三分文章思路-1
image这篇3分文章思路记录下来,其实前面没有展示生信的图图,但是文章introduction部分,描述了通过TCGA数据库TCGA_CESC_exp_HiSeqV22015-02-24数据集,筛选的出的差异基因-KIF18B,应该是用了生信方面的分析,后面又用了Human Protein Atlas IHC数据库,进一步确定了KIF18B在宫颈癌肿瘤组织和正常组织中的表达量是不一样的。所以前面生信筛选基因,后面试验+生信验证,是这样的一个思路吧。
文章是-KIF18B promotes tumor progression through activating the Wnt/β-catenin pathway in cervical cancer
摘要
oncogenes 致癌基因
The Wnt/β-catenin pathway plays key roles in embryogenesis, homeostasis, and stem cell regeneration, and pluripotency. In the canonical pathway, Wnt activation disrupts the destruction complex, allowing β-catenin to accumulate and subsequently translocate to the nucleus,where it interacts with a transcription factor of the TCF/LEF-1 family; the result is increased expression of oncogenes, such as c-Myc and CyclinD1.
Wnt /β-catenin途径在胚胎发生,体内稳态,干细胞再生和多能性中起关键作用。 在经典途径中,Wnt激活破坏了破坏复合物,使β-连环蛋白积累并随后易位至细胞核,在其中它与TCF / LEF-1家族的转录因子相互作用; 结果是增加了癌基因的表达,例如c-Myc和CyclinD1。
Regulation of Wnt/β-catenin activity is closely related to the development of various cancers, including lung cancer, breast cancer, liver cancer, colon cancer, and cervical cancer.Thus, targeting Wnt/β-catenin signaling is a promising strategy for treating cancers, with many drugs currently in clinical trials.
Wnt /β-catenin活性的调节与多种癌症的发生密切相关,包括肺癌,乳腺癌,肝癌,结肠癌和宫颈癌。因此,针对Wnt /β-catenin信号传导是治疗癌症的一种有前途的策略,目前有许多药物正在临床试验中。
Analysis of The Cancer Genome Atlas (TCGA) database showed that the KIF18B gene is highly expressed in cervical cancer tissue but exhibits low expression in paracancerous tissue. It is also associated positively with a large primary tumor size and an advanced TNM stage. KIF18B is a member of the kinesin family of motor proteins, which is closely related to the pairing and separation of chromosomes in mitosis.
癌症基因组图谱(TCGA)数据库的分析表明,KIF18B基因在宫颈癌组织中高表达,而在癌旁组织中低表达。 它也与大的原发肿瘤大小和晚期TNM分期呈正相关。 KIF18B是运动蛋白驱动蛋白家族的成员,其与有丝分裂中染色体的配对和分离密切相关。
De et al showed that overexpression of KIFC1, KIF1A, KIF5A, and KIFC3 can increase docetaxel chemotherapy resistance in breast cancer cells, and Liao et al21 found that KIF18A is closely related to the overall survival and progression-free survival in hepatic carcinoma patients. Moreover, overexpression of KIF18B indicates a poor prognosis in hepatic carcinoma.
De等显示KIFC1,KIF1A,KIF5A和KIFC3的过表达可以增加乳腺癌细胞中的多西他赛化疗耐药性,Liao等人21发现KIF18A与肝癌患者的总体生存和无进展生存密切相关。 此外,KIF18B的过度表达预示着肝癌的不良预后。
To predict whether KIF18B is a cancer driver gene with carcinogenic effects, we in a previous study retrieved only literature on the relationship between KIF18B and cancer, which primarily included bioinformatic analyses.22 However, the function of KIF18B in humans has remained unclear. In the present study, we show that KIF18B is a potential oncogene that promotes cervical cancer cell proliferation and migration in vitro and in vivo. Furthermore, our results indicate that the Wnt/β-catenin pathway may contribute to the carcinogenicity of KIF18B overexpression.
为了预测KIF18B是否是具有致癌作用的癌症驱动基因,我们在先前的研究中仅检索到有关KIF18B与癌症之间关系的文献,其中主要包括生物信息学分析。然而,KIF18B在人类中的功能仍不清楚。 在本研究中,我们显示KIF18B是潜在的致癌基因,可在体外和体内促进宫颈癌细胞的增殖和迁移。 此外,我们的结果表明Wnt /β-catenin途径可能与KIF18B过表达的致癌性有关。
结论
1.KIF18B is overexpressed in cervical cancer tumor tissues and correlates with more aggressive clinical characteristics
(1)利用TCGA的数据
HeLa and Siha cell这两种细胞
siRNA-1, siRNA-2, and siRNA-3三种干扰
通过分析TCGA_CESC_exp_HiSeqV22015-02-24数据集,与正常宫颈组织相比,宫颈癌组织显示KIF18B的过表达高3.4倍(P <0.0001),与大的原发肿瘤大小和晚期FIGO阶段密切相关.
image(2)利用Human Protein Atlas数据库进一步研究KIF18B在正常组织和肿瘤组织中的表达,原文表述如下
Subsequently, ==Human Protein Atlas IHC== analyses showed that KIF18B was not expressed in normal cervical tissues but was expressed in 11 of 12 (91.7%) cervical cancer tissue samples
image(3)自己的数据集做验证
KIF18B在30个肿瘤组织中有26个高表达
image(4)肿瘤恶性程度代表照片,免疫组化图片来自Human Protein Atlas 数据库
image(5)KIF18B的表达量和什么有关
image2.Knockdown of KIF18B inhibits cervical cancer cell proliferation, invasion, and migration in vitro.
(1)KIF18B在3种细胞中的表达量
image(2)三种干扰RNA的干扰效率
image(3)si-KIF18B转染的细胞现实较慢的生成速度
image(4)si-KIF18B转染的细胞有较少的菌落
image(5)siRNA介导的KIF18B敲低可抑制HeLa和Siha细胞的迁移
image(6)通过流式细胞术评估KIF18B对细胞周期分布和凋亡的影响。
image(7)转染si-KIF18B的HeLa细胞和Siha细胞在G1期的阻滞性高于转染si-NC的细胞。
image(8)对于HeLa和Siha细胞,在si-NC和si-KIF18B组之间未观察到凋亡的显着差异。
image3.Overexpression of KIF18B promotes cervical cancer cell proliferation, invasion, and migration in vitro
(A)伤口愈合试验表明,oe-KIF18B C33A细胞的迁移增加。
(B)CCK-8分析表明,KIF18B的过度表达促进了C33A细胞的增殖。
(C)oe-KIF18B转染的C33A细胞比对照pcDNA3.1转染的细胞具有更多的集落。
(D)迁移和侵袭测定表明oe-KIF18B处理损害了C33A细胞的迁移和侵袭能力。
image4.KIF18B plays a carcinogenic role by activating Wnt/β-catenin signaling
(1)与KIF18B共表达的大多数基因都发现了细胞周期(cell cycle)途径的富集
image(2)考虑到KIF18B敲低会降低癌细胞的增殖,迁移和侵袭并促进G1期细胞周期停滞,我们使用qRT-PCR和Western blot分析方法检查了KIF18B敲低细胞中细胞周期相关基因的表达。 与富集分析一致,与si-NC处理相比,si-KIF18B处理可降低CyclinD1的mRNA和蛋白质水平,而p21,p27和CyclinE的表达不受影响。这个CyclinD1正好和Wnt /β-catenin以前被证明是相关的, ==在introduction 做过铺垫==
image(3)评估了与Wnt /β-catenin途径相关的蛋白质,发现与si-NC组相比,si-KIF18B组的C-myc,β-catenin和GSK3β磷酸化水平降低,但总 GSK3β水平无明显差异。干扰组-C-myc降低,也是 ==在introduction 做过铺垫==
image5.Knockdown of KIF18B suppresses tumor growth in vivo
敲除后对肿瘤的影响
image image总结
1.就是我这个基因的筛选用了TCGA数据库TCGA_CESC_exp_HiSeqV22015-02-24数据集,筛选的出的差异基因-KIF18B,应该是用了生信方面的分析,后面又用了Human Protein Atlas IHC数据库,进一步确定了KIF18B在宫颈癌肿瘤组织和正常组织中的表达量是不一样的。
2.此外,作者在introduction对KIF18B家族的其他基因进行了描述,英文原文如下:
KIF4 is considered the main tumor trigger, and the absence of this motor protein will lead to aneuploidy in mouse embryonic stem cells or tumor formation in nude mice. A previous study showed that KIF4 is associated with a poor prognosis in breast cancer.Furthermore, Ishikawa et alobserved higher KIF2C mRNA expression in 120 cases of colorectal cancer than in adjacent normal tissues. KIF2C/MCAK is also upregulated in proliferative tumors, suggesting that KIF2C is associated with cell hyperproliferation. Shimo et aldetected 27,648 genes in 81 patients with breast cancer by gene chip analysis and found KIF2C gene expression to be significantly enhanced. Additionally, examination of 10 breast cancer cell lines revealed high KIF2C expression in nine. De et alshowed that overexpression of KIFC1, KIF1A, KIF5A, and KIFC3 can increase docetaxel chemotherapy resistance in breast cancer cells, and Liao et al found that KIF18A is closely related to the overall survival and progression-free survival in hepatic carcinoma patients. Moreover, overexpression of KIF18B indicates a poor prognosis in hepatic carcinoma.
借鉴过来的就是可以如果自己写作时,如果有同一家族的基因,把其他也写上。
image3.**关于Human Protein Atlas数据库 **,另一篇思路相近的中文文章-《基于多数据库联合挖掘研究PTP4A3的
表达对肝细胞癌发生发展的影响》也引用了这个数据库,这篇文章中的方法是:基于Oncomine 及癌症和肿瘤基因图谱(the Cancer Genome Atlas,TCGA)数据库联合数据分析PTP4A3在肝细胞癌 组织和正常组织中的表达水平;通过Human Protein Atlas数据库,进一步研究PTP4A3在肝细胞癌和正 常组织中的表达;同时基于Kaplan-Meier Plotter数据库进一步分析PTP4A3表达水平与肝细胞癌预后的 关系。
关于如何生成==免疫组织化学图==方法:生成免疫组织化学图 Human Protein Atlas 数据 库(www. proteinatlas.org) 的 免 疫 组 织 化 学 数 据 中,在“Tissue Atlas”和“Pathology Atlas”中输入 PTP4A3,分别选择“liver”和“liver cancer”,生 成免疫组织化学图。
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