Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis

Molecular Cytogenetics, Jan 2014

Background The MCF7 (ER+/HER2-), T47D (ER+/HER2-), BT474 (ER+/HER2+) and SKBR3 (ER-/HER2+) breast cancer cell lines are widely used in breast cancer research as paradigms of the luminal and HER2 phenotypes. Although they have been subjected to cytogenetic analysis, their chromosomal abnormalities have not been carefully characterized, and their differential cytogenetic profiles have not yet been established. In addition, techniques such as comparative genomic hybridization (CGH), microarray-based CGH and multiplex ligation-dependent probe amplification (MLPA) have described specific regions of gains, losses and amplifications of these cell lines; however, these techniques cannot detect balanced chromosomal rearrangements (e.g., translocations or inversions) or low frequency mosaicism. Results A range of 19 to 26 metaphases of the MCF7, T47D, BT474 and SKBR3 cell lines was studied using conventional (G-banding) and molecular cytogenetic techniques (multi-color fluorescence in situ hybridization, M-FISH). We detected previously unreported chromosomal changes and determined the content and frequency of chromosomal markers. MCF7 and T47D (ER+/HER2-) cells showed a less complex chromosomal make up, with more numerical than structural alterations, compared to BT474 and SKBR3 (HER2+) cells, which harbored the highest frequency of numerical and structural aberrations. Karyotype heterogeneity and clonality were determined by comparing all metaphases within and between the four cell lines by hierarchical clustering. The latter analysis identified five main clusters. One of these clusters was characterized by numerical chromosomal abnormalities common to all cell lines, and the other four clusters encompassed cell-specific chromosomal abnormalities. T47D and BT474 cells shared the most chromosomal abnormalities, some of which were shared with SKBR3 cells. MCF7 cells showed a chromosomal pattern that was markedly different from those of the other cell lines. Conclusions Our study provides a comprehensive and specific characterization of complex chromosomal aberrations of MCF7, T47D, BT474 and SKBR3 cell lines. The chromosomal pattern of ER+/HER2- cells is less complex than that of ER+/HER2+ and ER-/HER2+ cells. These chromosomal abnormalities could influence the biologic and pharmacologic response of cells. Finally, although gene expression profiling and aCGH studies have classified these four cell lines as luminal, our results suggest that they are heterogeneous at the cytogenetic level.

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Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis

Molecular Cytogenetics Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis Milena Rondn-Lagos 1 2 Ludovica Verdun Di Cantogno 0 3 Caterina Marchi 0 1 3 Nelson Rangel 1 Cesar Payan-Gomez 2 4 Patrizia Gugliotta 1 Cristina Botta 1 Gianni Bussolati 1 Sandra R Ramrez-Clavijo 2 Barbara Pasini 1 Anna Sapino 0 1 3 0 Department of Laboratory Medicine, Azienda Ospedaliera Citta della Salute e della Scienza di Torino , Turin , Italy 1 Department of Medical Sciences, University of Turin , Via Santena 7, 10126 Turin , Italy 2 Natural and Mathematical Sciences Faculty, Universidad del Rosario , Bogota , Colombia 3 Department of Laboratory Medicine, Azienda Ospedaliera Citta della Salute e della Scienza di Torino , Turin , Italy 4 Medical Genetics Center, Department of Cell Biology and Genetics, Center of Biomedical Genetics , P.O. Box 1738, 3000 DR Erasmus MC, Rotterdam , The Netherlands Background: The MCF7 (ER+/HER2-), T47D (ER+/HER2-), BT474 (ER+/HER2+) and SKBR3 (ER-/HER2+) breast cancer cell lines are widely used in breast cancer research as paradigms of the luminal and HER2 phenotypes. Although they have been subjected to cytogenetic analysis, their chromosomal abnormalities have not been carefully characterized, and their differential cytogenetic profiles have not yet been established. In addition, techniques such as comparative genomic hybridization (CGH), microarray-based CGH and multiplex ligation-dependent probe amplification (MLPA) have described specific regions of gains, losses and amplifications of these cell lines; however, these techniques cannot detect balanced chromosomal rearrangements (e.g., translocations or inversions) or low frequency mosaicism. Results: A range of 19 to 26 metaphases of the MCF7, T47D, BT474 and SKBR3 cell lines was studied using conventional (G-banding) and molecular cytogenetic techniques (multi-color fluorescence in situ hybridization, M-FISH). We detected previously unreported chromosomal changes and determined the content and frequency of chromosomal markers. MCF7 and T47D (ER+/HER2-) cells showed a less complex chromosomal make up, with more numerical than structural alterations, compared to BT474 and SKBR3 (HER2+) cells, which harbored the highest frequency of numerical and structural aberrations. Karyotype heterogeneity and clonality were determined by comparing all metaphases within and between the four cell lines by hierarchical clustering. The latter analysis identified five main clusters. One of these clusters was characterized by numerical chromosomal abnormalities common to all cell lines, and the other four clusters encompassed cell-specific chromosomal abnormalities. T47D and BT474 cells shared the most chromosomal abnormalities, some of which were shared with SKBR3 cells. MCF7 cells showed a chromosomal pattern that was markedly different from those of the other cell lines. Conclusions: Our study provides a comprehensive and specific characterization of complex chromosomal aberrations of MCF7, T47D, BT474 and SKBR3 cell lines. The chromosomal pattern of ER+/HER2- cells is less complex than that of ER+/HER2+ and ER-/HER2+ cells. These chromosomal abnormalities could influence the biologic and pharmacologic response of cells. Finally, although gene expression profiling and aCGH studies have classified these four cell lines as luminal, our results suggest that they are heterogeneous at the cytogenetic level. Cytogenetic; Chromosomal abnormalities; Breast cancer cell lines; Hierarchical cluster - Background The MCF7, T47D, BT474 and SKBR3 breast cancer cell lines are commonly used in experimental studies of cellular function, and much of the current knowledge of molecular alterations in breast cancer has been obtained from these cell lines [1-4]. Whole-genome studies using microarray expression analyses have identified distinct subtypes of breast carcinomas (the luminal, HER2+, and basal-like subtypes) based on the expression of approximately 500 genes (the socalled intrinsic gene list) [5-7]. These molecular subtypes have been approximated using immunohistochemical markers. In this way, estrogen (ER) and progesterone receptor (PR)+/HER2- tumors are classified as belonging to the luminal A molecular subtype, ER+/PR+/HER2+ tumors to the luminal B subtype, ER-/PR-/HER2+ tumors to the HER2 subtype, and triple negative (ER-/PR-/HER2-) tumors to the basal-like carcinomas [8]. As determined by immunohistochemistry, the receptor profile classifies MCF7 and T47D cells (ER+/PR+/HER2-) as belonging to the luminal A subtype, BT474 cells (ER+/PR+/HER2+) as luminal B and SKBR3 cells (ER-/ HER2+) as HER2 [9,10]. However, the RNA transcriptional profile determined by whole genome oligonucleotide microarrays [1,4,11] characterized all four-cell lines as luminal because of the expression of both ER-regulated genes (e.g., MYB, RET, EGR3, and TFF1) [1] and genes associated with luminal epithelial differentiati (...truncated)


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Milena Rondón-Lagos, Ludovica Verdun Di Cantogno, Caterina Marchiò, Nelson Rangel, Cesar Payan-Gomez, Patrizia Gugliotta, Cristina Botta, Gianni Bussolati, Sandra R Ramírez-Clavijo, Barbara Pasini, Anna Sapino. Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis, Molecular Cytogenetics, 2014, pp. 8, 7, DOI: 10.1186/1755-8166-7-8