High frequency of common DNA copy number abnormalities detected by bacterial artificial chromosome array comparative genomic hybridization in 24 breast cancer cell lines

Saito, Soichiro; Morita, Keiko; Hirano, Takashi

doi:10.1111/j.1749-0774.2008.00061.x

Cited by 16 publications

(31 citation statements)

References 33 publications

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“…Furthermore, the 4 demarcated MCORs in the 17q12 locus encompassed the ERBB2, STARD3 and GRB7 genes that demonstrated amplifications of ≥4 copies, detected in 16% of our samples. Similar rates were also formerly depicted in this region (18,23), in contrast to the study by Saito et al (27) which displayed a gain of 71%. This disparity could be due to the incorporation of breast cancer cell lines in their analyses, which have been linked with higher rates of aberration compared to primary tumours.…”

Section: Discussioncontrasting

confidence: 54%

Integrated analysis of copy number and loss of heterozygosity in primary breast carcinomas using high-density SNP array

et al. 2011

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Abstract. Breast cancer is a heterogeneous disease, marked by extensive chromosomal aberrations. In this study, we aimed to explicate the underlying chromosomal copy number (CN) alterations and loss of heterozygosity (LOH) implicated in a cohort of Malaysian hospital-based primary breast carcinoma samples using a single nucleotide polymorphism (SNP) array platform. The analysis was conducted by hybridizing the extracted DNA of 70 primary breast carcinomas and 37 normal peripheral blood samples to the Affymetrix 250K Sty SNP arrays. Locus-specific CN aberrations and LOH were statistically summarized using the binary segmentation algorithm and hidden Markov model. Selected genes from the SNP array analysis were also validated using quantitative real-time PCR. The merging of CN and LOH data fabricated distinctive integrated alteration profiles, which were comprised of finely demarcated minimal sites of aberrations. The most prevalent gains (≥30%) were detected at the 8q arm: 8q23.1, 8q23.3, 8q24.11, 8q24.13, 8q24.21, 8q24.22, 8q24.23 and 8q24.3, whilst the most ubiquitous losses (≥20%) were noted at the 8p12, 8p21.1, 8p21.2, 8p21.1-p21.2, 8p21.3, 8p22, 8p23.1, 8p23.1-p23.2, 8p23.3, 17p11.2, 17p12, 17p11.2-p12, 17p13.1 and 17p13.2 regions. Copy-neutral LOH was characterized as the most prevailing LOH event, in which the most frequent distributions (≥30%) were revealed at 3p21.31, 5q33.2, 12q24.12, 12q24.12-q24.13 and 14q23.1. These findings offer comprehensive genome-wide views on breast cancer genomic changes, where the most recurrent gain, loss and copy-neutral LOH events were harboured within the 8q24.21, 8p21.1 and 14q23.1 loci, respectively. This will facilitate the uncovering of true driver genes pertinent to breast cancer biology and the development of prospective therapeutics.

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Section: Discussioncontrasting

confidence: 54%

Integrated analysis of copy number and loss of heterozygosity in primary breast carcinomas using high-density SNP array

et al. 2011

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“…CNVs affect the gene expression patterns by altering the gene dosage in human breast cancer 32–34 , hMBCs 7,32 , and breast cancer cell lines 35 . Additionally, specific CNGs are concordant with EMT-related genes up-regulation in multiple human cancer types 36 .…”

Section: Introductionmentioning

confidence: 99%

TiHo-0906: a new feline mammary cancer cell line with molecular, morphological, and immunocytological characteristics of epithelial to mesenchymal transition

Granados-Soler

Junginger

Hewicker‐Trautwein

et al. 2018

Sci Rep

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Feline mammary carcinomas (FMCs) with anaplastic and malignant spindle cells histologically resemble the human metaplastic breast carcinoma (hMBC), spindle-cell subtype. hMBCs display epithelial-to-mesenchymal transition (EMT) characteristics. Herein we report the establishment and characterization of a cell line (TiHoCMglAdcar0906; TiHo-0906) exhibiting EMT-like properties derived from an FMC with anaplastic and malignant spindle cells. Copy-number variations (CNVs) by next-generation sequencing and immunohistochemical characteristics of the cell line and the tumour were compared. The absolute qPCR expression of EMT-related markers HMGA2 and CD44 was determined. The growth, migration, and sensitivity to doxorubicin were assessed. TiHo-0906 CNVs affect several genomic regions harbouring known EMT-, breast cancer-, and hMBCs-associated genes as AKT1, GATA3, CCND2, CDK4, ZEB1, KRAS, HMGA2, ESRP1, MTDH, YWHAZ, and MYC. Most of them were located in amplified regions of feline chromosomes (FCAs) B4 and F2. TiHo-0906 cells displayed an epithelial/mesenchymal phenotype, and high HMGA2 and CD44 expression. Growth and migration remained comparable during subculturing. Low-passaged cells were two-fold more resistant to doxorubicin than high-passaged cells (IC50: 99.97 nM, and 41.22 nM, respectively). The TiHo-0906 cell line was derived from a poorly differentiated cellular subpopulation of the tumour consistently displaying EMT traits. The cell line presents excellent opportunities for studying EMT on FMCs.

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“…A previous analysis on 24 breast cancer cell lines showed a high frequency of DNA copy number loss at the short arm of chromosome 8 (Cooke et al, 2008;Saito et al, 2009). The 8p23 cytogenetic band contains PINX1, a possible telomerase inhibitor and a putative tumor suppressor whose overexpression is known to inhibit telomerase activity, shorten telomeres, and induce crisis.…”

Section: Discussionmentioning

confidence: 98%

Determining and Interpreting New Predictive Rules for Breast Cancer Familial Inheritance

Tommasi¹,

Iannelli²,

Menolascina

et al. 2011

OMICS: A Journal of Integrative Biology

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DNA copy number alterations have been discovered to be key genetic events in development and progression of cancer. No clear data of familial and sporadic breast cancer are available. We focused on looking for an independent platform as a tool to identify the chromosomal profile in familial versus sporadic breast cancer patients. A total of 124 breast cancer patients were studied utilizing aCGH. The dataset was analyzed using Gaussian Mixture Models to determine the thresholds in order to assess gene copy number changes and to minimize the impact of noise on further data analyses. The identification of regions of consistent aberration across samples was carried out with statistical approaches and machine learning tools to draw profiles for familial and sporadic groups. Familial and sporadic cases resulted with a chromosome imbalance of 15% [false discovery rate (FDR): q=718E-5] and 18% (FDR: q=632E-13), respectively. The differential map evidenced two cytogenetic bands (8p23 and 11q13-11q14) significantly altered in familial versus sporadic cases (FDR: q=7E-4). The application of a new bioinformatics tool that discovers fuzzy classification rules (IFRAIS) let to individualize association of genes alterations that identify familial or sporadic cases. These results are comparable to those of the other systems used and are consistent from the biological point of view.

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High frequency of common DNA copy number abnormalities detected by bacterial artificial chromosome array comparative genomic hybridization in 24 breast cancer cell lines

Cited by 16 publications

References 33 publications

Integrated analysis of copy number and loss of heterozygosity in primary breast carcinomas using high-density SNP array

Integrated analysis of copy number and loss of heterozygosity in primary breast carcinomas using high-density SNP array

TiHo-0906: a new feline mammary cancer cell line with molecular, morphological, and immunocytological characteristics of epithelial to mesenchymal transition

Determining and Interpreting New Predictive Rules for Breast Cancer Familial Inheritance

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