卵巢癌肝转移灶高表达基因SFT2D1的生物信息学分析

目的:研究肿瘤原发灶和转移灶的基因表达差异,并采用生物信息学方法对一条卵巢癌肝转移灶高表达基因SFT2D1进行初步分析。方法:分别将卵巢癌原发灶和肝转移灶组织标本mRNA用Cy3-dUTP和Cy5-dUTP标记后与表达谱芯片杂交,通过信号扫描、处理后获得两者的表达差异基因。并用生物信息学方法对一条无功能研究的新基因SFT2D1进行初步分析,阐明了它的基因结构、染色体定位、编码蛋白质的理化性质、亚细胞定位、蛋白质功能域等信息。并对多物种中的相似性蛋白进行了系统进化分析。结果:表达谱芯片发现了共272条差异表达基因。对新基因SFT2D1的上述性质进行了有效的预测,基本明确了该基因编码蛋白为一内质网跨膜蛋白,可能参与肿瘤转移相关蛋白的合成与加工。结论:表达谱芯片技术是一种研究肿瘤转移基因表达差异的有效的高通量研究方法。通过生物信息学分析,表明新基因SFT2D1是一个有肿瘤转移研究价值的新靶点。     

FASN基因的原核表达及生物信息学分析

脂肪酸合成酶(FASN)在生物体内起着重要的作用,主要参与恶性肿瘤的数量调控。本研究旨在构建pET28a-FASN原核表达载体,并表达重组His-FASN蛋白,对该基因进行结构与功能的生物信息学分析。设计FASN基因特异性引物,通过PCR扩增获得的目的基因与原核表达载体pET28a连接,经IPTG诱导表达His-FASN蛋白。获得基因片段大小为1 320 bp,编码440个氨基酸;成功构建至pET28a原核表达载体,通过优化表达,确定在温度为35℃、IPTG浓度0.5 mmol/L、诱导时间为6 h的条件下融合蛋白表达量较高,获得蛋白大小约为53 kD;生物信息学分析结果表明FASN基因编码的蛋白是一个不稳定且具有亲水性的蛋白,不存在信号肽及跨膜区,可成为蛋白激酶磷酸化位点有12个Ser、5个Thr、3个Tyr。此外,从蛋白相互作用网络中发现,相互作用的蛋白包括主要酰基辅酶A合成酶长链家族成员及乙酰辅酶A羧化酶家族成员,为开发抑制剂药物提供了理论依据。     

卵巢癌侵袭转移机制的生物信息学研究进展

卵巢癌因其侵袭转移特性,致死率极高,居所有妇科恶性肿瘤之首。近年来随着高通量测序技术及生物信息学方法的快速发展,越来越多调控卵巢癌侵袭转移机制的相关生物大分子被发现。本文对卵巢癌侵袭转移机制的研究背景及现状进行了综述,归纳总结了侵袭转移机制相关调控因素,并对蛋白质组学和单细胞组学的生物信息学分析工具及数据库进行了汇总和介绍,以期为卵巢肿瘤细胞侵袭转移机制的深入研究提供理论依据和科研线索。     

人LRG1基因的原核表达及生物信息学分析

为了探讨LRG1基因结构与功能,对该基因进行克隆并构建到原核表达载体上,并对其进行表达及生物信息学分析。用Trizol法提取人肝癌HepG2细胞总RNA后,PCR扩增得到LRG1片段,经鉴定后将目的基因与原核表达载体pET28a连接,经诱导表达获得His-LRG1蛋白。LRG1基因cDNA片段大小为1 044 bp,编码347个氨基酸;成功构建pET28a原核表达载体,经多次不同条件诱导后,得到大小约40 kD目的蛋白;利用软件对LRG1蛋白的一级、二级结构进行了预测,分析总结得LRG1基因编码的蛋白是一个不稳定且具有亲水性的蛋白,可与多种信号开关相互作用。LRG1属于高度保守的富亮氨酸重复家族成员,其原核表达载体不易诱导产生大量目的蛋白,克隆表达该基因有利于验证其结构与功能关系。     

强直性脊柱炎差异表达基因的生物信息学分析

目的探讨强直性脊柱炎(AS)患者差异表达基因,并基于差异基因探讨强直性脊柱炎发病相关的可能生物学过程和信号通路。方法检索基因表达谱数据库(GEO)并筛选AS相关基因表达谱数据集。应用GEO在线分析功能GEO2R分析AS组和正常对照组的差异表达基因,用Cytoscape软件clueGO插件进行基因本体论和京都基因与基因组百科全书分析,采用String蛋白-蛋白相互作用(PPI)数据库分析差异表达基因编码蛋白间的相互作用;应用Cytoscape绘制蛋白相互作用网络图,并软件筛选信号通路关键基因分析。结果选取AS患者全血表达数据集GSE25101为研究对象,分析获得差异表达基因72个。72个差异表达基因分子功能主要为参与高迁移率族盒染色体蛋白1(HMGB1)转导机制;生物学过程主要富集于巨噬细胞迁移、骨髓细胞凋亡过程、线粒体呼吸链复合体装配、ATP合成偶联电子传输、线粒体ATP合成耦合电子输运等;细胞成分主要富集于呼吸链复合体、线粒体呼吸体等。信号通路富集于氧化磷酸化信号通路和帕金森综合征相关信号通路。PPI网络经过cytohubba插件筛选,ATP5J、NDUFS4、UQCRB、UQCRH、NDUFB3、COX7B、LSM3、ATP5EP2、ENY2、PSMA4被筛选为网络中的核心基因。结论通过生物信息学方法进行预测了AS的潜在机制,并筛选出10个潜在的与AS相关的重要分子,其中氧化磷酸化可能在AS发病机制中发挥了重要的作用。     

浆液性卵巢癌铁死亡关键基因的筛选及生物信息学分析

利用生物信息学方法筛选浆液性卵巢癌相关铁死亡关键基因,并预测其生物学功能。从GEO数据库中获得有关浆液性卵巢癌的数据集GSE54388和GSE12470,采用R语言中的“Limma”包分析挑选浆液性卵巢癌上皮组织与正常卵巢上皮组织中差异表达基因,绘制火山图、热图。利用Venn软件在线工具绘制GSE54388,GSE12470,FerrDb三个数据集韦恩图。对相关基因进行功能富集分析、蛋白互作分析、生存分析,对关键基因绘制ROC曲线进行诊断分析。采用GEPIA2 数据库对筛选基因进行验证,并进行免疫浸润分析。结果发现:从GSE54388中筛选出2458个差异基因,其中上调1309个,下调1149个。从GSE12470中筛选出3534个差异基因,其中上调1 837个,下调1 697个。与铁死亡基因数据集取交集,共得到16个差异基因,蛋白互作网络筛选出7个基因构建的关键模块,绘制生存曲线发现浆液性卵巢癌患者中5个基因与患者总生存率不良相关,其中NRAS,PSAT1,CDKN2A,GDF15这4个基因高表达,CAV1低表达。ROC曲线显示这5个基因中CAV1,NRAS,PSAT1的AUC诊断曲线面积大于0.95,有较高的诊断价值。GEPIA2 数据库验证发现5个基因的表达情况与预测相符,仅NRAS基因表达在浆液性卵巢癌患者Ⅱ期、Ⅲ期、Ⅳ期有显著差异(P<0.05)。免疫浸润分析发现CDKN2A表达与aDC细胞浸润水平呈正相关(P<0.05,spearman相关系数0.353);CAV1表达与Mast细胞浸润正向关(P<0.05,spearman相关系数0.327);NRAS与T helper细胞浸呈正向关(P<0.05,spearman相关系数0.362)。通过生物信息学方法筛选出与浆液性卵巢癌铁死亡相关的5个基因CAV1,NRAS,PSAT1,CDKN2A,GDF15,可能在浆液性卵巢癌的发生发展中起重要作用,有望成为该病诊断、治疗和预后的潜在分子生物标志物。     

丹参SmHB12基因生物信息学及表达分析

植物同源异型域-亮氨酸拉链Ⅰ(homeodomain-leucine zipperⅠ, HD-ZipⅠ)转录因子在响应非生物胁迫方面发挥了重要作用。本研究根据干旱胁迫下丹参(Salvia miltiorrhiza Bunge)幼苗根转录组数据,克隆获得丹参HB12(SmHB12)基因片段并进行测序验证,其开放阅读框长度603bp,编码200个氨基酸。蛋白理化性质分析表明蛋白质相对分子量为22.95 kDa,理论等电点为5.42,含有丝氨酸、苏氨酸和酪氨酸磷酸化位点。亚细胞定位结果表明SmHB12蛋白定位于细胞核。实时荧光定量PCR结果表明SmHB12基因在不同组织中均有表达,花中表达量最高,其次是茎和叶,根中最低,并受脱落酸(ABA)和聚乙二醇-6000 (PEG-6000)胁迫强烈诱导。上述结果为后续开展SmHB12基因的功能研究提供理论依据。     

水稻低温响应基因OsCR1的克隆与表达分析

低温、高温、干旱等非生物胁迫是影响水稻产量与品质的重要非生物逆境因子.为了探索水稻耐逆的分子机理并挖掘新的水稻耐逆基因,采用Affymetrix 60K水稻基因表达芯片分析了培矮64S全基因组在上述逆境下的表达谱变化,筛选出一个受低温诱导表达水平显著升高的基因OsCR1( Oryza sativaL.cold responsive gene 1,GenBank登录号:AK066066).实时定量PCR进一步证实该基因受低温诱导高表达.利用RT-PCR方法扩增获得其cDNA序列.生物信息学分析表明,OsCR1位于水稻第10号染色体上,包含两个内含子并存在选择性剪接现象,可编码含195个氨基酸残基的蛋白质,其蛋白等电点为5.78,分子量为21.9 kD.拓扑结构预测显示OsCR1蛋白上含有2个Ser/Thr蛋白激酶磷酸化位点;疏水性分析显示该基因为亲水性蛋白;启动子区域分析发现5类逆境相关的顺式作用元件.氨基酸序列比对分析显示OsCR1为未知功能基因.     

肾透明细胞癌Caki-1细胞系差异表达基因的生物信息学分析

目的比较肾透明细胞癌Caki-1细胞系与正常肾上皮细胞系ASE-5063中的差异表达基因（DEGs）,寻找潜在的肾透明细胞癌特异性分子标志物。 方法利用GEO数据库自带的GEO2R在线分析工具分析基因芯片GSE78179,将筛选出的DEGs分别导入Metascape、STRING以及Cytoscape进行综合分析并筛选出核心基因。最后使用FunRich等软件对筛选出的核心基因进行GO和KEGG富集分析。 结果共筛选出562个DEGs,其中上调基因345个,下调基因217个。进一步使用MCODE筛选出36个关键基因,GO功能分析发现这些基因与细胞粘附分子活性、趋化因子活性、细胞通讯和信号转导等密切相关;KEGG通路富集结果则表明差异基因主要集中在趋化因子信号通路、TNF信号通路以及NF-κB信号通路等多种与肿瘤相关的通路上。 结论运用生物信息学方法筛选出肾透明细胞癌Caki-1细胞系中DEGs,其中数个核心基因广泛参与多种肿瘤的病理进程,但尚未在肾透明细胞癌有相关研究报道,提示其可能是治疗肾透明细胞癌的潜在靶点。     

Mathematical modeling of ovarian cancer treatments: sequencing of surgery and chemotherapy

Ovarian cancer has long been one of the most common forms of cancer in women. The main treatment for ovarian cancer comprises a combination of surgery and chemotherapy. In an effort to improve treatment strategies, a variety of mathematical models have been developed in the literature. In this paper, we consider a simple mathematical model that incorporates tumor growth as well as the effects of chemotherapeutic and surgical treatments in ovarian cancer. We consider several growth models and combine them with different cell-kill hypotheses. Surgery is assumed to eliminate a fixed fraction of tumor cells instantaneously. We discuss how different models predict the optimal sequencing of chemotherapeutic and surgical treatments. This work has been carried out in the context of ovarian cancer; however, the results may also be useful for other kind of cancers.     

Prognostic significance of tumor-infiltrating T-lymphocytes in primary and metastatic lesions of advanced stage ovarian cancer

Purpose  Ovarian cancer patients with intra-tumoral CD3⁺ T-lymphocytes in primary tumor tissue have a better prognosis. This study aims to analyze the presence and relative influence of three important T-lymphocyte subsets, tumor-infiltrating CD8⁺ cytotoxic T-lymphocytes (CTL), CD45R0⁺ memory T-lymphocytes, and FoxP3⁺ regulatory T-lymphocytes (Treg), in primary tumor tissue and omental metastases of patients with ovarian cancer. Experimental design  The number of CD8⁺, CD45R0⁺, and FoxP3⁺ T-lymphocytes was determined by immunohistochemistry on a tissue micro array containing ovarian tumor tissue and/or omental metastases obtained at primary debulking surgery from 306 FIGO stage I–IV ovarian cancer patients. Immunohistochemistry data were correlated to clinicopathological parameters and survival data. Results  High number of CD8⁺ CTL and a high CD8⁺/FoxP3⁺ ratio in ovarian-derived tumor tissue were associated with increased disease-specific survival and proved to be independent prognostic factors in multivariate analyses. In advanced stage patients, the presence of CD8⁺ CTL, CD45R0⁺ memory T-lymphocytes, FoxP3⁺ Treg or a high CD8⁺/FoxP3⁺ ratio in ovarian-derived tumor tissue was associated with an increased disease specific survival in univariate analysis, as was the presence of CD45R0⁺ memory T-lymphocytes and FoxP3⁺ Treg in omental metastases. Furthermore, in advanced stage patients CD8⁺ cytotoxic and FoxP3⁺ regulatory T-lymphocytes infiltrating ovarian-derived tumor tissue were independent predictors of increased prognosis. Conclusions  T-lymphocytes infiltrating primary and metastatic ovarian cancer sites are associated with improved prognosis. These associations are especially distinct in advanced stage patients, underlining the potential for immunotherapy as a broadly applicable therapeutic strategy. Ninke Leffers and Marloes J. M. Gooden contributed equally.     

Inhibition of colon cancer growth and metastasis by NK4 gene repetitive delivery in mice

NK4, originally prepared as a competitive antagonist for hepatocyte growth factor (HGF), is a bifunctional molecule that acts as an HGF-antagonist and angiogenesis inhibitor. When the expression plasmid for NK4 gene was administered into mice by hydrodynamics-based delivery, the repetitive increase in the plasma NK4 protein level was achieved by repetitive administration of NK4 gene. Mice were subcutaneously implanted with colon cancer cells and weekly given with the NK4 plasmid. The repetitive delivery and expression of NK4 gene inhibited angiogenesis and invasiveness of colon cancer cells in subcutaneous tumor tissue and this was associated with suppression of primary tumor growth. By fifty days after tumor implantation, cancer cells naturally metastasized to the liver, whereas NK4 gene expression potently inhibited liver metastasis. Inhibition of the HGF-Met receptor pathway and tumor angiogenesis by NK4 gene expression has potential therapeutic value toward inhibition of invasion, growth, and metastasis of colon cancer.     

TNF inhibitor suppresses bone metastasis in a breast cancer cell line

In the evolution of cancer, tumor necrosis factor-alpha (TNF-α) plays a paradoxical role. High doses induce significant anticancer effects, but conversely, physiologic and pathologic levels of TNF-α may be involved in cancer promotion, tumor growth, and metastasis.Infliximab is a chimeric murine monoclonal antibody that binds with high affinity to soluble and membrane TNF-α and inhibits binding of TNF-α to its receptors. In the present study, we investigated the effect of infliximab, a TNF-α antagonist, on breast cancer aggressiveness and bone metastases.Infliximab greatly reduced cell motility and bone metastases in a metastatic breast cancer cell line, MDA-MB-231. The mechanism of bone metastasis inhibition involved decreased expression of CXC chemokine receptor 4 (CXCR4) and increased expression of decorin, which is the prototype of an expanding family of small leucine-rich proteoglycans. These results suggest a novel role for TNF-α inhibition in the reduction or prevention of bone metastases in this breast cancer model. Our study suggests that inhibition of TNF-α using infliximab may become a preventive therapeutic option for breast cancer.     

Bone metastasis as a prognostic factor in breast cancer patients with liver metastasis given OK-432-combined adoptive immunotherapy via the hepatic artery

The outcome in 31 patients with liver metastases from breast cancer given OK-432-combined adoptive immunotherapy via the hepatic artery was analyzed. Patients received intraarterial OK-432, a streptococcal preparation, followed by the transfer of autologous lymphocytes cultured with autologous tumor extract and interleukin-2 for 9–13 days. Liver lesions were evaluable in 11 of the 12 patients with bone metastasis (group A) and in 16 of the 19 patients without bone metastasis (group B). Complete response (CR) in the liver was attained in 8 patients in group A, but in only 1 in group B (p < 0.01). In group A, radiological features of all metastatic foci of bone improved after CR in the liver. Moreover, the median survival time (MST) of group A (20 months) was longer (p=0.06) than that of group B patients with extra-hepatic metastasis (n=12; MST=6 months), while group B patients with liver metastasis alone (n=7) showed a MST similar to that of group A. Thus, loco-regional immunotherapy via the hepatic artery was found to be useful in controlling both liver and bone metastasis from breast cancer. Moreover, in breast cancer patients with liver metastasis, bone metastasis appears to be a prognostic factor associated with good response to this immunotherapy.Abbreviations MST median survival time - CR complete response - PR partial response - MDP metyl-diphosphonate     

Structural and expression analysis of hepatic vitellogenin gene during ovarian maturation in Anguilla japonica

Vitellogenin (Vtg), the precursor molecule for yolk, is synthesized in the liver under estrogenic control. In all oviparous species, including fish, the process of vitellogenesis is crucial to subsequent embryonic development. This study attempted to obtain the cDNA encoding for Vtg from female Japanese eels, Anguilla japonica. Rapid amplification of cDNA ends (RACE) and polymerase chain reaction (PCR) were used to amplify Vtg cDNA prepared from liver extracts. Obtained PCR products were subcloned and sequenced. The overall sequence of eel Vtg cDNA isolated in this study contained 5395 bp nucleotides. This Vtg sequence encodes 1743 amino acids of the precursor molecule, and is entirely composed of the characteristic N-terminal lipovitellin-I region, an internal polyserine domain region, and a c-terminal lipovitellin-II region. The deduced amino acid sequence from these clones shares 34–61% identity with other teleost Vtgs. Northern blot assays of Vtg gene expression following hormonal treatment demonstrated that this Vtg is synthesized in the liver under stimulation by estradiol injection. However, Vtg synthesis may not be enhanced by salmon pituitary homogenate (SPH) induction for the developing ovarian follicles. Notably, the effect of methyltestosterone, following SPH injection, may be more appropriate for the uptake of Vtg by ovarian follicle maturation during the artificial maturation of Japanese female eels.     

MiR-126-3p inhibits ovarian cancer proliferation and invasion via targeting PLXNB2

Ovarian cancer is one of the leading malignancies in women and the 5-year survival rate of ovarian cancer still remains poor. In the present study, we aimed to investigate the interaction between the miR-126-3p and PLXNB2 in the progression of ovarian cancer. The qRT-PCR data revealed a reduction of miR-126-3p level in ovarian cancer tissues comparing to the adjacent normal tissues. Over-expression of miR-126-3p in ovarian cancer cells suppressed cell proliferation and invasion and the phosphorylation of AKT and ERK1/2. The cell cycle assay results showed that the over-expression of miR-126-3p induced cells in G1-phase and reduced cells in S-phase. We further performed bioinformatics analysis and luciferase assay to investigate the relationship between miR-126-3p and PLXNB2 in ovarian cancer cells. The results of TargetScan suggested that PLXNB2 is a direct target of miR-126-3p in ovarian cancer cells, and luciferase assay confirmed bioinformatics prediction. Knocking down of PLXNB2 with PLXNB2 siRNA results in repressed ovarian cancer cell proliferation and invasion, and decreased phosphorylation of AKT and ERK1/2, which is similar to the effect of over-expression of miR-126-3p in OC cells. The synergistic effect of combination of miR-126-3p over-expression and PLXNB2 down-regulation on the cell growth viability, cell colony, and cell invasion was also identified. All these findings indicated that miR-126-3p is involved in the progression of ovarian cancer via direct regulating PLXNB2.