Breakpoint Junction of Interstitial Homozygous Deletion at Chromosome 2q33 in a Small Cell Lung Carcinoma

We have characterized the breakpoint junction of the homozygousdeletion at chromosome 2q33 in a small cell lung carcinoma cellline. Cloning and sequencing of the genomic regions surroundingthe breakpoint junction of the deletion revealed that the homozygousdeletion was caused by a simple interstitial deletion of a 220-kbsegment. An AT-dinucleotide of contributing germline sequenceswas overlapped at the junction. Since there were one or twonucleotide overlaps of germline sequences at breakpoint junctionsin all four cases of interstitial deletions analyzed to date,this may reflect a common mechanism underlying the occurrenceof chromosomal interstitial deletion.     

Sequence Analysis of the 36-kb Region Between gntZ and trnY Genes of Bacillus Subtilis Genome*

Within the framework of an international Bacillus subtilis genomesequencing project, we have determined a 36-kb sequence coveringthe region between the gntZ and trnY genes. In addition to fivegenes sequenced and characterized previously, 27 putative proteincoding sequences (open reading frame; ORF) were identified.A homology search for the newly identified ORFs revealed thatsix of them had similarities to known proteins. It is notablethat new ORFs belonging to response-regulator aspartate phosphatase(Rap) and its regulator (Phr) families, and response regulatorand sensory kinase families of two-component signal transductionsystems have been identified. Furthermore, we found that some180-bp non-coding sequence, that might be an remnant of an ancientIS element, is preserved in at least five loci of the B. subtilisgenome.     

Alu-PCR Approach to Isolating NotI-Linking Clones from the 3p14-p21 Region Frequently Deleted in Renal Cell Carcinoma

In the mammalian genome CpG islands are associated with functional genes and cloning of these islands could be an alternative approach for cloning functional genes. Recently we have developed a new approach for cloning CpG islands and constructing NotI linking libraries. We have initiated the construction of a NotI restriction map for chromosome 3, especially focusing on the rearrangements in the 3p14-p21 region, which are associated with different malignancies. CpG islands from this region are useful for isolation of candidate tumor suppressor genes that map to this region and for isolating NotI-linking clones from 3p14-p21 for mapping purposes. Here we suggest a modification of Alu-PCR as an approach to isolating Not I sites (e.g., CpG islands) from defined regions of the chromosome. Instead of using whole chromosomal DNA for Alu-PCR, we have used representative NotI-linking libraries from hybrid cell lines containing either whole or deleted human chromosome 3 (MCH903.1 and MCH924.4, respectively). This decreases the complexity of the Alu-PCR products 10-100 times compared to the whole human genome. Using this modification, we can isolate NotI-linking clones, which are natural markers on the chromosome, rather than random genomic fragments. Among eight clones selected by this method, seven were from the region deleted in MCH924.4. The results clearly demonstrate the feasibility of Alu-PCR for isolating CpG islands from defined regions of the genome.     

The Chromosomal Organization of the Human Endogenous Retrovirus-like Sequence HERV-H: Clustering of the HERV-H Sequences in a 300-kb Region Close to the GRPR Locus on the X Chromosome

Within the haploid genome there are approximately 1,000 copiesof the human endogenous retroviruslike sequence, HERV-H. Althoughthese sequences are scattered throughout the entire genome,in situ hybridization experiments revealed that there are discreteclusters positioned on chromosomes 1p and 7q. In this study,we have located three HERV-H sequences which were unexpectedlyclustered within a 300-kilobase region close to the GRPR locuson the X chromosome. In previous studies, no clusteringof thissequence has been reported at this locus. Our finding demonstratesthat, like other repetitive sequences, clustering of HERV-Hoccurs in the human genome, although these sequences may notalways be detected by in situ hybridization methods.     

Sequence Analysis of a 32-kb Region Including the Major Ribosomal Protein Gene Clusters from Alkaliphilic Bacillus sp. Strain C-125

Forty-one open reading frames (ORFs) were identified in a 32-kb DNA fragment of alkaliphilic Bacillus sp. C-125. A similarity search using the BSORF database found 37 ORFs with significant sequence similarity to B. subtilis RNA polymerase subunits, elongation factor G, elongation factor Tu, and ribosomal proteins. Each ORF product showed more than 70% identity to those of B. subtilis. Gene organization in the region of str, S10, spc, and the α cluster was highly conserved among three strains, C-125, B. subtilis, and B. stearothermophilus.     

TTC4,a Novel Human Gene Containing the Tetratricopeptide Repeat and Mapping to the Region of Chromosome 1p31 That Is Frequently Deleted in Sporadic Breast Cancer

The 1p31 region shows loss of heterozygosity in up to 50% of human breast cancers, indicating the presence of a tumor suppressor gene in this location. We have mapped six novel ESTs to a 15-Mb contig of yeast artificial chromosomes spanning the critical region of 1p31. One of these ESTs was localized within the contig to the region most commonly undergoing loss of heterozygosity in breast cancer. The corresponding gene sequence for this EST was established by cDNA cloning and RACE procedures. This gene is 2 kb long and contains a tetratricopeptide repeat motif and a coiled-coil domain. This family of genes has been implicated in a wide variety of functions, including tumorigenesis. This is the fourth member of the human gene family, and so we have named this geneTTC4.Northern blot analysis demonstrates a ubiquitous pattern of gene expression that includes breast tissue. A preliminary screen of human breast cancer cell lines shows thatTTC4is expressed in all cases, but SSCP analysis of the coding region of this gene following RT-PCR failed to reveal any mutations. Clearly, because of its map location, a more extensive analysis is warranted to establish whether subtle mutations are present in breast cancers.     

Sequence Analysis of a 25-kb Segment in the 17{degrees}-19{degrees} Region of the Bacillus subtilis Chromosome Containing ada Locus

As a part of the Bacillus subtilis genome sequencing project,we have determined a 25-kb sequence covering the 17°–19°region. This region contains 26 complete open reading frames(ORFs) including the alkA and adaA/B operon, which encode genesfor adaptive response to DNA alkylation. A homology search forthe newly identified 21 ORFs revealed that 4 of them exhibita significant similarity to known proteins, e.g., methicillin-resistantStaphylococcus aureus (MRSA) protein homolog, proteins involvedin chloramphenicol resistance, glucosamine synthase and an ABCtransporter protein. The remaining 17 ORFs did not show anysignificant sequence similarities to known gene products inthe database.     

人类鼻咽癌细胞株CNE2的转化基因Tx的一个Eco RI片段的核苷酸序列分析

本文运用定点克隆法并结合鸟枪法,对人类鼻咽癌细胞抹CNE2转化基因Tx中一个与转化作用有关的Eco RI片段,进行了核苷酸序列分析。此种克隆方法的运用,大大减少了DNA模板的数量,并加快了测序的进展。将序列分析结果输入美国NCI的CRAY-2型超级电子计算机作进一步分析,以寻找基因库中的同源序列,酶切位点,开放阅读框架(ORF)。在人类DNA基因数据库中没有找到同源序列,从而证实Tx基因是一种新的人类转化基因。计算机的分析还得出了一系列有价值的结论,为进一步深入探讨这个基因在人类鼻咽癌发病学中的作用,提供了重要的资料。这是首次报道的Tx基因核苷酸序列分析结果。     

鼻咽癌恶性转化基因Tx核苷酸序列分析

从人类鼻咽癌细胞系CNE2基因组DNA文库中克隆一个恶性转化基因Tx转染小鼠JB6 + 细胞 ,使细胞恶性转化 ,宿主细胞具有停泊非依赖生长的特性 .已经报道的Tx中一个 3 0kb片段(Tx3 0 )的序列分析结果表明 ,Tx包含人类免疫球蛋白κ轻链完整的J区 .进一步对Tx全长进行亚克隆和测序 ,并采用生物信息学方法进行分析表明 ,Tx包含人类Igκ完整的J区、C区基因片段、还有 5个重组信号序列 ,1个核基质结合序列和 1个N segment的插入 .Tx与正常人IgκJ、C区比较只是在某些位点存在碱基的缺失、插入或置换 ,二者同源性高达 98% ,其电子定位于 2p11 2 ,这与人Igκ的染色体定位是一致的 .可以认为 ,Tx是一个缺乏V区的异常的人类免疫球蛋白kappa轻链基因     

Association Mapping and Haplotype Analysis of a 3.1-Mb Genomic Region Involved in Fusarium Head Blight Resistance on Wheat Chromosome 3BS

A previous study provided an in-depth understanding of molecular population genetics of European and Asian wheat gene pools using a sequenced 3.1-Mb contig (ctg954) on chromosome 3BS. This region is believed to carry the Fhb1 gene for response to Fusarium head blight. In this study, 266 wheat accessions were evaluated in three environments for Type II FHB response based on the single floret inoculation method. Hierarchical clustering (UPGMA) based on a Manhattan dissimilarity matrix divided the accessions into eight groups according to five FHB-related traits which have a high correlation between them; Group VIII comprised six accessions with FHB response levels similar to variety Sumai 3. Based on the compressed mixed linear model (MLM), association analysis between five FHB-related traits and 42 molecular markers along the 3.1-Mb region revealed 12 significant association signals at a threshold of P<0.05. The highest proportion of phenotypic variation (6.2%) in number of diseased spikelets (NDS) occurred at locus cfb6059, and the physical distance was about 2.9 Kb between umn10 and this marker. Haplotype block (HapB) analysis using a sliding window LD of 5 markers, detected six HapBs in the 3.1-Mb region at r²>0.1 and P<0.001 between random closely linked markers. F-tests among Haps with frequencies >0.05 within each HapB at r²>0.1 and P<0.001 showed significant differences between the Hap carried by FHB resistant resources, such as Sumai 3 and Wangshuibai, and susceptible genotypes in HapB3 and HapB6. These results suggest that Fhb1 is located within HapB6, with the possibility that another gene is located at or near HapB3. SSR markers and Haps detected in this study will be helpful in further understanding the genetic basis of FHB resistance, and provide useful information for marker-assisted selection of Fhb1 in wheat breeding.     

Chromosome 3q26 Gain Is an Early Event Driving Coordinated Overexpression of the PRKCI,SOX2, and ECT2 Oncogenes in Lung Squamous Cell Carcinoma

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Beagle犬血清与胎牛血清生化特性及其对体外培养的人肺癌细胞生长的影响

目的比较Beagle犬血清与胎牛血清生化特性,探讨它们对体外培养的人肺癌细胞生长的影响。方法收集、制备Beagle犬血清与胎牛血清,采用全自动血液生化分析仪测定23项血清生化指标,比较分析两组血清生化特征差异。取对数期人肺癌细胞QG-56,分别培养于含10%FBS或Beagle-S的RPMI-1640合成培养基中,于第0、24、48、72、96、120和144 h各取出一块培养板进行检测,观察不同血清对细胞生长MTT曲线、细胞形态学的影响。结果FBS中CK、CK-MB、LDH、HBDH、GGT水平明显高于Beagle-S（P〈0.05）;CHE水平却明显低于Beagle-S,两者之间比较,均具有显著统计学意义。血清中的BUN、CRE、GLU、TP、ALB、ALT、ALP、TBIL、DBIL、TG、K^＋、Na^＋、Cl^-、Ca^2＋、Pi^3-水平在Beagle犬与胎牛间无显著性差异。MTT曲线和细胞形态学观察,两组于干预后24、48、72、96、120、144 h对QG-56细胞株生长的影响无显著性差异（P〈0.05）。结论Beagle犬的血清生化特性及其对体外肺癌细胞生长的影响与胎牛相似,可作为血清药理研究的优选动物之一。     

8p22 MTUS1 Gene Product ATIP3 Is a Novel Anti-Mitotic Protein Underexpressed in Invasive Breast Carcinoma of Poor Prognosis

Background

Breast cancer is a heterogeneous disease that is not totally eradicated by current therapies. The classification of breast tumors into distinct molecular subtypes by gene profiling and immunodetection of surrogate markers has proven useful for tumor prognosis and prediction of effective targeted treatments. The challenge now is to identify molecular biomarkers that may be of functional relevance for personalized therapy of breast tumors with poor outcome that do not respond to available treatments. The Mitochondrial Tumor Suppressor (MTUS1) gene is an interesting candidate whose expression is reduced in colon, pancreas, ovary and oral cancers. The present study investigates the expression and functional effects of MTUS1 gene products in breast cancer.

Methods and Findings

By means of gene array analysis, real-time RT-PCR and immunohistochemistry, we show here that MTUS1/ATIP3 is significantly down-regulated in a series of 151 infiltrating breast cancer carcinomas as compared to normal breast tissue. Low levels of ATIP3 correlate with high grade of the tumor and the occurrence of distant metastasis. ATIP3 levels are also significantly reduced in triple negative (ER- PR- HER2-) breast carcinomas, a subgroup of highly proliferative tumors with poor outcome and no available targeted therapy. Functional studies indicate that silencing ATIP3 expression by siRNA increases breast cancer cell proliferation. Conversely, restoring endogenous levels of ATIP3 expression leads to reduced cancer cell proliferation, clonogenicity, anchorage-independent growth, and reduces the incidence and size of xenografts grown in vivo. We provide evidence that ATIP3 associates with the microtubule cytoskeleton and localizes at the centrosomes, mitotic spindle and intercellular bridge during cell division. Accordingly, live cell imaging indicates that ATIP3 expression alters the progression of cell division by promoting prolonged metaphase, thereby leading to a reduced number of cells ungergoing active mitosis.

Conclusions

Our results identify for the first time ATIP3 as a novel microtubule-associated protein whose expression is significantly reduced in highly proliferative breast carcinomas of poor clinical outcome. ATIP3 re-expression limits tumor cell proliferation in vitro and in vivo, suggesting that this protein may represent a novel useful biomarker and an interesting candidate for future targeted therapies of aggressive breast cancer.     

定位于染色体9p21-22的一个新基因UBAP1的克隆测序及在鼻咽癌中的表达分析

 在染色体 9p2 1 2 2鼻咽癌杂合性丢失 (lossofheterozygosity,LOH)高频区 ,应用EST介导的定位 侯选克隆策略 ,用RT PCR及Northern杂交检测了 2 2个表达序列标记 (expressedsequencetag ,EST)在鼻咽癌细胞株HNE1和原代培养的正常鼻咽上皮细胞中的表达差异 ,并对其中一个在鼻咽癌细胞株HNE1中表达下调的EST检测了在鼻咽癌活检组织中的表达 .用生物信息学方法获得其全长cDNA序列 ,GenBank登录号AF2 2 2 0 4 3.该基因cDNA全长 2 70 1bp ,其开放阅读框 (openreadingframe ,ORF)编码一个含 50 2个氨基酸、分子量为 55kD的碱性蛋白质 ,在蛋白羧基端含有 2个连续的重要UBA功能域 (ubiquitinassociateddomain) ,属于遍在蛋白相关蛋白家族的一个新成员 ,经国际人类基因命名委员会同意 ,将其命名为UBAP1 (ubiquitinassociatedprotein 1 ) .Northern表达分析显示UBAP1在所检测的人组织中广泛表达 ,但在人的心脏、骨骼肌及肝脏中的表达较强 .UBAP1基因在63 2 % ( 1 2 1 9)的鼻咽癌活检组织中表达下调 .UBAP1基因作为一个遍在蛋白相关蛋白家族的新成员 ,结合其在 9p的重要定位信息 ,有必要进一步研究其表达下调参与鼻咽癌发生发展的可能机制 .     

Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q,and SOX4 as a Possible Auxiliary Target on 6p

Background

Urothelial carcinoma shows frequent amplifications at 6p22 and 1q21–24. The main target gene at 6p22 is believed to be E2F3, frequently co-amplified with CDKAL1 and SOX4. There are however reports on 6p22 amplifications that do not include E2F3. Previous analyses have identified frequent aberrations occurring at 1q21–24. However, due to complex rearrangements it has been difficult to identify specific 1q21–24 target regions and genes.

Methods

We selected 29 cases with 6p and 37 cases with 1q focal genomic amplifications from 261 cases of urothelial carcinoma analyzed by array-CGH for high resolution zoom-in oligonucleotide array analyses. Genomic analyses were combined with gene expression data and genomic sequence analyses to characterize and fine map 6p22 and 1q21–24 amplifications.

Results

We show that the most frequently amplified gene at 6p22 is SOX4 and that SOX4 can be amplified and overexpressed without the E2F3 or CDKAL1 genes being included in the amplicon. Hence, our data point to SOX4 as an auxiliary amplification target at 6p22. We further show that at least three amplified regions are observed at 1q21–24. Copy number data, combined with gene expression data, highlighted BCL9 and CHD1L as possible targets in the most proximal region and MCL1, SETDB1, and HIF1B as putative targets in the middle region, whereas no obvious targets could be determined in the most distal amplicon. We highlight enrichment of G4 quadruplex sequence motifs and a high number of intraregional sequence duplications, both known to contribute to genomic instability, as prominent features of the 1q21–24 region.

Conclusions

Our detailed analyses of the 6p22 amplicon suggest SOX4 as an auxiliary target gene for amplification. We further demonstrate three separate target regions for amplification at 1q21–24 and identified BCL9, CHD1L, and MCL1, SETDB1, and HIF1B as putative target genes within these regions.     

Inactivation of p16INK4a in Primary Tumors and Cell Lines of Head and Neck Squamous Cell Carcinoma

Inactivation of the p16^INK4a gene by mutation and deletion is common in head and neck squamous cell carcinoma (HNSCC). The present study demonstrates that hypermethylation of the 5 CpG islands can serve as an alternative mechanism for the inactivation of the p16^INK4a gene in this tumor. We studied 11 HNSCC cell lines and 17 oral squamous cell carcinoma (OSCC) primary tumors for p16^INK4a gene status by protein/mRNA and DNA genetic/epigenetic analyses to determine the incidence of its inactivation. Our study indicates that: (1) inactivation of p16 protein is frequent in HNSCC cell lines (6/11, 54.5%) and OSCC primary tumors (15/17, 88.2%), (2) inactivation of p16^INK4a protein is commonly associated with the presence of gene alteration such as mutation, homozygous deletion and especially aberrant methylation, and (3) genomic sequencing of bisulfite-modified DNA shows that the carcinoma develops a heterogeneous pattern of hypermethylation.     

Structure of Bovine P2 Basic Protein: Sequence of a Carboxyterminal Segment That Is a Neuritogen in Rabbits

The sequence of the carboxyterminal 18 amino acids released by cyanogen bromide digestion of the bovine P2 protein was determined. It has several interesting structural and immunological properties. It contains the only two half-cystines in the molecule that have the capacity to form an intrachain disulfide bond. Using the rabbit as a test animal, this carboxyterminal peptide was capable of producing experimental allergic neuritis. The sequence of this peptide is Val-Val-Glu-Cys-Lys-Met-Lys-Asp-Val-Val-Cys-Thr-Arg-Ile-Tyr-Glu-Lys-Val.     

shASPP2 H22稳转肝癌细胞系的构建及ASPP2敲低对H22移植瘤小鼠血管生成的影响

摘要 目的：构建小鼠shASPP2 H22稳转肝癌细胞系,观察ASPP2敲低对血管生成的影响。方法：针对小鼠ASPP2基因设计了3个不同的shRNA干扰序列（Y18421,Y18422,Y18423）及1个对照序列（GL427NC2）,采用双酶切（Age Ⅰ和EcoR Ⅰ）及质粒连接构建重组质粒,使用菌落PCR和测序比对进行鉴定;使用293T细胞将各重组质粒包装慢病毒并测定滴度;将 shASPP2和对照慢病毒质粒转染H22细胞,采用流式细胞术测定转染效率;采用qRT-PCR、Western Blot法观察shASPP2慢病毒对H22细胞ASPP2的干扰效果;采用CCK8法观察ASPP2敲低对H22细胞增殖的影响;采用Western Blot法观察ASPP2敲低对H22细胞及上清VEGF表达和分泌的影响;采用细胞注射法建立小鼠ASPP2敲低H22细胞皮下移植瘤模型,游标卡尺法观察肿瘤体积大小,采用活体激光共聚焦观察肿瘤血管生成情况,采用Western Blot法观察肿瘤组织VEGF的表达。结果：双酶切、菌落PCR和测序鉴定结果表示各重组质粒构建成功;各重组质粒经慢病毒包装后,测定显示Y18421、Y18422、Y18423和GL427NC2慢病毒质粒的滴度分别为3.40×10⁸ TU/mL、4.08×10⁸ TU/mL、5.49×10⁸ TU/mL和1.7×10⁹ TU/mL;Y18421、Y18422、Y18423及GL427NC2慢病毒质粒转染效率分别为：86.2 %、69.6 %、60.8 %和76.9 %。与GL427NC2 H22细胞相比,Y18421 H22细胞的ASPP2 mRNA及蛋白的表达明显降低（P<0.01,P<0.05）;Y18421细胞在培养24,48,72 h后增殖速率显著增加（P<0.0001,P<0.001,P<0.01）;Y18421细胞及上清的VEGF表达显著升高（P<0.001,P<0.01,P<0.05）。与GL427NC2 细胞移植瘤相比,Y18421细胞移植瘤体积明显增大（P<0.05）,总血管长度显著增加（P<0.05）,VEGF蛋白的表达明显上调（P<0.05）。结论：小鼠shASPP2 H22稳转肝癌细胞系构建成功,ASPP2敲低可能通过上调VEGF的表达促进小鼠H22细胞移植瘤血管生成。