公开(公告)号：US20120183967A1

公开(公告)日：2012-07-19

申请号：US13311120

申请日：2011-12-05

申请人： Devin DRESSMAN ,  Hai YAN ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

发明人： Devin DRESSMAN ,  Hai YAN ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6858 ,  C07H21/04 ,  C12N15/1075 ,  C12Q1/686 ,  C12Q2565/537 ,  C12Q2563/149 ,  C12Q2563/143

摘要： Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently-labeled particles via flow cytometry. Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and employed for further experimentation. This approach can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues.

摘要翻译： 生物医学研究的许多领域取决于对个别基因或转录本中不常见变异的分析。 在这里，我们描述一种可以量化这种变化的方法，其规模和容易度迄今为止是无法实现的。 将这样的分子的集合中的每个DNA分子转化成单个颗粒，其中与原始序列顺序相同的数千个拷贝的DNA被结合。 这种珠子群对应于起始DNA分子的一对一表示。 然后可以通过流式细胞术对荧光标记的颗粒进行计数，简单地评估原始DNA分子群体内的变异。 可以用标准实验室设备以这种方式评估数百万个单独的DNA分子。 此外，可以通过流动分选分离特定的变体并用于进一步的实验。 该方法可用于鉴定和定量稀有突变，并研究特定群体或组织中基因序列或转录本的变异。

公开(公告)号：US20120202207A1

公开(公告)日：2012-08-09

申请号：US13412696

申请日：2012-03-06

申请人： Bert VOGELSTEIN ,  Kenneth W. KINZLER ,  D. Williams PARSONS ,  Xiaosong ZHANG ,  Jimmy Cheng-Ho LIN ,  Rebecca J. LEARY ,  Philipp ANGENENDT ,  Nickolas PAPADOPOULOS ,  Victor VELCULESCU ,  Giovanni PARMIGIANI ,  Rachel KARCHIN ,  Sian JONES ,  Hai YAN ,  Darell BIGNER ,  Chien-Tsun KUAN ,  Gregory J. RIGGINS

发明人： Bert VOGELSTEIN ,  Kenneth W. KINZLER ,  D. Williams PARSONS ,  Xiaosong ZHANG ,  Jimmy Cheng-Ho LIN ,  Rebecca J. LEARY ,  Philipp ANGENENDT ,  Nickolas PAPADOPOULOS ,  Victor VELCULESCU ,  Giovanni PARMIGIANI ,  Rachel KARCHIN ,  Sian JONES ,  Hai YAN ,  Darell BIGNER ,  Chien-Tsun KUAN ,  Gregory J. RIGGINS

IPC分类号： C12Q1/68 ,  C07K16/40 ,  C07H21/04 ,  G01N33/574

CPC分类号： C12Q1/6886 ,  C12Q2600/112 ,  C12Q2600/118 ,  C12Q2600/136 ,  C12Q2600/156

摘要： We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in glioblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.

摘要翻译： 我们发现大多数II级和III级星形细胞瘤和少突胶质细胞瘤中异柠檬酸脱氢酶1（IDH1）的R132残基突变以及从这些较低级别病变发展的成胶质细胞瘤。 那些没有IDH1突变的肿瘤在紧密相关的IDH2基因的类似R172残基中经常具有突变。 这些发现对恶性胶质瘤的发病机制和诊断具有重要意义。

公开(公告)号：US20110201004A1

公开(公告)日：2011-08-18

申请号：US13071105

申请日：2011-03-24

申请人： Bert VOGELSTEIN ,  Kenneth W. KINZLER

发明人： Bert VOGELSTEIN ,  Kenneth W. KINZLER

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q1/6818 ,  C12Q1/6851 ,  C12Q1/686 ,  C12Q1/6874 ,  C12Q2600/156 ,  C12Q2600/158

摘要： The identification of pre-defined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. The exponential, analog nature of the polymerase chain reaction is transformed into a linear, digital signal suitable for this purpose. Single molecules can be isolated by dilution and individually amplified; each product is then separately analyzed for the presence of pre-defined mutations. The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample.

摘要翻译： 预期存在于细胞群体的较小部分中的预定义突变的鉴定对于各种基础研究和临床应用是重要的。 聚合酶链反应的指数模拟性质被转化为适合于此目的的线性数字信号。 单分子可以通过稀释和单独扩增分离; 然后分别分析每种产品是否存在预先定义的突变。 该过程提供了DNA样品中变体序列比例的可靠和定量测量。

公开(公告)号：US20120095086A1

公开(公告)日：2012-04-19

申请号：US13275958

申请日：2011-10-18

申请人： Zhenghe WANG ,  Victor VELCULESCU ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

发明人： Zhenghe WANG ,  Victor VELCULESCU ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

IPC分类号： A61K31/7052 ,  C12Q1/42 ,  A61P35/00 ,  C12N15/55 ,  C12N5/10 ,  C12Q1/68 ,  C12N9/16

CPC分类号： C12Q1/6886 ,  C12N9/16 ,  C12Q2600/112 ,  C12Q2600/136 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Y301/03048 ,  G01N33/5011 ,  G01N2333/916

摘要： Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs (PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14), affecting 26% of colorectal cancers and a smaller fraction of lung, breast and gastric cancers. Fifteen mutations were nonsense, frameshift or splice site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP (PTPRT) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the tyrosine phosphatase genes are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.

摘要翻译： 由蛋白酪氨酸磷酸酶（PTP）和激酶（PTK）调节的酪氨酸磷酸化在肿瘤发生的信号通路中是重要的。 人类癌症中酪氨酸磷酸酶基因超家族的突变分析鉴定了六种PTP（PTPRF，PTPRG，PTPRT，PTPN3，PTPN13，PTPN14）中的83个体细胞突变，影响26％的结肠直肠癌和较小部分的肺癌，乳腺癌和胃癌 。 十五个突变是无义，移位或剪接位点改变，预计会导致截短的蛋白质缺乏磷酸酶活性。 在生物化学检查中发现最常改变的PTP（PTPRT）中的五个错义突变被发现可以减少磷酸酶活性。 野生型但不是突变PTPRT在人类癌细胞中的表达抑制细胞生长。 这些观察结果表明酪氨酸磷酸酶基因是肿瘤抑制基因，调节可能适合于治疗干预的细胞途径。

公开(公告)号：US20130196312A1

公开(公告)日：2013-08-01

申请号：US13247552

申请日：2011-09-28

申请人： Laura D. WOOD ,  Williams D. PARSONS ,  Sian JONES ,  Jimmy LIN ,  Tobias SJÖBLOM ,  Thomas BARBER ,  Giovanni PARMIGIANI ,  Victor VELCULESCU ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

发明人： Laura D. WOOD ,  Williams D. PARSONS ,  Sian JONES ,  Jimmy LIN ,  Tobias SJÖBLOM ,  Thomas BARBER ,  Giovanni PARMIGIANI ,  Victor VELCULESCU ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q2600/112 ,  C12Q2600/156

摘要： Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalogue the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene “mountains” and a much larger number of gene “hills” that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.

摘要翻译： 人类癌症是由致癌基因和肿瘤抑制基因突变的积累引起的。 为了列出肿瘤发生过程中发生的遗传变化，我们从11个乳腺和11个结肠直肠肿瘤中分离出DNA，并在这些样品中确定了参考序列数据库中的基因序列。 根据对18,191个基因的20,857个转录本的外显子的分析，我们得出结论，乳腺癌和结肠直肠癌的基因组景观由少数常见的突变基因“山”组成，更多的基因“山”在低位突变 频率。 我们描述了统计和生物信息学工具，可以帮助识别在肿瘤发生中发挥作用的突变。 这些结果有助于了解人类癌症的性质和异质性以及使用个人基因组学进行肿瘤诊断和治疗。

公开(公告)号：US20130035404A1

公开(公告)日：2013-02-07

申请号：US13461268

申请日：2012-05-01

申请人： Bert VOGELSTEIN ,  Kenneth W. KINZLER ,  Rebecca J. LEARY ,  Victor E. VELCULESCU

发明人： Bert VOGELSTEIN ,  Kenneth W. KINZLER ,  Rebecca J. LEARY ,  Victor E. VELCULESCU

IPC分类号： C40B30/04 ,  A61K35/00 ,  A61P35/00 ,  C40B20/00

CPC分类号： C12Q1/6886 ,  C12Q2600/156

摘要： Genome-wide analysis of copy number changes in breast and colorectal tumors used approaches that can reliably detect homozygous deletions and amplifications. The number of genes altered by major copy number changes—deletion of all copies or amplification of at least twelve copies per cell—averaged thirteen per tumor. These data were integrated with previous mutation analyses of the Reference Sequence genes in these same tumor types to identify genes and cellular pathways affected by both copy number changes and point alterations. Pathways enriched for genetic alterations include those controlling cell adhesion, intracellular signaling, DNA topological change, and cell cycle control. These analyses provide an integrated view of copy number and sequencing alterations on a genome-wide scale and identify genes and pathways that are useful for cancer diagnosis and therapy.

摘要翻译： 使用可以可靠地检测纯合缺失和扩增的方法对乳腺和结肠直肠肿瘤的拷贝数变化进行全基因组分析。 通过主要拷贝数变化改变的基因数量 - 全部拷贝的缺失或每个细胞至少12个拷贝的扩增，平均每个肿瘤13个。 这些数据与这些相同肿瘤类型中的参考序列基因的先前突变分析相结合，以鉴定受拷贝数变化和点改变影响的基因和细胞途径。 富含遗传改变的途径包括控制细胞粘附，细胞内信号转导，DNA拓扑变化和细胞周期控制的途径。 这些分析提供了在全基因组范围内的拷贝数和排序变化的综合视图，并确定了可用于癌症诊断和治疗的基因和途径。

公开(公告)号：US20110104059A1

公开(公告)日：2011-05-05

申请号：US12436444

申请日：2009-05-06

申请人： Brad ST. CROIX ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

发明人： Brad ST. CROIX ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

IPC分类号： A61K49/00 ,  C07K16/24 ,  C07K16/18 ,  C07K16/40 ,  C07K16/42 ,  C07K16/28 ,  C07K16/10 ,  A61K39/395 ,  C07K2/00 ,  C07K14/56 ,  C07K16/00 ,  A61K38/02 ,  A61K38/21 ,  A61K38/48 ,  A61K35/12 ,  A61K38/44 ,  G01N33/68 ,  C12Q1/68 ,  A61K39/21 ,  A61K39/00 ,  A61P35/00 ,  A61P19/02 ,  A61P17/06 ,  A61P27/02

CPC分类号： C07K14/705 ,  A61K38/00 ,  A61K2039/505 ,  C12Q1/6886 ,  C12Q2600/136 ,  C12Q2600/158

摘要： To gain a better understanding of tumor angiogenesis endothelial cells (ECs) were isolated and gene expression patterns were evaluated. When transcripts from ECs derived from normal and malignant colorectal tissues were compared with transcripts from non-endothelial cells, over 170 genes predominantly expressed in the endothelium were identified. Comparison between normal- and tumor-derived endothelium revealed differentially expressed genes, including many that were specifically elevated in tumor-associated endothelium. Experiments with representative genes from this group demonstrated that most were similarly expressed in the endothelium of primary lung, breast, brain, and pancreatic cancers as well as in metastatic lesions of the liver. These results demonstrate that neoplastic and normal endothelium in humans are distinct at the molecular level.

摘要翻译： 为了更好地了解肿瘤血管生成，分离内皮细胞（ECs），评估基因表达模式。 将来自正常和恶性结肠直肠组织的ECs的转录物与来自非内皮细胞的转录物进行比较，鉴定了主要在内皮中表达的170个以上的基因。 正常和肿瘤衍生的内皮的比较显示差异表达的基因，包括在肿瘤相关内皮中特异性升高的许多基因。 来自该组的代表性基因的实验表明，大多数类似物在原发性肺癌，乳腺癌，脑癌和胰腺癌的内皮以及肝转移性损伤中都表达。 这些结果表明，人类的肿瘤和正常内皮在分子水平上是不同的。

公开(公告)号：US20110319477A1

公开(公告)日：2011-12-29

申请号：US13210736

申请日：2011-08-16

申请人： Yardena SAMUELS ,  Victor VELCULESCU ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

发明人： Yardena SAMUELS ,  Victor VELCULESCU ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

IPC分类号： A61K31/7088 ,  A61K31/713 ,  C07H21/04 ,  C12Q1/68 ,  C12N5/09 ,  C12Q1/48

摘要： Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the PI3K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the PI3K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.

摘要翻译： 已知磷脂酰肌醇3-激酶（PI3K）是信号通路的重要调控因子。 为了确定PI3K在癌症中的遗传改变，我们分析了PI3K基因家族的序列，发现一个家族成员PIK3CA在结肠癌和其他器官的癌症中经常发生突变。 大多数突变聚集在PI3K螺旋或激酶结构域内的两个位置附近。 PIK3CA代表人类癌症中尚未鉴定的最高突变型癌基因之一，可用作诊断和治疗靶点。

公开(公告)号：US20110311500A1

公开(公告)日：2011-12-22

申请号：US13198850

申请日：2011-08-05

申请人： Long DANG ,  Chetan BETTEGOWDA ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

发明人： Long DANG ,  Chetan BETTEGOWDA ,  Kenneth W. KINZLER ,  Bert VOGELSTEIN

IPC分类号： A61K35/74 ,  A61P35/00

CPC分类号： A61K35/742 ,  A61K31/337 ,  A61K31/427 ,  A61K45/06 ,  Y10S435/842 ,  A61K2300/00

摘要： Current approaches for treating cancer are limited, in part, by the inability of drugs to affect the poorly vascularized regions of tumors. We have found that spores of anaerobic bacteria in combination with agents which interact with microtubules can cause the destruction of both the vascular and avascular compartments of tumors. Two classes of microtubule inhibitors were found to exert markedly different effects. Some agents that inhibited microtubule synthesis, such as vinorelbine, caused rapid, massive hemorrhagic necrosis when used in combination with spores. In contrast, agents that stabilized microtubules, such as the taxane, docetaxel, resulted in slow tumor regressions that killed most neoplastic cells. Remaining cells in the poorly perfused regions of tumors could be eradicated by sporulated bacteria. Mechanistic studies showed that the microtubule destabilizers, but not the microtubule stabilizers, radically reduced blood flow to tumors, thereby enlarging the hypoxic niche in which spores could germinate. A single intravenous injection of spores plus selected microtubule-interacting agents was able to cause regressions of several tumors in the absence of excessive toxicity.

摘要翻译： 目前用于治疗癌症的方法在一定程度上受到药物不能影响肿瘤血管不足的区域的限制。 我们已经发现，厌氧细菌的孢子与与微管相互作用的药物组合可能导致肿瘤的血管和非血管性腔室的破坏。 发现两类微管抑制剂发挥显着不同的作用。 抑制微管合成的一些药物，如长春瑞滨，当与孢子结合使用时，引起快速，大规模的出血性坏死。 相比之下，稳定微管（如紫杉烷，多西紫杉醇）的药物导致肿瘤消退缓慢，导致大多数肿瘤细胞死亡。 肿瘤不良灌注区域的剩余细胞可以被孢子细菌消灭。 机理研究表明，微管不稳定剂，而不是微管稳定剂，从根本上减少了流向肿瘤的血液，从而扩大了孢子可以发芽的缺氧生态位。 在没有过量毒性的情况下，单次静脉注射孢子加选择的微管相互作用剂能够引起几种肿瘤的回归。