Limits...
Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines.

Cody NA, Zietarska M, Filali-Mouhim A, Provencher DM, Mes-Masson AM, Tonin PN - BMC Med Genomics (2008)

Bottom Line: An overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group.However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.The various alternative in vivo and in vitro growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the in vitro cell line models are a viable option for testing gene candidates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, McGill University, Montreal, Canada. neal.cody@mail.mcgill.ca

ABSTRACT

Background: Expression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease. A possible variable is the influence of growth conditions on discerning candidates. The present study examined the influence of growth conditions on the expression of chromosome 3 genes in the tumorigenic EOC cell lines, OV-90, TOV-21G and TOV-112D using Affymetrix GeneChip(R) HG-U133A expression microarray analysis.

Methods: Chromosome 3 gene expression profiles (n = 1147 probe sets, representing 735 genes) were extracted from U133A expression microarray analyses of the EOC cell lines OV-90, TOV-21G and TOV-112D that were grown as monolayers, spheroids or nude mouse xenografts and monolayers derived from these tumors. Hierarchical cluster analysis was performed to compare chromosome 3 transcriptome patterns of each growth condition. Differentially expressed genes were identified and characterized by two-way comparative analyses of fold-differences in gene expression between monolayer cultures and each of the other growth conditions, and between the maximum and minimum values of expression of all growth conditions for each EOC cell line.

Results: An overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group. Two-way comparative analysis of each EOC cell line grown in an alternative condition relative to the monolayer culture showed that overall less than 15% of probe sets exhibited at least a 3-fold difference in expression profile. Less than 23% of probe sets exhibited greater than 3-fold differences in gene expression in comparisons of the maximum and minimum value of expression of all growth conditions within each EOC cell line group. The majority of these differences were less than 5-fold. There were 17 genes in common which were differentially expressed in all EOC cell lines. However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.

Conclusion: The various alternative in vivo and in vitro growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the in vitro cell line models are a viable option for testing gene candidates.

No MeSH data available.


Related in: MedlinePlus

Range of expression of differentially expressed 3p genes for TOV-112D. The expression values of all of the growth conditions are shown for genes exhibiting greater than 3-fold differences in gene expression between the monolayer cultures and any alternative growth condition for TOV-112D; and greater than 3-fold differences between the maximum and minimum value of expression determined for any growth condition for TOV-112D. The growth conditions are abbreviated as follows: monolayer culture (L), and alternative growth conditions consisting of spheroid cultures (S), xenograft tumors derived from subcutaneous (TSC) or intraperitoneal (TIP) injection sites in nude mice, and monolayer cultures derived from these tumors (LSC and LIP). For comparative purposes the expression values of the monolayer cultures are linked with a line. The gene name and probe set number are indicated, and are ordered (not to scale) based on the Human Genome Browser March 2006 (hg 18) assembly (UCSC Genome Bioinformatics database). The expression profiles are organized relative to the position of the probe sets (genes) for the 3ptel – 3pcen chromosome arm for TOV-112D. The arrows indicate the genes exhibiting differential expression greater than 3-fold in any comparative analyses that were found in common with all three EOC cell lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2519080&req=5

Figure 9: Range of expression of differentially expressed 3p genes for TOV-112D. The expression values of all of the growth conditions are shown for genes exhibiting greater than 3-fold differences in gene expression between the monolayer cultures and any alternative growth condition for TOV-112D; and greater than 3-fold differences between the maximum and minimum value of expression determined for any growth condition for TOV-112D. The growth conditions are abbreviated as follows: monolayer culture (L), and alternative growth conditions consisting of spheroid cultures (S), xenograft tumors derived from subcutaneous (TSC) or intraperitoneal (TIP) injection sites in nude mice, and monolayer cultures derived from these tumors (LSC and LIP). For comparative purposes the expression values of the monolayer cultures are linked with a line. The gene name and probe set number are indicated, and are ordered (not to scale) based on the Human Genome Browser March 2006 (hg 18) assembly (UCSC Genome Bioinformatics database). The expression profiles are organized relative to the position of the probe sets (genes) for the 3ptel – 3pcen chromosome arm for TOV-112D. The arrows indicate the genes exhibiting differential expression greater than 3-fold in any comparative analyses that were found in common with all three EOC cell lines.

Mentions: There were 17 genes which were found differentially expressed greater than 3-fold in all EOC cell lines (Additional file 1). These genes may represent those that could be affected by growth condition or tumor microenvironment [13]. Notable is that the patterns of expression of these 17 genes were not necessarily the same for each growth condition when one cell line is compared with another. For example in OV-90, the maximum value of expression of RIS1 was found with the monolayer culture (L) and both subcutaneous (TSC) and intraperitoneal (TIP) xenografts exhibited the lowest values of expression of this gene (Figure 5), whereas the highest level of expression of RIS1 in TOV-112D was found with the subcutaneous (TSC) xenograft sample and the lowest value was observed with intraperitoneal (TIP) xenograft (Figure 9).


Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines.

Cody NA, Zietarska M, Filali-Mouhim A, Provencher DM, Mes-Masson AM, Tonin PN - BMC Med Genomics (2008)

Range of expression of differentially expressed 3p genes for TOV-112D. The expression values of all of the growth conditions are shown for genes exhibiting greater than 3-fold differences in gene expression between the monolayer cultures and any alternative growth condition for TOV-112D; and greater than 3-fold differences between the maximum and minimum value of expression determined for any growth condition for TOV-112D. The growth conditions are abbreviated as follows: monolayer culture (L), and alternative growth conditions consisting of spheroid cultures (S), xenograft tumors derived from subcutaneous (TSC) or intraperitoneal (TIP) injection sites in nude mice, and monolayer cultures derived from these tumors (LSC and LIP). For comparative purposes the expression values of the monolayer cultures are linked with a line. The gene name and probe set number are indicated, and are ordered (not to scale) based on the Human Genome Browser March 2006 (hg 18) assembly (UCSC Genome Bioinformatics database). The expression profiles are organized relative to the position of the probe sets (genes) for the 3ptel – 3pcen chromosome arm for TOV-112D. The arrows indicate the genes exhibiting differential expression greater than 3-fold in any comparative analyses that were found in common with all three EOC cell lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2519080&req=5

Figure 9: Range of expression of differentially expressed 3p genes for TOV-112D. The expression values of all of the growth conditions are shown for genes exhibiting greater than 3-fold differences in gene expression between the monolayer cultures and any alternative growth condition for TOV-112D; and greater than 3-fold differences between the maximum and minimum value of expression determined for any growth condition for TOV-112D. The growth conditions are abbreviated as follows: monolayer culture (L), and alternative growth conditions consisting of spheroid cultures (S), xenograft tumors derived from subcutaneous (TSC) or intraperitoneal (TIP) injection sites in nude mice, and monolayer cultures derived from these tumors (LSC and LIP). For comparative purposes the expression values of the monolayer cultures are linked with a line. The gene name and probe set number are indicated, and are ordered (not to scale) based on the Human Genome Browser March 2006 (hg 18) assembly (UCSC Genome Bioinformatics database). The expression profiles are organized relative to the position of the probe sets (genes) for the 3ptel – 3pcen chromosome arm for TOV-112D. The arrows indicate the genes exhibiting differential expression greater than 3-fold in any comparative analyses that were found in common with all three EOC cell lines.
Mentions: There were 17 genes which were found differentially expressed greater than 3-fold in all EOC cell lines (Additional file 1). These genes may represent those that could be affected by growth condition or tumor microenvironment [13]. Notable is that the patterns of expression of these 17 genes were not necessarily the same for each growth condition when one cell line is compared with another. For example in OV-90, the maximum value of expression of RIS1 was found with the monolayer culture (L) and both subcutaneous (TSC) and intraperitoneal (TIP) xenografts exhibited the lowest values of expression of this gene (Figure 5), whereas the highest level of expression of RIS1 in TOV-112D was found with the subcutaneous (TSC) xenograft sample and the lowest value was observed with intraperitoneal (TIP) xenograft (Figure 9).

Bottom Line: An overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group.However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.The various alternative in vivo and in vitro growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the in vitro cell line models are a viable option for testing gene candidates.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, McGill University, Montreal, Canada. neal.cody@mail.mcgill.ca

ABSTRACT

Background: Expression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease. A possible variable is the influence of growth conditions on discerning candidates. The present study examined the influence of growth conditions on the expression of chromosome 3 genes in the tumorigenic EOC cell lines, OV-90, TOV-21G and TOV-112D using Affymetrix GeneChip(R) HG-U133A expression microarray analysis.

Methods: Chromosome 3 gene expression profiles (n = 1147 probe sets, representing 735 genes) were extracted from U133A expression microarray analyses of the EOC cell lines OV-90, TOV-21G and TOV-112D that were grown as monolayers, spheroids or nude mouse xenografts and monolayers derived from these tumors. Hierarchical cluster analysis was performed to compare chromosome 3 transcriptome patterns of each growth condition. Differentially expressed genes were identified and characterized by two-way comparative analyses of fold-differences in gene expression between monolayer cultures and each of the other growth conditions, and between the maximum and minimum values of expression of all growth conditions for each EOC cell line.

Results: An overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group. Two-way comparative analysis of each EOC cell line grown in an alternative condition relative to the monolayer culture showed that overall less than 15% of probe sets exhibited at least a 3-fold difference in expression profile. Less than 23% of probe sets exhibited greater than 3-fold differences in gene expression in comparisons of the maximum and minimum value of expression of all growth conditions within each EOC cell line group. The majority of these differences were less than 5-fold. There were 17 genes in common which were differentially expressed in all EOC cell lines. However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.

Conclusion: The various alternative in vivo and in vitro growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the in vitro cell line models are a viable option for testing gene candidates.

No MeSH data available.


Related in: MedlinePlus