bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2020–11–29
fifty papers selected by
Christian Frezza, , University of Cambridge, MRC Cancer Unit
  1. Warburg-like Metabolic Reprogramming in Aging Intestinal Stem Cells Contributes to Tissue Hyperplasia.
  2. Unexpected obesity, rather than tumorigenesis, in a conditional mouse model of mitochondrial complex II deficiency.
  3. KRAS-regulated glutamine metabolism requires UCP2-mediated aspartate transport to support pancreatic cancer growth.
  4. Redox activation of ATM enhances GSNOR translation to sustain mitophagy and tolerance to oxidative stress.
  5. Mitochondrial Ca2+ Signaling Is an Electrometabolic Switch to Fuel Phagosome Killing.
  6. SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease.
  7. Altered mitochondria functionality defines a metastatic cell state in lung cancer and creates an exploitable vulnerability.
  8. Cytosolic serine hydroxymethyltransferase controls lung adenocarcinoma cells migratory ability by modulating AMP kinase activity.
  9. Mitochondrial metabolism and DNA methylation: a review of the interaction between two genomes.
  10. The energetic cost of NNT-dependent ROS removal.
  11. IGF2R-initiated proton rechanneling dictates an anti-inflammatory property in macrophages.
  12. Mitochondrial DNA analysis efficiently contributes to the identification of metastatic contralateral breast cancers.
  13. Oncogenic activation of PI3K-AKT-mTOR signaling suppresses ferroptosis via SREBP-mediated lipogenesis.
  14. Cysteine metabolic circuitries: druggable targets in cancer.
  15. Overexpression of DJ-1 alleviates autosomal dominant polycystic kidney disease by regulating cell proliferation, apoptosis, and mitochondrial metabolism in vitro and in vivo.
  16. Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence.
  17. PGC1α regulates mitochondrial oxidative phosphorylation involved in cisplatin resistance in ovarian cancer cells via nucleo-mitochondrial transcriptional feedback.
  18. Visualizing Mitochondrial Ribosomal RNA and Mitochondrial Protein Synthesis in Human Cell Lines.
  19. mito-Ψ-Seq: A High-Throughput Method for Systematic Mapping of Pseudouridine Within Mitochondrial RNA.
  20. ATP13A2-mediated endo-lysosomal polyamine export counters mitochondrial oxidative stress.
  21. Mitochondrial Metabolism in Astrocytes Regulates Brain Bioenergetics, Neurotransmission and Redox Balance.
  22. Mitochondria-Associated Endoplasmic Reticulum Membranes in Cardiovascular Diseases.
  23. The Power of Plasticity-Metabolic Regulation of Hepatic Stellate Cells.
  24. Mitophagy protects beta cells from inflammatory damage in diabetes.
  25. Post-transcriptional control of mitochondrial protein composition in changing environmental conditions.
  26. Role of the KEAP1-NRF2 Axis in Renal Cell Carcinoma.
  27. A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism.
  28. An enolase inhibitor for the targeted treatment of ENO1-deleted cancers.
  29. Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism.
  30. Transcriptional Regulation of NK Cell Development by mTOR Complexes.
  31. An expanded palette of improved SPLICS reporters detects multiple organelle contacts in vitro and in vivo.
  32. pHLARE: A New Biosensor Reveals Decreased Lysosome pH in Cancer Cells.
  33. Tracing Metabolic Fate of Mitochondrial Glycine Cleavage System Derived Formate In Vitro and In Vivo.
  34. Evidences of a Direct Relationship between Cellular Fuel Supply and Ciliogenesis Regulated by Hypoxic VDAC1-ΔC.
  35. Targeting copper metabolism to defeat KRAS-driven colorectal cancer.
  36. Mitochondrial quality control in kidney injury and repair.
  37. In Vitro Analysis of mtDNA Replication.
  38. Blue-Native Electrophoresis to Study the OXPHOS Complexes.
  39. Engineered diets to improve cancer outcomes.
  40. Identification of new OPA1 cleavage site reveals that short isoforms regulate mitochondrial fusion.
  41. Autophagy compensates for Lkb1 loss to maintain adult mice homeostasis and survival.
  42. Normal Somatic Mutations in Cancer Transformation.
  43. G6PD overexpression protects from oxidative stress and age-related hearing loss.
  44. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.
  45. Metabolic Compartmentalization at the Leading Edge of Metastatic Cancer Cells.
  46. Mitoribosome Profiling from Human Cell Culture: A High Resolution View of Mitochondrial Translation.
  47. Detection of 5-formylcytosine in Mitochondrial Transcriptome.
  48. The epigenetic basis of cellular heterogeneity.
  49. DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage?
  50. Modification of Proteins by Metabolites in Immunity.
  1. Cell Rep. 2020 Nov 24. pii: S2211-1247(20)31412-1. [Epub ahead of print]33(8): 108423
    Warburg-like Metabolic Reprogramming in Aging Intestinal Stem Cells Contributes to Tissue Hyperplasia.
    Otto Morris, Hansong Deng, Christine Tam, Heinrich Jasper.
      In many tissues, stem cell (SC) proliferation is dynamically adjusted to regenerative needs. How SCs adapt their metabolism to meet the demands of proliferation and how changes in such adaptive mechanisms contribute to age-related dysfunction remain poorly understood. Here, we identify mitochondrial Ca2+ uptake as a central coordinator of SC metabolism. Live imaging of genetically encoded metabolite sensors in intestinal SCs (ISCs) of Drosophila reveals that mitochondrial Ca2+ uptake transiently adapts electron transport chain flux to match energetic demand upon proliferative activation. This tight metabolic adaptation is lost in ISCs of old flies, as declines in mitochondrial Ca2+ uptake promote a "Warburg-like" metabolic reprogramming toward aerobic glycolysis. This switch mimics metabolic reprogramming by the oncogene RasV12 and enhances ISC hyperplasia. Our data identify a critical mechanism for metabolic adaptation of tissue SCs and reveal how its decline sets aging SCs on a metabolic trajectory reminiscent of that seen upon oncogenic transformation.
    Keywords:  Drosophila; Warburg; aging; calcium; cancer; intestine; metabolism; mitochondria; stem cell; tissue homeostasis
    DOI:  https://doi.org/10.1016/j.celrep.2020.108423
  2. FASEB J. 2020 Nov 27.
    Unexpected obesity, rather than tumorigenesis, in a conditional mouse model of mitochondrial complex II deficiency.
    Fatimah Al Khazal, Seungwoo Kang, Molly Nelson Holte, Doo-Sup Choi, Ravinder Singh, Patricia Ortega-Sáenz, José López-Barneo, L James Maher.
      Mutations in any of the genes encoding the four subunits of succinate dehydrogenase (SDH), a mitochondrial membrane-bound enzyme complex that is involved in both the tricarboxylic acid cycle and the electron transport chain, can lead to a variety of disorders. Recognized conditions with such mutations include Leigh syndrome and hereditary tumors such as pheochromocytoma and paraganglioma (PPGL), renal cell carcinoma, and gastrointestinal stromal tumor. Tumors appear in SDH mutation carriers with dominant inheritance due to loss of heterozygosity in susceptible cells. Here, we describe a mouse model intended to reproduce hereditary PPGL through Cre-mediated loss of SDHC in cells that express tyrosine hydroxylase (TH), a compartment where PPGL is known to originate. We report that while there is modest expansion of TH+ glomus cells in the carotid body upon SDHC loss, PPGL is not observed in such mice, even in the presence of a conditional dominant negative p53 protein and chronic hypoxia. Instead, we report an unexpected phenotype of nondiabetic obesity beginning at about 20 weeks of age. We hypothesize that this obesity is caused by TH+ cell loss or altered phenotype in key compartments of the central nervous system responsible for regulating feeding behavior, coupled with metabolic changes due to loss of peripheral catecholamine production.
    Keywords:  catecholamines; dopaminergic cells; familial paraganglioma; mitochondrial disease; mouse; obesity; succinate dehydrogenase; tyrosine hydroxylase
    DOI:  https://doi.org/10.1096/fj.202002100R
  3. Nat Metab. 2020 Nov 23.
    KRAS-regulated glutamine metabolism requires UCP2-mediated aspartate transport to support pancreatic cancer growth.
    Susanna Raho, Loredana Capobianco, Rocco Malivindi, Angelo Vozza, Carmela Piazzolla, Francesco De Leonardis, Ruggiero Gorgoglione, Pasquale Scarcia, Francesca Pezzuto, Gennaro Agrimi, Simona N Barile, Isabella Pisano, Stephan J Reshkin, Maria R Greco, Rosa A Cardone, Vittoria Rago, Yuan Li, Carlo M T Marobbio, Wolfgang Sommergruber, Christopher L Riley, Francesco M Lasorsa, Edward Mills, Maria C Vegliante, Giuseppe E De Benedetto, Deborah Fratantonio, Luigi Palmieri, Vincenza Dolce, Giuseppe Fiermonte.
      The oncogenic KRAS mutation has a critical role in the initiation of human pancreatic ductal adenocarcinoma (PDAC) since it rewires glutamine metabolism to increase reduced nicotinamide adenine dinucleotide phosphate (NADPH) production, balancing cellular redox homeostasis with macromolecular synthesis1,2. Mitochondrial glutamine-derived aspartate must be transported into the cytosol to generate metabolic precursors for NADPH production2. The mitochondrial transporter responsible for this aspartate efflux has remained elusive. Here, we show that mitochondrial uncoupling protein 2 (UCP2) catalyses this transport and promotes tumour growth. UCP2-silenced KRASmut cell lines display decreased glutaminolysis, lower NADPH/NADP+ and glutathione/glutathione disulfide ratios and higher reactive oxygen species levels compared to wild-type counterparts. UCP2 silencing reduces glutaminolysis also in KRASWT PDAC cells but does not affect their redox homeostasis or proliferation rates. In vitro and in vivo, UCP2 silencing strongly suppresses KRASmut PDAC cell growth. Collectively, these results demonstrate that UCP2 plays a vital role in PDAC, since its aspartate transport activity connects the mitochondrial and cytosolic reactions necessary for KRASmut rewired glutamine metabolism2, and thus it should be considered a key metabolic target for the treatment of this refractory tumour.
    DOI:  https://doi.org/10.1038/s42255-020-00315-1
  4. EMBO Rep. 2020 Nov 27. e50500
    Redox activation of ATM enhances GSNOR translation to sustain mitophagy and tolerance to oxidative stress.
    Claudia Cirotti, Salvatore Rizza, Paola Giglio, Noemi Poerio, Maria Francesca Allega, Giuseppina Claps, Chiara Pecorari, Ji-Hoon Lee, Barbara Benassi, Daniela Barilà, Caroline Robert, Jonathan S Stamler, Francesco Cecconi, Maurizio Fraziano, Tanya T Paull, Giuseppe Filomeni.
      The denitrosylase S-nitrosoglutathione reductase (GSNOR) has been suggested to sustain mitochondrial removal by autophagy (mitophagy), functionally linking S-nitrosylation to cell senescence and aging. In this study, we provide evidence that GSNOR is induced at the translational level in response to hydrogen peroxide and mitochondrial ROS. The use of selective pharmacological inhibitors and siRNA demonstrates that GSNOR induction is an event downstream of the redox-mediated activation of ATM, which in turn phosphorylates and activates CHK2 and p53 as intermediate players of this signaling cascade. The modulation of ATM/GSNOR axis, or the expression of a redox-insensitive ATM mutant influences cell sensitivity to nitrosative and oxidative stress, impairs mitophagy and affects cell survival. Remarkably, this interplay modulates T-cell activation, supporting the conclusion that GSNOR is a key molecular effector of the antioxidant function of ATM and providing new clues to comprehend the pleiotropic effects of ATM in the context of immune function.
    Keywords:  ATM; GSNOR; ROS; T cell; mitophagy
    DOI:  https://doi.org/10.15252/embr.202050500
  5. Cell Rep. 2020 Nov 24. pii: S2211-1247(20)31400-5. [Epub ahead of print]33(8): 108411
    Mitochondrial Ca2+ Signaling Is an Electrometabolic Switch to Fuel Phagosome Killing.
    Philip V Seegren, Taylor K Downs, Marta E Stremska, Logan R Harper, Ruofan Cao, Rachel J Olson, Clint M Upchurch, Catherine A Doyle, Joel Kennedy, Eric L Stipes, Norbert Leitinger, Ammasi Periasamy, Bimal N Desai.
      Phagocytes reallocate metabolic resources to kill engulfed pathogens, but the intracellular signals that rapidly switch the immunometabolic program necessary to fuel microbial killing are not understood. We report that macrophages use a fast two-step Ca2+ relay to meet the bioenergetic demands of phagosomal killing. Upon detection of a fungal pathogen, macrophages rapidly elevate cytosolic Ca2+ (phase 1), and by concurrently activating the mitochondrial Ca2+ (mCa2+) uniporter (MCU), they trigger a rapid influx of Ca2+ into the mitochondria (phase 2). mCa2+ signaling reprograms mitochondrial metabolism, at least in part, through the activation of pyruvate dehydrogenase (PDH). Deprived of mCa2+ signaling, Mcu-/- macrophages are deficient in phagosomal reactive oxygen species (ROS) production and defective at killing fungi. Mice lacking MCU in their myeloid cells are highly susceptible to disseminated candidiasis. In essence, this study reveals an elegant design principle that MCU-dependent Ca2+ signaling is an electrometabolic switch to fuel phagosome killing.
    Keywords:  MCU; NADPH; calcium; citrate; electrometabolic; immunometabolism; mitochondria, Ca(2+); phagosome; pyruvate dehydrogenase
    DOI:  https://doi.org/10.1016/j.celrep.2020.108411
  6. Nat Commun. 2020 11 23. 11(1): 5927
    SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease.
    Philipp Gut, Sanna Matilainen, Jesse G Meyer, Pieti Pällijeff, Joy Richard, Christopher J Carroll, Liliya Euro, Christopher B Jackson, Pirjo Isohanni, Berge A Minassian, Reem A Alkhater, Elsebet Østergaard, Gabriele Civiletto, Alice Parisi, Jonathan Thevenet, Matthew J Rardin, Wenjuan He, Yuya Nishida, John C Newman, Xiaojing Liu, Stefan Christen, Sofia Moco, Jason W Locasale, Birgit Schilling, Anu Suomalainen, Eric Verdin.
      Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper-succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper-succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper-succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications.
    DOI:  https://doi.org/10.1038/s41467-020-19743-4
  7. Cancer Res. 2020 Nov 25. pii: canres.1865.2020. [Epub ahead of print]
    Altered mitochondria functionality defines a metastatic cell state in lung cancer and creates an exploitable vulnerability.
    Chen-Hua Chuang, Madeleine Dorsch, Philip Dujardin, Sukrit Silas, Kristina Ueffing, Johanna M Hölken, Dian Yang, Monte M Winslow, Barbara M Grüner.
      Lung cancer is a prevalent and lethal cancer type that leads to more deaths than the next four major cancer types combined. Metastatic cancer spread is responsible for most cancer deaths but the cellular changes that enable cancer cells to leave the primary tumor and establish inoperable and lethal metastases remain poorly understood. To uncover genes that are specifically required to sustain metastasis survival or growth, we performed a genome-scale pooled lentiviral-shRNA library screen in cells that represent non-metastatic and metastatic states of lung adenocarcinoma. Mitochondrial ribosome and mitochondria-associated genes were identified as top gene sets associated with metastasis-specific lethality. Metastasis-derived cell lines in vitro and metastases analyzed ex vivo from an autochthonous lung cancer mouse model had lower mitochondrial membrane potential and reduced mitochondrial functionality than non-metastatic primary tumors. Electron microscopy of metastases uncovered irregular mitochondria with bridging and loss of normal membrane structure. Consistent with these findings, compounds that inhibit mitochondrial translation or replication had a greater effect on the growth of metastasis-derived cells. Finally, mice with established tumors developed fewer metastases upon treatment with phenformin in vivo. These results suggest that the metastatic cell state in lung adenocarcinoma is associated with a specifically altered mitochondrial functionality that can be therapeutically exploited.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1865
  8. Cell Death Dis. 2020 Nov 26. 11(11): 1012
    Cytosolic serine hydroxymethyltransferase controls lung adenocarcinoma cells migratory ability by modulating AMP kinase activity.
    Amani Bouzidi, Maria Chiara Magnifico, Alessandro Paiardini, Alberto Macone, Giovanna Boumis, Giorgio Giardina, Serena Rinaldo, Francesca Romana Liberati, Clotilde Lauro, Cristina Limatola, Chiara Lanzillotta, Antonella Tramutola, Marzia Perluigi, Gianluca Sgarbi, Giancarlo Solaini, Alessandra Baracca, Alessio Paone, Francesca Cutruzzolà.
      Nutrient utilization and reshaping of metabolism in cancer cells is a well-known driver of malignant transformation. Less clear is the influence of the local microenvironment on metastasis formation and choice of the final organ to invade. Here we show that the level of the amino acid serine in the cytosol affects the migratory properties of lung adenocarcinoma (LUAD) cells. Inhibition of serine or glycine uptake from the extracellular milieu, as well as knockdown of the cytosolic one-carbon metabolism enzyme serine hydroxymethyltransferase (SHMT1), abolishes migration. Using rescue experiments with a brain extracellular extract, and direct measurements, we demonstrate that cytosolic serine starvation controls cell movement by increasing reactive oxygen species formation and decreasing ATP levels, thereby promoting activation of the AMP sensor kinase (AMPK) by phosphorylation. Activation of AMPK induces remodeling of the cytoskeleton and finally controls cell motility. These results highlight that cytosolic serine metabolism plays a key role in controlling motility, suggesting that cells are able to dynamically exploit the compartmentalization of this metabolism to adapt their metabolic needs to different cell functions (movement vs. proliferation). We propose a model to explain the relevance of serine/glycine metabolism in the preferential colonization of the brain by LUAD cells and suggest that the inhibition of serine/glycine uptake and/or cytosolic SHMT1 might represent a successful strategy to limit the formation of brain metastasis from primary tumors, a major cause of death in these patients.
    DOI:  https://doi.org/10.1038/s41419-020-03215-0
  9. Clin Epigenetics. 2020 Nov 23. 12(1): 182
    Mitochondrial metabolism and DNA methylation: a review of the interaction between two genomes.
    Amanda F C Lopes.
      Mitochondria are controlled by the coordination of two genomes: the mitochondrial and the nuclear DNA. As such, variations in nuclear gene expression as a consequence of mutations and epigenetic modifications can affect mitochondrial functionality. Conversely, the opposite could also be true. However, the relationship between mitochondrial dysfunction and epigenetics, such as nuclear DNA methylation, remains largely unexplored. Mitochondria function as central metabolic hubs controlling some of the main substrates involved in nuclear DNA methylation, via the one carbon metabolism, the tricarboxylic acid cycle and the methionine pathway. Here, we review key findings and highlight new areas of focus, with the ultimate goal of getting one step closer to understanding the genomic effects of mitochondrial dysfunction on nuclear epigenetic landscapes.
    Keywords:  DNA; DNA methylation; Haplogroups; Metabolism; Mitochondria; Nucleus
    DOI:  https://doi.org/10.1186/s13148-020-00976-5
  10. J Biol Chem. 2020 Nov 27. 295(48): 16217-16218
    The energetic cost of NNT-dependent ROS removal.
    Nina Kaludercic, Fabio Di Lisa.
      Under conditions of high nutrient availability and low ATP synthesis, mitochondria generate reactive oxygen species (ROS) that must be removed to avoid cell injury. Among the enzymes involved in this scavenging process, peroxidases play a crucial role, using NADPH provided mostly by nicotinamide nucleotide transhydrogenase (NNT). However, scarce information is available on how and to what extent ROS formation is linked to mitochondrial oxygen consumption. A new study by Smith et al. shows that NNT activity maintains low ROS levels by means of a fine modulation of mitochondrial oxygen utilization.
    DOI:  https://doi.org/10.1074/jbc.H120.016368
  11. Sci Adv. 2020 Nov;pii: eabb7389. [Epub ahead of print]6(48):
    IGF2R-initiated proton rechanneling dictates an anti-inflammatory property in macrophages.
    Xuefeng Wang, Liangyu Lin, Bin Lan, Yu Wang, Liming Du, Xiaodong Chen, Qing Li, Keli Liu, Mingyuan Hu, Yueqing Xue, Arthur I Roberts, Changshun Shao, Gerry Melino, Yufang Shi, Ying Wang.
      Metabolic traits of macrophages can be rewired by insulin-like growth factor 2 (IGF2); however, how IGF2 modulates macrophage cellular dynamics and functionality remains unclear. We demonstrate that IGF2 exhibits dual and opposing roles in controlling inflammatory phenotypes in macrophages by regulating glucose metabolism, relying on the dominant activation of the IGF2 receptor (IGF2R) by low-dose IGF2 (L-IGF2) and IGF1R by high-dose IGF2. IGF2R activation leads to proton rechanneling to the mitochondrial intermembrane space and enables sustained oxidative phosphorylation. Mechanistically, L-IGF2 induces nucleus translocation of IGF2R that promotes Dnmt3a-mediated DNA methylation by activating GSK3α/β and subsequently impairs expression of vacuolar-type H+-ATPase (v-ATPase). This sequestrated assembly of v-ATPase inhibits the channeling of protons to lysosomes and leads to their rechanneling to mitochondria. An IGF2R-specific IGF2 mutant induces only the anti-inflammatory response and inhibits colitis progression. Together, our findings highlight a previously unidentified role of IGF2R activation in dictating anti-inflammatory macrophages.
    DOI:  https://doi.org/10.1126/sciadv.abb7389
  12. J Cancer Res Clin Oncol. 2020 Nov 24.
    Mitochondrial DNA analysis efficiently contributes to the identification of metastatic contralateral breast cancers.
    Giulia Girolimetti, Lorena Marchio, Antonio De Leo, Miriam Mangiarelli, Laura Benedetta Amato, Simone Zanotti, Mario Taffurelli, Donatella Santini, Giuseppe Gasparre, Claudio Ceccarelli.
       PURPOSE: In daily practice, a contralateral breast cancer (CBC) is usually considered as a new independent tumor despite the indications of several studies showing that the second neoplasia may be a metastatic spread of the primary tumor. Recognition of clonal masses in the context of multiple synchronous or metachronous tumors is crucial for correct prognosis, therapeutic choice, and patient management. Mitochondrial DNA (mtDNA) sequencing shows high informative potential in the diagnosis of synchronous neoplasms, based on the fact that somatic mtDNA mutations are non-recurrent events, whereas tumors sharing them have a common origin. We here applied this technique to reveal clonality of the CBC with respect to the first tumor.
    METHODS: We analyzed 30 sample pairs of primary breast cancers and synchronous or metachronous CBCs with detailed clinical information available and compared standard clinico-pathological criteria with mtDNA sequencing to reveal the metastatic nature of CBCs.
    RESULTS: MtDNA analysis was informative in 23% of the cases, for which it confirmed a clonal origin of the second tumor. In addition, it allowed to solve two ambiguous cases where histopathological criteria had failed to be conclusive and to suggest a clonal origin for two additional cases that had been classified as independent by pathologists.
    CONCLUSION: Overall, the mtDNA-based classification showed a more accurate predictive power than standard histopathology in identifying cases of metastatic rather than bilateral breast cancers in our cohort, suggesting that mtDNA sequencing may be a more precise and easy-to-use method to be introduced in daily routine to support and improve histopathological diagnoses.
    Keywords:  Breast cancer metastasis; Contralateral breast cancers; Mitochondrial DNA mutations
    DOI:  https://doi.org/10.1007/s00432-020-03459-5
  13. Proc Natl Acad Sci U S A. 2020 Nov 23. pii: 202017152. [Epub ahead of print]
    Oncogenic activation of PI3K-AKT-mTOR signaling suppresses ferroptosis via SREBP-mediated lipogenesis.
    Junmei Yi, Jiajun Zhu, Jiao Wu, Craig B Thompson, Xuejun Jiang.
      Ferroptosis, a form of regulated necrosis driven by iron-dependent peroxidation of phospholipids, is regulated by cellular metabolism, redox homeostasis, and various signaling pathways related to cancer. In this study, we found that activating mutation of phosphatidylinositol 3-kinase (PI3K) or loss of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) function, highly frequent events in human cancer, confers ferroptosis resistance in cancer cells, and that inhibition of the PI3K-AKT-mTOR signaling axis sensitizes cancer cells to ferroptosis induction. Mechanistically, this resistance requires sustained activation of mTORC1 and the mechanistic target of rapamycin (mTOR)C1-dependent induction of sterol regulatory element-binding protein 1 (SREBP1), a central transcription factor regulating lipid metabolism. Furthermore, stearoyl-CoA desaturase-1 (SCD1), a transcriptional target of SREBP1, mediates the ferroptosis-suppressing activity of SREBP1 by producing monounsaturated fatty acids. Genetic or pharmacologic ablation of SREBP1 or SCD1 sensitized ferroptosis in cancer cells with PI3K-AKT-mTOR pathway mutation. Conversely, ectopic expression of SREPB1 or SCD1 restored ferroptosis resistance in these cells, even when mTORC1 was inhibited. In xenograft mouse models for PI3K-mutated breast cancer and PTEN-defective prostate cancer, the combination of mTORC1 inhibition with ferroptosis induction resulted in near-complete tumor regression. In conclusion, hyperactive mutation of PI3K-AKT-mTOR signaling protects cancer cells from oxidative stress and ferroptotic death through SREBP1/SCD1-mediated lipogenesis, and combination of mTORC1 inhibition with ferroptosis induction shows therapeutic promise in preclinical models.
    Keywords:  SREBP1; cancer; ferroptosis; lipogenesis; mTOR
    DOI:  https://doi.org/10.1073/pnas.2017152117
  14. Br J Cancer. 2020 Nov 23.
    Cysteine metabolic circuitries: druggable targets in cancer.
    Vasco D B Bonifácio, Sofia A Pereira, Jacinta Serpa, João B Vicente.
      To enable survival in adverse conditions, cancer cells undergo global metabolic adaptations. The amino acid cysteine actively contributes to cancer metabolic remodelling on three different levels: first, in its free form, in redox control, as a component of the antioxidant glutathione or its involvement in protein s-cysteinylation, a reversible post-translational modification; second, as a substrate for the production of hydrogen sulphide (H2S), which feeds the mitochondrial electron transfer chain and mediates per-sulphidation of ATPase and glycolytic enzymes, thereby stimulating cellular bioenergetics; and, finally, as a carbon source for epigenetic regulation, biomass production and energy production. This review will provide a systematic portrayal of the role of cysteine in cancer biology as a source of carbon and sulphur atoms, the pivotal role of cysteine in different metabolic pathways and the importance of H2S as an energetic substrate and signalling molecule. The different pools of cysteine in the cell and within the body, and their putative use as prognostic cancer markers will be also addressed. Finally, we will discuss the pharmacological means and potential of targeting cysteine metabolism for the treatment of cancer.
    DOI:  https://doi.org/10.1038/s41416-020-01156-1
  15. Ann Transl Med. 2020 Sep;8(18): 1175
    Overexpression of DJ-1 alleviates autosomal dominant polycystic kidney disease by regulating cell proliferation, apoptosis, and mitochondrial metabolism in vitro and in vivo.
    Zhongxin Li, Jingjing Zhou, Yan Li, Fan Yang, Xiaoying Lian, Wenhu Liu.
       Background: DJ-1 is critical for the mitochondrial function associated with autosomal dominant polycystic kidney disease (ADPKD). We aimed to investigate DJ-1's function in the pathogenesis of ADPKD.
    Methods: DJ-1 was knocked-down in IMCD3 cells to evaluate the effects of DJ-1 on cell phenotype and mitochondrial function in vitro. Furthermore, we generated three groups of mice with different expression levels of DJ-1 within an established ADPKD model: ADPKD, ADPKDpcDNA, and ADPKDpcDNA-DJ-1.
    Results: DJ-1 knock-down significantly increased oxidative stress as well as the proliferation and apoptosis rate of IMCD3 cells, along with Bcl-2 down-regulation and the up-regulation of Ki67, PCNA, Bax, cleaved caspase-3, and cleaved caspase-9. DJ-1 knock-down suppressed the cellular respiration, Ca2+ absorption, and mitochondrial complex I activity in mitochondria. In vivo, we verified that DJ-1 was down-regulated in ADPKD models, and its overexpression attenuated the renal dysfunction in ADPKD models. The transgenic mice had a significantly smaller renal cyst and less interstitial fibrosis than control, accompanied byα-SMA, fibronectin, and TGF-β1 up-regulation. Moreover, in vivo results confirmed DJ-1 overexpression inhibited the proliferation and apoptosis of tubular epithelial cells along with down-regulation of Ki67, PCNA, p53, intracellular Cyt c, cleaved caspase-3, and cleaved caspase-9 and the up-regulation of Bcl-2.
    Conclusions: DJ-1 was down-regulated in ADPKD models, and its overexpression may attenuate the renal dysfunction and pathological damage by regulating the proliferation, apoptosis, oxidative stress and mitochondrial metabolism, which may be mediated by the p53 signaling pathway.
    Keywords:  Autosomal dominant polycystic kidney disease (ADPKD); DJ-1; mitochondrial dysfunction; mitochondrial metabolism
    DOI:  https://doi.org/10.21037/atm-20-5761
  16. Nat Commun. 2020 Nov 27. 11(1): 6049
    Transcription-dependent cohesin repositioning rewires chromatin loops in cellular senescence.
    Ioana Olan, Aled J Parry, Stefan Schoenfelder, Masako Narita, Yoko Ito, Adelyne S L Chan, Guy St C Slater, Dóra Bihary, Masashige Bando, Katsuhiko Shirahige, Hiroshi Kimura, Shamith A Samarajiwa, Peter Fraser, Masashi Narita.
      Senescence is a state of stable proliferative arrest, generally accompanied by the senescence-associated secretory phenotype, which modulates tissue homeostasis. Enhancer-promoter interactions, facilitated by chromatin loops, play a key role in gene regulation but their relevance in senescence remains elusive. Here, we use Hi-C to show that oncogenic RAS-induced senescence in human diploid fibroblasts is accompanied by extensive enhancer-promoter rewiring, which is closely connected with dynamic cohesin binding to the genome. We find de novo cohesin peaks often at the 3' end of a subset of active genes. RAS-induced de novo cohesin peaks are transcription-dependent and enriched for senescence-associated genes, exemplified by IL1B, where de novo cohesin binding is involved in new loop formation. Similar IL1B induction with de novo cohesin appearance and new loop formation are observed in terminally differentiated macrophages, but not TNFα-treated cells. These results suggest that RAS-induced senescence represents a cell fate determination-like process characterised by a unique gene expression profile and 3D genome folding signature, mediated in part through cohesin redistribution on chromatin.
    DOI:  https://doi.org/10.1038/s41467-020-19878-4
  17. Exp Cell Res. 2020 Nov 18. pii: S0014-4827(20)30622-4. [Epub ahead of print] 112369
    PGC1α regulates mitochondrial oxidative phosphorylation involved in cisplatin resistance in ovarian cancer cells via nucleo-mitochondrial transcriptional feedback.
    Luyan Shen, Li Zhou, Meihui Xia, Nan Lin, Jiaoyan Ma, Delu Dong, Liankun Sun.
      Mitochondria play an important role in effective cell energy production and cell survival under stress conditions, such as treatment with chemotherapeutic drugs. Mitochondrial biogenesis is increased in ovarian cancer tissues, which is accompanied by alteration of mitochondrial energy metabolism, structure, and dynamics. These factors are involved in tumorigenesis and apoptosis resistance, highlighting the role of mitochondria in resisting cisplatin toxicity. Cisplatin-resistant ovarian cancer cells are dependent on mitochondrial OXPHOS for energy supply, and intracellular PGC1α-mediated mitochondrial biogenesis levels are increased in this cell line, indicating the important role of mitochondrial oxidative phosphorylation in cisplatin resistance. As PGC1α is a key molecule for integrating and coordinating nuclear DNA and mitochondrial DNA transcriptional machinery, an investigation into the regulatory mechanism PGC1α in mitochondrial energy metabolism via transcription may provide new clues for solving chemotherapy resistance. In the present study, it was demonstrated that inhibiting the expression of PGC1α decreased nuclear and mitochondrial DNA transcription factor expression, leading to increased lactic acid production and decreased cellular oxygen consumption and mitochondrial oxidative phosphorylation. Furthermore, mitochondrial stress-induced ROS production, as a feedback signal from mitochondria to the cell nucleus, increased PGC1α expression in SKOV3/DDP cells, which was involved in mitochondrial oxidative phosphorylation regulation. Collectively, the present study provides evidence that PGC1α-mediated nuclear and mitochondrial transcription feedback regulates energy metabolism and is involved in ovarian cancer cells escaping apoptosis during cisplatin treatment.
    Keywords:  Cisplatin resistance; Mitochondria; OXPHOS; Ovarian cancer; mtDNA transcription
    DOI:  https://doi.org/10.1016/j.yexcr.2020.112369
  18. Methods Mol Biol. 2021 ;2192 159-181
    Visualizing Mitochondrial Ribosomal RNA and Mitochondrial Protein Synthesis in Human Cell Lines.
    Matthew Zorkau, Yasmin Proctor-Kent, Rolando Berlinguer-Palmini, Andrew Hamilton, Zofia M Chrzanowska-Lightowlers, Robert N Lightowlers.
      Human mitochondria contain their own DNA (mtDNA) that encodes 13 proteins all of which are core subunits of oxidative phosphorylation (OXPHOS) complexes. To form functional complexes, these 13 components need to be correctly assembled with approximately 70 nuclear-encoded subunits that are imported following synthesis in the cytosol. How this complicated coordinated translation and assembly is choreographed is still not clear. Methods are being developed to determine whether all members of a particular complex are translated in close proximity, whether protein synthesis is clustered in submitochondrial factories, whether these align with incoming polypeptides, and if there is evidence for co-translational translation that is regulated and limited by the interaction of the incoming proteins with synthesis of their mtDNA-encoded partners. Two methods are described in this chapter to visualize the distribution of mitochondrial ribosomal RNAs in conjunction with newly synthesized mitochondrial proteins. The first combines RNA Fluorescent In Situ Hybridization (FISH) and super-resolution immunocytochemistry to pinpoint mitochondrial ribosomal RNA. The second localizes nascent translation within the mitochondrial network through non-canonical amino acid labeling, click chemistry and fluorescent microscopy.
    Keywords:  Click chemistry; Fluorescence microscopy; Mitochondria; Mitochondrial RNA; Mitoribosome; Single-molecule RNA FISH; Stimulated emission depletion microscopy; Super-resolution microscopy; Translation
    DOI:  https://doi.org/10.1007/978-1-0716-0834-0_13
  19. Methods Mol Biol. 2021 ;2192 103-115
    mito-Ψ-Seq: A High-Throughput Method for Systematic Mapping of Pseudouridine Within Mitochondrial RNA.
    Aldema Sas-Chen, Ronit Nir, Schraga Schwartz.
      RNA modifications are present in most cellular RNAs and are formed posttranscriptionally by enzymatic machineries that involve hundreds of enzymes and cofactors. RNA modifications impact the life cycle of the RNA, its stability, folding, cellular localization, as well as interactions with RNA and protein partners. RNA modifications are important for mitochondrial function and are required for proper processing and function of mitochondrial (mt) tRNA and rRNA. Underscoring their importance, several mitochondrial diseases are caused by defects in mt-RNA modifications, stemming from mutations in mtDNA at or near mt-RNA modification sites or in nuclear-encoded mt-RNA modifying enzymes. A highly abundant RNA modification, involved in mitochondrial physiology and pathology is pseudouridylation (Ψ), which is catalyzed by enzymes of the Pseudouridine Synthase (PUS) family. Although some Ψ sites in mt-rRNA and mt-tRNA have been identified, little is known about the functional role of these modifications. Furthermore, it is unknown which enzyme facilitates the modification of each site and it is likely that many yet undiscovered mt-RNA modifications exist, as is evidenced by recent work showing some Ψ sites on mRNA. Here, we present mito-Ψ-Seq, a high-throughput method for semiquantitative mapping of Ψ in mt-RNA.
    Keywords:  Epitranscriptome; Misincorporation signatures; Mitochondria; Next-generation sequencing; Pseudouridine; RNA modification; Reverse-transcription arrest
    DOI:  https://doi.org/10.1007/978-1-0716-0834-0_9
  20. Proc Natl Acad Sci U S A. 2020 Nov 23. pii: 201922342. [Epub ahead of print]
    ATP13A2-mediated endo-lysosomal polyamine export counters mitochondrial oxidative stress.
    Stephanie Vrijsen, Laura Besora-Casals, Sarah van Veen, Jeffrey Zielich, Chris Van den Haute, Norin Nabil Hamouda, Christian Fischer, Bart Ghesquière, Ivailo Tournev, Patrizia Agostinis, Veerle Baekelandt, Jan Eggermont, Eric Lambie, Shaun Martin, Peter Vangheluwe.
      Recessive loss-of-function mutations in ATP13A2 (PARK9) are associated with a spectrum of neurodegenerative disorders, including Parkinson's disease (PD). We recently revealed that the late endo-lysosomal transporter ATP13A2 pumps polyamines like spermine into the cytosol, whereas ATP13A2 dysfunction causes lysosomal polyamine accumulation and rupture. Here, we investigate how ATP13A2 provides protection against mitochondrial toxins such as rotenone, an environmental PD risk factor. Rotenone promoted mitochondrial-generated superoxide (MitoROS), which was exacerbated by ATP13A2 deficiency in SH-SY5Y cells and patient-derived fibroblasts, disturbing mitochondrial functionality and inducing toxicity and cell death. Moreover, ATP13A2 knockdown induced an ATF4-CHOP-dependent stress response following rotenone exposure. MitoROS and ATF4-CHOP were blocked by MitoTEMPO, a mitochondrial antioxidant, suggesting that the impact of ATP13A2 on MitoROS may relate to the antioxidant properties of spermine. Pharmacological inhibition of intracellular polyamine synthesis with α-difluoromethylornithine (DFMO) also increased MitoROS and ATF4 when ATP13A2 was deficient. The polyamine transport activity of ATP13A2 was required for lowering rotenone/DFMO-induced MitoROS, whereas exogenous spermine quenched rotenone-induced MitoROS via ATP13A2. Interestingly, fluorescently labeled spermine uptake in the mitochondria dropped as a consequence of ATP13A2 transport deficiency. Our cellular observations were recapitulated in vivo, in a Caenorhabditis elegans strain deficient in the ATP13A2 ortholog catp-6 These animals exhibited a basal elevated MitoROS level, mitochondrial dysfunction, and enhanced stress response regulated by atfs-1, the C. elegans ortholog of ATF4, causing hypersensitivity to rotenone, which was reversible with MitoTEMPO. Together, our study reveals a conserved cell protective pathway that counters mitochondrial oxidative stress via ATP13A2-mediated lysosomal spermine export.
    Keywords:  P5B-type ATPase; antioxidant; mitochondria; neurodegeneration; polyamine transport
    DOI:  https://doi.org/10.1073/pnas.1922342117
  21. Front Neurosci. 2020 ;14 536682
    Mitochondrial Metabolism in Astrocytes Regulates Brain Bioenergetics, Neurotransmission and Redox Balance.
    Jordan Rose, Christian Brian, Aglaia Pappa, Mihalis I Panayiotidis, Rodrigo Franco.
      In the brain, mitochondrial metabolism has been largely associated with energy production, and its dysfunction is linked to neuronal cell loss. However, the functional role of mitochondria in glial cells has been poorly studied. Recent reports have demonstrated unequivocally that astrocytes do not require mitochondria to meet their bioenergetics demands. Then, the question remaining is, what is the functional role of mitochondria in astrocytes? In this work, we review current evidence demonstrating that mitochondrial central carbon metabolism in astrocytes regulates overall brain bioenergetics, neurotransmitter homeostasis and redox balance. Emphasis is placed in detailing carbon source utilization (glucose and fatty acids), anaplerotic inputs and cataplerotic outputs, as well as carbon shuttles to neurons, which highlight the metabolic specialization of astrocytic mitochondria and its relevance to brain function.
    Keywords:  anaplerotic; astrocytes; bioenergetics; cataplerotic; fatty acid oxidation; glycolysis; mitochondria; redox
    DOI:  https://doi.org/10.3389/fnins.2020.536682
  22. Front Cell Dev Biol. 2020 ;8 604240
    Mitochondria-Associated Endoplasmic Reticulum Membranes in Cardiovascular Diseases.
    Peng Gao, Zhencheng Yan, Zhiming Zhu.
      The endoplasmic reticulum (ER) and mitochondria are physically connected to form dedicated structural domains known as mitochondria-associated ER membranes (MAMs), which participate in fundamental biological processes, including lipid and calcium (Ca2+) homeostasis, mitochondrial dynamics and other related cellular behaviors such as autophagy, ER stress, inflammation and apoptosis. Many studies have proved the importance of MAMs in maintaining the normal function of both organelles, and the abnormal amount, structure or function of MAMs is related to the occurrence of cardiovascular diseases. Here, we review the knowledge regarding the components of MAMs according to their different functions and the specific roles of MAMs in cardiovascular physiology and pathophysiology, focusing on some highly prevalent cardiovascular diseases, including ischemia-reperfusion, diabetic cardiomyopathy, heart failure, pulmonary arterial hypertension and systemic vascular diseases. Finally, we summarize the possible mechanisms of MAM in cardiovascular diseases and put forward some obstacles in the understanding of MAM function we may encounter.
    Keywords:  SR-mitochondrial contact; cardiovascular diseases; metabolic transition; mitochondria-associated ER membrane; mitochondrial bioenergetics
    DOI:  https://doi.org/10.3389/fcell.2020.604240
  23. Cell Metab. 2020 Nov 17. pii: S1550-4131(20)30595-7. [Epub ahead of print]
    The Power of Plasticity-Metabolic Regulation of Hepatic Stellate Cells.
    Parth Trivedi, Shuang Wang, Scott L Friedman.
      Hepatic stellate cells (HSCs) are resident non-parenchymal liver pericytes whose plasticity enables them to regulate a remarkable range of physiologic and pathologic responses. To support their functions in health and disease, HSCs engage pathways regulating carbohydrate, mitochondrial, lipid, and retinoid homeostasis. In chronic liver injury, HSCs drive hepatic fibrosis and are implicated in inflammation and cancer. To do so, the cells activate, or transdifferentiate, from a quiescent state into proliferative, motile myofibroblasts that secrete extracellular matrix, which demands rapid adaptation to meet a heightened energy need. Adaptations include reprogramming of central carbon metabolism, enhanced mitochondrial number and activity, endoplasmic reticulum stress, and liberation of free fatty acids through autophagy-dependent hydrolysis of retinyl esters that are stored in cytoplasmic droplets. As an archetype for pericytes in other tissues, recognition of the HSC's metabolic drivers and vulnerabilities offer the potential to target these pathways therapeutically to enhance parenchymal growth and modulate repair.
    DOI:  https://doi.org/10.1016/j.cmet.2020.10.026
  24. JCI Insight. 2020 Nov 24. pii: 141138. [Epub ahead of print]
    Mitophagy protects beta cells from inflammatory damage in diabetes.
    Vaibhav Sidarala, Gemma L Pearson, Vishal S Parekh, Benjamin Thompson, Lisa Christen, Morgan A Gingerich, Jie Zhu, Tracy Stromer, Jianhua Ren, Emma C Reck, Biaoxin Chai, John A Corbett, Thomas Mandrup-Poulsen, Leslie S Satin, Scott A Soleimanpour.
      Inflammatory damage contributes to β-cell failure in type 1 and 2 diabetes (T1D and T2D). Mitochondria are damaged by inflammatory signaling in β-cells, resulting in impaired bioenergetics and initiation of pro-apoptotic machinery. Hence, the identification of protective responses to inflammation could lead to new therapeutic targets. Here we report that mitophagy serves as a protective response to inflammatory stress in both human and rodent β-cells. Utilizing in vivo mitophagy reporters, we observed that diabetogenic pro-inflammatory cytokines induced mitophagy in response to nitrosative/oxidative mitochondrial damage. Mitophagy-deficient β-cells were sensitized to inflammatory stress, leading to the accumulation of fragmented dysfunctional mitochondria, increased β-cell death, and hyperglycemia. Overexpression of CLEC16A, a T1D gene and mitophagy regulator whose expression in islets is protective against T1D, ameliorated cytokine-induced human β-cell apoptosis. Thus, mitophagy promotes β-cell survival and prevents diabetes by countering inflammatory injury. Targeting this pathway has the potential to prevent β-cell failure in diabetes and may be beneficial in other inflammatory conditions.
    Keywords:  Apoptosis survival pathways; Diabetes; Endocrinology; Mitochondria
    DOI:  https://doi.org/10.1172/jci.insight.141138
  25. Biochem Soc Trans. 2020 Nov 27. pii: BST20200250. [Epub ahead of print]
    Post-transcriptional control of mitochondrial protein composition in changing environmental conditions.
    Tatsuhisa Tsuboi, Jordan Leff, Brian M Zid.
      In fluctuating environmental conditions, organisms must modulate their bioenergetic production in order to maintain cellular homeostasis for optimal fitness. Mitochondria are hubs for metabolite and energy generation. Mitochondria are also highly dynamic in their function: modulating their composition, size, density, and the network-like architecture in relation to the metabolic demands of the cell. Here, we review the recent research on the post-transcriptional regulation of mitochondrial composition focusing on mRNA localization, mRNA translation, protein import, and the role that dynamic mitochondrial structure may have on these gene expression processes. As mitochondrial structure and function has been shown to be very important for age-related processes, including cancer, metabolic disorders, and neurodegeneration, understanding how mitochondrial composition can be affected in fluctuating conditions can lead to new therapeutic directions to pursue.
    Keywords:  mRNA; mRNA localization; mRNA translation; mitochondria; mitochondrial morphology; protein import
    DOI:  https://doi.org/10.1042/BST20200250
  26. Cancers (Basel). 2020 Nov 20. pii: E3458. [Epub ahead of print]12(11):
    Role of the KEAP1-NRF2 Axis in Renal Cell Carcinoma.
    Sara Clerici, Alessandra Boletta.
      NRF2 is a transcription factor that coordinates the antioxidant response in many different tissues, ensuring cytoprotection from endogenous and exogenous stress stimuli. In the kidney, its function is essential in appropriate cellular response to oxidative stress, however its aberrant activation supports progression, metastasis, and resistance to therapies in renal cell carcinoma, similarly to what happens in other nonrenal cancers. While at the moment direct inhibitors of NRF2 are not available, understanding the molecular mechanisms that regulate its hyperactivation in specific tumor types is crucial as it may open new therapeutic perspectives. Here, we focus our attention on renal cell carcinoma, describing how NRF2 hyperactivation can contribute to tumor progression and chemoresistance. Furthermore, we highlight the mechanism whereby the many pathways that are generally altered in these tumors converge to dysregulation of the KEAP1-NRF2 axis.
    Keywords:  KEAP1; NRF2; PRCC; ccRCC; kidney injury
    DOI:  https://doi.org/10.3390/cancers12113458
  27. J Biol Chem. 2020 Nov 26. pii: jbc.RA120.015402. [Epub ahead of print]
    A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism.
    Elisa Enriquez-Hesles, Daniel L Smith, Nazif Maqani, Margaret B Wierman, Matthew D Sutcliffe, Ryan D Fine, Agata Kalita, Sean M Santos, Michael J Muehlbauer, James R Bain, Kevin A Janes, John L Hartman, Matthew D Hirschey, Jeffrey S Smith.
      Caloric restriction (CR) improves healthspan and lifespan of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging associated diseases. In budding yeast, Saccharomyces cerevisiae, CR is commonly defined by reduced glucose in the growth medium, which extends both replicative and chronological lifespan (CLS). We found that conditioned media collected from stationary phase CR cultures extended CLS when supplemented into non-restricted (NR) cultures, suggesting a potential cell non-autonomous mechanism of CR-induced lifespan regulation. Chromatography and untargeted metabolomics of the conditioned media, as well as transcriptional responses associated with the longevity effect, pointed to specific amino acids enriched in the CR conditioned media (CRCM) as functional molecules, with L-serine being a particularly strong candidate. Indeed, supplementing L-serine into NR cultures extended CLS through a mechanism dependent on the one-carbon metabolism pathway, thus implicating this conserved and central metabolic hub in lifespan regulation.
    Keywords:  Saccharomyces cerevisiae; aging; amino acid; caloric restriction; cell non-autonomous; chronological lifespan; one-carbon metabolism; serine
    DOI:  https://doi.org/10.1074/jbc.RA120.015402
  28. Nat Metab. 2020 Nov 23.
    An enolase inhibitor for the targeted treatment of ENO1-deleted cancers.
    Yu-Hsi Lin, Nikunj Satani, Naima Hammoudi, Victoria C Yan, Yasaman Barekatain, Sunada Khadka, Jeffrey J Ackroyd, Dimitra K Georgiou, Cong-Dat Pham, Kenisha Arthur, David Maxwell, Zhenghong Peng, Paul G Leonard, Barbara Czako, Federica Pisaneschi, Pijus Mandal, Yuting Sun, Rafal Zielinski, Susana Castro Pando, Xiaobo Wang, Theresa Tran, Quanyu Xu, Qi Wu, Yongying Jiang, Zhijun Kang, John M Asara, Waldemar Priebe, William Bornmann, Joseph R Marszalek, Ronald A DePinho, Florian L Muller.
      Inhibiting glycolysis remains an aspirational approach for the treatment of cancer. We have previously identified a subset of cancers harbouring homozygous deletion of the glycolytic enzyme enolase (ENO1) that have exceptional sensitivity to inhibition of its redundant paralogue, ENO2, through a therapeutic strategy known as collateral lethality. Here, we show that a small-molecule enolase inhibitor, POMHEX, can selectively kill ENO1-deleted glioma cells at low-nanomolar concentrations and eradicate intracranial orthotopic ENO1-deleted tumours in mice at doses well-tolerated in non-human primates. Our data provide an in vivo proof of principle of the power of collateral lethality in precision oncology and demonstrate the utility of POMHEX for glycolysis inhibition with potential use across a range of therapeutic settings.
    DOI:  https://doi.org/10.1038/s42255-020-00313-3
  29. Cell Syst. 2020 Nov 18. pii: S2405-4712(20)30418-X. [Epub ahead of print]
    Multi-omics Analysis of CRISPRi-Knockdowns Identifies Mechanisms that Buffer Decreases of Enzymes in E. coli Metabolism.
    Stefano Donati, Michelle Kuntz, Vanessa Pahl, Niklas Farke, Dominik Beuter, Timo Glatter, José Vicente Gomes-Filho, Lennart Randau, Chun-Ying Wang, Hannes Link.
      Enzymes maintain metabolism, and their concentration affects cellular fitness: high enzyme levels are costly, and low enzyme levels can limit metabolic flux. Here, we used CRISPR interference (CRISPRi) to study the consequences of decreasing E. coli enzymes below wild-type levels. A pooled CRISPRi screen with 7,177 strains demonstrates that metabolism buffers fitness defects for hours after the induction of CRISPRi. We characterized the metabolome and proteome responses in 30 CRISPRi strains and elucidated three gene-specific buffering mechanisms: ornithine buffered the knockdown of carbamoyl phosphate synthetase (CarAB) by increasing CarAB activity, S-adenosylmethionine buffered the knockdown of homocysteine transmethylase (MetE) by de-repressing expression of the methionine pathway, and 6-phosphogluconate buffered the knockdown of 6-phosphogluconate dehydrogenase (Gnd) by activating a bypass. In total, this work demonstrates that CRISPRi screens can reveal global sources of metabolic robustness and identify local regulatory mechanisms that buffer decreases of specific enzymes. A record of this paper's transparent peer review process is included in the Supplemental Information.
    Keywords:  CRISPR interference; allosteric regulation; metabolic robustness; metabolomics; proteomics; transcriptional regulation
    DOI:  https://doi.org/10.1016/j.cels.2020.10.011
  30. Front Cell Dev Biol. 2020 ;8 566090
    Transcriptional Regulation of NK Cell Development by mTOR Complexes.
    Chao Yang, Subramaniam Malarkannan.
      The mechanistic target of Rapamycin (mTOR) is essential for multiple cellular processes. The unique roles of mTOR complex 1 (mTORC1) or mTOR2 in regulating immune functions are emerging. NK cells are the major lymphocyte subset of innate immunity, and their development and effector functions require metabolic reprogramming. Recent studies demonstrate that in NK cells, conditionally disrupting the formation of mTORC1 or mTOR complex 2 (mTORC2) alters their development significantly. Transcriptomic profiling of NK cells at the single-cell level demonstrates that mTORC1 was critical for the early developmental progression, while mTORC2 regulated the terminal maturation. In this review, we summarize the essential roles of mTOR complexes in NK development and functions.
    Keywords:  NK cell development; mTORC1; mTORC2; raptor; rictor
    DOI:  https://doi.org/10.3389/fcell.2020.566090
  31. Nat Commun. 2020 Nov 27. 11(1): 6069
    An expanded palette of improved SPLICS reporters detects multiple organelle contacts in vitro and in vivo.
    Francesca Vallese, Cristina Catoni, Domenico Cieri, Lucia Barazzuol, Omar Ramirez, Valentina Calore, Massimo Bonora, Flavia Giamogante, Paolo Pinton, Marisa Brini, Tito Calì.
      Membrane contact sites between virtually any known organelle have been documented and, in the last decades, their study received momentum due to their importance for fundamental activities of the cell and for the subtle comprehension of many human diseases. The lack of tools to finely image inter-organelle proximity hindered our understanding on how these subcellular communication hubs mediate and regulate cell homeostasis. We develop an improved and expanded palette of split-GFP-based contact site sensors (SPLICS) for the detection of single and multiple organelle contact sites within a scalable distance range. We demonstrate their flexibility under physiological conditions and in living organisms.
    DOI:  https://doi.org/10.1038/s41467-020-19892-6
  32. Mol Biol Cell. 2020 Nov 25. mbcE20060383
    pHLARE: A New Biosensor Reveals Decreased Lysosome pH in Cancer Cells.
    Bradley A Webb, Francesca M Aloisio, Rabab A Charafeddine, Jessica Cook, Torsten Wittmann, Diane L Barber.
      Many lysosome functions are determined by a lumenal pH of ∼5.0, including the activity of resident acid-activated hydrolases. Lysosome pH (pHlys) is often increased in neurodegenerative disorders and predicted to be decreased in cancers, making it a potential target for therapeutics to limit the progression of these diseases. Accurately measuring pHlys, however, is limited by currently used dyes that accumulate in multiple intracellular compartments and cannot be propagated in clonal cells for longitudinal studies or used for in vivo determinations. To resolve this limitation, we developed a genetically encoded ratiometric pHlys biosensor, pHLARE (pHLysosomal Activity REporter), which localizes predominantly in lysosomes, has a dynamic range of pH 4.0 to 6.5, and can be stably expressed in cells. Using pHLARE we show decreased pHlys with inhibiting activity of the mammalian target of rapamycin complex 1 (mTORC1), in breast, pancreatic, colon, and glioblastoma cancer cells compared with untransformed cells, and with the activated oncogenes H-RasV12 and R-RasV12. pHLARE is a new tool to accurately measure pHlys, for improved understanding of lysosome dynamics that could be a promising therapeutic target.
    DOI:  https://doi.org/10.1091/mbc.E20-06-0383
  33. Int J Mol Sci. 2020 Nov 20. pii: E8808. [Epub ahead of print]21(22):
    Tracing Metabolic Fate of Mitochondrial Glycine Cleavage System Derived Formate In Vitro and In Vivo.
    Yee-Ling Tan, Nga-Lai Sou, Feng-Yao Tang, Hsin-An Ko, Wei-Ting Yeh, Jian-Hau Peng, En-Pei Isabel Chiang.
      Folate-mediated one-carbon (1C) metabolism is a major target of many therapies in human diseases. Studies have focused on the metabolism of serine 3-carbon as it serves as a major source for 1C units. The serine 3-carbon enters the mitochondria transferred by folate cofactors and eventually converted to formate and serves as a major building block for cytosolic 1C metabolism. Abnormal glycine metabolism has been reported in many human pathological conditions. The mitochondrial glycine cleavage system (GCS) catalyzes glycine degradation to CO2 and ammonium, while tetrahydrofolate (THF) is converted into 5,10-methylene-THF. GCS accounts for a substantial proportion of whole-body glycine flux in humans, yet the particular metabolic route of glycine 2-carbon recycled from GCS during mitochondria glycine decarboxylation in hepatic or bone marrow 1C metabolism is not fully investigated, due to the limited accessibility of human tissues. Labeled glycine at 2-carbon was given to humans and primary cells in previous studies for investigating its incorporations into purines, its interconversion with serine, or the CO2 production in the mitochondria. Less is known on the metabolic fate of the glycine 2-carbon recycled from the GCS; hence, a model system tracing its metabolic fate would help in this regard. We took the direct approach of isotopic labeling to further explore the in vitro and in vivo metabolic fate of the 2-carbon from [2-13C]glycine and [2-13C]serine. As the 2-carbon of glycine and serine is decarboxylated and catabolized via the GCS, the original 13C-labeled 2-carbon is transferred to THF and yield methyleneTHF in the mitochondria. In human hepatoma cell-lines, 2-carbon from glycine was found to be incorporated into deoxythymidine (dTMP, dT + 1), M + 3 species of purines (deoxyadenine, dA and deoxyguanine, dG), and methionine (Met + 1). In healthy mice, incorporation of GCS-derived formate from glycine 2-carbon was found in serine (Ser + 2 via cytosolic serine hydroxy methyl transferase), methionine, dTMP, and methylcytosine (mC + 1) in bone marrow DNA. In these experiments, labeled glycine 2-carbon directly incorporates into Ser + 1, A + 2, and G + 2 (at C2 and C8 of purine) in the cytosol. It is noteworthy that since the serine 3-carbon is unlabeled in these experiments, the isotopic enrichments in dT + 1, Ser + 2, dA + 3, dG + 3, and Met + 1 solely come from the 2-carbon of glycine/serine recycled from GCS, re-enters the cytosolic 1C metabolism as formate, and then being used for cytosolic syntheses of serine, dTMP, purine (M + 3) and methionine. Taken together, we established model systems and successfully traced the metabolic fate of mitochondrial GCS-derived formate from glycine 2-carbon in vitro and in vivo. Nutritional supply significantly alters formate generation from GCS. More GCS-derived formate was used in hepatic serine and methionine syntheses, whereas more GCS-derived formate was used in dTMP synthesis in the bone marrow, indicating that the utilization and partitioning of GCS-derived 1C unit are tissue-specific. These approaches enable better understanding concerning the utilization of 1C moiety generated from mitochondrial GCS that can help to further elucidate the role of GCS in human disease development and progression in future applications. More studies on GCS using these approaches are underway.
    Keywords:  glycine; glycine cleavage system; metabolic kinetics; one-carbon metabolism; serine; stable isotopic tracers
    DOI:  https://doi.org/10.3390/ijms21228808
  34. Cancers (Basel). 2020 Nov 23. pii: E3484. [Epub ahead of print]12(11):
    Evidences of a Direct Relationship between Cellular Fuel Supply and Ciliogenesis Regulated by Hypoxic VDAC1-ΔC.
    Monique Meyenberg Cunha-de Padua, Lucilla Fabbri, Maeva Dufies, Sandra Lacas-Gervais, Julie Contenti, Charles Voyton, Sofia Fazio, Marie Irondelle, Baharia Mograbi, Matthieu Rouleau, Nirvana Sadaghianloo, Amandine Rovini, Catherine Brenner, William J Craigen, Jérôme Bourgeais, Olivier Herault, Frédéric Bost, Nathalie M Mazure.
      Metabolic flexibility is the ability of a cell to adapt its metabolism to changes in its surrounding environment. Such adaptability, combined with apoptosis resistance provides cancer cells with a survival advantage. Mitochondrial voltage-dependent anion channel 1 (VDAC1) has been defined as a metabolic checkpoint at the crossroad of these two processes. Here, we show that the hypoxia-induced cleaved form of VDAC1 (VDAC1-ΔC) is implicated in both the up-regulation of glycolysis and the mitochondrial respiration. We demonstrate that VDAC1-ΔC, due to the loss of the putative phosphorylation site at serine 215, concomitantly with the loss of interaction with tubulin and microtubules, reprograms the cell to utilize more metabolites, favoring cell growth in hypoxic microenvironment. We further found that VDAC1-ΔC represses ciliogenesis and thus participates in ciliopathy, a group of genetic disorders involving dysfunctional primary cilium. Cancer, although not representing a ciliopathy, is tightly linked to cilia. Moreover, we highlight, for the first time, a direct relationship between the cilium and cancer cell metabolism. Our study provides the first new comprehensive molecular-level model centered on VDAC1-ΔC integrating metabolic flexibility, ciliogenesis, and enhanced survival in a hypoxic microenvironment.
    Keywords:  ciliopathy; glycolysis; mitochondrial respiration; primary cilium; tubulin; voltage-dependent anion channel 1
    DOI:  https://doi.org/10.3390/cancers12113484
  35. Mol Cell Oncol. 2020 Oct 07. 7(6): 1822123
    Targeting copper metabolism to defeat KRAS-driven colorectal cancer.
    Léo Aubert, Neethi Nandagopal, Philippe P Roux.
      KRAS-driven cancers acquire profound metabolic dependencies that are intimately linked to tumor growth. Our work revealed that colorectal cancers that harbor KRAS mutations are addicted to copper metabolism. This adaptation renders tumor cells critically dependent on the copper transporter ATP7A, which reveals copper metabolism as a promising therapeutic target for KRAS-driven colorectal cancers.
    Keywords:  ATP7A; Copper; KRAS; TTM; chelators; colorectal cancer; micronutrients
    DOI:  https://doi.org/10.1080/23723556.2020.1822123
  36. Nat Rev Nephrol. 2020 Nov 24.
    Mitochondrial quality control in kidney injury and repair.
    Chengyuan Tang, Juan Cai, Xiao-Ming Yin, Joel M Weinberg, Manjeri A Venkatachalam, Zheng Dong.
      Mitochondria are essential for the activity, function and viability of eukaryotic cells and mitochondrial dysfunction is involved in the pathogenesis of acute kidney injury (AKI) and chronic kidney disease, as well as in abnormal kidney repair after AKI. Multiple quality control mechanisms, including antioxidant defence, protein quality control, mitochondrial DNA repair, mitochondrial dynamics, mitophagy and mitochondrial biogenesis, have evolved to preserve mitochondrial homeostasis under physiological and pathological conditions. Loss of these mechanisms may induce mitochondrial damage and dysfunction, leading to cell death, tissue injury and, potentially, organ failure. Accumulating evidence suggests a role of disturbances in mitochondrial quality control in the pathogenesis of AKI, incomplete or maladaptive kidney repair and chronic kidney disease. Moreover, specific interventions that target mitochondrial quality control mechanisms to preserve and restore mitochondrial function have emerged as promising therapeutic strategies to prevent and treat kidney injury and accelerate kidney repair. However, clinical translation of these findings is challenging owing to potential adverse effects, unclear mechanisms of action and a lack of knowledge of the specific roles and regulation of mitochondrial quality control mechanisms in kidney resident and circulating cell types during injury and repair of the kidney.
    DOI:  https://doi.org/10.1038/s41581-020-00369-0
  37. Methods Mol Biol. 2021 ;2192 1-20
    In Vitro Analysis of mtDNA Replication.
    Jay P Uhler, Maria Falkenberg.
      Human mitochondrial DNA is a small circular double-stranded molecule that is essential for cellular energy production. A specialized protein machinery replicates the mitochondrial genome, with DNA polymerase γ carrying out synthesis of both strands. According to the prevailing mitochondrial DNA replication model, the two strands are replicated asynchronously, with the leading heavy-strand initiating first, followed by the lagging light-strand. By using purified recombinant forms of the replication proteins and synthetic DNA templates, it is possible to reconstitute mitochondrial DNA replication in vitro. Here we provide details on how to differentially reconstitute replication of the leading- and lagging-strands.
    Keywords:  DNA polymerase; In vitro; Mitochondria; Replication; mtDNA
    DOI:  https://doi.org/10.1007/978-1-0716-0834-0_1
  38. Methods Mol Biol. 2021 ;2192 287-311
    Blue-Native Electrophoresis to Study the OXPHOS Complexes.
    Erika Fernandez-Vizarra, Massimo Zeviani.
      Blue-native polyacrylamide gel electrophoresis (BN-PAGE) is a technique optimized for the analysis of the five components of the mitochondrial oxidative phosphorylation (OXPHOS) system. BN-PAGE is based on the preservation of the interactions between the individual subunits within the integral complexes. To achieve this, the complexes are extracted from the mitochondrial inner membrane using mild detergents and separated by electrophoresis in the absence of denaturing agents. The electrophoretic procedures can then be combined with a variety of downstream detection techniques. Since its development in the 1990s, BN-PAGE has been applied in the study of mitochondria from all kinds of organisms and extensive amounts of data have been produced using this technique, being key for the understanding of many aspects of OXPHOS physiopathology.
    Keywords:  Blue-native gel electrophoresis; First-dimension BN-PAGE; In gel activity assays; Mitochondrial complexes I, II, III, IV, and V; Oxidative phosphorylation system; Second-dimension BN-PAGE
    DOI:  https://doi.org/10.1007/978-1-0716-0834-0_20
  39. Curr Opin Biotechnol. 2020 Nov 21. pii: S0958-1669(20)30156-7. [Epub ahead of print]70 29-35
    Engineered diets to improve cancer outcomes.
    Marcus D Goncalves, Oliver Dk Maddocks.
      Cancer cells acquire a diverse range of metabolic adaptations that support their enhanced rates of growth and proliferation. While these adaptations help tune metabolism to support higher anabolic output and bolster antioxidant defenses, they can also decrease metabolic flexibility and increase dependence on nutrient uptake versus de novo synthesis. Diet is the major source of nutrients that ultimately support tumor growth, yet the potential impact of diet is currently underutilized during the treatment of cancer. Here, we review several forms of dietary augmentation therapy including those that alter the content of food, such as energy or macronutrient restriction, and those that alter the timing of food consumption, like intermittent fasting regimens. We discuss how these dietary strategies can be combined with pharmacologic therapies to exaggerate the metabolic liabilities of different cancer types.
    DOI:  https://doi.org/10.1016/j.copbio.2020.10.007
  40. Mol Biol Cell. 2020 Nov 25. mbcE20090605
    Identification of new OPA1 cleavage site reveals that short isoforms regulate mitochondrial fusion.
    Ruohan Wang, Prashant Mishra, Spiros D Garbis, Annie Moradian, Michael J Sweredoski, David C Chan.
      OPA1, a large GTPase of the dynamin superfamily, mediates fusion of the mitochondrial inner membranes, regulates cristae morphology, and maintains respiratory chain function. Inner-membrane-anchored long forms of OPA1 (l-OPA1) are proteolytically processed by the OMA1 or YME1L proteases, acting at cleavage sites S1 and S2 respectively, to produce short forms (s-OPA1). In both mouse and human, half of the mRNA splice forms of Opa1 are constitutively processed to yield exclusively s-OPA1. However, the function of s-OPA1 in mitochondrial fusion has been debated, because in some stress conditions, s-OPA1 is dispensable for fusion. By constructing cells in which the Opa1 locus no longer produces transcripts with S2 cleavage sites, we generated a simplified system to identify the new YME1L-dependent site S3 that mediates constitutive and complete cleavage of OPA1. We show that mitochondrial morphology is highly sensitive to the ratio of l-OPA1 to s-OPA1, indicating that s-OPA1 regulates mitochondrial fusion.
    DOI:  https://doi.org/10.1091/mbc.E20-09-0605
  41. Elife. 2020 Nov 25. pii: e62377. [Epub ahead of print]9
    Autophagy compensates for Lkb1 loss to maintain adult mice homeostasis and survival.
    Khoosheh Khayati, Vrushank Bhatt, Zhixian Sherrie Hu, Sajid Fahumy, Xuefei Luo, Jessie Yanxiang Guo.
      Liver Kinase B1 (LKB1), also known as serine/threonine kinase 11 (STK11) is the major energy sensor for cells to respond to metabolic stress. Autophagy degrades and recycles proteins, macromolecules, and organelles for cells to survive starvation. To access the role and cross-talk between autophagy and Lkb1 in normal tissue homeostasis, we generated genetically engineered mouse models where we can conditionally delete Stk11 and autophagy essential gene, Atg7, respectively or simultaneously, throughout the adult mice. We found that Lkb1 was essential for the survival of adult mice, and autophagy activation could temporarily compensate for the acute loss of Lkb1 and extend mouse life span. We further found that acute deletion of Lkb1 in adult mice led to impaired intestinal barrier function, hypoglycemia, and abnormal serum metabolism, which was partly rescued by the Lkb1 loss-induced autophagy upregulation via inhibiting p53 induction. Taken together, we demonstrated that autophagy and Lkb1 work synergistically to maintain adult mouse homeostasis and survival.
    Keywords:  cell biology; infectious disease; microbiology; mouse
    DOI:  https://doi.org/10.7554/eLife.62377
  42. Cancer Cell. 2020 Nov 17. pii: S1535-6108(20)30594-8. [Epub ahead of print]
    Normal Somatic Mutations in Cancer Transformation.
    Neshika Wijewardhane, Lisa Dressler, Francesca D Ciccarelli.
      Gene alterations play a prominent role in driving cancer initiation and progression. However, the genetic events that occur in normal cells prior to tumorigenesis are still unknown. Recent studies have started to map somatic mutations in normal human tissues, and here we discuss their implications for our understanding of tumorigenesis.
    DOI:  https://doi.org/10.1016/j.ccell.2020.11.002
  43. Aging Cell. 2020 Nov 22. e13275
    G6PD overexpression protects from oxidative stress and age-related hearing loss.
    Jose M Bermúdez-Muñoz, Adelaida M Celaya, Sara Hijazo-Pechero, Jing Wang, Manuel Serrano, Isabel Varela-Nieto.
      Aging of the auditory system is associated with the incremental production of reactive oxygen species (ROS) and the accumulation of oxidative damage in macromolecules, which contributes to cellular malfunction, compromises cell viability, and, ultimately, leads to functional decline. Cellular detoxification relies in part on the production of NADPH, which is an important cofactor for major cellular antioxidant systems. NADPH is produced principally by the housekeeping enzyme glucose-6-phosphate dehydrogenase (G6PD), which catalyzes the rate-limiting step in the pentose phosphate pathway. We show here that G6PD transgenic mice (G6PD-Tg), which show enhanced constitutive G6PD activity and NADPH production along life, have lower auditory thresholds than wild-type mice during aging, together with preserved inner hair cell (IHC) and outer hair cell (OHC), OHC innervation, and a conserved number of synapses per IHC. Gene expression of antioxidant enzymes was higher in 3-month-old G6PD-Tg mice than in wild-type counterparts, whereas the levels of pro-apoptotic proteins were lower. Consequently, nitration of proteins, mitochondrial damage, and TUNEL+ apoptotic cells were all lower in 9-month-old G6PD-Tg than in wild-type counterparts. Unexpectedly, G6PD overexpression triggered low-grade inflammation that was effectively resolved in young mice, as shown by the absence of cochlear cellular damage and macrophage infiltration. Our results lead us to propose that NADPH overproduction from an early stage is an efficient mechanism to maintain the balance between the production of ROS and cellular detoxification power along aging and thus prevents hearing loss progression.
    Keywords:  ARHL; NADPH; TrxR; aging; glutathione
    DOI:  https://doi.org/10.1111/acel.13275
  44. Cell. 2020 Nov 20. pii: S0092-8674(20)31451-3. [Epub ahead of print]
    Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.
    Children’s Brain Tumor Network
      We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses. Proteomics data further reveal functional effects of somatic mutations and copy number variations (CNVs) not evident in transcriptomics data. Kinase-substrate association and co-expression network analysis identify important biological mechanisms of tumorigenesis. This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
    Keywords:  BRAF alteration; CPTAC; CTNNB1 mutation; kinase activity score; kinase substrate regulation; pediatric brain tumor; post-translational modification; proteomic cluster; recurrent versus primary tumors; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2020.10.044
  45. Front Oncol. 2020 ;10 554272
    Metabolic Compartmentalization at the Leading Edge of Metastatic Cancer Cells.
    Kara Wolfe, Ryo Kamata, Kester Coutinho, Takanari Inoue, Atsuo T Sasaki.
      Despite advances in targeted therapeutics and understanding in molecular mechanisms, metastasis remains a substantial obstacle for cancer treatment. Acquired genetic mutations and transcriptional changes can promote the spread of primary tumor cells to distant tissues. Additionally, recent studies have uncovered that metabolic reprogramming of cancer cells is tightly associated with cancer metastasis. However, whether intracellular metabolism is spatially and temporally regulated for cancer cell migration and invasion is understudied. In this review, we highlight the emergence of a concept, termed "membraneless metabolic compartmentalization," as one of the critical mechanisms that determines the metastatic capacity of cancer cells. In particular, we focus on the compartmentalization of purine nucleotide metabolism (e.g., ATP and GTP) at the leading edge of migrating cancer cells through the uniquely phase-separated microdomains where dynamic exchange of nucleotide metabolic enzymes takes place. We will discuss how future insights may usher in a novel class of therapeutics specifically targeting the metabolic compartmentalization that drives tumor metastasis.
    Keywords:  GTP-metabolism; cancer; leading edge; liquid-liquid phase separation; membraneless metabolic compartmentalization; metabolon; metastasis; purine biosynthesis
    DOI:  https://doi.org/10.3389/fonc.2020.554272
  46. Methods Mol Biol. 2021 ;2192 183-196
    Mitoribosome Profiling from Human Cell Culture: A High Resolution View of Mitochondrial Translation.
    Sarah F Pearce, Miriam Cipullo, Betty Chung, Ian Brierley, Joanna Rorbach.
      Ribosome profiling (Ribo-Seq) is a technique that allows genome-wide, quantitative analysis of translation. In recent years, it has found multiple applications in studies of translation in diverse organisms, tracking protein synthesis with single codon resolution. Traditional protocols applied for generating Ribo-Seq libraries from mammalian cell cultures are not suitable to study mitochondrial translation due to differences between eukaryotic cytosolic and mitochondrial ribosomes. Here, we present an adapted protocol enriching for mitoribosome footprints. In addition, we describe the preparation of small RNA sequencing libraries from the resultant mitochondrial ribosomal protected fragments (mtRPFs).
    Keywords:  MitoRibo-Seq; Mitochondria; Mitoribosome; Ribosome profiling
    DOI:  https://doi.org/10.1007/978-1-0716-0834-0_14
  47. Methods Mol Biol. 2021 ;2192 59-68
    Detection of 5-formylcytosine in Mitochondrial Transcriptome.
    Lindsey Van Haute, Michal Minczuk.
      Posttranscriptional RNA modifications have recently emerged as essential posttranscriptional regulators of gene expression. Here we present two methods for single nucleotide resolution detection of 5-formylcytosine (f5C) in RNA. The first relies on chemical protection of f5C against bisulfite treatment, the second method is based on chemical reduction of f5C to hm5C. In combination with regular bisulfite treatment of RNA, the methods allow for precise mapping of f5C. The protocol is used for f5C detection in mtDNA-encoded RNA, however, it can be straightforwardly applied for transcriptome-wide analyses.
    Keywords:  5-formylcytosine; Next-generation sequencing; RNA modification; RedBS RNA-Seq; epitranscriptome; fCAB RNA-Seq
    DOI:  https://doi.org/10.1007/978-1-0716-0834-0_5
  48. Nat Rev Genet. 2020 Nov 26.
    The epigenetic basis of cellular heterogeneity.
    Benjamin Carter, Keji Zhao.
      Single-cell sequencing-based methods for profiling gene transcript levels have revealed substantial heterogeneity in expression levels among morphologically indistinguishable cells. This variability has important functional implications for tissue biology and disease states such as cancer. Mapping of epigenomic information such as chromatin accessibility, nucleosome positioning, histone tail modifications and enhancer-promoter interactions in both bulk-cell and single-cell samples has shown that these characteristics of chromatin state contribute to expression or repression of associated genes. Advances in single-cell epigenomic profiling methods are enabling high-resolution mapping of chromatin states in individual cells. Recent studies using these techniques provide evidence that variations in different aspects of chromatin organization collectively define gene expression heterogeneity among otherwise highly similar cells.
    DOI:  https://doi.org/10.1038/s41576-020-00300-0
  49. Bioessays. 2020 Nov 27. e2000243
    DNA adenine methylation in eukaryotes: Enzymatic mark or a form of DNA damage?
    Matthias Bochtler, Humberto Fernandes.
      6-methyladenine (6mA) is fairly abundant in nuclear DNA of basal fungi, ciliates and green algae. In these organisms, 6mA is maintained near transcription start sites in ApT context by a parental-strand instruction dependent maintenance methyltransferase and is positively associated with transcription. In animals and plants, 6mA levels are high only in organellar DNA. The 6mA levels in nuclear DNA are very low. They are attributable to nucleotide salvage and the activity of otherwise mitochondrial METTL4, and may be considered as a price that cells pay for adenine methylation in RNA and/or organellar DNA. Cells minimize this price by sanitizing dNTP pools to limit 6mA incorporation, and by converting 6mA that has been incorporated into DNA back to adenine. Hence, 6mA in nuclear DNA should be described as an epigenetic mark only in basal fungi, ciliates and green algae, but not in animals and plants.
    Keywords:  6mA; DNA damage; DNA modifications; cancer; epitranscriptome/epigenome; nucleotide salvage; transcription
    DOI:  https://doi.org/10.1002/bies.202000243
  50. Immunity. 2020 Nov 17. pii: S1074-7613(20)30408-8. [Epub ahead of print]
    Modification of Proteins by Metabolites in Immunity.
    C Diskin, T A J Ryan, L A J O'Neill.
      Immunometabolism has emerged as a key focus for immunologists, with metabolic change in immune cells becoming as important a determinant for specific immune effector responses as discrete signaling pathways. A key output for these changes involves post-translational modification (PTM) of proteins by metabolites. Products of glycolysis and Krebs cycle pathways can mediate these events, as can lipids, amino acids, and polyamines. A rich and diverse set of PTMs in macrophages and T cells has been uncovered, altering phenotype and modulating immunity and inflammation in different contexts. We review the recent findings in this area and speculate whether they could be of use in the effort to develop therapeutics for immune-related diseases.
    DOI:  https://doi.org/10.1016/j.immuni.2020.09.014
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