Synthetic lethality occurs when the inhibition of two genes is lethal while the inhibition of each single gene is not. It can be harnessed to selectively treat cancer by identifying inactive genes in ...a given cancer and targeting their synthetic lethal (SL) partners. We present a data-driven computational pipeline for the genome-wide identification of SL interactions in cancer by analyzing large volumes of cancer genomic data. First, we show that the approach successfully captures known SL partners of tumor suppressors and oncogenes. We then validate SL predictions obtained for the tumor suppressor VHL. Next, we construct a genome-wide network of SL interactions in cancer and demonstrate its value in predicting gene essentiality and clinical prognosis. Finally, we identify synthetic lethality arising from gene overactivation and use it to predict drug efficacy. These results form a computational basis for exploiting synthetic lethality to uncover cancer-specific susceptibilities.
Display omitted
•Genome-scale data-driven identification of synthetic lethality in cancer•Synthetic lethality networks successfully predict cancer gene essentiality•Synthetic lethality networks predict 15 year survival in breast cancer patients•Synthetic dosage lethality networks predict drug response in cancer
A data-driven computational pipeline named DAISY captures known and novel synthetic lethal (SL) interactions, enabling the utilization of genome-wide cancer SL networks to predict gene essentiality, drug response, and clinical prognosis.
Background: Tumor patients exhibit an increased peripheral demand of fatty acids and protein. Contrarily, tumors utilize glucose as their main source of energy supply. Thus, a diet supplying the ...cancer patient with sufficient fat and protein for his demands while restricting the carbohydrates (CHO) tumors thrive on, could be a helpful strategy in improving the patients' situation. A ketogenic diet (KD) fulfills these requirements. Therefore, we performed a pilot study to investigate the feasibility of a KD and its influence on the quality of life of patients with advanced metastatic tumors. Methods: Sixteen patients with advanced metastatic tumors and no conventional therapeutic options participated in the study. The patients were instructed to follow a KD (less than 70 g CHO per day) with normal groceries and were provided with a supply of food additives to mix a protein/fat shake to simplify the 3-month intervention period. Quality of life assessed by EORTC QLQ-C30 (version 2), serum and general health parameters were determined at baseline, after every two weeks of follow-up, or after drop out. The effect of dietary change on metabolism was monitored daily by measuring urinary ketone bodies. Results: One patient did not tolerate the diet and dropped out within 3 days. Among those who tolerated the diet, two patients died early, one stopped after 2 weeks due to personal reasons, one felt unable to stick to the diet after 4 weeks, one stopped after 6 and two stopped after 7 and 8 weeks due to progress of the disease, one had to discontinue after 6 weeks to resume chemotherapy and five completed the 3 month intervention period. These five and the one who resumed chemotherapy after 6 weeks report an improved emotional functioning and less insomnia, while several other parameters of quality of life remained stable or worsened, reflecting their very advanced disease. Except for temporary constipation and fatigue, we found no severe adverse side effects, especially no changes in cholesterol or blood lipids. Conclusions: These pilot data suggest that a KD is suitable for even advanced cancer patients. It has no severe side effects and might improve aspects of quality of life and blood parameters in some patients with advanced metastatic tumors.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK, VSZLJ
Among the most prominent metabolic alterations in cancer cells are the increase in glucose consumption and the conversion of glucose to lactic acid via the reduction of pyruvate even in the presence ...of oxygen. This phenomenon, known as aerobic glycolysis or the Warburg effect, may provide a rationale for therapeutic strategies that inhibit tumour growth by administration of a ketogenic diet with average protein but low in carbohydrates and high in fat enriched with omega-3 fatty acids and medium-chain triglycerides (MCT).
Twenty-four female NMRI nude mice were injected subcutaneously with tumour cells of the gastric adenocarcinoma cell line 23132/87. The animals were then randomly split into two feeding groups and fed either a ketogenic diet (KD group; n = 12) or a standard diet (SD group; n = 12) ad libitum. Experiments were ended upon attainment of the target tumor volume of 600 mm3 to 700 mm3. The two diets were compared based on tumour growth and survival time (interval between tumour cell injection and attainment of target tumour volume).
The ketogenic diet was well accepted by the KD mice. The tumour growth in the KD group was significantly delayed compared to that in the SD group. Tumours in the KD group reached the target tumour volume at 34.2 +/- 8.5 days versus only 23.3 +/- 3.9 days in the SD group. After day 20, tumours in the KD group grew faster although the differences in mean tumour growth continued significantly. Importantly, they revealed significantly larger necrotic areas than tumours of the SD group and the areas with vital tumour cells appear to have had fewer vessels than tumours of the SD group. Viable tumour cells in the border zone surrounding the necrotic areas of tumours of both groups exhibited a glycolytic phenotype with expression of glucose transporter-1 and transketolase-like 1 enzyme.
Application of an unrestricted ketogenic diet enriched with omega-3 fatty acids and MCT delayed tumour growth in a mouse xenograft model. Further studies are needed to address the impact of this diet on other tumour-relevant functions such as invasive growth and metastasis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Currently available cell culture media may not reproduce the in vivo metabolic environment of tumors. To demonstrate this, we compared the effects of a new physiological medium, Plasmax, with ...commercial media. We prove that the disproportionate nutrient composition of commercial media imposes metabolic artifacts on cancer cells. Their supraphysiological concentrations of pyruvate stabilize hypoxia-inducible factor 1α in normoxia, thereby inducing a pseudohypoxic transcriptional program. In addition, their arginine concentrations reverse the urea cycle reaction catalyzed by argininosuccinate lyase, an effect not observed in vivo, and prevented by Plasmax in vitro. The capacity of cancer cells to form colonies in commercial media was impaired by lipid peroxidation and ferroptosis and was rescued by selenium present in Plasmax. Last, an untargeted metabolic comparison revealed that breast cancer spheroids grown in Plasmax approximate the metabolic profile of mammary tumors better. In conclusion, a physiological medium improves the metabolic fidelity and biological relevance of in vitro cancer models.
Overexpression of transketolase-like 1 protein TKTL1 in cancer cells has been reported to correlate with enhanced glycolysis and lactic acid production. Furthermore, enhanced TKTL1 expression was put ...into context with resistance to chemotherapy and ionizing radiation. Here, a panel of human malign and benign cells, which cover a broad range of chemotherapy and radiation resistance as well as reliance on glucose metabolism, was analyzed in vitro for TKTL1 expression.
17 malign and three benign cell lines were characterized according to their expression of TKTL1 on the protein level with three commercially available anti-TKTL1 antibodies utilizing immunohistochemistry and Western blot, as well as on mRNA level with three published primer pairs for RT-qPCR. Furthermore, sensitivities to paclitaxel, cisplatin and ionizing radiation were assessed in cell survival assays. Glucose consumption and lactate production were quantified as surrogates for the "Warburg effect".
Considerable amounts of tktl1 mRNA and TKTL1 protein were detected only upon stable transfection of the human embryonic kidney cell line HEK293 with an expression plasmid for human TKTL1. Beyond that, weak expression of endogenous tktl1 mRNA was measured in the cell lines JAR and U251. Western blot analysis of JAR and U251 cells did not detect TKTL1 at the expected size of 65 kDa with all three antibodies specific for TKTL1 protein and immunohistochemical staining was observed with antibody JFC12T10 only. All other cell lines tested here revealed expression of tktl1 mRNA below detection limits and were negative for TKTL1 protein. However, in all cell lines including TKTL1-negative HEK293-control cells, antibody JFC12T10 detected multiple proteins with different molecular weights. Importantly, JAR and U251 did neither demonstrate an outstanding production of lactic acid nor increased resistance against chemotherapeutics or to ionizing radiation, respectively.
Using RT-qPCR and three different antibodies we observed only exceptional occurrence of TKTL1 in a panel of malignant human cell lines in vitro. The presence of TKTL1 was unrelated to either the rate of glucose consumption/lactic acid production or resistance against chemo- and radiotherapy.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Charakteristisch für viele maligne Tumorzellen ist eine erhöhte Aufnahme von Glucose und die Bildung großer Mengen Milchsäure auch in Anwesenheit von Sauerstoff (Warburg Effekt) und eine verminderte ...Nutzung des Zitratzyklus. Als Grund werden Defekte in der mitochondrialen Atmungskette diskutiert. Aber auch eine durch Onkogene gesteigerte Glykolyserate, könnte ursächlich sein. Ein weiterer für Tumorzellen wichtiger Stoffwechselweg, in dem Glucose abgebaut wird, ist der Pentosephosphatweg, dessen Blockade das Wachstum der Krebszellen hemmen könnte. Zudem stellt die Manipulation derjenigen Signalwege, die in den Tumorstoffwechsel involviert und in Tumorzellen überaktiviert (Ras/PI3K/Akt/mTOR- und Raf/MEK/ERK-Signalweg) oder unterdrückt (oxidative Phosphorylierung) sind, mögliche Ansatzpunkte dar. In dieser Arbeit wurde daher in vitro die Wirkung von 15 Substanzen an drei verschiedenen Tumorzelllinien und vier verschiedenen benignen Zellen untersucht, welche in die oben genannten charakteristischen Stoffwechselwege von Tumorzellen eingreifen und gegenwärtig intensiv als mögliche Tumortherapeutika diskutiert werden. Ziel war es, geeignete Kandidaten für eine zielgerichtete Therapie zu identifizieren. Der Schwerpunkt dieser Arbeit war die Beeinflussung des Glucosestoffwechsels in Tumorzellen. Da Glucose sowohl aerob als auch anaerob verstoffwechselt werden kann, wurden in einem ersten Ansatz zum einen Substanzen gestestet, die die Glykolyse auf verschiedenen Ebenen hemmen, zum anderen wurden Substanzen untersucht, die den mitochondrialen Stoffwechsel beeinflussen. Die Wirkung aller 15 Substanzen wurde zunächst jeweils als Einzelbehandlung getestet. Hierbei führten nur sehr hohe Konzentrationen in Tumorzellen zu einem drastisch verminderten ATP-Gehalt, die für benigne Zellen aber ebenfalls toxisch waren. Daher wurde in einem zweiten Schritt untersucht, ob durch die gleichzeitige Manipulation des Glucosestoffwechsels und des mitochondrialen Stoffwechsels mit jeweils subtoxischen Konzentrationen eine tumorselektive Wirkung erreicht werden kann. Bei der Kombination der Substanzen Oxythiamin/NaDCA bzw. 2-DG/Rotenon ergaben sich zwar synergistische Effekte auf die Verminderung des ATP-Gehaltes in den getesteten Tumorzellen, eine generelle tumorselektive Wirkung konnte jedoch durch die kombinierte Behandlung nicht erreicht werden. In jüngster Zeit mehren sich die Hinweise, dass die Glutaminolyse einen sehr wichtigen Stoffwechselweg für Energiegewinnung und Syntheseprozesse von Tumorzellen darstellt. Deshalb wurde in einem dritten Schritt untersucht, ob durch die Hemmung der Glutaminolyse mit der Substanz 6-Diazo-5-oxo-L-norleuzin (DON) eine tumorspezifische Wirkung erreicht werden kann. In der Tat konnte durch DON eine andeutungsweise tumorselektive Wirkung auf den ATP-Gehalt der Zellen erzielt werden, jedoch war das therapeutische Fenster sehr eng. Durch die Hemmung der oxidativen Phosphorylierung wurde in allen drei untersuchten Tumorzelllinien eine gesteigerte Milchsäureproduktion nachgewiesen. Dies ist ein eindeutiger Hinweis dafür, dass in diesen Tumorzellen die Mitochondrien keine Defekte aufweisen. Die hier untersuchten benignen und malignen Zellen wurden hinsichtlich des Glucosestoffwechsels mit verschiedenen Methoden näher charakterisiert, um zu beurteilen, ob sich die Zellen in ihrem Stoffwechselphänotyp unterscheiden. Bei der Quantifizierung der Glucoseaufnahme wurde deutlich, dass auch manche benigne Zellen deutliche Mengen an Glucose aufnehmen, welche allerdings nur der Tumorzelllinie mit der niedrigsten Aufnahme glich. Mittels immunhistochemischer Färbungen wurden charakteristische Proteine des Zuckerstoffwechsels dargestellt. Zudem wurde die Expression von zentralen Genen des Stoffwechsels auf mRNA- bzw. Proteinebene untersucht. Hierbei wurde deutlich, dass sowohl Tumorzellen als auch manche benigne Zellen für die Glykolyse typische Proteine bzw. mRNA stark exprimieren. Fazit der Charakterisierung ist, dass es zwischen den hier verwendeten malignen und benignen Zellen keine eindeutige Differenzierung aufgrund des Stoffwechselprofils gibt, sondern sich die getesteten Zellen nur graduell unterscheiden. Dieses Ergebnis erklärt möglicherweise die geringe Tumorspezifität der getesteten Substanzen. Im Vergleich mit den vielversprechenden Ergebnissen aus der Literatur zeigten die hier gewonnenen in vitro-Daten eindeutig, dass die Wirkung von potenziell tumorhemmenden Substanzen je nach Tumorzelltyp extrem verschieden war. Dies beruht darauf, dass der vorherrschende Stoffwechseltyp (oxidativ bzw. glykolytisch) für jede Tumorentität verschieden ist. Daher muss vermutlich für jede Tumorentität bzw. sogar für jeden Patienten individuell die Wirkung und der Nutzen einer Hemmung des Tumorstoffwechsels untersucht werden, bevor künftig an eine zielgerichtete Therapie gedacht werden kann.
A characteristic feature of aggressive tumour cells is a high uptake of glucose and enhanced lactic acid production even in the presence of oxygen (aerobic glycolysis, “Warburg effect”) with a reduced use of the tricarboxylic acid cycle. Defects in mitochondrial function and oncogene activation are supposed to contribute to increased glycolysis, that is not subjected to the Pasteur effect (reduced rate of glycolysis in the presence of oxygen). The pentose phosphate pathway (PPP) is an important metabolic pathway in cancer cells, supplying building blocks for nucleotide synthesis and NADPH for proper redox control. Hence, inhibition of the PPP might block tumour cell growth. Perturbation of signalling pathways that are involved in tumour cell metabolism and are hyperactivated (Ras/PI3K/Akt/mTOR- and Raf/MEK/ERK-pathway) or suppressed (oxidative phosphorylation, p53) in cancer cells are possible targets for anticancer drugs. Thus, in this work the effect of 15 substances highly discussed as potential anticancer agents which influence the aforementioned metabolic and signalling pathways was evaluated in vitro on three different tumour cells lines two breast cancer cells lines with different metastatic phenotype (MDA-MB 231 and 468) and one gastric cancer cell line (23132/87) and four normal cell types endometrial fibroblasts, endothelial cells (HUVEC), peripheral blood leukocytes and skin keratinocytes. Aim of the study was to identify suitable candidates for targeted therapies. ATP-level was measured as readout to determine the efficacy of the substances, because the ATP content of cells correlates well with cell viability. The main focus of this work was to selectively modulate the glucose metabolism of cancer cells. Because glucose can be metabolized aerobically and anaerobically, we first tested substances that inhibit glycolysis at different steps and substances that interfere with mitochondrial metabolism. All of the 15 substances were tested as single treatment. Here, only very high concentrations of the respective substance significantly decreased ATP-levels in cancer cells - but to a much greater extend in normal cells. Therefore, in the next step we determined if impairing glucose and mitochondrial metabolism simultaneously with less toxic drug concentrations would be more specific in targeting cancer cells. Although synergistic effects were observed by co-treatment with oyxthiamine/NaDCA and 2-DG/rotenone respectively on reducing ATP-levels, this effect was not selective for tumour cells too. Recently, evidence is coming up that glutaminolysis (degradation of glutamine) is an important metabolic pathway for cancer cells providing energy substrates and building blocks. Thus, we examined if a tumour-specific effect could be achieved by inhibition of glutaminolysis with 6-Diazo-5-oxo-L-norleuzin (DON). Actually, other than the substances interfering with glucose metabolism, DON showed a tumour-specific effect to some extent, although the therapeutical range was very small. Inhibition of oxidative mitochondrial metabolism with the substances rotenone, oligomycin, 2,4-dinitrophenol and rhodamine 123 increased lactic acid production in all three cancer cell lines. Thus, it was possible to impede oxidative phosphorylation and to force the cells to increase glycolysis, indicating that mitochondria had no defects. To determine if tumour cells and normal cells differ in regard of their metabolic phenotype, the cells were analyzed for parameters concerning glucose metabolism with different methods. Quantifying glucose uptake of the cells revealed that some normal cells (fibroblasts, T-cells) take up significant amounts of glucose that are similar to those of cancer cells (MDA-MB 231) which showed the lowest glucose uptake among the three tumour cell lines tested. Characteristic proteins of glucose metabolism were analyzed using immunohistochemistry. Furthermore expression patterns of crucial genes involved in glucose metabolism were analyzed on mRNA and protein level. Thereby, it became obvious that both tumour cells as well as normal cells have very similar expression patterns regarding these typical genes. In conclusion, the characterization of tumour and normal cells did not show any substantial but rather gradual differences concerning the metabolic phenotype. These results might explain the marginal tumour specific effect of the drugs tested herein Compared to the promising results from the literature our in vitro data clearly show that the effect of potential anticancer drugs is extremely different for several tumour cell types. This might be due to the predominant metabolic phenotype (oxidative or glycolytic) of different tumour entities. Thus, we suppose that inhibition of tumour cell metabolism has to be evaluated for every single cancer cell type or even every cancer patient on regard of effect and benefit for implementation of selective cancer pharmacotherapy.
Background: Overexpression of transketolase-like 1 protein TKTL1 in cancer cells has been reported to correlate with enhanced glycolysis and lactic acid production. Furthermore, enhanced TKTL1 ...expression was put into context with resistance to chemotherapy and ionizing radiation. Here, a panel of human malign and benign cells, which cover a broad range of chemotherapy and radiation resistance as well as reliance on glucose metabolism, was analyzed in vitro for TKTL1 expression. Methods: 17 malign and three benign cell lines were characterized according to their expression of TKTL1 on the protein level with three commercially available anti-TKTL1 antibodies utilizing immunohistochemistry and Western blot, as well as on mRNA level with three published primer pairs for RT-qPCR. Furthermore, sensitivities to paclitaxel, cisplatin and ionizing radiation were assessed in cell survival assays. Glucose consumption and lactate production were quantified as surrogates for the "Warburg effect". Results: Considerable amounts of tktl1 mRNA and TKTL1 protein were detected only upon stable transfection of the human embryonic kidney cell line HEK293 with an expression plasmid for human TKTL1. Beyond that, weak expression of endogenous tktl1 mRNA was measured in the cell lines JAR and U251. Western blot analysis of JAR and U251 cells did not detect TKTL1 at the expected size of 65 kDa with all three antibodies specific for TKTL1 protein and immunohistochemical staining was observed with antibody JFC12T10 only. All other cell lines tested here revealed expression of tktl1 mRNA below detection limits and were negative for TKTL1 protein. However, in all cell lines including TKTL1-negative HEK293-control cells, antibody JFC12T10 detected multiple proteins with different molecular weights. Importantly, JAR and U251 did neither demonstrate an outstanding production of lactic acid nor increased resistance against chemotherapeutics or to ionizing radiation, respectively. Conclusion: Using RT-qPCR and three different antibodies we observed only exceptional occurrence of TKTL1 in a panel of malignant human cell lines in vitro. The presence of TKTL1 was unrelated to either the rate of glucose consumption/lactic acid production or resistance against chemo-and radiotherapy.