HER2 over-expression and response to different chemotherapy regimens in breast cancer

Purpose： To exam the relationship between HER2 over-expression and different adjuvant chemotherapies in breast cancer. Patients and Methods： A total of 1625 primary breast cancer patients who received post-surgery adjuvant chemotherapy in Tianjin Cancer Hospital, China, from July 2002 to November 2005 were included in the study. Among them, 600 patients were given CMF （CTX＋MTX＋5-Fu） regimen, 600 given CEF （CTX＋E-ADM＋5-Fu） regimen, and 425 given anthracyclines plus taxanes regimen, with mean follow-up time of 42 months. Results： In CMF treatment group, the 3-year disease free survival （DFS） in HER2 over-expressed patients was lower than that of the HER2-negative ones （89.80% vs 91.24%, P=0.0348）; in node-positive subgroup, the 3-year DFS was 84.72% in HER2 over-expressed patients, and 90.18% in the HER-2-negative ones （P=0.0271）. Compared to CMF regimen, anthracyclines and anthracyclines plus taxanes regimens are more effective （P〈0.05） in node-positive HER2 over-expression than those in the node-negative. Conclusion： HER2 over-expression is an independent index for predicting poor prognosis and short DFS for breast cancer patients. HER2 over-expressed patients are resistant to CMF regimen chemotherapy, but sensitive to anthracyclines-based or anthracyclines plus taxanes regimen. HER2 expression can be taken as a marker for therapies in breast cancer.     

新型多酸化合物对人乳腺癌细胞增殖的抑制作用

采用MTT法、形态学方法和Western blot方法,检测了3种新型多酸化合物[SbW9、（SbW9）2-（SnR）4、（SbW9）2-（SnR-CH3）4]对人乳腺癌MCF7和MDA-MB-231细胞生长抑制作用,细胞形态学变化及细胞PCNA蛋白表达变化,并探讨该3种化合物抑癌的机制.实验结果表明：3种化合物对人乳腺癌细胞MCF7和MDA-MB-231的生长均具有明显的抑制作用（P〈0.01）,细胞形态发生明显变化,细胞皱缩并且增殖速度明显减慢;其中,（SbW9）2-（SnR）4可使MCF7细胞PCNA蛋白表达下降（P〈0.05）,且呈浓度剂量依赖性.说明该3种新型多酸化合物均具有抗肿瘤活性,其活性部位可能是以{SbW9}为基本建筑单元的聚阴离子,作用机制可能与其抑制细胞DNA的合成有关.     

Sparse discriminant analysis for breast cancer biomarker identification and classification

Biomarker identification and cancer classification are two important procedures in microarray data analysis. We propose a novel unified method to carry out both tasks. We first preselect biomarker candidates by eliminating unrelated genes through the BSS/WSS ratio filter to reduce computational cost, and then use a sparse discriminant analysis method for simultaneous biomarker identification and cancer classification. Moreover, we give a mathematical justification about automatic biomarker identification. Experimental results show that the proposed method can identify key genes that have been verified in biochemical or biomedical research and classify the breast cancer type correctly.     

乳腺癌诊断指标的数理统计分析

以UCI机器学习知识库提供的683个乳腺癌数据为基础，利用相关分析、逐步线性回归和主成分分析等数理统计方法，对用于诊断检测乳腺癌各指标间的相互关系及主要判断指标进行了深入研究，指出细胞大小的均匀性(X2)、细胞形状的均匀性(X3)是检测乳腺癌诸指标中最重要的指标。     

基于条件关联互补基因的乳腺癌预后分析

为了提高乳腺癌患者的生存率,改善病人的临床治疗效果,从分子机制上研究了乳腺癌的致病基因。首先对113个正常组织和1 109个癌症组织的表达量进行差异分析,然后对差异表达的基因采用条件联合分析方式对互补基因进行分组,并用逐步Cox回归挑选出一组基因拟合预后模型。研究结果显示:VWCE,SPDYC,CRYBG3,DEFB1,SEL1L2,NMNAT2 6个基因对患者生存率是有害的,AMZ1,GJB2,CXCL2,ALDOC 4个基因对患者生存率是有利的,最终确定10个基因的预后模型能够显著地将样本分为高风险组和低风险组,并且对乳腺癌患者5年和10年的生存率进行了预测,依赖时间的AUC值均可达0.7以上。所提方法能够利用基因与基因之间的关联性,很好地对高维数据进行降维,消除基因与基因之间的共线性问题,10个基因的预后模型可以对患者的临床预测提供帮助。     

CTAB调控乳腺癌干细胞抑制迁移

乳腺癌转移是限制其临床治疗的主要因素.十六烷基三甲基溴化铵(CTAB)作为一种潜在的抗癌化合物具有明显的抗肿瘤作用.使用划痕和Transwell实验证明了CTAB可抑制ZR-75-1细胞迁移.乳腺癌干细胞是导致乳腺癌转移的一个重要因素.通过免疫荧光、流式细胞术和细胞成球实验证明CTAB降低了乳腺癌干细胞比例,并且抑制了干性标记物CD44和CD133的表达.实验证明CTAB抑制乳腺癌干细胞并且抑制乳腺癌细胞迁移.     

乳腺癌脑转移差异表达基因的生物学功能分析

乳腺癌脑转移(breast cancer brain metastasis,BCBM)的发病机制尚未明确。为了探究BCBM的发病机制,对BCBM差异表达基因的生物学功能进行研究并筛选关键调控基因。从基因表达综合数据库(gene expression omnibus,GEO)下载4个BCBM基因表达谱数据(GSE12237、GSE100534、GSE125989以及GSE43837),采用R语言筛选差异表达基因,采用富集分析包括基因本体分析(gene ontology,GO)和京都基因与基因组百科全书分析(Kyoto encyclopedia of genes and genomes,KEGG)进行生物学功能分析,采用STRING和Cytoscape分析蛋白质相互作用网络,采用Kaplan-Meier进行生存分析。结果表明,同时存在于2个及以上基因表达谱数据中的差异表达基因261个,GO分析主要涉及细胞外基质组织、细胞外结构组织等生物过程,细胞外基质结构组成、胶原结合等分子功能,含有胶原的细胞外基质、胶原蛋白三聚物等细胞组分;KEGG分析主要涉及蛋白质消化和吸收、局部黏附等通路。蛋白质相互作用网络分析得到9个关键调控基因,其中,DCN、COL6A1与BCBM的生存率显著相关,可作为潜在的BCBM关键调控基因,并为BCBM分子机制的研究提供思路。     

TRIM24 links a non-canonical histone signature to breast cancer

Recognition of modified histone species by distinct structural domains within 'reader' proteins plays a critical role in the regulation of gene expression. Readers that simultaneously recognize histones with multiple marks allow transduction of complex chromatin modification patterns into specific biological outcomes. Here we report that chromatin regulator tripartite motif-containing 24 (TRIM24) functions in humans as a reader of dual histone marks by means of tandem plant homeodomain (PHD) and bromodomain (Bromo) regions. The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional unit for combinatorial recognition of unmodified H3K4 (that is, histone H3 unmodified at lysine 4, H3K4me0) and acetylated H3K23 (histone H3 acetylated at lysine 23, H3K23ac) within the same histone tail. TRIM24 binds chromatin and oestrogen receptor to activate oestrogen-dependent genes associated with cellular proliferation and tumour development. Aberrant expression of TRIM24 negatively correlates with survival of breast cancer patients. The PHD-Bromo of TRIM24 provides a structural rationale for chromatin activation through a non-canonical histone signature, establishing a new route by which chromatin readers may influence cancer pathogenesis.     

Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype

Understanding the molecular underpinnings of cancer is of critical importance to the development of targeted intervention strategies. Identification of such targets, however, is notoriously difficult and unpredictable. Malignant cell transformation requires the cooperation of a few oncogenic mutations that cause substantial reorganization of many cell features and induce complex changes in gene expression patterns. Genes critical to this multifaceted cellular phenotype have therefore only been identified after signalling pathway analysis or on an ad hoc basis. Our observations that cell transformation by cooperating oncogenic lesions depends on synergistic modulation of downstream signalling circuitry suggest that malignant transformation is a highly cooperative process, involving synergy at multiple levels of regulation, including gene expression. Here we show that a large proportion of genes controlled synergistically by loss-of-function p53 and Ras activation are critical to the malignant state of murine and human colon cells. Notably, 14 out of 24 'cooperation response genes' were found to contribute to tumour formation in gene perturbation experiments. In contrast, only 1 in 14 perturbations of the genes responding in a non-synergistic manner had a similar effect. Synergistic control of gene expression by oncogenic mutations thus emerges as an underlying key to malignancy, and provides an attractive rationale for identifying intervention targets in gene networks downstream of oncogenic gain- and loss-of-function mutations.     

Interaction of cellular-localized signature modules in response to prostate cancer

Rapid progress in high-throughput biotechnologies (e.g. microarrays) and exponential accumulation of gene functional knowledge makes it promising for systematic understanding of complex human diseases at the functional modules level. Current modular categorizations can be defined and selected more specifically and precisely in terms of both biological processes and cellular locations, aiming at uncovering the modular molecular networks highly relevant to cancers. Based on Gene Ontology, we identifed the functional modules enriched with differentially expressed genes and characterized by biological processes and specific cellular locations. Then, according to the ranking of the disease discriminating abilities of the pre-selected functional modules, we further defined and filtered signature modules which have higher relevance to the cancer under study. Applications of the proposed method to the analysis of a prostate cancer dataset revealed insightful biological modules.     

Interaction of cellular-localized signature modules in response to prostate cancer

Rapid progress in high-throughput biotechnologies (e.g. microarrays) and exponential accumulation of gene functional knowledge makes it promising for systematic understanding of complex human diseases at the functional modules level. Current modular categorizations can be defined and selected more specifically and precisely in terms of both biological processes and cellular locations, aiming at uncovering the modular molecular networks highly relevant to cancers. Based on Gene Ontology, we identifed the functional modules enriched with differentially expressed genes and characterized by biological processes and specific cellular locations. Then, according to the ranking of the disease discriminating abilities of the pre-selected functional modules, we further defined and filtered signature modules which have higher relevance to the cancer under study. Applications of the proposed method to the analysis of a prostate cancer dataset revealed insightful biological modules.     

有机肥对水稻的肥效试验分析

水稻生产每1／15公顷施用等量N(11．15kg)、P2O5(3．13kg)、K2O(9kg)的丰都有机肥(养分含量为11，3，7)、挪威复合肥(15，15，15)、百康通用肥(12，5，8)，在相同管理水平下，肥效差异不明显。