Metabolomic Dynamic Analysis of Hypoxia in MDA-MB-231 and the Comparison with Inferred Metabolites from Transcriptomics Data

Exploratory Metabolomic Analysis Based on Reversed-Phase Liquid Chromatography-Mass Spectrometry to Study an In Vitro Model of Hypoxia-Induced Metabolic Alterations in HK-2 Cells

Oxygen deficiency in cells, tissues, and organs can not only prevent the proper development of biological functions but it can also lead to several diseases and disorders. In this sense, the kidney deserves special attention since hypoxia can be considered an important factor in the pathophysiology of both acute kidney injury and chronic kidney disease. To provide better knowledge to unveil the molecular mechanisms involved, new studies are necessary. In this sense, this work aims to study, for the first time, an in vitro model of hypoxia-induced metabolic alterations in human proximal tubular HK-2 cells because renal proximal tubules are particularly susceptible to hypoxia. Different groups of cells, cultivated under control and hypoxia conditions at 0.5, 5, 24, and 48 h, were investigated using untargeted metabolomic approaches based on reversed-phase liquid chromatography–mass spectrometry. Both intracellular and extracellular fluids were studied to obtain a large metabolite coverage. On the other hand, multivariate and univariate analyses were carried out to find the differences among the cell groups and to select the most relevant variables. The molecular features identified as affected metabolites were mainly amino acids and Amadori compounds. Insights about their biological relevance are also provided.

Exploring metabolomics biomarkers for evaluating the effectiveness of concurrent radiochemotherapy for cervical cancers

Background

Cervical cancer is the second most common female malignancy worldwide. The main method to evaluate the effect of concurrent chemoradiotherapy (CCRT) in the locally advanced stage is imaging which cannot meet the clinical needs. This study aimed to explore potential cervical cancer biomarkers via plasma metabolomics and evaluate the effectiveness of CCRT and disease progression.

Methods

Twenty-four primary and thirty recurrent patients were enrolled between November 2016 and November 2017. Plasma samples were obtained by centrifugation of whole blood collected from enrolled patients at admission and from primary patients after CCRT. Plasma metabolic profiles were determined via ultra-performance liquid chromatography with quadrupole time-of-flight mass spectrometry. Multivariate analyses and public databases were used to screen and identify differential metabolites. Pathway analysis was conducted using MetaboAnalyst.

Results

Metabolic profiles obtained were significantly different among primary, post-CCRT-treated, and recurrent patients. Multivariate analyses showed that 37 metabolites differed significantly among the three groups, of which the levels of 22 metabolites changed significantly after CCRT and recovered or even exceeded the levels in primary patients when the tumor reappeared. These 22 metabolites were mainly lipids involved in sphingolipid and glycerophospholipid metabolism. Among them, 8 metabolites with area under curve values above 0.75 between each pair of groups exhibited great potential for evaluating CCRT effectiveness and disease progression.

Conclusions

Our results show significantly different plasma metabolic profiles among the three cervical cancer groups; 8 metabolites were identified as potential biomarkers to evaluate the effectiveness of CCRT and disease progression, which can help evaluate the prognosis and treatment of cervical cancer in a timely manner.

Extracellular volatilomic alterations induced by hypoxia in breast cancer cells

INTRODUCTION

The metabolic shift induced by hypoxia in cancer cells has not been explored at volatilomic level so far. The volatile organic metabolites (VOMs) constitute an important part of the metabolome and their investigation could provide us crucial aspects of hypoxia driven metabolic reconfiguration in cancer cells.

OBJECTIVE

To identify the altered volatilomic response induced by hypoxia in metastatic/aggressive breast cancer (BC) cells.

METHODS

BC cells were cultured under normoxic and hypoxic conditions and VOMs were extracted using HS-SPME approach and profiled by standard GC-MS system. Univariate and multivariate statistical approaches (p < 0.05, Log₂ FC ≥ 0.58/≤ - 0.58, PC1 > 0.13/< - 0.13) were applied to select the VOMs differentially altered after hypoxic treatment. Metabolic pathway analysis was also carried out in order to identify altered metabolic pathways induced by the hypoxia in the selected BC cells.

RESULTS

Overall, 20 VOMs were found to be significantly altered (p < 0.05, PC1 > 0.13/< - 0.13) upon hypoxic exposure to BC cells. Further, cell line specific volatilomic alterations were extracted by comparative metabolic analysis of aggressive (MDA-MB-231) vs. non-aggressive (MCF-7) cells incubated under hypoxia and normoxia. In this case, 15 and 12 VOMs each were found to be significantly altered in aggressive cells when exposed to hypoxic and normoxic condition respectively. Out of these, 9 VOMs were found to be uniquely associated with hypoxia, 6 were specific to normoxia and 6 were found common to both the conditions. Formic acid was identified as the most prominent molecule with higher abundance levels in aggressive as compared to non-aggressive cells in both conditions. Furthermore, metabolic pathway analyses revealed that fatty acid biosynthesis and nicotinate and nicotinamide metabolism were significantly altered in aggressive as compared to non-aggressive cells in normoxia and hypoxia respectively.

CONCLUSIONS

Higher formate overflow was observed in aggressive cells compared to non-aggressive cells incubated under both the conditions, reinforcing its correlation with aggressive and invasive cancer type. Moreover, under hypoxia, aggressive cells preferred to be bioenergetically more efficient whereas, under normoxia, fatty acid biosynthesis was favoured when compared to non-aggressive cells.

Characterizing the effects of hypoxia on the metabolic profiles of mesenchymal stromal cells derived from three tissue sources using chemical isotope labeling liquid chromatography-mass spectrometry

Microenvironmental factors such as oxygen concentration mediate key effects on the biology of mesenchymal stromal cells (MSCs). Herein, we performed an in-depth characterization of the metabolic behavior of MSCs derived from the placenta, umbilical cord, and adipose tissue (termed hPMSCs, UC-MSCs, and AD-MSCs, respectively) at physiological (hypoxic; 5% oxygen [O₂]) and standardized (normoxic; 21% O₂) O₂ concentrations using chemical isotope labeling liquid chromatography-mass spectrometry. ¹²C- and ¹³C-isotope dansylation (Dns) labeling was used to analyze the amine/phenol submetabolome, and 2574 peak pairs or metabolites were detected and quantified, from which 52 metabolites were positively identified using a library of 275 Dns-metabolite standards; 2189 metabolites were putatively identified. Next, we identified six metabolites using the Dns library, as well as 14 hypoxic biomarkers from the human metabolome database out of 96 altered metabolites. Ultimately, metabolic pathway analyses were performed to evaluate the associated pathways. Based on pathways identified using the Kyoto Encyclopedia of Genes and Genomes, we identified significant changes in the metabolic profiles of MSCs in response to different O₂ concentrations. These results collectively suggest that O₂ concentration has the strongest influence on hPMSCs metabolic characteristics, and that 5% O₂ promotes arginine and proline metabolism in hPMSCs and UC-MSCs but decreases gluconeogenesis (alanine-glucose) rates in hPMSCs and AD-MSCs. These changes indicate that MSCs derived from different sources exhibit distinct metabolic profiles.

Characterization of triple-negative breast cancer preclinical models provides functional evidence of metastatic progression

Triple-negative breast cancer (TNBC), an aggressive, metastatic and recurrent breast cancer (BC) subtype, currently suffers from a lack of adequately described spontaneously metastatic preclinical models that faithfully reproduce the clinical scenario. We describe two preclinical spontaneously metastatic TNBC orthotopic murine models for the development of advanced therapeutics: an immunodeficient human MDA-MB-231-Luc model and an immunocompetent mouse 4T1 model. Furthermore, we provide a broad range of multifactorial analysis for both models that could provide relevant information for the development of new therapies and diagnostic tools. Our comparisons uncovered differential growth rates, stromal arrangements and metabolic profiles in primary tumors, and the presence of cancer-associated adipocyte infiltration in the MDA-MB-231-Luc model. Histopathological studies highlighted the more rapid metastatic spread to the lungs in the 4T1 model following a lymphatic route, while we observed both homogeneous (MDA-MB-231-Luc) and heterogeneous (4T1) metastatic spread to axillary lymph nodes. We encountered unique metabolomic signatures in each model, including crucial amino acids and cell membrane components. Hematological analysis demonstrated severe leukemoid and lymphoid reactions in the 4T1 model with the partial reestablishment of immune responses in the immunocompromised MDA-MB-231-Luc model. Additionally, we discovered β-immunoglobulinemia and increased basal levels of G-CSF correlating with a metastatic switch, with G-CSF also promoting extramedullary hematopoiesis (both models) and causing hepatosplenomegaly (4T1 model). Overall, we believe that the characterization of these preclinical models will foster the development of advanced therapeutic strategies for TNBC treatment, especially for the treatment of patients presenting both, primary tumors and metastatic spread.

Effects of hypoxic preconditioning on neuroblastoma tumour oxygenation and metabolic signature in a chick embryo model

Hypoxia episodes and areas in tumours have been associated with metastatic dissemination and poor prognosis. Given the link between tumour tissue oxygen levels and cellular metabolic activity, we hypothesised that the metabolic profile between metastatic and non-metastatic tumours would reveal potential new biomarkers and signalling cues. We have used a previously established chick embryo model for neuroblastoma growth and metastasis, where the metastatic phenotype can be controlled by neuroblastoma cell hypoxic preconditioning (3 days at 1% O₂). We measured, with fibre-optic oxygen sensors, the effects of the hypoxic preconditioning on the tumour oxygenation, within tumours formed by SK-N-AS cells on the chorioallantoic membrane (CAM) of chick embryos. We found that the difference between the metastatic and non-metastatic intratumoural oxygen levels was small (0.35% O₂), with a mean below 1.5% O₂ for most tumours. The metabolomic profiling, using NMR spectroscopy, of neuroblastoma cells cultured in normoxia or hypoxia for 3 days, and of the tumours formed by these cells showed that the effects of hypoxia in vitro did not compare with in vivo tumours. One notable difference was the high levels of the glycolytic end-products triggered by hypoxia in vitro, but not by hypoxia preconditioning in tumours, likely due to the very high basal levels of these metabolites in tumours compared with cells. In conclusion, we have identified high levels of ketones (3-hydroxybutyrate), lactate and phosphocholine in hypoxic preconditioned tumours, all known to fuel tumour growth, and we herein point to the poor relevance of in vitro metabolomic experiments for cancer research.

Untargeted and stable isotope-assisted metabolomic analysis of MDA-MB-231 cells under hypoxia

INTRODUCTION

Hypoxia commonly occurs in cancers and is highly related with the occurrence, development and metastasis of cancer. Treatment of triple negative breast cancer remains challenge. Knowledge about the metabolic status of triple negative breast cancer cell lines in hypoxia is valuable for the understanding of molecular mechanisms of this tumor subtype to develop effective therapeutics.

OBJECTIVES

Comprehensively characterize the metabolic profiles of triple negative breast cancer cell line MDA-MB-231 in normoxia and hypoxia and the pathways involved in metabolic changes in hypoxia.

METHODS

Differences in metabolic profiles affected pathways of MDA-MB-231 cells in normoxia and hypoxia were characterized using GC-MS based untargeted and stable isotope assisted metabolomic techniques.

RESULTS

Thirty-three metabolites were significantly changed in hypoxia and nine pathways were involved. Hypoxia increased glycolysis, inhibited TCA cycle, pentose phosphate pathway and pyruvate carboxylation, while increased glutaminolysis in MDA-MB-231 cells.

CONCLUSION

The current results provide metabolic differences of MDA-MB-231 cells in normoxia and hypoxia conditions as well as the involved metabolic pathways, demonstrating the power of combined use of untargeted and stable isotope-assisted metabolomic methods in comprehensive metabolomic analysis.

HIF-1α inhibition by diethylstilbestrol and its polyacetal conjugate in hypoxic prostate tumour cells: insights from NMR metabolomics

In this study, we have employed ¹H NMR metabolomics to assess the metabolic responses of PC3 prostate tumour cells to hypoxia and to pharmacological HIF-1α inhibition by DES or its polyacetal conjugate tert-DES. Oxygen deprivation prompted a number of changes in intracellular composition and metabolic activity, mainly reflecting upregulated glycolysis, amino acid catabolism and other compensatory mechanisms used by hypoxic cells to deal with oxidative imbalance and energy deficit. Cell treatment with a non-cytotoxic concentration of DES, under hypoxia, triggered significant changes in 17 metabolites. Among these, lactate, phosphocreatine and reduced glutathione, whose levels showed opposite variations in hypoxic and drug-treated cells, emerged as possible markers of DES-induced HIF-1α inhibition. Furthermore, the free drug had a much higher impact on the cellular metabolome than tert-DES, particularly concerning polyamine and pyrimidine biosynthetic pathways, known to be tightly involved in cell proliferation and growth. This is likely due to the different cell pharmacokinetics observed between free and conjugated DES. Overall, this study has revealed a number of unanticipated metabolic changes that inform on DES and tert-DES direct cellular effects, providing further insight into their mode of action at the biochemical level.

Optimized Method for Untargeted Metabolomics Analysis of MDA-MB-231 Breast Cancer Cells

Cancer cells often have dysregulated metabolism, which is largely characterized by the Warburg effect-an increase in glycolytic activity at the expense of oxidative phosphorylation-and increased glutamine utilization. Modern metabolomics tools offer an efficient means to investigate metabolism in cancer cells. Currently, a number of protocols have been described for harvesting adherent cells for metabolomics analysis, but the techniques vary greatly and they lack specificity to particular cancer cell lines with diverse metabolic and structural features. Here we present an optimized method for untargeted metabolomics characterization of MDA-MB-231 triple negative breast cancer cells, which are commonly used to study metastatic breast cancer. We found that an approach that extracted all metabolites in a single step within the culture dish optimally detected both polar and non-polar metabolite classes with higher relative abundance than methods that involved removal of cells from the dish. We show that this method is highly suited to diverse applications, including the characterization of central metabolic flux by stable isotope labelling and differential analysis of cells subjected to specific pharmacological interventions.

Application of metabolomics in drug resistant breast cancer research

The metabolic profiles of breast cancer cells are different from normal mammary epithelial cells. Breast cancer cells that gain resistance to therapeutic interventions can reprogram their endogenous metabolism in order to adapt and proliferate despite high oxidative stress and hypoxic conditions. Drug resistance in breast cancer, regardless of subgroups, is a major clinical setback. Although recent advances in genomics and proteomics research has given us a glimpse into the heterogeneity that exists even within subgroups, the ability to precisely predict a tumor’s response to therapy remains elusive. Metabolomics as a quantitative, high through put technology offers promise towards devising new strategies to establish predictive, diagnostic and prognostic markers of breast cancer. Along with other “omics” technologies that include genomics, transcriptomics, and proteomics, metabolomics fits into the puzzle of a comprehensive systems biology approach to understand drug resistance in breast cancer. In this review, we highlight the challenges facing successful therapeutic treatment of breast cancer and the innovative approaches that metabolomics offers to better understand drug resistance in cancer.

Deregulation of purine metabolism in Alzheimer's disease

The neuroprotective role of adenosine and the deregulation of adenosine receptors in Alzheimer's disease (AD) have been extensively studied in recent years. However, little is known about the involvement of purine metabolism in AD. We started by analyzing gene expression in the entorhinal cortex of human controls and AD cases with whole-transcript expression arrays. Once we identified deregulation of the cluster purine metabolism, messenger RNA expression levels of 23 purine metabolism genes were analyzed with qRT-PCR in the entorhinal cortex, frontal cortex area 8, and precuneus at stages I-II, III-IV, and V-VI of Braak and Braak and controls. APRT, DGUOK, POLR3B, ENTPD3, AK5, NME1, NME3, NME5, NME7, and ENTPD2 messenger RNAs were deregulated, with regional variations, in AD cases when compared with controls. In addition, liquid chromatography mass spectrometry based metabolomics in the entorhinal cortex identified altered levels of dGMP, glycine, xanthosine, inosine diphosphate, guanine, and deoxyguanosine, all implicated in this pathway. Our results indicate stage- and region-dependent deregulation of purine metabolism in AD.