Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling

Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumours of DLBCL patients, apparently reflecting the variation in tumour proliferation rate, host response and differentiation state of the tumour. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal centre B cells ('germinal centre B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal centre B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumours on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer.     

基于基因表达式编程的多数据流分类并行算法

针对传统决策树分类算法在多数据流分类的正确率和处理速度存在的不足,提出了一种基于基因表达式编程(GEP)的多数据流分类并行算法,以提高多数据流分类的正确率和处理速度.根据GEP在数据分类上的优势,运用GEP原理和数据流段中分类目标相似属性合并构造多数据流分类算法,并对多数据流分类算法进行并行设计与分析,在多核PC上进行对比实验.实验结果表明:该串行与并行分类算法均优于传统算法,且在多样本上具有较好的加速比.     

草鱼原肌球蛋白基因的克隆及其组织表达

为揭示原肌球蛋白基因在草鱼肌肉中的作用,利用RT-PCR和RACE技术克隆获得了草鱼原肌球蛋白基因c DNA,并对该基因在普通草鱼和脆肉鲩不同组织中的表达情况进行研究分析。结果表明原肌球蛋白基因c DNA全长序列为1 705 bp,包含387 bp的5′UTR序列,1 307 bp的3′UTR序列和855 bp开放阅读框(ORF)。其ORF编码284个氨基酸。系统进化分析表明普通草鱼与斑马鱼、墨西哥脂鲤的原肌球蛋白基因核苷酸同源性分别是93%和87%,氨基酸同源性分别是96%和93%。在聚类上普通草鱼原肌球蛋白基因与其他鲤科鱼类同源性较高,表明亲缘关系最近,与传统分类相一致。Real time-PCR结果表明原肌球蛋白基因在所检测的普通草鱼和脆肉鲩7个组织中均有表达,原肌球蛋白基因在普通草鱼腹肌中表达最高,其次为前肠。原肌球蛋白基因在脆肉鲩腹肌中的表达低于普通草鱼,而脆肉鲩中肌肉、肝脏、肾脏、前肠、后肠中原肌球蛋白基因表达量大于普通草鱼相对应组织,但差异不显著。     

纳豆激酶基因克隆及其在大肠杆菌中活性表达研究

以纳豆芽孢杆菌基因组DNA为模板，PCR扩增了纳豆激酶基因（natto kinase gene）中编码前肽、成熟肽的核苷酸序列（pro-NK），构建大肠杆菌表达质粒pTYB102，转化大肠杆菌ER2566。在IPTG诱导下，分别在15℃（14h）、30℃（3h）、37℃（2h）条件下培养，pTYB102均能表达出有活性的纳豆激酶。实验证实纳豆激酶基因得到活性表达需要Pro序列。SDS－PAGE表明，15℃和30℃和37℃培养表达的杂蛋白更少。薄层扫描测定表达的纳豆激酶占菌体总蛋白30％以上。     

Molecular characterization and expression of the gene encoding human erythroid-potentiating activity

Erythropoietin is the primary physiological regulator of erythropoiesis; however, in vitro studies have identified another class of mediators which appear to be important in stimulating erythroid progenitors. These factors have generally been referred to as burst-promoting activities (BPA), because they stimulate the growth of early erythroid progenitors referred to as burst-forming units-erythroid (BFU-E) which give rise to colonies of up to thousands of haemoglobinized cells. We recently reported purification of a burst-promoting activity from medium conditioned by the Mo T-lymphoblast cell line infected with human T-cell lymphotropic virus type II (HTLV-II). This purified glycoprotein of relative molecular mass (Mr) 28,000 also stimulates colony formation by more mature erythroid precursors (CFU-E) and is therefore referred to as erythroid-potentiating activity (EPA). Purified EPA specifically stimulates human and murine cells of the erythroid lineage, unlike murine interleukin-3 (IL-3) which stimulates precursor cells from all haematopoietic lineages. We report here the isolation of a complementary DNA molecular clone encoding EPA and its use in producing EPA in COS (monkey) cells and CHO (Chinese hamster ovary) cells. We also define the organization of the EPA gene in human DNA.     

基于模糊核判别分析的基因表达数据分析方法

针对基因表达数据空间分布的特性,提出了一种基于模糊核判别分析的基因表达数据分析方法.方法综合了模糊数学以及核判别分析方法的优点,提高了对基因表达数据分类识别的准确性.以多发性骨髓瘤的基因表达数据为例进行了实验,从实验结果可以看出,采用模糊核判别分析方法可以得到最佳的识别效果.     

Monoclonal antibodies define differential ras gene expression in malignant and benign colonic diseases

DNAS of some human tumours can transform NIH 3T3 fibroblast cells, thus demonstrating the transforming potential of human ras genes (Hu-rasHa, Hu-rasKi, and Hu-rasN, respectively Harvey, Kirsten and neuroblastoma ras genes). Only a small percentage of a given type of human carcinoma, however, scores positive in this assay system. Activation of ras and subsequent transformation of NIH 3T3 cells are either by a point mutation in the ras gene or enhanced expression of the normal, or proto-onc, ras gene. If the transformation of a given human tumour involves the enhanced expression of the normal or cellular ras gene and the resulting gene product, the tumour DNA would probably score negative in the NIH 3T3 transfection assay. In human colon carcinoma, for example, lesions at position 12 of Hu-rasKi have been found. None of nine colon carcinomas obtained at biopsy, however, contain the ras lesion at this position, using a Hu-rasHa probe; one other colon carcinoma does appear to contain amplified proto-onc ras, and other colon carcinomas do have increased levels of ras RNA. There are at least three explanations for these observations. Either very few colon carcinomas contain point-mutated ras, the lesion in the majority of colon carcinomas is at a position other than 12 or ras activation in many colon carcinomas involves the enhanced expression of either the point-mutated or proto-onc form of a ras gene. We have now used monoclonal antibodies directed against a synthetic peptide reflecting sequences of the human T24 ras gene product to define ras p21 protein expression in a spectrum of colonic disease states. Immunohistochemical analyses of individual cells within tissue sections reveal differences in ras p21 expression in colon carcinomas compared with normal colonic epithelium, benign colon tumours and inflammatory or dysplastic colon lesions. Our data suggest that ras p21 expression is correlated with depth of carcinoma within the bowel wall, and is probably a relatively late event in colon carcinogenesis.     

9例颅内黑色素瘤的CT、MRI诊断和治疗

目的:探讨颅内黑色素瘤的CT、MR影像特点及治疗方法.方法:回顾性分析我院1999年以来收治的9例颅内黑色素瘤的CT、MR影像特点.结果:原发性黑色素瘤3例,转移性黑色素瘤6例.6例CT平扫表现为类圆形高密度影5例,类圆形低密度影1例,增强扫描肿瘤不均匀增强.7例行MRI检查,6例MRIT1 WI肿瘤表现为高信号,1例为不均匀低信号;6例T2 WI低信号,1例低高信号.T1 WI增强扫描6例明显增强.结论:颅内黑色素性黑色素瘤MRI具有特征性表现,病理检查是确诊黑色素瘤的最后手段.在手术基础上进行包括伽玛刀治疗、放疗及化疗的综合治疗有望提高疗效.     

Inactivation of the apoptosis effector Apaf-1 in malignant melanoma

Metastatic melanoma is a deadly cancer that fails to respond to conventional chemotherapy and is poorly understood at the molecular level. p53 mutations often occur in aggressive and chemoresistant cancers but are rarely observed in melanoma. Here we show that metastatic melanomas often lose Apaf-1, a cell-death effector that acts with cytochrome c and caspase-9 to mediate p53-dependent apoptosis. Loss of Apaf-1 expression is accompanied by allelic loss in metastatic melanomas, but can be recovered in melanoma cell lines by treatment with the methylation inhibitor 5-aza-2'-deoxycytidine (5aza2dC). Apaf-1-negative melanomas are invariably chemoresistant and are unable to execute a typical apoptotic programme in response to p53 activation. Restoring physiological levels of Apaf-1 through gene transfer or 5aza2dC treatment markedly enhances chemosensitivity and rescues the apoptotic defects associated with Apaf-1 loss. We conclude that Apaf-1 is inactivated in metastatic melanomas, which leads to defects in the execution of apoptotic cell death. Apaf-1 loss may contribute to the low frequency of p53 mutations observed in this highly chemoresistant tumour type.     

Molecular cloning and expression of the gene for a human D1 dopamine receptor

The diverse physiological actions of dopamine are mediated by its interaction with two basic types of G protein-coupled receptor, D1 and D2, which stimulate and inhibit, respectively, the enzyme adenylyl cyclase. Alterations in the number or activity of these receptors may be a contributory factor in diseases such as Parkinson's disease and schizophrenia. Here we describe the isolation and characterization of the gene encoding a human D1 dopamine receptor. The coding region of this gene is intronless, unlike the gene encoding the D2 dopamine receptor. The D1 receptor gene encodes a protein of 446 amino acids having a predicted relative molecular mass of 49,300 and a transmembrane topology similar to that of other G protein-coupled receptors. Transient or stable expression of the cloned gene in host cells established specific ligand binding and functional activity characteristic of a D1 dopamine receptor coupled to stimulation of adenylyl cyclase. Northern blot analysis and in situ hybridization revealed that the messenger RNA for this receptor is most abundant in caudate, nucleus accumbens and olfactory tubercle, with little or no mRNA detectable in substantia nigra, liver, kidney, or heart. Several observations from this work in conjunction with results from other studies are consistent with the idea that other D1 dopamine receptor subtypes may exist.     

Gene expression profiling predicts clinical outcome of breast cancer

Breast cancer patients with the same stage of disease can have markedly different treatment responses and overall outcome. The strongest predictors for metastases (for example, lymph node status and histological grade) fail to classify accurately breast tumours according to their clinical behaviour. Chemotherapy or hormonal therapy reduces the risk of distant metastases by approximately one-third; however, 70-80% of patients receiving this treatment would have survived without it. None of the signatures of breast cancer gene expression reported to date allow for patient-tailored therapy strategies. Here we used DNA microarray analysis on primary breast tumours of 117 young patients, and applied supervised classification to identify a gene expression signature strongly predictive of a short interval to distant metastases ('poor prognosis' signature) in patients without tumour cells in local lymph nodes at diagnosis (lymph node negative). In addition, we established a signature that identifies tumours of BRCA1 carriers. The poor prognosis signature consists of genes regulating cell cycle, invasion, metastasis and angiogenesis. This gene expression profile will outperform all currently used clinical parameters in predicting disease outcome. Our findings provide a strategy to select patients who would benefit from adjuvant therapy.     

Control of gene expression by a natural metabolite-responsive ribozyme

Most biological catalysts are made of protein; however, eight classes of natural ribozymes have been discovered that catalyse fundamental biochemical reactions. The central functions of ribozymes in modern organisms support the hypothesis that life passed through an 'RNA world' before the emergence of proteins and DNA. We have identified a new class of ribozymes that cleaves the messenger RNA of the glmS gene in Gram-positive bacteria. The ribozyme is activated by glucosamine-6-phosphate (GlcN6P), which is the metabolic product of the GlmS enzyme. Additional data indicate that the ribozyme serves as a metabolite-responsive genetic switch that represses the glmS gene in response to rising GlcN6P concentrations. These findings demonstrate that ribozyme switches may have functioned as metabolite sensors in primitive organisms, and further suggest that modern cells retain some of these ancient genetic control systems.     

鳜鱼肥胖基因的克隆与组织表达

为了研究脊椎动物肥胖基因(obese gene, ob)结构与功能关系,利用PCR和RACE方法克隆得到鳜鱼肥胖基因全长序列:鳜鱼ob基因全长1 398 bp, 由2个外显子和1个内含子构成,其完整的开放阅读框由486 bp组成,编码161个氨基酸. 应用Genome Walker方法克隆得到一段长为357 bp的鳜鱼ob基因5′侧翼区序列,并利用相关软件预测其中具有多个保守的顺式调控元件. 我们将克隆得到的鳜鱼ob基因编码氨基酸序列leptin与其他物种leptin序列分别进行同源性比较,并构建系统进化树,发现虽然不同物种间leptin序列差异非常大,但进化树分析显示所有的leptin序列,包括哺乳动物、两栖动物和真骨鱼类,各自聚集成簇. 最后通过荧光实时定量PCR方法研究鳜鱼不同组织ob基因的表达水平,与哺乳动物ob基因主要在脂肪组织表达分布不同,鳜鱼ob基因在所有被检测组织中均有表达,在肝脏组织中大量表达,其次是脑,在肠道、脂肪、脾和肌肉中只有微量表达,说明鱼类ob基因的表达分布及其调控机制可能与哺乳动物存在差别.     

生物信息学技术克隆并分析新基因STRF7

为进一步研究信号转导相关的新基因片段BE644250,采用生物信息学方法克隆基全长cDNA,并分析了其ORF,电子表达谱,染色体定位等,之后对全长序列进行了实验验证。电子延伸（contig)获得了729bp的延伸产物,含一个典型的74aa的ORF,命名为STRF7。与已知蛋白无明显同源性,部分地相似于人的源框蛋白CDX－4和酵母的转录调节子ADR6,属一新发现的基因;RT－PCR从IL－6刺激后的U937中克隆了STRF7基因,基序列与电子延伸结果安全一致,进一步的分析显示STRF7在多种组织中表达并定位于第6号染色体上,上述结果显示,STRF7是一个新基因,编码含74aa的蛋白,并且是一个潜在的转录因子。     

Short Report： Cyclic patterns of incidence rate for skin malignant melanoma： association with heliogeophysical activity

Background： Our previous studies revealed cyclicity in the incidence rate of skin malignant melanoma （SMM; ICD9, Dx： 172） in the Czech Republic （period T=7.50～7.63 years）, UK （T= 11.00 years） and Bulgaria （T= 12.20 years）. Incidences com- pared with the sunspot index Rz （lag-period dT=＋2, ＋4, ＋6, ＋ 10 or ＋ 12 years） have indicated that maximal rates are most likely to appear on descending slopes of the ;ll-year solar cycle, i.e., out of phase. We summarized and explored more deeply these cyclic variations and discussed their possible associations with heliogeophysical activity （HGA） components exhibiting similar cyclicity. Methods： Annual incidences of SMM from 5 countries （Czech Republic, UK, Bulgaria, USA and Canada） over various time spans during the years 1964-1992 were analyzed and their correlations with cyclic Rz （sunspot number） and aa （planetary geomagnetic activity） indices were summarized. Periodogram regression analysis with trigonometric approximation and phase-correlation analysis were applied. Results： Previous findings on SMM for the Czech Republic, UK and Bulgaria have been validated, and cyclic patterns have been revealed for USA （T=8.63 years, P〈0.05） and Canada （Ontario, T=9.91 years, P〈0.10）. Also, various ＇hypercycles＇ were established （T=45.5, 42.0, 48.25, 34.5 and 26.5 years, respectively） describing long-term cyclic incidence patterns. The association of SMM for USA and Canada with Rz （dT=＋6 and ＋7 years, respectively） and aa （dT=-10 and ＋9 years, respectively） was described. Possible interactions of cyclic non-photic influences （UV irradiation, Schumann resonance signal, low-frequency geomagnetic fluctuations） with brain waves absorbance, neuronal calcium dynamics, neuro-endocrine axis modulation, melatonin/serotonin disbalance and skin neuro-immunity impairment as likely causal pathways in melanoma appearance, were also discussed. Conclusion： The above findings on cyclicity and temporal assoc     

Combinatorial regulation of gene expression by uORFs and microRNAs in Drosophila

Gene expression is tightly controlled at multiple levels by dif-ferent categories of cis-regulatory elements(CREs)and trans-acting factors(TAFs).Two different r...