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Exometabolom analysis of breast cancer cell lines: Metabolic signature.

Willmann L, Erbes T, Halbach S, Brummer T, Jäger M, Hirschfeld M, Fehm T, Neubauer H, Stickeler E, Kammerer B - Sci Rep (2015)

Bottom Line: Samples were analyzed by application of reversed phase chromatography coupled to a triple quadrupole mass spectrometer.Collectively, we determined 23 compounds from RNA metabolism, two from purine metabolism, five from polyamine/methionine cycle, one from histidine metabolism and two from nicotinate and nicotinamide metabolism.Differences in metabolite excretion resulting from cancerous metabolism can be integrated into altered processes on the cellular level.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.

ABSTRACT
Cancer cells show characteristic effects on cellular turnover and DNA/RNA modifications leading to elevated levels of excreted modified nucleosides. We investigated the molecular signature of different subtypes of breast cancer cell lines and the breast epithelial cell line MCF-10A. Prepurification of cell culture supernatants was performed by cis-diol specific affinity chromatography using boronate-derivatized polyacrylamide gel. Samples were analyzed by application of reversed phase chromatography coupled to a triple quadrupole mass spectrometer. Collectively, we determined 23 compounds from RNA metabolism, two from purine metabolism, five from polyamine/methionine cycle, one from histidine metabolism and two from nicotinate and nicotinamide metabolism. We observed major differences of metabolite excretion pattern between the breast cancer cell lines and MCF-10A, just as well as between the different breast cancer cell lines themselves. Differences in metabolite excretion resulting from cancerous metabolism can be integrated into altered processes on the cellular level. Modified nucleosides have great potential as biomarkers in due consideration of the heterogeneity of breast cancer that is reflected by the different molecular subtypes of breast cancer. Our data suggests that the metabolic signature of breast cancer cell lines might be a more subtype-specific tool to predict breast cancer, rather than a universal approach.

No MeSH data available.


Related in: MedlinePlus

Cellular RNA-metabolism (Abbrevations: DNA = Deoxyribonucleic acid; RNA = Ribonucleic acid; ER = Endoplasmatic reticulum; A-, G-, C-, UMP = Adenosine-, Guanosine-, Cytidine-, Uridine-mononucleotide; Involved enzymes: 1) e.g. RNA-Methyltransferases, 2) Nucleases, Phosphodiesterases (EC: 3.1.4) 3) Phosphatases (EC: 3.1.3) 4) Phosphorylases (EC: 2.4.1.1) 5) Nucleoside-phosphoribosyltransferases (EC: 2.7.1.48; EC: 2.7.1.20) 6) Nucleosidephosphatekinases (EC: 2.7.4.3; EC: 2.7.4.14) 7) Nucleoside-diphosphatekinases (EC: 2.7.4.10; EC: 2.7.4.6) 8) Helicase (EC: 3.6.4.12), DNA-Polymerase (EC: 2.7.7.7), DNA-Ligase (EC: 6.5.1.1); this figure has been drawn by LW).
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f1: Cellular RNA-metabolism (Abbrevations: DNA = Deoxyribonucleic acid; RNA = Ribonucleic acid; ER = Endoplasmatic reticulum; A-, G-, C-, UMP = Adenosine-, Guanosine-, Cytidine-, Uridine-mononucleotide; Involved enzymes: 1) e.g. RNA-Methyltransferases, 2) Nucleases, Phosphodiesterases (EC: 3.1.4) 3) Phosphatases (EC: 3.1.3) 4) Phosphorylases (EC: 2.4.1.1) 5) Nucleoside-phosphoribosyltransferases (EC: 2.7.1.48; EC: 2.7.1.20) 6) Nucleosidephosphatekinases (EC: 2.7.4.3; EC: 2.7.4.14) 7) Nucleoside-diphosphatekinases (EC: 2.7.4.10; EC: 2.7.4.6) 8) Helicase (EC: 3.6.4.12), DNA-Polymerase (EC: 2.7.7.7), DNA-Ligase (EC: 6.5.1.1); this figure has been drawn by LW).

Mentions: Nucleosides consist of a ribose moiety bound to a nucleobase via beta-glycosidic linkage. The common ribonucleosides adenosine, guanosine, uridine and cytidine as well as modified nucleosides are components of RNA. In the nucleolus, RNA can be modified post-transcriptionally by several enzymes resulting in modifications like methylation, hydroxylation, reduction, isomerization, sulfur/oxygen substitution or addition of sidechains11. Today over 100 modified nucleosides are known, present in different RNA types, such as tRNA, mRNA, rRNA and snRNA12. In general, all RNA types contain modifications, but tRNA is by far the most-modified RNA type regarding to extent and diversity of modifications. Modified RNA is degraded to modified nucleosides in the cytoplasm by nucleases, phosphodiesterases and phosphatases. Adenosine, guanosine, uridine and cytidine (Fig. 1) are phosphorylated, resulting in ribose-1-phosphate and the corresponding nucleobase. Afterwards the nucleobase is recycled to adenosine triphosphate (ATP), guanosine triphosphate (GTP), uridine triphosphate (UTP) or cytidine triphosphate (CTP) in the salvage pathway (Fig. 1) and returned into the nucleus. Alternatively, unmodified nucleosides can be excreted out of the cell and metabolized to uric acid, CO2, NH3, β-Aminoisobutyrate or β-Alanine. Due to the lack of specific kinases for synthesis of modified nucleoside triphosphates in mammalian cells, modified nucleosides do not enter the salvage pathway for RNA rebuilding and therefore they are excreted quantitatively as metabolic endproducts. Consequently, the insertion of modified nucleoside triphosphates into inappropriate positions in tRNA or rRNA is avoided13. In Fig. 2, some modified nucleosides are depicted.


Exometabolom analysis of breast cancer cell lines: Metabolic signature.

Willmann L, Erbes T, Halbach S, Brummer T, Jäger M, Hirschfeld M, Fehm T, Neubauer H, Stickeler E, Kammerer B - Sci Rep (2015)

Cellular RNA-metabolism (Abbrevations: DNA = Deoxyribonucleic acid; RNA = Ribonucleic acid; ER = Endoplasmatic reticulum; A-, G-, C-, UMP = Adenosine-, Guanosine-, Cytidine-, Uridine-mononucleotide; Involved enzymes: 1) e.g. RNA-Methyltransferases, 2) Nucleases, Phosphodiesterases (EC: 3.1.4) 3) Phosphatases (EC: 3.1.3) 4) Phosphorylases (EC: 2.4.1.1) 5) Nucleoside-phosphoribosyltransferases (EC: 2.7.1.48; EC: 2.7.1.20) 6) Nucleosidephosphatekinases (EC: 2.7.4.3; EC: 2.7.4.14) 7) Nucleoside-diphosphatekinases (EC: 2.7.4.10; EC: 2.7.4.6) 8) Helicase (EC: 3.6.4.12), DNA-Polymerase (EC: 2.7.7.7), DNA-Ligase (EC: 6.5.1.1); this figure has been drawn by LW).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544000&req=5

f1: Cellular RNA-metabolism (Abbrevations: DNA = Deoxyribonucleic acid; RNA = Ribonucleic acid; ER = Endoplasmatic reticulum; A-, G-, C-, UMP = Adenosine-, Guanosine-, Cytidine-, Uridine-mononucleotide; Involved enzymes: 1) e.g. RNA-Methyltransferases, 2) Nucleases, Phosphodiesterases (EC: 3.1.4) 3) Phosphatases (EC: 3.1.3) 4) Phosphorylases (EC: 2.4.1.1) 5) Nucleoside-phosphoribosyltransferases (EC: 2.7.1.48; EC: 2.7.1.20) 6) Nucleosidephosphatekinases (EC: 2.7.4.3; EC: 2.7.4.14) 7) Nucleoside-diphosphatekinases (EC: 2.7.4.10; EC: 2.7.4.6) 8) Helicase (EC: 3.6.4.12), DNA-Polymerase (EC: 2.7.7.7), DNA-Ligase (EC: 6.5.1.1); this figure has been drawn by LW).
Mentions: Nucleosides consist of a ribose moiety bound to a nucleobase via beta-glycosidic linkage. The common ribonucleosides adenosine, guanosine, uridine and cytidine as well as modified nucleosides are components of RNA. In the nucleolus, RNA can be modified post-transcriptionally by several enzymes resulting in modifications like methylation, hydroxylation, reduction, isomerization, sulfur/oxygen substitution or addition of sidechains11. Today over 100 modified nucleosides are known, present in different RNA types, such as tRNA, mRNA, rRNA and snRNA12. In general, all RNA types contain modifications, but tRNA is by far the most-modified RNA type regarding to extent and diversity of modifications. Modified RNA is degraded to modified nucleosides in the cytoplasm by nucleases, phosphodiesterases and phosphatases. Adenosine, guanosine, uridine and cytidine (Fig. 1) are phosphorylated, resulting in ribose-1-phosphate and the corresponding nucleobase. Afterwards the nucleobase is recycled to adenosine triphosphate (ATP), guanosine triphosphate (GTP), uridine triphosphate (UTP) or cytidine triphosphate (CTP) in the salvage pathway (Fig. 1) and returned into the nucleus. Alternatively, unmodified nucleosides can be excreted out of the cell and metabolized to uric acid, CO2, NH3, β-Aminoisobutyrate or β-Alanine. Due to the lack of specific kinases for synthesis of modified nucleoside triphosphates in mammalian cells, modified nucleosides do not enter the salvage pathway for RNA rebuilding and therefore they are excreted quantitatively as metabolic endproducts. Consequently, the insertion of modified nucleoside triphosphates into inappropriate positions in tRNA or rRNA is avoided13. In Fig. 2, some modified nucleosides are depicted.

Bottom Line: Samples were analyzed by application of reversed phase chromatography coupled to a triple quadrupole mass spectrometer.Collectively, we determined 23 compounds from RNA metabolism, two from purine metabolism, five from polyamine/methionine cycle, one from histidine metabolism and two from nicotinate and nicotinamide metabolism.Differences in metabolite excretion resulting from cancerous metabolism can be integrated into altered processes on the cellular level.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.

ABSTRACT
Cancer cells show characteristic effects on cellular turnover and DNA/RNA modifications leading to elevated levels of excreted modified nucleosides. We investigated the molecular signature of different subtypes of breast cancer cell lines and the breast epithelial cell line MCF-10A. Prepurification of cell culture supernatants was performed by cis-diol specific affinity chromatography using boronate-derivatized polyacrylamide gel. Samples were analyzed by application of reversed phase chromatography coupled to a triple quadrupole mass spectrometer. Collectively, we determined 23 compounds from RNA metabolism, two from purine metabolism, five from polyamine/methionine cycle, one from histidine metabolism and two from nicotinate and nicotinamide metabolism. We observed major differences of metabolite excretion pattern between the breast cancer cell lines and MCF-10A, just as well as between the different breast cancer cell lines themselves. Differences in metabolite excretion resulting from cancerous metabolism can be integrated into altered processes on the cellular level. Modified nucleosides have great potential as biomarkers in due consideration of the heterogeneity of breast cancer that is reflected by the different molecular subtypes of breast cancer. Our data suggests that the metabolic signature of breast cancer cell lines might be a more subtype-specific tool to predict breast cancer, rather than a universal approach.

No MeSH data available.


Related in: MedlinePlus