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Global gene expression analysis of early response to chemotherapy treatment in ovarian cancer spheroids.

L'Espérance S, Bachvarova M, Tetu B, Mes-Masson AM, Bachvarov D - BMC Genomics (2008)

Bottom Line: However, the induction of genes linked to mechanisms of DNA replication and repair in cisplatin- and topotecan-treated OC spheroids could be associated with immediate adaptive response to treatment.Finally, multicellular growth conditions that are known to alter gene expression (including cell adhesion and cytoskeleton organization), could substantially contribute in reducing the initial effectiveness of CT drugs in OC spheroids.Results described in this study underscore the potential of the microarray technology for unraveling the complex mechanisms of CT drugs actions in OC spheroids and early cellular response to treatment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, Laval University, Québec (Québec), Canada. syles@hotmail.com

ABSTRACT

Background: Chemotherapy (CT) resistance in ovarian cancer (OC) is broad and encompasses diverse unrelated drugs, suggesting more than one mechanism of resistance. To better understand the molecular mechanisms controlling the immediate response of OC cells to CT exposure, we have performed gene expression profiling in spheroid cultures derived from six OC cell lines (OVCAR3, SKOV3, TOV-112, TOV-21, OV-90 and TOV-155), following treatment with 10,0 microM cisplatin, 2,5 microM paclitaxel or 5,0 microM topotecan for 72 hours.

Results: Exposure of OC spheroids to these CT drugs resulted in differential expression of genes associated with cell growth and proliferation, cellular assembly and organization, cell death, cell cycle control and cell signaling. Genes, functionally involved in DNA repair, DNA replication and cell cycle arrest were mostly overexpressed, while genes implicated in metabolism (especially lipid metabolism), signal transduction, immune and inflammatory response, transport, transcription regulation and protein biosynthesis, were commonly suppressed following all treatments. Cisplatin and topotecan treatments triggered similar alterations in gene and pathway expression patterns, while paclitaxel action was mainly associated with induction of genes and pathways linked to cellular assembly and organization (including numerous tubulin genes), cell death and protein synthesis. The microarray data were further confirmed by pathway and network analyses.

Conclusion: Most alterations in gene expression were directly related to mechanisms of the cytotoxics actions in OC spheroids. However, the induction of genes linked to mechanisms of DNA replication and repair in cisplatin- and topotecan-treated OC spheroids could be associated with immediate adaptive response to treatment. Similarly, overexpression of different tubulin genes upon exposure to paclitaxel could represent an early compensatory effect to this drug action. Finally, multicellular growth conditions that are known to alter gene expression (including cell adhesion and cytoskeleton organization), could substantially contribute in reducing the initial effectiveness of CT drugs in OC spheroids. Results described in this study underscore the potential of the microarray technology for unraveling the complex mechanisms of CT drugs actions in OC spheroids and early cellular response to treatment.

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Network analysis of dynamic gene expression in OC spheroids based on the 1.5-fold common gene expression list obtained following treatment with all CT drugs used (cisplatin, topotecan and paclitaxel). The five top-scoring networks were merged and are displayed graphically as node (genes/gene product) and edges (the biological relationships between the nodes). Intensity of the node color indicates the degree of up- (red) or downregulation (green). Nodes are displayed using various shapes that represent the functional class of the gene product (square, cytokine, vertical oval, transmembrane receptor, rectangle, nuclear receptor, diamond, enzyme, rhomboid, transporter, hexagon, translation factor, horizontal oval, transcription factor, circle, other). Edges are displayed with various labels that describe the nature of relationship between the nodes: ---- binding only, → acts on. The length of an edge reflect the evidence supporting that node-to-node relationship, in that edges supported by article from literature are shorter. Dotted edges represent indirect interaction.
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Figure 2: Network analysis of dynamic gene expression in OC spheroids based on the 1.5-fold common gene expression list obtained following treatment with all CT drugs used (cisplatin, topotecan and paclitaxel). The five top-scoring networks were merged and are displayed graphically as node (genes/gene product) and edges (the biological relationships between the nodes). Intensity of the node color indicates the degree of up- (red) or downregulation (green). Nodes are displayed using various shapes that represent the functional class of the gene product (square, cytokine, vertical oval, transmembrane receptor, rectangle, nuclear receptor, diamond, enzyme, rhomboid, transporter, hexagon, translation factor, horizontal oval, transcription factor, circle, other). Edges are displayed with various labels that describe the nature of relationship between the nodes: ---- binding only, → acts on. The length of an edge reflect the evidence supporting that node-to-node relationship, in that edges supported by article from literature are shorter. Dotted edges represent indirect interaction.

Mentions: A network analysis identified 34 highly significant networks with score ≥ 13 [see Additional file 2]. As expected, the five top-scoring networks were associated with functions linked to cellular growth and proliferation, cell cycle, cell death, cellular movement and metabolism (Table 3A). A common network obtained upon merging the five top-scoring networks (Figure 2) recognized several important nodes linked with numerous interaction partners, including cyclin-dependent kinase inhibitor 1A (CDKN1A, p21, Cip1), caspase 3 (CASP3), breast cancer 1 (BRCA1), proliferating cell nuclear antigen (PCNA), peroxisome proliferative activated receptor alpha (PPARA), cyclin D1 (CCND1), insulin receptor (INSR), integrin beta 1 (ITGB1), guanine nucleotide binding protein beta polypeptide 2-like 1 (GNB2L1), protein kinase C epsilon (PRKCE), SWI/SNF related, matrix associated actin dependent regulator of chromatin subfamily b, member 1 (SMARCB1), protein tyrosine phosphatase, non-receptor type 11 (PTPN11), low density lipoprotein receptor (LDLR), major histocompatibility complex class IA (HLA-A), discs, large homolog 1 (Drosophila) (DLG1), polo-like kinase 1 (PLK1) and colony stimulating factor 3 (CSF3). While the up-regulated gene nodes and related pathways were mostly associated with cell cycle arrest, induction of apoptosis (CASP3, CDKN1A) and DNA repair (BRCA1, PCNA), the down-regulated gene nodes were predominantly linked to control of cell cycle progression and cell proliferation (CCND1,GNB2L1,SMARCB1,DLG1,PLK1), carbohydrate and lipid metabolism (INSR, LDLR), intracellular signaling (PRKCE, PTPN11), cell adhesion (ITGB1) and immune response (HLA-A, CSF3). PPARA up-regulation could also contribute to reduced metabolism rates in treated spheroids by negatively regulating genes implicated in carbohydrate (PKLR) and mostly lipid (ACOT8, ACAA1, MGLL, PPARGC1B, DHCR24) metabolism (Figure 2).


Global gene expression analysis of early response to chemotherapy treatment in ovarian cancer spheroids.

L'Espérance S, Bachvarova M, Tetu B, Mes-Masson AM, Bachvarov D - BMC Genomics (2008)

Network analysis of dynamic gene expression in OC spheroids based on the 1.5-fold common gene expression list obtained following treatment with all CT drugs used (cisplatin, topotecan and paclitaxel). The five top-scoring networks were merged and are displayed graphically as node (genes/gene product) and edges (the biological relationships between the nodes). Intensity of the node color indicates the degree of up- (red) or downregulation (green). Nodes are displayed using various shapes that represent the functional class of the gene product (square, cytokine, vertical oval, transmembrane receptor, rectangle, nuclear receptor, diamond, enzyme, rhomboid, transporter, hexagon, translation factor, horizontal oval, transcription factor, circle, other). Edges are displayed with various labels that describe the nature of relationship between the nodes: ---- binding only, → acts on. The length of an edge reflect the evidence supporting that node-to-node relationship, in that edges supported by article from literature are shorter. Dotted edges represent indirect interaction.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279123&req=5

Figure 2: Network analysis of dynamic gene expression in OC spheroids based on the 1.5-fold common gene expression list obtained following treatment with all CT drugs used (cisplatin, topotecan and paclitaxel). The five top-scoring networks were merged and are displayed graphically as node (genes/gene product) and edges (the biological relationships between the nodes). Intensity of the node color indicates the degree of up- (red) or downregulation (green). Nodes are displayed using various shapes that represent the functional class of the gene product (square, cytokine, vertical oval, transmembrane receptor, rectangle, nuclear receptor, diamond, enzyme, rhomboid, transporter, hexagon, translation factor, horizontal oval, transcription factor, circle, other). Edges are displayed with various labels that describe the nature of relationship between the nodes: ---- binding only, → acts on. The length of an edge reflect the evidence supporting that node-to-node relationship, in that edges supported by article from literature are shorter. Dotted edges represent indirect interaction.
Mentions: A network analysis identified 34 highly significant networks with score ≥ 13 [see Additional file 2]. As expected, the five top-scoring networks were associated with functions linked to cellular growth and proliferation, cell cycle, cell death, cellular movement and metabolism (Table 3A). A common network obtained upon merging the five top-scoring networks (Figure 2) recognized several important nodes linked with numerous interaction partners, including cyclin-dependent kinase inhibitor 1A (CDKN1A, p21, Cip1), caspase 3 (CASP3), breast cancer 1 (BRCA1), proliferating cell nuclear antigen (PCNA), peroxisome proliferative activated receptor alpha (PPARA), cyclin D1 (CCND1), insulin receptor (INSR), integrin beta 1 (ITGB1), guanine nucleotide binding protein beta polypeptide 2-like 1 (GNB2L1), protein kinase C epsilon (PRKCE), SWI/SNF related, matrix associated actin dependent regulator of chromatin subfamily b, member 1 (SMARCB1), protein tyrosine phosphatase, non-receptor type 11 (PTPN11), low density lipoprotein receptor (LDLR), major histocompatibility complex class IA (HLA-A), discs, large homolog 1 (Drosophila) (DLG1), polo-like kinase 1 (PLK1) and colony stimulating factor 3 (CSF3). While the up-regulated gene nodes and related pathways were mostly associated with cell cycle arrest, induction of apoptosis (CASP3, CDKN1A) and DNA repair (BRCA1, PCNA), the down-regulated gene nodes were predominantly linked to control of cell cycle progression and cell proliferation (CCND1,GNB2L1,SMARCB1,DLG1,PLK1), carbohydrate and lipid metabolism (INSR, LDLR), intracellular signaling (PRKCE, PTPN11), cell adhesion (ITGB1) and immune response (HLA-A, CSF3). PPARA up-regulation could also contribute to reduced metabolism rates in treated spheroids by negatively regulating genes implicated in carbohydrate (PKLR) and mostly lipid (ACOT8, ACAA1, MGLL, PPARGC1B, DHCR24) metabolism (Figure 2).

Bottom Line: However, the induction of genes linked to mechanisms of DNA replication and repair in cisplatin- and topotecan-treated OC spheroids could be associated with immediate adaptive response to treatment.Finally, multicellular growth conditions that are known to alter gene expression (including cell adhesion and cytoskeleton organization), could substantially contribute in reducing the initial effectiveness of CT drugs in OC spheroids.Results described in this study underscore the potential of the microarray technology for unraveling the complex mechanisms of CT drugs actions in OC spheroids and early cellular response to treatment.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Medicine, Laval University, Québec (Québec), Canada. syles@hotmail.com

ABSTRACT

Background: Chemotherapy (CT) resistance in ovarian cancer (OC) is broad and encompasses diverse unrelated drugs, suggesting more than one mechanism of resistance. To better understand the molecular mechanisms controlling the immediate response of OC cells to CT exposure, we have performed gene expression profiling in spheroid cultures derived from six OC cell lines (OVCAR3, SKOV3, TOV-112, TOV-21, OV-90 and TOV-155), following treatment with 10,0 microM cisplatin, 2,5 microM paclitaxel or 5,0 microM topotecan for 72 hours.

Results: Exposure of OC spheroids to these CT drugs resulted in differential expression of genes associated with cell growth and proliferation, cellular assembly and organization, cell death, cell cycle control and cell signaling. Genes, functionally involved in DNA repair, DNA replication and cell cycle arrest were mostly overexpressed, while genes implicated in metabolism (especially lipid metabolism), signal transduction, immune and inflammatory response, transport, transcription regulation and protein biosynthesis, were commonly suppressed following all treatments. Cisplatin and topotecan treatments triggered similar alterations in gene and pathway expression patterns, while paclitaxel action was mainly associated with induction of genes and pathways linked to cellular assembly and organization (including numerous tubulin genes), cell death and protein synthesis. The microarray data were further confirmed by pathway and network analyses.

Conclusion: Most alterations in gene expression were directly related to mechanisms of the cytotoxics actions in OC spheroids. However, the induction of genes linked to mechanisms of DNA replication and repair in cisplatin- and topotecan-treated OC spheroids could be associated with immediate adaptive response to treatment. Similarly, overexpression of different tubulin genes upon exposure to paclitaxel could represent an early compensatory effect to this drug action. Finally, multicellular growth conditions that are known to alter gene expression (including cell adhesion and cytoskeleton organization), could substantially contribute in reducing the initial effectiveness of CT drugs in OC spheroids. Results described in this study underscore the potential of the microarray technology for unraveling the complex mechanisms of CT drugs actions in OC spheroids and early cellular response to treatment.

Show MeSH
Related in: MedlinePlus