There is increasing evidence showing that the stromal cells surrounding cancer epithelial cells, rather than being passive bystanders, might have a role in modifying tumor outgrowth. The molecular basis of this aspect of carcinoma etiology is controversial. Some studies have reported a high frequency of genetic aberrations in carcinoma-associated fibroblasts (CAFs), whereas other studies have reported very low or zero mutation rates. Resolution of this contentious area is of critical importance in terms of understanding both the basic biology of cancer as well as the potential clinical implications of CAF somatic alterations. We undertook genome-wide copy number and loss of heterozygosity (LOH) analysis of CAFs derived from breast and ovarian carcinomas using a 500K SNP array platform. Our data show conclusively that LOH and copy number alterations are extremely rare in CAFs and cannot be the basis of the carcinomapromoting phenotypes of breast and ovarian CAFs. © 2008 Nature Publishing GroupCorrespondence should be addressed to I.G.C. ian.campbell@petermac.org. AUTHOR CONTRIBUTIONS I.G.C., I.H. and W.Q. designed the study and wrote the paper. W.Q. undertook the bulk of the experimental work including tissue microdissection, SNP genotyping and microsatellite analysis. K.P. provided cell lines, academic support and assisted in manuscript preparation. A.S., E.R.T., M.R. and K.L.G. assisted in SNP genotyping. However, not all studies have identified genetic alterations in CAFs; for example, one study did not find any clonally selected somatic genetic alterations in CAFs separated from fresh breast cancer biopsies using array comparative genomic hybridization (CGH) and SNP array analysis 17 , although these CAFs were epigenetically distinct from those from normal breast tissue, as demonstrated by subsequent genome-wide DNA methylation studies 18 .The evidence for somatic genetic alterations as important mediators of the CAF phenotype is controversial and conflicting. We hypothesized that the contradictory data may in part be a reflection of inherent technical limitations of the various methodologies used. Therefore, we took advantage of innovative SNP array-based technologies 19 to investigate in detail the genomic integrity of CAFs microdissected from fresh frozen primary human ovarian and breast cancers as well as short-term cultures of primary breast CAFs.We assessed the sensitivity of the Affymetrix 500K SNP array platform to detect copy number and LOH in the context of normal DNA contamination in a mixing experiment using tumor epithelial cell DNA from a microdissected primary ovarian cancer that was mixed with various ratios of matched normal DNA. This tumor harbors a complex copy number profile on chromosome 17, including regions of high level copy number gain and regions of LOH with and without associated copy number loss. As shown in Supplementary Figure 1a online, the single copy number gain was clearly visible at 70% tumor DNA, and the high level gain was still discernible at 25% tumor DNA. LOH w...

Purpose: Genetic changes in sporadic ovarian cancer are relatively poorly characterized compared with other tumor types.We have evaluated the use of high-resolution whole genome arrays for the genetic profiling of epithelial ovarian cancer. Experimental Design: We have evaluated 31 primary ovarian cancers and matched normal DNA for loss of heterozygosity and copy number alterations using 500K single nucleotide polymorphism arrays. Results: In addition to identifying the expected large-scale genomic copy number changes, >380 small regions of copy number gain or loss (<500 kb) were identified among the 31 tumors, including 33 regions of high-level gain (>5 copies) and 27 homozygous deletions. The existence of such a high frequency of small regions exhibiting copy number alterations had not been previously suspected because earlier genomic array platforms lacked comparable resolution. Interestingly, many of these regions harbor known cancer genes. For example, one tumor harbored a 350-kb high-level amplification centered on FGFR1 and three tumors showed regions of homozygous loss 109 to 216 kb in size involving the RB1 tumor suppressor gene only. Conclusions: These data suggest that novel cancer genes may be located within the other identified small regions of copy number alteration. Analysis of the number of copy number breakpoints and the distribution of the small regions of copy number change indicate high levels of structural chromosomal genetic instability in ovarian cancer.

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Cancer stem cells (CSCs) constitute a subpopulation of cancer cells that have the potential for self-renewal, multipotent differentiation, and tumorigenicity. Studies on CSC biology and CSC-targeted therapies depend on CSC isolation and/or enrichment methodologies. Scientists have conducted extensive research in this field since John Dick's group successfully isolated CSCs based on the expression of the CD34 and CD38 surface markers. Progress in CSC research has been greatly facilitated by the enrichment and isolation of these cells. In this review, we summarize the current strategies used in our and other laboratories for CSC isolation and enrichment, including methods based on stem cell surface markers, intracellular enzyme activity, the concentration of reactive oxygen species, the mitochondrial membrane potential, promoter-driven fluorescent protein expression, autofluorescence, suspension/adherent culture, cell division, the identification of side population cells, resistance to cytotoxic compounds or hypoxia, invasiveness/adhesion, immunoselection, and physical property. Although many challenges remain to be overcome, it is reasonable to believe that more reliable, efficient, and convenient methods will be developed in the near future.