Bench to bedside: recent advances in lung cancer pathological research with implications for diagnostic clinical practice

After decades of relative stagnation lung cancer is emerging as a disease type where rapid progress is being made in diagnosis and therapy, as well as in our understanding of disease biology. Much of this progress is of immediate impact to diagnosticians, and more is likely to affect diagnostic practice in the near future. In this review we seek to briefly summarize several key areas of active research of immediate or probable imminent value to trainee and consultant pulmonary pathologists alike. We cover some major changes in tumour classification, grading, and patient stratification, as well as considering the state of the art in machine-assisted interpretation of lung cancer histology, and the use of genetically modified lung cancer models.     

Age-related variations in gene expression patterns of renal cell carcinoma

Background

Clear cell renal cell carcinoma (ccRCC) is known to occur across the adult lifetime traversing the spectrum of age-related organismal changes. Little is known as to how the aging process may affect the course of renal cell carcinoma (RCC) and the repertoire of genes involved.

不同区域晶状体上皮细胞基因表达差异分析

【目的】比较不同区域猪晶状体上皮细胞的基因表达在转录组水平上的差异。【方法】解剖显微镜下分离晶状体前囊膜，将附着于其上的上皮细胞分为中央（直径为10．56mm）和周边两部分。分别提取两个样本的总RNAs并经PCR扩增，以Cy3和Cy5分别标记扩增的中央与周边部分的cDNA。与含7548个基因的表达谱芯片杂交，经图像分析，生物信息学处理获得基因表达在转录水平差异的相关信息。【结果】中央与周边区域的猪晶状体上皮细胞在转录组水平共鉴定出952个有效表达的基因点，其中差异表达基因261个．以中央区域为参照，周边上皮细胞mRNA上调137个，下调124个。差异表达基因主要涉及的功能有：细胞周期与凋亡、细胞骨架蛋白及细胞外基质、转录、细胞信号分子等。【结论】中央与周边区域猪晶状体上皮细胞基因表达在转录组水平上差异明显。这类差异呈明显的功能聚类。     

RNA干扰（RNAi）技术及其在功能基因组学研究中的应用

近年来的研究表明 ,一些小的双链RNA可以高效、特异的阻断体内某些基因致使mRNA降解 ,诱使细胞表现出特定基因缺失的表型 ,称为RNA干扰 (RNAinterference ,RNAi)。由于可以作为代替基因敲除的遗传工具 ,RNAi技术正在改变着功能基因组学 (functionalgenomics)领域的研究步伐。《科学》杂志和美国科学促进会将RNAi技术评选为2 0 0 2年十大重大科学成就之首。1　RNAi及其作用机制1.1　RNAi回顾首次发现双链RNA (doublestrandRNA ,dsR NA)能够导致基因沉默的现象来源于对线虫Caenorhabditiselegans的研究。1995年 ,康乃尔大学的…     

Integration of the cytogenetic and physical maps of chicken chromosome 17

The chicken genome, like those of most avian species, contains numerous microchromosomes that cannot be distinguished by size alone. Unique properties attributed to the microchromosomes include high GC content and gene density, and an enhanced recombination rate. Previously, microchromosome GGA 17 was shown to align with the consensus genetic linkage group E41W17, and bacterial artificial chromosome (BAC) clones containing E41W17 markers were isolated and assigned on the physical BAC map as well as the recently assembled draft chicken genome sequence. For this study, these same BACS were utilized as probes for fluorescence in-situ hybridization (FISH) to develop the GGA 17 cytogenetic map. Here we detail the chromosome order of ten BAC DNAs, thereby deriving a cytogenetic map of GGA 17 that is simultaneously integrated with both the linkage map and genome sequence. The location of the FISH probes together with the morphological appearance of the chromosome suggested that GGA 17 is an acrocentric chromosome whose cytogenetic map orientation is reversed from that currently indicated by the linkage map and draft genome sequence. The reversed orientation and the centromere location of GGA 17 were confirmed experimentally by dual-colour FISH hybridization using terminal BACs and the centromere-specific CNM oligonucleotide as probes. An advantage of this cyto-genomic approach is the improved alignment of the sequence and linkage maps with cytogenetic features such as the centromere, telomeres, p and q arms, and staining patterns indicating GC versus AT content.     

Intracellular antibodies for proteomics

The intracellular antibody technology has many applications for proteomics studies.

The potential of intracellular antibodies for the systematic study of the proteome has been made possible by the development of new experimental strategies that allow the selection of antibodies under conditions of intracellular expression. The Intracellular Antibody Capture Technology (IACT) is an in vivo two-hybrid-based method originally developed for the selection of antibodies readily folded for ectopic expression. IACT has been used for the rapid and effective identification of novel antigen–antibody pairs in intracellular compartments and for the in vivo identification of epitopes recognized by selected intracellular antibodies. IACT opens the way to the use of intracellular antibody technology for large-scale applications in proteomics. In its present format, its use is however somewhat limited by the need of a preselection of the input phage antibody libraries on protein antigens or by the construction of an antibody library from mice immunized against the target protein(s), to provide an enriched input library to compensate for the suboptimal efficiency of transformation of the yeast cells. These enrichment steps require expressing the corresponding proteins, which represents a severe bottleneck for the scaling up of the technology.

We describe here the construction of a single pot library of intracellular antibodies (SPLINT), a naïve library of scFv fragments expressed directly in the yeast cytoplasm in a format such that antigen-specific intrabodies can be isolated directly from gene sequences, with no manipulation whatsoever of the corresponding proteins. We describe also the isolation from SPLINT of a panel of intrabodies against a number of different proteins.

The application of SPLINT on a genome-wide scale should help the systematic study of the functional organization of cell proteome.     

An improved and highly standardised transformation procedure allows efficient production of single and multiple targeted gene-knockouts in a moss,<Emphasis Type="Italic"> Physcomitrella patens</Emphasis>

The moss Physcomitrella patens is the only land plant known to date with highly efficient homologous recombination in its nuclear DNA, making it a unique model for plant functional genomics approaches. For high-throughput production of knockout plants, a robust transformation system based on polyethylene glycol-mediated transfection of protoplasts was developed and optimised. Both the DNA conformation and pre-culture of plants used for protoplast isolation significantly affected transformation efficiencies. Employing a newly developed PCR high-throughput method, the gene-targeting efficiency in more than 1,000 plants transformed with different cDNA-based knockout constructs was determined and analysed with regard to the length and intron/exon structure of the homologous gene locus. Different targeting constructs, each containing an identical selectable marker gene, were applied as batch DNA in a single transformation experiment and resulted in double-knockout plants. Thus, the fast and efficient generation of multiple targeted gene-knockouts is now feasible in Physcomitrella.Communicated by U. Kück     

我国人类基因组研究面临的机遇与挑战

中国的人类基因组计划自１９９３年启动以来，已在各民族的遗传资源保存和遗传多态性研究、建立较完整的基因组研究技术、致病基因及其相关基因的ｃＤＮＡ克隆３个方面取得了显著成绩。与此同时，一支高层次研究人员队伍和一批研究基地已经形成。中国人类基因组计划下一阶段的任务是：根据中国的国情和优势：（１）继续扩大中华民族基因资源库（包括ＤＮＡ和永生细胞株库），并开展微卫星和单核苷酸多态性研究与基因分型工作；（２）发展疾病基因组学，做好疾病遗传资源的调查、登记、采集和保存，形成现代化管理的样品库和数据库，并争取在肿瘤、遗传病和多基因病相关基因的定位、克隆，突变检测与大规模测序方面有所突破，获得一批重要的疾病基因；（３）启动以生物信息学、基因转录和翻译表达谱测定为主的功能基因组学研究，并以疾病基因组为研究基因组功能的重点；（４）加强与基因组科学有关的伦理、法律和社会问题的研究