Are practically secondary metastases (Fig. 7C).Figure 5. CD44 `fingerprint’ of HT168M1 human melanoma cell line growing on different matrices namely plastic (a), fibronectin (b), laminin (c), collagen (d) and matrigel (e). L stands for molecular weight marker. doi:10.1371/journal.pone.0053883.gCD44 Alternative Splicing Pattern of MelanomaFigure 6. Relative quantitative expression of CD44 variable exons in cell cultures from metastatic (newborn) and non-metastatic human xenograft model (Real-Time PCR measurement) of HT199, a human melanoma cell line of originally low variable exon expression level. A. The relative expression level of all variable exons is raised in circulating metastatic cells (NCTC) and metastatic cells (NM) compared to their levels in primary tumours [newborn primary (NP) and adult primary (AP)] and lung colony (IVLC) B. The qualitative fingerprint (bottom line) remains unchanged. doi:10.1371/journal.pone.0053883.gDiscussionDue to the possibility of a large number of different CD44 isoforms present at the same time in the examined sample, it was important to establish a method that would give a good representation of them. Our first step was to determine which variable exons, other than the ones most studied in the literature, are expressed at mRNA level in human melanoma. We showed that all the variable exons are expressed in human melanomas and predicted a number of paralelly expressed CD44 isoforms. We also found that v1 was missing from some of the isoforms, although 
it is not considered as a variable exon, also that some of the isoforms contained a truncated v1 exon. This was confirmed by direct sequencing of our cloned molecules. However, next generation sequencing studies have surfaced a whole other level of `complications’ by identifying a number of deletions across the variable exons. As a surrogate for representation of all of the expressed alternative splice variants of CD44, we developed a method to determine a `fingerprint’ of expression in human melanoma. This appeared to be stable in cell culture and mouse xenograft models and differed SPDP substantively from that found in MedChemExpress Nobiletin colorectal adenocarcinoma, squamous cell carcinoma and primary cultures of human melanocytes, kerationcytes and fibroblasts. This technique bypasses the attempts to link the 
expression or co-expression of individual variable exons to metastasis formation, a strategy whichloses crucial contextual information about the complex ASP underlying the CD44 protein set. This oversimplification may also account for some of the contradictory evidence on the associations of CD44 expression with the generation of a metastatic phenotype [35,36]. Previous work in our laboratory has shown that under the effect of host derived selection factors, xenografts of tumour cells growing in new born scid mice differ in gene expression pattern than those growing in adult mice. It is not yet clear whether this pattern is related to formation of metastasis or reflects a summation of changes resulting from local effects of graft:host interaction. Adaptation to a new microenvironment is a crucial factor in the formation of metastasis: This may require events in changing patterns of gene expression prior to implantation or may reflect post hoc modification of expression in response to the metastatic niche. To be able to study the pattern of expression during tumour progression we have established an experimental mouse model in which the expression pattern of pure cultur.Are practically secondary metastases (Fig. 7C).Figure 5. CD44 `fingerprint’ of HT168M1 human melanoma cell line growing on different matrices namely plastic (a), fibronectin (b), laminin (c), collagen (d) and matrigel (e). L stands for molecular weight marker. doi:10.1371/journal.pone.0053883.gCD44 Alternative Splicing Pattern of MelanomaFigure 6. Relative quantitative expression of CD44 variable exons in cell cultures from metastatic (newborn) and non-metastatic human xenograft model (Real-Time PCR measurement) of HT199, a human melanoma cell line of originally low variable exon expression level. A. The relative expression level of all variable exons is raised in circulating metastatic cells (NCTC) and metastatic cells (NM) compared to their levels in primary tumours [newborn primary (NP) and adult primary (AP)] and lung colony (IVLC) B. The qualitative fingerprint (bottom line) remains unchanged. doi:10.1371/journal.pone.0053883.gDiscussionDue to the possibility of a large number of different CD44 isoforms present at the same time in the examined sample, it was important to establish a method that would give a good representation of them. Our first step was to determine which variable exons, other than the ones most studied in the literature, are expressed at mRNA level in human melanoma. We showed that all the variable exons are expressed in human melanomas and predicted a number of paralelly expressed CD44 isoforms. We also found that v1 was missing from some of the isoforms, although it is not considered as a variable exon, also that some of the isoforms contained a truncated v1 exon. This was confirmed by direct sequencing of our cloned molecules. However, next generation sequencing studies have surfaced a whole other level of `complications’ by identifying a number of deletions across the variable exons. As a surrogate for representation of all of the expressed alternative splice variants of CD44, we developed a method to determine a `fingerprint’ of expression in human melanoma. This appeared to be stable in cell culture and mouse xenograft models and differed substantively from that found in colorectal adenocarcinoma, squamous cell carcinoma and primary cultures of human melanocytes, kerationcytes and fibroblasts. This technique bypasses the attempts to link the expression or co-expression of individual variable exons to metastasis formation, a strategy whichloses crucial contextual information about the complex ASP underlying the CD44 protein set. This oversimplification may also account for some of the contradictory evidence on the associations of CD44 expression with the generation of a metastatic phenotype [35,36]. Previous work in our laboratory has shown that under the effect of host derived selection factors, xenografts of tumour cells growing in new born scid mice differ in gene expression pattern than those growing in adult mice. It is not yet clear whether this pattern is related to formation of metastasis or reflects a summation of changes resulting from local effects of graft:host interaction. Adaptation to a new microenvironment is a crucial factor in the formation of metastasis: This may require events in changing patterns of gene expression prior to implantation or may reflect post hoc modification of expression in response to the metastatic niche. To be able to study the pattern of expression during tumour progression we have established an experimental mouse model in which the expression pattern of pure cultur.
