bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022‒08‒14
fifty-two papers selected by
Christian Frezza, Universität zu Köln
  1. Lipid droplets promote efficient mitophagy.
  2. Rapid and selective generation of H2S within mitochondria protects against cardiac ischemia-reperfusion injury.
  3. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes.
  4. Insights on how mitochondrial NAD(P)+ transhydrogenase plays a central metabolic role in proinflammatory macrophages.
  5. MYC sensitises cells to apoptosis by driving energetic demand.
  6. Lactate is an epigenetic metabolite that drives survival in model systems of glioblastoma.
  7. Ischemia-Selective Cardioprotection by Malonate for Ischemia/Reperfusion Injury.
  8. Miro proteins and their role in mitochondrial transfer in cancer and beyond.
  9. Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion.
  10. Nicotinamide riboside alleviates exercise intolerance in ANT1-deficient mice.
  11. Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer.
  12. The circadian clock mediates daily bursts of cell differentiation by periodically restricting cell-differentiation commitment.
  13. Inner Mitochondrial Membrane Sensitivity to Na+ Reveals Partially Segmented Functional CoQ Pools.
  14. Connections between metabolism and epigenetics: mechanisms and novel anti-cancer strategy.
  15. Thy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis.
  16. The mitochondrial enzyme FAHD1 regulates complex II activity in breast cancer cells and is indispensable for basal BT-20 cells in vitro.
  17. Interplay of carbon dioxide and peroxide metabolism in mammalian cells.
  18. Keeping the beat against time: Mitochondrial fitness in the aging heart.
  19. Nitric oxide-based regulation of metabolism: Hints from TRAP1 and SIRT3 crosstalk.
  20. Microbe capture by splenic macrophages triggers sepsis via T cell-death-dependent neutrophil lifespan shortening.
  21. Cooperative assembly of the mitochondrial respiratory chain.
  22. Mitochondrial impairment and repair in the pathogenesis of systemic lupus erythematosus.
  23. In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.
  24. Loss of Mitochondrial Fatty Acid β-Oxidation Protein Short Chain Enoyl-CoA Hydratase Disrupts Oxidative Phosphorylation Protein Complex Stability and Function.
  25. Why low temperatures could help starve tumours of fuel.
  26. The Circadian Regulation of Nutrient Metabolism in Diet-Induced Obesity and Metabolic Disease.
  27. Location matters: hexokinase 1 in glucose metabolism and inflammation.
  28. mTORC1 controls Golgi architecture and vesicle secretion by phosphorylation of SCYL1.
  29. Raptor downregulation rescues neuronal phenotypes in mouse models of Tuberous Sclerosis Complex.
  30. Mitofusin 2 Integrates Mitochondrial Network Remodelling, Mitophagy and Renewal of Respiratory Chain Proteins in Neurons after Oxygen and Glucose Deprivation.
  31. Acute lymphoblastic leukemia necessitates GSH-dependent ferroptosis defenses to overcome FSP1-epigenetic silencing.
  32. The mitochondrial NAD+ transporter SLC25A51 is a fasting-induced gene affecting SIRT3 functions.
  33. Different platforms for mitomiRs in mitochondria: Emerging facets in regulation of mitochondrial functions.
  34. OPA1 regulation of mitochondrial dynamics in skeletal and cardiac muscle.
  35. Interaction of LATS1 with SMAC links the MST2/Hippo pathway with apoptosis in an IAP-dependent manner.
  36. Blocking ActRIIB and restoring appetite reverses cachexia and improves survival in mice with lung cancer.
  37. Stressed to death: Mitochondrial stress responses connect respiration and apoptosis in cancer.
  38. High-throughput sequencing analysis of nuclear-encoded mitochondrial genes reveals a genetic signature of human longevity.
  39. The expanding role of BAP1 in clear cell renal cell carcinoma.
  40. Mitochondria and ischemia reperfusion injury.
  41. MCU proteins dominate in vivo mitochondrial Ca2+ uptake in Arabidopsis roots.
  42. Heterogeneity in RAS mutations: One size does not fit all.
  43. Effect of metformin on intact mitochondria from liver and brain: Concept revisited.
  44. Immunodeficiency, autoimmunity, and increased risk of B cell malignancy in humans with TRAF3 mutations.
  45. Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli.
  46. Cancer nanomedicine.
  47. Navigating ferroptosis via an NADPH sensor.
  48. Systematic comparison of pancreatic ductal adenocarcinoma models identifies a conserved highly plastic basal cell state.
  49. A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag.
  50. Balanced control of thermogenesis by nuclear receptor corepressors in brown adipose tissue.
  51. Untangling the web of intratumour heterogeneity.
  52. DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma.
  1. Autophagy. 2022 Aug 08. 1-2
    Lipid droplets promote efficient mitophagy.
    Maeve Long, Thomas G McWilliams.
      Mitophagy neutralizes defective mitochondria via lysosomal elimination. Increased levels of mitophagy hallmark metabolic transitions and are induced by iron depletion, yet its metabolic basis has not been studied in-depth. How mitophagy integrates with different homeostatic mechanisms to support metabolic integrity is incompletely understood. We examined metabolic adaptations in cells treated with deferiprone (DFP), a therapeutic iron chelator known to induce PINK1-PRKN-independent mitophagy. We found that iron depletion profoundly rewired the cellular metabolome, remodeling lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurs upstream of mitochondrial turnover, with many LDs bordering mitochondria upon iron chelation. Surprisingly, DGAT1 inhibition restricts mitophagy in vitro by lysosomal dysfunction. Genetic depletion of mdy/DGAT1 in vivo impairs neuronal mitophagy and locomotor function in Drosophila, demonstrating the physiological relevance of our findings.
    Keywords:  DGAT1; iron; lipid droplet; metabolism; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2022.2089956
  2. Redox Biol. 2022 Aug 05. pii: S2213-2317(22)00201-4. [Epub ahead of print]55 102429
    Rapid and selective generation of H2S within mitochondria protects against cardiac ischemia-reperfusion injury.
    Jan Lj Miljkovic, Nils Burger, Justyna M Gawel, John F Mulvey, Abigail A I Norman, Takanori Nishimura, Yoshiyuki Tsujihata, Angela Logan, Olga Sauchanka, Stuart T Caldwell, Jordan L Morris, Tracy A Prime, Stefan Warrington, Julien Prudent, Georgina R Bates, Dunja Aksentijević, Hiran A Prag, Andrew M James, Thomas Krieg, Richard C Hartley, Michael P Murphy.
      Mitochondria-targeted H2S donors are thought to protect against acute ischemia-reperfusion (IR) injury by releasing H2S that decreases oxidative damage. However, the rate of H2S release by current donors is too slow to be effective upon administration following reperfusion. To overcome this limitation here we develop a mitochondria-targeted agent, MitoPerSulf that very rapidly releases H2S within mitochondria. MitoPerSulf is quickly taken up by mitochondria, where it reacts with endogenous thiols to generate a persulfide intermediate that releases H2S. MitoPerSulf is acutely protective against cardiac IR injury in mice, due to the acute generation of H2S that inhibits respiration at cytochrome c oxidase thereby preventing mitochondrial superoxide production by lowering the membrane potential. Mitochondria-targeted agents that rapidly generate H2S are a new class of therapy for the acute treatment of IR injury.
    Keywords:  Hydrogen sulfide donors; Ischemia-reperfusion injury; Mitochondria; Mitochondria targeting; Reverse electron transport (RET)
    DOI:  https://doi.org/10.1016/j.redox.2022.102429
  3. Genome Biol. 2022 Aug 09. 23(1): 170
    Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes.
    Iliana Soto, Mary Couvillion, Katja G Hansen, Erik McShane, J Conor Moran, Antoni Barrientos, L Stirling Churchman.
      BACKGROUND: Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome.RESULTS: We resolve features of mitochondrial translation initiation and identify a small ORF in the 3' UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways.
    CONCLUSIONS: Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.
    DOI:  https://doi.org/10.1186/s13059-022-02732-9
  4. Am J Physiol Cell Physiol. 2022 08 01. 323(2): C648-C649
    Insights on how mitochondrial NAD(P)+ transhydrogenase plays a central metabolic role in proinflammatory macrophages.
    Tiago R Figueira, Roger F Castilho.
      
    Keywords:  Kreb’s cycle; immune cell; mitochondria; peroxide; redox balance
    DOI:  https://doi.org/10.1152/ajpcell.00090.2022
  5. Nat Commun. 2022 Aug 09. 13(1): 4674
    MYC sensitises cells to apoptosis by driving energetic demand.
    Joy Edwards-Hicks, Huizhong Su, Maurizio Mangolini, Kubra K Yoneten, Jimi Wills, Giovanny Rodriguez-Blanco, Christine Young, Kevin Cho, Heather Barker, Morwenna Muir, Ania Naila Guerrieri, Xue-Feng Li, Rachel White, Piotr Manasterski, Elena Mandrou, Karen Wills, Jingyu Chen, Emily Abraham, Kianoosh Sateri, Bin-Zhi Qian, Peter Bankhead, Mark Arends, Noor Gammoh, Alex von Kriegsheim, Gary J Patti, Andrew H Sims, Juan Carlos Acosta, Valerie Brunton, Kamil R Kranc, Maria Christophorou, Erika L Pearce, Ingo Ringshausen, Andrew J Finch.
      The MYC oncogene is a potent driver of growth and proliferation but also sensitises cells to apoptosis, which limits its oncogenic potential. MYC induces several biosynthetic programmes and primary cells overexpressing MYC are highly sensitive to glutamine withdrawal suggesting that MYC-induced sensitisation to apoptosis may be due to imbalance of metabolic/energetic supply and demand. Here we show that MYC elevates global transcription and translation, even in the absence of glutamine, revealing metabolic demand without corresponding supply. Glutamine withdrawal from MRC-5 fibroblasts depletes key tricarboxylic acid (TCA) cycle metabolites and, in combination with MYC activation, leads to AMP accumulation and nucleotide catabolism indicative of energetic stress. Further analyses reveal that glutamine supports viability through TCA cycle energetics rather than asparagine biosynthesis and that TCA cycle inhibition confers tumour suppression on MYC-driven lymphoma in vivo. In summary, glutamine supports the viability of MYC-overexpressing cells through an energetic rather than a biosynthetic mechanism.
    DOI:  https://doi.org/10.1038/s41467-022-32368-z
  6. Mol Cell. 2022 Aug 09. pii: S1097-2765(22)00647-5. [Epub ahead of print]
    Lactate is an epigenetic metabolite that drives survival in model systems of glioblastoma.
    Consuelo Torrini, Trang Thi Thu Nguyen, Chang Shu, Angeliki Mela, Nelson Humala, Aayushi Mahajan, Erin Heather Seeley, Guoan Zhang, Mike-Andrew Westhoff, Georg Karpel-Massler, Jeffrey N Bruce, Peter Canoll, Markus D Siegelin.
      Lactate accumulates to a significant amount in glioblastomas (GBMs), the most common primary malignant brain tumor with an unfavorable prognosis. However, it remains unclear whether lactate is metabolized by GBMs. Here, we demonstrated that lactate rescued patient-derived xenograft (PDX) GBM cells from nutrient-deprivation-mediated cell death. Transcriptome analysis, ATAC-seq, and ChIP-seq showed that lactate entertained a signature of oxidative energy metabolism. LC/MS analysis demonstrated that U-13C-lactate elicited substantial labeling of TCA-cycle metabolites, acetyl-CoA, and histone protein acetyl-residues in GBM cells. Lactate enhanced chromatin accessibility and histone acetylation in a manner dependent on oxidative energy metabolism and the ATP-citrate lyase (ACLY). Utilizing orthotopic PDX models of GBM, a combined tracer experiment unraveled that lactate carbons were substantially labeling the TCA-cycle metabolites. Finally, pharmacological blockage of oxidative energy metabolism extended overall survival in two orthotopic PDX models in mice. These results establish lactate metabolism as a novel druggable pathway for GBM.
    Keywords:  ATAC-seq; ChIP-seq; glioblastoma; lactate; metabolic flux analysis; tumor metabolism
    DOI:  https://doi.org/10.1016/j.molcel.2022.06.030
  7. Circ Res. 2022 Aug 12. 101161CIRCRESAHA121320717
    Ischemia-Selective Cardioprotection by Malonate for Ischemia/Reperfusion Injury.
    Hiran A Prag, Dunja Aksentijevic, Andreas Dannhorn, Abigail V Giles, John F Mulvey, Olga Sauchanka, Luping Du, Georgina Bates, Johannes Reinhold, Duvaraka Kula-Alwar, Zhelong Xu, Luc Pellerin, Richard J A Goodwin, Michael P Murphy, Thomas Krieg.
      BACKGROUND: Inhibiting SDH (succinate dehydrogenase), with the competitive inhibitor malonate, has shown promise in ameliorating ischemia/reperfusion injury. However, key for translation to the clinic is understanding the mechanism of malonate entry into cells to enable inhibition of SDH, its mitochondrial target, as malonate itself poorly permeates cellular membranes. The possibility of malonate selectively entering the at-risk heart tissue on reperfusion, however, remains unexplored.METHODS: C57BL/6J mice, C2C12 and H9c2 myoblasts, and HeLa cells were used to elucidate the mechanism of selective malonate uptake into the ischemic heart upon reperfusion. Cells were treated with malonate while varying pH or together with transport inhibitors. Mouse hearts were either perfused ex vivo (Langendorff) or subjected to in vivo left anterior descending coronary artery ligation as models of ischemia/reperfusion injury. Succinate and malonate levels were assessed by LC-MS/MS, in vivo by mass spectrometry imaging, and infarct size by TTC staining.
    RESULTS: Malonate was robustly protective against cardiac ischemia/reperfusion injury, but only if administered at reperfusion and not when infused before ischemia. The extent of malonate uptake into the heart was proportional to the duration of ischemia. Malonate entry into cardiomyocytes in vivo and in vitro was dramatically increased at the low pH (≈6.5) associated with ischemia. This increased uptake of malonate was blocked by selective inhibition of MCT1 (monocarboxylate transporter 1). Reperfusion of the ischemic heart region with malonate led to selective SDH inhibition in the at-risk region. Acid-formulation greatly enhances the cardioprotective potency of malonate.
    CONCLUSIONS: Cardioprotection by malonate is dependent on its entry into cardiomyocytes. This is facilitated by the local decrease in pH that occurs during ischemia, leading to its selective uptake upon reperfusion into the at-risk tissue, via MCT1. Thus, malonate's preferential uptake in reperfused tissue means it is an at-risk tissue-selective drug that protects against cardiac ischemia/reperfusion injury.
    Keywords:  ischemia; mitochondria; myocardial infarction; reactive oxygen species; reperfusion
    DOI:  https://doi.org/10.1161/CIRCRESAHA.121.320717
  8. Front Cell Dev Biol. 2022 ;10 937753
    Miro proteins and their role in mitochondrial transfer in cancer and beyond.
    Zuzana Nahacka, Jaromir Novak, Renata Zobalova, Jiri Neuzil.
      Mitochondria are organelles essential for tumor cell proliferation and metastasis. Although their main cellular function, generation of energy in the form of ATP is dispensable for cancer cells, their capability to drive their adaptation to stress originating from tumor microenvironment makes them a plausible therapeutic target. Recent research has revealed that cancer cells with damaged oxidative phosphorylation import healthy (functional) mitochondria from surrounding stromal cells to drive pyrimidine synthesis and cell proliferation. Furthermore, it has been shown that energetically competent mitochondria are fundamental for tumor cell migration, invasion and metastasis. The spatial positioning and transport of mitochondria involves Miro proteins from a subfamily of small GTPases, localized in outer mitochondrial membrane. Miro proteins are involved in the structure of the MICOS complex, connecting outer and inner-mitochondrial membrane; in mitochondria-ER communication; Ca2+ metabolism; and in the recycling of damaged organelles via mitophagy. The most important role of Miro is regulation of mitochondrial movement and distribution within (and between) cells, acting as an adaptor linking organelles to cytoskeleton-associated motor proteins. In this review, we discuss the function of Miro proteins in various modes of intercellular mitochondrial transfer, emphasizing the structure and dynamics of tunneling nanotubes, the most common transfer modality. We summarize the evidence for and propose possible roles of Miro proteins in nanotube-mediated transfer as well as in cancer cell migration and metastasis, both processes being tightly connected to cytoskeleton-driven mitochondrial movement and positioning.
    Keywords:  Miro; cancer; intercellular transfer; metastasis; migration; mitochondria; respiration
    DOI:  https://doi.org/10.3389/fcell.2022.937753
  9. Nucleic Acids Res. 2022 Aug 10. pii: gkac661. [Epub ahead of print]
    Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion.
    Jelena Misic, Dusanka Milenkovic, Ali Al-Behadili, Xie Xie, Min Jiang, Shan Jiang, Roberta Filograna, Camilla Koolmeister, Stefan J Siira, Louise Jenninger, Aleksandra Filipovska, Anders R Clausen, Leonardo Caporali, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli, Thomas J Nicholls, Anna Wredenberg, Maria Falkenberg, Nils-Göran Larsson.
      The in vivo role for RNase H1 in mammalian mitochondria has been much debated. Loss of RNase H1 is embryonic lethal and to further study its role in mtDNA expression we characterized a conditional knockout of Rnaseh1 in mouse heart. We report that RNase H1 is essential for processing of RNA primers to allow site-specific initiation of mtDNA replication. Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is initiated at non-canonical sites and becomes impaired. Importantly, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed accompanied by mtDNA depletion. The steady-state levels of mitochondrial transcripts follow the levels of mtDNA, and RNA processing is not altered in the absence of RNase H1. Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain of RNase H1 causing impaired mtDNA replication. In contrast to catalytically inactive variants of RNase H1, this mutant version has enhanced enzyme activity but shows impaired primer formation. This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.
    DOI:  https://doi.org/10.1093/nar/gkac661
  10. Mol Metab. 2022 Aug 06. pii: S2212-8778(22)00129-6. [Epub ahead of print] 101560
    Nicotinamide riboside alleviates exercise intolerance in ANT1-deficient mice.
    Patrick M Schaefer, Jessica Huang, Arrienne Butic, Caroline Perry, Tal Yardeni, Wendy Tan, Ryan Morrow, Joseph A Baur, Douglas C Wallace.
      OBJECTIVE: Mitochondrial disorders are often characterized by muscle weakness and fatigue. Null mutations in the heart-muscle adenine nucleotide translocator isoform 1 (ANT1) of both humans and mice cause cardiomyopathy and myopathy associated with exercise intolerance and muscle weakness. Here we decipher the molecular underpinnings of ANT1-deficiency-mediated exercise intolerance.METHODS: This was achieved by correlating exercise physiology, mitochondrial function and metabolomics of mice deficient in ANT1 and comparing this to control mice.
    RESULTS: We demonstrate a peripheral limitation of skeletal muscle mitochondrial respiration and a reduced complex I respiration in ANT1-deficient mice. Upon exercise, this results in a lack of NAD+ leading to a substrate limitation and stalling of the TCA cycle and mitochondrial respiration, further limiting skeletal muscle mitochondrial respiration. Treatment of ANT1-deficient mice with nicotinamide riboside increased NAD+ levels in skeletal muscle and liver, which increased the exercise capacity and the mitochondrial respiration.
    CONCLUSION: Increasing NAD + levels with nicotinamide riboside can alleviate the exercise intolerance associated to ANT1-deficiency, indicating the therapeutic potential of NAD+-stimulating compounds in mitochondrial myopathies.
    Keywords:  Exercise; Mitochondrial disorder; NAD(+)/NADH; Nicotinamide riboside
    DOI:  https://doi.org/10.1016/j.molmet.2022.101560
  11. Sci Adv. 2022 Aug 12. 8(32): eabo2389
    Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer.
    Sung Kook Chun, Bridget M Fortin, Rachel C Fellows, Amber N Habowski, Amandine Verlande, Wei A Song, Alisa L Mahieu, Austin E Y T Lefebvre, Jason N Sterrenberg, Leandro M Velez, Michelle A Digman, Robert A Edwards, Nicholas R Pannunzio, Marcus M Seldin, Marian L Waterman, Selma Masri.
      An alarming rise in young onset colorectal cancer (CRC) has been reported; however, the underlying molecular mechanism remains undefined. Suspected risk factors of young onset CRC include environmental aspects, such as lifestyle and dietary factors, which are known to affect the circadian clock. We find that both genetic disruption and environmental disruption of the circadian clock accelerate Apc-driven CRC pathogenesis in vivo. Using an intestinal organoid model, we demonstrate that clock disruption promotes transformation by driving Apc loss of heterozygosity, which hyperactivates Wnt signaling. This up-regulates c-Myc, a known Wnt target, which drives heightened glycolytic metabolism. Using patient-derived organoids, we show that circadian rhythms are lost in human tumors. Last, we identify that variance between core clock and Wnt pathway genes significantly predicts the survival of patients with CRC. Overall, our findings demonstrate a previously unidentified mechanistic link between clock disruption and CRC, which has important implications for young onset cancer prevention.
    DOI:  https://doi.org/10.1126/sciadv.abo2389
  12. Proc Natl Acad Sci U S A. 2022 Aug 16. 119(33): e2204470119
    The circadian clock mediates daily bursts of cell differentiation by periodically restricting cell-differentiation commitment.
    Zhi-Bo Zhang, Joydeb Sinha, Zahra Bahrami-Nejad, Mary N Teruel.
      Most mammalian cells have an intrinsic circadian clock that coordinates metabolic activity with the daily rest and wake cycle. The circadian clock is known to regulate cell differentiation, but how continuous daily oscillations of the internal clock can control a much longer, multiday differentiation process is not known. Here, we simultaneously monitor circadian clock and adipocyte-differentiation progression live in single cells. Strikingly, we find a bursting behavior in the cell population whereby individual preadipocytes commit to differentiate primarily during a 12-h window each day, corresponding to the time of rest. Daily gating occurs because cells irreversibly commit to differentiate within only a few hours, which is much faster than the rest phase and the overall multiday differentiation process. The daily bursts in differentiation commitment result from a differentiation-stimulus driven variable and slow increase in expression of PPARG, the master regulator of adipogenesis, overlaid with circadian boosts in PPARG expression driven by fast, clock-driven PPARG regulators such as CEBPA. Our finding of daily bursts in cell differentiation only during the circadian cycle phase corresponding to evening in humans is broadly relevant, given that most differentiating somatic cells are regulated by the circadian clock. Having a restricted time each day when differentiation occurs may open therapeutic strategies to use timed treatment relative to the clock to promote tissue regeneration.
    Keywords:  adipogenesis; cell differentiation; cell-fate decision; circadian rhythms; positive feedback
    DOI:  https://doi.org/10.1073/pnas.2204470119
  13. J Vis Exp. 2022 Jul 20.
    Inner Mitochondrial Membrane Sensitivity to Na+ Reveals Partially Segmented Functional CoQ Pools.
    Pablo Hernansanz-Agustín, José Antonio Enríquez.
      Ubiquinone (CoQ) pools in the inner mitochondrial membrane (IMM) are partially segmented to either complex I or FAD-dependent enzymes. Such subdivision can be easily assessed by a comparative assay using NADH or succinate as electron donors in frozen-thawed mitochondria, in which cytochrome c (cyt c) reduction is measured. The assay relies on the effect of Na+ on the IMM, decreasing its fluidity. Here, we present a protocol to measure NADH-cyt c oxidoreductase activity and succinate-cyt c oxidoreductase activities in the presence of NaCl or KCl. The reactions, which rely on the mixture of reagents in a cuvette in a stepwise manner, are measured spectrophotometrically during 4 min in the presence of Na+ or K+. The same mixture is performed in parallel in the presence of the specific enzyme inhibitors in order to subtract the unspecific change in absorbance. NADH-cyt c oxidoreductase activity does not decrease in the presence of any of these cations. However, succinate-cyt c oxidoreductase activity decreases in the presence of NaCl. This simple experiment highlights: 1) the effect of Na+ in decreasing IMM fluidity and CoQ transfer; 2) that supercomplex I+III2 protects ubiquinone (CoQ) transfer from being affected by lowering IMM fluidity; 3) that CoQ transfer between CI and CIII is functionally different from CoQ transfer between CII and CIII. These facts support the existence of functionally differentiated CoQ pools in the IMM and show that they can be regulated by the changing Na+ environment of mitochondria.
    DOI:  https://doi.org/10.3791/63729
  14. Front Pharmacol. 2022 ;13 935536
    Connections between metabolism and epigenetics: mechanisms and novel anti-cancer strategy.
    Chen Chen, Zehua Wang, Yanru Qin.
      Cancer cells undergo metabolic adaptations to sustain their growth and proliferation under several stress conditions thereby displaying metabolic plasticity. Epigenetic modification is known to occur at the DNA, histone, and RNA level, which can alter chromatin state. For almost a century, our focus in cancer biology is dominated by oncogenic mutations. Until recently, the connection between metabolism and epigenetics in a reciprocal manner was spotlighted. Explicitly, several metabolites serve as substrates and co-factors of epigenetic enzymes to carry out post-translational modifications of DNA and histone. Genetic mutations in metabolic enzymes facilitate the production of oncometabolites that ultimately impact epigenetics. Numerous evidences also indicate epigenome is sensitive to cancer metabolism. Conversely, epigenetic dysfunction is certified to alter metabolic enzymes leading to tumorigenesis. Further, the bidirectional relationship between epigenetics and metabolism can impact directly and indirectly on immune microenvironment, which might create a new avenue for drug discovery. Here we summarize the effects of metabolism reprogramming on epigenetic modification, and vice versa; and the latest advances in targeting metabolism-epigenetic crosstalk. We also discuss the principles linking cancer metabolism, epigenetics and immunity, and seek optimal immunotherapy-based combinations.
    Keywords:  cancer metabolism; epigenetics; immunity; novel anti-cancer strategy; oncology
    DOI:  https://doi.org/10.3389/fphar.2022.935536
  15. Nat Commun. 2022 Aug 08. 13(1): 4628
    Thy1 marks a distinct population of slow-cycling stem cells in the mouse epidermis.
    Elle Koren, Alona Feldman, Marianna Yusupova, Avihay Kadosh, Egor Sedov, Roi Ankawa, Yahav Yosefzon, Waseem Nasser, Stefanie Gerstberger, Liam B Kimel, Noa Priselac, Samara Brown, Sam Sharma, Travis Gorenc, Ruby Shalom-Feuerstein, Hermann Steller, Tom Shemesh, Yaron Fuchs.
      The presence of distinct stem cells that maintain the interfollicular epidermis is highly debated. Here, we report a population of keratinocytes, marked by Thy1, in the basal layer of the interfollicular epidermis. We find that epidermal cells expressing differential levels of Thy1 display distinct transcriptional signatures. Thy1+ keratinocytes do not express T cell markers, express a unique transcriptional profile, cycle significantly slower than basal epidermal progenitors and display significant expansion potential in vitro. Multicolor lineage tracing analyses and mathematical modeling reveal that Thy1+ basal keratinocytes do not compete neutrally alike interfollicular progenitors and contribute long-term to both epidermal replenishment and wound repair. Importantly, ablation of Thy1+ cells strongly impairs these processes, thus indicating the non-redundant function of Thy1+ stem cells in the epidermis. Collectively, these results reveal a distinct stem cell population that plays a critical role in epidermal homeostasis and repair.
    DOI:  https://doi.org/10.1038/s41467-022-31629-1
  16. FEBS Lett. 2022 Aug 02.
    The mitochondrial enzyme FAHD1 regulates complex II activity in breast cancer cells and is indispensable for basal BT-20 cells in vitro.
    Max Holzknecht, Lena Guerrero-Navarro, Michele Petit, Eva Albertini, Elisabeth Damisch, Anna Simonini, Fernando Schmitt, Walther Parson, Heidelinde Fiegl, Alexander Weiss, Pidder Jansen-Duerr.
      The mitochondrial enzyme fumarylacetoacetate hydrolase domain-containing protein 1 (FAHD1) was identified to be upregulated in breast cancer tissues. Here, we show that FAHD1 is indispensable for the survival of BT-20 cells, representing the basal breast cancer cell type. A lentiviral knock-down of FAHD1 in the breast cancer cell lines MCF-7 and BT-20 results in lower succinate dehydrogenase (complex II) activity. In luminal MCF-7 cells, this leads to reduced proliferation when cultured in medium containing only glutamine as the carbon source. Of note, both cell lines show attenuated protein levels of the enzyme glutaminase (GLS) which activates programmed cell death in BT-20. These findings demonstrate that FAHD1 is crucial for the functionality of complex II in breast cancer cells and acts on glutaminolysis in the mitochondria.
    Keywords:  FAHD1; MCF-7; TNBC; glutaminase; oxaloacetate; succinate dehydrogenase
    DOI:  https://doi.org/10.1002/1873-3468.14462
  17. J Biol Chem. 2022 Aug 09. pii: S0021-9258(22)00801-8. [Epub ahead of print] 102358
    Interplay of carbon dioxide and peroxide metabolism in mammalian cells.
    Rafael Radi.
      The carbon dioxide/bicarbonate (CO2/HCO3-) molecular pair is ubiquitous in mammalian cells and tissues, mainly as a result of oxidative decarboxylation reactions that occur during intermediary metabolism. CO2 is in rapid equilibrium with HCO3-via the hydration reaction catalyzed by carbonic anhydrases. Far from being an inert compound in redox biology, CO2 enhances or redirects the reactivity of peroxides, modulating the velocity, extent, and type of one- and two-electron oxidation reactions mediated by hydrogen peroxide (H2O2) and peroxynitrite (ONOO-/ONOOH). Herein, we review the biochemical mechanisms by which CO2 engages in peroxide-dependent reactions, free radical production, redox signaling, and oxidative damage. First, we cover the metabolic formation of CO2 and its connection to peroxide formation and decomposition. Next, the reaction mechanisms, kinetics, and processes by which the CO2/peroxide interplay modulates mammalian cell redox biology are scrutinized in-depth. Importantly, CO2 also regulates gene expression related to redox and nitric oxide metabolism and as such influences oxidative and inflammatory processes. Accumulated biochemical evidence in vitro, in cellula, and in vivo unambiguously show that the CO2 and peroxide metabolic pathways are intertwined and together participate in key redox events in mammalian cells.
    DOI:  https://doi.org/10.1016/j.jbc.2022.102358
  18. Front Aging. 2022 ;3 951417
    Keeping the beat against time: Mitochondrial fitness in the aging heart.
    Arielys Mendoza, Jason Karch.
      The process of aging strongly correlates with maladaptive architectural, mechanical, and biochemical alterations that contribute to the decline in cardiac function. Consequently, aging is a major risk factor for the development of heart disease, the leading cause of death in the developed world. In this review, we will summarize the classic and recently uncovered pathological changes within the aged heart with an emphasis on the mitochondria. Specifically, we describe the metabolic changes that occur in the aging heart as well as the loss of mitochondrial fitness and function and how these factors contribute to the decline in cardiomyocyte number. In addition, we highlight recent pharmacological, genetic, or behavioral therapeutic intervention advancements that may alleviate age-related cardiac decline.
    Keywords:  ROS; autophagy; cell death; metabolism; mitochondria; mitochondrial biogenesis; mitochondrial fitness; mitophagy
    DOI:  https://doi.org/10.3389/fragi.2022.951417
  19. Front Mol Biosci. 2022 ;9 942729
    Nitric oxide-based regulation of metabolism: Hints from TRAP1 and SIRT3 crosstalk.
    Fiorella Faienza, Andrea Rasola, Giuseppe Filomeni.
      
    Keywords:  SDH; metabolism; mitochondria; nitric oxide; nitrosylation
    DOI:  https://doi.org/10.3389/fmolb.2022.942729
  20. Nat Commun. 2022 Aug 09. 13(1): 4658
    Microbe capture by splenic macrophages triggers sepsis via T cell-death-dependent neutrophil lifespan shortening.
    Marianna Ioannou, Dennis Hoving, Iker Valle Aramburu, Mia I Temkin, Nathalia M De Vasconcelos, Theodora-Dorita Tsourouktsoglou, Qian Wang, Stefan Boeing, Robert Goldstone, Spyros Vernardis, Vadim Demichev, Markus Ralser, Sascha David, Klaus Stahl, Christian Bode, Venizelos Papayannopoulos.
      The mechanisms linking systemic infection to hyperinflammation and immune dysfunction in sepsis are poorly understood. Extracellular histones promote sepsis pathology, but their source and mechanism of action remain unclear. Here, we show that by controlling fungi and bacteria captured by splenic macrophages, neutrophil-derived myeloperoxidase attenuates sepsis by suppressing histone release. In systemic candidiasis, microbial capture via the phagocytic receptor SIGNR1 neutralizes myeloperoxidase by facilitating marginal zone infiltration and T cell death-dependent histone release. Histones and hyphae induce cytokines in adjacent CD169 macrophages including G-CSF that selectively depletes mature Ly6Ghigh neutrophils by shortening their lifespan in favour of immature Ly6Glow neutrophils with a defective oxidative burst. In sepsis patient plasma, these mediators shorten mature neutrophil lifespan and correlate with neutrophil mortality markers. Consequently, high G-CSF levels and neutrophil lifespan shortening activity are associated with sepsis patient mortality. Hence, by exploiting phagocytic receptors, pathogens degrade innate and adaptive immunity through the detrimental impact of downstream effectors on neutrophil lifespan.
    DOI:  https://doi.org/10.1038/s41467-022-32320-1
  21. Trends Biochem Sci. 2022 Aug 09. pii: S0968-0004(22)00187-6. [Epub ahead of print]
    Cooperative assembly of the mitochondrial respiratory chain.
    Erika Fernández-Vizarra, Cristina Ugalde.
      Deep understanding of the pathophysiological role of the mitochondrial respiratory chain (MRC) relies on a well-grounded model explaining how its biogenesis is regulated. The lack of a consistent framework to clarify the modes and mechanisms governing the assembly of the MRC complexes and supercomplexes (SCs) works against progress in the field. The plasticity model was postulated as an attempt to explain the coexistence of mammalian MRC complexes as individual entities and associated in SC species. However, mounting data accumulated throughout the years question the universal validity of the plasticity model as originally proposed. Instead, as we argue here, a cooperative assembly model provides a much better explanation to the phenomena observed when studying MRC biogenesis in physiological and pathological settings.
    Keywords:  assembly factors; cooperative assembly model; mitochondria; plasticity model; respiratory chain organization; supercomplexes
    DOI:  https://doi.org/10.1016/j.tibs.2022.07.005
  22. Front Immunol. 2022 ;13 929520
    Mitochondrial impairment and repair in the pathogenesis of systemic lupus erythematosus.
    Like Zhao, Xianda Hu, Fei Xiao, Xuan Zhang, Lidan Zhao, Min Wang.
      Nucleic acid autoantibodies, increase type I interferon (IFN-α) levels, and immune cell hyperactivation are hallmarks of systemic lupus erythematosus (SLE). Notably, immune cell activation requires high level of cellular energy that is predominately generated by the mitochondria. Mitochondrial reactive oxygen species (mROS), the byproduct of mitochondrial energy generation, serves as an essential mediator to control the activation and differentiation of cells and regulate the antigenicity of oxidized nucleoids within the mitochondria. Recently, clinical trials on normalization of mitochondrial redox imbalance by mROS scavengers and those investigating the recovery of defective mitophagy have provided novel insights into SLE prophylaxis and therapy. However, the precise mechanism underlying the role of oxidative stress-related mitochondrial molecules in skewing the cell fate at the molecular level remains unclear. This review outlines distinctive mitochondrial functions and pathways that are involved in immune responses and systematically delineates how mitochondrial dysfunction contributes to SLE pathogenesis. In addition, we provide a comprehensive overview of damaged mitochondrial function and impaired metabolic pathways in adaptive and innate immune cells and lupus-induced organ tissues. Furthermore, we summarize the potential of current mitochondria-targeting drugs for SLE treatment. Developing novel therapeutic approaches to regulate mitochondrial oxidative stress is a promising endeavor in the search for effective treatments for systemic autoimmune diseases, particularly SLE.
    Keywords:  mitochondria targeting therapeutics; mitochondrial dysfunction; mitochondrial reactive oxygen species; mitophagy; oxidative stress; systemic lupus erythematosus
    DOI:  https://doi.org/10.3389/fimmu.2022.929520
  23. Sci Rep. 2022 Aug 12. 12(1): 13719
    In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.
    Toshiya Kokaji, Miki Eto, Atsushi Hatano, Katsuyuki Yugi, Keigo Morita, Satoshi Ohno, Masashi Fujii, Ken-Ichi Hironaka, Yuki Ito, Riku Egami, Saori Uematsu, Akira Terakawa, Yifei Pan, Hideki Maehara, Dongzi Li, Yunfan Bai, Takaho Tsuchiya, Haruka Ozaki, Hiroshi Inoue, Hiroyuki Kubota, Yutaka Suzuki, Akiyoshi Hirayama, Tomoyoshi Soga, Shinya Kuroda.
      Metabolic regulation in skeletal muscle is essential for blood glucose homeostasis. Obesity causes insulin resistance in skeletal muscle, leading to hyperglycemia and type 2 diabetes. In this study, we performed multiomic analysis of the skeletal muscle of wild-type (WT) and leptin-deficient obese (ob/ob) mice, and constructed regulatory transomic networks for metabolism after oral glucose administration. Our network revealed that metabolic regulation by glucose-responsive metabolites had a major effect on WT mice, especially carbohydrate metabolic pathways. By contrast, in ob/ob mice, much of the metabolic regulation by glucose-responsive metabolites was lost and metabolic regulation by glucose-responsive genes was largely increased, especially in carbohydrate and lipid metabolic pathways. We present some characteristic metabolic regulatory pathways found in central carbon, branched amino acids, and ketone body metabolism. Our transomic analysis will provide insights into how skeletal muscle responds to changes in blood glucose and how it fails to respond in obesity.
    DOI:  https://doi.org/10.1038/s41598-022-17964-9
  24. FEBS J. 2022 Aug 13.
    Loss of Mitochondrial Fatty Acid β-Oxidation Protein Short Chain Enoyl-CoA Hydratase Disrupts Oxidative Phosphorylation Protein Complex Stability and Function.
    Harrison Burgin, Alice J Sharpe, Shuai Nie, Mark Ziemann, Jordan J Crameri, Diana Stojanovski, James Pitt, Akira Ohtake, Kei Murayama, Matthew McKenzie.
      Short chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short chain enoyl-CoA esters to short chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell 'knockout' model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 'knockout' cells showed reductions in key mitochondrial pathways, including the TCA cycle, receptor mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 'knockout' cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 'knockout' cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2 , complex IV, complex V and supercomplexes CIII2 /CIV and CI/CIII2 /CIV), which were associated with a defect in complex I assembly. Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2 , CIV, CV and the CI/CIII2 /CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
    Keywords:  ECHS1 deficiency; OXPHOS; fatty acid oxidation; mitochondria; mitochondrial disease; short chain enoyl-CoA hydratase
    DOI:  https://doi.org/10.1111/febs.16595
  25. Nature. 2022 Aug 10.
    Why low temperatures could help starve tumours of fuel.
    Benjamin Thompson.
      
    Keywords:  Cancer; Climate change; Metabolism
    DOI:  https://doi.org/10.1038/d41586-022-02171-3
  26. Nutrients. 2022 Jul 29. pii: 3136. [Epub ahead of print]14(15):
    The Circadian Regulation of Nutrient Metabolism in Diet-Induced Obesity and Metabolic Disease.
    Lauren N Woodie, Kaan T Oral, Brianna M Krusen, Mitchell A Lazar.
      Obesity and other metabolic diseases are major public health issues that are particularly prevalent in industrialized societies where circadian rhythmicity is disturbed by shift work, jet lag, and/or social obligations. In mammals, daylight entrains the hypothalamic suprachiasmatic nucleus (SCN) to a ≈24 h cycle by initiating a transcription/translation feedback loop (TTFL) of molecular clock genes. The downstream impacts of the TTFL on clock-controlled genes allow the SCN to set the rhythm for the majority of physiological, metabolic, and behavioral processes. The TTFL, however, is ubiquitous and oscillates in tissues throughout the body. Tissues outside of the SCN are entrained to other signals, such as fed/fasting state, rather than light input. This system requires a considerable amount of biological flexibility as it functions to maintain homeostasis across varying conditions contained within a 24 h day. In the face of either circadian disruption (e.g., jet lag and shift work) or an obesity-induced decrease in metabolic flexibility, this finely tuned mechanism breaks down. Indeed, both human and rodent studies have found that obesity and metabolic disease develop when endogenous circadian pacing is at odds with the external cues. In the following review, we will delve into what is known on the circadian rhythmicity of nutrient metabolism and discuss obesity as a circadian disease.
    Keywords:  circadian rhythms; metabolism; molecular clock; obesity
    DOI:  https://doi.org/10.3390/nu14153136
  27. Trends Endocrinol Metab. 2022 Aug 08. pii: S1043-2760(22)00140-0. [Epub ahead of print]
    Location matters: hexokinase 1 in glucose metabolism and inflammation.
    Sivaraj M Sundaram, Luke A Doughty, Michael W Sereda.
      Hexokinase (HK)-1 mitochondrial-binding mechanisms and consequential physiological relevance remain unclear. Recently, De Jesus et al. studied myeloid cells with HK1 carrying mutated mitochondrial-binding domains (MBDs) and provided evidence that HK1 localization controls glucose metabolic fate. Increases in cytosolic HK1 may also contribute to the inflammation associated with diabetes and aging.
    Keywords:  aging; deacetylation; diabetes; glucose metabolism; inflammation; nitrosylation
    DOI:  https://doi.org/10.1016/j.tem.2022.07.005
  28. Nat Commun. 2022 Aug 10. 13(1): 4685
    mTORC1 controls Golgi architecture and vesicle secretion by phosphorylation of SCYL1.
    Stéphanie Kaeser-Pebernard, Christine Vionnet, Muriel Mari, Devanarayanan Siva Sankar, Zehan Hu, Carole Roubaty, Esther Martínez-Martínez, Huiyuan Zhao, Miguel Spuch-Calvar, Alke Petri-Fink, Gregor Rainer, Florian Steinberg, Fulvio Reggiori, Jörn Dengjel.
      The protein kinase mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth and proliferation, supporting anabolic reactions and inhibiting catabolic pathways like autophagy. Its hyperactivation is a frequent event in cancer promoting tumor cell proliferation. Several intracellular membrane-associated mTORC1 pools have been identified, linking its function to distinct subcellular localizations. Here, we characterize the N-terminal kinase-like protein SCYL1 as a Golgi-localized target through which mTORC1 controls organelle distribution and extracellular vesicle secretion in breast cancer cells. Under growth conditions, SCYL1 is phosphorylated by mTORC1 on Ser754, supporting Golgi localization. Upon mTORC1 inhibition, Ser754 dephosphorylation leads to SCYL1 displacement to endosomes. Peripheral, dephosphorylated SCYL1 causes Golgi enlargement, redistribution of early and late endosomes and increased extracellular vesicle release. Thus, the mTORC1-controlled phosphorylation status of SCYL1 is an important determinant regulating subcellular distribution and function of endolysosomal compartments. It may also explain the pathophysiology underlying human genetic diseases such as CALFAN syndrome, which is caused by loss-of-function of SCYL1.
    DOI:  https://doi.org/10.1038/s41467-022-32487-7
  29. Nat Commun. 2022 Aug 09. 13(1): 4665
    Raptor downregulation rescues neuronal phenotypes in mouse models of Tuberous Sclerosis Complex.
    Vasiliki Karalis, Franklin Caval-Holme, Helen S Bateup.
      Tuberous Sclerosis Complex (TSC) is a neurodevelopmental disorder caused by mutations in the TSC1 or TSC2 genes, which encode proteins that negatively regulate mTOR complex 1 (mTORC1) signaling. Current treatment strategies focus on mTOR inhibition with rapamycin and its derivatives. While effective at improving some aspects of TSC, chronic rapamycin inhibits both mTORC1 and mTORC2 and is associated with systemic side-effects. It is currently unknown which mTOR complex is most relevant for TSC-related brain phenotypes. Here we used genetic strategies to selectively reduce neuronal mTORC1 or mTORC2 activity in mouse models of TSC. We find that reduction of the mTORC1 component Raptor, but not the mTORC2 component Rictor, rebalanced mTOR signaling in Tsc1 knock-out neurons. Raptor reduction was sufficient to improve several TSC-related phenotypes including neuronal hypertrophy, macrocephaly, impaired myelination, network hyperactivity, and premature mortality. Raptor downregulation represents a promising potential therapeutic intervention for the neurological manifestations of TSC.
    DOI:  https://doi.org/10.1038/s41467-022-31961-6
  30. Mol Neurobiol. 2022 Aug 13.
    Mitofusin 2 Integrates Mitochondrial Network Remodelling, Mitophagy and Renewal of Respiratory Chain Proteins in Neurons after Oxygen and Glucose Deprivation.
    Piotr Wojtyniak, Anna Boratynska-Jasinska, Karolina Serwach, Joanna Gruszczynska-Biegala, Barbara Zablocka, Jacek Jaworski, Maria Kawalec.
      In attempts to develop effective therapeutic strategies to limit post-ischemic injury, mitochondria emerge as a key element determining neuronal fate. Mitochondrial damage can be alleviated by various mechanisms including mitochondrial network remodelling, mitochondrial elimination and mitochondrial protein biogenesis. However, the mechanisms regulating relationships between these phenomena are poorly understood. We hypothesized that mitofusin 2 (Mfn2), a mitochondrial GTPase involved in mitochondrial fusion, mitochondria trafficking and mitochondria and endoplasmic reticulum (ER) tethering, may act as one of linking and regulatory factors in neurons following ischemic insult. To verify this assumption, we performed temporal oxygen and glucose deprivation (OGD/R) on rat cortical primary culture to determine whether Mfn2 protein reduction affected the onset of mitophagy, subsequent mitochondrial biogenesis and thus neuronal survival. We found that Mfn2 knockdown increased neuronal susceptibility to OGD/R, prevented mitochondrial network remodelling and resulted in prolonged mitophagosomes formation in response to the insult. Next, Mfn2 knockdown was observed to be accompanied by reduced Parkin protein levels and increased Parkin accumulation on mitochondria. As for wild-type neurons, OGD/R insult was followed by an elevated mtDNA content and an increase in respiratory chain proteins. Neither of these phenomena were observed for Mfn2 knockdown neurons. Collectively, our findings showed that Mfn2 in neurons affected their response to mild and transient OGD stress, balancing the extent of defective mitochondria elimination and positively influencing mitochondrial respiratory protein levels. Our study suggests that Mfn2 is one of essential elements for neuronal response to ischemic insult, necessary for neuronal survival.
    Keywords:  Brain ischemia; Mitochondria; Mitochondrial DNA; Mitochondrial biogenesis; Mitofusin 2; Mitophagy; Primary neurons
    DOI:  https://doi.org/10.1007/s12035-022-02981-6
  31. Redox Biol. 2022 Jul 31. pii: S2213-2317(22)00180-X. [Epub ahead of print]55 102408
    Acute lymphoblastic leukemia necessitates GSH-dependent ferroptosis defenses to overcome FSP1-epigenetic silencing.
    Lucas B Pontel, Alberto Bueno-Costa, Agustín E Morellato, Juliana Carvalho Santos, Gaël Roué, Manel Esteller.
      Ferroptosis is a form of cell death triggered by phospholipid hydroperoxides (PLOOH) generated from the iron-dependent oxidation of polyunsaturated fatty acids (PUFAs). To prevent ferroptosis, cells rely on the antioxidant glutathione (GSH), which serves as cofactor of the glutathione peroxidase 4 (GPX4) for the neutralization of PLOOHs. Some cancer cells can also limit ferroptosis through a GSH-independent axis, centered mainly on the ferroptosis suppressor protein 1 (FSP1). The significance of these two anti-ferroptosis pathways is still poorly understood in cancers from hematopoietic origin. Here, we report that blood-derived cancer cells are selectively sensitive to compounds that block the GSH-dependent anti-ferroptosis axis. In T- and B- acute lymphoblastic leukemia (ALL) cell lines and patient biopsies, the promoter of the gene coding for FSP1 is hypermethylated, silencing the expression of FSP1 and creating a selective dependency on GSH-centered anti-ferroptosis defenses. In-trans expression of FSP1 increases the resistance of leukemic cells to compounds targeting the GSH-dependent anti-ferroptosis pathway. FSP1 over-expression also favors ALL-tumor growth in an in vivo chick chorioallantoic membrane (CAM) model. Hence, our results reveal a metabolic vulnerability of ALL that might be of therapeutic interest.
    Keywords:  Acute lymphoblastic leukemia; DNA Methylation; FSP1; Ferroptosis; GPX4; Glutathione
    DOI:  https://doi.org/10.1016/j.redox.2022.102408
  32. Metabolism. 2022 Aug 04. pii: S0026-0495(22)00153-6. [Epub ahead of print]135 155275
    The mitochondrial NAD+ transporter SLC25A51 is a fasting-induced gene affecting SIRT3 functions.
    Zhiyao Fu, Hyunbae Kim, Paul T Morse, Mu-Jie Lu, Maik Hüttemann, Xiaolu A Cambronne, Kezhong Zhang, Ren Zhang.
      INTRODUCTION: Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism and energy production. NAD+-dependent deacetylase sirtuin 3 (SIRT3) regulates the acetylation levels of mitochondrial proteins that are involved in mitochondrial homeostasis. Fasting up-regulates hepatic SIRT3 activity, which requires mitochondrial NAD+. What is the mechanism, then, to transport more NAD+ into mitochondria to sustain enhanced SIRT3 activity during fasting?OBJECTIVE: SLC25A51 is a recently discovered mitochondrial NAD+ transporter. We tested the hypothesis that, during fasting, increased expression of SLC25A51 is needed for enhanced mitochondrial NAD+ uptake to sustain SIRT3 activity. Because the fasting-fed cycle and circadian rhythm are closely linked, we further tested the hypothesis that SLC25A51 is a circadian regulated gene.
    METHODS: We examined Slc25a51 expression in the liver of fasted mice, and examined its circadian rhythm in wild-type mice and those with liver-specific deletion of the clock gene BMAL1 (LKO). We suppressed Slc25a51 expression in hepatocytes and the mouse liver using shRNA-mediated knockdown, and then examined mitochondrial NAD+ levels, SIRT3 activities, and acetylation levels of SIRT3 target proteins (IDH2 and ACADL). We measured mitochondrial oxygen consumption rate using Seahorse analysis in hepatocytes with reduced Slc25a51 expression.
    RESULTS: We found that fasting induced the hepatic expression of Slc25a51, and its expression showed a circadian rhythm-like pattern that was disrupted in LKO mice. Reduced expression of Slc25a51 in hepatocytes decreased mitochondrial NAD+ levels and SIRT3 activity, reflected by increased acetylation of SIRT3 targets. Slc25a51 knockdown reduced the oxygen consumption rate in intact hepatocytes. Mice with reduced Slc25a51 expression in the liver manifested reduced hepatic mitochondrial NAD+ levels, hepatic steatosis and hypertriglyceridemia.
    CONCLUSIONS: Slc25a51 is a fasting-induced gene that is needed for hepatic SIRT3 functions.
    Keywords:  Mitochondria; NAD; SIRT3; SLC25A51
    DOI:  https://doi.org/10.1016/j.metabol.2022.155275
  33. Mitochondrion. 2022 Aug 06. pii: S1567-7249(22)00072-1. [Epub ahead of print]
    Different platforms for mitomiRs in mitochondria: Emerging facets in regulation of mitochondrial functions.
    Dhruv Gohel, Rajesh Singh.
      Mitochondria are one of the central organelles involved in cellular energy metabolism and play a regulatory role in various human pathologies ranging from inborn errors of metabolism, cancer, inflammation, and infections. Mitochondrial DNA encodes limited number of genes that is not sufficient for its optimal functioning. Hence, mitochondria import ∼1500 of proteins and ncRNAs from the nucleus depending on energy requirement of cell, tissue size, complexity and diversity of functions. Mitochondrial outer membrane can serve as a platform for regulation of local translation of nuclear-encoded mRNAs for mitochondrial proteins (nmRNAmp); however, underlying molecular mechanism for translational regulation of nmRNAmp at mitochondria is unexplored. Emerging evidence now suggest that mitochondria are enriched with specific miRNAs known as mitomiRs, which may be nuclear or mitochondrial DNA encoded. MitomiRs may modulate mitochondrial function and metabolism by fine-tuning protein levels related to mitochondria. The discovery of mitomiRs raised the questions of elucidating molecular pathways for their biogenesis, translocation, action sites and mechanism of action. Here, we have reviewed the existing reports describing the role of mitomiRs in sub mitochondrial compartments and discussed possible molecular mechanisms of mitomiRs in the regulation of nmRNAmp and mito-genome encoded transcripts. Further understanding of mitomiRs will uncover their implication in various pathophysiological conditions associated with mitochondria.
    Keywords:  Ago2; Mitochondria; MitomiRs; RISC; nmRNAmp
    DOI:  https://doi.org/10.1016/j.mito.2022.08.003
  34. Trends Endocrinol Metab. 2022 Aug 06. pii: S1043-2760(22)00134-5. [Epub ahead of print]
    OPA1 regulation of mitochondrial dynamics in skeletal and cardiac muscle.
    John Noone, Donal J O'Gorman, Helena C Kenny.
      The mitochondria are double-membrane organelles integral for energy metabolism. Mitochondrial dynamics is regulated by inner and outer mitochondrial membrane (IMM and OMM) proteins, which promote fission and fusion. Optic atrophy 1 (OPA1) regulates IMM fusion, prevents apoptosis, and is a key regulator of morphological change in skeletal and cardiac muscle physiology and pathophysiology. OPA1 fuses the inner membranes of adjacent mitochondria, allowing for an increase in oxidative phosphorylation (OXPHOS). Considering the importance of energy metabolism in whole-body physiology, OPA1 and its regulators have been proposed as novel targets for the treatment of skeletal muscle atrophy and heart failure. Here, we review the role and regulation of OPA1 in skeletal muscle and cardiac pathophysiology, epitomizing its critical role in the cell.
    Keywords:  exercise; heart; metabolism; mitochondria; skeletal muscle
    DOI:  https://doi.org/10.1016/j.tem.2022.07.003
  35. Cell Death Dis. 2022 Aug 08. 13(8): 692
    Interaction of LATS1 with SMAC links the MST2/Hippo pathway with apoptosis in an IAP-dependent manner.
    Lucía García-Gutiérrez, Emma Fallahi, Nourhan Aboud, Niall Quinn, David Matallanas.
      Metastatic malignant melanoma is the deadliest skin cancer, and it is characterised by its high resistance to apoptosis. The main melanoma driving mutations are part of ERK pathway, with BRAF mutations being the most frequent ones, followed by NRAS, NF1 and MEK mutations. Increasing evidence shows that the MST2/Hippo pathway is also deregulated in melanoma. While mutations are rare, MST2/Hippo pathway core proteins expression levels are often dysregulated in melanoma. The expression of the tumour suppressor RASSF1A, a bona fide activator of the MST2 pathway, is silenced by promoter methylation in over half of melanomas and correlates with poor prognosis. Here, using mass spectrometry-based interaction proteomics we identified the Second Mitochondria-derived Activator of Caspases (SMAC) as a novel LATS1 interactor. We show that RASSF1A-dependent activation of the MST2 pathway promotes LATS1-SMAC interaction and negatively regulates the antiapoptotic signal mediated by the members of the IAP family. Moreover, proteomic experiments identified a common cluster of apoptotic regulators that bind to SMAC and LATS1. Mechanistic analysis shows that the LATS1-SMAC complex promotes XIAP ubiquitination and its subsequent degradation which ultimately results in apoptosis. Importantly, we show that the oncogenic BRAFV600E mutant prevents the proapoptotic signal mediated by the LATS1-SMAC complex while treatment of melanoma cell lines with BRAF inhibitors promotes the formation of this complex, indicating that inhibition of the LATS1-SMAC might be necessary for BRAFV600E-driven melanoma. Finally, we show that LATS1-SMAC interaction is regulated by the SMAC mimetic Birinapant, which requires C-IAP1 inhibition and the degradation of XIAP, suggesting that the MST2 pathway is part of the mechanism of action of Birinapant. Overall, the current work shows that SMAC-dependent apoptosis is regulated by the LATS1 tumour suppressor and supports the idea that LATS1 is a signalling hub that regulates the crosstalk between the MST2 pathway, the apoptotic network and the ERK pathway.
    DOI:  https://doi.org/10.1038/s41419-022-05147-3
  36. Nat Commun. 2022 Aug 08. 13(1): 4633
    Blocking ActRIIB and restoring appetite reverses cachexia and improves survival in mice with lung cancer.
    Andre Lima Queiroz, Ezequiel Dantas, Shakti Ramsamooj, Anirudh Murthy, Mujmmail Ahmed, Elizabeth R M Zunica, Roger J Liang, Jessica Murphy, Corey D Holman, Curtis J Bare, Gregory Ghahramani, Zhidan Wu, David E Cohen, John P Kirwan, Lewis C Cantley, Christopher L Axelrod, Marcus D Goncalves.
      Cancer cachexia is a common, debilitating condition with limited therapeutic options. Using an established mouse model of lung cancer, we find that cachexia is characterized by reduced food intake, spontaneous activity, and energy expenditure accompanied by muscle metabolic dysfunction and atrophy. We identify Activin A as a purported driver of cachexia and treat with ActRIIB-Fc, a decoy ligand for TGF-β/activin family members, together with anamorelin (Ana), a ghrelin receptor agonist, to reverse muscle dysfunction and anorexia, respectively. Ana effectively increases food intake but only the combination of drugs increases lean mass, restores spontaneous activity, and improves overall survival. These beneficial effects are limited to female mice and are dependent on ovarian function. In agreement, high expression of Activin A in human lung adenocarcinoma correlates with unfavorable prognosis only in female patients, despite similar expression levels in both sexes. This study suggests that multimodal, sex-specific, therapies are needed to reverse cachexia.
    DOI:  https://doi.org/10.1038/s41467-022-32135-0
  37. Mol Cell. 2022 Aug 09. pii: S1097-2765(22)00708-0. [Epub ahead of print]
    Stressed to death: Mitochondrial stress responses connect respiration and apoptosis in cancer.
    Jacob M Winter, Tarun Yadav, Jared Rutter.
      Mitochondrial energetics and respiration have emerged as important factors in how cancer cells respond to or evade apoptotic signals. The study of the functional connection between these two processes may provide insight into following questions old and new: how might we target respiration or downstream signaling pathways to amplify apoptotic stress in the context of cancer therapy? Why are respiration and apoptotic regulation housed in the same organelle? Here, we briefly review mitochondrial respiration and apoptosis and then focus on how the intersection of these two processes is regulated by cytoplasmic signaling pathways such as the integrated stress response.
    Keywords:  CRISPR; apoptosis; cancer; electron transport chain; integrated stress response; leukemia; mitochondria; oncology; oxidative phosphorylation; respiration; stress; venetoclax
    DOI:  https://doi.org/10.1016/j.molcel.2022.07.012
  38. Geroscience. 2022 Aug 10.
    High-throughput sequencing analysis of nuclear-encoded mitochondrial genes reveals a genetic signature of human longevity.
    Brenda Gonzalez, Archana Tare, Seungjin Ryu, Simon C Johnson, Gil Atzmon, Nir Barzilai, Matt Kaeberlein, Yousin Suh.
      Mitochondrial dysfunction is a well-known contributor to aging and age-related diseases. The precise mechanisms through which mitochondria impact human lifespan, however, remain unclear. We hypothesize that humans with exceptional longevity harbor rare variants in nuclear-encoded mitochondrial genes (mitonuclear genes) that confer resistance against age-related mitochondrial dysfunction. Here we report an integrated functional genomics study to identify rare functional variants in ~ 660 mitonuclear candidate genes discovered by target capture sequencing analysis of 496 centenarians and 572 controls of Ashkenazi Jewish descent. We identify and prioritize longevity-associated variants, genes, and mitochondrial pathways that are enriched with rare variants. We provide functional gene variants such as those in MTOR (Y2396Lfs*29), CPS1 (T1406N), and MFN2 (G548*) as well as LRPPRC (S1378G) that is predicted to affect mitochondrial translation. Taken together, our results suggest a functional role for specific mitonuclear genes and pathways in human longevity.
    Keywords:  Aging; Centenarian; Genetic variant; Longevity; Mitochondria
    DOI:  https://doi.org/10.1007/s11357-022-00634-z
  39. Hum Pathol. 2022 Aug 03. pii: S0046-8177(22)00206-4. [Epub ahead of print]
    The expanding role of BAP1 in clear cell renal cell carcinoma.
    Payal Kapur, Satwik Rajaram, James Brugarolas.
      Mutations drive renal cell carcinoma (RCC) biology and tumor growth. The BRCA1 associated protein-1 (BAP1) gene is frequently mutated in clear cell renal cell carcinoma (ccRCC) and has emerged as a prognostic and putative predictive biomarker. In this review, we discuss the role of BAP1 as a signature event of a subtype of ccRCC marked by aggressiveness, inflammation and a heightened response to immunotherapy.
    Keywords:  BAP1; PBRM1; RCC; ccRCC
    DOI:  https://doi.org/10.1016/j.humpath.2022.07.022
  40. Curr Opin Organ Transplant. 2022 Aug 04.
    Mitochondria and ischemia reperfusion injury.
    Rebecca Panconesi, Jeannette Widmer, Mauricio Flores Carvalho, Janina Eden, Daniele Dondossola, Philipp Dutkowski, Andrea Schlegel.
      PURPOSE OF REVIEW: This review describes the role of mitochondria in ischemia-reperfusion-injury (IRI).RECENT FINDINGS: Mitochondria are the power-house of our cells and play a key role for the success of organ transplantation. With their respiratory chain, mitochondria are the main energy producers, to fuel metabolic processes, control cellular signalling and provide electrochemical integrity. The mitochondrial metabolism is however severely disturbed when ischemia occurs. Cellular energy depletes rapidly and various metabolites, including Succinate accumulate. At reperfusion, reactive oxygen species are immediately released from complex-I and initiate the IRI-cascade of inflammation. Prior to the development of novel therapies, the underlying mechanisms should be explored to target the best possible mitochondrial compound. A clinically relevant treatment should recharge energy and reduce Succinate accumulation before organ implantation. While many interventions focus instead on a specific molecule, which may inhibit downstream IRI-inflammation, mitochondrial protection can be directly achieved through hypothermic oxygenated perfusion (HOPE) before transplantation.
    SUMMARY: Mitochondria are attractive targets for novel molecules to limit IRI-associated inflammation. Although dynamic preservation techniques could serve as delivery tool for new therapeutic interventions, their own inherent mechanism should not only be studied, but considered as key treatment to reduce mitochondrial injury, as seen with the HOPE-approach.
    DOI:  https://doi.org/10.1097/MOT.0000000000001015
  41. Plant Cell. 2022 Aug 08. pii: koac242. [Epub ahead of print]
    MCU proteins dominate in vivo mitochondrial Ca2+ uptake in Arabidopsis roots.
    Cristina Ruberti, Elias Feitosa-Araujo, Zhaolong Xu, Stephan Wagner, Matteo Grenzi, Essam Darwish, Sophie Lichtenauer, Philippe Fuchs, Ambra Selene Parmagnani, Daria Balcerowicz, Sébastjen Schoenaers, Carolina de la Torre, Khansa Mekkaoui, Adriano Nunes-Nesi, Markus Wirtz, Kris Vissenberg, Olivier Van Aken, Bettina Hause, Alex Costa, Markus Schwarzländer.
      Ca2+ signaling is central to plant development and acclimation. While Ca2+-responsive proteins have been investigated intensely in plants, only a few Ca2+-permeable channels have been identified, and our understanding of how intracellular Ca2+ fluxes are facilitated remains limited. Arabidopsis thaliana homologues of the mammalian channel-forming mitochondrial calcium uniporter (MCU) protein showed Ca2+ transport activity in vitro. Yet, the evolutionary complexity of MCU proteins, as well as reports about alternative systems and unperturbed mitochondrial Ca2+ uptake in knockout lines of MCU genes, leave critical questions about the in vivo functions of the MCU protein family in plants unanswered. Here, we demonstrate that MCU proteins mediate mitochondrial Ca2+ transport in planta and that this mechanism is the major route for fast Ca2+ uptake. Guided by the subcellular localization, expression, and conservation of MCU proteins, we generated an mcu triple knockout line. Using Ca2+ imaging in living root tips and the stimulation of Ca2+ transients of different amplitudes, we demonstrated that mitochondrial Ca2+ uptake became limiting in the triple mutant. The drastic cell physiological phenotype of impaired subcellular Ca2+ transport coincided with deregulated jasmonate-related signaling and thigmomorphogenesis. Our findings establish MCUs as a major mitochondrial Ca2+ entry route in planta and link mitochondrial Ca2+ transport with phytohormone signaling.
    DOI:  https://doi.org/10.1093/plcell/koac242
  42. Sci Signal. 2022 Aug 09. 15(746): eadc9816
    Heterogeneity in RAS mutations: One size does not fit all.
    Nancy E Sealover, Robert L Kortum.
      Although oncogenic driver mutations in RAS occur in 20% of cancers, heterogeneity in the biologic outputs of different RAS mutants has hampered efforts to develop effective treatments for RAS-mutated cancers. In this issue of Science Signaling, Huynh et al. show that even among KRASQ61 mutants, the specific amino acid that is substituted substantially affects mutant KRAS biologic activity and oncogenicity.
    DOI:  https://doi.org/10.1126/scisignal.adc9816
  43. Eur J Pharmacol. 2022 Aug 04. pii: S0014-2999(22)00438-1. [Epub ahead of print] 175177
    Effect of metformin on intact mitochondria from liver and brain: Concept revisited.
    Belem Yoval-Sánchez, Fariha Ansari, Dmitry Lange, Alexander Galkin.
      Metformin is an antihyperglycemic drug which is being examined as a repurposed treatment for cardiovascular disease for individuals without diabetes mellitus. Despite evidence that mitochondrial respiratory complex I is a target of metformin and inhibition of the enzyme is one of the mechanisms of its therapeutic actions, no systematic studies of the metformin effect on intact mitochondria have been reported. In the presented paper, we described the effect of metformin on respiration and ROS release by intact mitochondria from the liver and brain. By comparing the effect of metformin on mitochondria oxidizing different substrates, we found direct inhibition of respiration and stimulation of ROS release when complex I-based respiration is measured (forward electron transfer). Metformin had no effect on respiration rates but inhibited ROS release when mitochondria oxidize succinate or glycerol 3-phosphate in conditions of reverse electron transfer in complex I. In addition, we found that metformin is a weak effector of the active/deactive (A/D) transition of mitochondrial complex I. At high concentrations, metformin increases the rate of spontaneous deactivation of complex I (A→D transition). The results obtained are consistent with the concept of metformin inhibition of complex I and that it can either stimulate or inhibit mitochondrial ROS production depending on the preferential respiratory substrate. This is relevant during the reperfusion process, to counteract the damage produced by ROS when a high level of reverse electron transfer substrates is generated after an ischemic event.
    Keywords:  A/D transition; Metformin; Mitochondrial complex I; ROS production; Respiration
    DOI:  https://doi.org/10.1016/j.ejphar.2022.175177
  44. Sci Immunol. 2022 Aug 12. 7(74): eabn3800
    Immunodeficiency, autoimmunity, and increased risk of B cell malignancy in humans with TRAF3 mutations.
    William Rae, John M Sowerby, Dorit Verhoeven, Mariam Youssef, Prasanti Kotagiri, Natalia Savinykh, Eve L Coomber, Alexis Boneparth, Angela Chan, Chun Gong, Machiel H Jansen, Romy du Long, Giorgia Santilli, Ilenia Simeoni, Jonathan Stephens, Kejia Wu, Marta Zinicola, Hana Lango Allen, Helen Baxendale, Dinakantha Kumararatne, Effrossyni Gkrania-Klotsas, Selma C Scheffler Mendoza, Marco Antonio Yamazaki-Nakashimada, Laura Berrón Ruiz, Cesar Mauricio Rojas-Maruri, Saul O Lugo Reyes, Paul A Lyons, Anthony P Williams, Daniel J Hodson, Gail A Bishop, Adrian J Thrasher, David C Thomas, Michael P Murphy, Timothy J Vyse, Joshua D Milner, Taco W Kuijpers, Kenneth G C Smith.
      Tumor necrosis factor receptor-associated factor 3 (TRAF3) is a central regulator of immunity. TRAF3 is often somatically mutated in B cell malignancies, but its role in human immunity is not defined. Here, in five unrelated families, we describe an immune dysregulation syndrome of recurrent bacterial infections, autoimmunity, systemic inflammation, B cell lymphoproliferation, and hypergammaglobulinemia. Affected individuals each had monoallelic mutations in TRAF3 that reduced TRAF3 expression. Immunophenotyping showed that patients' B cells were dysregulated, exhibiting increased nuclear factor-κB 2 activation, elevated mitochondrial respiration, and heightened inflammatory responses. Patients had mild CD4+ T cell lymphopenia, with a reduced proportion of naïve T cells but increased regulatory T cells and circulating T follicular helper cells. Guided by this clinical phenotype, targeted analyses demonstrated that common genetic variants, which also reduce TRAF3 expression, are associated with an increased risk of B cell malignancies, systemic lupus erythematosus, higher immunoglobulin levels, and bacterial infections in the wider population. Reduced TRAF3 conveys disease risks by driving B cell hyperactivity via intrinsic activation of multiple intracellular proinflammatory pathways and increased mitochondrial respiration, with a likely contribution from dysregulated T cell help. Thus, we define monogenic TRAF3 haploinsufficiency syndrome and demonstrate how common TRAF3 variants affect a range of human diseases.
    DOI:  https://doi.org/10.1126/sciimmunol.abn3800
  45. Curr Biol. 2022 Aug 06. pii: S0960-9822(22)01162-9. [Epub ahead of print]
    Connecting single-cell ATP dynamics to overflow metabolism, cell growth, and the cell cycle in Escherichia coli.
    Wei-Hsiang Lin, Christine Jacobs-Wagner.
      Adenosine triphosphate (ATP) is an abundant and essential metabolite that cells consume and regenerate in large amounts to support growth. Although numerous studies have inferred the intracellular concentration of ATP in bacterial cultures, what happens in individual bacterial cells under stable growth conditions is less clear. Here, we use the QUEEN-2m biosensor to quantify ATP dynamics in single Escherichia coli cells in relation to their growth rate, metabolism, cell cycle, and cell lineage. We find that ATP dynamics are more complex than expected from population studies and are associated with growth-rate variability. Under stable nutrient-rich condition, cells can display large fluctuations in ATP level that are partially coordinated with the cell cycle. Abrogation of aerobic acetate fermentation (overflow metabolism) through genetic deletion considerably reduces both the amplitude of ATP level fluctuations and the cell-cycle trend. Similarly, growth in media in which acetate fermentation is lower or absent results in the reduction of ATP level fluctuation and cell-cycle trend. This suggests that overflow metabolism exhibits temporal dynamics, which contributes to fluctuating ATP levels during growth. Remarkably, at the single-cell level, growth rate negatively correlates with the amplitude of ATP fluctuation for each tested condition, linking ATP dynamics to growth-rate heterogeneity in clonal populations. Our work highlights the importance of single-cell analysis in studying metabolism and its implication to phenotypic diversity and cell growth.
    Keywords:  acetate fermentation; adenosine triphosphate; bacterial cell cycle; fluorescence biosensor; overflow metabolism; single-cell dynamics
    DOI:  https://doi.org/10.1016/j.cub.2022.07.035
  46. Nat Rev Cancer. 2022 Aug 08.
    Cancer nanomedicine.
    Sangeeta N Bhatia, Xiaoyuan Chen, Marina A Dobrovolskaia, Twan Lammers.
      
    DOI:  https://doi.org/10.1038/s41568-022-00496-9
  47. Nat Cell Biol. 2022 Aug;24(8): 1186-1187
    Navigating ferroptosis via an NADPH sensor.
    Chao Mao, Boyi Gan.
      
    DOI:  https://doi.org/10.1038/s41556-022-00963-3
  48. Cancer Res. 2022 Aug 11. pii: CAN-22-1742. [Epub ahead of print]
    Systematic comparison of pancreatic ductal adenocarcinoma models identifies a conserved highly plastic basal cell state.
    Kenneth L Pitter, Olivera Grbovic-Huezo, Simon Joost, Anupriya Singhal, Melissa Blum, Katherine Wu, Matilda Holm, Alexander Ferrena, Arjun Bhutkar, Anna Hudson, Nicolas Lecomte, Elisa de Stanchina, Ronan Chaligne, Christine A Iacobuzio-Donahue, Dana Pe'er, Tuomas Tammela.
      Intra-tumoral heterogeneity and cellular plasticity have emerged as hallmarks of cancer, including pancreatic ductal adenocarcinoma (PDAC). As PDAC portends a dire prognosis, a better understanding of the mechanisms underpinning cellular diversity in PDAC is crucial. Here, we investigated the cellular heterogeneity of PDAC cancer cells across a range of in vitro and in vivo growth conditions using single-cell genomics. Heterogeneity contracted significantly in 2D and 3D cell culture models but was restored upon orthotopic transplantation. Orthotopic transplants reproducibly acquired cell states identified in autochthonous PDAC tumors, including a basal state exhibiting co-expression and co-accessibility of epithelial and mesenchymal genes. Lineage-tracing combined with single-cell transcriptomics revealed that basal cells display high plasticity in situ. This work defines the impact of cellular growth conditions on phenotypic diversity and uncovers a highly plastic cell state with the capacity to facilitate state transitions and promote intra-tumoral heterogeneity in PDAC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-1742
  49. Elife. 2022 Aug 08. pii: e78923. [Epub ahead of print]11
    A pulse-chasable reporter processing assay for mammalian autophagic flux with HaloTag.
    Willa Wen-You Yim, Hayashi Yamamoto, Noboru Mizushima.
      Monitoring autophagic flux is necessary for most autophagy studies. The autophagic flux assays currently available for mammalian cells are generally complicated and do not yield highly quantitative results. Yeast autophagic flux is routinely monitored with the GFP-based processing assay, whereby the amount of GFP proteolytically released from GFP-containing reporters (e.g., GFP-Atg8), detected by immunoblotting, reflects autophagic flux. However, this simple and effective assay is typically inapplicable to mammalian cells because GFP is efficiently degraded in lysosomes while the more proteolytically resistant RFP accumulates in lysosomes under basal conditions. Here, we report a HaloTag (Halo)-based reporter processing assay to monitor mammalian autophagic flux. We found that Halo is sensitive to lysosomal proteolysis but becomes resistant upon ligand binding. When delivered into lysosomes by autophagy, pulse-labeled Halo-based reporters (e.g., Halo-LC3 and Halo-GFP) are proteolytically processed to generate Haloligand when delivered into lysosomes by autophagy. Hence, the amount of free Haloligand detected by immunoblotting or in-gel fluorescence imaging reflects autophagic flux. We demonstrate the applications of this assay by monitoring the autophagy pathways, macroautophagy, selective autophagy, and even bulk nonselective autophagy. With the Halo-based processing assay, mammalian autophagic flux and lysosome-mediated degradation can be monitored easily and precisely.
    Keywords:  cell biology; human; mouse
    DOI:  https://doi.org/10.7554/eLife.78923
  50. Proc Natl Acad Sci U S A. 2022 Aug 16. 119(33): e2205276119
    Balanced control of thermogenesis by nuclear receptor corepressors in brown adipose tissue.
    Hannah J Richter, Amy K Hauck, Kirill Batmanov, Shin-Ichi Inoue, Bethany N So, Mindy Kim, Matthew J Emmett, Ronald N Cohen, Mitchell A Lazar.
      Brown adipose tissue (BAT) is a key thermogenic organ whose expression of uncoupling protein 1 (UCP1) and ability to maintain body temperature in response to acute cold exposure require histone deacetylase 3 (HDAC3). HDAC3 exists in tight association with nuclear receptor corepressors (NCoRs) NCoR1 and NCoR2 (also known as silencing mediator of retinoid and thyroid receptors [SMRT]), but the functions of NCoR1/2 in BAT have not been established. Here we report that as expected, genetic loss of NCoR1/2 in BAT (NCoR1/2 BAT-dKO) leads to loss of HDAC3 activity. In addition, HDAC3 is no longer bound at its physiological genomic sites in the absence of NCoR1/2, leading to a shared deregulation of BAT lipid metabolism between NCoR1/2 BAT-dKO and HDAC3 BAT-KO mice. Despite these commonalities, loss of NCoR1/2 in BAT does not phenocopy the cold sensitivity observed in HDAC3 BAT-KO, nor does loss of either corepressor alone. Instead, BAT lacking NCoR1/2 is inflamed, particularly with respect to the interleukin-17 axis that increases thermogenic capacity by enhancing innervation. Integration of BAT RNA sequencing and chromatin immunoprecipitation sequencing data revealed that NCoR1/2 directly regulate Mmp9, which integrates extracellular matrix remodeling and inflammation. These findings reveal pleiotropic functions of the NCoR/HDAC3 corepressor complex in BAT, such that HDAC3-independent suppression of BAT inflammation counterbalances stimulation of HDAC3 activity in the control of thermogenesis.
    Keywords:  brown adipose tissue; corepressor; inflammation; thermogenesis; transcription
    DOI:  https://doi.org/10.1073/pnas.2205276119
  51. Nat Cell Biol. 2022 Aug;24(8): 1192-1201
    Untangling the web of intratumour heterogeneity.
    Zheqi Li, Marco Seehawer, Kornelia Polyak.
      Intratumour heterogeneity (ITH) is a hallmark of cancer that drives tumour evolution and disease progression. Technological and computational advances have enabled us to assess ITH at unprecedented depths, yet this accumulating knowledge has not had a substantial clinical impact. This is in part due to a limited understanding of the functional relevance of ITH and the inadequacy of preclinical experimental models to reproduce it. Here, we discuss progress made in these areas and illuminate future directions.
    DOI:  https://doi.org/10.1038/s41556-022-00969-x
  52. JCI Insight. 2022 Aug 09. pii: e153836. [Epub ahead of print]
    DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma.
    Thale Kristin Olsen, Cecilia Dyberg, Bethel Tesfai Embaie, Adele M Alchahin, Jelena Milosevic, Jane Ding, Jörg Otte, Conny Tümmler, Ida Hed Myrberg, Ellen M Westerhout, Jan Koster, Rogier Versteeg, Han-Fei Ding, Per Kogner, John Inge Johnsen, David B Sykes, Ninib Baryawno.
      Despite intensive therapy, children with high-risk neuroblastoma are at risk of treatment failure. We applied a multi-omic system approach to evaluate metabolic vulnerabilities in human neuroblastoma. We combined metabolomics, CRISPR screening and transcriptomic data across >700 solid tumor cell lines and identified dihydroorotate dehydrogenase (DHODH), a critical enzyme in pyrimidine synthesis, as a potential treatment target. Of note, DHODH inhibition is currently under clinical investigation in patients with hematologic malignancies. In neuroblastoma, DHODH expression was identified as an independent risk factor for aggressive disease, and high DHODH levels correlated to worse overall and event-free survival. A subset of tumors with the highest DHODH expression was associated with a dismal prognosis, with a 5-year survival of <10%. In xenograft and transgenic neuroblastoma mouse models treated with the DHODH inhibitor brequinar, tumor growth was dramatically reduced, and survival was extended. Furthermore, brequinar treatment was shown to reduce the expression of MYC targets in three different neuroblastoma models in vivo. A combination of brequinar and temozolomide was curative in the majority of transgenic TH-MYCN neuroblastoma mice, indicating a highly active clinical combination therapy. Overall, DHODH inhibition combined with temozolomide has therapeutic potential in neuroblastoma and we propose this combination for clinical testing.
    Keywords:  Cancer; Oncology; Therapeutics
    DOI:  https://doi.org/10.1172/jci.insight.153836
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