用比较基因组杂交技术(CGH)检测肾癌染色体畸变

目的应用比较基因组杂交技术(CGH)分析原发性肾癌肿瘤组织中染色体异常变化,探讨肾癌细胞遗传物质的改变,揭示肾癌发生发展的内在本质及其与临床特征之间的关系。方法采用CGH技术对12例肾癌组织提取的全基因组DNA进行检测,以了解肾癌全基因组的变化。结果CGH技术检测的12例肾癌标本中均有染色体的畸变(扩增和/或缺失),常见的扩增区是1p、4p、5q、7p、9p、16p,常见的缺失区是3q、4q、6q、9q、14q、18q。结论原发性肾癌存在广泛的遗传物质不平衡现象,肾癌细胞染色体扩增和/或缺失可能是肾癌发生发展的基础。     

Chromosomal imbalances revealed in primary renal cell carcinomas by comparative genomic hybridization

Renal cell carcinoma (RCC) accounts for approximately 3% of all new cancer cases. Although the classification of RCC is based mainly on histology, this method is not always accurate. We applied comparative genomic hybridization (CGH) to determine genomic alterations in 46 cases of different RCC histological subtypes [10 cases of clear cell RCC (CCRCC), 13 cases of papillary RCC (PRCC), 12 cases of chromophobe RCC (CRCC), 9 cases of Xp11.2 translocation RCC (Xp11.2RCC), 2 cases of undifferentiated RCC (unRCC)], and investigated the relationships between clinical parameters and genomic aberrations. Changes involving one or more regions of the genome were seen in all RCC patients; DNA sequence gains were most frequently (>30%) seen in chromosomes 7q, 16p, and 20q; losses from 1p, 3p, 13q, 14q, and 8p. We conclude CGH is a useful complementary method for differential diagnosis of RCC. Loss of 3p21-25, 15q, and gain of 16p11-13 are relatively particular to CCRCC vs. other types of RCC. Gain of 7p13-22, 8q21-24, and loss of 18q12-ter, 14q13-24, and Xp11-q13/Y are more apparent in PRCC, and gain of 8q21-24 is characteristic of type 2 PRCC vs. type 1 PRCC. Loss of 2q12-32, 10p12-15, and 11p11-15, 13p are characteristic of CRCC, and gain of 3p and loss of 11p11-15 and 13p are significant differentiators between common CRCC and CRCC accompanied by sarcomatous change groups. Gain of Xp11-12 is characteristic of the Xp11.2RCC group. Based on Multivariate Cox regression analysis, aberration in 5 chromosome regions were poor prognostic markers of RCC, and include the gain of chromosome 12p12-ter (P = 0.034, RR = 3.502, 95% CI 1.097-11.182), 12q14-ter (P = 0.002, RR = 5.115, 95% CI 1.847-14.170), 16q21-24 (P = 0.044, RR = 2.629, 95% CI 1.027-6.731), 17p12-ter (P = 0.017, RR = 3.643, 95% CI 1.262-10.512) and the loss of 18q12-23 (P = 0.049, RR = 2.911, 95% CI 1.006-8.425), which may provide clues of new genes involved in RCC tumorigenesis.     

Chromosomal abnormalities in renal cell neoplasms associated with acquired renal cystic disease. A series studied by comparative genomic hybridization and fluorescence in situ hybridization

Sporadic renal cell carcinomas (RCCs) display different chromosomal abnormalities according to their morphology; gains of chromosomes 7 and 17 and loss of Y are commonly observed in papillary lesions, whereas loss of 3p sequences and multiple losses of specific chromosomes are found in non-papillary and chromophobe cell carcinomas, respectively. Acquired renal cystic disease (ARCD) is associated with an increased incidence of renal cell tumours, especially papillary lesions. The aim of this study was to examine a series of ARCD-related tumours for chromosomal abnormalities and to compare the findings with those abnormalities commonly observed in sporadic RCCs. Nine tumours from four patients with ARCD were examined using comparative genomic hybridization (CGH) and interphase cytogenetics. Gain of chromosomes 7 and 17 was observed in all four papillary lesions and loss of Y in three. In addition, gain of chromosome 16 was observed in three papillary tumours. Three chromophobe RCCs originating from the same kidney showed different genomic profiles; two had no abnormalities, whereas one showed loss of chromosome 17p. Two non-papillary RCCs failed to show chromosome 3p alterations. In conclusion, renal cell tumours developing in ARCD may show chromosomal abnormalities both similar to and different from those seen in sporadic tumours. Copyright © 1999 John Wiley & Sons, Ltd.     

Unclassified renal cell carcinoma: a clinicopathological,comparative genomic hybridization,and whole-genome exon sequencing study

Unclassified renal cell carcinoma (URCC) is a rare variant of RCC, accounting for only 3-5% of all cases. Studies on the molecular genetics of URCC are limited, and hence, we report on 2 cases of URCC analyzed using comparative genome hybridization (CGH) and the genome-wide human exon GeneChip technique to identify the genomic alterations of URCC. Both URCC patients (mean age, 72 years) presented at an advanced stage and died within 30 months post-surgery. Histologically, the URCCs were composed of undifferentiated, multinucleated, giant cells with eosinophilic cytoplasm. Immunostaining revealed that both URCC cases had strong p53 protein expression and partial expression of cluster of differentiation-10 and cytokeratin. The CGH profiles showed chromosomal imbalances in both URCC cases: gains were observed in chromosomes 1p11-12, 1q12-13, 2q20-23, 3q22-23, 8p12, and 16q11-15, whereas losses were detected on chromosomes 1q22-23, 3p12-22, 5p30-ter, 6p, 11q, 16q18-22, 17p12-14, and 20p. Compared with 18 normal renal tissues, 40 mutated genes were detected in the URCC tissues, including 32 missense and 8 silent mutations. Functional enrichment analysis revealed that the missense mutation genes were involved in 11 different biological processes and pathways, including cell cycle regulation, lipid localization and transport, neuropeptide signaling, organic ether metabolism, and ATP-binding cassette transporter signaling. Our findings indicate that URCC may be a highly aggressive cancer, and the genetic alterations identified herein may provide clues regarding the tumorigenesis of URCC and serve as a basis for the development of targeted therapies against URCC in the future.     

Comparative genomic hybridization and karyotyping of human embryonic stem cells reveals the occurrence of an isodicentric X chromosome after long-term cultivation

Human embryonic stem (hES) cells are important research toolsin studies of the physiology of early tissue differentiation.In addition, prospects are high regarding the use of these cellsfor successful cell transplantation. However, one concern hasbeen that cultivation of these cells over many passages mightinduce chromosomal changes. It is thus important to investigatethese cell lines, and check that a normal chromosomal contentis retained even during long-term in vitro culture. Comparativegenomic hybridization (CGH) was used to analyse three hES celllines derived in our laboratory and cultured continuously for30–42 weeks, comprising 35–39 cell passages. CGHcould be successfully performed in 48 out of a total of 50 isolatedsingle cells (96%). All three lines (HS181, HS235 and HS237)were shown to have a normal chromosomal content when analysedby both single cell CGH and by karyotyping up to passages 39,39 and 35 respectively. No aneuploidies or larger deletionsor amplifications were detected, and they were female (46,XX).However, HS237 was reanalysed at passage 61, and at that pointan aberrant X chromosome was detected by karyotyping. The aberrationwas confirmed and characterized by single cell CGH and fluorescencein situ hybridization analysis, 46,X,idic(X)(q21). Thus, chromosomalaberrations may occur over time in stem cell lines, and continuousanalysis of these cells during cultivation is crucial. Singlecell CGH is a method that can be used for continuous analysisof the hES cell lines during cultivation, in order to detectchromosome imbalance.     

Comparative genomic hybridization as a tool in tumour cytogenetics

The quality of cytogenetic analysis of solid tumours has greatly improved in the past decade, but a number of technical difficulties remain which limit the characterization of solid tumour chromosomes by conventional cytogenetics alone. The identification of regions of chromosomal abnormality has been aided by the introduction of molecular cytogenetic techniques such as fluorescence in situ hybridization (FISH). Of these, a recently developed approach, comparative genomic hybridization (CGH), has had a particular impact on the cytogenetic analysis of solid tumours. It incorporates the sensitivity of in situ techniques and overcomes many of the drawbacks of conventional cytogenetic analysis. This review first outlines the CGH method, giving details for the preparation of DNA probes and target human metaphase chromosomes together with information on the in situ technique and data handling criteria used in our laboratory. It then presents an overview of some of the current applications of CGH, together with a discussion of future directions in the field. Copyright © 1999 John Wiley & Sons, Ltd.     

应用微阵列比较基因组杂交技术精确诊断不平衡染色体畸变

目的 探讨微阵列比较基因组杂交技术(array-based comparative genomic hybridization,array-CGH)在诊断不平衡染色体畸变中的应用价值.方法 选取4例常规G显带染色体核型分析未能确诊的不平衡染色体畸变病例,按照标准的Affymetrix SNP 6.0微阵列的操作手册进行杂交、洗涤及全基因组扫描,并通过相应的计算机软件分析结果.结果 通过array-CGH技术分析,明确了所有4例染色体不平衡畸变的诊断并且进行精确定位,其中对2例患者镜下染色体出现无法确定来源的额外条带进行了自身直接重复的确诊;对2例患者G显带无法识别的缺失合并重复的衍生染色体进行了精确诊断.结论 array-CGH技术在DNA水平上对染色体不平衡畸变的诊断具有独特的高分辨率、高敏感性和高特异性,并且能够精确定位,对染色体疾病作出基因型-表型关系的诊断具有重大的应用价值.     

Uniparental isodisomy 13 in a normal female due to transmission of a maternal t(13q13q)

Chromosomes from a normal 23-year-old, primigravid woman were examined at 10 weeks of gestation because of her mother's history: 8 miscarriages and two liveborn infants (the proposita and a brother who died at 3 days with multiple anomalies). Karyotypes of the proposita and her normal mother were 45,XX, t(13q13q). No evidence of mosaicism was encountered. When the proposita inherited the t(13q13q), she received two copies of 13q from her mother. Moreover, she and her mother shared the same homozygous pattern of alleles from 7 highly polymorphic microsatellite repeats localized along 13q. No evidence of paternal markers from 13 was detected, although biparental inheritance was demonstrated with DNA markers from chromosomes 2 and 17. Cytogenetic and molecular findings indicated that the proposita's chromosomal complement included mUPD 13q. The proposita's normal phenotype suggested that no maternally imprinted genes map to 13q. © 1995 Wiley-Liss, Inc.     

Array—CGH技术用于产前诊断可疑胎儿染色体异常

目的探讨微阵列比较基因组杂交技术（array—based comparative genomic hybridization,array—CGH）在产前诊断胎儿染色体异常中的应用价值。方法产前诊断发现4例常规G显带染色体核型分析不能明确的胎儿染色体异常,按照标准的array—CGH操作分析对这些病例进行全基因组检测。结果通过array—CGH技术分析,明确了4例胎儿可疑染色体异常的诊断并且进行精确定位,1例染色体部分缺失,1例正常,1例染色体部分重复,1例不平衡易位。结论array—CGH技术对产前诊断胎儿染色体异常具有高分辨率,能够精确定位异常片段,明确胎儿预后,对产前诊断具有重要应用价值。     

Comparative genomic hybridization in a case of melanoma that loses expression of S100, HMB45, Melan A and tyrosinase in metastasis

We recently reported three cases of metastatic melanoma that does not express S100, HMB45, Melan A and Tyrosinase. A concurrent cutaneous scalp primary melanoma was identified later in one of the cases, which showed strong expression of these markers. The difference in immunophenotype between the primary melanoma and its metastasis in the parotid gland in this case raised the question of the biological significance of the expression of these markers and metastatic potential. To address this question, we utilized microarray comparative genomic hybridization (aCGH) to compare the cytogenetic features between the primary and metastatic melanoma. We observed chromosomal gains including 6p, entire chromosome 7, and 8q11.1-q24.3 in both primary and metastatic tumors. However, the metastatic lesion showed unique additional copy of chromosomal 7q, and loss of chromosome 9p24.3-q13 and chromosome 4, which included Melan A encoding gene region in 9p24.1. The above findings suggest the unique cytogenetic changes in the parotid lesion are most likely related to the metastatic behavior, as well as responsible for loss of multiple melanocytic marker expression in the metastatic melanoma for this case.     

光谱核型分析联合微阵列比较基因组杂交诊断15号环状染色体综合征

目的 探讨联合应用光谱核型分析技术(spectral karyotyping,SKY)和微阵列比较基因组杂交技术(microarray-based comparative genomic hybridization,array-CGH)在诊断复杂疑难的环状染色体畸变中的价值.方法 对1例常规G显带染色体核型分析疑诊为46,XY,r(15)?的8岁男性生长发育迟缓患儿依次应用SKY及array-CGH技术常规进行制片杂交,并通过相应的显微摄像系统和计算机软件分析结果.结果 SKY技术明确了该患儿环状染色体来源于15号染色体,array-CGH技术明确患儿15q26.3末端存在约594 kb的缺失,染色体基因位点编码范围为99689349-100282878.结论 联合应用现代分子细胞遗传学技术可以从细胞到分子水平精确诊断复杂疑难的环状染色体病例,是常规染色体核型分析的有益补充,也有利于细胞遗传学向分子水平深入.     

多发性骨髓瘤1q染色体异常与13q缺失的相关性研究

目的 探讨多发性骨髓瘤(multiple myeloma,MM)中13q14的缺失[del(13q14)]和1q染色体异常的相关性.方法 应用CD138单克隆抗体磁珠分选系统纯化48例初治MM患者的骨髓浆细胞,结合SpectrumorangeTM直接标记的位于13q14和1q12的序列特异性DNA探针和间期荧光原位杂交技术检测48例MM患者del(13q14)及1q染色体异常情况.结果 48例MM患者中,用D13S319探针检测,del(13q14)异常22例(45.8%);用CEP1探针检测.23例(47.9%)发现1q染色体异常.其中2例为1q缺失,21例为1q重复.22例伴有del(13q14)MM患者中16例出现1q染色体异常;26例未检测到del(13q14)MM患者中仅7例发现1q染色体异常.经X2检验两者间差异有统计学意义(X2=10.02,P＜0.01).结论 del(13q14)及1q染色体异常在MM中的发生率较高,两者间存在高度相关性.     

人食管鳞癌细胞系EC9706的建立及其比较基因组杂交分析

目的 以中国男性食管鳞癌为来源，建立一个可良好传代的细胞系，从而提价七个有用的体外模式用于食管癌的研究。方法 采用组织块培养法，以新鲜的食管癌组织细胞系EC9706，做了初步的生物学特性观察，并采用比较基因组杂交的方法进行细胞遗传学的检测。结果 食管癌细胞系EC9706生长曲线显示其生长良好，易于培养。传代时间为26h，平皿集落形成率为91．9％，且能够在软琼脂中形成集落。经异种接种到裸鼠中均形成移植性肿瘤，肿瘤的病理诊断为中－低分化鳞状细胞癌。比较基因组杂交结果得出染色体1p1,q2-4,2p1,5p,7p14,7q21,11q1,11q2,20q扩增，其中5p表现出高水平的扩增。而染色体2p2,2q2,3p,4,9p,14,18,Xq缺失。结论 建立的细胞系EC9706可用于研究食管癌的癌变过程。     

Comparative genomic hybridization reveals genetic progression of oral squamous cell carcinoma from dysplasia via two different tumourigenic pathways

To clarify the genetic pathway(s) involved in the development and progression of oral squamous cell carcinoma (OSCC), as well as the relationship between genetic aberrations and biological characteristics of OSCC tumours, comparative genomic hybridization was used to analyse genetic alterations in both primary OSCCs and adjacent dysplastic lesions of the same biopsy specimens from 35 patients. Gain of 8q22-23 was the most frequent alteration in both OSCC and mild dysplasia, and was considered the earliest event in the process of oral tumourigenesis. The average number of DNA sequence copy number aberrations (DSCNAs) increased with progression from mild dysplasia to invasive carcinoma (r = 0.737, n = 70, p < 0.001). OSCC samples were classified as having a large or small number of DSCNAs (OSCC-L, 21.4 +/- 4.7 DSCNAs or OSCC-S, 10.0 +/- 1.7 DSCNAs, respectively; p < 0.0001). Gains of 3q26-qter, 8q, 11q13, 14q, and 20q and losses of 4q, 5q12-22, 6q, 8p, 13q, and 18q22-qter were common to OSCC-L and OSCC-S. Gains of 5p15, 7p, 17q11-22, and 18p and losses of 3p14-21, 4p, and 9p were detected exclusively in OSCC-L. The average number of DSCNAs depended on whether the samples showed OSCC- L or dysplasia plus OSCC-L, or showed OSCC-S or dysplasia plus OSCC-S (p = 0.001). Gain of 5p15 and losses of 4p and 9p were detected even in dysplastic lesions adjacent to OSCC-L samples. Loss of 4p was associated with node metastasis by multivariate analysis (p = 0.013). OSCC-L tumours were more often T3-T4 stage tumours than T1-T2 stage tumours (p = 0.03). These findings suggest that two different types of OSCC, OSCC-L associated with high-stage cancer and OSCC-S associated with low-stage cancer, arise from different types of dysplasia via different genetic pathways.     

河南食管/贲门癌高发区人群食管癌和贲门癌比较基因组杂交分析

目的探讨食管癌/贲门癌高发区人群食管癌和贲门癌染色体基因组变化特征。方法应用比较基因组杂交技术分析37例原发性食管癌和30例贲门癌患者染色体基因组的变化。结果比较基因组杂交发现,食管癌组织染色体8q发生DNA扩增的频率最高(78%),其它依次为3q、5p、6q和7p;3p发生DNA丢失的频率最高(57%),其它依次为8p、9q和11q。贲门癌组织染色体20q发生DNA扩增频率最高(43%),其它依次为6q、8q和6p;17p发生DNA丢失的频率最高(57%),其它依次为19p、1p和4p。结论8q、3q和5pDNA扩增和3p、8p和9qDNA丢失是河南高发区食管癌患者基因组DNA变化特征;而20q、6qDNA扩增和17p、19p、1pDNA丢失可能是河南高发区贲门癌患者基因组DNA变化特征。这些结果为进一步定位筛选和克隆与食管癌/贲门癌相关基因提供了重要的理论信息。     

A novel microdeletion at chromosome 2q31.1-31.2 in a three-generation family presenting duplication of great toes with clinodactyly

HOXD gene cluster maps to chromosome 2q31 and plays a key role in embryonic limb morphogenesis. Mutations of the HOXD13 and HOXD10 genes have been found to be associated with digital and limb malformations. In addition, dysregulation of HOXD gene cluster has been proposed to account for the limb abnormalities in patients with chromosome 2q rearrangements. In this report, we investigated a three-generation family presenting clinical phenotypes of duplication of great toes, tapering fingers, and clinodactyly of the fifth finger in both hands, which were transmitted in a dominant fashion in this family. We identified and validated an interstitial microdeletion of ∼3.4 Mb at chromosome 2q31.1-31.2 by array-based comparative genomic hybridization, fluorescence in situ hybridization, and real-time quantitative polymerase chain reaction that cosegregates with the clinical phenotypes in this family. The microdeletion removes 30 labeled genes including the entire HOXD gene cluster, suggesting that the digital abnormalities of this family may be attributed to the haploinsufficiency of the HOXD gene cluster. The delineation of the microdeletion region may contribute to the genotype–phenotype correlation study in patients with genomic rearrangements of the long arm of chromosome 2 and helps to understand the pathogenesis of haploinsufficiency of the HOXD gene cluster.     

Novel candidate tumour suppressor gene loci on chromosomes 11q23-24 and 22q13 involved in human insulinoma tumourigenesis

Insulinomas represent the predominant syndromic subtype of endocrine pancreatic tumours. Previous molecular studies have shown that gain of chromosome 9q rather than MEN1 gene mutation is an important early event in tumour development and that chromosomal instability is associated with metastatic disease. In order to identify new gene loci and to define further the critical genetic events in insulinoma tumourigenesis, 27 insulinomas were investigated by array-based comparative genomic hybridization (array CGH) on 3.7 k genomic BAC arrays (resolution < or =1 Mb). Fluorescence in situ hybridization was used to validate alterations in a subset of tumours. Array CGH most frequently detected loss of chromosomes 11q and 22q and gains of chromosome 9q. The chromosomal regions of interest (CRI) included 11q24.1 (56%), 22q13.1 (67%), 22q13.31 (56%), and 9q32 (63%). Evaluation of the simultaneous occurrence of these aberrations in the individual tumours revealed that gain of 9q32 and loss of 22q13.1 are early genetic events in insulinomas, occurring independently of the other alterations. In tumours with increased genomic complexity, these alterations were often detected simultaneously, occurring in the same tumour cells. Losses of 11q24.1 and 22q13.31 were also associated with these more advanced tumour cases. The CRIs identified most likely harbour crucial candidate genes important in insulinoma tumourigenesis.     

A case of chromophobe renal cell carcinoma with sarcomatoid foci and a small daughter lesion

Chromophobe renal cell carcinoma (RCC), which has recently been recognized to be a distinct type of RCC, comprises approximately 5% of renal cell tumors. It has been hypothesized that the cells that comprise chromophobe RCC show a phenotype similar to that of intercalated cells of the collecting duct Although the number of research reports on this type of tumor has recently been increasing, only nine cases of chromophobe RCC showing sarcomatoid transformation have been described. Herein, a case of chromophobe RCC with sarcomatoid foci and a small daughter lesion is reported.