Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis

1. Download high-res image (190KB)
2. Download full-size image

     

Pan cancer patterns of allelic imbalance from chromosomal alterations in 33 tumor types

Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities (“B allele” frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the “B allele” frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.     

Characterization of Postmortem Human Brain Proteins by Two-Dimensional Gel Electrophoresis

Abstract: The proteins of membrane and cytosol fractions from frozen human postmortem brain were analyzed by two-dimensional gel electrophoresis (isoelectric range: 5.1–6.0) and both Coomassie-blue and ammoniacal silver staining. Cytosol preparations were analyzed from six different postmortem brains from patients with various neurologic diagnoses and immediate causes of death. Intervals between death and brain freezing (−70^oC) ranged from 2 to 20 h. The vast majority of proteins detected in these cytosol fractions had identical molecular weights and isoelectric points in each of six human brains examined. However, in some tissue samples tubulin was either quantitatively decreased or undetectable. The possibility that this partial or complete depletion of tubulin was related to postmortem interval and/or brain freezing was studied using rat forebrain tissue. Rat brain incubated at room temperature for up to 24 h did not reproduce the changes seen in the region of human cytosol tubulin. However, other changes seen in the two-dimensional electrophoretic pattern of rat cytosol proteins did relate to postmortem interval, brain freezing, or both. Rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum were prepared from three human brains, with highly reproducible two-dimensional patterns. Protein analysis of these membrane fractions revealed that human RER contained significant amounts of tubulin, in contrast to rat RER which contained no detectable tubulin. This discrepancy was elucidated by allowing rat brains to remain at room temperature for 24 h before freezing; gels of rat RER prepared from this tissue showed that tubulin subunits were present.     

人乳腺癌cAMP结合蛋白

建立了测定人乳腺癌胞浆ｃＡＭＰ结合蛋白（ｃＡＭＰｂ．ｐ．）方法。综合研究了其温度、保温时间、配体浓度、稳定性等条件。ｃＡＭＰｂ．ｐ．的Ｋ_Ｄ值为２．９０×１０~（－８）ｍｏｌ／Ｌ．并测定了６０例雌激素受体（ＥＲ）Ｆｕ性乳腺癌标本的ｃＡＭＰｂ．ｐ．含量。此组病人术后均接受系统的内分泌治疗,ＥＲ／ｃＡＭＰｂｐ,比值范围为７．７～３６２×１０~（－３）,ＥＲ／ｃＡＭＰｂ．ｐ．比值≥４０×１０~（－３）的五年生存率明显高于比值＜４０×１０~（－３）组,（ｐ＜０．００５）．表明测定ＥＲ／ｃＡＭＰｂ．ｐ．比值对预测患者内分泌治疗疗效,优于单独测定ＥＲ．     

Role of genomic factors beyond thymidylate synthase in the prediction of response to 5-fluorouracil

ABSTRACT

5-Fluorouracil (5FU) is still a major drug in combinations regimens for the treatment of colorectal cancer (CRC) both in the adjuvant and palliative setting. 5FU or its oral prodrug capecitabine is usually combined with irinotecan/oxaliplatin and the novel agents bevacizumab/cetuximab. Although this improved the outcome, the overall prognosis in patients with metastasized disease is still relatively poor. Although the target for 5FU, thymidylate synthase was shown to have a predictive value, this could only predict response in a subset of patients. Given the heterogeneous and complex nature of CRC, it is likely that other aberrations can affect therapeutic response. As an alternative, we investigated Copy number alterations using oligonucleotide-based high-throughput array-comparative-genomic-hybridization (aCGH) to obtain an unbiased screening of the whole genetic spectrum. Chromosomal aberrations have been identified in 85% of CRC patients and include genomic regions harboring copy number alterations in the DNA. These alterations may change the expression of many genes and might explain the differential response to therapy as shown in recent studies with several 5FU combinations. In order to clarify new predictive parameters for 5FU, we used aCGH in a historical cohort of patients, which received treatment with single agent 5FU, and an unsupervised clustering analysis showed a statistical (p < 0.05) difference between responding and nonresponding patients. We also find that several regions showed differences between responders/non-responders, such as losses in 12p12.3–12q15 and in 18p (where TS is located) in responding patients. Genome-wide analysis may provide an additional tool to discriminate between responders and nonresponders.     

Loss of chromosome Y in primary tumors

1. Download : Download high-res image (162KB)
2. Download : Download full-size image

     

Chromosome instability region analysis and identification of the driver genes of the epithelial ovarian cancer cell lines A2780 and SKOV3

Epithelial ovarian cancer (EOC) is one of the most prevalent gynaecological cancers worldwide. The molecular mechanisms of serous ovarian cancer (SOC) remain unclear and not well understood. SOC cases are primarily diagnosed at the late stage, resulting in a poor prognosis. Advances in molecular biology techniques allow us to obtain a better understanding of precise molecular mechanisms and to identify the chromosome instability region and key driver genes in the carcinogenesis and progression of SOC. Whole-exome sequencing was performed on the normal ovarian cell line IOSE80 and the EOC cell lines SKOV3 and A2780. The single-nucleotide variation burden, distribution, frequency and signature followed the known ovarian mutation profiles, without chromosomal bias. Recurrently mutated ovarian cancer driver genes, including LRP1B, KMT2A, ARID1A, KMT2C and ATRX were also found in two cell lines. The genome distribution of copy number alterations was found by copy number variation (CNV) analysis, including amplification of 17q12 and 4p16.1 and deletion of 10q23.33. The CNVs of MED1, GRB7 and MIEN1 located at 17q12 were found to be correlated with the overall survival of SOC patients (MED1: p = 0.028, GRB7: p = 0.0048, MIEN1: p = 0.0051), and the expression of the three driver genes in the ovarian cell line IOSE80 and EOC cell lines SKOV3 and A2780 was confirmed by western blot and cell immunohistochemistry.     

Theoretical framework of population genetics with somatic mutations taken into account: application to copy number variations in humans

Traditionally, population genetics focuses on the dynamics of frequencies of alleles acquired by mutations on germ-lines, because only such mutations are heritable. Typical genotyping experiments, however, use DNA from some somatic tissues such as blood, which harbors somatic mutations at the current generation in addition to germ-line mutations accumulated since the most recent common ancestor of the sample. This common practice may sometimes cause erroneous interpretations of polymorphism data, unless we properly understand the role of somatic mutations in population genetics. We here introduce a very basic theoretical framework of population genetics with somatic mutations taken into account. It is easy to imagine that somatic mutations at the current generation simply add individual-specific variations, as errors in mutation detection do. Our theory quantifies this increment under various conditions. We find that the major contribution of somatic mutations plus errors is to very rare variants, particularly to singletons. The relative contribution is markedly large when mutations are deleterious. Because negative selection also increases rare variants, it is important to distinguish the roles of these mutually confounding factors when we interpret the data, even after correcting for demography. We apply this theory to human copy number variations (CNVs), for which the composite effect of somatic mutations and errors may not be negligible. Using genome-wide CNV data, we demonstrate how the joint action of the two factors, selection and somatic mutations plus errors, shapes the observed pattern of polymorphism.     

Genomic instability of the DYZ1 repeat in patients with Y chromosome anomalies and males exposed to natural background radiation.

We assessed genomic instability of 3.4 kb DYZ1 repeat arrays in patients encompassing prostate cancer (PC), cases of repeated abortion (RA) and males exposed to natural background radiation (NBR) using real-time PCR and fluorescence in situ hybridization (FISH). Normal males showed DYZ1 copies ranging from 3000 to 4300, RA, 0-2237; PC, 550; and males exposed to NBR, 1577-5700. FISH showed organizational variation of DYZ1 in these samples substantiating the data obtained from real-time PCR. Of the 10 RA samples, 7 were found to be affected of which, 5 showed deletion of 265 bp from nt 25 to 290 and 773 bp from 1347 to 2119 and 2 showed deletion of 275 bp from nt 3128 to 3402. Copy number variation of DYZ1 in these males correlated with genetic constrains/anomalies. Although precise mechanisms of genomic instability of DYZ1 remains unclear, we construe that this repeat plays a critical role in maintaining the structural integrity of the Y chromosome, possibly by absorbing the load of mutations. This may be used as a marker system to analyze genetic integrity of the DYZ1 repeat array(s) across the spectrum of patients.     

HER2基因组DNA标准物质互通性研究

采用实验室建立的数字PCR方法 (ddPCR)和荧光定量PCR (qPCR)方法研究HER2基因组DNA标准物质的互通性,评价HER2基因组DNA标准物质与临床样本的互通性,为临床实验室检测提供具有互通性的可溯源标准物质.将研制的5个水平标准物质随机穿插于29例临床样本间,使用ddPCR方法与qPCR方法同时进行检测.参考美国临床实验室标准化协会(CLSI)指南文件EP30和中华人民共和国卫生行业标准基质效应与互通性评估指南WS/T356-2011的推荐,采用Deming回归法评价标准物质的互通性.结果显示,5种标准物质与临床样本之间具有良好的互通性,可以用于临床实验室对HER2基因拷贝数变异检测方法的方法验证和质量控制.     

胃癌相关新蛋白Raf激酶抑制蛋白相互作用蛋白质的鉴定

Raf激酶抑制蛋白(RKIP)的异常表达在胃癌的发生发展中起重要的作用,为了阐明其作用机制,应用脂质体将RKIP-3xFLAG-pcDNA3.1质粒转染至SGC7901细胞,建立RKIP-3xFLAG高表达的SGC7901细胞;并利用3xFLAG标签的亲和层析技术联合质谱分析,分离、鉴定与RKIP相互作用的蛋白质,并应用免疫共沉淀联合Western-blot进一步验证质谱结果．共鉴定出66个RKIP相互作用蛋白质,功能分类包括蛋白质代谢酶类、生物氧化相关酶类,细胞骨架蛋白、分子伴侣、信号转导相关蛋白、酶解相关蛋白等．并首次证实14-3-3蛋白与RKIP存在相互作用．为阐明RKIP在胃癌发生发展中的作用机制提供了重要的线索,为胃癌的早期诊治及预后监测提供了新的靶点．     

Characterization and Use of Green Fluorescent Proteins from Renilla mulleri and Ptilosarcus guernyi for the Human Cell Display of Functional Peptides

Green fluorescent protein (GFP) is useful as an intracellular scaffold for the display of random peptide libraries in yeast. GFPs with a different sequence from Aequorea victoria have recently been identified from Renilla mulleri and Ptilosarcus gurneyi. To examine these proteins as intracellular scaffolds for peptide display in human cells, we have determined the expression level of retrovirally delivered human codon-optimized versions in Jurkat-E acute lymphoblastic leukemia cells using fluorescence activated cell sorting and Western blots. Each wild type protein is expressed at 40% higher levels than A. victoria mutants optimized for maximum fluorescence. We have compared the secondary structure and stability of these GFPs with A. victoria GFP using circular dichroism (CD). All three GFPs essentially showed a perfect -strand conformation and their melting temperatures (T_m) are very similar, giving an experimental evidence of a similar overall structure. Folded Renilla GFP allows display of an influenza hemagglutinin epitope tag in several internal insertion sites, including one which is not permissive for such display in Aequorea GFP, giving greater flexibility in peptide display options. To test display of a functional peptide, we show that the SV-40 derived nuclear localization sequence PPKKKRKV, when inserted into two different potential loops, results in the complete localization of Renilla GFP to the nucleus of human A549 cells.     

应用二维电泳和质谱技术筛选喉癌及癌旁组织中的差异表达蛋白质

目的分离并鉴定喉癌和癌旁正常粘膜组织的差异表达蛋白质,为喉癌早期临床诊断、治疗提供新的有关的肿瘤生物学标记和靶标。方法收集5对人喉癌组织和对应的癌旁正常粘膜组织,提取组织总蛋白质,采用二维凝胶电泳技术分离蛋白并进行比较。选择在喉癌中明显差异表达的蛋白质点,进行质谱分析。结果获得了分辨率和重复性均较好的凝胶蛋白图谱。筛选出的在喉癌及癌旁正常粘膜组织中明显差异表达的10个蛋白质点,并成功鉴定。其中在喉癌组织中高表达的7个,低表达的3个。结论喉癌组织与癌旁正常粘膜组织蛋白存在明显的差异,筛选并鉴定出的这些蛋白质可能成为喉癌早期临床诊断、治疗的标志物和靶标。