Loss Of Heterozygosity For Chromosome Research Articles

Microsatellite instability and/or loss of heterozygosity in young gastric cancer patients in Italy.

Gastric cancers are rarely diagnosed before the age of 40 years and the incidence reaches a peak during the 7th decade in the general population. A molecular mechanism of early tumor onset may be determined by comparing microsatellite instability (MSI), indicative of error-prone mismatch repair, and loss of heterozygosity (LOH) between gastric cancers in patients < or = 40 years of age and those of older ages. Three to 5 chromosomal loci, where MSI and/or LOH are commonly found in gastric cancers in the general population, were examined in formalin-fixed, paraffin-embedded samples from 102 patients < or = 40 years of age using a polymerase chain reaction-based non-radioactive screening method. MSI and/or LOH at a minimum of 1 locus were detected in 11/102 patients. The frequency of MSI and/or LOH at the D11S904 locus was significantly higher than that at the D2S119, D2S123, D5S409 and IFNA regions. No preferential genetic changes at the D11S904 locus were observed in elderly patients. Among several clinicopathological variables, a statistically significant association with MSI and/or LOH was observed only for tumors located at the cardia, compared with tumors at the antrum and the corpus. Our findings suggest that a unique mechanism may be involved in increasing the susceptibility of the D11S904 locus for either MSI or LOH, especially for cardia tumors in young patients. Early onset of gastric cancers in patients < or = 40 years of age is associated with genetic changes at preferential chromosomal loci, including D11S904.

Frequent Loss of Heterozygosity for Chromosome 10 in Uterine Leiomyosarcoma in Contrast to Leiomyoma

Distinction of malignant uterine leiomyosarcomas from benign leiomyomas by morphological criteria is not always possible. Leiomyosarcomas typically have complex cytogenetic abnormalities; in contrast, leiomyomas have simple or no cytogenetic abnormalities. To understand better the biological distinction(s) between these tumors, we analyzed two other potential markers of genomic instability, loss of heterozygosity (LOH) and microsatellite instability. We examined archival materials from 16 leiomyosarcomas and 13 benign leiomyomas by polymerase chain reaction for 26 microsatellite polymorphisms. Markers were selected based on previous reports of cytogenetic or molecular genetic abnormalities in leiomyosarcomas or leiomyomas and surveyed chromosomes 7, 9, 10, 11, 12, 14, 15, 16, 18, 21, and X. LOH for markers on chromosomes 15, 18, 21, and X was infrequent in leiomyosarcomas (1 of 6 tumors for each chromosome) and not observed for markers on chromosomes 7, 9, 11, 12, 14, or 16. Interestingly, 8 of 14 (57.2%) informative leiomyosarcomas had LOH for at least one marker on chromosome 10 and involved both chromosomal arms in 45.5% (5 of 11). In contrast to leiomyosarcomas, LOH for chromosome 10 was not found in 13 benign leiomyomas. Microsatellite instability was found infrequently in leiomyosarcomas and not detected in leiomyoma. Clinicopathological features (eg, atypia, necrosis, and clinical outcome) did not appear to correlate with LOH for chromosome 10. In contrast to other chromosomes studied, LOH on chromosome 10 was frequent in leiomyosarcomas and absent in benign leiomyomas.

Both the rate and spectrum of loss of heterozygosity differ between human lymphoblastoid cells derived from various donors

Loss of heterozygosity (LOH) contributes significantly to the inactivation of tumor suppressor genes and may involve a variety of mechanisms. Studying loss of HLA-A2 alleles in human lymphoblastoid cell lines, we previously showed that mitotic recombination and chromosome loss with concomitant duplication of the non-selected chromosome were the most frequent mechanisms of LOH. In the present study we used the HLA system to determine the rate and spectrum of LOH mutations in the EBV transformed lymphoblastoid cell line R83-4915. Spontaneous loss of HLA-A2 in R83-4915 occurred with a rate of 7.9×10 −7 which was 5 to 10-times lower compared to the previously observed rate of loss of HLA-A2 in other lymphoblastoid cell lines. Among the HLA-A2 mutants, 27% did not show LOH of additional chromosome 6 markers. Molecular analysis showed that neither large deletion nor gene conversion was the cause for their mutant phenotype. The remaining mutants showed LOH, which was caused by mitotic recombination (40%) and chromosome loss (33%). However, the chromosome loss observed in mutants of R83-4915 was not accompanied by the duplication of the remaining chromosome. Instead 3 out of 5 mutants became polyploid suggesting that different mechanisms exist to compensate for chromosome loss. In conclusion, the rate and types of LOH that can be observed in cell lines obtained from various donors may depend on the genetic make-up or the transformation status of these cells

Allelic loss and prognosis in carcinoma of the uterine cervix.

Cervical carcinomas develop as a result of multiple genetic alterations. As the genetic alterations are the cause of malignant transformation, it is likely that specific genetic alterations lead to specific clinical behaviour. The aim of this study was (i) to localise chromosome arms that harbour likely tumour-suppressor genes, by analysing loss of heterozygosity (LOH) and (ii) to study the association of LOH with clinicopathological parameters. To define the regions of interest, we studied the presence of loss of heterozygosity at all chromosomes in 67 cervical carcinomas (stages IB and IIA) with 81 polymorphic markers. In addition, all frequent allelic imbalances were correlated with HPV status and clinicopathologic parameters including survival, FIGO-stage, lymph-node metastasis, tumour size, number of mitoses, vaso-invasion and histologic type. LOH at a frequency over 25% was observed at sites on 9 chromosome arms: 3p21, 4p16.1-15, 6p, 6q22.3-23.1, 11q22-24, 15q11-21.1, 17p13.3, 18q22-qter and Xq. LOH of chromosome 6q14-16.2, 6p22 and 17p13 correlated marginally with HPV-16 positivity. LOH on chromosome 3p21 was weakly correlated with high mitotic activity, while LOH on chromosomes 11q23.3, 15q21.1 and 17p13 correlated with low mitotic activity. LOH at chromosome 17p13 associated marginally with FIGO stage I, while LOH at chromosome 15q associated weakly with FIGO stage II. When chromosome 18q showed LOH in the tumour, the patients had decreased survival (p = 0.024). We conclude that, in carcinoma of the uterine cervix, a novel tumour-suppressor gene may be present on chromosome 15q21 and that patients with LOH on chromosome 18q have relatively poor survival (p = 0.025).

Molecular mechanism of hepatocarcinogenesis.

To clarify the relative role of hepatitis C virus (HCV) and hepatitis B virus (HBV) in hepatocarcinogenesis in hepatitis B surface antigen (HBsAg)-negative hepatocellular carcinoma (HCC) in Taiwan, polymerase chain reaction (PCR) was used to detect the HCV-RNA and HBV-DNA sequences in the serum and liver tissues from 31 HBsAg-negative HCC patients. Twenty-one were positive for antibody to HCV (group 1) and 10 were negative (group 2). Hepatitis C virus-RNA was detected by PCR in the serum of 16 group 1 patients and in the liver tissue of 17; while HBV-DNA was found in the liver tissue of only four, and no HBV-DNA was found in the serum. Hepatitis C virus RNA was detected in the serum of one group 2 patient and in the liver tissue of another. In contrast, HBV viral DNA was found in the serum of four group 2 patients and in the liver tissues of five patients. This indicates that HCV plays an important role in hepatocarcinogenesis in HBsAg-negative patients in Taiwan, especially in those with antibody to HCV. In those without antibody to HCV, HBV might still be associated with the development of HCC in a significant proportion of such patients. In order to study the role of the p53 mutation in hepatocarcinogenesis, we investigated the status of the p53 mutation in 61 HCC samples from Taiwan. The exon 5 to 8 of the p53 gene in the tumour tissue of 61 HCC were amplified and sequenced. A total of 20 cases (32.8%) were found to have mutations: 36.6% (15/41) from the HBsAg-positive group and 25.0% (5/20) from the HBsAg-negative group. The corresponding normal liver showed no mutation. The mutation is widely distributed throughout the exon 5 to 8. Only four cases (6.6%), all positive for HBsAg, had a specific hotspot mutation at codon 249 with G to T transversion. These results show that scattered point mutations in p53 are not uncommon in HCC samples from Taiwan and may be important in the development of this cancer. However, the aflatoxin-related specific mutation seems much less related to the genesis of HCC in Taiwan. To study the role of telomerase activity in hepatocarcinogenesis, a total of 39 HCC tissues and the corresponding non-tumour liver tissues were analysed. The results showed that telomerase activity was detected in all the 39 tumour tissues, while it could be detected in six of the 39 non-tumour liver tissues. The high positive rate of telomerase activity in HCC samples suggests that telomerase activity is closely related to the development or progression of HCC. To determine whether exon 1 and exon 2 of the p16 gene are altered in HCC, thirty-four tumours from 30 HCC patients were examined by DNA sequencing analysis of PCR-amplified genomic DNA. Homozygous deletions of MTS1/p16/CDKN2 exon 1 were identified in 1/34 primary tumours (3%), no mutations or rearrangements were found in these specimens. These data suggest that alterations of MTS1/p16/CDKN2 gene are rarely found in HCC, and might play little role in the development of this cancer. To study the clonality of HCC, 18 patients with multiple HCC, most of them small in size, were analysed by DNA fingerprinting. In patients positive for hepatitis B surface antigen, the integration pattern of hepatitis B viral DNA in liver tissue was also analysed. The results by both methods showed that 8/9 hepatitis B surface antigen-positive patients were different in clonality. In the remaining nine patients negative for hepatitis B surface antigen, four had different band patterns in their tumours by DNA fingerprinting. This study indicated that polyclonality of multiple HCC was rather frequent and it highlighted the importance of eliminating the underlying cause of liver injury to improve the survival of these patients. Microsatellite markers were used to study the genetic changes of HCC. Thirty cases of HCC, most of them small in size, were studied. A total of 242 microsatellite markers mapping to 1-22 and X chromosomes was used. The results showed that the range of loss of het

Loss of heterozygosity induced by a chromosomal double-strand break.

The repair of chromosomal double-strand breaks (DSBs) is necessary for genomic integrity in all organisms. Genetic consequences of misrepair include chromosomal loss, deletion, and duplication resulting in loss of heterozygosity (LOH), a common finding in human solid tumors. Although work with radiation-sensitive cell lines suggests that mammalian cells primarily rejoin DSBs by nonhomologous mechanisms, alternative mechanisms that are implicated in chromosomal LOH, such as allelic recombination, may also occur. We have examined chromosomal DSB repair between homologs in a gene targeted mammalian cell line at the retinoblastoma (Rb) locus. We have found that allelic recombinational repair occurs in mammalian cells and is increased at least two orders of magnitude by the induction of a chromosomal DSB. One consequence of allelic recombination is LOH at the Rb locus. Some of the repair events also resulted in other types of genetic instability, including deletions and duplications. We speculate that mammalian cells may have developed efficient nonhomologous DSB repair processes to bypass allelic recombination and the potential for reduction to homozygosity.

Basal cell carcinoma occurring in multiple familial trichoepithelioma: detection of loss of heterozygosity in chromosome 9q

Basal cell carcinoma (BCC) occasionally arises from the preexisting lesions of multiple familial trichoepithelioma (MFT). 1 The gene for BCC has been assigned to chromosome 9q22.3-q31, 2 and the gene for Bazex-Dupre-Christol syndrome, characterized by the early onset of multiple BCCs, has been mapped to chromosome Xq24-q27.1. 3 Recently, we carried out a linkage analysis in 3 families with MFT and mapped the gene for MFT to chromosome 9p21. 4 Therefore, trichoepithelioma does not seem to be allelic with BCC despite their histological similarities. To assess the involvement of the BCC genes in the development of BCC in MFT lesions, we examined the possibility of loss of heterozygosity in 2 different BCC specimens from the same patient using microsatellite markers of chromosomes 9q22-q31, Xq24-q27, and 9p21. Only the markers of chromosome 9q22-q31, the locus for sporadic BCCs and nevoid BCC syndrome, showed loss of heterozygosity in 1 of the 2

Microsatellite instability and loss of heterozygosity in chromosomes 9 and 16 in human breast epithelial cells transformed by chemical carcinogens.

Microsatellite instability (MSI) and loss of heterozygosity (LOH) in chromosomes 9 and 16 have been reported in human breast cancers. In order to determine whether changes in these chromosomes play a role in the initiation and progression of this disease, we performed microsatellite polymorphism analyses in human breast epithelial cells (HBEC) transformed by chemical carcinogens, an in vitro system that recapitulates various stages of neoplastic transformation. In this experimental system we studied the mortal HBEC MCF-10M, immortal MCF-10F cells, derived from MCF-10M cells, and clones derived from MCF-10F cells treated with benzo[a]pyrene (B[a]P) (BP1 and BP1E) and 7,12-dimethylbenz[a]anthracene (DMBA) (D3 and D3-1). The four clones of transformed cells were injected into severe combined immunodeficient (SCID) mice. Only BP1-E cells induced the formation of tumors, designated BP1E-Tp cells. These cells originated six additional tumors, designated BP1E-Tf no. 1 through Tf no. 6. Microsatellite analyses were carried out using five markers for chromosome 9 and 20 for chromosome 16. There was no evidence of MSI or LOH in clones BP1 and BP1E when compared with the MCF-10M and MCF-10F cells, whereas BP1E-Tp cells and Bp1E-Tf no. 1-Tf no. 6 tumors exhibited MSI at loci p23 and p21, and LOH at p21-22 of chromosome 9. They also exhibited MSI and LOH at multiple loci of both the short and long arms of chromosome 16, i.e. p13.13, p13.3, p12, q12.1, q12.2, q23 and q24, to which putative tumor suppressor genes have been localized. Clones D3 and D3-1 exhibited no genomic changes in chromosome 9, but did show MSI at locus q12.1 of chromosome 16 using marker D16S285. Although the cells treated with DMBA expressed early phenotypes of neoplastic transformation, they were not tumorigenic, and also manifested fewer changes than the tumorigenic BP1E-Tp cells and the tumors BP1E-Tf. The changes in chromosomes 9 and 16 observed in these latter ones indicated an association with the expression of tumorigenesis, which represents a late event in the progression of the neoplastic transformation of HBEC. Of interest was the observation that HBEC transformed by chemical carcinogens in vitro express genomic changes similar to those found in spontaneous breast carcinomas.

Basal Cell Carcinoma Occurring in Multiple Familial Trichoepithelioma: Detection of Loss of Heterozygosity in Chromosome 9q

Basal cell carcinoma (BCC) occasionally arises from the preexisting lesions of multiple familial trichoepithelioma (MFT).¹The gene for BCC has been assigned to chromosome 9q22.3-q31,²and the gene for Bazex-Dupré-Christol syndrome, characterized by the early onset of multiple BCCs, has been mapped to chromosome Xq24-q27.1.³Recently, we carried out a linkage analysis in 3 families with MFT and mapped the gene for MFT to chromosome 9p21.⁴Therefore, trichoepithelioma does not seem to be allelic with BCC despite their histological similarities. To assess the involvement of the BCC genes in the development of BCC in MFT lesions, we examined the possibility of loss of heterozygosity in 2 different BCC specimens from the same patient using microsatellite markers of chromosomes 9q22-q31, Xq24-q27, and 9p21. Only the markers of chromosome 9q22-q31, the locus for sporadic BCCs and nevoid BCC syndrome, showed loss of heterozygosity in 1 of the 2

Analysis of loss of heterozygosity and KRAS2 mutations in ovarian neoplasms: clinicopathological correlations.

The molecular events that give rise to ovarian epithelial neoplasms are not well understood. In particular, it is not known whether adenocarcinomas arise from benign or low malignant potential (LMP) precursors. We have examined a large series of benign (25) and LMP (31) ovarian tumors for loss of heterozygosity (LOH) at multiple loci on 17 chromosomes. LOH was observed in benign tumors on chromosomes 6 (14%) and 9 (5%) and on the X chromosome (33%) only. LOH on these chromosomes was also detected in a small number of LMP neoplasms, suggesting that these may derive sometimes from benign precursors. In addition, we examined LOH in 93 adenocarcinomas. Analysis of associations between LOH events showed that LOH on chromosomes 5 and 17 (P = 0.0002) and on chromosomes 17 and 18 (P = 0.00007) were associated significantly with each other, which suggests that these may represent cooperative, progressive events. No novel significant associations were identified between LOH events and stage, grade, or histology, which would indicate the existence of genetic heterogeneity in ovarian neoplasms. KRAS2 mutations were detected more often in LMP neoplasms than in malignant tumors (P = 0.004) and were detected more often in Stage I/II malignant tumors than in Stage III/IV malignant tumors (P = 0.033), suggesting that LMP tumors with KRAS2 mutations are unlikely to progress to frank malignancy. Univariate (but not multivariate) survival analysis showed that LOH of chromosomes 11 (P = 0.039) and 17 (P = 0.04) was associated with a significantly worse prognosis. Replication of these novel findings is necessary, and the identification, isolation, and characterization of the critical genes affected by LOH will determine their importance in the pathogenesis of ovarian malignancies.

Loss of heterozygosity analysis in a human fibrosarcoma cell line.

Loss of heterozygosity (LOH) is an important event in tumor formation. We have used polymorphic microsatellite repeat markers to identify and characterize LOH in spontaneous mutants of a human cell line, MR12-1, that is heterozygous for the adenine phosphoribosyltransferase gene (APRT+/-) located on chromosome 16q24.3. Initially, clones without extensive LOH (which are likely derived as a consequence of intragenic point mutations) and clones with multilocus LOH (which are likely due to major chromosome alterations) were identified. Clones with major regions of LOH were further characterized by assaying additional informative microsatellite markers. Analysis of 20 spontaneously-arising, independent APRT-/- clones from MR12-1 demonstrated that nine of the mutants retained both copies of APRT and 11 had undergone multilocus genetic alterations. The nature of LOH in four of the latter clones has been examined in detail by karyotype and fluorescence in situ hybridization analysis (Shao et al., 1996). These data demonstrate that LOH of chromosome 16 may be due to mitotic recombination, interstitial or partial deletion, or to more complex mechanisms. LOH in these clones may be a consequence of events similar to those observed in many tumors.

Potential role of the inactivated X chromosome in ovarian epithelial tumor development.

Ovarian epithelial tumors can be divided into subcategories often regarded as different stages of neoplastic transformation. Cystadenomas belong to the least aggressive subgroup and are noninvasive and nonmetastatic. Ovarian tumors of low malignant potential (LMP) are intermediate between cystadenomas and carcinomas and show markedly reduced invasive and metastatic abilities. Invasion and metastasis are the hallmarks of carcinomas, which constitute the most aggressive subgroup and can be further subdivided into different grades. We performed comparative allelotype analyses of ovarian cystadenomas, LMP tumors, and carcinomas, reasoning that such analyses could provide clues about the molecular determinants of their phenotypic differences. Because we realized that allelic losses involving the X chromosome might be associated with LMP tumor development, we determined whether such losses were interstitial and whether they involved the active or the inactive X chromosome. Frequencies of loss of heterozygosity (LOH) at specific loci in every chromosomal arm were determined in 16 ovarian cystadenomas, 23 ovarian LMP tumors, 15 low-grade ovarian carcinomas, and 35 high-grade ovarian carcinomas by use of either the polymerase chain reaction (PCR) or Southern blot analyses. We took advantage of the fact that DNA methylation is an important mechanism of X-chromosome inactivation to determine whether losses involving the X chromosome were in the active or the inactive copy. We analyzed the methylation status of retained alleles on the X chromosome by determining whether they could be amplified by PCR after digestion with the methylation-sensitive restriction endonuclease Hpa II. High-grade carcinomas contained frequent(>50%) LOH in four autosomal chromosome arms, i.e., 6q, 13q, 17p, and 17q. Except for 13q, these same chromosomal arms showed frequent LOH in low-grade carcinomas. LOH in autosomal chromosomes was comparatively rare in LMP tumors and was absent in cystadenomas. In contrast, half (eight of 16) of LMP tumors informative for a locus in the proximal portion of chromosome Xq showed LOH at that locus. These losses were the result of interstitial deletions in six of the eight cases and involved the inactive copy of the X chromosome exclusively. Similar losses in the X chromosome were not seen in either cystadenomas or low-grade carcinomas. LOH at multiple loci is associated with the development of ovarian carcinomas but not with the development of cystadenomas and LMP tumors. However, the integrity of a locus in chromosome Xq that possibly escapes X-chromosome inactivation is important for the control of LMP tumor development. The fact that this locus does not appear to be involved in the genesis of low-grade carcinomas suggests that LMP tumors are not precursors of such carcinomas.

Relationship Between Sunlight Exposure and a Key Genetic Alteration in Basal Cell Carcinoma

Basal cell carcinoma (BCC) of the skin is the most common cancer in humans. Epidemiologic studies implicate sunlight exposure as one risk factor, but the limited association between BCCs and UVB radiation (i.e., UV radiation of a wavelength of 280-320 nm) suggests that additional factors must be involved. At the molecular level, not much is known about the role of specific environmental agents in the pathogenesis of BCCs. Point mutations of the types produced by UVB radiation are seen in the p53 gene (also known as TP53; chromosome 17p) of 40%-56% of BCCs. Loss of heterozygosity (LOH) on chromosome 9q22, however, is the most frequent genetic alteration in these tumors, and its causative agent is unknown. We investigated whether the genetic alteration in chromosome 9 is common to all clinical subtypes of BCCs and whether inactivation of this putative tumor suppressor is related to sunlight exposure. The presence of UVB radiation-related point mutations in the p53 gene was used as an internal control for sunlight exposure to the precursor cells. Tumor and blood samples were obtained from skin cancer patients by a surgeon who used Mohs' micrographic surgical technique. Clinical information on each tumor included location, size, histologic, subtype and whether it was primary or recurrent and sporadic or hereditary. Sixty BCCs from 58 patients were evaluated for LOH with 12 polymorphic markers that span chromosome 9. A subset of 18 tumors was evaluated for point mutations in exons 2-11 of the p53 gene, and a subset of 26 tumors was evaluated for LOH by use of a polymorphism in exon 4 of the p53 gene. Associations between tumor characteristics and molecular alterations were tested by a two-tailed chi-squared analysis or a two-tailed Fisher's exact test, depending on sample size. In a clinically diverse series of 47 informative tumors, 32 (68%) showed LOH for chromosome 9q markers, irrespective of histologic characteristics or clinical behavior. Forty-four (94%) of the 47 tumors were from sun-exposed areas of the body, defined as the head and neck in both sexes, shoulders or chest in males, and legs in females. No association was found between chromosome 9q LOH and sunlight exposure, as assessed by either the location of tumors on the body or the presence of UVB radiation-related p53 mutations. Of note, there was a striking difference between the frequency of LOH on chromosome 17p (two [12.5%] of 16 informative tumors) and on chromosome 9q (32 [68%] of 47 informative tumors; P < .001). Inactivation of a gene on chromosome 9q22 may be a necessary event for basal cell carcinogenesis. The pathogenesis of mutations in this gene may involve factors other than sunlight in a large proportion of tumors. The limited association between sunlight exposure and BCC incidence may reflect an etiologic contribution of additional environmental agents.

Loss of Heterozygosity in Chromosome-1, Chromosome-5, Chromosome-7 and Chromosome-13 in Mouse Hepatoma Detected by Systematic Genome-Wide Scanning Using Rlgs Genetic-Map

We have developed an RLGS-based scanning system to detect DNA alteration in tumor tissues, using 575 mapped spots/loci in a single gel. This system is very powerful for screening and identifying not only loss of heterozygosity (LOH) but also DNA methylation change. In this study, we applied this system to search for the LOH of hepatoma from an interspecific F1 hybrid between Mus spretus and C57BL/6 with SV40 early T antigen transgene connected to a mouse major urinary protein enhancer/promoter. Comparing the RLGS profiles of each tumor to that of the normal tissue showed significant LOH in chromosomes 1,5,7 and 13.

Genetic alterations on chromosome 17 distinguish different types of epithelial ovarian tumors

Epithelial tumors of the ovary are the most common ovarian tumors of adult women. They exist in several different histological patterns and exhibit varying degrees of aggressiveness. Molecular genetic studies in epithelial ovarian cancer have shown that loss of heterozygosity (LOH) for regions of chromosome 17 is a common event, probably reflecting the inactivation of one or more tumor suppressor genes present on this chromosome. We examined 87 sporadic epithelial ovarian tumors of different grade and histological type at 16 loci on this chromosome and found that 35% of them showed LOH for chromosome 17. Of these, 84% showed LOH for all informative markers, suggesting that loss of the entire chromosome 17 homologue may have occurred. Interestingly, chromosome 17 loss was observed frequently in serous tumors (49%), was less common in endometrioid tumors (15%), and was rare in mucinous tumors (4%) ( P = .01 and P = .0002, respectively). Our findings support the concept that the histological subtypes of epithelial ovarian cancer may be the result of different molecular genetic events.

Loss of heterozygosity for DNA polymorphisms mapping to chromosomes 10 and 17 and prognosis in patients with gliomas.

Twenty nine patients with gliomas were investigated for loss of heterozygosity for 40 DNA polymorphisms in tumour DNA, particularly concentrating on those mapping to chromosomes 10 and 17. Eight of 18 grade IV gliomas showed loss of sequences from chromosomes 10, 17, or both. The data suggested total loss of one copy of chromosome 10, but there were interstitial deletions of the short arm of chromosome 17 in three of five tumours. Heterogeneous interstitial deletions of chromosome 17 were also found in two lower grade astrocytomas and one benign oligodendroglioma. The striking finding of this study was that patients with high grade gliomas whose tumours exhibited loss of heterozygosity for chromosomes 10, 17, or both survived significantly longer after surgery (median 17.4 months) than those whose tumours did not show loss of these chromosomes (median 6.7 months). These findings suggest that there is a subset of particularly aggressive high grade gliomas with no currently known molecular genetic abnormalities.

Extensive loss of heterozygosity accounts for differential mutation rate on chromosome 17q in human lymphoblasts

In order to investigate the influence of loss of heterozygosity (LOH) events on mutation rate, we studied two closely related human lymphoblastoid cell lines, AHH-1 (h2E1.v2) and MCL-5, which are heterozygous at the tk locus (chromosome 17q23-25). Although they have similar mutant fractions at the hprt locus, the mutant fraction and rate at tk is four to five times higher in AHH-1. Analysis of 58 spontaneous TK- mutants from AHH-1 and MCL-5 showed that the occurrence of LOH events was more frequent (23/24) in AHH-1 than MCL-5 (16/34). A set of five microsatellite polymorphism loci was used to map the extent of LOH along chromosome 17q. In AHH-1 cells, 15/23 of the LOH events encompassed at least 35% of the sex-averaged genetic length of chromosome 17q (98 cM). Additionally, the next most extensive category of LOH accounted for 5/23 TK- mutants, and encompassed at least 17 cM. In contrast, LOH events observed in MCL-5 are very restricted in extent; only one LOH tract extended as far as 4 cM from tk. The higher mutation rate at tk in AHH-1 can, therefore, be entirely attributed to the recovery of chromosomal scale LOH in viable, normal growth TK- mutants. Furthermore, these data demonstrate that the regional potential for LOH is likely to be an important determinant of mutation rate for loci within that chromosomal segment.

Molecular analysis of genomic abnormalities in human gliomas

A series of 57 malignant gliomas, including 27 astrocytomas grade III–IV (glioblastoma multiforme), 15 astrocytomas grade I–II, and 15 tumors with major oligodendroglial component, was examined to detect molecular abnormalities of loci at specific chromosome regions. At the cytogenetic level, these regions have been shown to be nonrandomly involved in neoplastic development of these histologic subtypes of tumor. We used a panel of 24 polymorphic DNA probes to analyze loss of heterozygosity (LOH) at loci on chromosomes 7, 9, 10, 13, 17p, and 22q. In addition, the retinoblastoma ( RB1) oncosuppressor gene, the platelet-derived growth factor A ( PDGFA) gene, and the epidermal growth factor receptor ( EGFR) gene were analyzed directly. Loss of genetic information on the short arm of chromosome 17 was observed in both low- and high-grade astrocytomas, whereas no oligodendroglial tumor was characterized by this type of aberration. LOH for chromosome 10, mainly compatible with loss of the entire chromosome, was primarily evidenced in the more malignant forms and in isolated cases diagnosed as low-grade astrocytomas. Again, no oligodendroglial tumor displayed losses of chromosome 10. In contrast, four tumors with major oligodendroglial component showed losses involving 9p markers, primarily interferon A and B ( IFNA, IFNB); this feature was also observed in two low-grade astrocytomas and in 11 high-grade tumors. Isolated cases displayed LOH for markers on chromosomes 13 and 22, whereas EGFR amplification was almost exclusively evidenced in the more malignant forms which, in most instances, also presented LOH for chromosome 10. In general, the samples with lower malignancy stage displayed a lesser grade of abnormalities, mainly restricted to losses at 17p and chromosome 10 in astrocytomas grade I–II and at 9p in oligodendrogliomas. In contrast, about 50% of the high-grade tumor samples analyzed included abnormalities at two or more loci, with a recurrent association of EGFR amplification and LOH for chromosome 10; this association was evident in 26% of the high-grade astrocytomas.

Clonal analysis of human astrocytomas.

Clonal analysis of many human cancers have generally confirmed that they are monoclonal. Although astrocytic neoplasms are the most frequently occurring primary tumors in the central nervous system, their clonal composition has not been systematically studied. In this report, the clonal composition of 22 human astrocytomas of all histological grades (2 well-differentiated astrocytomas, 3 anaplastic astrocytomas and 17 glioblastoma multiforme) was determined by analysis of the pattern of X-chromosome inactivation. Leukocyte and non-tumor brain DNA were used as controls. In addition, specimens from different parts of four glioblastoma multiforme were analyzed to determine whether remote areas of the same tumor had the same clonal composition. Eighteen of nineteen informative astrocytomas had a monoclonal pattern of X-chromosome inactivation; one glioblastoma multiforme had loss of heterozygosity on the X chromosome. Specimens from different areas of the same tumor all had identical patterns of X-chromosome inactivation. Leukocytes and non-tumor brain used as controls uniformly had a polyclonal pattern of X-chromosome inactivation. Furthermore, loss of heterozygosity for chromosomes 10 or 17 p loci was found in 64% (9/14) of informative specimens and identical allelic patterns were observed in specimens from different areas of the same tumor. Our results demonstrate that human astrocytomas from low to high-grade are characterized by monoclonal cell populations. The presence of monoclonality in even low-grade neoplasms suggests that in astrocytic tumors the establishment of monoclonality occurs quite early. Also, the finding of a monoclonal pattern in intermediate- and high-grade astrocytomas further supports the hypothesis that clonal expansion underlies astrocytic tumor progression.

Malignant melanoma: From subcutaneous nodule to brain metastasis

A thirteen-year-old patient, diagnosed with melanoma was followed cytogenetically using short-term cultures of specimens from a subcutaneous nodule, lymph node, and brain metastases. Simple hypodiploid karyotypes with loss of heterozygosity for chromosomes 5, 9, 10, 16 and 17 and two structural changes in 3 and between 13 and 21 increased in complexity to near triploid in the lymph node. Two cell types of the lymph node showed a progression of structural rearrangements prior to metastasis to the brain. Translocation of 6p to chromosome 2, deletions of 8, and a translocation (2;19) preceded p and q arm deletions of both chromosomes 9 and 11 in the lymph node. Cells metastasizing to the brain showed the accumulation of all previous aberrations and had acquired a direct duplication of distal 17 long arm. Whether or not elevated levels of protein kinase C, located on chromosome 17q contribute to tumor adhesion and growth on the brain remains to be elucidated. Identification of most chromosomes undergoing rearrangement was carried out using whole chromosome painting probes in in situ hybridizations. Some of these rearrangements would have been impossible to identify by standard karyotyping.