Identification of multiple chromosome 12 abnormalities in human testicular germ cell tumors by two-color fluorescence in situ hybridization (FISH)

Fluorescent In Situ Hybridization Analysis for 12p Alterations in Sarcomatoid Yolk Sac Tumors

"Sarcomas" in patients with testicular germ cell tumors (GCTs) are a common form of "somatic-type malignancy." There is support, based on morphology and immunohistochemistry, that many such sarcomatous tumors represent an unusual form of yolk sac tumor (YST). A virtually universal chromosomal anomaly in GCTs is increase in 12p copy number, often in the form of isochromosome 12p [i(12p)], but this aspect of sarcomatoid YSTs has not hitherto been studied. We performed interphase fluorescent in situ hybridization assay for detection of increased 12p copy number in sarcomatoid YSTs using a bacterial artificial chromosome-derived probe localized to 12p12.1 and a commercially available centromeric probe. Sixteen formalin-fixed, paraffin-embedded specimens from 11 patients, along with normal controls, were studied. Overrepresentation of 12p was expressed as a ratio between the number of signals for 12p and the number of signals for centromere 12. A ratio ≥1.3 was considered overrepresentation. All cases were postchemotherapy recurrences or metastases. Ages ranged 22 to 38 years (mean: 36). Most tumors (12/16) showed myxoid or fibromyxoid stroma and 15 of 16 were high grade. Thirteen of 16 specimens (81%) showed overrepresentation of 12p by the above criteria. Two cases exhibited loss of 12p and 1 case had gain of a whole chromosome 12 (trisomy 12). We conclude that, as in other GCTs, sarcomatous differentiation of YST demonstrates 12p alterations that can be identified by interphase fluorescent in situ hybridization. Apart from 12p overrepresentation, these tumors may exhibit loss of 12p or even gain of an entire chromosome 12 (trisomy 12). Increase in 12p copy number of a sarcomatous neoplasm provides support for sarcomatoid YST in clinically ambiguous settings.

Fluorescence in situ hybridization analysis of chromosome 12p in paraffin-embedded tissue is useful for establishing germ cell origin of metastatic tumors

The over-representation of chromosome 12p sequences is crucial for the development of invasive testicular germ cell tumors. Testicular cancer patients may have metastatic tumors of diverse histologic types, including adenocarcinoma, undifferentiated carcinoma, sarcoma, or other malignancies that lack features of germ cell tumors. We sought to investigate the possible germ cell origin of such tumors using interphase fluorescence in situ hybridization. In all, 10 metastatic malignant somatic-type tumors from patients with histories of testicular cancer, as well as one malignant somatic-type tumor from a patient with primary mediastinal germ cell tumor were studied and included: adenocarcinoma (five cases), poorly differentiated carcinoma (one), sarcoma (four), and neuroendocrine carcinoma (one). The tumors were analyzed using fluorescence in situ hybridization using 12p spectrum green and 12 centromeric spectrum orange probes in paraffin sections. The patients ranged in age from 27 to 55 years (mean, 43). Colon and lung cancers from patients without germ cell tumors were used as controls. Adequate signals were observed in all tumors. Gain of chromosome 12p was seen in six tumors. None of the control tumors showed 12p amplification. Fluorescence in situ hybridization for 12p amplification in routinely processed surgical specimens is a useful adjuvant diagnostic tool in confirming the germ cell origin of metastatic tumors having the histologic appearance of somatic-type neoplasms.

Characterization of gains, losses, and regional amplification in testicular germ cell tumor cell lines by comparative genomic hybridization

We have performed comparative genomic hybridization on 12 testicular germ cell tumor (TGCT) cell lines and one paraffin-embedded surgical specimen to identify and characterize genome-wide gains and losses of chromosomes in these specimens. All specimens demonstrated overrepresentation of 12p. Other significant chromosomal gains, apart from 12p, included the X chromosome and chromosome arms 1q and 20q. Chromosomal losses were observed for chromosomes 4 and 18 and chromosome arms 2q, 9q, and 13q. Genomic differences were observed between an embryonal carcinoma component of a mixed tumor, 833K, and its cisplastin-resistant derivative line, 64CP, including losses of 6q23 approximately qter and 9p22 approximately q21. Five lines also demonstrated gain of 12p and additional 12p12 approximately p13 material. Similarly, two lines demonstrated gain of 12p and additional 12p11.2 approximately p12 material. The data supports the consistent gain of 12p in adult TGCT cell lines and additional regional amplification of 12p in some lines. This regional amplification has been observed in both primary tumor specimens and TGCT cell lines and may support a hypothesis that at least two different regions of 12p, one proximal and one distal, harbor genes important for the pathogenesis of testicular germ cell neoplasia.

Overrepresentation of the short arm of chromosome 12 in seminoma and nonseminoma groups of testicular germ cell tumors

The amplification of the short arm of the chromosome 12, especially as the i(12p) marker chromosome, has been found to be a highly nonrandom chromosome abnormality associated with testicular germ cell tumors (TGCT). A series of adult TGCT consisting of seven seminomas (SE) and eight nonseminomas (NS) was analyzed by conventional cytogenetics and fluorescent in situ hybridization. Multiplied chromosome 12 material originating from typical i(12p) and from other markers carrying chromosome 12-derived material was found in almost all analyzed tumors (6 of 7 SE cases and 8 of 8 NS cases). Heterogeneity in the copy number of i(12p) and other 12p-derived markers, as well as chromosome 12 aneuploidy, were higher in NS tumors than in SE.

Definition of chromosome aberrations in testicular germ cell tumor cell lines by 24-color karyotyping and complementary molecular cytogenetic analyses

Many of the reported karyotypes for adult testicular germ cell tumors (GCTs) are complex and incomplete, although the presence of an isochromosome 12p, i(12p), and gain of 12p material have consistently been found. Here, an accurate definition of the chromosome aberrations associated with four cell lines derived from GCTs (GCT27, H12.1, Tera1, and Tera2) has been produced using 24-color karyotyping by mulifluor in situ hybridization, comparative genomic hybridization analysis, and further fluorescence in situ hybridization analysis to confirm some chromosomal assignments and refine involvement of specific regions of 12p. There was karyotypic heterogeneity. Isochromosomes in addition to i(12p) were found, as were other rearrangements with breakpoints at or near centromeric regions. The most frequent non-centromeric breakpoints were at 1p31 approximately p32, 1p21 approximately p22, 11q13, and Xq22, although consistent partner chromosomes were not involved. One cell line (Tera1) showed a subtle dosage increase in the copy number of a 12p probe known to be within the smallest overlapping region of amplification that has been defined in a number of testicular GCTs with amplicons at 12p11 approximately p12. The chromosome rearrangements and associated imbalances may be significant in GCT progression and the characterized cell lines can be used to investigate these further.

Variation in microdeletions of the cyclic AMP-responsive element-binding protein gene at chromosome band 16p13.3 in the Rubinstein-Taybi syndrome

Most reported microdeletions of the CREB-binding protein (CBP) gene in the Rubinstein-Taybi syndrome (RTS) were detected by fluorescence in situ hybridization (FISH) with a single cosmid probe specific to the 3' region of the gene. In order to test the hypothesis that the rate of microdeletion-positive cases would be greater if the entire gene was evaluated, we performed FISH on 66 patients with an established diagnosis of RTS, using a panel of five cosmids that span the CBP gene. Five of 66 patients had deletions by FISH (9%), consistent with those rates reported in various series that ranged between 3-25%. Among our cases, different deletions were observed; one was deleted for the 5' but not the 3' region of the CBP gene (case 055). Other deletions included a total CBP deletion extending from the 5' through the 3' region (case 017), a deletion of all but the 5' region (cases 006 and 060), and an interstitial deletion in the 3' region (case 028). Fine breakpoint mapping with additional cosmid and yeast artificial chromosome (YAC) constructs was performed on these patients. The findings of a partial 5' deletion and of interstitial deletions of the CBP gene add to the known spectrum of mutations of this gene in RTS and demonstrate the need for evaluation of the entire CBP gene region for deletions rather than only the 3' region in RTS patients. These results further suggest that the true rate of microdeletion across the CBP gene detectable by FISH has yet to be established firmly. No phenotypic differences between partial deletion, complete deletion, and nondeletion patients were observed, supporting a haploinsufficiency model for RSTS.

Amplifications of DNA primase 1 (PRIM1) in human osteosarcoma

We studied the involvement of PRIM1 in osteosarcoma by differential display, Northern and Southern hybridization, as well as fluorescence in situ hybridization (FISH) on interphase nuclei. In total, 22 pediatric oncology specimens were tested. PRIM1 was found to be amplified in 41% of the samples. PRIM1 is coamplified with the core 12q13 amplicon genes CDK4, SAS, and OS9, and was physically mapped very close to them. PRIM1 is therefore a new candidate for the role of a major target gene of 12q13 amplifications in human cancers. Genes Chromosomes Cancer 26:62-69, 1999.

Cytogenetic analyses of 85 testicular germ cell tumors: comparison of postchemotherapy and untreated tumors

Cytogenetic analyses of 85 testicular germ cell tumors, of which 54 were karyotypically abnormal, showed recurrent breakpoints at chromosome bands 1p36, 1p13-1qh, 11q23, 19q13, and the pericentromeric regions of the acrocentric chromosomes. Postchemotherapy tumors had significantly more rearrangements of bands 3p25-p26, 6q16-q21, 8p22-p23 when compared with untreated tumors, while untreated tumors had more rearrangements of 9p22-p24 when compared with postchemotherapy tumors. Frequent breakpoints also were identified at 15q15 and 9qh in untreated tumors. Tumors of different histopathology, clinical stage, and treatment status showed no significant differences in the frequencies of i(12p)-positive and i(12p)-negative tumors.

Characterization of multiple 12p rearrangements in testicular germ cell tumor cell line 833K and its subclone 64CP by chromosome microdissection

Rearrangements of chromosome arm 12p are known to be common in germ cell tumors (GCT). Previous studies, using fluorescence in situ hybridization (FISH) with a whole chromosome 12 painting probe, showed unusual distributions of chromosome 12-derived chromatin in GCT cell line 833K and its cisplatin-resistant subclone, 64CP, located next to AgNOR (silver staining nucleolus organizer regions), some of which were ectopic. In this study, the ectopic stalk regions were shown by FISH to be composed of 18s and 28s rDNA, but were flanked by beta-satellite DNA, which may form a barrier around the rDNA. In order to determine the specific origins of the rearranged chromosome 12 segments, three different derived chromosome 12 regions were isolated from 64CP, using chromosomal microdissection. The microdissected fragments were labeled and hybridized by FISH to normal human chromosomes. All three segments localized to distal 12p; 12p12-->12pter, but with apparently different breakpoints for each segment. Furthermore, three-color FISH experiments with 12p band-specific probes demonstrated that the derivative chromosome 12 regions in 833K also originate from distal 12p (12p12-->p13). These sequences now can be evaluated for degree of overlap or common breakpoints which may be of significance in the development or progression of GCT.

Testicular germ cell tumors: molecular understanding and clinical implications

It was recognized in the 1960s that testicular germ cell tumors were curable with chemotherapeutic drugs. Since that time, newer drugs including cisplatin have increased the cure rate of these tumors to over 80%, even in patients with metastatic disease. Germ cell tumors also exhibit a unique biology and genetics that distinguish them from other solid tumors and might contribute to their routine curability.

Fluorescence in situ hybridization on nuclei from paraffin-embedded tissue in low stage pure embryonal carcinoma of the testis

Approximately 30% of patients who present with clinical stage A nonseminomatous testis cancer are in fact pathologic stage B. In previous studies an increasing volume of embryonal carcinoma in the orchiectomy specimen was associated with a higher likelihood of being pathologic stage B. However, not all patients with pure embryonal carcinoma in the primary tumor were pathologic stage B. In an effort to discriminate patients with pure embryonal carcinoma in the testicular specimen relative to pathologic stage, archival specimens from patients presenting with clinical stage A pure embryonal carcinoma were examined by fluorescence in situ hybridization (FISH) with newly developed probes for chromosome arms 12p and 12q. Whole nuclei from archival material from 14 patients (six pathologic stage A, seven pathologic stage B and one stage C) with 100% embryonal carcinoma in the orchiectomy specimen were studied using bicolor FISH with chromosome arm 12p- and 12q-specific painting probes developed by chromosome microdissection. In all cases a blinded analysis showed distinct regions of 12p and 12q probe hybridization simultaneously and allowed identification of probable normal chromosomes 12, as well as regions of amplification of 12p sequences, including possible i(12p). In 5/14 specimens, a distinct and peculiar pattern of 12p hybridization was observed which resembled 12p "disarray" or "multifocal 12p". Of the five specimens demonstrating multifocal 12p, four were pathologic stage B, while one was pathologic stage A. Whether the trend toward multifocal 12p predicts metastatic potential in primary testicular embryonal carcinoma will need to be assessed using a larger series of patients.

DNA sequence, chromosomal localization, and tissue expression of the mouse proteasome subunit lmp10 (Psmb10) gene

Proteasomes are nonlysosomal multicatalytic proteases involved in antigen processing. Three of the 10 mammalian proteasome beta subunits (LMP2, LMP7, and LMP10) are induced by IFN-gamma. Two of these (LMP2 and LMP7) are encoded in the major histocompatibility complex of both human (chromosome 6) and mouse (chromosome 17). However, the human homologue of Lmp10, MECL1, is found on chromosome 16. Here we show that in mice, Lmp10 is a single-copy gene localized to chromosome 8, in a region of conserved synteny with human chromosome 16. Sequencing of a 129/SvJ strain genomic clone revealed that the gene has eight exons spanning 2.3 kb. Characterization of a full-length mouse cDNA clone indicates that Lmp10 encodes a protein of 273 amino acids with a calculated molecular weight of 29 kDa and an isoelectric point of 6.86. Northern analysis of Lmp2, Lmp7, and Lmp10 showed expression in heart, liver, thymus, lung, and spleen, but not in brain, kidney, skeletal muscle, or testis.

Bicolor fluorescence in situ hybridization on nuclei from formalin-fixed, paraffin-embedded testicular germ cell tumors: comparison with standard metaphase analysis

Rearrangements of chromosome 12, especially i(12p), are common in testicular germ cell tumors (TGCT). We have developed 12p and 12q chromosome arm-specific painting probes for fluorescence in situ hybridization (FISH) through the use of chromosome microdissection. We developed a method to hybridize these probes to interphase nuclei released from formalin-fixed, paraffin-embedded tumors (PET). In this study, we compared simultaneous bicolor PET FISH painting with metaphase chromosome analysis of fresh tissue from the same tumor. Bicolor PET FISH produced patterns of 12p and 12q hybridization consistent with expectations based on metaphase chromosome analysis; adjoined 12p and 12q regions appeared to detect "normal" chromosome 12s, whereas relatively large isolated regions of 12p were suggestive of i(12p), and small 12p regions probably represent cryptic rearrangements of 12p. Fourteen tumors with successful cytogenetic analyses and available archival material from the same tumor source were selected for study. In a blinded analysis, PET FISH painting assessment was in very close agreement with karyotypic findings in seven subjects, in close agreement in five, and showed less agreement in two. Differences may be due in part to clonal selection during culture for metaphase studies, or regional selection within the tumor. Although PET FISH painting should not replace standard chromosome analysis, this study shows that it can reliably predict chromosome 12 constitution in TGCT, can serve as a useful adjunct to standard cytogenetics when such analysis is unsuccessful, and can provide limited karyotyping of archival materials.

Use of fluorescence in situ hybridization and comparative genomic hybridization in the cytogenetic analysis of testicular germ cell tumors and uveal melanomas

Fluorescence in situ hybridization (FISH) with specific DNA probes and comparative genomic hybridization (CGH) are molecular cytogenetic methods that provide powerful supplementations of classical cancer cytogenetics. We present two examples of successful application of these new techniques in solid tumors in which basic information about specific cytogenetic aberrations had been gained previously by conventional karyotyping. In the first, testicular germ cell tumors (TGCT), FISH analysis allowed further characterization of the i(12p) marker chromosome. By CGH, chromosomal subregions that may harbor genes important for tumorigenesis or progression could be identified. In the second, uveal melanoma, CGH enabled a retrospective study in which monosomy 3 was statistically proved to be a relevant marker for poor prognosis.