Analysis of gene expression in co-culture of PBMCs with Head and Neck cancer cells line by High-Throughput Sequencing

(Objectives) The goal of this study is to investigate paracrine effect of Peripheral Blood Mononuclear Cells (PBMCs) on Head and Neck cancer cell lines. (Method) Transcription profiles of PBMCs (control) and PBMCs co-cultured with Head and Neck cancer cell lines (treatment) were generated by deep sequencing, in triplicate for HN17 and duplicate for HN4, using Illumina HiSeq 4000. (Results and conclusion) Transcriptome analysis of PBMCs has shown the gene expression changed when co-cultured with HN cell lines. The result revealed significantly down-regulated genes. On the other hand, up-regulated gene, ZCCHC6 were used to validated with qRT-PCR in HNSCC patient blood. The synopsis of this study demonstrates paracrine effect on PBMC of HNSCC patient to significantly up expression of ZCCHC6 gene when compared with healthy donors. Transcription profiles of PBMC (control) and PBMC co-cultured with Head and Neck cancer cell lines (treatment) were generated by deep sequencing, in triplicate for HN17 and duplicate for HN4, using Illumina HiSeq 4000.

【研究目标】本研究旨在探究外周血单个核细胞（Peripheral Blood Mononuclear Cells, PBMCs）对头颈部癌细胞系的旁分泌效应。
【研究方法】本研究采用Illumina HiSeq 4000测序平台对两组样本进行深度测序以获取转录组谱：一组为未共培养的PBMCs（对照组），另一组为与头颈部癌细胞系共培养的PBMCs（处理组）；其中HN17样本设置3次生物学重复，HN4样本设置2次生物学重复。
【结果与结论】PBMCs的转录组分析结果显示，当与HN细胞系共培养时，其基因表达发生显著改变。研究发现存在大量显著下调的基因。此外，本研究选取上调基因ZCCHC6，在头颈部鳞状细胞癌（Head and Neck Squamous Cell Carcinoma, HNSCC）患者的血液样本中通过定量实时聚合酶链反应（qRT-PCR）进行了验证。本研究结果表明，与健康供体相比，头颈部鳞状细胞癌患者来源的PBMCs在共培养后可显著上调ZCCHC6基因的表达水平，证实了其旁分泌效应。
本研究再次采用Illumina HiSeq 4000测序平台对两组样本进行深度测序以获取转录组谱：一组为未共培养的PBMCs（对照组），另一组为与头颈部癌细胞系共培养的PBMCs（处理组）；其中HN17样本设置3次生物学重复，HN4样本设置2次生物学重复。