Benz, Christopher C.; Fedele, Vita; Xu, Fan; Ylstra, Bauke; Ginzinger, David; Yu, Mamie; Moore, Dan; Hall, Rayna Kneuper; Wolff, Daynna J.; Disis, Mary L.; Eppenberger‐Castori, Serenella; Eppenberger, Urs; Schittulli, Francesco; Tommasi, Stefania;
doi: 10.1002/gcc.20364pmid: 16883574
Analysis of a collection of human breast cancers (n = 150), enriched in ERBB2‐positive cases (n = 57) and involving tumor genotyping relative to population‐matched blood genotyping (n = 749) for a common ERBB2 single nucleotide polymorphism Ala(G)1170Pro(C), revealed that ERBB2 amplification in breast cancer is invariably monoallelic. Analysis of paired breast cancer and blood samples from informative (G1170C heterozygotic) ERBB2‐positive (n = 12) and ERBB2‐negative (n = 17) cases not only confirmed monoallelic amplification and ERBB2 transcriptional overexpression but also revealed that most low ERBB2 expressing breast cancers (12/17) exhibit unbalanced allelic transcription, showing 3‐fold to nearly 5,000‐fold preferential expression from one of two inherited alleles. To explore cis‐acting transcriptional mechanisms potentially selected during ERBB2 amplification, levels of four different ERBB2 transcript variants (5.2, 4.7, 2.1, and 1.4 kb) were correlated with total (4.6 kb) ERBB2 mRNA levels in ERBB2‐positive (n = 14) versus ERBB2‐negative (n = 43) primary breast cancers. Relative expression of only the 2.1 kb extracellular domain‐encoding splice variant and a 4.7 kb mRNA variant that uses an alternative start site were significantly increased in association with ERBB2‐positivity, implicating altered promoter usage and selective transcript regulation within the ERBB2 amplicon. Altogether, these findings provide new mechanistic insights into the development of ERBB2‐positive breast cancer and strong rationale for delineating candidate cis‐acting regulatory elements that may link allele‐specific ERBB2 transcription in premalignant breast epithelia with subsequent development of breast cancers bearing monoallelic ERBB2 amplicons. © 2006 Wiley‐Liss, Inc.
Zahn, Susanne; Sievers, Sonja; Alemazkour, Katayoun; Orb, Sandra; Harms, Dieter; Schulz, Wolfgang A.; Calaminus, Gabriele; Göbel, Ulrich; Schneider, Dominik T.
doi: 10.1002/gcc.20363pmid: 16897744
Previous studies on childhood germ cell tumors (GCTs) report highly variable frequencies of losses at chromosome arm 1p. Since deletions at 1p portend a poor prognosis in other embryonal tumors, this study aims to clarify the question of the frequency of true allelic loss at 1p and whether it constitutes a prognostic parameter. We analyzed 13 GCTs from different gonadal and extragonadal sites of children (4 teratomas, 9 malignant GCTs) and 18 GCTs of adolescents and adults (3 teratomas; 15 malignant GCTs) using automated microsatellite analysis with 23 polymorphic markers and chromosomal “high resolution” comparative genomic hybridization (HR‐CGH). With this combined approach, we detected loss of heterozygosity (LOH) at 1p in 8/9 childhood malignant GCTs with concordant data from HR‐CGH and microsatellite analyses. In contrast, LOH at 1p was not detected in childhood teratomas (0/4) and constituted a rare event in GCTs of adolescence and adulthood (3/18). The commonly deleted region was located at distal 1p36‐pter, with a proximal boundary between the markers D1S450 and D1S2870. These data unequivocally demonstrate that deletion at 1p is common in childhood GCTs and results in allelic loss. This observation argues for the presence of a classical tumor suppressor at distal 1p. Considering the high frequency of LOH at 1p and the overall favorable prognosis of childhood GCTs, a prognostic impact of LOH at 1p in childhood GCTs appears unlikely. However, since two postpubertal tumors with LOH at 1p progressed, a prognostic relevance in this age group seems possible, warranting a prospective evaluation. © 2006 Wiley‐Liss, Inc.
Mastracci, Teresa L.; Shadeo, Ashleen; Colby, Sarah M.; Tuck, Alan B.; O'Malley, Frances P.; Bull, Shelley B.; Lam, Wan L.; Andrulis, Irene L.
doi: 10.1002/gcc.20368pmid: 16897748
The identification of genomic alterations occurring in neoplastic lesions provides insight into both lesion occurrence and disease progression. In this study, we used microarray comparative genomic hybridization (CGH) to investigate genetic changes in atypical lobular hyperplasia (ALH) and lobular carcinoma in situ (LCIS), as the presence of these lobular neoplastic lesions is an indicator of risk in the development of invasive breast cancer. DNA was extracted from microdissected archival breast tissue containing ALH or LCIS, lacking adjacent invasive carcinoma, and subjected to whole‐genome tiling path microarray‐CGH using the submegabase resolution tiling set (SMRT)‐array platform. Twelve ALH and 13 LCIS lesions were examined. Copy number alterations were identified using statistical criteria and validated with Real‐Time PCR and fluorescence in situ hybridization. From statistical analysis, a greater number of alterations were observed in ALH compared to LCIS. Alterations common to ALH include gain at 2p11.2 and loss at 7p11–p11.1 and 22q11.1. Alterations common to LCIS include gain at 20q13.13 and loss at 19q13.2–q13.31. In both ALH and LCIS, we observed loss of 16q21–q23.1, an altered region previously identified in lobular neoplasia and invasive carcinoma. The validation of select alterations reinforces the genomic signature. This study represents the first whole‐genome investigation of lobular neoplastic breast lesions using clinical archival specimens. The identified genomic signature includes copy number alterations not previously identified for lobular neoplasia. This genomic signature, common to ALH and LCIS, suggests a role for the acquisition of novel genomic alterations in the aberrant cellular proliferation that defines lobular neoplasia. © 2006 Wiley‐Liss, Inc.
Liu, Wennuan; Chang, Baoli; Sauvageot, Jurga; Dimitrov, Latchezar; Gielzak, Marta; Li, Tao; Yan, Guifang; Sun, Jishan; Sun, Jielin; Adams, Tamara S.; Turner, Aubrey R.; Kim, Jin Woo; Meyers, Deborah A.; Zheng, Siqun Lilly; Isaacs, William B.; Xu, Jianfeng
doi: 10.1002/gcc.20369pmid: 16897747
Although multiple recurrent chromosomal alterations have been identified in prostate cancer cells, the specific genes driving the apparent selection of these changes remain largely unknown. In part, this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high‐resolution genome‐wide method, Affymetrix 100K SNP mapping array, to screen for somatic DNA copy number (CN) alterations among 22 pairs of samples from primary prostate cancers and matched nonmalignant tissues. We detected 355 recurrent deletions and 223 recurrent gains, many of which were novel. As expected, the sizes of novel alterations tend to be smaller. Importantly, among tumors with increasing grade, Gleason sum 6, 7, and 8, we found a significant trend of larger number of alterations in the tumors with higher grade. Overall, gains are significantly more likely to occur within genes (74%) than are deletions (49%). However, when we looked at the most frequent CN alterations, defined as those in ≥4 subjects, we observed that both gains (85%) and deletions (57%) occur preferentially within genes. An example of a novel, recurrent alteration observed in this study was a deletion between the ERG and TMPRSS2 genes on chromosome 21, presumably related to the recently identified fusion transcripts from these two genes. Results from this study provide a basis for a systematic and comprehensive cataloging of CN alterations associated with grades of prostate cancer, and the subsequent identification of specific genes that associated with initiation and progression of the disease. This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045‐2257/suppmat. © 2006 Wiley‐Liss, Inc.
Bergamaschi, Anna; Kim, Young H.; Wang, Pei; Sørlie, Therese; Hernandez‐Boussard, Tina; Lonning, Per E.; Tibshirani, Robert; Børresen‐Dale, Anne‐Lise; Pollack, Jonathan R.
doi: 10.1002/gcc.20366pmid: 16897746
Breast cancer is a leading cause of cancer‐death among women, where the clinicopathological features of tumors are used to prognosticate and guide therapy. DNA copy number alterations (CNAs), which occur frequently in breast cancer and define key pathogenetic events, are also potentially useful prognostic or predictive factors. Here, we report a genome‐wide array‐based comparative genomic hybridization (array CGH) survey of CNAs in 89 breast tumors from a patient cohort with locally advanced disease. Statistical analysis links distinct cytoband loci harboring CNAs to specific clinicopathological parameters, including tumor grade, estrogen receptor status, presence of TP53 mutation, and overall survival. Notably, distinct spectra of CNAs also underlie the different subtypes of breast cancer recently defined by expression‐profiling, implying these subtypes develop along distinct genetic pathways. In addition, higher numbers of gains/losses are associated with the “basal‐like” tumor subtype, while high‐level DNA amplification is more frequent in “luminal‐B” subtype tumors, suggesting also that distinct mechanisms of genomic instability might underlie their pathogenesis. The identified CNAs may provide a basis for improved patient prognostication, as well as a starting point to define important genes to further our understanding of the pathobiology of breast cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045‐2257/suppmat. © 2006 Wiley‐Liss, Inc.
Strehl, Sabine; König, Margit; Meyer, Claus; Schneider, Björn; Harbott, Jochen; Jäger, Ulrich; von Bergh, Anne R. M.; Loncarevic, Ivan F.; Jarosova, Marie; Schmidt, Helmut H.; Moore, Steven D. P.; Marschalek, Rolf; Haas, Oskar A.
doi: 10.1002/gcc.20372pmid: 16897742
The majority of translocations that involve the long arms of chromosomes 11 and 17 in acute myeloid leukemia appear identical on the cytogenetic level. Nevertheless, they are diverse on the molecular level. At present, two genes are known in 11q23 and four in 17q12‐25 that generate five distinct fusion genes: MLL‐MLLT6/AF17, MLL‐LASP1, MLL‐ACACA or MLL‐SEPT9/MSF, and ZBTB16/PLZF‐RARA. We analyzed 14 cases with a t(11;17) by fluorescence in situ hybridization and molecular genetic techniques and determined the molecular characteristics of their fusion genes. We identified six different gene fusions that comprised seven cases with a MLL‐MLLT6/AF17, three with a MLL‐SEPT9/MSF, and one each with MLL‐LASP1, MLL‐ACACA, and ZBTB16/PLZF‐RARA fusions. In the remaining case, a MLL‐SEPT6/Xq24 fusion suggested a complex rearrangement. The MLL‐MLLT6/AF17 transcripts were extremely heterogeneous and the detection of seven different in‐frame transcript and splice variants enabled us to predict the protein domains relevant for leukemogenesis. The putative MLL‐MLLT6 consensus chimeric protein consists of the AT‐hook DNA‐binding, the methyltransferase, and the CXXC zinc‐finger domains of MLL and the highly conserved octapeptide and the leucine‐zipper dimerization motifs of MLLT6. The MLL‐SEPT9 transcripts showed a similar high degree of variability. These analyses prove that the diverse types of t(11;17)‐associated fusion genes can be reliably identified and delineated with a proper combination of cytogenetic and molecular genetic techniques. The heterogeneity of transcripts encountered in cases with MLL‐MLLT6/AF17 and MLL‐SEPT9/MSF fusions clearly demonstrates that thorough attention has to be paid to the appropriate selection of primers to cover all these hitherto unrecognized fusion variants. © 2006 Wiley‐Liss, Inc.
Katoh, Hiroto; Shibata, Tatsuhiro; Kokubu, Akiko; Ojima, Hidenori; Kosuge, Tomoo; Kanai, Yae; Hirohashi, Setsuo
doi: 10.1002/gcc.20362pmid: 16897741
Although activated Wnt/β‐catenin pathway is considered to be one of the main driving forces of hepatocarcinogenesis, no somatic mutations of the adenomatous polyposis coli (APC) gene have been found in sporadic hepatocellular carcinoma (HCC) to date. Here we present a case of a sporadic nodule‐in‐nodule‐type HCC that provides the first evidence that biallelic genetic inactivation of the APC gene contributed to the development of the tumor. High‐density array‐based comparative genomic hybridization (aCGH) was performed to clarify genome‐wide chromosomal structural alteration profiles of both early and advanced components of this nodule‐in‐nodule HCC. aCGH analysis revealed a chromosomal loss of the APC gene locus only in the inner advanced component of this tumor. Direct sequencing of the remaining allele revealed a nonsense mutation at codon 682 in the Armadillo repeats, resulting in a truncated protein that lacked all of the β‐catenin‐binding motifs. Nonsense mutations at this location are rare among other types of cancer. In conclusion, combined with an immunohistochemical analysis of the β‐catenin protein, this case provides the first evidence that genetic inactivation of the APC gene can play a significant role in the progression of sporadic HCC, probably by activating the Wnt/β‐catenin pathway. © 2006 Wiley‐Liss, Inc.
Huang, Xin; Godfrey, Tony E.; Gooding, William E.; McCarty, Kenneth S.; Gollin, Susanne M.
doi: 10.1002/gcc.20371pmid: 16906560
11q13 amplification occurs in a wide variety of tumors, including almost half of oral squamous cell carcinomas (OSCC) where it has been correlated with a poor outcome. In this study, we compiled 3.6 Mb of DNA sequence in the 11q13 amplicon core and refined the physical map of the amplicon. In the process, we determined the genomic structure and normal tissue expression patterns of two recently identified genes, TAOS2/TMEM16A and MRGF, which reside in the amplicon core. We then quantified DNA copy number and mRNA expression of all genes in the 11q13 amplicon in cell lines and primary tumors from OSCC. With the exception of FGF3, FGF4, FGF19, and MRGF, all genes were overexpressed in most tumors with genomic amplification. Furthermore, we found that the expression of genes in the amplicon appeared to be highly coordinated, making it difficult to determine which gene or genes are driving amplification. However, in nonamplified primary tumors, three genes, TAOS2/TMEM16A, OCIM, and TPCN2, are frequently overexpressed, whereas CCND1 and EMS1 are not. These results suggest that in addition to CCND1 and EMS1, other important genes also may be target genes driving 11q13 amplification. We hypothesize that 11q13 amplification may be driven by a cassette of genes that provide growth or metastatic advantage to cancer cells. This is supported by the finding that the human 11q13 amplicon core is syntenic to mouse chromosomal band 7F5, which is frequently amplified in chemically induced murine OSCC. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045‐2257/suppmat. © 2006 Wiley‐Liss, Inc.
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