Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer.

Departamento de Bioquímica, Faculdade de Medicina, Universidade de São Paulo, Brazil.
Cancer Research (Impact Factor: 9.28). 04/2005; 65(5):1693-9. DOI: 10.1158/0008-5472.CAN-04-3506
Source: PubMed

ABSTRACT A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including six transcripts mapped to well-studied chromosomes such as 22, as well as transcripts that mapped to 253 intergenic regions. In addition, 2,251 noncoding intronic RNAs, eventually involved in transcriptional regulation, were found. A set of 250 candidate markers for loss of heterozygosis or gene amplification was selected by identifying transcripts that mapped to genomic regions previously known to be frequently amplified or deleted in head, neck, and thyroid tumors. Three of these markers were evaluated by quantitative reverse transcription-PCR in an independent set of individual samples. Along with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers that can be used for future studies on the molecular basis of these tumors. Similar analysis is warranted for a number of other tumors for which large EST data sets are available.

  • [Show abstract] [Hide abstract]
    ABSTRACT: Recent large-scale transcriptome analyses have revealed that the human genome contains more than just protein-coding genes. Indeed, a large number of transcripts, including long non-coding RNAs (lncRNAs), lack protein-coding capacity, and increasing evidence suggests that lncRNAs could have a critical role in the regulation of diverse cellular processes, such as stem cell pluripotency, development, cell growth and apoptosis, and cancer invasion and/or metastasis. Furthermore, the aberrant expression of several lncRNAs is closely linked to cancer invasion and/or metastasis. Although the underlying molecular mechanisms by which lncRNAs regulate cancer invasion and/or metastasis are not clearly understood, recent studies have revealed that aberrant lncRNAs expression affects the progression of cancer. In this review, we highlight recent findings regarding the roles of lncRNAs in cancer invasion and/or metastasis.Modern Pathology advance online publication, 13 June 2014; doi:10.1038/modpathol.2014.75.
    Modern Pathology 06/2014; · 6.36 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma (HNSCC) is unclear. Our study queried exon-level expression to implicate splice variants in HNSCC tumors. We performed a comparative genome-wide analysis of 44 HNSCC tumors and 25 uvulopalatopharyngoplasty (UPPP) tissue samples at an exon expression level. In our comparison we ranked genes based upon a novel score-the Maximum-Minimum Exon Score (MMES) - designed to predict the likelihood of an alternative splicing event occurring. We validated predicted alternative splicing events using quantitative RT-PCR on an independent cohort. After MMES scoring of 17,422 genes, the top 900 genes with the highest scores underwent additional manual inspection of expression patterns in a graphical analysis. The genes LAMA3, DST, VEGFC, SDHA, RASIP1, and TP63 were selected for further validation studies because of a high frequency of alternative splicing suggested in our graphical analysis, and literature review showing their biological relevance and known splicing patterns. We confirmed TP63 as having dominant expression of the short DeltaNp63 isoform in HNSCC tumor samples, consistent with prior reports. Two of the six genes (LAMA3 and DST) validated by quantitative RT-PCR for tumor-specific alternative splicing events (Student's t test, P<0.001). Alternative splicing events of oncologically relevant proteins occur in HNSCC. The number of genes expressing tumor-specific splice variants needs further elucidation, as does the functional significance of selective isoform expression.
    PLoS ONE 03/2014; 9(3):e91263. · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Long non-coding RNAs (lncRNAs) are novel transcripts that may play important roles in cancer. Our study aimed to resolve the lncRNA profile of larynx squamous cell carcinoma (LSCC) and to determine its clinical significance. The global lncRNA expression profile in LSCC tissues was measured by lncRNA microarray. Distinctly expressed lncRNAs were identified and levels of AC026166.2-001 and RP11-169D4.1-001 lncRNAs in 87 LSCC samples and paired adjacent normal tissue were analyzed by real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The clinical significance of these lncRNAs in laryngeal cancer was analyzed and survival data were estimated by the Kaplan-Meier method and the log-rank test. A receiver operating characteristic (ROC) curve was constructed to check the diagnostic value. In the lncRNA expression profile of tumor samples, 684 lncRNAs were upregulated and 747 lncRNAs were downregulated (fold-change >2.0). Of these, AC026166.2-001 and RP11-169D4.1-001 were distinctly dysregulated, with AC026166.2-001 exhibiting lower expression in cancer tissues and RP11-169D4.1-001 higher expression. We verified that both AC026166.2-001 and RP11-169D4.1-001 were expressed at a lower level in cervical lymph nodes compared with paired laryngeal cancer tissues and paired normal tissues. RP11-169D4.1-001 levels were positively correlated with lymph node metastasis (P = 0.007). From the survival analysis, decreased levels of AC026166.2-001 and RP11-169D4.1-001 were associated with poorer prognosis. The area under the ROC curve was up to 0.65 and 0.67, respectively, and the cut-off point of ΔCt was 11.23 and 10.53, respectively. AC026166.2-001 and RP11-169D4.1-001 may act as novel biomarkers in LSCC and may be potential therapeutic targets for LSCC patients. Both AC026166.2-001 and RP11-169D4.1-001 could be independent prognostic factors for survival in LSCC.
    PLoS ONE 09/2014; 9(9):e108237. · 3.53 Impact Factor

Full-text (2 Sources)

Available from
May 20, 2014