Lower frequency of allele loss on chromosome 18q in human breast cancer than in colorectal tumors

Inactivation of tumor suppressor genes is thought to be a critical step in tumorigenesis. TheDCC (deleted in colorectal carcinoma) gene, located on the long arm of chromosome 18, has been shown to be frequently deleted in colorectal tumors. To investigate the involvement of allelic deletions on chromosome 18q in breast cancer tumorigenesis we analyzed 28 primary breast tumors and 28 colorectal, tumors (24 carcinomas, 4 adenomas) with four different polymorphic DNA markers detecting RFLPs on chromosome 18q. In breast cancer we found loss of heterozygosity (LOH) in 4 of 27 (15%) informative cases whereas 15 of 25 (60%) colorectal tumors showed allelic deletions. In all cases of allelic loss theDCC locus or its proximal vicinity (locus SSAV1) were involved. LOH on chromosome 18q occurs both in breast and colorectal cancer, yet the frequency of these deletions in breast tumors is lower than in colorectal tumors. Moreover, in breast cancer these mutations were only detected in large and undifferentiated tumors.Abbreviations LOH Loss of heterozygosity     

Clonal divergence in lung cancer development is associated with allelic loss on chromosome 4

Patients who receive curative treatment for lung cancer can develop additional lung tumors that may or may not be related to the original tumor and thus require different clinical management. If a subsequent tumor has a pattern of allele loss, revealed by allelotype analysis, overlapping that of the first tumor, it is believed to be a local recurrence or metastasis. In this case history, we present loss of heterozygosity analyses of the original primary tumor, and two second primary tumors occurring in the ipsilateral and the contra-lateral lungs. The allelotyping suggests that these tumors are all clonally related but concordance is not complete. Our interpretation is that the original primary tumor and the two new primary tumors have developed to full malignancy independently, but are clonally related, possibly via a clone of motile progenitor cells. Deletion mapping of DNA from biopsies of this patient delineated a region in 4p16 that we had previously shown to be lost in the transition from carcinoma in situ to invasive tumor. We identified a minimally deleted region encompassing six genes including two candidate tumor suppressor genes, CRMP1 a lung cancer metastasis-suppressing gene and PPP2R2C a gene for a regulatory subunit of the PP2 complex known to suppress tumorigenesis, particularly viral induced transformation.     

Identification of a 100-kb region of common allelic loss on chromosome bands 10q25–q26 in human endometrial cancer

In human endometrial cancer, we have previously identified a 790-kb region of common allelic loss in chromosome bands 10q25–q26, flanked by D10S587 and D10S1723. We constructed a contig covering the entire deleted region using YACs, PACs, and BACs. Five overlapping cosmid clones derived from YAC clones completely covered the entire deleted region: its size was estimated to be no larger than 200 kb. We further performed two-color fluorescence in situ hybridization (FISH) analysis to confirm the deletion and narrowed down the deleted region to 100 kb or less; it was covered by three overlapping cosmid clones that were included in one BAC clone. Restriction endonuclease mapping identified a region in which NotI, SalI, SmaI, and XhoI were clustered, suggesting the possible existence of a CpG island. Genes Chromosomes Cancer 23:74–77, 1998. © 1998 Wiley-Liss, Inc.     

Identification of a 910-Kb region of common allelic loss in chromosome bands 16q24.1–q24.2 in human lung cancer

To understand the molecular pathogenesis of human lung cancer, we analyzed allelic deletions on the long arm of chromosome 16 by PCR amplification of microsatellite markers. A total of 203 lung cancer specimens (78 squamous cell carcinomas and 125 adenocarcinomas) were analyzed. In both cell types, a common region of allelic loss was identified in 16q24.1–q24.2; it is flanked by the two markers D16S534 and D16S422 that spanned at most 910 kb. These results were confirmed by fluorescence in situ hybridization. There was no correlation between allelic loss and histopathologic diagnosis or clinical stage. These results suggest the existence of a tumor-suppressor gene that plays an important role in the course of carcinogenesis in both squamous cell carcinoma and adenocarcinoma of the lungs. Genes Chromosomes Cancer 22:1–8, 1998. © 1998 Wiley-Liss, Inc.     

17q allele loss is associated with lymph node metastasis in locally aggressive human colorectal cancer

A consecutive series of 87 colorectal tumours were studied for loss of a polymorphic probe on chromosome 17q and of the 64 informative cases, 13 (20 per cent) showed loss of heterozygosity (LOH). Examples of LOH were found in carcinomas of all stages and in a large non-invasive adenoma. There was no correlation between 17q LOH and patient age, sex, standard clinicopathological variables (differentiation and nature of tumour margin), DNA ploidy, or tumour site, nor was 17q LOH associated with 17p LOH defined at four loci adjacent to p53. However, comparison of Dukes' B and C carcinomas revealed that tumours which had metastasized to regional lymph nodes at the time of primary surgery were significantly more likely to have lost this 17q allele. Clinical follow-up of this cohort of patients showed no significant difference in survival between patients whose tumours had lost or retained 17q. Thus, we conclude that 17q allele loss is associated with lymph node metastasis in locally aggressive colorectal tumours but probably not with blood-borne metastasis.     

Peripherin gene is linked to keratin 18 gene on human chromosome 12

Peripherin is a neuron-specific intermediate filament (IF) protein, found primarily in phylogenetically old regions of the nervous system. Whereas other neuronal IF genes have only two to three introns and are scattered in the genome, the peripherin gene (PRPH) has a complex intron-exon structure like nonneuronal IF genes that are clustered in tandem arrays, e.g., those encoding the keratins. We used a cosmid containing the human peripherin gene (PRPH) to determine its chromosomal location in relationship to nonneuronal IF genes. Using a rodenthuman mapping panel, we localized thePRPH gene to human chromosome 12. Since a cluster of keratin genes maps to 12q12–13, polymorphic markers were developed forPRPH and for one of the keratin genes presumed to be in the cluster, keratin 18 (KRT18). Both markers were typed in CEPH reference families. Pairwise and multipoint analyses of the CEPH data revealed thatKRT17 is tightly linked to DNA markersD12S4, D12S22, D12S90, D12S96 andD12S103, which lie betweenD12S18 andD12S8, with odds greater than 10001. These markers are physically located at 12q11–13, thus supporting the fine localization ofKRT18 in or near the group of type II keratins in this region. Furthermore, linkage analysis showed that the peripherin gene (PRPH) is tightly linked toKRT18 (=15.73, =0.013), and therefore appears to be in close proximity to the cluster.     

Genetic and epigenetic alterations of the candidate tumor-suppressor gene MYO18B, on chromosome arm 22q, in colorectal cancer

Allelic imbalance (AI) on chromosome arm 22q has been detected in 20%-40% of colorectal cancers, suggesting that this chromosome arm has a tumor-suppressor gene involved in colorectal carcinogenesis. Recently, we isolated a candidate tumor-suppressor gene, MYO18B, at 22q12.1, that is deleted, mutated, and hypermethylated in more than 50% of lung cancers. In the present study, we analyzed genetic and epigenetic alterations of the MYO18B gene in colorectal cancers. AI at the MYO18B locus was detected in 16 of 43 (40%) informative cases. Mutations of the MYO18B gene were detected in 2 of 11 (18%) cell lines and 1 of 47 (2%) surgical specimens. Nine of 11 (82%) cell lines showed reduced MYO18B expression, which was restored in all 9 by treatment with 5-aza-2'-deoxycytidine and/or trichostatin A (TSA). Although hypermethylation of the promoter CpG island for MYO18B was not detected, a significant correlation was observed between the level of MYO18B expression and the level of acetylation of histones H3 and H4 in 6 cell lines with and without TSA treatment. Thus, it was suggested that MYO18B is inactivated in a considerable fraction of colorectal cancers by several mechanisms, especially silencing by histone deacetylation and/or AI. Furthermore, restoration of MYO18B expression in colorectal cancer cell lines HT29 and DLD-1 suppressed anchorage-independent growth, whereas it did not affect the growth rate in vitro. These results suggest that genetic and epigenetic inactivation of the MYO18B gene play an important role in colorectal carcinogenesis.     

肺癌患者PTEN基因启动子高甲基化的检测

目的 探讨肺癌患者组织、外周血浆及支气管肺泡灌洗液(BALF)中张力蛋白同源的磷酸酶基因(PTEN)启动子异常基因化状况及其在肺癌诊断中的价值.方法 用甲基化特异性PCR方法检测组织、血浆及BALF中的PTEN基因启动子区CpG岛甲基化.结果 45例肺癌患者中,PTEN基因启动子异常甲基化率组织为26.67%(12/45)、血浆为15.56%(7/45),BALF为22.22%(10/45);而非肺癌组织、正常对照血浆、非肺癌患者BALF中未检出甲基化;血浆、BALF中甲基化改变与肿瘤组织甲基化状况显著相关(P<0.01).结论 血浆、BALF中PTEN基因异常甲基化改变的检测在肺癌的早期特异诊断等方面有一定的价值.     

Loss of cables, a novel gene on chromosome 18q, in ovarian cancer.

Cables, a cyclin-dependent kinase (cdk) interacting protein, has recently been identified and mapped to human chromosome 18q11. Cables appears to be primarily involved in cell cycle regulation and cell proliferation. Overexpression of Cables in Hela and other cell lines inhibits cell proliferation and tumor formation. We hypothesize that loss of Cables expression is associated with ovarian cancer. To test our hypothesis, we examined Cables expression in the four most common subtypes of ovarian carcinomas: serous, endometrioid, mucinous, and clear cell. In addition, mucinous and serous borderline tumors were also included. Loss of Cables expression was observed at high frequency in ovarian serous (11 of 14 cases, 79%) and endometrioid (5 of 10 cases, 50%) carcinomas. In contrast, strong Cables staining was detected in all clear cell carcinomas (10 cases) and mucinous tumors (5 carcinomas and 5 borderline tumors). The majority of serous borderline tumors (11 of 14 cases, 79%) showed positive Cables staining, with the rest showing focal loss of Cables expression. Furthermore, RT-PCR revealed the lack of Cables mRNA in a human ovarian cancer xenograft. No correlation was noted between loss of Cables and histologic grade, tumor stage, and survival. In conclusion, our results indicate that loss of Cables is common in ovarian serous and endometrioid carcinomas and imply that Cables may be involved in the pathogenesis of these two types of ovarian carcinomas.     

Detection of frequent allelic loss of 6q23–q25.2 in microdissected human breast cancer tissues

Detection of allelic loss in human breast cancer is hindered by the fact that breast cancer tissues are frequently infiltrated by stromal and inflammatory cells. For this study, we carefully microdissected infiltrating breast cancer tumor cells from contaminating normal cells and analyzed the DNA from these samples for allelic loss on the long arm of chromosome 6 by using a panel of 15 dinucleotide repeat markers. We found 53 of the 66 cases studied (80%) to have allelic loss of either the entire chromosomal arm (37 cases) or a portion of the chromosomal arm (16 cases). One common region that was identified for all tumors with deletions of 6q was the area between markers D6S310/314 and D6S473/255, consistent with a tumor suppressor gene locus at 6q23–6q25.2. The use of tissue microdissection allowed the detection of allelic loss in this chromosomal region in human breast cancer at a much higher frequency than was previously recognized. Genes Chromosom Cancer 16:35–39 (1996). © 1996 Wiley-Liss, Inc.     

Recurrent allelic deletions of chromosome arms 15q and 16q in human small cell lung carcinomas

The genetic lesions that lead to the development of small cell lung carcinoma (SCLC) remain incompletely defined. To identify recurrent allelic deletions in specific chromosomal regions that could serve as markers for tumor suppressor gene (TSG) inactivation in SCLC, we performed a comprehensive allelotype analysis of all 39 nonacrocentric autosomal arms. Alterations in 158 polymorphic microsatellite alleles were examined in 24 pairs of human SCLC tumor and normal control DNA samples. A total of 2,107 informative reactions were analyzed. This analysis revealed allelic losses of 100% on chromosome arm 3p, >85% loss within chromosome arms 13q and 17p, and >70% loss within chromosome arms 4q, 5q, 15q, and 16q. The allelic deletions on chromosome arms 15q and 16q have not been defined previously for SCLC and are candidate regions to harbor novel TSGs. Genes Chromosomes Cancer 27:323-331, 2000.     

The putative melanoma tumor-suppressor gene on human chromosome 6q.

The tumorigenicity of malignant melanoma cells may be suppressed experimentally by the introduction into these cells of human chromosome 6 or mouse chromosome 4. These chromosomes share a homologous region, contained in human chromosome 6q12-21. Abnormalities of this human chromosomal region have been found frequently not only in cutaneous and uveal malignant melanomas, but also in a range of other tumors. In all these, mutations of tumor-suppressor genes on human chromosome 6q may be involved. Identification of this putative tumor-suppressor gene may give new insights into the biology of malignant melanomas, and could pave the way for new treatment for such tumors, based upon the tumor-suppressor protein which this gene is likely to encode.     

Clinical significance of allelic loss of chromosome region 5q22.3 approximately q23.2 in nonpapillary renal cell carcinoma

To analyze the clinical significance of copy number gain and loss at chromosome region 5q21 approximately q23, 105 nonpapillary renal cell carcinomas (RCC) were examined by interphase cytogenetic analysis using the dual-color fluorescence in situ hybridization (FISH) technique. DNA probes for D5S23 (5p15.2), cCI5-243 (5q21.2 approximately q21.3), and cCI5-215 (5q22.3 approximately q23.2) were used, and the signals for cCI5-243 and cCI5-215 were compared with those for D5S23 as the numerical control. Aneusomy (three or more copies) of chromosome 5 was found in 22 tumors (21.0%). Aneusomy was significantly correlated with loss at 5q21 approximately q23, while disomy with gain at 5q21 approximately q23 (P<0.05). Aneusomy was also significantly related to poor disease-specific survival (P<0.01). Gain and loss at cCI5-243 were seen in 34 (32.4%) and 59 (56.2%) tumors, respectively, while gain and loss at cCI5-215 occurred in 55 (52.4%) and 45 (42.9%) cases, respectively. The frequency of gain at cCI5-215 was significantly correlated with a smaller tumor diameter (7 cm or less, P<0.05), while loss with a larger one (>7 cm, P<0.05). Both loss at cCI5-215 and aneusomy of chromosome 5 were significantly related to poor disease-specific survival (P<0.05). In conclusion, alterations of chromosome 5 (including allelic loss of 5q22.3 approximately q23.2) could be a useful genetic marker for predicting the patient prognosis of RCC.     

Overrepresentation of 3q and 8q material and loss of 18q material are recurrent findings in advanced human ovarian cancer

In order to define the ability of comparative genomic hybridization (CGH) to detect and map genetic imbalances, we investigated 47 malignant ovarian tumors and 2 ovarian tumors of low malignant potential. The most common genetic changes in order of frequency included DNA gains of chromosome arms 8q (53%), 3q (51%), 20q (43%), 1p (32%), 19q (30%), 1q (28%), 12p (28%), 6p (21%), and 2q (19%). The smallest regions of overrepresentation could be defined in 3q26-qter, 8q23-qter, 1p35-pter, 12p12, and 6p21-22, respectively. Losses were detected on 18q (23%), chromosome 4 (23%), 13q (17%), and 16q (17%) with the smallest underrepresented regions on 18q22-qter, 13q21, and 16q23-qter. Also, losses of the X chromosome (19%) were detected, correlating with higher ages of the patients. Therefore, some of these X chromosome losses might be due to a well-known aging phenomenon and in these cases will be more preferably lost during cell division and tumor progression. Our findings show that ovarian carcinomas reveal consistent chromosomal abnormalities. Further detailed studies of these regions with specific molecular genetic techniques may lead to the identification of oncogenes and/or tumor suppressor genes playing an important role in the tumorigenesis of ovarian carcinomas. Genes Chromosom Cancer 16:46–54 (1996). © 1996 Wiley-Liss, Inc.     

The gene for human αaL-lactalbumin is assigned to chromosome 12q13

A cDNA clone complementary to the mRNA encoding human αaL-lactalbumin (ALA) has been used as a probe in the analysis of DNA from panels of rodent/human somatic cell hybrids. The presence of the ALA gene correlates with the presence of chromosome 12. In situ hybridization localizes the ALA gene to 12q13.     

Evidence by allelic association-dependent methods for a type 1 diabetes polygene (IDDM6) on chromosome 18q21

Type 1 diabetes is a common polygenic disease. Fine mapping of polygenes by affected sibpair linkage analysis is not practical and allelic association or linkage disequilibrium mapping will have to be employed to attempt to detect founder chromosomes. Given prior evidence of linkage of the Jk-D18S64 region of chromosome 18q12-q21 to type 1 diabetes, we evaluated the 12 informative microsatellite markers in the region for linkage with disease by the transmission disequilibrium test (TDT) in a UK data set of type 1 diabetic families (n = 195). Increased transmission of allele 4 of marker D18S487 to affected children was detected (P = 0.02). Support for this was extended in a total of 1067 families from four different countries by isolating, and evaluating by the TDT, two novel microsatellites within 70 kb of D18S487. Evidence for linkage and association was P = 5 x 10(-5) and 3 x 10(-4), respectively. There was no evidence for increased transmission of associated alleles to nonaffected siblings. Analysis of an additional 390 families by the TDT did not extend the evidence further, and reduced support in the total 1457 families to P = 0.001 for linkage and P = 0.003 for association. However, evidence for linkage by affected sibpair allele sharing was strong (P = 3.2 x 10(-5)) in the second data set. Heterogeneity in TDT results between data sets was, in part, accounted for by the presence of more than one common disease- associated haplotype (allelic heterogeneity) which confounds the analysis of individual alleles by the TDT. Guidelines for strategies for the mapping of polygenes are suggested with the emphasis on collections of large numbers of families from multiple populations that should be as genetically homogeneous as possible.      

Evidence by allelic association-dependent methods for a type 1 diabetes polygene (IDDM6) on chromosome 18q21

Human Molecular Genetics