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Molecular and phenotypic characterisation of paediatric glioma cell lines as models for preclinical drug development.

Bax DA, Little SE, Gaspar N, Perryman L, Marshall L, Viana-Pereira M, Jones TA, Williams RD, Grigoriadis A, Vassal G, Workman P, Sheer D, Reis RM, Pearson AD, Hargrave D, Jones C - PLoS ONE (2009)

Bottom Line: All lines proliferate as adherent monolayers and express glial markers.Copy number profiling revealed complex genomes including amplification and deletions of genes known to be pivotal in core glioblastoma signalling pathways.Expression profiling identified 93 differentially expressed genes which were able to distinguish between the adult and paediatric high grade cell lines, including a number of kinases and co-ordinated sets of genes associated with DNA integrity and the immune response.

View Article: PubMed Central - PubMed

Affiliation: Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom.

ABSTRACT

Background: Although paediatric high grade gliomas resemble their adult counterparts in many ways, there appear to be distinct clinical and biological differences. One important factor hampering the development of new targeted therapies is the relative lack of cell lines derived from childhood glioma patients, as it is unclear whether the well-established adult lines commonly used are representative of the underlying molecular genetics of childhood tumours. We have carried out a detailed molecular and phenotypic characterisation of a series of paediatric high grade glioma cell lines in comparison to routinely used adult lines.

Principal findings: All lines proliferate as adherent monolayers and express glial markers. Copy number profiling revealed complex genomes including amplification and deletions of genes known to be pivotal in core glioblastoma signalling pathways. Expression profiling identified 93 differentially expressed genes which were able to distinguish between the adult and paediatric high grade cell lines, including a number of kinases and co-ordinated sets of genes associated with DNA integrity and the immune response.

Significance: These data demonstrate that glioma cell lines derived from paediatric patients show key molecular differences to those from adults, some of which are well known, whilst others may provide novel targets for evaluation in primary tumours. We thus provide the rationale and demonstrate the practicability of using paediatric glioma cell lines for preclinical and mechanistic studies.

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Expression profiling of paediatric and adult glioblastoma cell lines.(A) Heatmap demonstrating hierarchical clustering of 93 differentially expressed genes between paediatric (SF188, KNS42, UW479) and adult (LN229, A172, U118MG, U87MG, SF268) high grade glioma cell lines. (B) Quantitative real-time (TaqMan) RT-PCR confirming differential expression of CRKL, LYN, EPHA6 and AXL. Expression values are plotted relative to Universal Human Reference RNA. (C) Gene Set Enrichment Analysis highlighting co-ordinated differential expression of gene sets defined a priori. Enriched in paediatric high grade glioma cell lines - MORF_MSH2, GNF2_MLH1, GCM_RAD21, DNA_replication_reactome; enriched in adult lines IL6_SCAR_FIBRO_UP, CROONQUIST_IL6_RAS_UP, TGFBETA_C1_UP. Nominal p value<0.001.
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pone-0005209-g004: Expression profiling of paediatric and adult glioblastoma cell lines.(A) Heatmap demonstrating hierarchical clustering of 93 differentially expressed genes between paediatric (SF188, KNS42, UW479) and adult (LN229, A172, U118MG, U87MG, SF268) high grade glioma cell lines. (B) Quantitative real-time (TaqMan) RT-PCR confirming differential expression of CRKL, LYN, EPHA6 and AXL. Expression values are plotted relative to Universal Human Reference RNA. (C) Gene Set Enrichment Analysis highlighting co-ordinated differential expression of gene sets defined a priori. Enriched in paediatric high grade glioma cell lines - MORF_MSH2, GNF2_MLH1, GCM_RAD21, DNA_replication_reactome; enriched in adult lines IL6_SCAR_FIBRO_UP, CROONQUIST_IL6_RAS_UP, TGFBETA_C1_UP. Nominal p value<0.001.

Mentions: In order to investigate the differences between the paediatric- and adult-derived cell lines at the gene expression level, we carried out expression profiling using Affymetrix U133 Plus2.0 arrays. For the comparison, we excluded the lines Res259 and Res186, derived from low-grade tumours, in order to avoid the possible confounding factors of grade. Despite the small number of lines profiled, we were able to identify 93 genes significantly differentially expressed between paediatric and adult high grade glioma cell lines (Figure 4A). The differentially expressed genes included several kinases which were validated by quantitative real-time RT-PCR (Figure 4B). These included members of the Src family kinases - LYN and the adaptor molecule CRKL, highly expressed in paediatric lines, along with SRC itself and also YES1. Also upregulated in the paediatric vs adult lines were several early response genes including FOS and FOSB. Highly expressed in the adult lines were the receptor tyrosine kinases EPHA6 and AXL, and also CDK9 and ILK.


Molecular and phenotypic characterisation of paediatric glioma cell lines as models for preclinical drug development.

Bax DA, Little SE, Gaspar N, Perryman L, Marshall L, Viana-Pereira M, Jones TA, Williams RD, Grigoriadis A, Vassal G, Workman P, Sheer D, Reis RM, Pearson AD, Hargrave D, Jones C - PLoS ONE (2009)

Expression profiling of paediatric and adult glioblastoma cell lines.(A) Heatmap demonstrating hierarchical clustering of 93 differentially expressed genes between paediatric (SF188, KNS42, UW479) and adult (LN229, A172, U118MG, U87MG, SF268) high grade glioma cell lines. (B) Quantitative real-time (TaqMan) RT-PCR confirming differential expression of CRKL, LYN, EPHA6 and AXL. Expression values are plotted relative to Universal Human Reference RNA. (C) Gene Set Enrichment Analysis highlighting co-ordinated differential expression of gene sets defined a priori. Enriched in paediatric high grade glioma cell lines - MORF_MSH2, GNF2_MLH1, GCM_RAD21, DNA_replication_reactome; enriched in adult lines IL6_SCAR_FIBRO_UP, CROONQUIST_IL6_RAS_UP, TGFBETA_C1_UP. Nominal p value<0.001.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2666263&req=5

pone-0005209-g004: Expression profiling of paediatric and adult glioblastoma cell lines.(A) Heatmap demonstrating hierarchical clustering of 93 differentially expressed genes between paediatric (SF188, KNS42, UW479) and adult (LN229, A172, U118MG, U87MG, SF268) high grade glioma cell lines. (B) Quantitative real-time (TaqMan) RT-PCR confirming differential expression of CRKL, LYN, EPHA6 and AXL. Expression values are plotted relative to Universal Human Reference RNA. (C) Gene Set Enrichment Analysis highlighting co-ordinated differential expression of gene sets defined a priori. Enriched in paediatric high grade glioma cell lines - MORF_MSH2, GNF2_MLH1, GCM_RAD21, DNA_replication_reactome; enriched in adult lines IL6_SCAR_FIBRO_UP, CROONQUIST_IL6_RAS_UP, TGFBETA_C1_UP. Nominal p value<0.001.
Mentions: In order to investigate the differences between the paediatric- and adult-derived cell lines at the gene expression level, we carried out expression profiling using Affymetrix U133 Plus2.0 arrays. For the comparison, we excluded the lines Res259 and Res186, derived from low-grade tumours, in order to avoid the possible confounding factors of grade. Despite the small number of lines profiled, we were able to identify 93 genes significantly differentially expressed between paediatric and adult high grade glioma cell lines (Figure 4A). The differentially expressed genes included several kinases which were validated by quantitative real-time RT-PCR (Figure 4B). These included members of the Src family kinases - LYN and the adaptor molecule CRKL, highly expressed in paediatric lines, along with SRC itself and also YES1. Also upregulated in the paediatric vs adult lines were several early response genes including FOS and FOSB. Highly expressed in the adult lines were the receptor tyrosine kinases EPHA6 and AXL, and also CDK9 and ILK.

Bottom Line: All lines proliferate as adherent monolayers and express glial markers.Copy number profiling revealed complex genomes including amplification and deletions of genes known to be pivotal in core glioblastoma signalling pathways.Expression profiling identified 93 differentially expressed genes which were able to distinguish between the adult and paediatric high grade cell lines, including a number of kinases and co-ordinated sets of genes associated with DNA integrity and the immune response.

View Article: PubMed Central - PubMed

Affiliation: Paediatric Oncology, The Institute of Cancer Research, Sutton, United Kingdom.

ABSTRACT

Background: Although paediatric high grade gliomas resemble their adult counterparts in many ways, there appear to be distinct clinical and biological differences. One important factor hampering the development of new targeted therapies is the relative lack of cell lines derived from childhood glioma patients, as it is unclear whether the well-established adult lines commonly used are representative of the underlying molecular genetics of childhood tumours. We have carried out a detailed molecular and phenotypic characterisation of a series of paediatric high grade glioma cell lines in comparison to routinely used adult lines.

Principal findings: All lines proliferate as adherent monolayers and express glial markers. Copy number profiling revealed complex genomes including amplification and deletions of genes known to be pivotal in core glioblastoma signalling pathways. Expression profiling identified 93 differentially expressed genes which were able to distinguish between the adult and paediatric high grade cell lines, including a number of kinases and co-ordinated sets of genes associated with DNA integrity and the immune response.

Significance: These data demonstrate that glioma cell lines derived from paediatric patients show key molecular differences to those from adults, some of which are well known, whilst others may provide novel targets for evaluation in primary tumours. We thus provide the rationale and demonstrate the practicability of using paediatric glioma cell lines for preclinical and mechanistic studies.

Show MeSH
Related in: MedlinePlus