Chinese Journal of Tissue Engineering Research ›› 2024, Vol. 28 ›› Issue (16): 2481-2487.doi: 10.12307/2024.309
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Huang Ting1, Liu Xia1, Wang Zhu2, Chen Ting2, Chen Bin2, Bai Guohui1, Wu Jiayuan1, Tian Yuan1
Received:
2023-02-14
Accepted:
2023-04-24
Online:
2024-06-08
Published:
2023-07-29
Contact:
Tian Yuan, Chief physician, Affiliated Stomatology Hospital of Zunyi Medical University, Zunyi 563000, Guizhou Province, China
About author:
Huang Ting, Master, Physician, Affiliated Stomatology Hospital of Zunyi Medical University, Zunyi 563000, Guizhou Province, China
Supported by:
CLC Number:
Huang Ting, Liu Xia, Wang Zhu, Chen Ting, Chen Bin, Bai Guohui, Wu Jiayuan, Tian Yuan. Screening and analysis of differentially expressed genes for calcium homeostasis in ameloblasts with high fluoride intervention[J]. Chinese Journal of Tissue Engineering Research, 2024, 28(16): 2481-2487.
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2.3 转录组测序分析结果 根据CCK-8实验得出NaF 处理LS8细胞 24 h 的半抑制浓度为1.640 mmol/L,因此实验选择NaF 浓度为1.6 mmol/L处理LS8细胞24 h作为中间浓度组(T1)、NaF 浓度为3.2 mmol/L处理LS8细胞24 h作为高浓度组(T2),选择NaF浓度为0 mmol/L(不加NaF)作为对照组,分为3 个组,每组3 个生物学重复,一共9 个样本,进行转录组测序,每个样品平均产出6.74 G数据,一共检测到16 517个基因。测序的原始数据去除低质量、接头污染以及未知碱基N含量过高的reads,过滤后reads质量统计见表3,整体测序数据质量达到分析要求。"
2.3.1 差异表达基因分析结果 基因差异表达分析显示,NaF浓度为1.6 mmol/L组上调的基因有4 074 个、下调的有3 951 个,NaF浓度为3.2 mmol/L组上调的基因有4 838 个、下调的有4 728 个,由于NaF浓度为1.6 mmol/L和3.2 mmol/L两组差异表达基因数目过多不利于分析,为了更好地说明NaF对成釉细胞的影响,筛选NaF浓度为1.6 mmol/L和3.2 mmol/L两组共同差异表达基因进行分析,Venn分析表明,如图5A绿色部分(T1 up)是NaF浓度为1.6 mmol/L处理LS8细胞24 h 的转录组测序分析,结果得出上调的差异表达基因有779 个;粉色部分(T2 up)是NaF浓度为3.2 mmol/L处理LS8细胞24 h的转录组测序分析,结果得出上调的差异表达基因有1 543 个,两组共同上调的基因有3 295 个。如图5B绿色部分(T1 down)是NaF浓度为1.6 mmol/L处理LS8细胞24 h的转录组测序分析,结果得出下调调的差异表达基因有673 个;粉色部分(T2 down)是NaF浓度为3.2 mmol/L处理LS8细胞24 h的转录组测序分析,结果得出下调的差异表达基因有1 450 个,共同下调基因有3 278 个。"
通过KEGG对差异表达基因进行信号通路富集分析,显著富集的通路主要有蛋白质在内质网中的加工、钙信号通路及代谢通路等,并具有统计学意义。通过对富集的信号通路进一步分析发现,蛋白质在内质网中加工信号通路显著富集的基因(如:Hsp90b1、Canx、Calr、Hspa5、Bax、Xbp1、Atf6、upd1、Sec61a1、Sec61a1)和钙信号通路中显著富集的基因(如:Cacna1a、Itpka、Ptk2b、Ptgf、Calml4、Plcd1、Camk2b、Adra1d、Gna14、Nos1)参与调控细胞的Ca2+浓度。 2.4 RT-qPCR 验证测序结果 为进一步验证RNA-seq筛选出的基因的表达水平,实验选择了5 个显著差异基因采用RT-qPCR进行验证,选择差异倍数较高的基因Cacna1a、Hsp90b1、Canx、Calr、Hspa5。RT-qPCR检测结果显示,Hsp90b1、Canx、Calr、Hspa5的表达显著上调,Cacna1a的表达显著下调(P < 0.05),见图11。通过上述结果进一步验证 RNA-seq测序结果可靠,同时证明了NaF影响LS8细胞基因的表达水平。"
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