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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Cancer Discov. Author manuscript; available in PMC 2013 December 1.
Published in final edited form as:
PMCID: PMC3531869
NIHMSID: NIHMS415801

Metabolomics strategy reveals subpopulation of liposarcomas sensitive to gemcitabine treatment

Abstract

Unlike many cancers which exhibit glycolytic metabolism, high grade liposarcomas often exhibit low FDG uptake by PET despite rapid tumor growth. Here, we used liquid chromatography tandem mass spectrometry to identify carbon sources taken up by liposarcoma cell lines derived from patient xenograft tumors. Interestingly, we found that liposarcoma cell lines consume nucleosides from culture media, suggesting nucleoside salvage pathway activity. The nucleoside salvage pathway is dependent on deoxycytidine kinase (dCK) (1) and can be imaged in vivo by PET with 1-(2′-deoxy-2′-[18F]fluoroarabinofuranosyl) cytosine (FAC) (2). We found that liposarcoma cell lines and xenograft tumors exhibit dCK activity and dCK-dependent FAC uptake in vitro and in vivo. Additionally, liposarcoma cell lines and xenograft tumors are sensitive to treatment with the nucleoside analog prodrug gemcitabine, and gemcitabine sensitivity is dependent on dCK expression. Elevated dCK activity is evident in 7 out of 68 clinical liposarcoma samples analyzed. This data suggests that a subpopulation of liposarcoma patients have tumors with nucleoside salvage pathway activity that can be identified non-invasively using [18F]-FAC-PET and targeted using gemcitabine.

Keywords: deoxycytidine kinase, nucleoside salvage pathway, gemcitabine, liposarcoma, metabolomics, FAC-PET, cancer metabolism

Introduction

Sarcomas are tumors of mesenchymal origin with over 50 distinct histological subtypes (3). Liposarcomas are the most common soft tissue sarcomas accounting for roughly 20% of sarcomas (4). Based on cell morphology, liposarcomas can be classified into well-differentiated/dedifferentiated (WDLPS/DDLPS), myxoid/round cell, and pleomorphic subtypes (5). In over 90% of cases, WDLPS/DDLPS show an amplification of chromosome 12q13–15, which harbors genes such as CDK4 (regulates cell cycle) and MDM2 (negatively regulates p53 stability) (6). Patients with high grade liposarcoma have poor prognoses, and surgery is currently the best treatment option (7). However, tumors are frequently found in a visceral location which makes surgery difficult or impossible. Patients with unresectable liposarcomas are commonly treated with anthracyclines (doxorubicin), DNA alkylating agents (ifosfamide), anti-mitotic drugs (docetaxel), or anti-metabolites such as gemcitabine, but response to treatment is rare (3, 8), and biomarkers that stratify responders from non-responders are currently lacking (9).

Liposarcoma cells are difficult to propagate under cell culture conditions and few stable cell lines have been generated from tumor samples. We recently generated three dedifferentiated liposarcoma cell lines (LPS 1–3) from patient tumor xenografts in mice, all of which exhibit glycolytic metabolism by FDG-PET (Supplemental Figure 1). These cell lines recapitulate morphological and gene expression characteristics of the primary tumors even after continuous passages as xenograft tumors in mice and under cell culture conditions in vitro (10).

In this study, we used an unbiased metabolomics approach to assess nutrient uptake of liposarcoma cell lines and identified nucleoside salvage pathway activity. Using PET imaging with the cytidine derivative tracer FAC, we confirmed nucleoside salvage activity in liposarcoma xenograft tumors. Since the chemotherapeutic pro-drug gemcitabine is metabolized the same way as FAC, we found that liposarcoma cell lines are sensitive to nM amounts of gemcitabine in vitro, and liposarcoma xenograft tumors in mice regress upon gemcitabine treatment. These results suggest that PET imaging with cytidine derivative tracers can be used to detect liposarcoma patients who will benefit from gemcitabine treatment.

Results

Since patients with high grade liposarcoma frequently present to the clinic with low FDG uptake despite rapid tumor growth (Supplemental Figure 2), we took an unbiased approach to assess alternative carbon sources than glucose used by these fatal tumors to fuel proliferation. To this end, we analyzed changes in metabolite concentrations over time in liposarcoma cell culture media using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) and a NOVA BioProfile analyzer (Figure 1A and Supplemental Figures 3 and 4). We hypothesized that cellular uptake of nutrients would result in continuous decrease in media metabolite concentration over time. Ten metabolites were consistently consumed by the three liposarcoma cell lines analyzed (Figure 1B). In accordance with previous reports for other cancer types, multiple amino acids and amino acid precursors were among the consumed metabolites identified (1113). Interestingly, the nucleosides cytidine, thymidine and uridine were also continuously consumed by the liposarcoma cells analyzed (Figures 1C–E). These findings suggest that liposarcoma cell lines have nucleoside salvage pathway activity.

Figure 1
Mass spectrometry-based metabolomics identifies nucleosides amongst other nutrients consumed by liposarcoma cell lines in vitro

Figure 2A depicts the nucleoside salvage pathway which enables nucleoside uptake and conversion to nucleotide triphosphates that can be incorporated into DNA (14). dCK is required to catalyze the initial and rate-limiting phosphorylation of the nucleoside that traps the nucleotide inside the cell. To assess nucleoside salvage pathway activity in liposarcoma cell lines, we measured dCK activity and FAC uptake in vitro. Liposarcoma cell lines exhibit dCK expression and activity (Figure 2B) as well as tritiated FAC (3H-FAC) uptake in vitro (Figure 2C). Stable knockdown of dCK using short hairpin (sh)RNA reduces dCK activity and 3H-FAC uptake to background levels (Figures 2B and 2C). These results confirm dCK-dependent nucleoside salvage activity in liposarcoma cell lines in vitro.

Figure 2
Liposarcoma cell lines and xenograft tumors exhibit nucleoside salvage pathway activity

To determine whether liposarcoma cells exhibit nucleoside salvage activity in vivo, we established liposarcoma xenografts in immunocompromised NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice by subcutaneously injecting 5 × 105 liposarcoma cells into the neck area of the mouse. Imaging the mice with microPET/CT using D-18F-FAC (Figure 2D) revealed a similar biodistribution as seen in C57/BL6 mice(15), and quantification of three-dimensional regions of interest (ROIs) showed medium-high to high 18F-FAC uptake in liposarcoma xenografts (%ID/g >9) confirming nucleoside salvage activity in vivo.

To determine whether nucleoside salvage pathway activity contributes to proliferation in liposarcoma cell lines, we compared proliferation rates in the presence/absence of media nucleosides and dCK expression. Incubation of cultured liposarcoma cells in medium lacking nucleosides had no effect on proliferation rates (data not shown). Additionally, dCK knockdown did not affect proliferation rates nor glucose consumption, glutamine consumption, and lactate production rates (Supplemental Figures 5A and 5B). These data suggest that although liposarcoma cells exhibit nucleoside salvage activity, they are not dependent on this metabolic pathway for proliferation and survival. This phenotype is consistent with previously published results on the dCK knockout mouse which has a phenotype predominantly restricted to T- and B-lymphogenesis (16).

In order to determine whether the nucleoside salvage pathway activity observed in liposarcoma cell lines and xenograft tumors is reflective of the primary tumor from which they were derived, we measured dCK activity in protein lysates from the primary tumor, xenograft, and cell line for LPS1-3. As shown in Figure 2E, the amount of dCK activity is unchanged between samples from LPS2 and LPS3, while the amount of dCK activity in the LPS1-derived cell line is 2-fold lower compared to the corresponding primary and xenograft tumor tissue samples. These data suggest that all three primary liposarcoma tumors likely also exhibited nucleoside salvage pathway activity and that nucleoside salvage activity is unlikely to be an artifact of cell culture conditions.

A variety of chemotherapeutic prodrugs depend on nucleoside salvage activity in tumors for uptake and drug activation (17). For example, gemcitabine (dFdC), a derivative of cytidine and FAC, is critically dependent on dCK for its activation. Recent studies have suggested use of dCK as a potential prognostic marker for gemcitabine sensitivity in patients with pancreatic cancer (1821). Phosphorylated gemcitabine can be incorporated into DNA causing DNA synthesis to stall (22). In addition, diphosphorylated gemcitabine can bind and block the function of ribonucleotide reductase, an enzyme required for de novo nucleotide synthesis (18). This block in de novo synthesis causes a positive feedback loop that increases nucleoside salvage activity and potentiates the cytotoxic effect of gemcitabine (19). The nucleoside salvage pathway activity in liposarcoma cell lines and xenograft tumors suggests potential sensitivity to gemcitabine and other nucleoside derivative prodrugs.

To determine whether liposarcoma cell lines are sensitive to gemcitabine treatment, we incubated three liposarcoma cell lines for five days in the presence of various concentrations of gemcitabine and assessed cell viability. As demonstrated in Figure 3A, all three liposarcoma cell lines tested showed decreased viability upon incubation with gemcitabine with LC50 values in the low nM range. We confirmed cytotoxicity in the liposarcoma cell lines by observing increased propidium iodide staining upon treatment with 100 nM gemcitabine (Supplemental Figure 6). To determine whether gemcitabine also has a cytotoxic effect on liposarcoma cells in vivo, we treated mice with liposarcoma xenograft tumors with gemcitabine and measured the effect on tumor growth (schematic in Figure 3B). As shown in Figures 3C–E, gemcitabine treatment led to immediate and complete regression of tumors derived from each of the liposarcoma cell lines, while tumors in vehicle-treated mice exhibited continuous growth (see also Supplemental Figures 7A–D). Similar results were obtained on passaged xenograft tumors derived from a patient’s primary liposarcoma sample (Supplemental Figure 8). These data suggest that gemcitabine has a cytotoxic effect on liposarcoma tumors that exhibit nucleoside salvage pathway activity.

Figure 3
The nucleoside prodrug gemcitabine is cytotoxic to liposarcoma cell lines and xenograft tumors in mice

To estimate the population of liposarcoma patients with tumor nucleoside salvage pathway activity, we analyzed our previously published mRNA expression data generated from the tumors of patients with various liposarcoma subtypes (23). As shown in Supplemental Figure 9A, we assessed the transcriptional expression levels of nucleoside transporters (SLC28A1, SLC29A1) and enzymes in the nucleoside salvage pathway (dCK, CDA, dCTD, NT5E). 10 out of 74 patient samples (13.5%) showed increased dCK mRNA expression levels. We also assessed dCK, CDA and DCTD protein expression levels in 9 primary liposarcoma tumors, including those used to generate the liposarcoma cell lines, LPS1-3. As shown in Supplemental Figures 9B and 9C, dCK, CDA and DCTD protein expression varies across liposarcoma samples. However, recent publications have shown that dCK can be post-translationally modified (24); therefore, the relationship between dCK expression and activity is not precise. To overcome this limitation, we measured dCK activity in liposarcoma tumor samples from patients. Tumor tissue samples from 68 liposarcoma patients with various histological subtypes were analyzed for dCK activity. As shown in Figure 4A, four additional liposarcoma tumor samples (LPS12, 17, 51, and 55) had dCK kinase activity levels comparable to the liposarcoma samples from which we generated cell lines (LPS1-3). Together, 7 out of 68 (10%) tumor tissues showed elevated dCK kinase activity. These results raise the interesting possibility that a subset of liposarcoma patients have tumors with nucleoside salvage activity that may be detectable using PET with FAC (or a FAC derivative) and targeted using gemcitabine.

Figure 4
dCK activity is elevated in 10% of liposarcomas and is required for response to gemcitabine treatment

To determine whether nucleoside salvage activity is required for gemcitabine sensitivity in liposarcomas, we reduced nucleoside salvage activity in the LPS2 liposarcoma cell line by stable knockdown of dCK and examined the resultant effects on gemcitabine response in vitro and in vivo. Similar to the results shown in Figure 2, dCK knockdown in LPS2 cells led to reduced dCK activity, reduced dCK protein expression, and reduced [3H]-FAC uptake when compared to the scrambled shRNA-expressing control cells (Supplemental Figures 10A–C). dCK knockdown in LPS2 cells showed a 1000-fold decrease in gemcitabine sensitivity – the LC50 values for gemcitabine in scrambled shRNA-expressing cells were in the nanomolar range, whereas the LC50 values for gemcitabine in dCK shRNA-expressing cells were in the micromolar range (Figure 4B). To determine whether PET imaging using [18F]-FAC can distinguish between xenografted tumors from dCK knockdown versus scrambled shRNA-expressing control cells in the same mouse, we injected 5×105 cells of each liposarcoma cell line into the flanks of immunocompromised mice (Scr cells into the left and ΔdCK cells into the right flanks). We imaged the mice with [18F]-FAC-PET and quantified tumor FAC uptake using AMIDE software (Figure 4C and Supplemental Figures 10D and E). Tumors from LPS2 cells expressing scrambled shRNA had a 2.8-fold higher FAC uptake compared to tumors of the same size expressing dCK knockdown shRNA (Figure 4C). Mice bearing both dCK knockdown and scrambled shRNA control tumors of equal size were treated with gemcitabine. As shown in Figures 4C and D, tumors expressing scrambled shRNA decreased in size when treated with gemcitabine, however dCK knockdown tumors exhibited continuous growth. In contrast, both tumors in PBS-treated mice grew at roughly the same speed and exhibited similar [18F]-FDG uptake when imaged with microPET/CT (Supplemental Figures 10E and F). These results suggest that dCK and nucleoside salvage activity are necessary for gemcitabine response in liposarcomas, and PET imaging with [18F]-FAC (or FAC derivative) could be employed to identify liposarcoma patients with this metabolic phenotype.

Discussion

Liposarcomas are deadly tumors, and surgical intervention remains the best treatment option. However, surgery is not an option for patients with tumors in visceral locations. Unfortunately, the success rate for chemotherapeutic agents in liposarcoma is low, and biomarkers indicating patients likely to respond are lacking. In this study, we set out to identify alternative carbon sources than glucose used by liposarcoma cell lines derived from patient xenograft tumors. To this end, we employed mass spectrometry-based metabolic footprint analysis, and identified nucleosides amongst other metabolites consumed by liposarcoma cell lines. We confirmed nucleoside salvage activity in liposarcoma cell lines and xenograft tumors using the cytidine-derivative PET tracer FAC.

Nucleoside derivative pro-drugs such as gemcitabine rely on nucleoside salvage activity, which is dependent on the activity of various proteins including nucleoside transporters and kinases. The rate limiting step in the nucleoside salvage pathway is the initial phosphorylation catalyzed by dCK (20). While expression of nucleoside transporters and dCK is critical for nucleoside salvage activity, metabolic flux through this pathway is complex and determined by various mechanisms of regulation. For instance, dCK is post-transcriptionally regulated by HuR (25), post-translationally regulated by phosphorylation at Ser-74 by DNA damage-sensing kinases (24, 26), and biochemically regulated in a negative feedback mechanism by elevated dCTP levels (26). Flux through the nucleoside salvage pathway and gemcitabine sensitivity can also be negatively modulated by cytidine deaminase (CDA) activity, which deaminates cytidine/deoxycytidine into uridine/deoxyuridine and inactivates gemcitabine (27). Since we found that liposarcoma cell lines and xenograft tumors are not dependent on nucleoside salvage activity for proliferation, decreased dCK or increased CDA activity are potential mechanisms of gemcitabine resistance in liposarcoma patients.

Several recent publications have discussed relationships between dCK and CDA expression levels and sensitivity to gemcitabine treatment in pancreatic cancer (18, 19, 21, 26, 27). Marechal et al. found that dCK protein expression levels can be used as a predictive marker for disease-free survival and overall survival after adjuvant gemcitabine treatment in pancreatic adenocarcinoma (21). Frese et al. found that decreased CDA protein expression associated with paclitaxel treatment enhanced gemcitabine sensitivity in pancreatic (27). However, given the complex regulation of nucleoside salvage activity (22, 23, 24), use of dCK and/or CDA expression levels as markers for gemcitabine sensitivity may not be as valuable as PET imaging with FAC. Since FAC is subjected to the same metabolic processes as gemcitabine, FAC-PET is a functional readout of gemcitabine sensitivity and likely more suitable for stratification of patient responders to nucleoside pro-drug treatments such as gemcitabine.

Here we show that dCK expression and activity is elevated in about 10% of primary liposarcoma tumors and that the efficacy of gemcitabine treatment is dependent on dCK activity. However, the molecular mechanisms by which dCK activity is elevated in liposarcomas remain unknown. The dCK promoter contains an E-box element conserved across primates, suggesting potential transcriptional regulation by MYC. However, patient liposarcoma samples with elevated dCK activity did not consistently exhibit elevated MYC expression or transcriptional activity (data not shown). Additionally, we analyzed mRNA expression data from 74 primary liposarcoma tumors for a potential connection between dCK and CDK4 and/or MDM2 expression; however, our analysis did not indicate any correlation between dCK and CDK4 or MDM2 at the transcriptional level (data not shown).

In addition to nucleosides, we also identified other metabolites commonly consumed by liposarcoma cell lines including amino acids and amino acid precursors. Our preliminary studies have shown that liposarcoma cell lines are highly dependent on glutamine consumption (data not shown), consistent with findings in other cancer cell types (28). It is interesting to note that various genes important for glutaminolysis are under the transcriptional control of the MYC oncogene (29). Therefore MYC could potentially drive metabolic reprogramming in liposarcoma cells towards both increased amino acid consumption (predominantly glutamine) and nucleoside salvage activity. However, primary liposarcoma tumors show varying levels of MYC protein expression (data not shown), and further investigation is necessary to determine whether MYC plays a role in liposarcoma transformation.

In summary, we used a mass spectrometry-based metabolomics approach to analyze liposarcoma metabolism and identified nucleoside salvage pathway activity in a subset of patients’ tumors. Additionally, we showed that liposarcoma xenograft tumors with nucleoside salvage activity can be imaged in vivo using the cytidine-derivative PET tracer [18F]-FAC and respond to treatment with the nucleoside-based prodrug gemcitabine. By analyzing dCK activity in primary liposarcoma samples, we estimate the population of liposarcoma patients with tumor nucleoside salvage activity to be around 10%. Together, these findings could directly impact management and treatment of liposarcoma patients since they suggest that PET imaging with cytidine-derivative PET tracers may identify potential responders to gemcitabine treatment. However, further work is needed to determine whether liposarcoma nucleoside salvage activity can successfully stratify gemcitabine responders from non-responders in the clinic. Nonetheless, identification of nucleoside salvage activity in a subset of liposarcomas suggests a promising new strategy to identify patients with this otherwise fatal disease who will benefit from nucleoside prodrug treatment.

Materials and Methods

Generation and culturing conditions of liposarcoma cell lines

The generation of the liposarcoma cell lines has been described previously (10) and was confirmed by histology and microarray analysis. All cell lines were originally grown in DMEM/F12 medium; LPS2 was subsequently grown in DMEM medium (10% FBS, 1% Pen/Strep). Cell numbers were counted using a Beckman Coulter Z1 Particle Counter.

Xenograft models, drug efficacy assay, and microPET/CT imaging

Liposarcoma tumor xenografts were generated by subcutaneously injecting 2.5x (LPS2) or 5x 105 (LPS1 and 3) cells into female NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice. Drug treatment was started once tumors reached a size of 5×5 to 8×8 mm2 and was performed by i.p. injection of 360 mg/kg gemcitabine (Eli Lilly) dissolved in PBS and, subsequently, 180 mg/kg every fourth day. Control animals were injected with an equal volume of PBS. Tumor size was monitored every second day with a caliper, and animals were euthanized once the tumors reached a size of 15×15 mm2. For microPET imaging, animals were anesthetized with 1.5% isoflurane, USP (Phoenix Pharmaceutical Inc.) and injected i.v. with 200 μCi 18F-FAC. PET imaging was performed on a Focus 220 microPET scanner (Siemens) and, subsequently, CT recorded using a MicroCAT II CT instrument (Siemens). Data was analyzed by drawing three-dimensional ROIs using AMIDE software (30).

Mass spectrometry-based metabolomic analysis of cell culture medium

5×105 liposarcoma cells per well were seeded onto a 6-well plate, medium replaced after 24 hours, and 20 μl cell-free medium samples taken every 24 hours thereafter. Metabolites were extracted by adding 300 μl 80% methanol (−80 °C) to the medium samples followed by centrifugation for 5 min at 13 krpm at 4 °C. The supernatant was transferred into a fresh tube, and the solvent was evaporated using a SpeedVac. Dried metabolites were resolved in HPLC-grade water and analyzed as described previously (31).

Significance

Patients with high grade liposarcoma have poor prognoses and often fail to respond to chemotherapy. This report identifies elevated nucleoside salvage activity in a subset of liposarcomas that are identifiable using non-invasive PET imaging with FAC and sensitive to gemcitabine. Thus we suggest a new treatment paradigm for liposarcoma patients involving stratification of gemcitabine-responders from non-responders in the clinic using FAC-PET.

Supplementary Material

Acknowledgments

Grant support: HRC is a Damon Runyon-Rachleff Innovation Awardee supported (in part) by the Damon Runyon Cancer Research Foundation, the Searle Scholars Program, the NIH Director’s New Innovator Award (DP2 OD008454-01), and the Caltech/UCLA Nanosystems Biology Cancer Center (NCI U54 CA151819). This work was supported in part by the NIH (P50CA0863062 to HW and FCE).

We kindly thank Drs. Caius Radu and Johannes Czernin for invaluable discussions on experimental design and manuscript preparation, Dr. David Stout and Waldemar Ladno for expert help with the microPET/CT, and Dr. Nagichettiar Satyamurthy and the cyclotron staff for the production of [18F]-FDG and [18F]-FAC.

Abbreviations

dCK
deoxycytidine kinase
PET
positron emission tomography
FAC
1-(2′-deoxy-2′-[18F]fluoroarabinofuranosyl) cytosine
LC-MS/MS
liquid chromatography coupled with tandem mass spectrometry
WDLPS/DDLPS
well-differentiated/dedifferentiated liposarcoma

Footnotes

Conflict of interest statement: ONW is an inventor of national and Patent Cooperation Treaty (PCT) patent applications for FAC technology referred to in the article. ONW is also involved in Sofie Biosciences, a startup company that has licensed this intellectual property. All other authors declare no conflict of interest.

Additional materials and methods can be found in the Supplemental Information.

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