressão em plataformas de microarranjos de tecidos contendo as áreas do tumor e do fronte de invasão. Foi realizada também a análise de marcadores polimórficos de microssatélites mapeados em 3q e 18q em um grupo independente de 33 amostras (DNA tumoral e do sangue periférico) cujos resultados confirmaram as perdas encontradas nestas regiões cromossômicas. A expressão do gene CTTN (mapeada em 11q13) e de sua proteína foram avaliadas e revelaram que os altos níveis de expressão proteica foram correlacionados com invasão perineural nas células do fronte de invasão, sugerindo que esta área pode ser considerada como ferramenta prognóstica em carcinomas de laringe. Foram investigados os ganhos detectados em 2q24...

Distribución relativa de genotipos de virus papiloma humano en muestras de carcinoma escamoso de laringe / Relative distribution of human papilloma virus in laryngeal squamous cell carcinoma

Introducción: La relación entre virus papiloma humano (VPH) y cáncer escamoso de la vía aéreo-digestiva superior está claramente establecida en la literatura. Objetivo: El objetivo del presente trabajo es conocer la frecuencia de identificación de ADN de VPH y la distribución relativa de genotipos en muestras de carcinoma escamoso de laringe. Material y método: Se extrajo ADN desde muestras fijadas en formalina e incluidas en parafina, de biopsias de carcinoma escamoso de laringe de pacientes operados en el Servicio de Otorrinolaringología del Hospital San Juan de Dios. La detección de ADN viral se realizó mediante PCR con partidores de consenso MY09/11, y la genotipificación se realizó mediante endonucleasas de restricción Rsal. La calidad de la muestra se controló mediante amplificación de beta-globina. Resultados: Se incluyeron 90 casos. En 24 de ellos (27 por ciento) se identificó la presencia de ADN de VPH. Los genotipos más frecuentes fueron VPH18 (7/24), VPH16 (5/24), VPH54 (2/ 24). En 3 casos no se logró identificar el genotipo. No se detectaron infecciones múltiples. Conclusiones: La presencia de genotipos de VPH de alto riesgo oncogénico sugieren que el virus papiloma humano tendría un rol en la etiopatogenia de un subgrupo de pacientes portadores de carcinoma escamoso de laringe.

Introduction: Human papillomaviruses (HPV) have been detected in benign and neoplastic laryngeal lesions, with variable frequency (20-60 percent). These viral agents are proposed as an adjuvant or cofactor in head and neck carcinogenesis because of their oncogenic properties. Aim: The aim of this study was to identify HPV in laryngeal carcinoma samples and to describe their genotype distribution. Material and method: Tumor samples from patients with newly diagnosed laryngeal carcinomas were collected, fixed in formalin and paraffin-embedded. HPV genome was identified by use of polymerase chain reaction (PCR) using primers complementary to the conserved region L1 (MY09-11). Genotyping was accomplished by restriction fragment length polymorphism. Results: 24 of the 90 samples were positive for HPVDNA (27 percent), all of the samples were positive for human 3-globin. The genotypes identified were HPV 16(5 cases), HPV 18 (7 cases), and HPV 39, 45, 51, 58, 59, 61, and 66 (1 case each). Conclusions: High-risk HPV genotypes were identified, suggesting a role of human papilloma virus in the etiology of a subgroup of laryngeal squamous cell carcinomas.

DNA Gains and Losses of Chromosome in Laryngeal Squamous Cell Carcinoma Using Comparative Genomic Hybridization

PURPOSE: A larynx squamous cell carcinoma (LSCC) is one of the most common forms of cancer and may exhibit various complex karyotypes. MATERIALS AND METHODS: We used comparative genomic hybridization (CGH) to analyze DNA gains and losses in 15 squamous cell carcinomas that consisted of 4 glottic, 10 supraglottic, and 1 transglottic localization samples. RESULTS: The majority of the chromosomal alterations detected were gains: 3 samples of LSCCs revealed high level amplification, while 6 samples displayed gains in various chromosomal regions (17p, 3p, 4p, 5p, 6q, 8p, 9p, 14q, 18p and Xq). One sample was found to have losses (chromosomes 15q and 22q) and 5 had normal CGH profiles. CONCLUSION: Many of these gained regions (4p, 5p, 8p, 10q, 18q and Xq) were novel sites, which may harbor oncogene(s) that potentially play an important role in squamous cell tumorigenesis and progression at supraglottic localizations.

Promoter hypermethylation of DNA repair gene MGMT in laryngeal squamous cell carcinoma / 华中科技大学学报（医学）（英德文版）

The relationship between hypermethylation of CpG islands in the promoter regions of O6-methylguanine DNA methyltransferase (MGMT) genes and laryngeal squamous cell carcinoma was explored. Methylation-specific PCR and semi-quantitative RT-PCR were used to study the promoter methylation and mRNA expression of the MGMT gene in laryngeal carcinoma tissues, tissues adjacent to the tumor and normal laryngeal tissues. Hypermethylation of MGMT gene was detected in 16 samples of 46 (34.8%) laryngeal squamous cell carcinoma samples. However, the MGMT hypermethylation was not detected in all tissues adjacent to the tumors and normal tissues. No significant difference in MGMT gene hypermethylation was found in samples with different histological grades (chi2 = 3.130, P = 0.077) or in samples from patients with different TNM status (chi2 = 3.957, P = 0.138). No expression of MGMT mRNA was detected in all hypermethylated laryngeal carcinoma tissues. The expression of MGMT mRNA was detected in all unmethylated laryngeal carcinoma tissues, tissues adjacent to the tumors and normal tissues. It suggests that MGMT gene promoter hypermethylation is associated with MGMT gene transcription loss in laryngeal carcinoma tissues and possibly plays an important role in carcinogenesis of laryngeal tissues.

Loss of Heterozygosity on Chromosomes 3p,8p,9p and 17p in the Progression of Squamous Cell Carcinoma of the Larynx

Previous molecular genetic studies of laryngeal squamous cell carcinoma (SCC)have shown certain chromosomal regions with recurring alterations. But studies of sequential molecular alterations and genetic progression model of laryngeal SCC have not been clearly defined. To identify the chromosomal alterations associated with the carcinogenesis of laryngeal SCC, we analyzed genomic DNA from microdissected squamous metaplasia, squamous dysplasia, invasive SCC, and metastatic carcinoma samples from 22 laryngeal SCC patients for loss of heterozygosity (LOH) at microsatellite loci. Ten microsatellite markers on chromosome 3p, 8p, 9p, and 17p were used. LOH at 9p21 was observed in the all stages including squamous metaplasia, squamous dysplasia, invasive SCC and metastatic carcinoma. LOH at 17p13.1, 3p25 and 3p14.2 was observed from the squamous dysplasia, invasive SCC and metastatic carcinoma. LOH at 8p21.3-p22 was observed mainly from the invasive SCC and metastatic carcinoma. The results suggest that 9p21 in the early event, 17p13.1, 3p25 and 3p14.2 in the intermediate event and 8p21.3- p22 in the late event may be involved in the laryngeal carcinogenesis.

Caracterización citogenética en cáncer laríngeo / Cytogenetic characterization in laryngeal cancer

El cáncer laríngeo representa un 23 por ciento de las neoplasias malignas en la práctica clínica del otorrinolaringólogo. Mediante técnicas de citogenética se ha logrado describior cambios en el DNA de tumores epiteliales de cabeza y cuello, siendo lo mas frecuentes pérdida de 3p, 8p y 18q. Entre Mayo de 1996 y Julio de 1997 se estudiaron 13 pacientes con diagnóstico de cáncer laríngeo. Las alteraciones encontrada corresponden a pérdida del cromosoma Y, alteraciones del cromosoma 5, 4q+, 2p-y manosomía del cromosoma 15