HGPGD: the human gene population genetic difference database

Transcriptome Analysis Identified 2 New lncRNAs Associated with the Metastasis of Papillary Thyroid Carcinoma

INTRODUCTION

Papillary thyroid microcarcinoma (PTMC) is a specific subgroup of papillary thyroid carcinoma and defined with the dimension ≤1 cm by the WHO. Although it shows a relatively high 10-year livability, the metastasis of PTMC into other tissues and organs seriously affects the daily life of patients with relatively high mortality. Therefore, the genetic basis for the metastasis of PTMC needs to be explored for effective therapeutic targets. Here, we conducted a series of comparative analysis of the transcriptional expression profile between PTMC patients with and without lymph node metastasis.

METHODS

Gene expression profile and gene function were analyzed using RNA extracted from pathological tissues of 12 patients with PTMC, and the core biomarkers closely related to its metastasis were identified.

RESULTS

Our results showed that 7,507 genes and 42 RNAs showed remarkably different expression patterns. More sophisticated analysis showed that the high expression of 2 lncRNAs (T077499 and T004533) resulted in the metastasis of PTMC, which suggests that the expression pattern of the 2 lncRNAs may act as a potential biomarker for pathogenesis and prognosis of PTMC metastasis.

CONCLUSION

Our findings preliminarily reveal the molecular mechanisms for PTMC metastasis, which will provide vital reference for subsequent studies about the genetic basis and molecular targeted therapy for PTMC metastasis.

The identification of induction chemo-sensitivity genes of laryngeal squamous cell carcinoma and their clinical utilization

PURPOSE

To identify potential molecular markers for induction chemotherapy of Laryngeal squamous cell carcinoma (LSCC).

METHODS

Differently expressed genes between chemo-sensitive group (seven cases) and chemo-insensitive (five cases) group after induction chemotherapy by TPF were identified by microarrays. Bayes network and Random forest analyses were employed to identify core genes for induction chemotherapy. The diagnostic value of these core genes was also evaluated by ROC analysis.

RESULTS

Six genes (SPP1, FOLR3, KYNU, LOC653219, ADH7 and XAGE1A) are highly expressed, while seven gene (CADM1, NDUFA4L2, CCND2, RARRES3, ERAP2, LYD6 and CNTNAP2) present significantly low expression. Among these genes, genes CADM1, FOLR3, KYNU, and CNTNAP2 are core candidates for LSCC chemo-sensitivity. And that the low expression of CADM1 may result in chemo-sensitivity, which leads to high expression of gene FOLR3 and KYNU, and low expression of gene CNTNAP2. Besides, ROC analysis shows that these four genes exhibit effective diagnostic value for induction chemo-sensitivity.

CONCLUSIONS

CADM1 may be a potential molecular marker for LSCC induction chemotherapy, while CADM1, FOLR3, KYNU, and CNTNAP2 may provide essential guidance for LSCC diagnosis and follow-up treatment strategies.

Microarray gene expression analysis of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma

BACKGROUND

Laryngeal squamous cell carcinoma (LSCC) is the most common type in head and neck squamous cell carcinoma (HNSCC), and the development and progression of LSCC are multistep processes accompanied by changes of molecular biology.

OBJECTIVE

The purpose of this study was to investigate the molecular basis of tumorigenesis and regional lymph node metastasis in LSCC, and provide a set of genes that may be useful for the development of novel diagnostic markers and/or more effective therapeutic strategies.

METHODS

A total number of 10 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for microarray analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by Illumina mRNA microarrays, and LSCC tissues with regional lymph node metastasis and LSCC tissues without regional lymph node metastasis were analyzed in the same manner. The most frequently differently expressed genes screened by microarrays were also validated by qRT-PCR in another 42 patients diagnosed for LSCC.

RESULTS

Analysed by Illumina mRNA microarrays, there were 361 genes significantly related to tumorigenesis while 246 genes significantly related to regional lymph node metastasis in LSCC. We found that the six genes (CDK1, CDK2, CDK4, MCM2, MCM3, MCM4) were most frequently differently expressed functional genes related to tumorigenesis while eIF3a and RPN2 were most frequently differently expressed functional genes related to regional lymph node metastasis in LSCC. The expressions of these genes were also validated by qRT-PCR.

CONCLUSIONS

The research revealed a gene expression signature of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma. Of the total, the deregulation of several genes (CDK1, CDK2, CDK4, MCM2, MCM3, MCM4, EIF3a and RPN2) were potentially associated with disease development and progression. The result will contribute to the understanding of the molecular basis of LSCC and help to improve diagnosis and treatment.