Localization of tumor suppressor gene candidates by cytogenetic and short tandem repeat analyses in tumorigenic human bronchial epithelial cells

Radon exposure is associated with increased risk for bronchogenic carcinoma. Mutagenesis analyses have revealed that radon induces mostly multi-locus chromosome deletions. Based on these findings, it was hypothesized that deletion analysis of multiple radon-induced malignant transformants would reveal common mutations in chromosomal regions containing tumor suppressor genes responsible for malignant transformation. This hypothesis was supported by a previous study in which tumorigenic derivatives of the human papillomavirus 18-immortalized human bronchial epithelial cell line BEP2D were established following irradiation with 30 cGy of high linear energy transfer radon-simulated alpha-particles. Herein, we describe the analyses of 10 additional tumorigenic derivative cell lines resulting from the irradiation of five additional independent BEP2D populations. The new transformants have common cytogenetic changes, including the loss of chromosome (ch)Y, one of three copies of ch8, one of two copies of ch11p15-pter and one of three copies of ch14. These changes are the same as those reported previously. Analysis of PCR-amplified short tandem repeats of informative loci confirmed the loss of heterozygosity (LOH) at 12 loci spanning the length of ch8 in cell lines from four of the total of eight irradiation treatments to date and the loss of chY in all cell lines (8 of 8). LOH analysis with a total of 17 informative loci confirmed loss on ch14 in transformants from seven of eight irradiation treatments and indicated a 0.5-1.7 cM region of common involvement centered around locus D14S306. No LOH was detected at any of the informative loci on ch11. The overall results support our stated hypothesis. Further studies are currently in progress to determine whether the ch8 and ch14 regions contain genes with tumor suppressor function in bronchial epithelial cells.     

Deletion mapping on the short arm of chromosome 1 in Merkel cell carcinoma

Twenty-two Merkel cell carcinoma (MCC) biopsies and six cell lines from 24 patients were examined for loss of heterozygosity (LOH) at 11 loci on 1p and one on 1q, to determine LOH regions on chromosome 1p. Sixteen (73%) tumors had LOH for at least one locus; 14 demonstrated LOH at more than one locus, and 7 (29%) samples had more than one region of loss, with 4 of these having loss at all informative loci on 1p. Three common regions of loss (SRO) were defined by LOH in multiple tumors. Eight samples demonstrated LOH between D1S214 and D1S160 (1p36), seven between D1S234 and D1S186 (1p35), and 11 for the region centromeric of D1S211 and D1S220 (1p32-1p33). Seven samples (29%) demonstrated more than one region of loss. LOH on 1p occurs frequently in MCC and more than one tumor suppressor gene on 1p is likely to play a role in the development of this tumor type.     

Allelic Loss of the Region of Chromosome 1p35-pter Is Associated with Progression of Human Gastric Carcinoma

In order to identify the region on distal chromosome 1p that is thought to include one or more tumor suppressor genes for gastric carcinoma, 39 gastric carcinomas were examined for allelic loss using 11 polymorphic microsatellite markers and 1 marker of single strand conformation polymorphism. Loss of heterozygosity (LOH) was found in 18 (46%) of 39 informative patients. The regions with high frequency of loss of heterozygosity were the loci at D1S548 (6/17; 35.3%) and D1S2843 (7/20; 35%), and we found three commonly deleted regions on chromosome 1p35-pter. The frequency of allelic loss in the region of chromosome 1p35-pter was significantly associated with advanced-stage gastric carcinoma, but not with early-stage tumor or with the histology. These results suggest that allelic loss at chromosome 1p35-pter may play a role in the progression of gastric carcinoma.     

Allelic loss of the region of chromosome 1p35-pter is associated with progression of human gastric carcinoma.

In order to identify the region on distal chromosome 1p that is thought to include one or more tumor suppressor genes for gastric carcinoma, 39 gastric carcinomas were examined for allelic loss using 11 polymorphic microsatellite markers and 1 marker of single strand conformation polymorphism. Loss of heterozygosity (LOH) was found in 18 (46%) of 39 informative patients. The regions with high frequency of loss of heterozygosity were the loci at D1S548 (6 / 17; 35.3%) and D1S2843 (7 / 20; 35%), and we found three commonly deleted regions on chromosome 1p35-pter. The frequency of allelic loss in the region of chromosome 1p35-pter was significantly associated with advanced-stage gastric carcinoma, but not with early-stage tumor or with the histology. These results suggest that allelic loss at chromosome 1p35-pter may play a role in the progression of gastric carcinoma.     

Characterization of genetic alteration patterns in human esophageal squamous cell carcinoma using selected microsatellite markers spanning multiple loci

In order to identify representative genetic alterations in esophageal squamous cell carcinomas (ESCC) and useful markers for future early detection, 34 ESCC samples with neighboring normal epithelia and 30 esophageal biopsy samples from Linzhou, P.R. China, were studied. Of the 38 microsatellite markers selected, half were linked with tumor suppressors. More than 40% of the tumor samples showed loss of heterozygosity (LOH) in at least one of the eight markers, D3S1067 and D3S1561 (both linked to hMLH1 locus), FABP2, D4S1613, D9S171 (p14ARF, p15INK4b, p16INK4a loci), Rb1 (intron), p53-2 (intron), and NM23-H1. Most of the 38 microsatellite markers did not display microsatellite instability (MSI) in more than 30% of the tumor samples, except D9S942 (p14ARF, p15INK4b, p16INK4a loci) and Bat26, which showed frequency at 32 and 41%, respectively. Of all the ESCC samples examined, 20 samples exhibited LOH in 25% or more of the informative markers. Three samples displayed MSI in more than 30% of the markers, indicating that MSI might be an important event in these subset ESCC cases. Statistically significant correlations were found between LOH of the hMLH1 locus and the general LOH status of the sample, and between the LOH of the hMLH1 locus and p53 mutations. In addition, correlation was found between MSI in D3S1067/D3S1561 and the general MSI status in the samples. However, MSI in the introns of hMLH1 and hMSH2 were not correlated with the general MSI status of the tumors. LOH analysis was also performed in 30 esophageal biopsy samples containing precancerous lesions with matching blood samples using nine microsatellite markers selected from the above studies. LOH frequence ranged from 0 to 33% in informative cases, mostly in the 9p21 and p53 gene regions, suggesting these regions are possible targets of genomic instability in early stage ESCC carcinogenesis. The results demonstrate the degree of genetic alterations at different loci of the chromosomes. Some of the microsatellite markers may be useful for the early detection of ESCC.     

Loss of heterozygosity at loci on chromosome 4, a common genetic event during the spontaneous immortalization of mouse embryonic fibroblasts

Spontaneously immortalized fibroblast cell lines derived from embryonic tissues of C3D2F₁ mice were analyzed for loss of heterozygosity (LOH) at multiple chromosomal loci to identify candidate suppressor loci for immortalization. Among 47 simple sequence repeat (SSR) loci selected for screening, those on chromosome 4 exhibited an exceptionally high LOH incidence of up to 89%. Only four other chromosomes (8, 11, 12, and 18) showed LOH, with the highest incidence being 33%. To further localize candidate suppressor genes on mouse chromosome 4, detailed deletion mapping was performed with 18 cell lines and 14 SSR markers. The greatest LOH incidence (94%) was observed at the D4Mit14 locus located on distal chromosome 4, indicating that a major suppressor gene resides in this region. On the other hand, at the D4Mit77 locus, 30 cM proximal to the D4Mit14 locus, we found the SSR to be homozygously lost in 39% of the cell lines. Because the D4Mit77 is tightly linked to the tumor suppressor gene p16, for which homozygous deletion has been reported in various human tumor cell lines, we also examined our fibroblast cell lines for gross aberrations of the p16 gene by using the Southern blot method. The p16 gene was found to be homozygously deleted in 56% of the cell lines. Although this result implies that the p16 gene plays a role as a suppressor gene for immortalization, the combined incidence of LOH ad homozygous deletion at the D4Mit77 locus was 72%, which is significantly lower than the observed incidence at the D4Mit14 locus. Consequently, we concluded that immortalization of mouse embryonic fibroblasts may involve more than one suppressor gene on chromosome 4. Mol. Carcinog. 19:17–24, 1997. © 1997 Wiley-Liss, Inc.     

MAD-related Genes on 18q21.1, Smad2 and Smad4, Are Altered Infrequently in Esophageal Squamous Cell Carcinoma

The MAD (mothers against decapentaplegic)-related genes, Smad2 (former name MA DR2 or JV18-1 ) and Smad4 (former name DPC4 ), have been identified on chromosome 18q21.1, We analyzed 30 primary esophageal squamous cell carcinomas (ESCC) and 7 cell lines derived from ESCC for intragenic mutations and loss of heterozygosity (LOH) of the Smad2 and Smad4 genes. LOH was detected in 5 of 14 (35%) informative cases. However, no mutations in either gene were detected in either the primary carcinomas or the cell lines, and only a G-to-A base transition within the 3'-untranslated region of the Smad4 gene was observed in a carcinoma. There were no homozygous deletions in either of the genes in the cell lines. MAD -related genes on chromosome 18q21.1 are altered infrequently in ESCC.     

Loss of heterozygosity on chromosomes 1, 11, 12, and 14 in hybrid mouse lung adenocarcinomas

An allelotype analysis of lung tumors in mouse hybrids was conducted to identify common regions of allelic loss. By using 50 informative genetic markers, the autosomes of 36 (A/J x C3H/HeJ) F₁ adenocarcinomas were examined. Additional adenocarcinomas from as many as 72 (C3H/HeJ x A/J) F₁ and 15 (BALB/cJ x DBA/2J) F₁ hybrids also were analyzed for DNA loss at some of the loci. Loss of heterozygosity (LOH) was observed at multiple loci and occurred with the most regularity at markers on chromosomes 12 (28%), 14 (28%), 11 (21%), and 1 (20%). The frequency of LOH was not greater than 11% on any of the other chromosomes. Chromosomes 11 and 14 often displayed allelic loss at markers located near the p53 and retinoblastoma tumor suppressor loci, respectively. LOH at markers on chromosomes 12 and 14 was associated with tumors having overall frequencies of allelic loss that exceeded the median value. Losses on chromosomes 1, 11, 12, and 14 also showed a significant association with the adenocarcinoma stage of mouse lung tumorigenesis, suggesting that the inactivation of tumor suppressor loci on these chromosomes may participate in the progression of these tumors. © 1996 Wiley-Liss, Inc.     

Identification of distinct regions of allelic loss on chromosome 13q in nasopharyngeal cancer from paraffin embedded tissues.

Our main purpose was to identify tumor suppressor gene loci on chromosome 13 responsible for nasopharyngeal cancer (NPC) development by analyzing loss of heterozygosity (LOH) and RB protein expression in paraffin embedded tissues. Normal and tumor DNA were extracted from microdissected samples, and their whole genomes were amplified using degenerate oligonucleotide primers. The polymerase chain reaction (PCR) products were analyzed by repeated amplification using primers derived from 16 microsatellite regions spanning the long arm of this chromosome. Among 50 informative cases, LOH was observed in 44 tumors. Thirty-one tumors displayed partial loss and provided an informative basis for detailed deletion mapping. Three minimal regions of loss were delineated; the first flanked by D13S120 and D13S219, the second by D13S126 and D13S119, and the third by D13S137 and 13qter. These 3 regions were linked to BRCA2 on 13q12, RB1 on 13q14, and 13q14.3-ter, respectively. Seven and 4 cases showed LOH either on 13q12 or 13q14, respectively. Nineteen cases showed LOH of both loci separately. One NPC displayed 13q12 and 13q14.3-ter LOH. RB protein expression was detectable in 76% of the cases. Ten out of 15 cases with the allelic losses limited to 13q14 showed RB protein expression. Contrasting that, 6 out of 7 cases devoid of RB protein expressions showed 13q14LOH. In conclusion, 13qLOH, involving 3 tumor suppressor gene loci, appears to be a frequent genetic event occurring during NPC development. However, other tumor suppressor genes besides RB1, may be responsible for the majority of 13q14LOH.     

10号染色体可能含有多个与胶质母细胞瘤相关的肿瘤抑制基因

目的 寻找胶质母细胞瘤（GBM）10号染色体上可能存在肿瘤抑制基因的杂合性丢失（LOH）区域,为发现和定位肿瘤抑制基因（TSG）提供线索和依据。方法 应用聚合酶链反应（PCR）方法,采用荧光标记的引物和先进的377型DNA序列自动分析仪,分析了21例GBM10号染色体上20个微卫星多态性标记的LOH。结果 在85．7％（18／21例）GBM的10号染色体上观察到LOH,在57．7％（162／281）可提供信息位点上存在LOH。10q的LOH率高于10p,分别是81．0％（17／21）、66．7％（14／21）。在下列位点或区域检测到较高的LOH率（＞60％）：10q22.3-23.3上的D10s185-D10s192间区域,10p14-15.1上的D10s591-D10s249间区域,10q24.2-26.3上的D10s1693-D10s212间区域,10p12.2-14上的D10s547位点,10q21.3上的D10537位点。结论 10号染色体可能在GBM的分子水平发病机制中发挥着重要作用,它上面的多个染色体区域可能存在与GBM相关的多个TSG。     

Localization of a tumour-suppressor gene associated with human oral cancer on 7q31.1

To search for the existence of a tumour-suppressor gene (TSG) associated with oral squamous cell carcinoma (SCC), PCR analysis of microsatellite polymorphisms corresponding to 14 loci which map to chromosome 7q21.3-qter was performed to screen 35 patients with oral SCC for loss of heterozygosity (LOH). LOH was observed in at least one of the loci in 19 of 34 (55.9%) informative cases. Among the loci tested, frequent LOH was restricted at D7S522 on chromosome 7q31.1, which was measured within 1 cM. Furthermore, we detected microsatellite instability (MI) in 11 of 35 (31.4%) cases tested. Our observations indicate that alterations of chromosome 7q are associated with oral SCC tumorigenesis and that 7q31.1 might harbour at least one putative TSG. Int. J. Cancer 75:671–674, 1998.© 1998 Wiley-Liss, Inc.     

Deletion mapping of chromosomes 14q and 1p in human neuroblastoma.

It has been suggested that loss of heterozygosity (LOH) on the short arm of chromosome 1 is a critical event for the development of neuroblastoma, and we have previously shown frequent LOH on chromosome 14 in neuroblastoma. To pursue these observations, especially to define further the regions which are commonly deleted in the tumor, we examined for allelic losses in 27 cases of neuroblastomas by using a number of polymorphic DNA markers for chromosomes 14q and 1p. LOH was observed in 10 out of the 25 informative cases (40%) on chromosome 14q and in eight out of the 21 informative cases (38%) on 1p. The commonly deleted regions were distal to the D14S13 locus (14q32-qter) on chromosome 14 and distal to the D1S112 locus (1p36.1-pter) on chromosome 1. These results strongly suggest that tumor-suppressor genes important in the pathogenesis of human neuroblastoma are located on the distal part of both chromosomes 14q and 1p.     

Frequent loss of heterozygosity on chromosome 4 in diethylnitrosamine-induced C3H/MSM mouse hepatocellular carcinomas in culture

Genetic changes, in particular the loss of heterozygosity (LOH) and the presence of c-Ha-ras codon 61 point mutations, were investigated in diethylnitrosamine-induced hepatocellular carcinomas (HCCs) in C3H/MSM F₁ mice. (MSM are wild mice.) LOH analysis of 48 primary tumors with microsatellite probes covering at least one proximal and one distal site of each autosome revealed no obvious positive results for LOH. Analysis of 23 cell lines established from seven of these HCCs, however, showed LOH on chromosome 4 in all (seven of seven), even in early passages (G2-G3). With regard to other chromosomes, LOH was observed only rarely on chromosomes 16 and 19. These allelotype features were maintained in later passages (G11-G14), with only a few additional occurrences of LOH appearing on chromosomes 1, 6, and 8. Extensive analyses with multiple micro-satellite probes from chromosome 4 and with 52 cell lines established from 24 HCCs of 18 mice revealed LOH in 22 of the tumors (92%), with the shortest region about 10 cM distal to the a-interferon gene. No c-Ha-ras oncogene activation in codon 61 was observed. These data indicate that loss of tumor suppressor genes on chromosome 4 may play an important role in mouse hepatocarcinogenesis in progression in vivo or in immortalization in vitro or both. © 1995 Wiley-Liss, Inc.     

Genetic alterations on chromosome 17 in human breast cancer: relationships to clinical features and DNA ploidy

Summary We analyzed DNA from 105 primary breast cancers to assess amplification of the ERBB2 gene and loss of heterozygosity (LOH) on chromosome 17 using 4 polymorphic markers, and investigated the relationships of these genetic alterations to clinicopathological characteristics including DNA ploidy. Amplification of the ERBB2 gene was observed in 28% of the tumors. ERBB2 was amplified in tumors of all clinical stages and amplification was significantly linked to lymph node metastasis. LOH atD17S5 was observed in 28 of 57 informative tumors, while 17 of 62 informative tumors showed allelic loss atTP53. Among the 37 tumors informative for both loci, 32% showed LOH at these loci and 49% retained both alleles, indicating that there was a significant relationship between LOH atD17S5 and atTP53. We also examined LOH at theD17S74 andNME1 loci on chromosome 17q. LOH atD17S74 andNME1 was observed in 20% and 22% of the informative tumors, respectively, but there was no significant association between LOH at these loci. Of the 4 loci tested, LOH atTP53, D17S74, andNME1 was associated with clinical stage. Lymph node metastasis was correlated with LOH atNME1. Moreover, allelic loss was more frequent in aneuploid tumors than in diploid tumors. These results suggest that certain combinations of genetic alterations on chromosome 17 may cooperate in the development and/or progression of breast cancer. Furthermore, it seems likely that analysis of these alterations in breast cancer patients may provide useful prognostic information.     

Loss of heterozygosity on the short arm of chromosome 3 in renal cancer

3% of human cancers are renal cell carcinomas (RCC). The most common chromosome abnormality found in this tumor is loss of heterozygosity (LOH) on the short arm of chromosome 3, which suggests that there must be one or more tumor suppressor genes between 3p14 and 3p21 near the VHL gene which play a relevant role in renal cancer development. DNA from normal and tumor tissue from 40 patients at various stages of RCC was analyzed for LOH at three microsatellites mapped to 3p (3p14.1-14.3; 3p21.2-21.3 and 3p25) by polymerase chain reaction). 42.5% of the tumors studied showed LOH on at least one locus. 30% showed LOH on only one locus; 5% on two loci and 7.5% on the three loci tested. LOH occurred only on nonpapillary tumors (p = 0.03). Interestingly, all the tumors with LOH on 3p21 were >/=25 mm (p = 0.04; relative risk 1.76, confidence interval: 1.3-2.3).     

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers

Cancers with chromosomal instability (CIN) are held to be aneuploid/polyploid with multiple large-scale gains/deletions, but the processes underlying CIN are unclear and different types of CIN might exist. We investigated colorectal cancer cell lines using array-comparative genomic hybridization (CGH) for copy number changes and single-copy number polymorphism (SNP) microarrays for allelic loss (LOH). Many array-based CGH changes were not found by LOH because they did not cause true reduction-to-homozygosity. Conversely, many regions of SNP-LOH occurred in the absence of copy number change, comprising an average per cell line of 2 chromosomes with complete LOH; 1-2 terminal regions of LOH (mitotic recombination); and 1 interstitial region of LOH. SNP-LOH detected many novel changes, representing possible locations of uncharacterized tumor suppressor loci. Microsatellite unstable (MSI+) lines infrequently showed gains/deletions or whole-chromosome LOH, but their near-diploid karyotypes concealed mitotic recombination frequencies similar to those of MSI- lines. We analyzed p53 and chromosome 18q (SMAD4) in detail, including mutation screening. Almost all MSI- lines showed LOH and/or deletion of p53 and 18q; some near-triploid lines had acquired three independent changes at these loci. We found consistent results in primary colorectal cancers. Overall, the distributions of mitotic recombination and whole-chromosome LOH in the MSI- cell lines differed significantly from random, with some lines having much higher than expected levels of these changes. Moreover, lines with more LOH changes had significantly fewer copy number changes. These data suggest that CIN is not synonymous with copy number change and some cancers have a specific tendency to whole-chromosome deletion and regain or to mitotic recombination.     

Loss of heterozygosity in sporadic breast tumours at the BRCA2 locus on chromosome 13q12-q13.

Loss of heterozygosity (LOH) on chromosome 13 occurs on 25-30% of breast tumours. This may reflect the inactivation of the retinoblastoma susceptibility gene RB1. However, recently another candidate tumour-suppressor gene has been identified on chromosome 13 by linkage analysis, the breast cancer susceptibility gene BRCA2. To investigate the involvement of BRCA2 in sporadic breast cancer 200 breast tumours were tested for LOH on chromosome band 13q12-q14, using 11 highly polymorphic microsatellite markers. LOH was found in 65 tumours, which all showed simultaneously loss of BRCA2 and RB1. Of 12 breast tumour cell lines tested with polymorphic microsatellite markers, seven showed a contiguous region of homozygosity on 13q12-q14, suggesting LOH in the tumour from which the cell line had been derived. One cell line showed homozygosity in the BRCA2 region and heterozygosity at RB1. This is the only indication that BRCA2 is a distinct target for LOH on chromosome 13 in addition to RB1.