bims-mepmim Biomed News
on Metabolites in pathological microenvironments and immunometabolism
Issue of 2022‒03‒20
43 papers selected by
Erika Mariana Palmieri
NIH/NCI Laboratory of Cancer ImmunoMetabolism

  1. Front Oncol. 2022 ;12 858462
      SLC7A11/xCT is an antiporter that mediates the uptake of extracellular cystine in exchange for glutamate. Cystine is reduced to cysteine, which is a rate-limiting precursor in glutathione synthesis; a process that protects cells from oxidative stress and is, therefore, critical to cell growth, proliferation, and metabolism. SLC7A11 is expressed in different tissues and plays diverse functional roles in the pathophysiology of various diseases, including cancer, by regulating the processes of redox homeostasis, metabolic flexibility/nutrient dependency, immune system function, and ferroptosis. SLC7A11 expression is associated with poor prognosis and drug resistance in cancer and, therefore, represents an important therapeutic target. In this review, we discuss the molecular functions of SLC7A11 in normal versus diseased tissues, with a special focus on how it regulates gastrointestinal cancers. Further, we summarize current therapeutic strategies targeting SLC7A11 as well as novel avenues for treatment.
    Keywords:  Cancer therapy; SLC7A11 (xCT); cysteine (Cys); ferroptosis; gastrointestinal tract; metabolism; oxidative stress
  2. PLoS Comput Biol. 2022 Mar 14. 18(3): e1009395
      Synthetic Lethality (SL) is currently defined as a type of genetic interaction in which the loss of function of either of two genes individually has limited effect in cell viability but inactivation of both genes simultaneously leads to cell death. Given the profound genomic aberrations acquired by tumor cells, which can be systematically identified with -omics data, SL is a promising concept in cancer research. In particular, SL has received much attention in the area of cancer metabolism, due to the fact that relevant functional alterations concentrate on key metabolic pathways that promote cellular proliferation. With the extensive prior knowledge about human metabolic networks, a number of computational methods have been developed to predict SL in cancer metabolism, including the genetic Minimal Cut Sets (gMCSs) approach. A major challenge in the application of SL approaches to cancer metabolism is to systematically integrate tumor microenvironment, given that genetic interactions and nutritional availability are interconnected to support proliferation. Here, we propose a more general definition of SL for cancer metabolism that combines genetic and environmental interactions, namely loss of gene functions and absence of nutrients in the environment. We extend our gMCSs approach to determine this new family of metabolic synthetic lethal interactions. A computational and experimental proof-of-concept is presented for predicting the lethality of dihydrofolate reductase (DHFR) inhibition in different environments. Finally, our approach is applied to identify extracellular nutrient dependences of tumor cells, elucidating cholesterol and myo-inositol depletion as potential vulnerabilities in different malignancies.
  3. Front Immunol. 2022 ;13 845923
      Although immunotherapy has achieved good results in various cancer types, a large proportion of patients are limited from the benefits. Hypoxia and metabolic reprogramming are the common and critical factors that impact immunotherapy response. Here, we present current research on the metabolism reprogramming induced by hypoxia on antitumor immunity and discuss the recent progression among preclinical and clinical trials exploring the therapeutic effects combining targeting hypoxia and metabolism with immunotherapy. By evaluating the little clinical translation of the combined therapy, we provide insight into "understanding and regulating cellular metabolic plasticity under the current tumor microenvironment (TME)," which is essential to explore the strategy for boosting immune responses by targeting the metabolism of tumor cells leading to harsh TMEs. Therefore, we highlight the potential value of advanced single-cell technology in revealing the metabolic heterogeneity and corresponding phenotype of each cell subtype in the current hypoxic lesion from the clinical patients, which can uncover potential metabolic targets and therapeutic windows to enhance immunotherapy.
    Keywords:  cancer immunotherapy; cell subtypes; hypoxia; metabolic reprogramming; single-cell analysis
  4. Cell Rep. 2022 Mar 15. pii: S2211-1247(22)00247-9. [Epub ahead of print]38(11): 110511
      An epithelial-to-mesenchymal transition (EMT) phenotype with cancer stem cell-like properties is a critical feature of aggressive/metastatic tumors, but the mechanism(s) that promote it and its relation to metabolic stress remain unknown. Here we show that Collapsin Response Mediator Protein 2A (CRMP2A) is unexpectedly and reversibly induced in cancer cells in response to multiple metabolic stresses, including low glucose and hypoxia, and inhibits EMT/stemness. Loss of CRMP2A, when metabolic stress decreases (e.g., around blood vessels in vivo) or by gene deletion, induces extensive microtubule remodeling, increased glutamine utilization toward pyrimidine synthesis, and an EMT/stemness phenotype with increased migration, chemoresistance, tumor initiation capacity/growth, and metastatic potential. In a cohort of 27 prostate cancer patients with biopsies from primary tumors and distant metastases, CRMP2A expression decreases in the metastatic versus primary tumors. CRMP2A is an endogenous molecular brake on cancer EMT/stemness and its loss increases the aggressiveness and metastatic potential of tumors.
    Keywords:  cytoskeleton; metabolism; metastasis; microtubule; mitochondria; stress
  5. Front Oncol. 2022 ;12 839880
      Fibroblasts in the tumor microenvironment have been proven to actively participate in tumor progression; they can be "educated" by cancer cells acquiring an activated state and, as such, are identified as cancer-associated fibroblasts (CAFs); CAFs, in turn, remodel tumor stroma to be more advantageous for cancer progression by modulating several processes, including angiogenesis, immunosuppression, and drug access, presumably driving the chemoresistance. That is why they are believed to hamper the response to clinical therapeutic options. The communication between cancer cells and fibroblasts can be mediated by extracellular vesicles (EVs), composed of both exosomes (EXOs) and microvesicles (MVs). To verify the role of different subpopulations of EVs in this cross-talk, a nearly pure subpopulation of EXO-like EVs and the second one of mixed EXO- and MV-like EVs were isolated from ovarian cancer cells and administered to fibroblasts. It turned out that EVs can activate fibroblasts to a CAF-like state, supporting their proliferation, motility, invasiveness, and enzyme expression; EXO-like EV subpopulation seems to be more efficient in some of those processes, suggesting different roles for different EV subpopulations. Moreover, the secretome of these "activated" fibroblasts, composed of both soluble and EV-associated molecules, was, in turn, able to modulate the response of bystander cells (fibroblasts, tumor, and endothelial cells), supporting the idea that EVs sustain the mutual cross-talk between tumor cells and CAFs.
    Keywords:  CAFs; cancer-associated fibroblasts; extracellular vesicles; ovarian cancer; tumor microenvironment; vesicles subpopulations
  6. Chem Sci. 2022 Feb 09. 13(6): 1641-1647
      Natural killer cells (NK cells) are important immune cells which have attracted increasing attention in cancer immunotherapy. Due to the heterogeneity of cells, individual cancer cells show different resistance to NK cytotoxicity, which has been revealed by flow cytometry. Here we used label-free mass cytometry (CyESI-MS) as a new tool to analyze the metabolites in Human Hepatocellular Carcinoma (HepG2) cells at the single-cell level after the interaction with different numbers of NK92 MI cells. A large amount of chemical information from individual HepG2 cells was obtained showing the process of cell apoptosis induced by NK cells. Nineteen metabolites which consecutively change during cell apoptosis were revealed by calculating their average relative intensity. Four metabolic pathways were impacted during cell apoptosis which hit 4 metabolites including glutathione (GSH), creatine, glutamic acid and taurine. We found that the HepG2 cells could be divided into two phenotypes after co-culturing with NK cells according to the bimodal distribution of concentration of these 4 metabolites. The correlation between metabolites and different apoptotic pathways in the early apoptosis cell group was established by the 4 metabolites at the single-cell level. This is a new idea of using single-cell specific metabolites to reveal the metabolic heterogeneity in cell apoptosis which would be a powerful means for evaluating the cytotoxicity of NK cells.
  7. Biochem Biophys Res Commun. 2022 Mar 10. pii: S0006-291X(22)00359-X. [Epub ahead of print]604 96-103
      Different regions and states of the human colon are likely to have a distinct influence on immune cell functions. Here we studied the immunometabolic mechanisms for spatial immune specialization and dysregulated immune response during ulcerative colitis at single-cell resolution. We revealed that the macrophages and CD8+ T cells in the lamina propria of the human colon possessed an effector phenotype and were more activated, while their lipid metabolism was suppressed compared with those in the epithelial. Also, IgA+ plasma cells accumulated in lamina propria of the sigmoid colon were identified to be more metabolically activated versus those in the cecum and transverse colon, and the improved metabolic activity was correlated with the expression of CD27. In addition to the immunometabolic reprogramming caused by spatial localization colon, we found dysregulated cellular metabolism was related to the impaired immune functions of macrophages and dendritic cells in patients with ulcerative colitis. The cluster of OSM+ inflammatory monocytes was also identified to play its role in resistance to anti-TNF treatment, and we explored targeted metabolic reactions that could reprogram them to a normal state. Altogether, this study revealed a landscape of metabolic reprogramming of human colonic immune cells in different locations and disease states, and offered new insights into treating ulcerative colitis by immunometabolic modulation.
    Keywords:  Anti-TNF therapy Resistance; Human colon; Immunometabolic modulation; Inflammation; Single-cell immunometabolism; Spatial immune specialization; Ulcerative colitis
  8. J Cell Mol Med. 2022 Mar 13.
      Angiopoietin-like protein (ANGPTL) 4 is a key factor in the regulation of lipid and glucose metabolism in metabolic diseases. ANGPTL4 is highly expressed in various cancers, but the regulation of energy metabolism in tumours remains to be determined. This study explored the role of ANGPTL4 in aerobic glycolysis, glutamine consumption and fatty acid oxidation in nonsmall cell lung cancer (NSCLC) cells. Two NSCLC cell lines (A549 and H1299) were used to investigate the role of ANGPTL4 in energy metabolism by tracer techniques and with Seahorse XF technology in ANGPTLs4 knockdown cells. RNA microarrays and specific inhibitors were used to identify targets in ANGPTLs4-overexpressing cells. The results showed that knockdown of ANGPTLs4 could inhibit energy metabolism and proliferation in NSCLC. ANGPTLs4 had no significant effect on glycolysis but affected glutamine consumption and fatty acid oxidation. Knockdown of ANGPTLs4 also significantly inhibited tumour metastasis and energy metabolism in mice and had a weak effect on glycolysis. RNA microarray analysis showed that ANGPTLs4 significantly affected glutaminase (GLS) and carnitine palmitoyl transferase 1 (CPT1). ANGPTLs4-overexpressing cells were exposed to a glutamine deprivation environment, and cell proliferation and energy metabolism were significantly decreased but still differed from normal NSCLC cells. Treatment of ANGPTLs4-overexpressing cells with GLS and CPT1 inhibitors simultaneously prevented the regulatory effects on cell proliferation and energy metabolism. ANGPTLs4 could promote glutamine consumption and fatty acid oxidation but not glycolysis or accelerate energy metabolism in NSCLC.
    Keywords:  ANGPTL4; NSCLC; aerobic glycolysis; fatty acid oxidation; glutamine
  9. FEBS Open Bio. 2022 Mar 18.
      Mutations in genes encoding cytochrome c oxidase (COX; mitochondrial complex IV) subunits and assembly factors (e.g., SCO1, SCO2, COA6) are linked to severe metabolic syndromes. Notwithstanding that SCO2 is under transcriptional control of tumour suppressor p53, the role of mitochondrial complex IV dysfunction in cancer metabolism remains obscure. Herein, we demonstrate that the loss of SCO2 in HCT116 colorectal cancer cells leads to significant metabolic and signaling perturbations. Specifically, abrogation of SCO2 increased NAD+ regenerating reactions and decreased glucose oxidation through citric acid cycle while enhancing pyruvate carboxylation. This was accompanied by a reduction in amino acid levels and the accumulation of lipid droplets. In addition, SCO2 loss resulted in hyperactivation of the IGF1R/AKT axis with paradoxical downregulation of mTOR signaling which was accompanied by increased AMPK activity. Accordingly, abrogation of SCO2 expression appears to increase the sensitivity of cells to IGF1R and AKT, but not mTOR inhibitors. Finally, the loss of SCO2 was associated with reduced proliferation and enhanced migration of HCT116 cells. Collectively, herein we describe potential adaptive signaling and metabolic perturbations triggered by mitochondrial complex IV dysfunction.
    Keywords:  AKT; AMPK; SCO2; cytochrome C oxidase; mTOR; metabolism; mitochondrial dysfunction
  10. Front Physiol. 2022 ;13 831829
      Cardiac function highly relies on sufficient energy supply. Perturbations in myocardial energy metabolism play a causative role in cardiac pathogenesis. Accumulating evidence has suggested that modifications of cardiac metabolism are also an essential part of the adaptive responses to various physiological conditions in the heart to meet specific energy needs. The review highlighted some new studies on basic myocardial energy substrate metabolism and updated recent findings regarding cardiac metabolic remodeling and their associated mechanisms under physiological conditions, including exercise and cardiac development. Studying basic metabolic profiles in the heart in these conditions can contribute to understanding the significance of metabolic regulation in the heart during physiological adaption and gaining further insights into the maladaptive metabolic changes associated with cardiac pathogenesis, thus opening up new avenues to exploring novel therapeutic strategies in cardiac diseases.
    Keywords:  cardiac disease; heart; metabolism; physiology; substrate utilization
  11. FEBS J. 2022 Mar 18.
      Mammalian metabolism comprises a series of interlinking pathways that include two major cycles: the folate and methionine cycles. The folate-mediated metabolic cycle uses several oxidation states of tetrahydrofolate to carry activated one-carbon units to be readily used and interconverted within the cell, which are required for nucleotide synthesis, methylation and metabolism, particularly for proliferation of cancer cells. Based on the latest progress in genome-wide CRISPR loss-of-function viability screening of 789 cell lines, we focus on the most cancer dependent enzymes in this pathway, especially those that are hyperactivated in cancer, to provide new insight into the chemical basis for cancer drug development. Since the complete 3D structure of several of these enzymes in their active form are not available, we used homology modeling integrated with the interpretation of the reaction mechanism, and have reconstructed the most likely scenario for the reactions to take place paired with their catalytic cycle that provides a testable framework for this pathway.
    Keywords:  DHFR; Enzyme catalysis; Enzyme reaction mechanism; Folate; Folate metabolism; Folate-mediated one-carbon pathway; MTHFD1; MTHFD2; MTHFD2L; SHMT2; TYMS
  12. Int J Biol Sci. 2022 ;18(4): 1695-1705
      Ferroptosis, a new form of programmed necrosis characterized by iron-dependent lethal accumulation of lipid hydroperoxides, is associated with many human diseases. Targeting amino acid (AA) availability can selectively suppress tumor growth and has been a promising therapeutic strategy for cancer therapy. Compelling studies have indicated that AA metabolism is also involved in ferroptosis, closely regulating its initiation and execution. This manuscript systematically summarizes the latest advances of AA metabolism in regulating ferroptosis and discusses the potential combination of therapeutic strategies that simultaneously target AA metabolism and ferroptosis in cancer to eliminate tumors or limit their invasiveness.
    Keywords:  amino acid metabolism; cancer; combinatorial therapy; ferroptosis
  13. Front Physiol. 2022 ;13 837001
      Adipose tissue is comprised of a heterogeneous population of cells that co-operate to perform diverse physiological roles including endocrine-related functions. The endocrine role of adipose tissue enables it to communicate nutritional and health cues to other organs, such as the liver, muscle, and brain, in order to regulate appetite and whole body metabolism. Adipose tissue dysfunction, which is often observed in obesity, is associated with changes in the adipose secretome, which can subsequently contribute to disease pathology. Indeed, secreted bioactive factors released from adipose tissue contribute to metabolic homeostasis and likely play a causal role in disease; however, what constitutes the entirety of the adipose tissue secretome is still poorly understood. Recent advances in nanotechnology have advanced this field substantially and have led to the identification of small, secreted particles known as extracellular vesicles (EVs). These small nano-sized lipid envelopes are released by most cell types and are capable of systemically delivering bioactive molecules, such as nucleic acids, proteins, and lipids. EVs interact with target cells to deliver specific cargo that can then elicit effects in various tissues throughout the body. Adipose tissue has recently been shown to secrete EVs that can communicate with the periphery to maintain metabolic homeostasis, or under certain pathological conditions, drive disease. In this review, we discuss the current landscape of adipose tissue-derived EVs, with a focus on their role in the regulation of metabolic homeostasis and disease pathology.
    Keywords:  adipose tissue; adipose tissue secretome; brown adipose tissue; exosome; extracellular vescicles; metabolic homeostasis; white adipose tissue
  14. Cancer Med. 2022 Mar 18.
      BACKGROUND: Metabolic reprogramming is one of the essential features of tumorigenesis. Herein, this study aimed to develop a novel metabolism-related gene signature for head and neck squamous cell carcinoma (HNSCC) patients.METHODS: The transcriptomic and clinical data of HNSCC samples were collected from The Cancer Genome Atlas (TCGA) and GSE65858 datasets. The metabolism-related gene-based prognostic signature (MRGPS) was constructed by the Least Absolute Shrinkage and Selection Operator (LASSO) regression model. The time-dependent receiver operating characteristic (ROC) and Kaplan-Meier (K-M) survival curves were plotted for evaluating its predicting performance. At the same time, univariate along with multivariate analysis was carried out to explore its correlation with clinicopathologic factors. Furthermore, GSEA analysis was performed to explore the signaling pathways affected by MRGPS. We also analyzed the associations of MRGPS with the tumor immune microenvironment (TIME), as well as identified potential compounds via Connectivity Map (CMap) and molecular docking.
    RESULTS: A total of 12 differentially expressed metabolism-related genes were identified and selected to construct the MRGPS. Notably, this signature performed well in predicting HNSCC patients' survival and could serve as an independent prognostic factor in multiple datasets. In addition to the metabolism-related pathway, this signature could also affect some immune-related pathways. The results indicated that MRGPS is correlated with immune cells infiltration and anti-cancer immune response. Furthermore, we identified cephaeline as a potential therapeutic compound for HNSCC.
    CONCLUSION: Taken together, we established an MRGs-based signature that has the potential to predict the clinical outcome and immune microenvironment, which help to search for potential combination immunotherapy compounds and provide a promising therapeutic strategy for treating HNSCC patients.
    Keywords:  head and neck squamous cell carcinoma; metabolic reprogramming; metabolism-related genes; prognostic signature; tumor immune microenvironment
  15. iScience. 2022 Mar 18. 25(3): 103955
      MYCT1 has been shown to function as a tumor suppressor in various tumors, but its role in metabolism has never been reported. Here, we showed that global inactivation of Myct1 in mice led to progressive accumulation of glycogen in the liver, which was accompanied by aberrant changes in intermediates of the glycogen metabolic pathway. Mechanistically, MYCT1 appeared to promote translation efficiency of PGM1, UGP2 and GSK3A in hepatic cells in a RACK1-dependent manner. Consequently, upregulation of the three enzymes enhanced the glycogen shunt. Our data reveal a critical role of MYCT1 as a switch for the glycogen shunt in tumor cells.
    Keywords:  Animal physiology; Molecular biology; Physiology
  16. Mayo Clin Proc. 2022 Mar 11. pii: S0025-6196(22)00042-8. [Epub ahead of print]
      A metabolically flexible state exists when there is a rapid switch between glucose and fatty acids during the transition between the fed and fasting state. This flexibility in fuel choice serves to prevent hyperglycemia following a meal and simultaneously ensures an adequate amount of blood glucose is available for delivery to the brain and exclusively glycolytic tissues during fasting. The modern era is characterized by chronic overnutrition in which a mixture of fuels is delivered to the mitochondria in an unabated manner thereby uncoupling the feast and famine situation. The continuous influx of fuel leads to accumulation of reducing equivalents in the mitochondria and an increase in the mitochondrial membrane potential. These changes create a microenvironment fostering the generation of reactive oxygen species and other metabolites leading to deleterious protein modification, cell injury, and ultimately clinical disease. Insulin resistance may also play a primary role in this deleterious effect. The imbalance between mitochondrial energy delivery and use is made worse with a sedentary lifestyle. Maneuvers that restore energy balance across the mitochondria activate pathways that remove or repair damaged molecules and restore the plasticity characteristic of normal energy metabolism. Readily available strategies to maintain energy balance across the mitochondria include exercise, various forms of caloric restriction, administration of sodium-glucose cotransporter-2 inhibitors, cold exposure, and hypobaric hypoxia.
  17. Cell Chem Biol. 2022 Mar 17. pii: S2451-9456(22)00092-7. [Epub ahead of print]29(3): 353-355
      In this issue of Cell Chemical Biology, Olszewski et al. (2022) address the challenge of developing small molecules to inhibit glucose uptake in cancer. They characterize a novel pan-GLUT inhibitor that suppresses tumor growth and uncover how cancer cells can adapt to glucose restriction.
  18. Sci Rep. 2022 Mar 16. 12(1): 4476
      Cellular redox status and the level of reactive oxygen species (ROS) are important regulators of apoptotic potential, playing a crucial role in the growth of cancer cell and their resistance to apoptosis. However, the relationships between the redox status and ROS production during apoptosis remain poorly explored. In this study, we present an investigation on the correlations between the production of ROS, the redox ratio FAD/NAD(P)H, the proportions of the reduced nicotinamide cofactors NADH and NADPH, and caspase-3 activity in cancer cells at the level of individual cells. Two-photon excitation fluorescence lifetime imaging microscopy (FLIM) was applied to monitor simultaneously apoptosis using the genetically encoded sensor of caspase-3, mKate2-DEVD-iRFP, and the autofluorescence of redox cofactors in colorectal cancer cells upon stimulation of apoptosis with staurosporine, cisplatin or hydrogen peroxide. We found that, irrespective of the apoptotic stimulus used, ROS accumulation correlated well with both the elevated pool of mitochondrial, enzyme-bound NADH and caspase-3 activation. Meanwhile, a shift in the contribution of bound NADH could develop independently of the apoptosis, and this was observed in the case of cisplatin. An increase in the proportion of bound NADPH was detected only in staurosporine-treated cells, this likely being associated with a high level of ROS production and their resulting detoxification. The results of the study favor the discovery of new therapeutic strategies based on manipulation of the cellular redox balance, which could help improve the anti-tumor activity of drugs and overcome apoptotic resistance.
  19. Int J Mol Med. 2022 May;pii: 65. [Epub ahead of print]49(5):
      Radiotherapy is an essential and effective treatment modality for cancer. Excessive levels of reactive oxygen species (ROS) induced by ionizing radiation disrupt the redox homeostasis and lead to oxidative stress that may result in cell death. However, the tumor cell microenvironment is dynamic and responds to radiotherapy by activating numerous cellular signaling pathways. By scavenging excess ROS, the activity levels of the endogenous antioxidant enzymes result in radioresistance and worsen the clinical outcomes. To assess the full potential of radiotherapy, it is essential to explore the underlying mechanisms of oxidative stress in radiotherapy for potential target identification. The present review article summarized recent data demonstrating nuclear factor‑erythroid factor 2‑related factor 2 (Nrf2) as a powerful transcription factor and one of the major cellular defense mechanisms that protect against oxidative stress in response to radiotherapy; the glutathione (GSH) and thioredoxin (Trx) systems complement each other and are effective antioxidant mechanisms associated with the protection of cancer cells from radiation damage. In addition, it is suggested that dual targeting to inhibit GSH and Trx enzymes may be a potential strategy for the development of radiosensitive and radioprotective drugs.
    Keywords:  glutathione metabolism; oxidative stress; radiosensitivity; radiotherapy; thioredoxin
  20. Heliyon. 2022 Mar;8(3): e09068
      Single-driver molecular events specific to the metabolic colorectal cancer (CRC) have not been clearly elucidated. Herein, we identified 12 functional miRNAs linked to activated metabolism by integrating multi-omics features in metabolic CRC. These miRNAs exhibited significantly enriched CRC driver miRNAs, significant impacts on CRC cell growth and significantly correlated metabolites. Importantly, miR-20a is minimally expressed in normal colorectal tissues but highly expressed in metabolic CRC, suggesting the potential therapeutic target. Bioinformatics analyses further revealed miR-20a as the most powerful determinant that regulates a cascade of dysregulated events, including Wnt signaling pathway, core enzymes involved in FA metabolism program and triacylglycerol abundances. In vitro assays demonstrated that elevated miR-20a up-regulated FA synthesis enzymes via Wnt/β-catenin signaling, and finally promoted proliferative and migration of metabolic CRC cells. Overall, our study revealed that miR-20a promoted progression of metabolic CRC by regulating FA metabolism and served as a potential target for preventing tumor metastasis.
    Keywords:  Consensus molecular subtype; Fatty acid metabolism; Metabolic colorectal cancer; Wnt signaling pathway; miRNA
  21. Mol Cells. 2022 Mar 14.
      Excessive production of reactive oxygen species (ROS) is a key phenomenon in tumor necrosis factor (TNF)-α-induced cell death. However, the role of ROS in necroptosis remains mostly elusive. In this study, we show that TNF-α induces the mitochondrial accumulation of superoxide anions, not H2O2, in cancer cells undergoing necroptosis. TNF-α-induced mitochondrial superoxide anions production is strictly RIP3 expression-dependent. Unexpectedly, TNF-α stimulates NADPH oxidase (NOX), not mitochondrial energy metabolism, to activate superoxide production in the RIP3-positive cancer cells. In parallel, mitochondrial superoxide-metabolizing enzymes, such as manganese-superoxide dismutase (SOD2) and peroxiredoxin III, are not involved in the superoxide accumulation. Mitochondrial-targeted superoxide scavengers and a NOX inhibitor eliminate the accumulated superoxide without affecting TNF-α-induced necroptosis. Therefore, our study provides the first evidence that mitochondrial superoxide accumulation is a consequence of necroptosis.
    Keywords:  ; NADPH oxidase; necroptosis; superoxide anion; tumor necrosis factor-α
  22. Front Cell Dev Biol. 2022 ;10 829029
      Breast cancer is highly prevalent and fatal worldwide. Currently, breast cancer classification is based on the presence of estrogen, progesterone, and human epidermal growth factor 2. Because cancer and metabolism are closely related, we established a breast cancer classification system based on the metabolic gene expression profile. We performed typing of metabolism-related genes using The Cancer Genome Atlas-Breast Cancer and 2010 (YAU). We included 2,752 metabolic genes reported in previous literature, and the genes were further identified according to statistically significant variance and univariate Cox analyses. These prognostic metabolic genes were used for non-negative matrix factorization (NMF) clustering. Then, we identified characteristic genes in each metabolic subtype using differential analysis. The top 30 characteristic genes in each subtype were selected for signature construction based on statistical parameters. We attempted to identify standard metabolic signatures that could be used for other cohorts for metabolic typing. Subsequently, to demonstrate the effectiveness of the 90 Signature, NTP and NMF dimensional-reduction clustering were used to analyze these results. The reliability of the 90 Signature was verified by comparing the results of the two-dimensionality reduction clusters. Finally, the submap method was used to determine that the C1 metabolic subtype group was sensitive to immunotherapy and more sensitive to the targeted drug sunitinib. This study provides a theoretical basis for diagnosing and treating breast cancer.
    Keywords:  breast cancer; drug-targeted therapy; immunotherapy; metabolism phenotype; non-negative matrix factorization
  23. Int J Gen Med. 2022 ;15 2501-2513
      Purpose: Ferroptosis is an iron-dependent and reactive oxygen species (ROS)-reliant form of cell death, exhibiting cellular, molecular, and gene-level characteristics distinct from those of necrosis, autophagy, apoptosis, and pyroptosis. Solute carrier family 7 member 11 (SLC7A11), which encodes a cystine/glutamate antiporter transmembrane protein, inhibits ferroptosis by importing cystine and promoting glutathione (GSH) biosynthesis and was found to be overexpressed in multiple human cancers. However, the specific role and underlying mechanism of SLC7A11 in cancers remains poorly characterized. This research aimed to identify the relationship between SLC7A11 expression and tumor microenvironment and visualize its prognostic value in pan-cancer.Patients and Methods: Transcriptomic data for 6313 tumors and normal samples across 20 cancer types were acquired from The Cancer Genome Atlas (TCGA) database. Besides, we presented a novel bioinformatics pipeline that uncovered the impacts of SLC7A11 on cancer prognosis, tumor mutational burden (TMB), immune cell infiltration in tumor microenvironment, and drug responses. The Genotype-Tissue Expression (GTEx), cBioportal, TCGA and Connectivity Map (CMap) databases were used to explore the expression, genetic alterations, immune microenvironment, and drug responses of SLC7A11. A series of deconvolution algorithms, including EPIC, CIBERSORT and GSEA, were utilized for multidimensional analyses of the cancer transcriptomic data.
    Results: SLC7A11 was found to be highly expressed in the 20 types of cancer, especially in solid tumors. Survival analysis uncovered that most cancer patients with up-regulated expression of SLC7A11 showed poor prognosis, suggesting that SLC7A11 is a potential oncogene in most cancer types. Furthermore, the expression level of SLC7A11 was confirmed to be associated with immune cell infiltration in tumor microenvironment, TMB, and drug responses. Gene set enrichment analysis (GESA) revealed that dysregulation of SLC7A11 was associated with metabolic and immunity-related signaling pathways in the cancers.
    Conclusion: The comprehensive pan-cancer analyses identified SLC7A11 as an attractive biomarker for immune infiltration and poor prognosis in cancers, shedding new light on the therapeutics of cancers.
    Keywords:  SLC7A11; drug sensitivity; ferroptosis; immunotherapy; pan-cancer
  24. Analyst. 2022 Mar 16.
      Neurodevelopment is an intricately orchestrated program of cellular events that occurs with tight temporal and spatial regulation. While it is known that the development and proper functioning of the brain, which is the second most lipid rich organ behind adipose tissue, greatly rely on lipid metabolism and signaling, the temporal lipidomic changes that occur throughout the course of neurodevelopment have not been investigated. Smith-Lemli-Opitz syndrome is a metabolic disorder caused by genetic mutations in the DHCR7 gene, leading to defective 3β-hydroxysterol-Δ7-reductase (DHCR7), the enzyme that catalyzes the last step of the Kandutsch-Russell pathway of cholesterol synthesis. Due to the close regulatory relationship between sterol and lipid homeostasis, we hypothesize that altered or dysregulated lipid metabolism beyond the primary defect of cholesterol biosynthesis is present in the pathophysiology of SLOS. Herein, we applied our HILIC-IM-MS method and LiPydomics Python package to streamline an untargeted lipidomics analysis of developing mouse brains in both wild-type and Dhcr7-KO mice, identifying lipids at Level 3 (lipid species level: lipid class/subclass and fatty acid sum composition). We compared relative lipid abundances throughout development, from embryonic day 12.5 to postnatal day 0 and determined differentially expressed brain lipids between wild-type and Dhcr7-KO mice at specific developmental time points, revealing lipid metabolic pathways that are affected in SLOS beyond the cholesterol biosynthesis pathway, such as glycerolipid, glycerophospholipid, and sphingolipid metabolism. Implications of the altered lipid metabolic pathways in SLOS pathophysiology are discussed.
  25. Trends Biochem Sci. 2022 Mar 12. pii: S0968-0004(22)00065-2. [Epub ahead of print]
      Tricarboxylic acid (TCA) cycle is a major hub for catabolic and anabolic reactions, yet cellular metabolic adaptations following its inhibition are largely unknown. Using multi-tiered omics approaches, Ryan et al. have shown convergent activation of the integrated stress response (ISR) through ATF4-mediated rewiring of cellular amino acid and redox metabolic pathways.
    Keywords:  ATF4; TCA cycle; fumarate hydratase; glutathione synthesis; integrated stress response; succinate dehydrogenase
  26. Neoplasma. 2022 Mar 16. pii: 211006N1410. [Epub ahead of print]
      Colon cancer is a common cause of death in the world, and its main cause of therapy failure is chemoresistance. Apoptosis is de-regulated in colon cancer and is one key mechanism of cancer treatment. We recently reported that reduced expression of ARHGAP17, a Rho GTPase activating protein, correlated with a poor prognosis of colon cancer patients. Here we investigated the role of ARHGAP17 in apoptosis induced by 5-Fluorouracil (5-FU) in human colon cancer cells and in mouse xenograft tumor model. We observed a decreased protein level of ARHGAP17 in 5-FU resistant colon cancer cells (HCT116/5-FU and HCT8/5-FU). While ARHGAP17 knockdown attenuated apoptosis upon 5-FU treatment in HCT116 and HCT8, and ARHGAP17 overexpression in HCT116/5-FU and HCT8/5-FU cells increased apoptosis induced by 5-FU. We also found that ARHGAP17 knockdown led to a high level of active Rac1 in HCT116 and HCT8, but ARHGAP17 overexpression reduced active Rac1 in HCT116/5-FU and HCT8/5-FU cells. However, Rac1 inhibitor abolished the effect of ARHGAP17 knockdown, and Rac1 overexpression diminished the effect of ARHGAP17 overexpression on apoptosis induced by 5-FU. Apoptosis was also confirmed by cleaved Caspase-3 and cleaved PARP. Further, we observed that overexpression of ARHGAP17 promoted 5-FU-induced apoptosis and attenuated tumor growth in vivo. Collectively, our data indicate that ARHGAP17 sensitizes chemotherapy-resistant colon cancer cells to apoptosis induced by 5-FU, which is in part through suppressing Rac1.
  27. Nano Lett. 2022 Mar 14.
      Uncontrolled growth of tumor cells is highly dependent on the energy metabolism. Fasting-mimicking diet (FMD) is a low-calorie, low-protein, low-sugar diet representing a promising strategy for cancer treatment. However, triglyceride stored in adipose tissue is hydrolyzed into free fatty acids and glycerol for energy supply during FMD treatment. Herein, we design a nutrient-sensing nanodrug, VFETX, which is self-assembled with vitamin B1 (VB1), ferrous ions, and etomoxir (ETX). FMD treatment upregulate the expression of VB1 transporters on tumor cells, thereby increasing cellular uptake and tumor accumulation of VFETX. Importantly, treatments of VFETX and FMD synergistically inhibit the energy metabolism in tumor cells and subsequently markedly enhance cytotoxicity of ETX. As a result, VFETX nanodrugs efficiently inhibit the growth of two tumor models in vivo without obvious side effects. This study demonstrates the potential of FMD-assisted nutrient-sensing nanodrugs for cancer therapy.
    Keywords:  Biomolecule; cancer therapy; fasting-mimicking diet; self-assembly
  28. Antioxid Redox Signal. 2022 Mar 14.
      AIMS: Raloxifene, a selective estrogen receptor (ER) modulator, has been reported to exert the tumor-suppressive effects in both ER-positive and ER-negative cancer cells; however, the mechanisms underlying its ER-independent anti-cancer effects are poorly understood. The NLRP3 inflammasome, a critical component of the innate immune system, has recently received growing attention owing to its multifaceted roles in various aspects of cancer development. The present study aimed to examine the involvement of NLRP3 inflammasomes in the anti-breast cancer effects of raloxifene and its underlying mechanisms.RESULTS: Raloxifene significantly inhibited activation of NLRP3 inflammasomes in various breast cancer cell lines. Importantly, forced expression of a gain-of-function variant of NLRP3 rescued breast cancer cells from growth arrest by raloxifene, suggesting that suppression of NLRP3 inflammasomes activation mediates the raloxifene-induced inhibition of breast cancer growth. Mechanistically, raloxifene suppressed NLRP3 inflammasomes activation by lowering the cellular levels of ROS through the modulation of redox signaling mediated via aryl hydrocarbon receptor (AhR)-Nrf2-HO-1 axis or the impaired generation of mitochondrial ROS in a mitophagy-dependent manner. Furthermore, blockage of AhR signaling or inhibition of mitophagy abolished the tumor-suppressive effect of raloxifene in a human breast tumor xenograft model.
    INNOVATION: We elucidate a novel molecular mechanism underlying the breast tumor suppressing effect of raloxifene.
    CONCLUSIONS: The results observed in this study suggest that modulation of NLRP3 inflammasomes activation is a critical event in inhibition of breast tumor growth by raloxifene.
  29. Front Cell Dev Biol. 2022 ;10 768579
      Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is an important mediator of tumor immune surveillance. In addition, its potential to kill cancer cells without harming healthy cells led to the development of TRAIL receptor agonists, which however did not show the desired effects in clinical trials. This is caused mainly by apoptosis resistance mechanisms operating in primary cancer cells. Meanwhile, it has been realized that in addition to cell death, TRAIL also induces non-apoptotic pro-inflammatory pathways that may enhance tumor malignancy. Due to its late detection and resistance to current therapeutic options, pancreatic ductal adenocarcinoma (PDAC) is still one of the deadliest types of cancer worldwide. A dysregulated pH microenvironment contributes to PDAC development, in which the cancer cells become highly dependent on to maintain their metabolism. The impact of extracellular pH (pHe) on TRAIL-induced signaling in PDAC cells is poorly understood so far. To close this gap, we analyzed the effects of acidic and alkaline pHe, both in short-term and long-term settings, on apoptotic and non-apoptotic TRAIL-induced signaling. We found that acidic and alkaline pHe differentially impact TRAIL-induced responses, and in addition, the duration of the pHe exposition also represents an important parameter. Thus, adaptation to acidic pHe increases TRAIL sensitivity in two different PDAC cell lines, Colo357 and Panc1, one already TRAIL-sensitive and the other TRAIL-resistant, respectively. However, the latter became highly TRAIL-sensitive only by concomitant inhibition of Bcl-xL. None of these effects was observed under other pHe conditions studied. Both TRAIL-induced non-apoptotic signaling pathways, as well as constitutively expressed anti-apoptotic proteins, were regulated by acidic pHe. Whereas the non-apoptotic pathways were differently affected in Colo357 than in Panc1 cells, the impact on the anti-apoptotic protein levels was similar in both cell lines. In Panc1 cells, adaptation to either acidic or alkaline pHe blocked the activation of the most of TRAIL-induced non-apoptotic pathways. Interestingly, under these conditions, significant downregulation of the plasma membrane levels of TRAIL-R1 and TRAIL-R2 was observed. Summing up, extracellular pH influences PDAC cells' response to TRAIL with acidic pHe adaptation, showing the ability to strongly increase TRAIL sensitivity and in addition to inhibit TRAIL-induced pro-inflammatory signaling.
    Keywords:  TRAIL; TRAIL receptor; apoptosis; extracellular pH; non-apoptotic signaling; pancreatic ductal adenocarcinoma
  30. Commun Biol. 2022 Mar 17. 5(1): 198
      Tumor metastasis imposes metabolic requirements for escaping from primary tissues, producing vulnerability in treatment. This study aimed to explore the metabolic reprogramming relevant to lung adenocarcinoma (LUAD) metastasis and decode the underlying intercellular alterations. Using the gene expression profiles of 394 LUAD samples derived from The Cancer Genome Atlas (TCGA), we identified 11 metastasis-related metabolic genes involved in glycolysis and lipid metabolism, and defined three metabolic reprogramming phenotypes (MP-I, -II, and -III) using unsupervised clustering. MP-III with the highest glycolytic and lowest lipid metabolic levels exhibited the highest metastatic potency and poorest survival in TCGA and six independent cohorts totaling 1,235 samples. Genomic analyses showed that mutations in TP53 and KEAP1, and deletions in SETD2 and PBRM1 might drive metabolic reprogramming in MP-III. Single-cell RNA-sequencing data from LUAD validated a metabolic evolutionary trajectory from normal to MP-II and MP-III, through MP-I. The further intercellular communications revealed that MP-III interacted uniquely with endothelial cells and fibroblasts in the ANGPTL pathway, and had stronger interactions with endothelial cells in the VEGF pathway. Herein, glycolysis-lipid dysregulation patterns suggested metabolic reprogramming phenotypes relevant to metastasis. Further insights into the oncogenic drivers and microenvironmental interactions would facilitate the treatment of LUAD metastasis in the future.
  31. Arch Gynecol Obstet. 2022 Mar 14.
      BACKGROUND: Circular RNAs (circRNAs) have been reported to function as vital regulators in cancers, including triple-negative breast cancer (TNBC). This study aimed to explore the role of circ_0062558 in TNBC.METHODS: The real-time quantitative polymerase chain reaction (RT-qPCR) was conducted to quantify the expressions of circ_0062558, microRNA-876-3p (miR-876-3p), and solute carrier family 1 (neutral amino acid transporter), member 5 (SLC1A5) in TNBC tissues and cells. 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyl-2H-tetrazol-3-ium bromide (MTT), thymidine analog 5-ethynyl-2'-deoxyuridine (EdU), flow cytometry, wound healing, and Transwell assays were employed for cell phenotype analyses. Protein expression was tested by western blot analysis. Dual-luciferase reporter was used to confirm the association among circ_0062558, miR-876-3p, and SLC1A5 in TNBC. Xenograft experiments were performed to elucidate the function of circ_0062558 in vivo.
    RESULTS: TNBC tissues and cells showed the higher level of circ_0062558 when compared with control samples. Downregulation of circ_0062558 inhibited proliferation, migration, invasion, and glutamine metabolism, while enhanced apoptosis of TNBC cells, and silencing of circ_0062558 also inhibited the growth of tumor in vivo. MiR-876-3p was confirmed as a target of circ_0062558, and circ_0062558 knockdown repressed TNBC cell malignant behaviors by increasing miR-876-3p. Furthermore, miR-876-3p inhibited malignant behaviors of TNBC cells by down-regulating SLC1A5, a newly identified target of miR-876-3p.
    CONCLUSION: Circ_0062558 promoted TNBC progression by enhancing proliferation, survival, migration, invasion, and glutamine metabolism via miR-876-3p/SLC1A5 axis, which was helpful for understanding the carcinogenic roles of circ_0062558.
    Keywords:  CircRNA; Circ_0062558; MiR-876-3p; SLC1A5; TNBC
  32. Trends Biochem Sci. 2022 Mar 15. pii: S0968-0004(22)00050-0. [Epub ahead of print]
      Insulin stimulates glucose uptake into adipocytes via mTORC2/AKT signaling and GLUT4 translocation and directs glucose carbons into glycolysis, glycerol for TAG synthesis, and de novo lipogenesis. Adipocyte insulin resistance is an early indicator of type 2 diabetes in obesity, a worldwide health crisis. Thus, understanding the interplay between insulin signaling and central carbon metabolism pathways that maintains adipocyte function, blood glucose levels, and metabolic homeostasis is critical. While classically viewed through the lens of individual enzyme-substrate interactions, advances in mass spectrometry are beginning to illuminate adipocyte signaling and metabolic networks on an unprecedented scale, yet this is just the tip of the iceberg. Here, we review how 'omics approaches help to elucidate adipocyte insulin action in cellular time and space.
    Keywords:  glucose; insulin; metabolism; metabolomics; phosphoproteomics; white and brown adipose tissue
  33. J Exp Clin Cancer Res. 2022 Mar 14. 41(1): 98
      BACKGROUND: Macropinocytosis, an important nutrient-scavenging pathway in certain cancer cells, allows cells to compensate for intracellular amino acid deficiency under nutrient-poor conditions. Ferroptosis caused by cysteine depletion plays a pivotal role in sorafenib responses during hepatocellular carcinoma (HCC) therapy. However, it is not known whether macropinocytosis functions as an alternative pathway to acquire cysteine in sorafenib-treated HCC, and whether it subsequently mitigates sorafenib-induced ferroptosis. This study aimed to investigate whether sorafenib drives macropinocytosis induction, and how macropinocytosis confers ferroptosis resistance on HCC cells.METHODS: Macropinocytosis, both in HCC cells and HCC tissues, was evaluated by measuring TMR-dextran uptake or lysosomal degradation of DQ-BSA, and ferroptosis was evaluated via C11-BODIPY fluorescence and 4-HNE staining. Sorafenib-induced ferroptosis and macropinocytosis were validated in tumor tissues taken from HCC patients who underwent ultrasound-guided needle biopsy.
    RESULTS: Sorafenib increased macropinocytosis in human HCC specimens and xenografted HCC tissues. Sorafenib-induced mitochondrial dysfunction was responsible for activation of PI3K-RAC1-PAK1 signaling, and amplified macropinocytosis in HCC. Importantly, macropinocytosis prevented sorafenib-induced ferroptosis by replenishing intracellular cysteine that was depleted by sorafenib treatment; this rendered HCC cells resistant to sorafenib. Finally, inhibition of macropinocytosis by amiloride markedly enhanced the anti-tumor effect of sorafenib, and sensitized resistant tumors to sorafenib.
    CONCLUSION: In summary, sorafenib induced macropinocytosis, which conferred drug resistance by mitigating sorafenib-induced ferroptosis. Thus, targeting macropinocytosis is a promising therapeutic strategy to facilitate ferroptosis-based therapy for HCC.
    Keywords:  Ferroptosis; Hepatocellular carcinoma; Macropinocytosis; Sorafenib; Sorafenib resistance
  34. Biosci Biotechnol Biochem. 2022 Mar 14. pii: zbac037. [Epub ahead of print]
      Muscle atrophy is a major health problem that needs effective prevention and treatment approaches. Chronic exercise, an effective treatment strategy for atrophy, promotes muscle hypertrophy, which leads to dynamic metabolic changes; however, the metabolic changes vary among myofiber types. To investigate local metabolic changes due to chronic exercise, we utilized comprehensive proteome and mass spectrometry (MS) imaging analyses. Our training model exhibited hypertrophic features only in glycolytic myofibers. The proteome analyses demonstrated that exercise promoted anabolic pathways, such as protein synthesis, and significant changes in lipid metabolism, but not in glucose metabolism. Furthermore, the fundamental energy sources, glycogen, neutral lipids, and ATP, were sensitive to exercise, and the changes in these sources differed between glycolytic and oxidative myofibers. MS imaging revealed that the lipid composition differs among myofibers; arachidonic acid might be an effective target for promoting lipid metabolism during muscle hypertrophy in oxidative myofibers.
    Keywords:  exercise; mass spectrometry imaging; metabolites; muscle hypertrophy
  35. Front Cardiovasc Med. 2022 ;9 803510
      Objective: To explore the cardioprotective effects of exercise-derived β-aminoisobutyric (BAIBA) on cardiomyocyte apoptosis and energy metabolism in a rat model of heart failure (HF).Methods: In male Sprague-Dawley rats (8-week-old), myocardial infarction (MI) was used to induce HF by ligating the left anterior descending branch of the coronary artery. In the Sham group, the coronary artery was threaded but not ligated. After HF development, Sham and HF rats were exercised 60 min daily, 5 days/week on a treadmill for 8 weeks (50-60% maximal intensity) and exercise-induced cardiac remodeling after MI were assessed using echocardiography, hematoxylin and eosin (H&E), Masson's Trichrome, and TUNEL staining for the detection of apoptosis-associated factors in cardiac tissue. High-throughput sequencing and mass spectrometry were used to measure BAIBA production and to explore its cardioprotective effects and molecular actions. To further characterize the cardioprotective effects of BAIBA, an in vitro model of apoptosis was generated by applying H2 O 2 to H9C2 cells to induce mitochondrial dysfunction. In addition, cells were transfected with either a miR-208b analog or a miR-208b inhibitor. Apoptosis-related proteins were detected by Western Blotting (WB). ATP production was also assessed by luminometry. After administration of BAIBA and Compound C, the expression of proteins related to apoptosis, mitochondrial function, lipid uptake, and β-oxidative were determined. Changes in the levels of reactive oxygen species (ROS) were assessed by fluorescence microscopy. In addition, alterations in membrane potential (δψm) were obtained by confocal microscopy.
    Results: Rats with HF after MI are accompanied by mitochondrial dysfunction, metabolic stress and apoptosis. Reduced expression of apoptosis-related proteins was observed, together with increased ATP production and reduced mitochondrial dysfunction in the exercised compared with the Sham (non-exercised) HF group. Importantly, exercise increased the production of BAIBA, irrespective of the presence of HF. To assess whether BAIBA had similar effects to exercise in ameliorating HF-induced adverse cardiac remodeling, rats were treated with 75 mg/kg/ day of BAIBA and we found BAIBA had a similar cardioprotective effect. Transcriptomic analyses found that the expression of miR-208b was increased after BAIBA administration, and subsequent transfection with an miR-208b analog ameliorated both the expression of apoptosis-related proteins and energy metabolism in H2O2-treated H9C2 cells. In combining transcriptomic with metabolomic analyses, we identified AMPK as a downstream target for BAIBA in attenuating metabolic stress in HF. Further cell experiments confirmed that BAIBA increased AMPK phosphorylation and had a cardioprotective effect on downstream fatty acid uptake, oxidative efficiency, and mitochondrial function, which was prevented by the AMPK inhibitor Compound C.
    Conclusion: Exercise-generated BAIBA can reduce cardiomyocyte metabolic stress and apoptosis induced by mitochondrial dysfunction through the miR-208b/AMPK pathway.
    Keywords:  exercise; heart failure; lipid metabolism; metabolic stress; mitochondrial dysfunction
  36. Trends Cell Biol. 2022 Mar 14. pii: S0962-8924(22)00036-8. [Epub ahead of print]
      Gene transcription and cell metabolism are two fundamental biological processes that mutually regulate each other. Upregulated or altered expression of glucose metabolic genes in glycolysis and gluconeogenesis is a major driving force of enhanced aerobic glycolysis in tumor cells. Importantly, glycolytic and gluconeogenic enzymes in tumor cells acquire moonlighting functions and directly regulate gene expression by modulating chromatin or transcriptional complexes. The mutual regulation between cellular metabolism and gene expression in a feedback mechanism constitutes a unique feature of tumor cells and provides specific molecular and functional targets for cancer treatment.
    Keywords:  cancer; gene expression; gluconeogenesis; glycolysis; metabolism
  37. Front Toxicol. 2021 ;3 780778
      Immunotoxicology sensu lato comprises not only toxicity toward immune cells, but also biological reactions from immune cells exposed to toxicants, reactions that may have deleterious effects at the organismal level. Within this wide frame, a specific case of interest is represented by the response of macrophages to particulate materials, with the epitome examples of asbestos and crystalline silica. For such toxicants that are both persistent and often encountered in an occupational setting, i.e. at low but repeated doses, there is a need for in vitro systems that can take into account these two parameters. Currently, most in vitro systems are used in an acute exposure mode, i.e., with a single dose and a readout made shortly if not immediately after exposure. We describe here how adequate changes of the culture methods applied to the murine macrophage cell line J774A.1 enable longer periods of culture (several days), which represents a first opportunity to address the persistence and dose-rate issues. To respond to this, the protocol uses a reduction in the concentration of the animal serum used for cell culture, as well as a switch from fetal to adult serum, which is less rich in proliferation factors. By doing so, we have considerably reduced cell proliferation, which is a problem with cell lines when they are supposed to represent slowly-dividing cells such as resident macrophages. We also succeeded in maintaining the differentiated functions of macrophages, such as phagocytosis or inflammatory responses, over the whole culture period. Furthermore, the presence of serum, even at low concentrations, provides excellent cell viability and keeps the presence of a protein corona on particulate materials, a feature that is known to strongly modulate their effects on cells and is lost in serum-free culture. Besides data showing the impact of these conditions on macrophages cell line cultures, illustrative examples are shown on silica- and cobalt-based pigments.
    Keywords:  cobalt; effect persistence; immunotoxicology; macrophages; pigments; silica
  38. Mol Ther Methods Clin Dev. 2022 Mar 10. 24 380-393
      Ex vivo expansion conditions used to generate T cells for immunotherapy are thought to adopt metabolic phenotypes that impede therapeutic efficacy in vivo. The comparison of five different culture media used for clinical T cell expansion revealed unique optima based on different output variables, including proliferation, differentiation, function, activation, and mitochondrial phenotypes. The extent of proliferation and function depended on the culture media rather than stimulation conditions. Moreover, the expanded T cell end products adapted their metabolism when switched to a different media formulation, as shown by glucose and glutamine uptake and patterns of glucose isotope labeling. However, adoption of these metabolic phenotypes was uncoupled to T cell function. Expanded T cell products cultured in ascites from ovarian cancer patients displayed suppressed mitochondrial activity and function irrespective of the ex vivo expansion media. Thus, ex vivo T cell expansion media have profound impacts on metabolism and function.
    Keywords:  13C tracer analysis; T cell expansion; cell-based immunotherapy; culture media; metabolism; phenotype
  39. Front Genet. 2022 ;13 815476
      Motivation: The increasing availability of metabolomic data and their analysis are improving the understanding of cellular mechanisms and how biological systems respond to different perturbations. Currently, there is a need for novel computational methods that facilitate the analysis and integration of increasing volume of available data. Results: In this paper, we present Totoro a new constraint-based approach that integrates quantitative non-targeted metabolomic data of two different metabolic states into genome-wide metabolic models and predicts reactions that were most likely active during the transient state. We applied Totoro to real data of three different growth experiments (pulses of glucose, pyruvate, succinate) from Escherichia coli and we were able to predict known active pathways and gather new insights on the different metabolisms related to each substrate. We used both the E. coli core and the iJO1366 models to demonstrate that our approach is applicable to both smaller and larger networks. Availability: Totoro is an open source method (available at suitable for any organism with an available metabolic model. It is implemented in C++ and depends on IBM CPLEX which is freely available for academic purposes.
    Keywords:  metabolic networks; metabolic perturbation; metabolomics; omics integration; transient state
  40. IUBMB Life. 2022 Mar 18.
      Multiple mitochondrial matrix enzymes playing key roles in metabolism require cofactors for their action. Due to the high impermeability of the mitochondrial inner membrane, these cofactors need to be synthesized within the mitochondria or be imported, themselves or one of their precursors, into the organelles. Transporters belonging to the protein family of mitochondrial carriers have been identified to transport the coenzymes: thiamine pyrophosphate, coenzyme A, FAD and NAD+ , which are all structurally similar to nucleotides and derived from different B-vitamins. These mitochondrial cofactors bind more or less tightly to their enzymes and, after having been involved in a specific reaction step, are regenerated, spontaneously or by other enzymes, to return to their active form, ready for the next catalysis round. Disease-causing mutations in the mitochondrial cofactor carrier genes compromise not only the transport reaction but also the activity of all mitochondrial enzymes using that particular cofactor and the metabolic pathways in which the cofactor-dependent enzymes are involved. The mitochondrial transport, metabolism and diseases of the cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD+ are the focus of this review.
    Keywords:  coenzyme; coenzyme A; flavin adenine dinucleotide; mitochondria; mitochondrial carrier family SLC25; nicotinamide adenine dinucleotide; thiamine pyrophosphate
  41. Front Genet. 2022 ;13 812764
      Epigenetic modifiers (EM; methionine, choline, folate, and vitamin B12) are important for early embryonic development due to their roles as methyl donors or cofactors in methylation reactions. Additionally, they are essential for the synthesis of nucleotides, polyamines, redox equivalents, and energy metabolites. Despite their importance, investigation into the supplementation of EM in ruminants has been limited to one or two epigenetic modifiers. Like all biochemical pathways, one-carbon metabolism needs to be stoichiometrically balanced. Thus, we investigated the effects of supplementing four EM encompassing the methionine-folate cycle on bovine embryonic fibroblast growth, mitochondrial function, and DNA methylation. We hypothesized that EM supplemented to embryonic fibroblasts cultured in divergent glucose media would increase mitochondrial respiration and cell growth rate and alter DNA methylation as reflected by changes in the gene expression of enzymes involved in methylation reactions, thereby improving the growth parameters beyond Control treated cells. Bovine embryonic fibroblast cells were cultured in Eagle's minimum essential medium with 1 g/L glucose (Low) or 4.5 g/L glucose (High). The control medium contained no additional OCM, whereas the treated media contained supplemented EM at 2.5, 5, and 10 times (×2.5, ×5, and ×10, respectively) the control media, except for methionine (limited to ×2). Therefore, the experimental design was a 2 (levels of glucose) × 4 (levels of EM) factorial arrangement of treatments. Cells were passaged three times in their respective treatment media before analysis for growth rate, cell proliferation, mitochondrial respiration, transcript abundance of methionine-folate cycle enzymes, and DNA methylation by reduced-representation bisulfite sequencing. Total cell growth was greatest in High ×10 and mitochondrial maximal respiration, and reserve capacity was greatest (p < 0.01) for High ×2.5 and ×10 compared with all other treatments. In Low cells, the total growth rate, mitochondrial maximal respiration, and reserve capacity increased quadratically to 2.5 and ×5 and decreased to control levels at ×10. The biological processes identified due to differential methylation included the positive regulation of GTPase activity, molecular function, protein modification processes, phosphorylation, and metabolic processes. These data are interpreted to imply that EM increased the growth rate and mitochondrial function beyond Control treated cells in both Low and High cells, which may be due to changes in the methylation of genes involved with growth and energy metabolism.
    Keywords:  DNA methylation; cell growth; embryonic fibroblasts; mitochondrial respiration; one-carbon metabolism
  42. Front Toxicol. 2022 ;4 842396
      Fourteen to 26 percent of all hospitalized cases of acute kidney injury are explained by drug-induced toxicity, emphasizing the importance of proper strategies to pre-clinically assess renal toxicity. The MTT assay is widely used as a measure of cell viability, but largely depends on cellular metabolic activity. Consequently, MTT as a single assay may not be the best way to assess cytotoxicity of compounds that reduce mitochondrial function and cellular metabolic activity without directly affecting cell viability. Accordingly, we aim to highlight the limitations of MTT alone in assessing renal toxicity of compounds that interfere with metabolic activity. Therefore, we compared toxic effects observed by MTT with a fluorescent assay that determines compromised plasma membrane permeability. Exposure of proximal tubule epithelial cells to nephrotoxic compounds reduced cellular metabolic activity concentration- and time-dependently. We show that compared to our fluorescence-based approach, assessment of cellular metabolic activity by means of MTT provides a composite readout of cell death and metabolic impairment. An approach independent of cellular metabolism is thus preferable when assessing cytotoxicity of compounds that induce metabolic dysfunction. Moreover, combining both assays during drug development enables a first discrimination between compounds having a direct or indirect mitochondrial toxic potential.
    Keywords:  acute kidney injury; cell viability; cellular metabolic activity; drug-induced toxicity; metabolic toxicity
  43. Metab Eng. 2022 Mar 13. pii: S1096-7176(22)00042-8. [Epub ahead of print]
      Osteoarthritis (OA) is the most common degenerative joint disease and a major cause of age-related disability worldwide, mainly due to pain, the disease's main symptom. Although OA was initially classified as a non-inflammatory joint disease, recent attention has been drawn to the importance of synovitis and fibroblast-like synoviocytes (FLS) in the pathogenesis of OA. FLS can be divided into two major populations: thymus cell antigen 1 (THY1)- FLS are currently classified as quiescent cells and assumed to destroy bone and cartilage, whereas THY1+ FLS are invasively proliferative cells that drive synovitis. Both THY1- and THY1+ FLS share many characteristics with fibroblast-like progenitors - mesenchymal stromal cells (MSC). However, it remains unclear whether synovitis-induced metabolic changes exist in FLS from OA patients and whether metabolic differences may provide a mechanistic basis for the identification of approaches to precisely convert the pathologically proliferative synovitis-driven FLS phenotype into a healthy one. To identify novel pathological mechanisms of the perpetuation and manifestation of OA, we analyzed metabolic, proteomic, and functional characteristics of THY1+ FLS from patients with OA. Proteome data and pathway analysis revealed that an elevated expression of pyruvate dehydrogenase kinase (PDK) 3 was characteristic of proliferative THY1+ FLS from patients with OA. These FLS also had the highest podoplanin (PDPN) expression and localized to the sublining but also the lining layer in OA synovium in contrast to the synovium of ligament trauma patients. Inhibition of PDKs reprogrammed metabolism from glycolysis towards oxidative phosphorylation and reduced FLS proliferation and inflammatory cytokine secretion. This study provides new mechanistic insights into the importance of FLS metabolism in the pathogenesis of OA. Given the selective overexpression of PDK3 in OA synovium and its restricted distribution in synovial tissue from ligament trauma patients and MSC, PDKs may represent attractive selective metabolic targets for OA treatment. Moreover, targeting PDKs does not affect cells in a homeostatic, oxidative state. Our data provide an evidence-based rationale for the idea that inhibition of PDKs could restore the healthy THY1+ FLS phenotype. This approach may mitigate the progression of OA and thereby fundamentally change the clinical management of OA from the treatment of symptoms to addressing causes.
    Keywords:  Mesenchymal stromal cells; Metabolic engineering; Metabolism; Proteomics; Synovial fibroblasts; Synovitis; THY1