Profiling essential genes in human mammary cells by multiplex RNAi screening

By virtue of their accumulated genetic alterations, tumor cells may acquire vulnerabilities that create opportunities for therapeutic intervention. We have devised a massively parallel strategy for screening short hairpin RNA (shRNA) collections for stable loss-of-function phenotypes. We assayed from 6000 to 20,000 shRNAs simultaneously to identify genes important for the proliferation and survival of five cell lines derived from human mammary tissue. Lethal shRNAs common to these cell lines targeted many known cell-cycle regulatory networks. Cell line-specific sensitivities to suppression of protein complexes and biological pathways also emerged, and these could be validated by RNA interference (RNAi) and pharmacologically. These studies establish a practical platform for genome-scale screening of complex phenotypes in mammalian cells and demonstrate that RNAi can be used to expose genotype-specific sensitivities.     

BLV-miRNA跨界调控人类靶基因预测及生物信息学分析

[目的]评估牛白血病病毒(BLV)来源的miRNAs跨界调控人源基因的风险.对BLV-miRNA可能带来的食品安全问题及对人体健康可能造成何种影响进行前瞻性研究,为未来实际生产中地方流行性白血病防控措施执行的必要性研究奠定基础,对BLV与人类疾病间关联性的研究提供理论指导.[方法]首先使用mirbase网站对BLV m...     

Functional genomic analysis of the Wnt-wingless signaling pathway

The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.     

MicroRNA-34a影响宫颈癌细胞增殖及PTEN基因表达的研究

目的探讨microRNA-34a对宫颈癌细胞增殖及抑癌基因PTEN表达的影响。方法 Hela细胞株传代培养后分为上调组、下调组和对照组,分别转染microRNA-34a模拟物、抑制物和对照物,48 h后用CCK-8、定量PCR、Western blot法检测细胞增殖及PTEN mRNA、蛋白表达。采用生物信息软件预测microRNA-34a靶基因。结果上调组Hela细胞增殖比对照组降低23.43%（P〈0.01）,而下调组比对照组增加14.77%（P〈0.01）。上调组PTEN mRNA和蛋白表达升高（P〈0.01）,而下调组表达降低（P〈0.05）。靶基因预测分析显示microRNA-34a与PTEN基因mRNA的3UTR区无互补结合区。结论 microRNA-34a抑制宫颈癌细胞增殖,可能与促进抑癌基因PTEN表达有关。     

Phosphofructokinase 1 glycosylation regulates cell growth and metabolism

Cancer cells must satisfy the metabolic demands of rapid cell growth within a continually changing microenvironment. We demonstrated that the dynamic posttranslational modification of proteins by O-linked β-N-acetylglucosamine (O-GlcNAcylation) is a key metabolic regulator of glucose metabolism. O-GlcNAcylation was induced at serine 529 of phosphofructokinase 1 (PFK1) in response to hypoxia. Glycosylation inhibited PFK1 activity and redirected glucose flux through the pentose phosphate pathway, thereby conferring a selective growth advantage on cancer cells. Blocking glycosylation of PFK1 at serine 529 reduced cancer cell proliferation in vitro and impaired tumor formation in vivo. These studies reveal a previously uncharacterized mechanism for the regulation of metabolic pathways in cancer and a possible target for therapeutic intervention.     

Genome-wide RNAi analysis of growth and viability in Drosophila cells

A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale.     

Recurrent hemizygous deletions in cancers may optimize proliferative potential

Tumors exhibit numerous recurrent hemizygous focal deletions that contain no known tumor suppressors and are poorly understood. To investigate whether these regions contribute to tumorigenesis, we searched genetically for genes with cancer-relevant properties within these hemizygous deletions. We identified STOP and GO genes, which negatively and positively regulate proliferation, respectively. STOP genes include many known tumor suppressors, whereas GO genes are enriched for essential genes. Analysis of their chromosomal distribution revealed that recurring deletions preferentially overrepresent STOP genes and underrepresent GO genes. We propose a hypothesis called the cancer gene island model, whereby gene islands encompassing high densities of STOP genes and low densities of GO genes are hemizygously deleted to maximize proliferative fitness through cumulative haploinsufficiencies. Because hundreds to thousands of genes are hemizygously deleted per tumor, this mechanism may help to drive tumorigenesis across many cancer types.     

Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responses

Control of intracellular reactive oxygen species (ROS) concentrations is critical for cancer cell survival. We show that, in human lung cancer cells, acute increases in intracellular concentrations of ROS caused inhibition of the glycolytic enzyme pyruvate kinase M2 (PKM2) through oxidation of Cys(358). This inhibition of PKM2 is required to divert glucose flux into the pentose phosphate pathway and thereby generate sufficient reducing potential for detoxification of ROS. Lung cancer cells in which endogenous PKM2 was replaced with the Cys(358) to Ser(358) oxidation-resistant mutant exhibited increased sensitivity to oxidative stress and impaired tumor formation in a xenograft model. Besides promoting metabolic changes required for proliferation, the regulatory properties of PKM2 may confer an additional advantage to cancer cells by allowing them to withstand oxidative stress.     

黄芩苷通过上调miR-126诱导乳腺癌细胞凋亡的机制研究

目的 用黄芩苷干预人乳腺癌细胞株MDA-MB-231,观察黄芩苷对乳腺癌细胞增殖、凋亡的影响及作用机制。方法 用qRT-PCR检测miR-126的表达变化,Western-blot检测Bcl-2、Caspase-9、Caspase-3、p-p38和p53的表达,MTT法检测细胞增殖,流式细胞术检测细胞凋亡。结果 miR-126在乳腺癌MDA-MB-231细胞中的表达比正常乳腺细胞低,黄芩苷干预乳腺癌细胞后miR-126上调最为明显（P<0.05）。用miR-126 mimics、miR-126 inhibitors转染乳腺癌细胞,Western-blot显示黄芩苷及miR-126 mimics作用于人乳腺癌细胞后Bcl-2表达水平下降,Caspase-9和Caspase-3的裂解产物、p-p38、p53表达增加,差异有统计学意义（P<0.05）。MTT法显示黄芩苷和miR-126 均可抑制乳腺癌细胞的增殖,流式细胞术显示黄芩苷与miR-126 mimics促进癌细胞凋亡。结论 黄芩苷可以抑制乳腺癌细胞的增殖,促进其凋亡,其机制可能与通过上调miR-126调节凋亡相关基因有关。     

p53 regulates mitochondrial respiration

The energy that sustains cancer cells is derived preferentially from glycolysis. This metabolic change, the Warburg effect, was one of the first alterations in cancer cells recognized as conferring a survival advantage. Here, we show that p53, one of the most frequently mutated genes in cancers, modulates the balance between the utilization of respiratory and glycolytic pathways. We identify Synthesis of Cytochrome c Oxidase 2 (SCO2) as the downstream mediator of this effect in mice and human cancer cell lines. SCO2 is critical for regulating the cytochrome c oxidase (COX) complex, the major site of oxygen utilization in the eukaryotic cell. Disruption of the SCO2 gene in human cancer cells with wild-type p53 recapitulated the metabolic switch toward glycolysis that is exhibited by p53-deficient cells. That SCO2 couples p53 to mitochondrial respiration provides a possible explanation for the Warburg effect and offers new clues as to how p53 might affect aging and metabolism.     

A gene-coexpression network for global discovery of conserved genetic modules

To elucidate gene function on a global scale, we identified pairs of genes that are coexpressed over 3182 DNA microarrays from humans, flies, worms, and yeast. We found 22,163 such coexpression relationships, each of which has been conserved across evolution. This conservation implies that the coexpression of these gene pairs confers a selective advantage and therefore that these genes are functionally related. Many of these relationships provide strong evidence for the involvement of new genes in core biological functions such as the cell cycle, secretion, and protein expression. We experimentally confirmed the predictions implied by some of these links and identified cell proliferation functions for several genes. By assembling these links into a gene-coexpression network, we found several components that were animal-specific as well as interrelationships between newly evolved and ancient modules.     

Metabolite profiling identifies a key role for glycine in rapid cancer cell proliferation

Metabolic reprogramming has been proposed to be a hallmark of cancer, yet a systematic characterization of the metabolic pathways active in transformed cells is currently lacking. Using mass spectrometry, we measured the consumption and release (CORE) profiles of 219 metabolites from media across the NCI-60 cancer cell lines, and integrated these data with a preexisting atlas of gene expression. This analysis identified glycine consumption and expression of the mitochondrial glycine biosynthetic pathway as strongly correlated with rates of proliferation across cancer cells. Antagonizing glycine uptake and its mitochondrial biosynthesis preferentially impaired rapidly proliferating cells. Moreover, higher expression of this pathway was associated with greater mortality in breast cancer patients. Increased reliance on glycine may represent a metabolic vulnerability for selectively targeting rapid cancer cell proliferation.     

miR-423-5p在牛肌肉组织中表达及其靶基因预测

miR-423-5p在细胞中具有重要的生物学功能,如在肌细胞中能影响细胞的增殖.根据miRBase及NCBI网站显示的相关信息利用分析软件对miR-423在各物种之间的同源性进行了分析.取成年西门塔尔牛体内的骨骼肌、小肠、心脏组织利用茎环荧光定量PCR进行miR-423-5p表达量检测,将牛骨骼肌卫星细胞(MDSCs)...     

Hirschsprung disease is linked to defects in neural crest stem cell function

Genes associated with Hirschsprung disease, a failure to form enteric ganglia in the hindgut, were highly up-regulated in gut neural crest stem cells relative to whole-fetus RNA. One of these genes, the glial cell line-derived neurotrophic factor (GDNF) receptor Ret, was necessary for neural crest stem cell migration in the gut. GDNF promoted the migration of neural crest stem cells in culture but did not affect their survival or proliferation. Gene expression profiling, combined with reverse genetics and analyses of stem cell function, suggests that Hirschsprung disease is caused by defects in neural crest stem cell function.     

Landscape of somatic retrotransposition in human cancers

Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.     

石斑鱼虹彩病毒主要衣壳蛋白的表达及其生物学功能分析

【目的】明确石斑鱼虹彩病毒（Singapore grouper iridovirus,SGIV）主要衣壳蛋白（Major capsid protein,MCP）的生物学功能,为阐明SGIV感染致病机理及研发抗病毒产品提供理论依据。【方法】使用实时荧光定量PCR检测SGIV感染过程中MCP基因的转录时序及其在SGIV感染石斑鱼脾脏、肝脏、肾脏、肠道、胃和鳃组织中的表达水平;将SGIV MCP基因分别克隆至真核表达载体pEGFP-N3和pcDNA3.1上,构建重组质粒pEGFP-N3-MCP和pcDNA3.1-MCP,然后以重组质粒pEGFP-N3-MCP转染石斑鱼脾细胞（Grouper spleen cell,GS）进行亚细胞定位分析,同时以重组质粒pcDNA3.1-MCP转染胖头鲤细胞（Fathead minnow cells,FHM）构建能稳定表达MCP蛋白的FHM细胞系（FHM-MCP）,用于分析MCP蛋白对宿主细胞生长增殖及SGIV感染压力下细胞存活率和病毒复制的影响。【结果】在SGIV感染8 h后即可检测到MCP基因的特异性转录,即MCP基因是一个晚期基因。在SGIV感染24 h后,MCP基因在石斑鱼脾脏中的相对表达量最高,其次是在肝脏、肾脏和肠道组织中,而在胃和鳃组织中的相对表达量较低,提示胃和鳃组织并非SGIV感染的主要靶器官。SGIV的MCP蛋白主要定位于细胞核附近的胞质中。细胞生长增殖曲线和细胞计数结果均证实,MCP蛋白能调节细胞生长及促进细胞分裂增殖。在SGIV感染后24和48 h,FHM-MCP细胞的存活率均显著高于FHM-Vector细胞（真核表达载体pcDNA3.1转染FHM细胞）,其存活率分别是FHM-Vector细胞的1.12和1.15倍。此外,FHM-MCP细胞在SGIV感染24和48 h后,其病毒滴度均高于FHM-Vector细胞,即MCP蛋白能促进SGIV病毒复制。【结论】SGIV的MCP基因是一个晚期基因,其编码蛋白主要定位于细胞核附近的胞质中,通过促进宿主细胞分裂增殖及病毒复制,最终提高SGIV的病毒滴度和感染力。     

Myc-induced T cell leukemia in transgenic zebrafish

The zebrafish is an attractive model organism for studying cancer development because of its genetic accessibility. Here we describe the induction of clonally derived T cell acute lymphoblastic leukemia in transgenic zebrafish expressing mouse c-myc under control of the zebrafish Rag2 promoter. Visualization of leukemic cells expressing a chimeric transgene encoding Myc fused to green fluorescent protein (GFP) revealed that leukemias arose in the thymus, spread locally into gill arches and retro-orbital soft tissue, and then disseminated into skeletal muscle and abdominal organs. Leukemic cells homed back to the thymus in irradiated fish transplanted with GFP-labeled leukemic lymphoblasts. This transgenic model provides a platform for drug screens and for genetic screens aimed at identifying mutations that suppress or enhance c-myc- induced carcinogenesis.