Highly frequent allelic loss of chromosome 6q16-23 in osteosarcoma: involvement of cyclin C in osteosarcoma

The molecular pathogenesis of osteosarcoma is very complicated and associated with chaotic abnormalities on many chromosomal arms. We analyzed 12 cases of osteosarcomas with comparative genomic hybridization (CGH) to identify chromosomal imbalances, and detected highly frequent chromosomal alterations in chromosome 6q, 8p, 10p and 10q. To define the narrow rearranged region on chromosome 6 with higher resolution, loss of heterozygosity (LOH) analysis was performed with 21 microsatellite markers. Out of 31 cases, 23 cases (74%) showed allelic loss at least with one marker on chromosome 6q. We identified two distinct commonly deleted regions on chromosome 6 using markers D6S1565 located at 6q16 and 6q23MS1 at 6q23. The expression analysis of genes located at the deleted region was performed, and the decreased mRNA expression of the CCNC gene, one of the regulators of cell cycle, was detected. Growth of osteosarcoma cell line was significantly suppressed after the CCNC cDNA transfection. Fine mapping of the deleted region containing a possible tumor suppressor gene and the transfection assay suggest that the CCNC is a candidate tumor suppressor gene.     

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.     

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.     

Cervial intraepithelial neoplasia III shows frequent allelic loss in 3p and 6p

We have shown previously that a significant number of invasive cervical cancers (ICC) have nonrandom chromosomal losses in 3p, 6p, 11q, 2q, 6q, and 19q, thereby suggesting that genes involved in the suppression of tumor development or progression are located in these regions. Cervical intraepithelial neoplasia (CIN) III is considered the precursor lesion for ICC of squamous type and occurs frequently with ICC of glandular type. In an effort to define which chromosomal losses are present in the precursor lesions, we identified CIN III lesions from 24 ICC treated by radical hysterectomy. Thirty-three CIN III associated with 22 squamous carcinomas and 2 adenocarcinomas were carefully microdissected from the paraffin-embedded sections. The whole genomic DNA from CIN III was amplified with short random primers. DNA from ICC, CIN III, and normal tissue was analyzed at the six chromosomal regions with polymorphic markers. Thirty-eight percent of hysterectomy specimens had loss of heterozygosity (LOH) in at least one of the CIN III lesions from each case. Loss occurred in 30% of cases in 3p14.1–12 (37% for associated ICC), 21% in 6p23 (33%), 14% in 2q33–37 (27%), 0 in 11q23.3 (33%), 4% in 19q13.4 (13%), and 0 in 6q21–23.3 (18%). These results suggest that mutations in 3p and 6p are important early in tumorigenesis, whereas 11q and 6q contain genes important later in tumor progression. Invasive and preinvasive cervical lesions appear to develop from multifocal genetic events since consistent losses do not occur within all precursor lesions in the same patient. Genes Chromosomes Cancer 22:57–65, 1998. © 1998 Wiley-Liss, Inc.     

Homozygous deletion and frequent allelic loss of the 21q11.1-q21.1 region including the ANA gene in human lung carcinoma

The frequent occurrence of 21q deletions in human non-small cell lung carcinoma (NSCLC) indicates the presence of a tumor suppressor gene on this chromosome arm. Since the ANA (Abundant in Neuroepithelium Area) gene, a member of an antiproliferative gene family, was mapped to 21q11.2-q21.1, we searched for genetic alterations of the ANA gene in human lung cancers. The gene was homozygously deleted in a human NSCLC cell line, Ma17. The gene was mapped in the 0.33 Mb NotI fragment at 21q21.1 of the NotI restriction map for 21q. Loss of heterozygosity (LOH) at this locus was detected in 24/47 (51.1%) of NSCLC, and the frequency of LOH in brain metastases was significantly higher than that in stage I–II primary tumors (P = 0.018). These results suggested that the homozygously deleted region harbors a novel tumor suppressor gene involved in NSCLC progression. Since mutation of the ANA gene was not detected in other lung cancer cell lines and fresh lung tumors with LOH at this locus, it is unlikely that the ANA gene is a target gene inactivated by two mutational events in this chromosomal region. Physical mapping of the homozygously deleted region showed that the deletion had occurred interstitially at 21q11.1-q21.1 and the size of the deletion was estimated as being more than 3 Mb. Our mapping results will facilitate further efforts to identify a tumor suppressor gene on 21q. Genes Chromosomes Cancer 21:236–243, 1998. © 1998 Wiley-Liss, Inc.     

Detection of loss of heterozygosity on chromosome 9q22.3 in microdissected sporadic basal cell carcinoma

Identification of loss of heterozygosity (LOH) at specific genetic loci in cancer cells suggests the presence of a tumor suppressor gene within the deleted region. A basal cell carcinoma (BCC) susceptibility gene, human homolog of drosophila patched (PTC), has been recently cloned and localized on chromosome 9q22.3. Mutation and deletion of this region has been reported in BCCs using frozen tumor tissue. The objective of this study was to test whether LOH of human PTC on chromosome 9q22 could be detected in archival sporadic BCCs. We studied 20 randomly selected sporadic BCCs by microdissection and polymerase chain reaction using paraffin-embedded, formalin-fixed material on glass slides. In all cases, analysis was performed with the polymorphic markers D9S53, D9S15, D9S287, and D9S303. The LOH frequencies were 30%, 42%, 56%, and 75% with D9S15, D9S287, D9S53, and D9S303, respectively. LOH at 9q22 was identified in 12 of 20 cases (60%) with at least one marker. Seven cases showed LOH with two markers, two cases with three markers, and one case showed LOH with all four markers. The results indicate that BCC LOH can be frequently identified in paraffin-embedded BCC after routine processing.     

Frequent deletions of 6q23–24 in B-cell non-Hodgkin's lymphomas detected by fluorescence in situ hybridization

Deletions of the long arm of chromosome 6 (6q) are among the most frequent chromosome aberrations in malignant lymphomas and often occur as secondary changes in addition to typical translocations, such as t(14; 18). Using fluorescence in situ hybridization (FISH) with two YAC probes hybridizing to 6q23–24 and with the centromeric probe D6Z1 as internal control, we studied 31 cases of low-grade and eight cases of high-grade B-cell lymphoma. Deletions of 6q23–24 were detected in 21 patients (56.8%) by FISH, compared to 13 patients (33.3%) by chromosome analysis. Deletions of 6q23–24 were found by FISH in 5 of 13 cases of small lymphocytic lymphoma, in 2 of 3 cases of mantle cell lymphoma, in 10 of 14 cases of t(14; 18) positive low-grade follicular lymphoma, and in 4 of 8 cases of high-grade follicular lymphoma. This study shows that deletions of 6q23–24 are more frequent in B-cell lymphomas than previously suggested and that they can be detected more sensitively by FISH than by chromosome analysis. Contrary to previous reports indicating that the region 6q23–24 is preferentially deleted in low-grade lymphomas without t(14; 18), our results indicate that deletions of 6q23–24 appear to be common in other pathological subsets of B-cell lymphoma as well, especially in follicular lymphomas with t(14; 18). Genes Chromosom. Cancer 18:310–313, 1997. © 1997 Wiley-Liss, Inc.     

Retention of polysomy at 9p23–24 during karyotypic evolution in human breast cancer cell line COLO 824

Somatic genetic alterations of 9p have been seen in a wide range of human cancers, including breast cancer. Loss of heterozygosity analysis of primary breast cancer tumors has revealed a high frequency of deletion of DNA from 9p21–22 encompassing the MTS1 (P16/CDKN2A) gene. We report the approximately tenfold increase in copy number of DNA from 9p23–24, which is far distal to P16/CDKN2A in female breast cancer cell line COLO 824, as revealed by fluorescence in situ hybridization, comparative genomic hybridization, and microsatellite analysis. Amplification of DNA has been reported previously to encompass multiple sites of the genome of the breast cancer cell, but increase in DNA copy number has not been seen in distal 9p. Genes Chromosomes Cancer 24:87–93, 1999. © 1999 Wiley‐Liss, Inc.     

Diffuse large cell lymphomas exhibit frequent deletions in 9p21–22 and 9q31–34 regions

We have previously identified deletions of 9p and 9q in a cytogenetic analysis of a large series of non-Hodgkin's lymphomas (NHLs), which suggested loss of candidate tumor suppressor genes (TSGs). In order to define these deletions at the molecular level, we performed an LOH analysis of a panel of paired normal and tumor DNAs comprising 13 cases of diffuse lymphoma with a large cell component (DLLC) and 18 cases of Burkitt's lymphoma (BL). The loci tested comprised eight polymorphic probes mapped to 9p (D9S33, D9S25, IFNB, IFNA, IFNW, D9S126, D9S3, and D9S19) and seven polymorphic probes mapped to 9q (D9S29, ASS, AKI, ABL, D9S10, D9S7, and D9S14). In this analysis, among cases informative for all loci in each subset, 5/13 (38%) DLLC and 4/18 (22%) BL showed LOH at 9p loci, whereas 5/13 (38%) DLLC and 3/18 (16%) BL showed LOH at 9q loci. Among the 9p loci partial homozygous or heterozygous losses were observed in 20–50% of informative cases of DLLC at D9S25, IFNB, IFNA, IFNW, D9S126, and D9S3, whereas in BL, losses at these loci ranged from 0% to 11%. Among the 9q loci, heterozygous losses were observed in >20% of informative cases of DLLC at D9S7 (23%) and D9S29 (27%), whereas no losses were seen at these two loci in BL. These data demonstrate a high level of molecular deletion in DLLC, but not in BL, suggesting that loss of one or more TSGs on chromosome 9 plays an important role in DLLC development.     

Frequent allelic loss at the TOC locus on 17q25.1 in primary breast cancers

Sporadic breast cancers often show allelic losses on the long arm of chromosome 17. Since the BRCA1 gene lies at 17q21.1 and the TOC locus, associated with esophageal cancer, lies at 17q25.1, either gene could be the target of those losses. We examined both loci in 178 primary breast cancers, using microsatellite markers covering the relevant regions of 17q, and observed allelic losses in 97 tumors (55%). Losses were most frequent at markers around the TOC locus (48% at D7S1839 and 43% at D17S1603), where we identified a distinct commonly deleted region within a I -cM interval. Another larger, separate commonly deleted region including the BRCA1 gene was also identified, which exhibited 45% of allelic loss (at D17S934). Allelic loss on 17q was more frequent in tumors of the solid-tubular histologic type (P = 0.0129) and in estrogen-negative and progesterone-negative tumors (P = 0.0281 and 0.0196, respectively). The results indicated that BRCA1 and TOC are independent targets of allelic loss on 17q in primary breast cancers, and that inactivation of the TOC locus in particular may play an important role in the genesis of sporadic breast tumors.     

Proximal and distal 15q25.2 microdeletions–genotype–phenotype delineation of two neurodevelopmental susceptibility loci

Distal 15q25.2 microdeletions have recently been reported as a copy number variation (CNV) locus for neurodevelopmental and neuropsychiatric disorders with variable outcome. In addition, more proximal microdeletions of 15q25.2 have been described as a susceptibility locus for cognitive deficits, congenital diaphragmatic hernia (CDH), and Diamond–Blackfan anaemia (DBA). We describe two patients with 15q25.2 deletion, one with the more distal deletion and the other with a deletion overlapping both the distal and proximal 15q25.2 deletions and compare them to the 18 so far reported patients with 15q25.2 deletions. We provide a characterization of the 15q25.2 microdeletions and contribute to the genotype–phenotype delineation for these two novel microdeletion syndromes. © 2012 Wiley Periodicals, Inc.     

The Cables gene on chromosome 18q is silenced by promoter hypermethylation and allelic loss in human colorectal cancer

Cables is a cyclin-dependent kinase-binding nuclear protein that maps to chromosome 18q11-12. Here, we assessed Cables expression in 160 colorectal cancers (CRCs), its role in colon cancer cell growth, and the potential mechanisms of Cables inactivation. Expression levels, promoter methylation, and mutational status of Cables were investigated in colon cancer cell lines and primary colon tumors. Chromosome 18q loss of heterozygosity (LOH) was evaluated with multiple polymorphic markers. Cables inhibited cellular proliferation and colony formation in colon cancer cell lines. Cables expression was reduced in 65% of primary CRCs. No mutations were detected in 10 exons of Cables in 20 primary colon tumors. Cables promoter was methylated in cell lines with decreased Cables expression and vice versa. 5-Aza-2'-deoxycytidine resulted in increased Cables expression in methylated cell lines. There was a significant correlation between promoter methylation and Cables gene expression in primary colon tumors. Sixty-five percent of primary colon tumors demonstrated chromosome 18q LOH. LOH involving the Cables region was observed in 35% of cases, including those in which more distal portions of chromosome 18q were retained, and Cables expression was decreased in all such cases. Loss of Cables expression in 65% of CRCs suggests that it is a common event in colonic carcinogenesis, with promoter methylation and LOH appearing to be important mechanisms of Cables gene inactivation.     

Mapping of a new target region of allelic loss to a 6-cM interval at 21q21 in primary breast cancers

A detailed analysis of loss of heterozygosity (LOH) in breast cancers was performed with 11 microsatellite markers on the long arm of chromosome 21. Among the 142 tumors examined, 44 (31%) showed LOH at one or more loci. Peak LOH frequency was observed on band 21q21. Deletion mapping identified a new commonly deleted region in a 6-cM interval of 21q21 between loci D21S1432 and D21S1437, and raised the possibility that one or more tumor suppressor genes associated with breast cancer may exist in this region. Comparison of these alterations with clinicopathological parameters revealed an association of LOH on 21q with loss of progesterone receptor (P = 0.0013). Genes Chromosomes Cancer 23:244–247, 1998. © 1998 Wiley-Liss, Inc.     

Mutation at chromosome 11q23 in human non-familial breast cancer: A microdissection microsatellite analysis

Allelotypic evaluation of loss of heterozygosity (LOH) has been instrumental in the identification of tumour suppressor genes. Here we report a high incidence of LOH at chromosome 11q23 in non-familial breast cancers with in situ, invasive, and metastatic tumour cells microdissected from archival haematoxylin and eosin (H & E) sections for polymerase chain reaction (PCR)-LOH analysis at polymorphic microsatellite loci. Ninety-four cases of non-familial breast cancer were examined at the D11S29 microsatellite locus on chromosome 11q23. Eighty-three cases (88 per cent) were informative and 35 cases overall (42 per cent) had LOH at this locus, comprising 23 per cent of in situ, 36 per cent of invasive, and 28 per cent of metastatic cancers. The DNA from those cancer cells with LOH was amplified at microsatellite loci D11S554 (11p12–p11.2) and D11S534 (11q13). In 19 of 67 cases overall (28 per cent), LOH occurred solely at 11q23. There was an association between LOH at 11q23 and tumour size ≥2 cm (P<0.01) in the overall results and the invasive cancers. The data revealed heterogeneity for LOH at D11S29 in in situ, invasive, and metastatic cells from the same case. In general, however, there was concordance between LOH (or its absence) in in situ and invasive disease. We conclude that the distal part of the long arm of chromosome 11 contains a region involved in breast carcinogenesis and that there is molecular heterogeneity at this chromosomal region in individual breast cancer cells.     

Mapping of a new target region of allelic loss to a 2-cM interval at 22q13.1 in primary breast cancer

Allelic losses on chromosome arm 22q are frequently observed in human meningiomas and in carcinomas of the colon, ovary, and breast. Among 140 primary breast cancers we examined for loss of heterozygosity (LOH) at 16 polymorphic loci on the long arm of chromosome 22, 56 (40%) showed LOH for at least one locus. Eleven of these tumors had retained heterozygosity for markers proximal to the NF2 locus but showed LOH for markers distal to NF2. Deletion mapping indicated a new common region of deletion, 2-cM in extent, at q13.1 between Interleukin 2 receptor β (IL2RB) and D22S279. Our results raise the possibility that one or more tumor suppressor genes associated with breast cancer may exist at 22q13.1. Comparison of these results with clinicohistological data indicated that allelic losses on 22q tend to occur more frequently in tumors of malignant histological types. Genes Chromosomes Cancer 21:108–112, 1998. © 1998 Wiley-Liss, Inc.     

Study of allelic losses on 3p, 6q, and 17p in human urothelial cancer.

Forty-eight transitional cell carcinomas of the bladder and three transitional cell carcinomas of the renal pelvis were examined for loss of heterozygosity (LOH) on chromosomes 3p, 6q, and 17p. The most frequent allelic loss was seen on 17p (18/36, 50%) followed by 6q (6/22, 27%), and 3p (5/22, 23%). In cases with LOH at more than one locus, the same DNA sample often varied in degree of signal reduction for missing alleles. This observation indicates that LOH studies can serve to detect intratumor heterogeneity. No correlation was found between allelic losses at these chromosome arms and tumor grade and stage. Allelic losses on 6q were associated with tumors having a solid growth pattern; in this kind of tumors, allelic losses on 3p were associated with invasion.     

High incidence of familial breast cancer segregates with constitutional t(11;22)(q23;q11)

In a family with a high incidence of postmenopausal breast cancer and a case of glioblastoma, the constitutional translocation t(11;22)(q23;q11.2) was shown to segregate with the malignancies. The breakpoints in this family coincided with the common breakpoints in t(11;22) as shown by a translocation-specific PCR assay. Loss of heterozygosity analysis of breast tumor tissue revealed deletion of the normal chromosome 22, but retention of der(22) in the tumor cells, suggesting a predisposing effect of the der(22) for breast and brain tumor development in this family.