Clonal chromosome abnormalities in human breast carcinomas. I. Twenty-eight cases with primary disease

Genetics and genomics of breast fibroadenomas

Fibroadenomas of the breast are benign fibroepithelial tumours most frequently encountered in women of reproductive age, although they may be diagnosed at any age. The fibroadenoma comprises a proliferation of both stromal and epithelial components. The mechanisms underlying fibroadenoma pathogenesis remain incompletely understood. In the clinical setting, distinguishing cellular fibroadenomas from benign phyllodes tumours is a common diagnostic challenge due to subjective histopathological criteria and interobserver differences. Recent sequencing studies have demonstrated the presence of highly recurrent mutations in fibroadenomas, and also delineated the genomic landscapes of fibroadenomas and the closely related phyllodes tumours, revealing differences at the gene level, which may be of potential adjunctive diagnostic use. The present article provides an overview of key studies uncovering genetic and genomic abnormalities in fibroadenomas, from initial karyotype reports revealing myriad cytogenetic aberrations to next-generation sequencing-based approaches that led to the discovery of highly recurrent MED12 mutations. A thorough understanding of these abnormalities is important to further elucidate the mechanisms by which fibroadenomas arise and to refine diagnostic assessment of this very common tumour.

Molecular cytogenetic characterization of mammary neuroendocrine carcinoma

Primary mammary neuroendocrine carcinoma (NEC) is an uncommon entity that accounts for 2% to 5% of breast carcinomas. Recent reports have shown that NEC of the breast is an aggressive subtype of mammary carcinoma that is distinct from invasive ductal carcinoma, not otherwise specified, and have suggested that these tumors have a poorer prognosis than invasive ductal carcinoma, not otherwise specified. In this study, we provide the first cytogenetic characterization of mammary NEC using both conventional G-banding and spectral karyotype on a group of 7 tumors. We identified clonal chromosomal aberrations in 5 (71.4%) cases, with 4 of them showing complex karyotypes. Of these, recurrent numerical aberrations included gain of chromosome 7 (n = 2) and loss of chromosome 15 (n = 2). Recurrent clonal structural chromosomal aberrations involved chromosomes 1 (n = 3), 3 (n = 2), 6q (n = 3), and 17q (n = 3). Of the 4 (57.1%) cases with complex karyotypes, 2 showed evidence of chromothripsis, a phenomenon in which tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. One of these had evidence of chromothripsis involving chromosomes 1, 6, 8, and 15. The other also had evidence of chromosome 8 chromothripsis, making this a recurrent finding shared by both cases. We also found that mammary NEC shared some cytogenetic abnormalities--such as trisomy 7 and 12--with other neuroendocrine tumors in the lung and gastrointestinal tract, suggesting trisomy 7 and 12 as potential common molecular aberrations in neuroendocrine tumors. To our knowledge, this is the first report on molecular cytogenetic characterization of mammary NEC.

High SINE RNA Expression Correlates with Post-Transcriptional Downregulation of BRCA1

Short Interspersed Nuclear Elements (SINEs) are non-autonomous retrotransposons that comprise a large fraction of the human genome. SINEs are demethylated in human disease, but whether SINEs become transcriptionally induced and how the resulting transcripts may affect the expression of protein coding genes is unknown. Here, we show that downregulation of the mRNA of the tumor suppressor gene BRCA1 is associated with increased transcription of SINEs and production of sense and antisense SINE small RNAs. We find that BRCA1 mRNA is post-transcriptionally down-regulated in a Dicer and Drosha dependent manner and that expression of a SINE inverted repeat with sequence identity to a BRCA1 intron is sufficient for downregulation of BRCA1 mRNA. These observations suggest that transcriptional activation of SINEs could contribute to a novel mechanism of RNA mediated post-transcriptional silencing of human genes.

Evaluation of the prognostic role of centromere 17 gain and HER2/topoisomerase II alpha gene status and protein expression in patients with breast cancer treated with anthracycline-containing adjuvant chemotherapy: pooled analysis of two Hellenic Cooperative Oncology Group (HeCOG) phase III trials

BACKGROUND

The HER2 gene has been established as a valid biological marker for the treatment of breast cancer patients with trastuzumab and probably other agents, such as paclitaxel and anthracyclines. The TOP2A gene has been associated with response to anthracyclines. Limited information exists on the relationship of HER2/TOP2A gene status in the presence of centromere 17 (CEP17) gain with outcome of patients treated with anthracycline-containing adjuvant chemotherapy.

METHODS

Formalin-fixed paraffin-embedded tumor tissue samples from 1031 patients with high-risk operable breast cancer, enrolled in two consecutive phase III trials, were assessed in a central laboratory by fluorescence in situ hybridization for HER2/TOP2A gene amplification and CEP17 gain (CEP17 probe). Amplification of HER2 and TOP2A were defined as a gene/CEP17 ratio of >2.2 and ≥2.0, respectively, or gene copy number higher than 6. Additionally, HER2, TopoIIa, ER/PgR and Ki67 protein expression was assessed by immunohistochemistry (IHC) and patients were classified according to their IHC phenotype. Treatment consisted of epirubicin-based adjuvant chemotherapy followed by hormonal therapy and radiation, as indicated.

RESULTS

HER2 amplification was found in 23.7% of the patients and TOP2A amplification in 10.1%. In total, 41.8% of HER2-amplified tumors demonstrated TOP2A co-amplification. The median (range) of HER2, TOP2A and CEP17 gain was 2.55 (0.70-45.15), 2.20 (0.70-26.15) and 2.00 (0.70-26.55), respectively. Forty percent of the tumors had CEP17 gain (51% of those with HER2 amplification). Adjusting for treatment groups in the Cox model, HER2 amplification, TOP2A amplification, CEP17 gain and HER2/TOP2A co-amplification were not associated with time to relapse or time to death.

CONCLUSION

HER2 amplification, TOP2A amplification, CEP17 gain and HER2/TOP2A co-amplification were not associated with outcome in high-risk breast cancer patients treated with anthracycline-based adjuvant chemotherapy.

TRIAL REGISTRATION

Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12611000506998 and ACTRN12609001036202.

Relation between deletion of chromosome 1p36 and DNA ploidy in breast carcinoma: an interphase cytogenetic study

Aims-To investigate whether deletion of the 1p36 region of chromosome 1 is independent of DNA ploidy in breast cancer cells.Methods-Preparations of nuclei from 64 fresh primary breast tumours were studied using dual target fluorescence in situ hybridisation (FISH) combining probes specific for the 1q12 (pUC 1.77) and 1p36 (1p-79) regions of chromosome 1. Signals were counted in 100-300 nuclei and the percentage of cells showing fewer p1-79 than pUC 1.77 signals was measured in each sample. DNA ploidy was investigated by cytofluorimetry in 55 tumour samples.Results-Chromosome 1 aberrations were detected in 56 samples. There were fewer p1-79 than pUC 1.77 signals in 53 samples. The 1p36 region was deleted in 11 samples in which a single p1-79 signal was detected; seven of these samples were diploid. Abnormalities were found in 17/24 diploid and 30/31 aneuploid tumours.Conclusions-Chromosome 1 aberrations, including deletion of the 1p36 region, were observed in diploid breast tumours. Deletion of the 1p36 region may be an early event in tumorigenesis. Given the frequency and importance of chromosome 1 aberrations in the biological behaviour of breast tumours, FISH, used in conjunction with cytofluorimetry, may be helpful for determining prognosis in patients with diploid tumours.

Breast cancer and aneusomy 17: implications for carcinogenesis and therapeutic response

Abnormalities of chromosome 17, recognised over two decades ago to be important in tumorigenesis, often occur in breast cancer. Changes of specific loci on chromosome 17 including ERBB2 amplification, P53 loss, BRCA1 loss, and TOP2A amplification or deletion are known to have important roles in breast-cancer pathophysiology. Numerical aberrations of chromosome 17 are linked to breast-cancer initiation and progression, and possibly to treatment response. However, the clinical importance of chromosome 17 anomalies, in particular the effect on ERBB2 protein expression, is unknown. Reports are conflicting regarding the association of copy gain of chromosome 17 (polysomy 17) with strong ERBB2 protein expression in the absence of true ERBB2 gene amplification. Copy-number anomalies in chromosome 17 seem to be common in tumours that show discrepant ERBB2 expression and in tumours with discordant ERBB2-protein and ERBB2 gene copy number measurements. The mechanisms of ERBB2 dosage changes-gene amplification versus chromosome gain and loss-probably differ in primary and metastatic disease; however, a correction for chromosome 17 copy-number is necessary to completely distinguish between these mechanisms. A better understanding of how polysomy 17 affects gene-copy number and protein expression will help to select patients who will respond to therapies targeting ERBB2 and other protein products of chromosome 17 loci.

High-resolution array CGH clarifies events occurring on 8p in carcinogenesis

Background

Rearrangement of the short arm of chromosome 8 (8p) is very common in epithelial cancers such as breast cancer. Usually there is an unbalanced translocation breakpoint in 8p12 (29.7 Mb – 38.5 Mb) with loss of distal 8p, sometimes with proximal amplification of 8p11-12. Rearrangements in 8p11-12 have been investigated using high-resolution array CGH, but the first 30 Mb of 8p are less well characterised, although this region contains several proposed tumour suppressor genes.

Methods

We analysed the whole of 8p by array CGH at tiling-path BAC resolution in 32 breast and six pancreatic cancer cell lines. Regions of recurrent rearrangement distal to 8p12 were further characterised, using regional fosmid arrays. FISH, and quantitative RT-PCR on over 60 breast tumours validated the existence of similar events in primary material.

Results

We confirmed that 8p is usually lost up to at least 30 Mb, but a few lines showed focal loss or copy number steps within this region. Three regions showed rearrangements common to at least two cases: two regions of recurrent loss and one region of amplification. Loss within 8p23.3 (0 Mb – 2.2 Mb) was found in six cell lines. Of the genes always affected, ARHGEF10 showed a point mutation of the remaining normal copies in the DU4475 cell line. Deletions within 12.7 Mb – 19.1 Mb in 8p22, in two cases, affected TUSC3. A novel amplicon was found within 8p21.3 (19.1 Mb – 23.4 Mb) in two lines and one of 98 tumours.

Conclusion

The pattern of rearrangements seen on 8p may be a consequence of the high density of potential targets on this chromosome arm, and ARHGEF10 may be a new candidate tumour suppressor gene.

Chromosome alterations associated with positive and negative lymph node involvement in breast cancer

Genetic heterogeneity is high in breast cancer, and hence it is difficult to link a specific chromosome alteration to a specific clinicopathologic feature. We examined clonal chromosome alterations in 45 breast carcinomas and statistically correlated the findings with clinical-histopathological parameters of the patients. The most common abnormalities were losses of chromosomes 19, 22, 21, X, and 17 and gains of chromosomes 9 and 18. A statistically significant correlation was found between clonal aberrations in chromosomes 17, 20, and 21 and positive lymph node involvement (LN+) and between clonal aberrations in chromosomes X and 6 and negative involvement (LN-). The average number of chromosome abnormalities was the same for both LN- and LN+ groups, and numerical and structural alterations were equally distributed. The mean number of chromosome aberrations did not differ significantly among tumor grades, but when aberrations were analyzed as monosomies, trisomies, and structural aberrations, a heterogeneous distribution was observed. Further cytogenetic investigation of breast tumors and their variable pathological features is undoubtedly necessary. The recognition and ultimately the molecular understanding of these abnormalities may improve breast cancer taxonomy and provide important prognostic information for both the patient and clinician.

Comparative oncogenomics identifies NEDD9 as a melanoma metastasis gene

Genomes of human cancer cells are characterized by numerous chromosomal aberrations of uncertain pathogenetic significance. Here, in an inducible mouse model of melanoma, we characterized metastatic variants with an acquired focal chromosomal amplification that corresponds to a much larger amplification in human metastatic melanomas. Further analyses identified Nedd9, an adaptor protein related to p130CAS, as the only gene within the minimal common region that exhibited amplification-associated overexpression. A series of functional, biochemical, and clinical studies established NEDD9 as a bona fide melanoma metastasis gene. NEDD9 enhanced invasion in vitro and metastasis in vivo of both normal and transformed melanocytes, functionally interacted with focal adhesion kinase and modulated focal contact formation, and exhibited frequent robust overexpression in human metastatic melanoma relative to primary melanoma. Thus, comparative oncogenomics has enabled the identification and facilitated the validation of a highly relevant cancer gene governing metastatic potential in human melanoma.

Gene expression profile of an adenomyoepithelioma of the breast with a reciprocal translocation involving chromosomes 8 and 16

Myoepithelium is an integral part of the mammary ductal and lobular architecture, positioned between luminal cells and the basement membrane. We describe the first report on cytogenetic findings in an adenomyoepithelioma of the breast with a balanced t(8;16)(p23;q21), and provide gene expression profile using Affymetrix GeneChip U95AV2 (Affymetrix, Santa Clara, CA). Differential analysis identified 857 genes with 2-fold or more mRNA change in comparison to pooled normal breast control; immunohistochemical analysis was used to confirm these results in a limited number of genes. Expression results were grouped based on the chromosomal location of the genes and associated protein function, and identified several potential pathogenetic mechanisms (autocrine and paracrine growth stimuli) in the development of myoepithelial tumors.

Ductal breast carcinoma develops through different patterns of chromosomal evolution

In a previous study that used comparative genomic hybridization (CGH) to analyze 43 ductal breast carcinomas selected for hyperdiploidy, we proposed the existence of two distinct pathways of chromosomal evolution. In the present study, in which we reassessed our cytogenetic findings on 158 ductal breast carcinomas selected for having a modal number of chromosomes of fewer than 60, we confirmed the existence of two subtypes of tumors. Along with the great majority of tumors (142 of 158) that evolved through structural rearrangements with no or very few whole-chromosome gains, we found that a minor subset (16 of 158) evolved through progressive gains of whole chromosomes with no or only a few associated rearrangements. In this article, we describe the karyotypes of these 16 tumors together with data from CGH, which was performed for 10 of them. Chromosomes 5, 7, 8, and 20 were the most frequently gained. Our findings support the evidence of a new pathway of chromosomal evolution in a small subset of ductal breast carcinomas characterized by numerical chromosome aberrations.

The acetyltransferase p300/CBP-associated factor is a p53 target gene in breast tumor cells

p300/CBP-associated factor (PCAF) is a coactivator of the tumor suppressor, p53. PCAF participates in p53's transactivation of target genes through acetylation of both bound p53 and histones within p53 target promoters. Using microarrays, we discovered that PCAF itself is induced by p53 in a panel of breast tumor cell lines. Two p53 mutant breast tumor cell lines, BT-549 and UACC-1179, were chosen for further study of PCAF induction by wild-type p53. PCAF induction following adenoviral transduction of p53 expression was confirmed with real-time polymerase chain reaction in a time course experiment. Chromatin immunoprecipitation experiments then showed that PCAF induction was associated with increased p53 binding to the PCAF promoter, which contains p53 consensus-binding sites. PCAF induction by p53 activity was further demonstrated in wild-type p53 MCF10A cells when PCAF expression was induced following activation of endogenous wild-type p53 with doxorubicin in a dose- and time-dependent manner. Furthermore, the doxorubicin-induced increase in PCAF expression was blocked by pretreatment of the MCF10A cells with siRNA (small interfering RNA) targeted against p53 mRNA. Taken together, the results show that PCAF expression can be induced by wild-type p53.

Molecular cytogenetic analysis of breast cancer: a combined multicolor fluorescence in situ hybridization and G-banding study of uncultured tumor cells

In six patients with breast cancer, uncultured tumor cells were investigated with G-banding and multicolor fluorescence in situ hybridization (M-FISH). A large number of numerical and structural aberrations could be analyzed. Among other structural abnormalities, reciprocal, hidden and complex translocations were found. Recurrent t(1;10) and t(6;16), not previously described, were identified, as well as t(15;22). The latter was also found in additional cases among our unpublished breast carcinomas. The significance of t(15;22) for breast cancer is discussed, taking into account also data drawn from the literature. Reciprocal translocations were a prominent feature in a pseudodiploid lobular carcinoma. Hidden translocations on 6p22-p24 were detected with M-FISH. Involvement of 6p22-p24 was observed in five cases. The analysis of various other translocations and different structural abnormalities revealed the following common breakpoints (according to frequency of involvement): 1p34-p36, 3p12-p13, 4p13-->q11, 14p11-->q11, 1q42, 8p11, 8q24, 10q22, 11q13, 11q23-q24, 13q13, and 18p10-p11. Loss of 3p and 1p34-p36-->pter and complete or partial loss of 13q and chromosome 17 were also found. With the combination of G-banding and M-FISH techniques, chromosome misclassification is avoided and the characterization of complex tumor karyotypes is more effective.

Detection of differentially expressed HES-6 gene in metastatic colon carcinoma by combination of suppression subtractive hybridization and cDNA library array

The molecular mechanisms involved in the progression of colon carcinomas from a primary to a metastatic tumor have been only partially elucidated and poorly understood. This study combines suppression subtractive hybridization and cDNA array hybridization to identify genes with expression differences between a primary human colon tumor cell line (HT29) and three isogenic lung tumor metastases. The positive clones isolated in this screen were further validated and quantitated with real-time reverse transcription polymerase chain reactions. HES-6 was identified as up-regulated in each of the individual tumor metastases, as well as in a panel of primary human tumors derived from the lung, breast and kidney. These findings demonstrate that it is possible to utilize longitudinal samples from an in vivo model of colon carcinoma to identify genes up-regulated in metastases and that HES-6 may be an important marker of a range of primary cancers as well as metastatic colon carcinoma.

Mutant p53 and aberrant cytosine methylation cooperate to silence gene expression

p53 is an important transcriptional regulator that is frequently mutated in cancer. Gene-profiling experiments of breast cancer cells infected with wt p53 revealed both MASPIN and desmocollin 3 (DSC3) to be p53-target genes, even though both genes are silenced in association with aberrant cytosine methylation of their promoters. Despite the transcriptional repression of these genes by aberrant DNA methylation, restoration of p53 resulted in the partial reactivation of both genes. This reactivation is a result of wt p53 binding to its consensus DNA-binding sites within the MASPIN and DSC3 promoters, stimulating histone acetylation, and enhancing chromatin accessibility of their promoters. Interestingly, wt p53 alone did not affect the methylation status of either promoter, suggesting that p53 itself can partially overcome the repressive barrier of DNA methylation. Pharmacologic inhibition of DNA methylation with 5-aza-2'-deoxycytidine in combination with restoration of wt p53 status resulted in a synergistic reactivation of these genes to near-normal levels. These results suggest that cancer treatments that target both genetic and epigenetic facets of gene regulation may be a useful strategy towards the therapeutic transcriptional reprogramming of cancer cells.

Episomally mediated overexpression of wild-type erbB-2 transforms MCF-10A breast epithelial cells

MCF-10A are human non-transformed, EGF and insulin dependent breast epithelial cells. The cells were transfected with an episomal pCEP4 vector library containing cDNA from SKBR3 breast carcinoma cells, and selected in media without EGF. After two cycles of expression cloning, morphologically transformed cells appeared. Extracted episomes contained a high proportion of erbB-2 cDNA with wild-type transmembrane domains. Transfection of MCF-10A with individual erbB-2 containing episomes induced significant foci formation in low serum (0.1%) without EGF. MCF-10A sublines expanded from these foci contained a high number of erbB-2 gene copies, highly expressed erbB-2, and lost E-cadherin expression. These results show that if wild-type erbB-2 is sufficiently overexpressed, erbB-2 alone can cause EGF independent transformation of these nonmalignant breast cells. This expression system may be useful for expression cloning in MCF-10A cells, and simulating the effects of high erbB-2 gene amplification in breast epithelial cells.

Reciprocal translocations in breast tumor cell lines: cloning of a t(3;20) that targets the FHIT gene

All molecular alterations that lead to breast cancer are not precisely known. We are evaluating the frequency and consequences of reciprocal translocations in breast cancer. We surveyed 15 mammary cell lines by multicolor fluorescence in situ hybridization (M-FISH). We identified nine apparently reciprocal translocations. Using mBanding FISH and FISH with selected YAC clones, we identified the breakpoints for four of them, and cloned the t(3;20)(p14;p11) found in the BrCa-MZ-02 cell line. We found that the breakpoint targets the potential tumor-suppressor gene FHIT (fragile histidine triad) in the FRA3B region; it is accompanied by homozygous deletion of exon 5 of the gene and absence of functional FHIT and fusion transcripts, which leads to the loss of FHIT protein expression. Additional experiments using comparative genomic hybridization provided further information on the genomic context in which the t(3;20)(p14;p11) reciprocal translocation was found.

Intragenic amplification and formation of extrachromosomal small circular DNA molecules from the PIP gene on chromosome 7 in primary breast carcinomas

The PIP gene is expressed in exocrine glands and, in pathologic conditions, in breast cysts and breast cancers exhibiting apocrine features. It is localized on the long arm of chromosome 7, a region frequently alterated in mammary tumors. We previously described an abnormal restriction pattern of the PIP gene in 33% of prostate carcinomas analyzed. Here, we analyze the structure of the PIP gene in primary breast carcinomas. We report that part of the 3' end, including exon 3, intron C, two-thirds of exon 4 and a small portion of intron B, is amplified and involved in the formation of extrachromosomal spcDNA molecules in 3/14 (21.4%) breast cancers analyzed. The involvement of a well-defined intragenic region of a gene in the formation of spcDNA appears to be unprecedented. Since spcDNA has been suggested to serve as an enhancer of genetic instability, the PIP gene may be the target of genomic variability processes in breast cancer.

Cytogenetic analysis and clinical significance in adult T-cell leukemia/lymphoma: a study of 50 cases from the human T-cell leukemia virus type-1 endemic area, Nagasaki

Identification of cytogenetic abnormalities is an important clue for the elucidation of carcinogenesis. However, the cytogenetic and clinical significance of adult T-cell leukemia/lymphoma (ATLL) is still unclear. To address this point, cytogenetic findings in 50 cases of ATLL were correlated with clinical characteristics. Karyotypes showed a high degree of diversity and complexity. Aneuploidy and multiple breaks (at least 6) were observed frequently in acute and lymphoma subtypes of ATLL. Breakpoints tended to cluster at specific chromosomal regions, although characteristic cytogenetic subgroups of abnormalities were not found. Of these, aberrations of chromosomes 1p, 1q, 1q10-21, 10p, 10p13, 12q, 14q, and 14q32 correlated with one or more of the following clinical features: hepatosplenomegaly, elevated lactate dehydrogenase, hypercalcemia, and unusual immunophenotype, all indicators of clinical severity of ATLL. Multiple breaks (at least 6); abnormalities of chromosomes 1p, 1p22, 1q, 1q10-21, 2q, 3q, 3q10-12, 3q21, 14q, 14q32, and 17q; and partial loss of chromosomes 2q, 9p, 14p, 14q, and 17q regions correlated with shorter survival. These cytogenetic findings are relevant in predicting clinical outcome and provide useful information to identify chromosomal regions responsible for leukemogenesis. This study also indicates that one model of an oncogenic mechanism, activation of a proto-oncogene by translocation of a T-cell–receptor gene, may not be applicable to the main pathway of development of ATLL and that a multistep process of leukemogenesis is required for the development of ATLL.

Differences in genetic alterations between primary lobular and ductal breast cancers detected by comparative genomic hybridization

Infiltrating ductal (DC) and lobular carcinoma (LC) of the breast represent the most frequently observed varieties of invasive breast cancer, characterized by differences in their histological and clinical properties. Although comparative genomic hybridization (CGH) of invasive breast carcinomas has revealed a complex and consistent pattern of DNA copy number changes, the data with regard to type specific aberrations are limited. A comprehensive study was therefore performed on 19 LCs and 29 DCs to ascertain type-specific differences of unbalanced DNA copy number changes by CGH. Statistical analysis revealed significantly higher frequencies for underrepresentation of chromosomes 16q (p<0.01), 22 (p<0.05), and 17q (p<0.05), and a lower frequency for overrepresentation of chromosome 8q (p<0.01) in LC. Similar frequencies of non-random chromosomal changes in LC and DC were obtained for gain of 1q (74%/59%) and loss of 19p (53%/52%), parts of 1p (42%/41%) and 11q (21%/24%). Less frequently, gains mainly involving parts of chromosomes 20q, 20p, 3q, and 5p and partial losses of chromosomes 17p and 13 were observed in both groups of tumours. Minimal regions of overlapping amplifications were mapped to 17q23 exclusively in DC (17%) and 11q13-q14 in both DC and LC (21% and 11%, respectively). High occurrences of DNA copy number decreases were detected at the distal part of chromosomes 1p, 19 and 22, but further analysis is required to confirm these imbalances. It is suggested that the observed differences are involved in the development of type-specific properties of DC and LC.

Transcriptional repression of BRCA1 by aberrant cytosine methylation, histone hypoacetylation and chromatin condensation of the BRCA1 promoter

BRCA1 expression is repressed by aberrant cytosine methylation in sporadic breast cancer. We hypothesized that aberrant cytosine methylation of the BRCA1 promoter was associated with the transcriptionally repressive effects of histone hypoacetylation and chromatin condensation. To address this question, we developed an in vitro model of study using normal cells and sporadic breast cancer cells with known levels of BRCA1 transcript to produce a 1.4 kb 5-methylcytosine map of the BRCA1 5' CpG island. While all cell types were densely methylated upstream of -728 relative to BRCA1 transcription start, all normal and BRCA1 expressing cells were non-methylated downstream of -728 suggesting that this region contains the functional BRCA1 5' regulatory region. In contrast, the non-BRCA1 expressing UACC3199 cells were completely methylated at all 75 CpGs. Chromatin immunoprecipitations showed that the UACC3199 cells were hypoacetylated at both histones H3 and H4 in the BRCA1 promoter compared to non-methylated BRCA1 expressing cells. The chromatin of the methylated UACC3199 BRCA1 promoter was inaccessible to DNA-protein interactions. These data indicate that the epigenetic effects of aberrant cytosine methylation, histone hypoacetylation and chromatin condensation act together in a discrete region of the BRCA1 5' CpG island to repress BRCA1 transcription in sporadic breast cancer.

Cytogenetic analysis of invasive breast cancer: a study of 27 Asian patients

Tumor cytogenetic analysis from 27 patients with breast cancer diagnosed at the Singapore General Hospital revealed complex karyotypic aberrations in 12 cases. The study group comprised 25 women and 2 men, ranging in age from 33 to 78 years (median 52 years). Ethnic distribution consisted of 22 Chinese, 3 Malaysian, and 2 Indian patients. Pathologic assessment disclosed 24 invasive ductal, 2 invasive mucinous, and 1 mixed invasive mucinous and ductal carcinomas. Histologic grading showed 3 grade 1, 10 grade 2, and 12 grade 3 tumors; 2 cancers were not graded, because they had been subjected to prior chemotherapy. Tumor sizes ranged from 1.5 to 10 cm (median 3 cm). Eleven cases were axillary node negative, whereas the remaining 16 node-positive cancers affected as many as 3 nodes in 8 cases and 4 or more nodes in another 8. Twenty cases demonstrated estrogen-receptor positivity, and 8 cases progesterone-receptor positivity. The spectrum of cytogenetic abnormalities involved chromosomes 1, 3, 6, 7, 8, 11, 16, and 17 and ranged from gains and deletions of both long and short arms, trisomy, monosomy, and other rearrangements. There was a trend toward the presence of karyotypic abnormalities in tumors of higher grade.

Allelic loss in chromosomal region 1q21-23 in breast cancer is associated with peritumoral angiolymphatic invasion and extensive intraductal component

AIMS

Breast cancer is the most frequent cancer in the female population and the involvement of chromosomal alterations is often implicated in the development of cancer. The aim of our study was to assess loss of heterozygosity (LOH) in chromosome 1 in relation to clinical and pathological parameters.

METHODS

Tumours, corresponding normal tissues and peripheral blood samples from 50 women with operable breast cancer, were analysed by polymerase chain reaction (PCR) at 16 polymorphic DNA markers, on both the long and short arm of chromosome 1.

RESULTS

There was a significant correlation between chromosomal region 1q21-23 and the presence of extensive intraductal component (EIC) and peritumoral angiolymphatic (PALI) invasion, both independent markers of local recurrence.

CONCLUSIONS

Allelic loss in region 1q21-23 may be a valuable prognostic biological marker for the detection of local relapse in breast cancer, in combination with other histological and clinical parameters.

Evaluation of numerical abnormalities of chromosomes 1 and 17 in proliferative epithelial breast lesions using fluorescence in situ hybridization

Our aim was to investigate the putative role of chromosome abnormalities of chromosomes 1 and 17 in the process of breast carcinogenesis. Numerical abnormalities of chromosomes 1 and 17 were investigated using fluorescence in situ hybridisation (FISH) in a series of 16 primary invasive breast carcinomas associated with intraductal proliferative epithelial lesions. Chromosome 1 aneusomy was detected in 55.6% of ductal hyperplasia (DH), 81.8% of ductal carcinomas in situ (DCIS) and 87.5% of invasive ductal carcinomas (IDC). Chromosome 17 aneusomy was not detected in the cases of DH and was present in 90.9% of DCIS and in 87.5% of IDC. Simultaneous aneusomy of chromosome 1 and 17 was found in 81.8% of DCIS and in 75.0% of IDC. Our results showed that the number of chromosome 1 and 17 copies increases from normal epithelium to invasive cancer. The numerical abnormalities of chromosome 1 were already detected in DH, suggesting that a gain in the copy number of chromosome 1 may be involved early in breast carcinogenesis.

Chromosome translocations in breast cancer with breakpoints at 8p12

Unbalanced chromosome translocations with breakpoints around 8p12, resulting in loss of distal 8p, are common in carcinomas. We have mapped the 8p12 breakpoints in three breast cancer cell lines, T-47D, MDA-MB-361, and ZR-75-1, using YACs and PACs between D8S540 and D8S255 by fluorescence in situ hybridization. All three lines had a breakpoint close to D8S505, proximal to HGL. Each breakpoint was distinct, but all were within 0.5 to 1.5 Mb of each other. The T-47D cell line had a straightforward translocation, but in MDA-MB-361 and ZR-75-1 the translocations were accompanied by local rearrangements of surprising complexity. Small regions of 8p from close to the breakpoint were duplicated or amplified as inserts in the attached chromosome fragment. ZR-75-1 also had retained a separate fragment of about 1 Mb, from the region 1 to 3 Mb telomeric to the common breakpoint, that included HGL. This line also had an interstitial deletion several megabases more centromeric. The data suggest that breakpoints on 8p12 are clustered in a small region and show that translocations breaking there may be accompanied by additional rearrangements.

Epigenetic silencing of maspin gene expression in human breast cancers

Maspin is a tumor suppressor whose expression is lost in many advanced breast cancers. Maspin has been shown to inhibit cell motility, invasion and metastasis; however, its precise role in normal mammary epithelium remains to be elucidated. Although expression of maspin mRNA is low or absent in most human breast cancer cells, the maspin gene is rarely re-arranged or deleted. We hypothesized that aberrant cytosine methylation and chromatin condensation of the maspin promoter participates in the silencing of maspin expression during neoplastic progression. To test this hypothesis, we compared cultured normal human mammary epithelial cells (HMECs) to 9 cultured human breast cancer cell lines. HMECs expressed maspin mRNA and displayed a completely non-methylated maspin gene promoter with an open chromatin structure. In contrast, 7 of 9 breast cancer cell lines had no detectable maspin expression and 6 of these 7 maspin-negative breast cancer cell lines also displayed an aberrant pattern of cytosine methylation of the maspin promoter. Interestingly, the maspin promoter was completely methylated in maspin-negative normal peripheral blood lymphocytes. This indicates that the maspin promoter is not a functional CpG island and that cytosine methylation of this region may contribute to normal tissue-restricted gene expression. Chromatin accessibility studies with MCF-7 cells, which lack maspin expression and have a methylated maspin promoter, showed a closed chromatin structure compared with HMECs. Moreover, maspin gene expression could be re-activated in MCF-7 cells by treatment with 5-aza-2;-deoxycytidine, a DNA demethylating agent. Thus, aberrant cytosine methylation and heterochromatinization of the maspin promoter may silence maspin gene expression, thereby contributing to the progression of human mammary cancer.

Gene therapy for carcinoma of the breast: Genetic ablation strategies

The gene therapy strategy of mutation compensation is designed to rectify the molecular lesions that are etiologic for neoplastic transformation. For dominant oncogenes, such approaches involve the functional knockout of the dysregulated cellular control pathways provoked by the overexpressed oncoprotein. On this basis, molecular interventions may be targeted to the transcriptional level of expression, via antisense or ribozymes, or post-transcriptionally, via intracellular single chain antibodies (intrabodies). For carcinoma of the breast, these approaches have been applied in the context of the disease linked oncogenes erbB-2 and cyclin D1, as well as the estrogen receptor. Neoplastic revision accomplished in modal systems has rationalized human trials on this basis.

Frequent multiplication of chromosome 1q in non-invasive and papillotubular carcinoma of the breast

Carcinogenesis is considered to be a multistep process that may involve cumulative genetic alterations; one of these mechanisms, gain of chromosomal material, has the potential to activate tumor-promoting genes in breast carcinogenesis. Using 12 polymorphic microsatellite markers on the long arm of chromosome 1 (1q), we examined 130 sporadic breast carcinomas for abnormalities in the copy numbers of these loci in tumor cells using a differential PCR method. We also sought correlations between alterations on 1q and several clinicopathological parameters. At every locus examined, a 2-3-fold increase in copy number of an allele in tumor material was observed in one third of the tumors (46 of 130, 35%), indicating 'multiplication' of 1q. This multiplication involved the entire long arm in majority of those tumors (43 cases, 93%). The multiplication of 1q was observed more frequently in non-invasive ductal and papillotubular histological types than in solid-tubular and scirrhous types (13/25, 52% vs. 27/90, 30%) (P = 0.041). The predominant chromosomal alterations on 1q in breast carcinomas are found to be multiplications rather than losses. The multiplication represents polysomy of the entire region of 1q, and may confer a growth advantage during development and/or progression of non-invasive ductal and papillotubular histologic types of breast carcinomas.

Genetic analysis of 53 lymph node-negative breast carcinomas by CGH and relation to clinical, pathological, morphometric, and DNA cytometric prognostic factors

Within the subgroup of lymph node-negative breast cancers, there is a need for accurate prognostic indicators to select high-risk patients. Comparative genomic hybridization (CGH) provides an opportunity to screen the whole genome for chromosomal aberrations which may be associated with poor clinical outcome. The results of CGH analysis of 53 lymph node-negative breast carcinomas are presented and correlated with a set of clinico-pathological and cytometric features with strong prognostic value. The most frequent chromosomal gains were, in descending order of frequency, 8q, 1q, Xq, 5q, 4q, and 3q. Recurring losses were observed at chromosomal arms 19p, 1p, 17p, 22q, 4q, and 8p. There was not a single, unique combination of chromosomal aberrations, but gains of 1q and 8q were frequently observed simultaneously (15/53 cases). DNA aneuploid tumours harboured more gains than DNA diploid tumours, but there was no correlation between the total number of events per tumour detected by CGH and any of the prognostic features. Of the many chromosomal aberrations found, only gains of chromosome 8q were strongly correlated with high values of mean nuclear area. A clearer picture was obtained when comparing only those cases which, according to their cytometric and morphometric features, had either the worst or the best prognosis. Gains occurred mainly in the 'poor prognostic features' group, in particular at 8q, 11q13, 17q, and 20q. It is hypothesized that these gains could be late, progression-related events and may be associated with aggressive clinical behaviour. These four chromosomal regions may therefore be of potential prognostic value. Correlation with real follow-up data will enable us better to identify those patients who have a high risk of recurrence within the subgroup of lymph node-negative breast cancer patients.

Unusual presentation of multiple myeloma with "jumping translocation" involving 1q21. A case report and review of the literature

We describe a case of multiple myeloma with unusual manifestations consisting of cutaneous xanthomatosis, temporal arteritis, retinal vasculitis with a complex karyotype, and a "jumping translocation" involving 1q21. The literature of cytogenetic studies of multiple myeloma and of jumping translocation is reviewed.

Cytogenetic findings in invasive breast carcinomas with prognostically favourable histology: a less complex karyotypic pattern?

Seventeen invasive primary breast carcinomas of histological types usually considered to be prognostically favourable (2 medullary, 3 papillary, 3 tubular, and 9 mucinous carcinomas) were analysed as part of an ongoing study of the cytogenetics of breast cancer. Thirteen of the tumours (7 mucinous, 2 medullary, 2 papillary, and 2 tubular carcinomas) showed clonal chromosome aberrations. Trisomy 7 and i(1q) were present as sole and recurrent aberrations in the mucinous tumours. The 2 tubular carcinomas and I papillary carcinoma had simple numerical changes only, whereas the second papillary tumour had a balanced translocation as the sole anomaly. Both medullary carcinomas had chromosome numbers in the triploid range, with clones displaying structural and numerical changes. Our data, especially when collated with information on previously published cases of mucinous, papillary, tubular, and medullary breast carcinomas, show that the former 3 histological types, in keeping with their recognised prognostic advantage, appear to exhibit relatively simple karyotypic changes, i.e., numerical aberrations, balanced translocations, and near-diploid chromosome numbers. Medullary carcinomas on the other hand, appear to have more complex karyotypes, similar to those described for the more common ductal and lobular subtypes of breast carcinoma.

Detection of numerical chromosome 17 abnormalities in fine-needle aspirates of breast cancer using a novel in situ hybridization signal amplification method

We describe a method of in situ hybridization (ISH) to assess numerical chromosome abnormalities on alcohol-fixed smears obtained by fine-needle aspiration from breast cancer patients, using a commercially available amplification kit to demonstrate numerical chromosome alterations of chromosome 17. In this staining procedure after detection of the biotin-labeled alpha-satellite probe for chromosome 17 with avidin-biotin-peroxidase, we incorporated a signal amplification based on the peroxidase-catalyzed deposition of a biotinylated phenolic compound followed by a secondary reaction with peroxidase. The reactions are revealed by deposition of diaminobenzidine and can be analyzed in an optical microscope, with total preservation of the morphology, allowing a direct morphologic-cytogenetic correlation. A series of 25 cases of aspirates from breast cancer were analyzed with this methodology. Aneusomy was found in 14 cases (56%), whereas 11 (44%) had a normal number of chromosome 17 copies. Polysomy occurred in all aneusome cases except one. We did not find concordance between numerical chromosome abnormalities of chromosome 17 and nuclear grading as well as with the immunoexpression of p53 and c-erbB2 studied in the smears. We conclude that the application of the ISH signal amplification method on alcohol-fixed smears will eliminate the need for fresh material and will provide several advantages, such as improvement of morphological concomitant analysis without the need for a fluorescence microscope; utilization, whenever malignancy is found, without necessity to reaspirate the patient; and adequacy of archival material.

Structural cues from the tissue microenvironment are essential determinants of the human mammary epithelial cell phenotype

Historically, the study of normal human breast function and breast disorders has been significantly impaired by limitations inherent to available model systems. Recent improvements in human breast epithelial cell lines and three-dimensional (3-D)3 culture systems have contributed to the development of in vitro model systems that recapitulate differentiated epithelial cell phenotypes with remarkable fidelity. Molecular characterization of these human breast cell models has demonstrated that normal breast epithelial cell behavior is determined in part by the precise interplay that exists between a cell and its surrounding microenvironment. Recent functional studies of integrins in a human model system provide evidence to support the idea that the structural stability afforded by integrin-mediated cell-extracellular matrix interactions is an important determinant of normal cellular behavior, and that alterations in tissue structure can give rise to tumorigenic progression.

Near haploidy in breast cancer: a particular pathway of chromosome evolution

In a series of 260 cytologically abnormal breast cancers studied in our laboratory, we observed a single case of near-haploid karyotype: 27,X, +der(1;16)(q10;p10), +7, +14, +15. A review of published cases of near-haploid malignancies suggests that near haploidy belongs to a process of chromosome evolution distinct from that of most epithelial cancers in which hypodiploidy is strongly associated with the occurrence of unbalanced structural rearrangements. In near-haploid tumors, chromosome loss is independent from chromosome rearrangements and may not be associated with an adverse prognosis.

Cytogenetic evaluation of 20 primary breast carcinomas

Chromosome analysis was performed on samples from 20 Brazilian patients with breast cancer. All the samples were from untreated patients who presented the clinical symptoms for months or years before surgical intervention. Six cases showed axillary lymph node metastases. Clonal chromosome abnormalities were detected in all cases. The numerical alterations most frequently observed involved the loss of chromosomes X, 19, 20, and 22 followed by gain of chromosomes 9 and 8. Among the structural anomalies observed, there was preferential involvement of chromosomes 11, 6, 1, 7, 3, and 12, supporting previous reports that these chromosomes may harbour genes of importance in the development of breast tumors. Two cases with a family history of breast cancer had in common total or partial trisomy 1.

A gene dosage effect is responsible for high overexpression of the MUC1 gene observed in human breast tumors

Alterations of the entire long arm of chromosome 1 are the most consistent cytogenetic abnormalities found in human breast carcinoma. Overexpression of a large number of genes, because of acquisition of additional copies of one arm or a whole chromosome, is one possible cause of the imbalance in cell metabolism. To investigate the existence of such a gene dosage effect in breast cancer, we chose to study the MUC1 mucin gene located at 1q21-q24. This gene is highly expressed in breast tumors, but the genetic mechanism for its ectopic overexpression is not clearly known. Thirty-two human primary breast tumors were examined, by Southern blot DNA and northern blot RNA analyses, for allelic dosage and expression of the MUC1 gene. A correlation was found between acquisition of additional copies of MUC1 gene and high mRNA levels (p < 0.0001). These results identify a genetic mechanism responsible for MUC1 gene overexpression and support the hypothesis that a gene dosage effect of the long arm of chromosome 1 may be involved in the pathogenesis of breast cancer.

Cytogenetic analysis of three breast carcinoma cell lines using reverse chromosome painting

Chromosome painting was used to determine the copy number and identity of virtually all the chromosomes in three breast cancer cell lines, T-47D, MDA-MB-361, and ZR-75-1. The karyotypes of all three cell lines were very complex, and were consistent with the monosomic pattern of evolution suggested by Dutrillaux, in which nonreciprocal translocations cause an initial reduction in chromosome number, followed by duplication of the entire genome and further chromosome loss. Twenty distinct abnormal chromosomes were identified in T-47D, seven of which were present as two copies. MDA-MB-361 had 27 abnormal chromosomes each as a single copy. Thirteen abnormal chromosomes in ZR-75-1 occurred singly, two were paired, and one was present as three copies. Most of the aberrant chromosomes were nonreciprocal translocations, although deletions, duplications, isochromosomes, and amplifications (HSR of 1q) were also found. Chromosome arms present in abnormal chromosomes in all three lines were 1q, 6p, 7p, 8p, 8q, 10q, 11p, 11q, 12p, 13q, 14q, 15q, 16p, 16q, 17q, and 20q. The only chromosome arms present in four or more copies in all three lines were 8q and proximal 12p, while 1p, 17p, and bands 11q12--13 were the only chromosome regions consistently reduced to two copies. The most striking feature common to all three lines was a translocation breakpoint on the short arm of chromosome 8 at 8p12.

Molecular genetics and cytogenetics of breast carcinomas: comparison of the two methods

Molecular genetics and cytogenetics are two different approaches to studying genetic changes in breast carcinoma. We have used karyotype analysis, fluorescence in situ hybridization, and molecular analysis of allelic imbalance on chromosomes 7q and 16q and on both arms of chromosome 17, to study 85 breast carcinomas. Twenty-five of these samples gave results that could be used to compare the two methods. Sixty-nine chromosome arms were compared, of which 48 (70%) gave concordant molecular and cytogenetical results. Samples were processed for karyotyping both by harvesting directly from the fresh tissue and after selective culture for a few days. Karyotypes among the direct harvest samples matched significantly better with the molecular genetics results than karyotypes among the cultured cell preparations.