Pericentromeric Probes For Chromosomes Research Articles

Abstract 810: Amplification of 8q21 in breast cancer is independent of MYC and associated with poor patient outcome

Abstract Introduction Copy number gains involving the long arm of chromosome 8 including high-level amplifications at 8q21 and 8q24 have been reported in up to 60% of breast cancers. While the role of the MYC gene is well established, the significance of the 8q21 amplicon is less clear. The aim of our study was to analyze 8q21 amplification in a large set of breast cancers with clinical follow up data. Experimental procedures The breast cancer tissue microarray used for this study contains a total of 2.197 tumors and has been described in detail. A fluorescence in situ hybridization (FISH) probe was generated from genomic clone RZPDB737E022003D (imaGenes GmbH, Germany) that maps to the centre of the 8q21 amplicon as previously described in the SK-BR-3 breast cancer cell line. The probe contains the entire TMEM70 gene (transmembrane protein 70) and locates 4 kb downstream from TCEB1 (transcription elongation factor B, polypeptide 1), amplification of which was recently described in prostate cancer. A commercially available pericentromeric probe for chromosome 8 was used as reference (CEP 8Z2 SpectrumOrange, Vysis Inc.). A tumor was considered amplified if the ratio of 8q21/centromere 8 was ≥2.0. Ratios >1.0 and <2.0 had been considered as gains and a ratio ≤1.0 as normal. Results A total of 1458 (66.4%) of arrayed cancer samples were assessable by FISH. Copy number alterations of the 8q21 locus were found in 157 (10.7%) interpretable breast cancers, including amplification in 50 (3.4%) tumors and gains in 107 (7.3%). Amplification at 8q21 was associated to high tumor grade (p=0.042). There was no association between aberrations of the 8q21 locus and tumor stage, presence of lymph node metastases or estrogen receptor status (p>0.05 each). Data on MYC amplification were available from a previous study. A combined analysis of MYC and 8q21 identified 90 tumors with amplifications of MYC and/or 8q21. Of these, 28 tumors were amplified for 8q21 only and 54 for MYC only. Co-amplification of both genes was found in the remaining eight tumors. 8q21 amplification was strongly linked to adverse prognosis (hazard ratio 2.18, confidence interval 1.36 to 3.46, p=0.001). There was no impact of 8q21 gains on patient survival (p=0.48). However, a multivariate Cox analysis did not reveal an independent prognostic value of 8q21 amplification (p=0.23). Conclusions In summary, amplification of 8q21 occurs in a subgroup of breast carcinomas with poor prognosis. Copy number changes of 8q21 are independent from MYC and represent a separate amplicon in this chromosomal region. TMEM70 and the close TCEB1 gene in the centre of the 8q21 amplicon are the most likely possible candidate driver genes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 810.

Assessment of chromosomal gains as compared to DNA content changes is more useful to detect dysplasia in Barrett's esophagus brush cytology specimens

Abnormal DNA ploidy status has been suggested as a prognostic factor for Barrett's esophagus progression into esophageal adenocarcinoma (EAC). The aim of the study was to compare image cytometry DNA analysis (ICDA) and fluorescent in situ hybridization (FISH) in the assessment of DNA ploidy status in Barrett's esophagus (BE), and to determine the value of these abnormalities as an adjunct to conventional cytology in detection of dysplasia and EAC. Brush cytology specimens of 90 BE patients were examined using ICDA and FISH with peri-centromeric probes for chromosomes 7 and 17. The results of ICDA and FISH were compared with each other, and with dysplasia grade or EAC as determined by histology and cytology. FISH and ICDA detected abnormalities in 41% (37/90) and 22% (19/90) of the BE cases, respectively. Gains of chromosome 7 and/or 17 were present in 13% of nondysplasia cases, which further increased with dysplasia stage, while overall DNA content aneuploidy was detected predominantly in high grade dysplasia (HGD) and EAC. Using FISH results combined with cytology, we were able to identify IND/LGD (indefinite/ low grade dysplasia) with a sensitivity and specificity of 75 and 76%, respectively. FISH alone detected HGD/EAC with a high sensitivity and specificity of 85 and 84%, which was superior to that of cytology alone. Thus, FISH is more sensitive than ICDA to detect chromosomal abnormalities in BE brush cytology specimens. FISH detects chromosomal gains in early stages of BE and represents a valuable adjunct to conventional cytology to detect dysplasia or EAC.

Basal keratinocyte tetrasomy in low-grade squamous intra-epithelial lesions of the cervix is restricted to high and intermediate risk HPV infection but is not type-specific.

Human papillomavirus (HPV) infection appears to be an early event in cervical carcinogenesis with additional abnormalities being required for biological transformation. We have analysed 179 low-grade cervical squamous intra-epithelial lesions (SILs) and 15 normal cervices for the presence of HPV using both in situ hybridization and polymerase chain reaction (PCR). PCR was performed with GP5+/GP6+ primers followed by hybridization using probes for low (HPV 6, 11, 40, 42, 43, 44), intermediate (HPV 31, 33, 35, 39, 51, 52, 58, 59, 66 and 68) and high-risk HPVs (HPV 16, 18, 45 and 56). Interphase cytogenetic analysis using pericentromeric probes for chromosomes 1, 3, 4, 6, 10, 11, 17, 18 and X was also performed to identify numerical chromosomal abnormalities. Tetrasomy of all nine chromosomes was identified within basal keratinocytes, was restricted to epithelia infected with high risk (17 of 46) or intermediate risk (23 of 83) HPVs but was not HPV type-specific. Tetrasomy was not identified in any of the epithelia infected with low risk HPVs (n = 62). These numbers include multiple infection. These findings indicate that the induction of tetrasomy is a property restricted to high and intermediate-risk HPV types but that it is not type-specific. The factors governing which lesions will develop this abnormality are as yet unclear. © 2000 Cancer Research Campaign

Chromosomal aberrations in transitional cell carcinoma that are predictive of disease outcome are independent of polyploidy.

To determine whether aneusomy for chromosomes 7, 9 and 17 (reported to predict recurrence in up to 65% of patients with superficial transitional cell bladder cancer and thus providing the opportunity for early and effective treatment) reflects specific genetic events on these chromosomes or merely wider unspecific genetic damage to the cell, e.g. that increased copy numbers for 7 and 17 reflect tumour polyploidy. The study comprised 25 primary tumours; 6 microm thick sections from formalin-fixed and paraffin-embedded tumours were analysed. Chromosome copy numbers were determined by fluorescence in situ hybridization (FISH) using pericentromeric probes for chromosomes 7, 8, 9, 10, 11 and 17. A minimum of 200 nuclei per tumour area were scored by two independent observers. Eight of the 25 tumours examined (32%) showed no evidence of chromosomal abnormalities as detected by FISH for any chromosomes analysed. Twelve tumours (48%) showed abnormalities for one or two chromosomes, five tumours (20%) showed abnormalities for multiple chromosomes and one tumour showed abnormalities for all chromosomes analysed, suggestive of polyploidy. Chromosomal abnormalities predictive of recurrence occur largely in the absence of other gross chromosomal lesions. In a small proportion of cases other chromosomes are affected, but this is almost always distinct from tumour polyploidy.

Is Chromosome 9 Loss a Marker of Disease Recurrence in Transitional Cell Carcinoma of the Urinary Bladder?

Investigation of transitional cell carcinoma of the urinary bladder (TCC) patients classified by recurrence and/or progression has demonstrated that loss of chromosome 9, as detected by FISH analysis of the pericentromeric classical satellite marker at 9q12, occurs early. A total of 105 TCCs from 53 patients were analysed in situ by two independent observers for loss of chromosome 9 using quantitative fluorescence in situ hybridization (FISH). All 53 primary tumours were evaluated for chromosomes 9, 7 and 17. Normal ranges for chromosomal copy number were defined for normal skin epidermis and bladder epithelium. Values for chromosome 9 copy number outwith the range 1.51-2.10 (mean +/- 3 x s.d. of normal values) were significantly abnormal. Twenty-five TCCs were detected with consistent monosomic scores. Of 89 TCCs, in which multiple tumour areas were analysed, 85 tumours (96%) demonstrated the same chromosome 9 copy number in all areas (2- 6) analysed; only three tumours demonstrated heterogeneity for this locus. A total of 36% (12 out of 33) of patients with subsequent disease recurrence demonstrated loss of chromosome 9 in their primary and all subsequent TCCs analysed. Only a single patient (n = 20) with non-recurrent TCC showed loss of chromosome 9 (P = 0.0085). Of 53 primary tumours, eight showed significant elevation of chromosome 17. Of these patients, six demonstrated elevation in chromosome 7 copy number. No abnormalities were observed in non-recurrent patients. This study describes rapid quantitation of chromosomal copy number by FISH using a pericentromeric probe for chromosome 9 in TCC of the urinary bladder. Routinely fixed and processed material was evaluated without disaggregation. Strict quality control of FISH demonstrated that this technique was reproducible in a clinical environment and could be used to detect genetic changes relevant to patient outcome. It is proposed that loss of chromosome 9 from primary TCC of the urinary bladder identified patients at high risk of recurrence and possible progression.

Chromosome 7 Abnormalities in Prostate Cancer Detected by Dual-Color Fluorescence In Situ Hybridization

Aneusomy of chromosome 7 and loss at 7q (especially 7q31.1) have been reported in prostate cancer. To further investigate abnormalities of 7q and the relationship with whole chromosome 7 changes, we have conducted a dual-color fluorescence in situ hybridization (FISH) analysis on isolated nuclei from 28 primary prostate cancers. A pericentromeric probe for chromosome 7, five newly isolated sequence-specific bacterial artificial chromosome (BAC) probes from 7q31.1, and one BAC for the epidermal growth factor receptor (EGFR) gene at 7p12 were used in dual color hybridizations. Pericentromeric probes for chromosomes X and 4 were also used as controls. Sixteen (57.1%) of the 28 tumors showed clonal aberrations. Nine of them were trisomy 7 and four were hypertetrasomy for chromosome 7. Deletions at 7q31.1 were found in two of the high grade tumors. With the exception of these two cases, all other cases showed concordant results using all probes. These findings confirm previous studies that aneusomy of 7 is associated with prostate cancer progression, and there may be a tumor suppressor gene (TSG) at 7q31.1 which is associated with tumor progression. In addition, our study indicates: (1) the deletion pattern of individual nuclei infers that deletions at 7q31.1 precede reduplications of chromosome 7; and (2) the amplification of EGFR was not detected at the DNA level, suggesting that activation of this oncogene may play a minor role in prostate cancer.

Is chromosome 9 loss a marker of disease recurrence in transitional cell carcinoma of the urinary bladder?

Investigation of transitional cell carcinoma of the urinary bladder (TCC) patients classified by recurrence and/or progression has demonstrated that loss of chromosome 9, as detected by FISH analysis of the pericentromeric classical satellite marker at 9q12, occurs early. A total of 105 TCCs from 53 patients were analysed in situ by two independent observers for loss of chromosome 9 using quantitative fluorescence in situ hybridization (FISH). All 53 primary tumours were evaluated for chromosomes 9, 7 and 17. Normal ranges for chromosomal copy number were defined for normal skin epidermis and bladder epithelium. Values for chromosome 9 copy number outwith the range 1.51-2.10 (mean +/- 3 x s.d. of normal values) were significantly abnormal. Twenty-five TCCs were detected with consistent monosomic scores. Of 89 TCCs, in which multiple tumour areas were analysed, 85 tumours (96%) demonstrated the same chromosome 9 copy number in all areas (2-6) analysed; only three tumours demonstrated heterogeneity for this locus. A total of 36% (12 out of 33) of patients with subsequent disease recurrence demonstrated loss of chromosome 9 in their primary and all subsequent TCCs analysed. Only a single patient (n = 20) with non-recurrent TCC showed loss of chromosome 9 (P = 0.0085). Of 53 primary tumours, eight showed significant elevation of chromosome 17. Of these patients, six demonstrated elevation in chromosome 7 copy number. No abnormalities were observed in non-recurrent patients. This study describes rapid quantitation of chromosomal copy number by FISH using a pericentromeric probe for chromosome 9 in TCC of the urinary bladder. Routinely fixed and processed material was evaluated without disaggregation. Strict quality control of FISH demonstrated that this technique was reproducible in a clinical environment and could be used to detect genetic changes relevant to patient outcome. It is proposed that loss of chromosome 9 from primary TCC of the urinary bladder identified patients at high risk of recurrence and possible progression.

Chromosomal Anomalies in Stage D1 Prostate Adenocarcinoma Primary Tumors and Lymph Node Metastases Detected by Fluorescence in Situ Hybridization

We determined if characteristic chromosomal anomalies exist within the primary tumors and lymph node metastases in patients with stage D1 prostate cancer, and compared the patterns of chromosomal alterations between primary tumors and nodal metastases. Fluorescence in situ hybridization analysis using peri-centromeric probes for chromosomes 6, 7, 8, 17, X and Y was performed on 5 mu. sections from paraffin embedded tissue blocks obtained from 23 consecutive patients who underwent radical prostatectomy and bilateral pelvic lymphadenectomy in 1990 for stage D1 prostate cancer. The dominant focus of primary tumor was compared to matched nodal metastases in 12 cases. Five of 12 primary tumor foci (41.7%) had similar chromosomal gains and the same fluorescence in situ hybridization ploidy result as the corresponding nodal metastases. Chromosomes 7 and X (73.2% of cases) were most frequently gained in the primary tumors, and chromosomes X and Y (81.2% of cases) were most frequently gained in the metastases. No primary tumor or metastasis demonstrated chromosomal loss. Three of 19 primary tumors (15.7%) were diploid, while 16 of 19 (84.3%) were nondiploid. Chromosomal aneusomy was inversely correlated with increasing Gleason summary score. These data indicate that the dominant primary tumor foci may not give rise to nodal metastases, gains of chromosomes 7, X and Y may be associated with metastatic behavior, and patients with stage D1 disease have a greater rate of aneuploidy than those with lower stage cancer.

Nonrandom chromosomal gains in pilocytic astrocytomas of childhood

Low-grade astrocytomas are the most common central nervous system (CNS) tumor occurring in the pediatric age group. Although many of these tumors are karyotypically normal, various studies have reported gains of chromosomes in a significant proportion of cases. We had the opportunity to karyotype two pilocytic astrocytomas occurring in 5- and 15-year-old children. These tumors were characterized by stemlines of 49,XY,+4,+7,+8 and 48,XX,+7,+8. Using these patients as index cases and based on additional karyotypic data that have been published, we performed fluorescence in situ hybridization on 25 additional cases of low-grade astrocytomas in children using pericentromeric probes for chromosomes 4, 6, 7, 8, 9, 10, 11, 12, 15, and 17. Six of 18 (excluding the two index cases), or one third, of the pilocytic astrocytomas were characterized by chromosomal gains, most commonly chromosomes 7 and 8, suggesting that trisomy 7 and 8 are relatively common events in the tumorigenesis of pilocytic astrocytomas. In contrast, chromosomal trisomies were not detected in seven well-differentiated fibrillary astrocytomas with any of the probes chosen.

Chromosomal aneuploidy in proliferative breast disease

Although some forms of proliferative breast disease have been associated with increased risk of breast cancer, substantial confirmatory evidence that the lesions are biologically premalignant has not been presented. Our intent was to identify cytogenetic aberrations in proliferative breast disease using fluorescence in situ hybridization probes selected for their relationship to aberrations previously reported in breast cancer. Application of fluorescence in situ hybridization techniques to paraffin tissue sections using pericentromeric probes for chromosomes 1, 16, 17, 18, and X revealed chromosome aneuploidy in proliferative and malignant lesions of the breast. Sectioning artifact that may result in nuclear truncation was controlled by establishing expected baseline frequencies for gain and loss in normal tissues from the same breast. Localization of chromosomal aberrations to proliferative breast disease lesions with concomitant retention of a normal chromosome complement in corresponding normal breast tissues indicates biologic significance of the results. The similarities of losses involving chromosomes 16, 17, and 18 in hyperplastic lesions and in malignant breast lesions suggest that some hyperplasias may be part of a sequence of progression to malignancy in breast cancer. Gains of chromosome 1 in both in situ and invasive carcinoma are consistent with reports of polysomy 1q as a common cytogenetic change in breast cancer. Its localization to advanced lesions suggests that this trisomy is probably not the initial cytogenetic change in breast cancer tumorigenesis.

Analysis of prostatic tumor cultures using fluorescence in-situ hybridization (FISH)

Analysis of ten primary prostatic tumor cultures using fluorescence in-situ hybridization (FISH) with pericentromeric probes for chromosomes 7, 8, 10, 16, 17, and 18 revealed aneusomies in nine of these specimens. Classical cytogenetics by G-banding indicated that only four of those same ten specimens had any (but not consistent) clonal abnormalities. This preliminary study suggests that aneusomy is a common event in early-stage prostatic tumors, and also supports the notion that multiple chromosomes are involved. In combination with routine cytogenetic analysis, FISH is thus likely to be a powerful tool in the evaluation of prostatic cancer.