bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020–01–05
48 papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Mitochondrial Integrity Regulated by Lipid Metabolism Is a Cell-Intrinsic Checkpoint for Treg Suppressive Function.
  2. Mutant IDH1 Differently Affects Redox State and Metabolism in Glial Cells of Normal and Tumor Origin.
  3. Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells.
  4. Modeling succinate dehydrogenase loss disorders in C. elegans through effects on hypoxia-inducible factor.
  5. Stimulating pyruvate dehydrogenase complex reduces itaconate levels and enhances TCA cycle anabolic bioenergetics in acutely inflamed monocytes.
  6. Peroxisomal fission is modulated by the mitochondrial Rho-GTPases, Miro1 and Miro2.
  7. Analyzing the Metabolism of Metastases in Mice.
  8. The mitochondrial iron exporter genes MMT1 and MMT2 in yeast are transcriptionally regulated by Aft1 and Yap1.
  9. Mitochondrial genetics cooperate with nuclear genetics to selectively alter immune cell development/trafficking.
  10. OGDHL silencing promotes hepatocellular carcinoma by reprogramming glutamine metabolism.
  11. Gut stem cell aging is driven by mTORC1 via a p38 MAPK-p53 pathway.
  12. Omics Integration for Mitochondria Systems Biology.
  13. Cysteine catabolism and the serine biosynthesis pathway support pyruvate production during pyruvate kinase knockdown in pancreatic cancer cells.
  14. Downregulation of the DNA 5-hydroxymethylcytosine is involved in mitochondrial dysfunction and neuronal impairment in high fat diet-induced diabetic mice.
  15. Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis.
  16. Immune-mediated anti-tumor effects of metformin; targeting metabolic reprogramming of T cells as a new possible mechanism for anti-cancer effects of metformin.
  17. TGFB-INHB/activin signaling regulates age-dependent autophagy and cardiac health through inhibition of MTORC2.
  18. Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy.
  19. Large-Scale Profiling of Cellular Metabolic Activities Using Deep 13C Labeling Medium.
  20. Interpreting pathways to discover cancer driver genes with Moonlight.
  21. Liquid Chromatography Methods for Separation of Polar and Charged Intracellular Metabolites for 13C Metabolic Flux Analysis.
  22. Fumarate and oxidative stress synergize to promote stability of C/EBP homologous protein in the adipocyte.
  23. Inferring Metabolic Flux from Time-Course Metabolomics.
  24. Variants in Miro1 Cause Alterations of ER-Mitochondria Contact Sites in Fibroblasts from Parkinson's Disease Patients.
  25. Mitochondrial residence of the apoptosis inducer BAX is more important than BAX oligomerization in promoting membrane permeabilization.
  26. SWATH: A Data-Independent Tandem Mass Spectrometry Method to Quantify 13C Enrichment in Cellular Metabolites and Fragments.
  27. Autophagy and disease: unanswered questions.
  28. Pediatric gastrointestinal stromal tumor: Report of two novel patients harboring germline variants in SDHB and SDHC genes.
  29. Mitochondrial TCA cycle metabolites control physiology and disease.
  30. The PAP/SAL1 retrograde signaling pathway is involved in iron homeostasis.
  31. Increased Drp1 Acetylation by Lipid Overload Induces Cardiomyocyte Death and Heart Dysfunction.
  32. Fat for fuel: lipid metabolism in haematopoiesis.
  33. Rescuing stalled mammalian mitoribosomes - what can we learn from bacteria?
  34. Mitochondrial Dynamics of Proximal Tubular Epithelial Cells in Nephropathic Cystinosis.
  35. ROCK inhibitors upregulate the neuroprotective Parkin-mediated mitophagy pathway.
  36. Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism.
  37. Molecular connections between circadian clocks and aging.
  38. Energy oversupply to tissues: a single mechanism possibly underlying multiple cancer risk factors.
  39. Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor.
  40. Exploring Targeted Degradation Strategy for Oncogenic KRASG12C.
  41. Mitochondrial Haplogroups and Lifespan in a Population Isolate.
  42. A systematic flux analysis approach to identify metabolic vulnerabilities in human breast cancer cell lines.
  43. Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases.
  44. CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer.
  45. Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects.
  46. Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes.
  47. A ketogenic diet attenuates proliferation and stemness of glioma stem‑like cells by altering metabolism resulting in increased ROS production.
  48. Proteome-wide observation of the phenomenon of life on the edge of solubility.
  1. Cell Metab. 2019 Dec 12. pii: S1550-4131(19)30665-5. [Epub ahead of print]
    Mitochondrial Integrity Regulated by Lipid Metabolism Is a Cell-Intrinsic Checkpoint for Treg Suppressive Function.
    Cameron S Field, Francesc Baixauli, Ryan L Kyle, Daniel J Puleston, Alanna M Cameron, David E Sanin, Keli L Hippen, Michael Loschi, Govindarajan Thangavelu, Mauro Corrado, Joy Edwards-Hicks, Katarzyna M Grzes, Edward J Pearce, Bruce R Blazar, Erika L Pearce.
      Regulatory T cells (Tregs) subdue immune responses. Central to Treg activation are changes in lipid metabolism that support their survival and function. Fatty acid binding proteins (FABPs) are a family of lipid chaperones required to facilitate uptake and intracellular lipid trafficking. One family member, FABP5, is expressed in T cells, but its function remains unclear. We show that in Tregs, genetic or pharmacologic inhibition of FABP5 function causes mitochondrial changes underscored by decreased OXPHOS, impaired lipid metabolism, and loss of cristae structure. FABP5 inhibition in Tregs triggers mtDNA release and consequent cGAS-STING-dependent type I IFN signaling, which induces heightened production of the regulatory cytokine IL-10 and promotes Treg suppressive activity. We find evidence of this pathway, along with correlative mitochondrial changes in tumor infiltrating Tregs, which may underlie enhanced immunosuppression in the tumor microenvironment. Together, our data reveal that FABP5 is a gatekeeper of mitochondrial integrity that modulates Treg function.
    Keywords:  FABP5; IL-10; Treg; cGAS-STING; immunometabolism; lipids; mtDNA; suppression; tumor; type I IFN
    DOI:  https://doi.org/10.1016/j.cmet.2019.11.021
  2. Cancers (Basel). 2019 Dec 16. pii: E2028. [Epub ahead of print]11(12):
    Mutant IDH1 Differently Affects Redox State and Metabolism in Glial Cells of Normal and Tumor Origin.
    Julia Biedermann, Matthias Preussler, Marina Conde, Mirko Peitzsch, Susan Richter, Ralf Wiedemuth, Khalil Abou-El-Ardat, Alexander Krüger, Matthias Meinhardt, Gabriele Schackert, William P Leenders, Christel Herold-Mende, Simone P Niclou, Rolf Bjerkvig, Graeme Eisenhofer, Achim Temme, Michael Seifert, Leoni A Kunz-Schughart, Evelin Schröck, Barbara Klink.
      IDH1R132H (isocitrate dehydrogenase 1) mutations play a key role in the development of low-grade gliomas. IDH1wt converts isocitrate to α-ketoglutarate while reducing nicotinamide adenine dinucleotide phosphate (NADP+), whereas IDH1R132H uses α-ketoglutarate and NADPH to generate the oncometabolite 2-hydroxyglutarate (2-HG). While the effects of 2-HG have been the subject of intense research, the 2-HG independent effects of IDH1R132H are still ambiguous. The present study demonstrates that IDH1R132H expression but not 2-HG alone leads to significantly decreased tricarboxylic acid (TCA) cycle metabolites, reduced proliferation, and enhanced sensitivity to irradiation in both glioblastoma cells and astrocytes in vitro. Glioblastoma cells, but not astrocytes, showed decreased NADPH and NAD+ levels upon IDH1R132H transduction. However, in astrocytes IDH1R132H led to elevated expression of the NAD-synthesizing enzyme nicotinamide phosphoribosyltransferase (NAMPT). These effects were not 2-HG mediated. This suggests that IDH1R132H cells utilize NAD+ to restore NADP pools, which only astrocytes could compensate via induction of NAMPT. We found that the expression of NAMPT is lower in patient-derived IDH1-mutant glioma cells and xenografts compared to IDH1-wildtype models. The Cancer Genome Atlas (TCGA) data analysis confirmed lower NAMPT expression in IDH1-mutant versus IDH1-wildtype gliomas. We show that the IDH1 mutation directly affects the energy homeostasis and redox state in a cell-type dependent manner. Targeting the impairments in metabolism and redox state might open up new avenues for treating IDH1-mutant gliomas.
    Keywords:  IDH-mutation; IDH1; NAD-synthesis; glioma; metabolism; redox state
    DOI:  https://doi.org/10.3390/cancers11122028
  3. Methods Mol Biol. 2020 ;2088 51-71
    Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells.
    Esther W Lim, Seth J Parker, Christian M Metallo.
      Oxidation-reduction (redox) reactions are ubiquitous in biology and typically occur in specific subcellular compartments. In cells, the electron transfer between molecules and organelles is commonly facilitated by pyridine nucleotides such as nicotinamide adenine dinucleotide phosphate (NADPH) and nicotinamide adenine dinucleotide (NADH). While often taken for granted, these metabolic reactions are critically important for maintaining redox homeostasis and biochemical potentials across membranes. While 13C tracing and metabolic flux analysis (MFA) have emerged as powerful tools to study intracellular metabolism, this approach is limited when applied to pathways catalyzed in multiple cellular compartments. To address this issue, we and others have applied 2H (deuterium) tracers to observe transfer of labeled hydride anions, which accompanies electron transfer. Furthermore, we have developed a reporter system for indirectly quantifying NADPH enrichment in specific subcellular compartments. Here, we provide a detailed description of 2H tracing applications and the interrogation of mitochondrial versus cytosolic NAD(P)H metabolism in cultured mammalian cells. Specifically, we describe the generation of reporter cell lines that express epitope-tagged R132H-IDH1 or R172K-IDH2 and produce (D)2-hydroxyglutarate in a doxycycline-dependent manner. These tools and methods allow for quantitation of reducing equivalent turnover rates, the directionality of pathways present in multiple compartments, and the estimation of pathway contributions to NADPH pools.
    Keywords:  Deuterium; Isotopomer spectral analysis; Mammalian cell culture; Metabolic flux analysis; Metabolite extraction; NADH; NADPH; Redox metabolism; Stable isotope tracing
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_4
  4. PLoS One. 2019 ;14(12): e0227033
    Modeling succinate dehydrogenase loss disorders in C. elegans through effects on hypoxia-inducible factor.
    Megan M Braun, Tamara Damjanac, Yuxia Zhang, Chuan Chen, Jinghua Hu, L James Maher.
      Mitochondrial disorders arise from defects in nuclear genes encoding enzymes of oxidative metabolism. Mutations of metabolic enzymes in somatic tissues can cause cancers due to oncometabolite accumulation. Paraganglioma and pheochromocytoma are examples, whose etiology and therapy are complicated by the absence of representative cell lines or animal models. These tumors can be driven by loss of the tricarboxylic acid cycle enzyme succinate dehydrogenase. We exploit the relationship between succinate accumulation, hypoxic signaling, egg-laying behavior, and morphology in C. elegans to create genetic and pharmacological models of succinate dehydrogenase loss disorders. With optimization, these models may enable future high-throughput screening efforts.
    DOI:  https://doi.org/10.1371/journal.pone.0227033
  5. J Leukoc Biol. 2020 Jan 02.
    Stimulating pyruvate dehydrogenase complex reduces itaconate levels and enhances TCA cycle anabolic bioenergetics in acutely inflamed monocytes.
    Xuewei Zhu, David Long, Manal Zabalawi, Brian Ingram, Barbara K Yoza, Peter W Stacpoole, Charles E McCall.
      The pyruvate dehydrogenase complex (PDC)/pyruvate dehydrogenase kinase (PDK) axis directs the universal survival principles of immune resistance and tolerance in monocytes by controlling anabolic and catabolic energetics. Immune resistance shifts to immune tolerance during inflammatory shock syndromes when inactivation of PDC by increased PDK activity disrupts the tricarboxylic acid (TCA) cycle support of anabolic pathways. The transition from immune resistance to tolerance also diverts the TCA cycle from citrate-derived cis-aconitate to itaconate, a recently discovered catabolic mediator that separates the TCA cycle at isocitrate and succinate dehydrogenase (SDH). Itaconate inhibits succinate dehydrogenase and its anabolic role in mitochondrial ATP generation. We previously reported that inhibiting PDK in septic mice with dichloroacetate (DCA) increased TCA cycle activity, reversed septic shock, restored innate and adaptive immune and organ function, and increased survival. Here, using unbiased metabolomics in a monocyte culture model of severe acute inflammation that simulates sepsis reprogramming, we show that DCA-induced activation of PDC restored anabolic energetics in inflammatory monocytes while increasing TCA cycle intermediates, decreasing itaconate, and increasing amino acid anaplerotic catabolism of branched-chain amino acids (BCAAs). Our study provides new mechanistic insight that the DCA-stimulated PDC homeostat reconfigures the TCA cycle and promotes anabolic energetics in monocytes by reducing levels of the catabolic mediator itaconate. It further supports the theory that PDC is an energy sensing and signaling homeostat that restores metabolic and energy fitness during acute inflammation.
    Keywords:  Anabolism; Catabolism; Dichloroacetate; Itaconate; Metabolomics; Pyruvate dehydrogenase complex; Pyruvate dehydrogenase kinase; Tolerance; Tricarboxylic acid cycle
    DOI:  https://doi.org/10.1002/JLB.3A1119-236R
  6. EMBO Rep. 2020 Jan 02. e49865
    Peroxisomal fission is modulated by the mitochondrial Rho-GTPases, Miro1 and Miro2.
    Christian Covill-Cooke, Viktoriya S Toncheva, James Drew, Nicol Birsa, Guillermo López-Doménech, Josef T Kittler.
      Peroxisomes are essential for a number of cellular functions, including reactive oxygen species metabolism, fatty acid β-oxidation and lipid synthesis. To ensure optimal functionality, peroxisomal size, shape and number must be dynamically maintained; however, many aspects of how this is regulated remain poorly characterised. Here, we show that the localisation of Miro1 and Miro2-outer mitochondrial membrane proteins essential for mitochondrial trafficking-to peroxisomes is not required for basal peroxisomal distribution and long-range trafficking, but rather for the maintenance of peroxisomal size and morphology through peroxisomal fission. Mechanistically, this is achieved by Miro negatively regulating Drp1-dependent fission, a function that is shared with the mitochondria. We further find that the peroxisomal localisation of Miro is regulated by its first GTPase domain and is mediated by an interaction through its transmembrane domain with the peroxisomal-membrane protein chaperone, Pex19. Our work highlights a shared regulatory role of Miro in maintaining the morphology of both peroxisomes and mitochondria, supporting a crosstalk between peroxisomal and mitochondrial biology.
    Keywords:  Fis1; Rhot1; Rhot2; oscillatory; tail-anchored
    DOI:  https://doi.org/10.15252/embr.201949865
  7. Methods Mol Biol. 2020 ;2088 93-118
    Analyzing the Metabolism of Metastases in Mice.
    Patricia Altea-Manzano, Dorien Broekaert, João A G Duarte, Juan Fernández-García, Mélanie Planque, Sarah-Maria Fendt.
      Metastasis formation is the leading cause of death in cancer patients. It has recently emerged that cancer cells adapt their metabolism to successfully transition through the metastatic cascade. Consequently, measuring and analyzing the in vivo metabolism of metastases has the potential to reveal novel treatment strategies to prevent metastasis formation. Here, we describe two different metastasis mouse models and how their metabolism can be analyzed with metabolomics and 13C tracer analysis.
    Keywords:  13C tracer analysis; In vivo metabolism; Metabolism; Metabolomics; Metastasis; Mouse infusions
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_6
  8. J Biol Chem. 2020 Jan 02. pii: jbc.RA119.011154. [Epub ahead of print]
    The mitochondrial iron exporter genes MMT1 and MMT2 in yeast are transcriptionally regulated by Aft1 and Yap1.
    Liangtao Li, Sophie Bertram, Jerry Kaplan, Xuan Jia, Diane M Ward.
      Budding yeast (Saccharomyces cerevisiae) responds to low cytosolic iron by up-regulating the expression of iron import genes where iron import can reflect iron transport into the cytosol or mitochondria. Mmt1 and Mmt2 are nuclear encoded mitochondrial proteins that export iron from the mitochondria into the cytosol. Here, we report that MMT1 and MMT2 expression is transcriptionally regulated by two pathways: the low-iron sensing transcription factor Aft1 and the oxidant-sensing transcription factor Yap1. We determined that MMT1 and MMT2 expression is increased under low-iron conditions and decreased when mitochondrial iron import is increased through overexpression of the high-affinity mitochondrial iron importer Mrs3. Moreover, loss of iron-sulfur cluster synthesis induced the expression of both MMT1 and MMT2. We show that exposure to the oxidant H2O2 induced MMT1 expression, but not MMT2 expression, and identified the transcription factor Yap1 as being involved in oxidant-mediated MMT1 expression. We defined Aft1- and Yap1-dependent transcriptional sites in the MMT1 promoter that are necessary for low iron- or oxidant-mediated MMT1 expression. We also found that the MMT2 promoter contains domains that are important for regulating its expression under low-iron conditions, including an upstream region that appears to partially repress expression under low-iron conditions. Our findings reveal that both MMT1 and MMT2 are induced under low-iron conditions and that the low-iron regulator Aft1 is required for this induction. We further uncover an Aft1-binding site in the MMT1 promoter sufficient for inducing MMT1 transcription and identify an MMT2 promoter region required for low-iron induction.
    Keywords:  Aft1; Yap1; iron; iron-sulfur protein; metal homeostasis; mitochondria; transcription; transport metal
    DOI:  https://doi.org/10.1074/jbc.RA119.011154
  9. Biochim Biophys Acta Mol Basis Dis. 2019 Dec 30. pii: S0925-4439(19)30378-3. [Epub ahead of print] 165648
    Mitochondrial genetics cooperate with nuclear genetics to selectively alter immune cell development/trafficking.
    T C Beadnell, C Fain, C J Vivian, J C G King, R Hastings, M A Markiewicz, D R Welch.
      The nuclear genome drives differences in immune cell populations and differentiation potentials, in part regulated by changes in metabolism. Despite this connection, the role of mitochondrial DNA (mtDNA) polymorphisms (SNP) in this process has not been examined. Using mitochondrial nuclear exchange (MNX) mice, we and others have shown that mtDNA strongly influences varying aspects of cell biology and disease. Based upon an established connection between mitochondria and immune cell polarization, we hypothesized that mtDNA SNP alter immune cell development, trafficking, and/or differentiation. Innate and adaptive immune cell populations were isolated and characterizated from the peritoneum and spleen. While most differences between mouse strains are regulated by nuclear DNA (nDNA), there are selective changes that are mediated by mtDNA differences (e.g., macrophage (CD11c) differentiation), These findings highlight how nuclear-mitochondrial crosstalk may alter pathology and physiology via regulation of specific components of the immune system.
    Keywords:  Differentiation; Immune; Macrophage; Mitochondria; Polymorphism; T cell
    DOI:  https://doi.org/10.1016/j.bbadis.2019.165648
  10. J Hepatol. 2019 Dec 30. pii: S0168-8278(19)30760-3. [Epub ahead of print]
    OGDHL silencing promotes hepatocellular carcinoma by reprogramming glutamine metabolism.
    W Q Dai, L Xu, X N Yu, G C Zhang, H Y Guo, H L Liu, G Q Song, S Q Weng, L Dong, J M Zhu, T T Liu, C Y Guo, X Z Shen.
       BACKGROUND & AIMS: Mitochondrial dysfunction and subsequent metabolic deregulation are commonly observed in cancers including hepatocellular carcinoma (HCC). When mitochondrial function is impaired, reductive glutamine metabolism is a major cellular carbon source for de novo lipogenesis to support cancer cell growth. The underlying regulators of reductively metabolized glutamine in mitochondrial dysfunction are not completely understood in tumorigenesis including in HCC.
    METHODS: We systematically investigated the role of oxoglutarate dehydrogenase-like (OGDHL), one of the rate-limiting components of the key mitochondrial multi-enzyme OGDH complex (OGDHC), in the regulation of lipid metabolism in hepatoma cells and explored the underlying molecular mechanisms.
    RESULTS: Lower expression of OGDHL was associated with advanced tumor stage, significantly worse survival and more frequent tumor recurrence in three independent cohorts totaling 681 postoperative HCC patients. Promoter hypermethylation and DNA copy deletion of OGDHL were independently correlated with reduced OGDHL expression in HCC specimens. Additionally, OGDHL overexpression significantly inhibited the growth of hepatoma cells as mouse xenografts while knockdown of OGDHL promoted proliferation in hepatoma cells. Mechanistically, OGDHL downregulation upregulated the α-ketoglutarate (αKG):citrate ratio by reducing OGDHC activity, which subsequently drove reductive carboxylation (RC) of glutamine-derived αKG for lipogenesis via retrograde TCA cycling in hepatoma cells. Notably, silencing of OGDHL activated the mTORC1 signaling pathway in an α-KG-dependent manner, which in turn transcriptionally induced expression of SCD1 and FASN, thus, enhancing de novo lipogenesis. Meanwhile, metabolic reprogramming in OGDHL-negative hepatoma cells provided an abundant supply of NADPH and GSH to support the cellular antioxidant system. The reduction of reductive glutamine metabolism through OGDHL overexpression or through use of glutaminase inhibitors sensitized tumor cells to sorafenib, a molecular-targeted therapy for HCC.
    CONCLUSION: Our findings established that silencing of OGDHL contributed to HCC development and survival by regulating glutamine metabolic pathways, and suggest OGDHL as a promising prognostic biomarker and therapeutic target for HCC.
    Keywords:  Glutamine metabolism; Liver cancer; OGDHL; Tricarboxylic acid cycle
    DOI:  https://doi.org/10.1016/j.jhep.2019.12.015
  11. Nat Commun. 2020 Jan 02. 11(1): 37
    Gut stem cell aging is driven by mTORC1 via a p38 MAPK-p53 pathway.
    Dan He, Hongguang Wu, Jinnan Xiang, Xinsen Ruan, Peike Peng, Yuanyuan Ruan, Ye-Guang Chen, Yibin Wang, Qiang Yu, Hongbing Zhang, Samy L Habib, Ronald A De Pinho, Huijuan Liu, Baojie Li.
      Nutrients are absorbed solely by the intestinal villi. Aging of this organ causes malabsorption and associated illnesses, yet its aging mechanisms remain unclear. Here, we show that aging-caused intestinal villus structural and functional decline is regulated by mTORC1, a sensor of nutrients and growth factors, which is highly activated in intestinal stem and progenitor cells in geriatric mice. These aging phenotypes are recapitulated in intestinal stem cell-specific Tsc1 knockout mice. Mechanistically, mTORC1 activation increases protein synthesis of MKK6 and augments activation of the p38 MAPK-p53 pathway, leading to decreases in the number and activity of intestinal stem cells as well as villus size and density. Targeting p38 MAPK or p53 prevents or rescues ISC and villus aging and nutrient absorption defects. These findings reveal that mTORC1 drives aging by augmenting a prominent stress response pathway in gut stem cells and identify p38 MAPK as an anti-aging target downstream of mTORC1.
    DOI:  https://doi.org/10.1038/s41467-019-13911-x
  12. Antioxid Redox Signal. 2019 Dec 31.
    Omics Integration for Mitochondria Systems Biology.
    Xin Hu, Young-Mi Go, Dean P Jones.
       SIGNIFICANCE: Elucidation of the central importance of mitophagy in homeostasis of cells and organisms emphasizes that mitochondrial functions extend far beyond short-term needs for energy production. In mitochondria systems biology, the mitochondrial genome, proteome and metabolome operate as a functional network in coordination of cell activities. Organization occurs through subnetworks interconnected by membrane potential, transport activities, allosteric and cooperative interactions, redox signaling mechanisms, rheostatic control by post-translational modifications, and metal ion homeostasis. These subnetworks enable use of varied energy precursors, defense against environmental stressors and macromolecular rewiring to titrate energy production, biosynthesis and detoxification according to cell-specific needs. Rewiring mechanisms, termed mitochondrial reprogramming, enhance fitness to respond to metabolic resources and challenges from the environment. Maladaptive responses can cause cell death. Maladaptive rewiring can cause disease. In cancer, adaptive rewiring can interfere with effective treatment. Recent Advances: Many recent advances have been facilitated by the development of new omics tools, which create opportunities to use data-driven analysis of omics data to address these complex adaptive and maladaptive mechanisms of mitochondrial reprogramming in human disease.
    CRITICAL ISSUES: Application of omics integration to model systems reveals a critical role for metal ion homeostasis broadly impacting mitochondrial reprogramming. Importantly, data show that trans-omics associations are more robust and biologically relevant than single omics associations.
    FUTURE DIRECTIONS: Application of omics integration to mitophagy research creates new opportunities to link the complex, interactive functions of mitochondrial form and function in mitochondria systems biology.
    DOI:  https://doi.org/10.1089/ars.2019.8006
  13. Cancer Metab. 2019 ;7 13
    Cysteine catabolism and the serine biosynthesis pathway support pyruvate production during pyruvate kinase knockdown in pancreatic cancer cells.
    Lei Yu, Shao Thing Teoh, Elliot Ensink, Martin P Ogrodzinski, Che Yang, Ana I Vazquez, Sophia Y Lunt.
       Background: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with limited treatment options. Pyruvate kinase, especially the M2 isoform (PKM2), is highly expressed in PDAC cells, but its role in pancreatic cancer remains controversial. To investigate the role of pyruvate kinase in pancreatic cancer, we knocked down PKM2 individually as well as both PKM1 and PKM2 concurrently (PKM1/2) in cell lines derived from a Kras G12D/- ; p53 -/- pancreatic mouse model.
    Methods: We used liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine metabolic profiles of wildtype and PKM1/2 knockdown PDAC cells. We further used stable isotope-labeled metabolic precursors and LC-MS/MS to determine metabolic pathways upregulated in PKM1/2 knockdown cells. We then targeted metabolic pathways upregulated in PKM1/2 knockdown cells using CRISPR/Cas9 gene editing technology.
    Results: PDAC cells are able to proliferate and continue to produce pyruvate despite PKM1/2 knockdown. The serine biosynthesis pathway partially contributed to pyruvate production during PKM1/2 knockdown: knockout of phosphoglycerate dehydrogenase in this pathway decreased pyruvate production from glucose. In addition, cysteine catabolism generated ~ 20% of intracellular pyruvate in PDAC cells. Other potential sources of pyruvate include the sialic acid pathway and catabolism of glutamine, serine, tryptophan, and threonine. However, these sources did not provide significant levels of pyruvate in PKM1/2 knockdown cells.
    Conclusion: PKM1/2 knockdown does not impact the proliferation of pancreatic cancer cells. The serine biosynthesis pathway supports conversion of glucose to pyruvate during pyruvate kinase knockdown. However, direct conversion of serine to pyruvate was not observed during PKM1/2 knockdown. Investigating several alternative sources of pyruvate identified cysteine catabolism for pyruvate production during PKM1/2 knockdown. Surprisingly, we find that a large percentage of intracellular pyruvate comes from cysteine. Our results highlight the ability of PDAC cells to adaptively rewire their metabolic pathways during knockdown of a key metabolic enzyme.
    Keywords:  Liquid chromatography mass spectrometry; Metabolism; PKM; Pancreatic cancer; Pyruvate kinase
    DOI:  https://doi.org/10.1186/s40170-019-0205-z
  14. Free Radic Biol Med. 2019 Dec 30. pii: S0891-5849(19)32226-9. [Epub ahead of print]
    Downregulation of the DNA 5-hydroxymethylcytosine is involved in mitochondrial dysfunction and neuronal impairment in high fat diet-induced diabetic mice.
    Run Liu, Lei Chen, Zhen Wang, Xuewei Zheng, Yan Wang, Hua Li, Mami Noda, Jiankang Liu, Jiangang Long.
      DNA 5-hydroxymethylcytosine (5hmC), converted from 5-methylcytosine (5mC), is highly enriched in the central nervous system and is dynamically regulated during neural development and metabolic disorders. However, whether and how neural 5hmC is involved in metabolic disorders shows little evidence. In this study, significant downregulation of the DNA 5hmC were observed in the cerebral cortex of HFD-induced diabetic mice, while phosphated AMP-activated protein kinase (p-AMPK) and ten-eleven translocation 2 (TET2) reduced, and mitochondrial dysfunction. We futher demonstrated that dysregulation of 5hmC preceded mitochondrial dysfunction in palmitic acid-treated HT22 cells and decreased level of 5hmC led to mitochondrial respiratory activity and apoptosis in HT22 cells. Taken together, our results reveal that neural 5hmC undergoes remodeling during HFD-induced metabolic disorder, and 5hmC downregulation significantly impacts on mitochondrial respiration and cell apoptosis. This study suggests a novel link between metabolic disorder and neural impairment through neural DNA 5hmC remodeling and resultant mitochondrial dysfunction.
    Keywords:  5-hydroxymethylcytosine; Metabolic disorders; Mitochondria; Neuronal impairment; TET2
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2019.12.042
  15. Neuron. 2019 Dec 13. pii: S0896-6273(19)31036-0. [Epub ahead of print]
    Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis.
    Takashi Namba, Judit Dóczi, Anneline Pinson, Lei Xing, Nereo Kalebic, Michaela Wilsch-Bräuninger, Katherine R Long, Samir Vaid, Janelle Lauer, Aliona Bogdanova, Barbara Borgonovo, Anna Shevchenko, Patrick Keller, David Drechsel, Teymuras Kurzchalia, Pauline Wimberger, Christos Chinopoulos, Wieland B Huttner.
      The human-specific gene ARHGAP11B is preferentially expressed in neural progenitors of fetal human neocortex and increases abundance and proliferation of basal progenitors (BPs), which have a key role in neocortex expansion. ARHGAP11B has therefore been implicated in the evolutionary expansion of the human neocortex, but its mode of action has been unknown. Here, we show that ARHGAP11B is imported into mitochondria, where it interacts with the adenine nucleotide translocase (ANT) and inhibits the mitochondrial permeability transition pore (mPTP). BP expansion by ARHGAP11B requires its presence in mitochondria, and pharmacological inhibition of ANT function or mPTP opening mimic BP expansion by ARHGAP11B. Searching for the underlying metabolic basis, we find that BP expansion by ARHGAP11B requires glutaminolysis, the conversion of glutamine to glutamate for the tricarboxylic acid (TCA) cycle. Hence, an ARHGAP11B-induced, mitochondria-based effect on BP metabolism that is a hallmark of highly mitotically active cells appears to underlie its role in neocortex expansion.
    Keywords:  evolution; metabolism; neocortex; neural progenitor cells
    DOI:  https://doi.org/10.1016/j.neuron.2019.11.027
  16. Biochem Pharmacol. 2019 Dec 26. pii: S0006-2952(19)30486-1. [Epub ahead of print] 113787
    Immune-mediated anti-tumor effects of metformin; targeting metabolic reprogramming of T cells as a new possible mechanism for anti-cancer effects of metformin.
    Saman Bahrambeigi, Vahid Shafiei-Irannejad.
      Immunotherapy-based cancer treatment has revolutionized the era of cancer patients recuperation and it has brought a strong hope to treatment of some types of cancers. Metformin, a widely used antidiabetic drug, which has intensely been studied for its anticancer effects, is believed to have positive influences on immune responses against tumor cells. Metformin can affect metabolic pathways within cells mainly through activation of AMPK. Metabolic restriction of tumor microenvironment on effector immune cells is one of the important strategies favoring tumor cells to escape from immunogenic cell death. The metabolism of T cells has an axial role in shaping and supporting immune responses and may have an important role in anticancer immunity, suggesting that the functionality and durability of tumor-specific T cells need sufficient energy and nutrients. Energy biogenesis of tumor-specific cytotoxic T cells has become an interesting field of study and it is suggested that activation and maintenance of effector T cell responses in tumor microenvironment may occur by metabolic reprogramming of T cells. AMPK has been noticed as the main intracellular energy sensor and mitochondrial biogenesis key regulator which can control and regulate metabolic reprogramming in immune cells and increase antitumor immunity. Metabolic reprogramming of T cells to overcome metabolic restriction in tumor microenvironment, maiming effector T cell responses against tumor cells, has been noticed by several studies. Here we represent metformin, an AMPK activator, as a new candidate drug for metabolic reprogramming of tumor-specific T cells to increase the efficacy and accountability of cancer immunotherapy.
    Keywords:  AMPK; immunotherapy; metabolic reprogramming of effector T cells; metformin; tumor cells metabolism
    DOI:  https://doi.org/10.1016/j.bcp.2019.113787
  17. Autophagy. 2019 Dec 29. 1-16
    TGFB-INHB/activin signaling regulates age-dependent autophagy and cardiac health through inhibition of MTORC2.
    Kai Chang, Ping Kang, Ying Liu, Kerui Huang, Ting Miao, Antonia P Sagona, Ioannis P Nezis, Rolf Bodmer, Karen Ocorr, Hua Bai.
      Age-related impairment of macroautophagy/autophagy and loss of cardiac tissue homeostasis contribute significantly to cardiovascular diseases later in life. MTOR (mechanistic target of rapamycin kinase) signaling is the most well-known regulator of autophagy, cellular homeostasis, and longevity. The MTOR signaling consists of two structurally and functionally distinct multiprotein complexes, MTORC1 and MTORC2. While MTORC1 is well characterized but the role of MTORC2 in aging and autophagy remains poorly understood. Here we identified TGFB-INHB/activin signaling as a novel upstream regulator of MTORC2 to control autophagy and cardiac health during aging. Using Drosophila heart as a model system, we show that cardiac-specific knockdown of TGFB-INHB/activin-like protein daw induces autophagy and alleviates age-related heart dysfunction, including cardiac arrhythmias and bradycardia. Interestingly, the downregulation of daw activates TORC2 signaling to regulate cardiac autophagy. Activation of TORC2 alone through overexpressing its subunit protein rictor promotes autophagic flux and preserves cardiac function with aging. In contrast, activation of TORC1 does not block autophagy induction in daw knockdown flies. Lastly, either daw knockdown or rictor overexpression in fly hearts prolongs lifespan, suggesting that manipulation of these pathways in the heart has systemic effects on longevity control. Thus, our studies discover the TGFB-INHB/activin-mediated inhibition of TORC2 as a novel mechanism for age-dependent decreases in autophagic activity and cardiac health.Abbreviations: AI: arrhythmia index; BafA1: bafilomycin A1; BMP: bone morphogenetic protein; CQ: chloroquine; CVD: cardiovascular diseases; DI: diastolic interval; ER: endoplasmic reticulum; HP: heart period; HR: heart rate; MTOR: mechanistic target of rapamycin kinase; NGS: normal goat serum; PBST: PBS with 0.1% Triton X-100; PDPK1: 3-phosphoinositide dependent protein kinase 1; RICTOR: RPTOR independent companion of MTOR complex 2; ROI: region of interest; ROUT: robust regression and outlier removal; ROS: reactive oxygen species; R-SMAD: receptor-activated SMAD; SI: systolic interval; SOHA: semi-automatic optical heartbeat analysis; TGFB: transformation growth factor beta; TSC1: TSC complex subunit 1.
    Keywords:  Atg8a; INHB/activin ligand; TOR complex 2; autophagic flux; dawdle; semi-automatic optical heartbeat analysis (SOHA)
    DOI:  https://doi.org/10.1080/15548627.2019.1704117
  18. Cell. 2019 Dec 21. pii: S0092-8674(19)31331-5. [Epub ahead of print]
    Local Fatty Acid Channeling into Phospholipid Synthesis Drives Phagophore Expansion during Autophagy.
    Maximilian Schütter, Patrick Giavalisco, Susanne Brodesser, Martin Graef.
      Autophagy is a conserved catabolic homeostasis process central for cellular and organismal health. During autophagy, small single-membrane phagophores rapidly expand into large double-membrane autophagosomes to encapsulate diverse cargoes for degradation. It is thought that autophagic membranes are mainly derived from preformed organelle membranes. Instead, here we delineate a pathway that expands the phagophore membrane by localized phospholipid synthesis. Specifically, we find that the conserved acyl-CoA synthetase Faa1 accumulates on nucleated phagophores and locally activates fatty acids (FAs) required for phagophore elongation and autophagy. Strikingly, using isotopic FA tracing, we directly show that Faa1 channels activated FAs into the synthesis of phospholipids and promotes their assembly into autophagic membranes. Indeed, the first committed steps of de novo phospholipid synthesis at the ER, which forms stable contacts with nascent autophagosomes, are essential for autophagy. Together, our work illuminates how cells spatially tune synthesis and flux of phospholipids for autophagosome biogenesis during autophagy.
    Keywords:  Acyl-CoA synthetase; autophagosome biogenesis; autophagy; de novo phospholipid synthesis; endoplasmic reticulum; fatty acid metabolism; membrane composition; membrane contact site; phagophore expansion; phospholipids
    DOI:  https://doi.org/10.1016/j.cell.2019.12.005
  19. Methods Mol Biol. 2020 ;2088 73-92
    Large-Scale Profiling of Cellular Metabolic Activities Using Deep 13C Labeling Medium.
    Nina Grankvist, Jeramie D Watrous, Mohit Jain, Roland Nilsson.
      The recently developed deep labeling method allows for large-scale profiling of metabolic activities in human cells or tissues using isotope tracing with a highly 13C enriched culture medium in combination with liquid chromatography-high resolution mass spectrometry. This method generates mass spectrometry data sets where endogenous cellular products can be identified, and active pathways can be determined from observed 13C mass isotopomers of the various metabolites measured. Here we describe in detail the experimental procedures for deep labeling experiments in cultured mammalian cells, including synthesis of the deep labeling medium, experimental considerations for cell culture, metabolite extractions and sample preparation, and liquid chromatography-mass spectrometry. We also outline a workflow for the downstream data analysis using publicly available software.
    Keywords:  Cell culture; LC-HRMS; Metabolism; Metabolomics; Stable isotope tracing experiments
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_5
  20. Nat Commun. 2020 Jan 03. 11(1): 69
    Interpreting pathways to discover cancer driver genes with Moonlight.
    Antonio Colaprico, Catharina Olsen, Matthew H Bailey, Gabriel J Odom, Thilde Terkelsen, Tiago C Silva, André V Olsen, Laura Cantini, Andrei Zinovyev, Emmanuel Barillot, Houtan Noushmehr, Gloria Bertoli, Isabella Castiglioni, Claudia Cava, Gianluca Bontempi, Xi Steven Chen, Elena Papaleo.
      Cancer driver gene alterations influence cancer development, occurring in oncogenes, tumor suppressors, and dual role genes. Discovering dual role cancer genes is difficult because of their elusive context-dependent behavior. We define oncogenic mediators as genes controlling biological processes. With them, we classify cancer driver genes, unveiling their roles in cancer mechanisms. To this end, we present Moonlight, a tool that incorporates multiple -omics data to identify critical cancer driver genes. With Moonlight, we analyze 8000+ tumor samples from 18 cancer types, discovering 3310 oncogenic mediators, 151 having dual roles. By incorporating additional data (amplification, mutation, DNA methylation, chromatin accessibility), we reveal 1000+ cancer driver genes, corroborating known molecular mechanisms. Additionally, we confirm critical cancer driver genes by analysing cell-line datasets. We discover inactivation of tumor suppressors in intron regions and that tissue type and subtype indicate dual role status. These findings help explain tumor heterogeneity and could guide therapeutic decisions.
    DOI:  https://doi.org/10.1038/s41467-019-13803-0
  21. Methods Mol Biol. 2020 ;2088 33-50
    Liquid Chromatography Methods for Separation of Polar and Charged Intracellular Metabolites for 13C Metabolic Flux Analysis.
    Damini Jaiswal, Anjali Mittal, Deepak Nagrath, Pramod P Wangikar.
      Accurate quantification of mass isotopolog distribution (MID) of intracellular metabolites is a key requirement for 13C metabolic flux analysis (13C-MFA). Liquid chromatography coupled with mass spectrometry (LC/MS) has emerged as a frontrunner technique that combines two orthogonal separation strategies. While metabolomics requires separation of monoisotopic peaks, 13C-MFA imposes additional demands for chromatographic separation as isotopologs of metabolites significantly add to the number of analytes. In this protocol chapter, we discuss two liquid chromatography methods, namely, reverse phase ion-pairing and hydrophilic interaction chromatography (HILIC) that together can separate a wide variety of metabolites that are typically used for 13C metabolic flux analysis.
    Keywords:  HILIC; Metabolic flux analysis; Nucleotides; Reverse phase ion-pairing; Sugar phosphates
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_3
  22. Free Radic Biol Med. 2019 Dec 26. pii: S0891-5849(19)31525-4. [Epub ahead of print]
    Fumarate and oxidative stress synergize to promote stability of C/EBP homologous protein in the adipocyte.
    Allison M Manuel, Michael D Walla, Margaret Dorn, Ross M Tanis, Gerardo G Piroli, Norma Frizzell.
      C/EBP homologous protein (CHOP) is a transcription factor that is elevated in adipose tissue across many models of diabetes and metabolic stress. Although increased CHOP levels are associated with the terminal response to endoplasmic reticulum stress and apoptosis, there is no evidence for CHOP mediated apoptosis in the adipose tissue during diabetes. CHOP protein levels increase in parallel with protein succination, a fumarate derived cysteine modification, in the adipocyte during metabolic stress. We investigated the factors contributing to sustained CHOP proteins levels in the adipocyte, with an emphasis on the regulation of CHOP protein turnover by metabolite-driven modification of Keap1 cysteines. CHOP protein stability was investigated in conditions of nutrient stress due to high glucose or elevated fumarate (fumarase knockdown model); where cysteine succination is specifically elevated. CHOP protein turnover is significantly reduced in models of elevated glucose and fumarate with a ∼30% increase in CHOP stability (p > 0.01), in part due to decreased CHOP phosphorylation. Sustained CHOP levels occur in parallel with elevated heme-oxygenase-1, a production of increased Nrf2 transcriptional activity and Keap1 modification. While Keap1 is directly succinated in the presence of excess fumarate derived from genetic knockdown of fumarase (fumarate levels are elevated >20-fold), it is the oxidative modification of Keap1 that predominates in adipocytes matured in high glucose (fumarate increases 4-5 fold). Elevated fumarate indirectly regulates CHOP stability through the induction of oxidative stress. The antioxidant N-acetylcysteine (NAC) reduces fumarate levels, protein succination and CHOP levels in adipocytes matured in high glucose. Elevated CHOP does not contribute elevated apoptosis in adipocytes, but plays a redox-dependent role in decreasing the adipocyte secretion of interleukin-13, an anti-inflammatory chemokine. NAC treatment restores adipocyte IL-13 secretion, confirming the redox-dependent regulation of a potent anti-inflammatory eotaxin. This study demonstrates that physiological increases in the metabolite fumarate during high glucose exposure contributes to the presence of oxidative stress and sustained CHOP levels in the adipocyte during diabetes. The results reveal a novel metabolic link between mitochondrial metabolic stress and reduced anti-inflammatory adipocyte signaling as a consequence of reduced CHOP protein turnover.
    Keywords:  Adipocytes; Adipose; ER stress; Glucotoxicity; Metabolism; Oxidative stress; Protein modification
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2019.12.037
  23. Methods Mol Biol. 2020 ;2088 299-313
    Inferring Metabolic Flux from Time-Course Metabolomics.
    Scott Campit, Sriram Chandrasekaran.
      The metabolic activity of a mammalian cell changes dynamically over time and is tied to the changing metabolic demands of cellular processes such as cell differentiation and proliferation. While experimental tools like time-course metabolomics and flux tracing can measure the dynamics of a few pathways, they are unable to infer fluxes at the whole network level. To address this limitation, we have developed the Dynamic Flux Activity (DFA) algorithm, a genome-scale modeling approach that uses time-course metabolomics to predict dynamic flux rewiring during transitions between metabolic states. This chapter provides a protocol for applying DFA to characterize the dynamic metabolic activity of various cancer cell lines.
    Keywords:  Cancer metabolism; Constraint-based modeling; Dynamic flux activity; Flux balance analysis; Genome-scale metabolic models; Time-course metabolomics
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_13
  24. J Clin Med. 2019 Dec 16. pii: E2226. [Epub ahead of print]8(12):
    Variants in Miro1 Cause Alterations of ER-Mitochondria Contact Sites in Fibroblasts from Parkinson's Disease Patients.
    Clara Berenguer-Escuder, Dajana Grossmann, Franҫois Massart, Paul Antony, Lena F Burbulla, Enrico Glaab, Sophie Imhoff, Joanne Trinh, Philip Seibler, Anne Grünewald, Rejko Krüger.
       BACKGROUND: Although most cases of Parkinson´s disease (PD) are idiopathic with unknown cause, an increasing number of genes and genetic risk factors have been discovered that play a role in PD pathogenesis. Many of the PD-associated proteins are involved in mitochondrial quality control, e.g., PINK1, Parkin, and LRRK2, which were recently identified as regulators of mitochondrial-endoplasmic reticulum (ER) contact sites (MERCs) linking mitochondrial homeostasis to intracellular calcium handling. In this context, Miro1 is increasingly recognized to play a role in PD pathology. Recently, we identified the first PD patients carrying mutations in RHOT1, the gene coding for Miro1. Here, we describe two novel RHOT1 mutations identified in two PD patients and the characterization of the cellular phenotypes.
    METHODS: Using whole exome sequencing we identified two PD patients carrying heterozygous mutations leading to the amino acid exchanges T351A and T610A in Miro1. We analyzed calcium homeostasis and MERCs in detail by live cell imaging and immunocytochemistry in patient-derived fibroblasts.
    RESULTS: We show that fibroblasts expressing mutant T351A or T610A Miro1 display impaired calcium homeostasis and a reduced amount of MERCs. All fibroblast lines from patients with pathogenic variants in Miro1, revealed alterations of the structure of MERCs.
    CONCLUSION: Our data suggest that Miro1 is important for the regulation of the structure and function of MERCs. Moreover, our study supports the role of MERCs in the pathogenesis of PD and further establishes variants in RHOT1 as rare genetic risk factors for neurodegeneration.
    Keywords:  Miro1; Parkinson´s disease; mitochondria-ER contact sites
    DOI:  https://doi.org/10.3390/jcm8122226
  25. J Biol Chem. 2020 Jan 03. pii: jbc.RA119.011635. [Epub ahead of print]
    Mitochondrial residence of the apoptosis inducer BAX is more important than BAX oligomerization in promoting membrane permeabilization.
    Tomomi Kuwana, Louise E King, Katia Cosentino, Julian Suess, Ana J García-Sáez, Andrew P Gilmore, Donald D Newmeyer.
      Permeabilization of the mitochondrial outer membrane is a key step in the intrinsic apoptosis pathway, triggered by the release of mitochondrial intermembrane space proteins into the cytoplasm. The BCL-2-associated X apoptosis regulator (BAX) protein critically contributes to this process by forming pores in the mitochondrial outer membrane. However, the relative roles of the mitochondrial residence of BAX and its oligomerization in promoting membrane permeabilization are unclear. To this end, using both cell-free and cellular experimental systems, including membrane permeabilization, size-exclusion chromatography-based oligomer, and retrotranslocation assays, along with confocal microscopy analysis, here we studied two BAX C-terminal variants, T182I and G179P. Neither variant formed large oligomers when activated in liposomes. Nevertheless, the G179P variant could permeabilize liposome membranes, suggesting that large BAX oligomers are not essential for the permeabilization. However, when G179P was transduced into BAX/BCL2 agonist killer (BAK) double-knockout mouse embryonic fibroblasts, its location was solely cytoplasmic, and it then failed to mediate cell death. In contrast, T182I was inefficient in both liposome insertion and permeabilization. Yet, when transduced into cells, BAXT182I resided predominantly on mitochondria, because of its slow retrotranslocation and mediated apoptosis as efficiently as wild-type BAX. We conclude that BAX's mitochondrial residence in vivo, regulated by both targeting and retrotranslocation, is more significant for its pro-apoptotic activity than its ability to insert and to form higher-order oligomers in model membranes. We propose that this finding should be taken into account when developing drugs that modulate BAX activity.
    Keywords:  Bax; anticancer drug; apoptosis; liposome; mitochondrial apoptosis; mitochondrial loacalization; mitochondrial outer membrane permeabilization (MOMP); molecular cell biology; protein oligomers; translocation
    DOI:  https://doi.org/10.1074/jbc.RA119.011635
  26. Methods Mol Biol. 2020 ;2088 189-204
    SWATH: A Data-Independent Tandem Mass Spectrometry Method to Quantify 13C Enrichment in Cellular Metabolites and Fragments.
    Damini Jaiswal, Pramod P Wangikar.
      Recently, the sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) method coupled with liquid chromatography has been demonstrated for the quantification of isotopic 13C enrichment in a large number of cellular metabolites and fragments. SWATH, a data-independent acquisition (DIA) method, alleviates the need for data deconvolution and shows greater accuracy in the quantification of low abundance isotopologs of fragments thereby resulting in a lower systematic error. Here we provide a detailed protocol for the design of Q1 mass isolation windows and the post-acquisition data analysis with emphasis on the untargeted nature of SWATH.
    Keywords:  13C metabolic flux analysis; Liquid chromatography–mass spectrometry; Mass isotopolog distribution; Multiple reaction monitoring; Parallel reaction monitoring
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_9
  27. Cell Death Differ. 2020 Jan 03.
    Autophagy and disease: unanswered questions.
    Ying Yang, Daniel J Klionsky.
      Autophagy is a process in which intracellular components and dysfunctional organelles are delivered to the lysosome for degradation and recycling. Autophagy has various connections to a large number of human diseases, as its functions are essential for cell survival, bioenergetic homeostasis, organism development, and cell death regulation. In the past two decades, substantial effort has been made to identify the roles of autophagy in tumor suppression and promotion, neurodegenerative disorders, and other pathophysiologies. This review summarizes the current advances and discusses the unanswered questions in understanding the involvement of autophagy in pathogenic mechanisms of disease, primarily focusing on cancer and neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41418-019-0480-9
  28. Cancer Genet. 2019 Dec 16. pii: S2210-7762(19)30433-8. [Epub ahead of print]
    Pediatric gastrointestinal stromal tumor: Report of two novel patients harboring germline variants in SDHB and SDHC genes.
    Martina Rinelli, Emanuele Agolini, Giuseppe Maria Milano, Ida Russo, Alessandro Crocoli, Rita De Vito, Angela Di Giannatale, Pier Luigi Di Paolo, Antonio Novelli.
      Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract and rarely occur in pediatric patients. 85% of pediatric GISTs and 15% of adult GISTs lack of KIT or PDGFRA mutations. 40% of these "wild-type" GISTs present loss of function mutations in genes encoding for the subunits of the succinate dehydrogenase (SDH) complex. Germline mutations in SDH complex genes have been described in patients with the Carney-Stratakis syndrome (CSS), a rare inherited condition that predisposes to GIST and paraganglioma. We report two pediatric patients with multifocal GIST, harboring respectively a novel and a previously reported loss-of-function germline variant, in SDHC and SDHB genes.
    Keywords:  Cancer predisposition syndrome; Gastrointestinal stromal tumors; SDH complex deficiency; SDH genes; Succinate dehydrogenase
    DOI:  https://doi.org/10.1016/j.cancergen.2019.12.002
  29. Nat Commun. 2020 Jan 03. 11(1): 102
    Mitochondrial TCA cycle metabolites control physiology and disease.
    Inmaculada Martínez-Reyes, Navdeep S Chandel.
      Mitochondria are signaling organelles that regulate a wide variety of cellular functions and can dictate cell fate. Multiple mechanisms contribute to communicate mitochondrial fitness to the rest of the cell. Recent evidence confers a new role for TCA cycle intermediates, generally thought to be important for biosynthetic purposes, as signaling molecules with functions controlling chromatin modifications, DNA methylation, the hypoxic response, and immunity. This review summarizes the mechanisms by which the abundance of different TCA cycle metabolites controls cellular function and fate in different contexts. We will focus on how these metabolites mediated signaling can affect physiology and disease.
    DOI:  https://doi.org/10.1038/s41467-019-13668-3
  30. Plant Mol Biol. 2020 Jan 03.
    The PAP/SAL1 retrograde signaling pathway is involved in iron homeostasis.
    Manuel Balparda, Alejandro M Armas, Gonzalo M Estavillo, Hannetz Roschzttardtz, María A Pagani, Diego F Gomez-Casati.
       KEY MESSAGE: There is a link between PAP/SAL retrograde pathway, ethylene signaling and Fe metabolism in Arabidopsis. Nuclear gene expression is regulated by a diversity of retrograde signals that travel from organelles to the nucleus in a lineal or classical model. One such signal molecule is 3'-phosphoadenisine-5'-phosphate (PAP) and it's in vivo levels are regulated by SAL1/FRY1, a phosphatase enzyme located in chloroplast and mitochondria. This metabolite inhibits the action of a group of exorribonucleases which participate in post-transcriptional gene expression regulation. Transcriptome analysis of Arabidopsis thaliana mutant plants in PAP-SAL1 pathway revealed that the ferritin genes AtFER1, AtFER3, and AtFER4 are up-regulated. In this work we studied Fe metabolism in three different mutants of the PAP/SAL1 retrograde pathway. Mutant plants showed increased Fe accumulation in roots, shoots and seeds when grown in Fe-sufficient condition, and a constitutive activation of the Strategy I Fe uptake genes. As a consequence, they grew more vigorously than wild type plants in Fe-deficient medium. However, when mutant plants grown in Fe-deficient conditions were sprayed with Fe in their leaves, they were unable to deactivate root Fe uptake. Ethylene synthesis inhibition revert the constitutive Fe uptake phenotype. We propose that there is a link between PAP/SAL pathway, ethylene signaling and Fe metabolism.
    Keywords:  Chloroplast; Iron homeostasis; Mitochondria; PAP/SAL1; Retrograde signals
    DOI:  https://doi.org/10.1007/s11103-019-00950-7
  31. Circ Res. 2020 Jan 03.
    Increased Drp1 Acetylation by Lipid Overload Induces Cardiomyocyte Death and Heart Dysfunction.
    Qingxun Hu, Huiliang Zhang, Nicolas Gutierrez Cortes, Dan Wu, Pei Wang, Jing Zhang, Julie A Mattison, Eric Smith, Lisa F Bettcher, Mingyi Wang, Edward G Lakatta, Shey-Shing Sheu, Wang Wang.
      Rationale: Lipid overload-induced heart dysfunction is characterized by cardiomyocyte death, myocardial remodeling, and compromised contractility, but the impact of excessive lipid supply on cardiac function remains poorly understood. Objective: To investigate the regulation and function of the mitochondrial fission protein dynamin-related protein 1 (Drp1) in lipid overload-induced cardiomyocyte death and heart dysfunction. Methods and Results: Mice fed a high-fat diet (HFD) developed signs of obesity and type II diabetes, including hyperlipidemia, hyperglycemia, hyperinsulinemia, and hypertension. HFD for 18 weeks also induced heart hypertrophy, fibrosis, myocardial insulin resistance, and cardiomyocyte death. HFD stimulated mitochondrial fission in mouse hearts. Furthermore, HFD increased the protein level, phosphorylation (at the activating serine 616 site), oligomerization, mitochondrial translocation, and GTPase activity of Drp1 in mouse hearts, indicating that Drp1 was activated. Monkeys fed a diet high in fat and cholesterol for 2.5 years also exhibited myocardial damage and Drp1 activation in the heart. Interestingly, HFD decreased NAD+ levels and increased Drp1 acetylation in the heart. In adult cardiomyocytes, palmitate increased Drp1 acetylation, phosphorylation, and protein levels, and these increases were abolished by restoration of the decreased NAD+ level. Proteomics analysis and in vitro screening revealed that Drp1 acetylation at lysine 642 (K642) was increased by HFD in mouse hearts and by palmitate incubation in cardiomyocytes. The non-acetylated Drp1 mutation (K642R) attenuated palmitate-induced Drp1 activation, its interaction with voltage-dependent anion channel 1, mitochondrial fission, contractile dysfunction, and cardiomyocyte death. Conclusions: These findings uncover a novel mechanism that contributes to lipid overload-induced heart hypertrophy and dysfunction. Excessive lipid supply created an intracellular environment that facilitated Drp1 acetylation, which, in turn, increased its activity and mitochondrial translocation, resulting in cardiomyocyte dysfunction and death. Thus, Drp1 may be a critical mediator of lipid overload-induced heart dysfunction as well as a potential target for therapy.
    Keywords:  Lipid overload; dynamin related protein 1; heart dysfunction in type II diabetes; mitochondrial dysfunction; protein acetylation
    DOI:  https://doi.org/10.1161/CIRCRESAHA.119.315252
  32. Clin Transl Immunology. 2019 ;8(12): e1098
    Fat for fuel: lipid metabolism in haematopoiesis.
    Gerard Pernes, Michelle C Flynn, Graeme I Lancaster, Andrew J Murphy.
      The importance of metabolic regulation in the immune system has launched back into the limelight in recent years. Various metabolic pathways have been examined in the context of their contribution to maintaining immune cell homeostasis and function. Moreover, this regulation is also important in the immune cell precursors, where metabolism controls their maintenance and cell fate. This review will discuss lipid metabolism in the context of haematopoiesis, that is blood cell development. We specifically focus on nonoxidative lipid metabolism which encapsulates the synthesis and degradation of the major lipid classes such as phospholipids, sphingolipids and sterols. We will also discuss how these metabolic processes are affected by haematological malignancies such as leukaemia and lymphoma, which are known to have altered metabolism, and how these different pathways contribute to the pathology.
    Keywords:  cellular metabolism; haematopoiesis; lipid metabolism
    DOI:  https://doi.org/10.1002/cti2.1098
  33. J Cell Sci. 2020 Jan 02. pii: jcs231811. [Epub ahead of print]133(1):
    Rescuing stalled mammalian mitoribosomes - what can we learn from bacteria?
    Shreya Ahana Ayyub, Fei Gao, Robert N Lightowlers, Zofia M Chrzanowska-Lightowlers.
      In the canonical process of translation, newly completed proteins escape from the ribosome following cleavage of the ester bond that anchors the polypeptide to the P-site tRNA, after which the ribosome can be recycled to initiate a new round of translation. Not all protein synthesis runs to completion as various factors can impede the progression of ribosomes. Rescuing of stalled ribosomes in mammalian mitochondria, however, does not share the same mechanisms that many bacteria use. The classic method for rescuing bacterial ribosomes is trans-translation. The key components of this system are absent from mammalian mitochondria; however, four members of a translation termination factor family are present, with some evidence of homology to members of a bacterial back-up rescue system. To date, there is no definitive demonstration of any other member of this family functioning in mitoribosome rescue. Here, we provide an overview of the processes and key players of canonical translation termination in both bacteria and mammalian mitochondria, followed by a perspective of the bacterial systems used to rescue stalled ribosomes. We highlight any similarities or differences with the mitochondrial translation release factors, and suggest potential roles for these proteins in ribosome rescue in mammalian mitochondria.
    Keywords:  ArfA; ArfB; ArfT; C12orf65; ICT1; Mammalian mitochondria; Mitoribosomes; MtRF1; Release factor; Stalled ribosome; Trans-translation; Translation termination
    DOI:  https://doi.org/10.1242/jcs.231811
  34. Int J Mol Sci. 2019 Dec 26. pii: E192. [Epub ahead of print]21(1):
    Mitochondrial Dynamics of Proximal Tubular Epithelial Cells in Nephropathic Cystinosis.
    Domenico De Rasmo, Anna Signorile, Ester De Leo, Elena V Polishchuk, Anna Ferretta, Roberto Raso, Silvia Russo, Roman Polishchuk, Francesco Emma, Francesco Bellomo.
      Nephropathic cystinosis is a rare lysosomal storage disorder caused by mutations in CTNS gene leading to Fanconi syndrome. Independent studies reported defective clearance of damaged mitochondria and mitochondrial fragmentation in cystinosis. Proteins involved in the mitochondrial dynamics and the mitochondrial ultrastructure were analyzed in CTNS-/- cells treated with cysteamine, the only drug currently used in the therapy for cystinosis but ineffective to treat Fanconi syndrome. CTNS-/- cells showed an overexpression of parkin associated with deregulation of ubiquitination of mitofusin 2 and fission 1 proteins, an altered proteolytic processing of optic atrophy 1 (OPA1), and a decreased OPA1 oligomerization. According to molecular findings, the analysis of electron microscopy images showed a decrease of mitochondrial cristae number and an increase of cristae lumen and cristae junction width. Cysteamine treatment restored the fission 1 ubiquitination, the mitochondrial size, number and lumen of cristae, but had no effect on cristae junction width, making CTNS-/- tubular cells more susceptible to apoptotic stimuli.
    Keywords:  Fanconi syndrome; cysteamine; mitochondrial cristae; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion; nephropathic cystinosis
    DOI:  https://doi.org/10.3390/ijms21010192
  35. Nat Commun. 2020 Jan 03. 11(1): 88
    ROCK inhibitors upregulate the neuroprotective Parkin-mediated mitophagy pathway.
    Natalia Moskal, Victoria Riccio, Mikhail Bashkurov, Rediet Taddese, Alessandro Datti, Peter N Lewis, G Angus McQuibban.
      The accumulation of damaged mitochondria causes the death of dopaminergic neurons. The Parkin-mediated mitophagy pathway functions to remove these mitochondria from cells. Targeting this pathway represents a therapeutic strategy for several neurodegenerative diseases, most notably Parkinson's disease. We describe a discovery pipeline to identify small molecules that increase Parkin recruitment to damaged mitochondria and ensuing mitophagy. We show that ROCK inhibitors promote the activity of this pathway by increasing the recruitment of HK2, a positive regulator of Parkin, to mitochondria. This leads to the increased targeting of mitochondria to lysosomes and removal of damaged mitochondria from cells. Furthermore, ROCK inhibitors demonstrate neuroprotective effects in flies subjected to paraquat, a parkinsonian toxin that induces mitochondrial damage. Importantly, parkin and rok are required for these effects, revealing a signaling axis which controls Parkin-mediated mitophagy that may be exploited for the development of Parkinson's disease therapeutics.
    DOI:  https://doi.org/10.1038/s41467-019-13781-3
  36. Methods Mol Biol. 2020 ;2088 223-269
    Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism.
    Sarah McGarrity, Sigurður T Karvelsson, Ólafur E Sigurjónsson, Óttar Rolfsson.
      Metabolic network flux analysis uses genome-scale metabolic reconstructions to integrate transcriptomics, proteomics, and/or metabolomics data to allow for comprehensive interpretation of genotype to metabolic phenotype relationships. The compilation of many Constraint-based model analysis methods into one MATLAB package, the COBRAtoolbox, has opened the possibility of using these methods to the many biologists with some knowledge of the commonly used statistical program, MATLAB. Here we outline the steps required to take a published genome-scale metabolic reconstruction and interrogate its consistency and biological feasibility. Subsequently, we demonstrate how mRNA expression data and metabolomics data, relating to one or more cell types or biological contexts, can be applied to constrain and generate metabolic models descriptive of metabolic flux phenotypes. Finally, we describe the comparison of the resulting models and model outputs with the aim of identifying metabolic biomarkers and changes in cellular metabolism.
    Keywords:  Constraint-based metabolic models; Data integration; Flux balance analysis; Genome-scale reconstruction; Metabolomics; Systems biology; Transcriptomics
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_11
  37. J Mol Biol. 2019 Dec 27. pii: S0022-2836(19)30746-6. [Epub ahead of print]
    Molecular connections between circadian clocks and aging.
    Patrick-Simon Welz, Salvador Aznar Benitah.
      The mammalian circadian clockwork has evolved as a timing system that allows the daily environmental changes to be anticipated, so that behavior and tissue physiology can be adjusted accordingly. The circadian clock synchronizes the function of all cells within tissues in order to temporally separate preclusive and potentially harmful physiologic processes, and to establish a coherent temporal organismal physiology. Thus, proper functioning of the circadian clockwork is essential for maintaining cellular and tissue homeostasis. Importantly, aging reduces the robustness of the circadian clock, resulting in disturbed sleep-wake cycles, a lowered capacity to synchronize circadian rhythms in peripheral tissues and reprogramming of the circadian clock output at the molecular function levels. These circadian clock-dependent behavioral and molecular changes in turn further accelerate the process of aging. Here we review the current knowledge about how aging affects the circadian clock, how the functional decline of the circadian clock affects aging and how the circadian clock machinery and the molecular processes that underlie aging are intertwined.
    Keywords:  SIRT1; circadian reprogramming; deregulated nutrient sensing; mTOR; mitochondrial dysfunction; stem cell exhaustion; tissue homeostasis
    DOI:  https://doi.org/10.1016/j.jmb.2019.12.036
  38. Evol Med Public Health. 2019 ;2019(1): 9-16
    Energy oversupply to tissues: a single mechanism possibly underlying multiple cancer risk factors.
    Daniel J Wu, Athena Aktipis, John W Pepper.
       Background and objectives: Several major risk factors for cancer involve vascular oversupply of energy to affected tissues. These include obesity, diabetes and chronic inflammation. Here, we propose a potential mechanistic explanation for the association between energy oversupply and cancer risk, which we call the metabolic cancer suppression hypothesis: We hypothesize that oncogenesis is normally suppressed by organismal physiology that regulates and strictly limits normal energy supply to somatic cells, and that this protection is removed by abnormal oversupply of energy.
    Methodology: We evaluate this hypothesis using a computational model of somatic cell evolution to simulate experimental manipulation of the vascular energy supply to a tissue. The model simulates the evolutionary dynamics of somatic cells during oncogenesis.
    Results: In our simulation experiment, we found that under plausible biological assumptions, elevated energy supply to a tissue led to the evolution of elevated energy uptake by somatic cells, leading to the rapid evolution of both defining traits of cancer cells: hyperproliferation, and tissue invasion.
    Conclusions and implications: Our results support the hypothesis of metabolic cancer suppression, suggesting that vascular oversupply of energetic resources to somatic cells removes normal energetic limitations on cell proliferation, and that this accelerates cellular evolution toward cancer. Various predictions of this hypothesis are amenable to empirical testing, and have promising implications for translational research toward clinical cancer prevention.
    Keywords:  cancer; cancer prevention; cell energetics; cell metabolism; oncogenesis
    DOI:  https://doi.org/10.1093/emph/eoz004
  39. Mol Syst Biol. 2019 Dec;15(12): e9071
    Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor.
    Francisca Monteiro, Georg Hubmann, Vakil Takhaveev, Silke R Vedelaar, Justin Norder, Johan Hekelaar, Joana Saldida, Athanasios Litsios, Hein J Wijma, Alexander Schmidt, Matthias Heinemann.
      Metabolic heterogeneity between individual cells of a population harbors significant challenges for fundamental and applied research. Identifying metabolic heterogeneity and investigating its emergence require tools to zoom into metabolism of individual cells. While methods exist to measure metabolite levels in single cells, we lack capability to measure metabolic flux, i.e., the ultimate functional output of metabolic activity, on the single-cell level. Here, combining promoter engineering, computational protein design, biochemical methods, proteomics, and metabolomics, we developed a biosensor to measure glycolytic flux in single yeast cells. Therefore, drawing on the robust cell-intrinsic correlation between glycolytic flux and levels of fructose-1,6-bisphosphate (FBP), we transplanted the B. subtilis FBP-binding transcription factor CggR into yeast. With the developed biosensor, we robustly identified cell subpopulations with different FBP levels in mixed cultures, when subjected to flow cytometry and microscopy. Employing microfluidics, we were also able to assess the temporal FBP/glycolytic flux dynamics during the cell cycle. We anticipate that our biosensor will become a valuable tool to identify and study metabolic heterogeneity in cell populations.
    Keywords:  biosensor; fructose-1,6-bisphosphate; glycolytic flux; single cell; yeast
    DOI:  https://doi.org/10.15252/msb.20199071
  40. Cell Chem Biol. 2019 Dec 23. pii: S2451-9456(19)30402-7. [Epub ahead of print]
    Exploring Targeted Degradation Strategy for Oncogenic KRASG12C.
    Mei Zeng, Yuan Xiong, Nozhat Safaee, Radosław P Nowak, Katherine A Donovan, Christine J Yuan, Behnam Nabet, Thomas W Gero, Frederic Feru, Lianbo Li, Sudershan Gondi, Lincoln J Ombelets, Chunshan Quan, Pasi A Jänne, Milka Kostic, David A Scott, Kenneth D Westover, Eric S Fischer, Nathanael S Gray.
      KRAS is the most frequently mutated oncogene found in pancreatic, colorectal, and lung cancers. Although it has been challenging to identify targeted therapies for cancers harboring KRAS mutations, KRASG12C can be targeted by small-molecule inhibitors that form covalent bonds with cysteine 12 (C12). Here, we designed a library of C12-directed covalent degrader molecules (PROTACs) and subjected them to a rigorous evaluation process to rapidly identify a lead compound. Our lead degrader successfully engaged CRBN in cells, bound KRASG12Cin vitro, induced CRBN/KRASG12C dimerization, and degraded GFP-KRASG12C in reporter cells in a CRBN-dependent manner. However, it failed to degrade endogenous KRASG12C in pancreatic and lung cancer cells. Our data suggest that inability of the lead degrader to effectively poly-ubiquitinate endogenous KRASG12C underlies the lack of activity. We discuss challenges for achieving targeted KRASG12C degradation and proposed several possible solutions which may lead to efficient degradation of endogenous KRASG12C.
    Keywords:  CRBN; KRAS(G12C); PROTAC; caner; degrader; targeted protein degradation; ubiquitination
    DOI:  https://doi.org/10.1016/j.chembiol.2019.12.006
  41. Mitochondrion. 2019 Dec 27. pii: S1567-7249(19)30104-7. [Epub ahead of print]
    Mitochondrial Haplogroups and Lifespan in a Population Isolate.
    Joseph Bonner, Rachel Fisher, Ellen Wilch, Debra Schutte, Brian Schutte.
      Physiochemical differences between mitochondrial DNA (mtDNA) haplogroups that favor oxidative phosphorylation efficiency during periods of caloric limitation can lead to lifespan lengthening when food calories are less abundant. For example, prior work demonstrated that older female haplogroup H carriers had modestly lengthened lifespans beyond 60 years during the Great Depression, a time of caloric limitation in North America. The objective of the current study is to replicate the prior findings in an independent cohort that includes both sexes and younger ages. By determining and cross-referencing the mtDNA genotypes of a culturally homogeneous population isolate to the lifespans of their ancestors, we found that between 1930 and 1939, haplogroup H compared to haplogroup U carriers had a modestly lengthened lifespan (3 years) past 60 years (hazard ratio 2.35; CI95 1.41-3.90; p-value: 0.0029). The lifespan-lengthening association was apparent in both sexes but only after the age of 60. Our results provide further support for the role of mitochondrial genetics in lengthening human lifespan.
    DOI:  https://doi.org/10.1016/j.mito.2019.12.004
  42. Cancer Metab. 2019 ;7 12
    A systematic flux analysis approach to identify metabolic vulnerabilities in human breast cancer cell lines.
    Sheree D Martin, Sean L McGee.
       Background: Increased flux through both glycolytic and oxidative metabolic pathways is a hallmark of breast cancer cells and is critical for their growth and survival. As such, targeting this metabolic reprograming has received much attention as a potential treatment approach. However, the heterogeneity of breast cancer cell metabolism, even within classifications, suggests a necessity for an individualised approach to treatment in breast cancer patients.
    Methods: The metabolic phenotypes of a diverse panel of human breast cancer cell lines representing the major breast cancer classifications were assessed using real-time metabolic flux analysis. Flux linked to ATP production, pathway reserve capacities and specific macromolecule oxidation rates were quantified. Suspected metabolic vulnerabilities were targeted with specific pathway inhibitors, and relative cell viability was assessed using the crystal violet assay. Measures of AMPK and mTORC1 activity were analysed through immunoblotting.
    Results: Breast cancer cells displayed heterogeneous energy requirements and utilisation of non-oxidative and oxidative energy-producing pathways. Quantification of basal glycolytic and oxidative reserve capacities identified cell lines that were highly dependent on individual pathways, while assessment of substrate oxidation relative to total oxidative capacity revealed cell lines that were highly dependent on individual macromolecules. Based on these findings, mild mitochondrial inhibition in ESH-172 cells, including with the anti-diabetic drug metformin, and mild glycolytic inhibition in Hs578T cells reduced relative viability, which did not occur in non-transformed MCF10a cells. The effects on viability were associated with AMPK activation and inhibition of mTORC1 signalling. Hs578T were also found to be highly dependent on glutamine oxidation and inhibition of this process also impacted viability.
    Conclusions: Together, these data highlight that systematic flux analysis in breast cancer cells can identify targetable metabolic vulnerabilities, despite heterogeneity in metabolic profiles between individual cancer cell lines.
    Keywords:  AMPK; Breast cancer; Metabolic flux analysis; Metabolism; Metformin; mTORC1
    DOI:  https://doi.org/10.1186/s40170-019-0207-x
  43. J Clin Invest. 2020 Jan 02. pii: 129202. [Epub ahead of print]130(1): 20-28
    Integrative omics approaches provide biological and clinical insights: examples from mitochondrial diseases.
    Sofia Khan, Gulayse Ince-Dunn, Anu Suomalainen, Laura L Elo.
      High-throughput technologies for genomics, transcriptomics, proteomics, and metabolomics, and integrative analysis of these data, enable new, systems-level insights into disease pathogenesis. Mitochondrial diseases are an excellent target for hypothesis-generating omics approaches, as the disease group is mechanistically exceptionally complex. Although the genetic background in mitochondrial diseases is in either the nuclear or the mitochondrial genome, the typical downstream effect is dysfunction of the mitochondrial respiratory chain. However, the clinical manifestations show unprecedented variability, including either systemic or tissue-specific effects across multiple organ systems, with mild to severe symptoms, and occurring at any age. So far, the omics approaches have provided mechanistic understanding of tissue-specificity and potential treatment options for mitochondrial diseases, such as metabolome remodeling. However, no curative treatments exist, suggesting that novel approaches are needed. In this Review, we discuss omics approaches and discoveries with the potential to elucidate mechanisms of and therapies for mitochondrial diseases.
    DOI:  https://doi.org/10.1172/JCI129202
  44. Cancer Cell. 2019 Dec 09. pii: S1535-6108(19)30523-9. [Epub ahead of print]
    CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer.
    Hua Zhang, Camilla L Christensen, Ruben Dries, Matthew G Oser, Jiehui Deng, Brian Diskin, Fei Li, Yuanwang Pan, Xuzhu Zhang, Yandong Yin, Eleni Papadopoulos, Val Pyon, Cassandra Thakurdin, Nicholas Kwiatkowski, Kandarp Jani, Alexandra R Rabin, Dayanne M Castro, Ting Chen, Heather Silver, Qingyuan Huang, Mirna Bulatovic, Catríona M Dowling, Belen Sundberg, Alan Leggett, Michela Ranieri, Han Han, Shuai Li, Annan Yang, Kristen E Labbe, Christina Almonte, Vladislav O Sviderskiy, Max Quinn, Jack Donaghue, Eric S Wang, Tinghu Zhang, Zhixiang He, Vamsidhar Velcheti, Peter S Hammerman, Gordon J Freeman, Richard Bonneau, William G Kaelin, Kate D Sutherland, Ariena Kersbergen, Andrew J Aguirre, Guo-Cheng Yuan, Eli Rothenberg, George Miller, Nathanael S Gray, Kwok-Kin Wong.
      Cyclin-dependent kinase 7 (CDK7) is a central regulator of the cell cycle and gene transcription. However, little is known about its impact on genomic instability and cancer immunity. Using a selective CDK7 inhibitor, YKL-5-124, we demonstrated that CDK7 inhibition predominately disrupts cell-cycle progression and induces DNA replication stress and genome instability in small cell lung cancer (SCLC) while simultaneously triggering immune-response signaling. These tumor-intrinsic events provoke a robust immune surveillance program elicited by T cells, which is further enhanced by the addition of immune-checkpoint blockade. Combining YKL-5-124 with anti-PD-1 offers significant survival benefit in multiple highly aggressive murine models of SCLC, providing a rationale for new combination regimens consisting of CDK7 inhibitors and immunotherapies.
    Keywords:  CDK7; YKL-5-124; anti-tumor immunity; cell cycle; genome instability; immune checkpoint blockade; immunotherapy; replication stress; single-cell analysis; small cell lung cancer
    DOI:  https://doi.org/10.1016/j.ccell.2019.11.003
  45. Methods Mol Biol. 2020 ;2088 315-330
    Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects.
    Kristopher Rawls, Bonnie V Dougherty, Jason Papin.
      The drug development pipeline has stalled because of the difficulty in identifying new drug targets while minimizing off-target effects. Computational methods, such as the use of metabolic network reconstructions, may provide a cost-effective platform to test new hypotheses for drug targets and prevent off-target effects. Here, we summarize available methods to identify drug targets and off-target effects using either reaction-centric, gene-centric, or metabolite-centric approaches with genome-scale metabolic network reconstructions.
    Keywords:  Constraint-based modeling; Drug targets; Flux balance analysis (FBA); Genome-scale metabolic network reconstruction (GENRE); Off-target effects
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_14
  46. Methods Mol Biol. 2020 ;2088 17-32
    Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes.
    Christian-Alexander Dudek, Lisa Schlicker, Karsten Hiller.
      Gas chromatography coupled with mass spectrometry can provide an extensive overview of the metabolic state of a biological system. Analysis of raw mass spectrometry data requires powerful data processing software to generate interpretable results. Here we describe a data processing workflow to generate metabolite levels, mass isotopomer distribution, similarity and variability analysis of metabolites in a nontargeted manner, using stable isotope labeling. Using our data analysis software, no bioinformatic or programming background is needed to generate results from raw mass spectrometry data.
    Keywords:  Data analysis; GCMS; Gas chromatography; Mass isotopomer distribution; Mass spectrometry; Metabolism; Nontargeted metabolomics; Stable isotope labeling
    DOI:  https://doi.org/10.1007/978-1-0716-0159-4_2
  47. Int J Oncol. 2019 Dec 13.
    A ketogenic diet attenuates proliferation and stemness of glioma stem‑like cells by altering metabolism resulting in increased ROS production.
    Chen-Chen Ji, Yi-Yang Hu, Guang Cheng, Liang Liang, Bo Gao, Ying-Peng Ren, Jin-Tao Liu, Xiu-Li Cao, Min-Hua Zheng, San-Zhong Li, Feng Wan, Hua Han, Zhou Fei.
      Abnormal metabolism serves a critical role in the development and progression of different types of malignancies including glioblastoma (GBM), and may therefore serve as a promising target for treatment of cancer. Preclinical studies have indicated that a ketogenic diet (KD) may exhibit beneficial effects in patients with GBM; however, the underlying mechanisms remain incompletely understood. The aim of the present study was to evaluate the effects of a KD on glioma stem‑like cells (GSCs), by culturing patient‑derived primary GSCs as well as a GSC cell line in glucose‑restricted, β‑hydroxybutyrate‑containing medium (BHB‑Glow) which was used to mimic clinical KD treatment. GSCs cultured in BHB‑Glow medium exhibited reduced proliferation and increased apoptosis compared with cells grown in the control medium. Furthermore, decreased expression of stem cell markers, diminished self‑renewal in vitro, and reduced tumorigenic capacity in vivo, providing evidence that the stemness of GSCs was compromised. Mechanistically, culturing in BHB‑Glow medium reduced glucose uptake and inhibited glycolysis in GSCs. Furthermore, culturing in the BHB‑Glow medium resulted in morphological and functional disturbances to the mitochondria of GSCs. These metabolic changes may have reduced ATP production, promoted lactic acid accumulation, and thus, increased the production of reactive oxygen species (ROS) in GSCs. The expression levels and activation of mammalian target of rapamycin, hypoxia‑inducible factor 1 and B‑cell lymphoma 2 were decreased, consistent with the reduced proliferation of GSCs in BHB‑Glow medium. ROS scavenging reversed the inhibitory effects of a KD on GSCs. Taken together, the results demonstrate that treatment with KD inhibited proliferation of GSCs, increased apoptosis and attenuated the stemness in GSCs by increasing ROS production.
    DOI:  https://doi.org/10.3892/ijo.2019.4942
  48. Proc Natl Acad Sci U S A. 2019 Dec 31. pii: 201910444. [Epub ahead of print]
    Proteome-wide observation of the phenomenon of life on the edge of solubility.
    Giulia Vecchi, Pietro Sormanni, Benedetta Mannini, Andrea Vandelli, Gian Gaetano Tartaglia, Christopher M Dobson, F Ulrich Hartl, Michele Vendruscolo.
      To function effectively proteins must avoid aberrant aggregation, and hence they are expected to be expressed at concentrations safely below their solubility limits. By analyzing proteome-wide mass spectrometry data of Caenorhabditis elegans, however, we show that the levels of about three-quarters of the nearly 4,000 proteins analyzed in adult animals are close to their intrinsic solubility limits, indeed exceeding them by about 10% on average. We next asked how aging and functional self-assembly influence these solubility limits. We found that despite the fact that the total quantity of proteins within the cellular environment remains approximately constant during aging, protein aggregation sharply increases between days 6 and 12 of adulthood, after the worms have reproduced, as individual proteins lose their stoichiometric balances and the cellular machinery that maintains solubility undergoes functional decline. These findings reveal that these proteins are highly prone to undergoing concentration-dependent phase separation, which on aging is rationalized in a decrease of their effective solubilities, in particular for proteins associated with translation, growth, reproduction, and the chaperone system.
    Keywords:  protein aggregation; protein homeostasis; protein misfolding diseases
    DOI:  https://doi.org/10.1073/pnas.1910444117
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