Primary study of the perineural invasion related genes of salivary adenoid cystic carcinoma by RNA-Seq

doi:10.19438/j.cjoms.2018.02.004

Abstract

Abstract: PURPOSE: To investigate the perineural invasion(PNI) related genes, the level of gene expression in single culture group and co-culture group of salivary adenoid cystic carcinoma (SACC) was analyzed by RNA-Seq technique. METHODS: Two groups of salivary adenoid cystic carcinoma (SACC) cells were analyzed for gene expression by co-culture system with rat Schwann cells (SCs). Then, cluster analysis, gene ontology (GO) function enrichment analysis, Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis were used to analyze gene function, qRT-PCR was used to verify the 6 key-genes. Differential expression analysis of two conditions was performed using edgeR package (3.12.1). P value of 0.05 and log2 (fold change) of 1 were set as the threshold for significantly differential expression. RESULTS: The results showed that a total of 395 genes were differentially expressed in two groups (P≤0.05, |logFC|≥1.0), 135 genes were up-regulated (34.2%) and 260 genes were down-regulated (65.8%). GO enrichment analysis results showed that these PNI related DEGs involved in angiogenesis, extracellular matrix, cell proliferation, apoptosis and epithelial morphogenesis; KEGG pathway enrichment analysis displayed that these genes participated in histidine metabolism, interactions of tumor necrosis factor, chemotactic factor and cytokine receptor. qRT-PCR was used to validate 6 key-genes, and the results were consistent with RNA-Seq. CONCLUSIONS: Differentially expressed genes related to PNI of SACC were obtained, which provides important experimental basis for elucidating the mechanism of PNI of SACC, and also provides a new strategy and target for treatment of perineural invasion.

Key words: Salivary gland, Adenoid cystic carcinoma, Sequence analysis, RNA, DEGs, Perineural invasion

CLC Number:

R739.8

LI Huan, YANG Xin-jie, WANG Wei-qi, LEI De-lin. Primary study of the perineural invasion related genes of salivary adenoid cystic carcinoma by RNA-Seq[J]. China Journal of Oral and Maxillofacial Surgery, 2018, 16(2): 114-119.

References

[1] Dodd RL, Slevin NJ.Salivary gland adenoid cystic carcinoma: a review of chemotherapy and molecular therapies[J]. Oral Oncol, 2006, 42(8): 759-769.
[2] Jia S, Wang W, Hu Z, et al.BDNF mediated TrkB activation contributes to the EMT progression and the poor prognosis in human salivary adenoid cystic carcinoma[J]. Oral Oncol, 2015, 51(1): 64-70.
[3] Yang X, Zhang P, Ma Q, et al.EMMPRIN contributes to the in vitro invasion of human salivary adenoid cystic carcinoma cells[J]. Oncol Rep, 2012, 27(4): 1123-1127.
[4] Zhu N, Yang J, Wang Y, et al.Study of the difference of high and low metastasis cell line's gene expression map and metastasis-related genes of adenoid cystic carcinoma[J]. Exp Mol Med, 2003, 35(4): 243-248.
[5] Patel KJ, Pambuccian SE, Ondrey FG, et al.Genes associated with early development, apoptosis and cell cycle regulation define a gene expression profile of adenoid cystic carcinoma[J]. Oral Oncol, 2006, 42(10): 994-1004.
[6] Wang Z, Gerstein M, Snyder M.RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009, 10(1): 57-63.
[7] Shan C, Wei J, Hou R, et al.Schwann cells promote EMT and the Schwann-like differentiation of salivary adenoid cystic carcinoma cells via the BDNF/TrkB axis[J]. Oncol Rep, 2016, 35(1): 427-435.
[8] Chen W, Zhang HL, Shao XJ, et al.Gene expression profile of salivary adenoid cystic carcinoma associated with perineural invasion[J]. Tohoku J Exp Med, 2007, 212(3): 319-334.
[9] 单春, 杨新杰, 吴宝磊, 等. 腺样囊性癌细胞与大鼠施万细胞共培养的实验研究[J]. 中国口腔颌面外科杂志, 2015, 13(6): 481-485.
[10] Conesa A, Madrigal P, Tarazona S, et al.A survey of best practices for RNA-seq data analysis[J]. Genome Biol, 2016, 17: 13.
[11] Young MD, Wakefield MJ, Smyth GK, et al.Gene ontology analysis for RNA-seq: accounting for selection bias[J]. Genome Biol, 2010, 11(2): R14.
[12] Kanehisa M, Goto S.KEGG: kyoto encyclopedia of genes and genomes[J]. Nucleic Acids Res, 2000, 28(1): 27-30.
[13] 杨宗珂, 王德林, 蓝建华, 等. LOXL4 mRNA在膀胱癌中的表达及意义[J]. 生命科学研究, 2009, 13(4): 292-295.
[14] 刘换新, 彭娟, 白义凤, 等. 上调Delta-Like1基因可增强小细胞肺癌化疗敏感性[J]. 中国肺癌杂志, 2013, 16(6): 282-288.
[15] Heatley MK.Keratin expression in human tissues and neoplasms[J]. Histopathology, 2002, 41(4): 365-366.
[16] Sakamoto K, Aragaki T, Morita K, et al.Down-regulation of keratin 4 and keratin 13 expression in oral squamous cell carcinoma and epithelial dysplasia: a clue for histopathogenesis[J]. Histopathology, 2011, 58(4): 531-542.
[17] Mikami T, Cheng J, Maruyama S, et al.Emergence of keratin 17 vs. loss of keratin 13: their reciprocal immunohistochemical profiles in oral carcinoma in situ[J]. Oral Oncol, 2011, 47(6): 497-503.
[18] 刘曼, 余远林, 高雪, 等. 反义角蛋白13慢病毒质粒对鼻咽癌细胞放射敏感性的影响[J]. 中国耳鼻咽喉颅底外科杂志, 2014, 20(2): 101-106.
[19] Tan Q, Cui J, Huang J, et al.Genomic alteration during metastasis of lung adenocarcinoma[J]. Cell Physiol Biochem, 2016, 38(2): 469-486.
[20] Gu W, Gao T, Sun Y, et al.LncRNA expression profile reveals the potential role of lncRNAs in gastric carcinogenesis[J]. Cancer Biomark, 2015, 15(3): 249-258.
[21] Mertins P, Mani DR, Ruggles KV, et al.Proteogenomics connects somatic mutations to signalling in breast cancer[J]. Nature, 2016, 534(7605): 55-62.