bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2022–12–04
fifty-two papers selected by
Christian Frezza, Universität zu Köln
  1. Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.
  2. Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.
  3. Mitochondria and cell death-associated inflammation.
  4. Metabolic determinants of tumour initiation.
  5. Mitochondrial copper in human genetic disorders.
  6. Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet.
  7. Extrinsic cell death pathway plasticity: a driver of clonal evolution in cancer?
  8. Mitochondria-originated redox signalling regulates KLF-1 to promote longevity in Caenorhabditis elegans.
  9. Mitochondrial respiration and dynamics of in vivo neural stem cells.
  10. Elevated FSP1 protects KRAS-mutated cells from ferroptosis during tumor initiation.
  11. PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response.
  12. Nicotinamide riboside kinases regulate skeletal muscle fiber-type specification and are rate-limiting for metabolic adaptations during regeneration.
  13. Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy.
  14. Mitochondrial fragmentation and ROS signaling in wound response and repair.
  15. Mitochondria in photosynthetic cells: Coordinating redox control and energy balance.
  16. Ferroptosis induction via targeting metabolic alterations in head and neck cancer.
  17. Phosphofructokinase P fine-tunes T regulatory cell metabolism, function, and stability in systemic autoimmunity.
  18. Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells.
  19. Inhibition of glutaminolysis restores mitochondrial function in senescent stem cells.
  20. BCAT2-BCKDH metabolon maintains BCAA homeostasis.
  21. The lysosomal Ragulator complex activates NLRP3 inflammasome in vivo via HDAC6.
  22. VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney.
  23. Emerging mitochondrial-mediated mechanisms involved in oligodendrocyte development.
  24. The signaling pathways and therapeutic potential of itaconate to alleviate inflammation and oxidative stress in inflammatory diseases.
  25. Kidney tumors associated with germline mutations of FH and SDHB show a CpG island methylator phenotype (CIMP).
  26. Acetyl-CoA-mediated autoacetylation of fatty acid synthase as a metabolic switch of de novo lipogenesis in Drosophila.
  27. Pyruvate dehydrogenase phosphatase 1 (PDP1) stimulates HIF activity by supporting histone acetylation under hypoxia.
  28. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription.
  29. Targeting Mitochondrial Calcium Handling to Treat Atrial Fibrillation.
  30. Cellular functions of cGAS-STING signaling.
  31. Genetically personalised organ-specific metabolic models in health and disease.
  32. STING Suppresses Mitochondrial VDAC2 to Govern RCC Growth Independent of Innate Immunity.
  33. Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.
  34. Dietary glucosamine overcomes the defects in αβ-T cell ontogeny caused by the loss of de novo hexosamine biosynthesis.
  35. Filling gaps in metabolism using hypothetical reactions.
  36. IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein.
  37. A Time and Place for Inhibiting Autophagy.
  38. Stimulation of RAS-dependent ROS signaling extends longevity by modulating a developmental program of global gene expression.
  39. D-2HG comes out of its shell: Metabolic effects on the immune environment.
  40. Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation.
  41. Tumor aneuploidy predicts survival following immunotherapy across multiple cancers.
  42. Active DNA demethylation promotes cell fate specification and the DNA damage response.
  43. Human cytomegalovirus induces neuronal enolase to support virally mediated metabolic remodeling.
  44. Ras drives malignancy through stem cell crosstalk with the microenvironment.
  45. Mitochondrial RNA stimulates beige adipocyte development in young mice.
  46. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis.
  47. Interferon-dependent SLC14A1+ cancer-associated fibroblasts promote cancer stemness via WNT5A in bladder cancer.
  48. An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.
  49. Decorating chromatin for enhanced genome editing using CRISPR-Cas9.
  50. Distinct changes in endosomal composition promote NLRP3 inflammasome activation.
  51. A self-powered ingestible wireless biosensing system for real-time in situ monitoring of gastrointestinal tract metabolites.
  52. The autophagy pathway beyond model organisms: an evolutionary perspective.
  1. Nat Metab. 2022 Nov 28.
    Metabolon formation regulates branched-chain amino acid oxidation and homeostasis.
    McKenzie Patrick, Zhimin Gu, Gen Zhang, R Max Wynn, Pranita Kaphle, Hui Cao, Hieu Vu, Feng Cai, Xiaofei Gao, Yuannyu Zhang, Mingyi Chen, Min Ni, David T Chuang, Ralph J DeBerardinis, Jian Xu.
      The branched-chain aminotransferase isozymes BCAT1 and BCAT2, segregated into distinct subcellular compartments and tissues, initiate the catabolism of branched-chain amino acids (BCAAs). However, whether and how BCAT isozymes cooperate with downstream enzymes to control BCAA homeostasis in an intact organism remains largely unknown. Here, we analyse system-wide metabolomic changes in BCAT1- and BCAT2-deficient mouse models. Loss of BCAT2 but not BCAT1 leads to accumulation of BCAAs and branched-chain α-keto acids (BCKAs), causing morbidity and mortality that can be ameliorated by dietary BCAA restriction. Through proximity labelling, isotope tracing and enzymatic assays, we provide evidence for the formation of a mitochondrial BCAA metabolon involving BCAT2 and branched-chain α-keto acid dehydrogenase. Disabling the metabolon contributes to BCAT2 deficiency-induced phenotypes, which can be reversed by BCAT1-mediated BCKA reamination. These findings establish a role for metabolon formation in BCAA metabolism in vivo and suggest a new strategy to modulate this pathway in diseases involving dysfunctional BCAA metabolism.
    DOI:  https://doi.org/10.1038/s42255-022-00689-4
  2. Nat Commun. 2022 Nov 28. 13(1): 7338
    Lysosomal damage drives mitochondrial proteome remodelling and reprograms macrophage immunometabolism.
    Claudio Bussi, Tiaan Heunis, Enrica Pellegrino, Elliott M Bernard, Nourdine Bah, Mariana Silva Dos Santos, Pierre Santucci, Beren Aylan, Angela Rodgers, Antony Fearns, Julia Mitschke, Christopher Moore, James I MacRae, Maria Greco, Thomas Reinheckel, Matthias Trost, Maximiliano G Gutierrez.
      Transient lysosomal damage after infection with cytosolic pathogens or silica crystals uptake results in protease leakage. Whether limited leakage of lysosomal contents into the cytosol affects the function of cytoplasmic organelles is unknown. Here, we show that sterile and non-sterile lysosomal damage triggers a cell death independent proteolytic remodelling of the mitochondrial proteome in macrophages. Mitochondrial metabolic reprogramming required leakage of lysosomal cathepsins and was independent of mitophagy, mitoproteases and proteasome degradation. In an in vivo mouse model of endomembrane damage, live lung macrophages that internalised crystals displayed impaired mitochondrial function. Single-cell RNA-sequencing revealed that lysosomal damage skewed metabolic and immune responses in alveolar macrophages subsets with increased lysosomal content. Functionally, drug modulation of macrophage metabolism impacted host responses to Mycobacterium tuberculosis infection in an endomembrane damage dependent way. This work uncovers an inter-organelle communication pathway, providing a general mechanism by which macrophages undergo mitochondrial metabolic reprograming after endomembrane damage.
    DOI:  https://doi.org/10.1038/s41467-022-34632-8
  3. Cell Death Differ. 2022 Nov 29.
    Mitochondria and cell death-associated inflammation.
    Esmee Vringer, Stephen W G Tait.
      Mitochondria have recently emerged as key drivers of inflammation associated with cell death. Many of the pro-inflammatory pathways activated during cell death occur upon mitochondrial outer membrane permeabilization (MOMP), the pivotal commitment point to cell death during mitochondrial apoptosis. Permeabilised mitochondria trigger inflammation, in part, through the release of mitochondrial-derived damage-associated molecular patterns (DAMPs). Caspases, while dispensable for cell death during mitochondrial apoptosis, inhibit activation of pro-inflammatory pathways after MOMP. Some of these mitochondrial-activated inflammatory pathways can be traced back to the bacterial ancestry of mitochondria. For instance, mtDNA and bacterial DNA are highly similar thereby activating similar cell autonomous immune signalling pathways. The bacterial origin of mitochondria suggests that inflammatory pathways found in cytosol-invading bacteria may be relevant to mitochondrial-driven inflammation after MOMP. In this review, we discuss how mitochondria can initiate inflammation during cell death highlighting parallels with bacterial activation of inflammation. Moreover, we discuss the roles of mitochondrial inflammation during cell death and how these processes may potentially be harnessed therapeutically, for instance to improve cancer treatment.
    DOI:  https://doi.org/10.1038/s41418-022-01094-w
  4. Nat Rev Endocrinol. 2022 Nov 29.
    Metabolic determinants of tumour initiation.
    Julia S Brunner, Lydia W S Finley.
      Tumours exhibit notable metabolic alterations compared with their corresponding normal tissue counterparts. These metabolic alterations can support anabolic growth, enable survival in hostile environments and regulate gene expression programmes that promote malignant progression. Whether these metabolic changes are selected for during malignant transformation or can themselves be drivers of tumour initiation is unclear. However, intriguingly, many of the major bottlenecks for tumour initiation - control of cell fate, survival and proliferation - are all amenable to metabolic regulation. In this article, we review evidence demonstrating a critical role for metabolic pathways in processes that support the earliest stages of tumour development. We discuss how cell-intrinsic factors, such as the cell of origin or transforming oncogene, and cell-extrinsic factors, such as local nutrient availability, promote or restrain tumour initiation. Deeper insight into how metabolic pathways control tumour initiation will improve our ability to design metabolic interventions to limit tumour incidence.
    DOI:  https://doi.org/10.1038/s41574-022-00773-5
  5. Trends Endocrinol Metab. 2022 Nov 23. pii: S1043-2760(22)00199-0. [Epub ahead of print]
    Mitochondrial copper in human genetic disorders.
    Natalie M Garza, Abhinav B Swaminathan, Krishna P Maremanda, Mohammad Zulkifli, Vishal M Gohil.
      Copper is an essential micronutrient that serves as a cofactor for enzymes involved in diverse physiological processes, including mitochondrial energy generation. Copper enters cells through a dedicated copper transporter and is distributed to intracellular cuproenzymes by copper chaperones. Mitochondria are critical copper-utilizing organelles that harbor an essential cuproenzyme cytochrome c oxidase, which powers energy production. Mutations in copper transporters and chaperones that perturb mitochondrial copper homeostasis result in fatal genetic disorders. Recent studies have uncovered the therapeutic potential of elesclomol, a copper ionophore, for the treatment of copper deficiency disorders such as Menkes disease. Here we review the role of copper in mitochondrial energy metabolism in the context of human diseases and highlight the recent developments in copper therapeutics.
    Keywords:  Menkes disease; Wilson disease; copper; elesclomol; mitochondria; mitochondrial disease
    DOI:  https://doi.org/10.1016/j.tem.2022.11.001
  6. J Biol Chem. 2022 Oct 28. pii: S0021-9258(22)01091-2. [Epub ahead of print]298(12): 102648
    Requirement of hepatic pyruvate carboxylase during fasting, high fat, and ketogenic diet.
    Ebru S Selen, Susana Rodriguez, Kyle S Cavagnini, Han-Byeol Kim, Chan Hyun Na, Michael J Wolfgang.
      Pyruvate has two major fates upon entry into mitochondria, the oxidative decarboxylation to acetyl-CoA via the pyruvate decarboxylase complex or the biotin-dependent carboxylation to oxaloacetate via pyruvate carboxylase (Pcx). Here, we have generated mice with a liver-specific KO of pyruvate carboxylase (PcxL-/-) to understand the role of Pcx in hepatic mitochondrial metabolism under disparate physiological states. PcxL-/- mice exhibited a deficit in hepatic gluconeogenesis and enhanced ketogenesis as expected but were able to maintain systemic euglycemia following a 24 h fast. Feeding a high-fat diet to PcxL-/- mice resulted in animals that were resistant to glucose intolerance without affecting body weight. However, we found that PcxL-/- mice fed a ketogenic diet for 1 week became severely hypoglycemic, demonstrating a requirement for hepatic Pcx for long-term glycemia under carbohydrate-limited diets. Additionally, we determined that loss of Pcx was associated with an induction in the abundance of lysine-acetylated proteins in PcxL-/- mice regardless of physiologic state. Furthermore, liver acetyl-proteomics revealed a biased induction in mitochondrial lysine-acetylated proteins. These data show that Pcx is important for maintaining the proper balance of pyruvate metabolism between oxidative and anaplerotic pathways.
    Keywords:  Pyruvate Carboxylase; acetylation; fasting; gluconeogenesis; mitochondria
    DOI:  https://doi.org/10.1016/j.jbc.2022.102648
  7. Cell Death Discov. 2022 Nov 26. 8(1): 465
    Extrinsic cell death pathway plasticity: a driver of clonal evolution in cancer?
    Eric Seidel, Silvia von Karstedt.
      Human cancers are known to adhere to basic evolutionary principles. During their journey from early transformation to metastatic disease, cancer cell populations have proven to be remarkably adaptive to different forms of intra- and extracellular selective pressure, including nutrient scarcity, oxidative stress, and anti-cancer immunity. Adaption may be achieved via the expansion of clones bearing driver mutations that optimize cellular fitness in response to the specific selective scenario, e.g., mutations facilitating evasion of cell death, immune evasion or increased proliferation despite growth suppression, all of which constitute well-established hallmarks of cancer. While great progress concerning the prevention, diagnosis and treatment of clinically apparent disease has been made over the last 50 years, the mechanisms underlying cellular adaption under selective pressure via the immune system during early carcinogenesis and its influence on cancer cell fate or disease severity remain to be clarified. For instance, evasion of cell death is generally accepted as a hallmark of cancer, yet recent decades have revealed that the extrinsic cell death machinery triggered by immune effector cells is composed of an astonishingly complex network of interacting-and sometimes compensating-modes of cell death, whose role in selective processes during early carcinogenesis remains obscure. Based upon recent advances in cell death research, here we propose a concept of cell death pathway plasticity in time shaping cancer evolution prior to treatment in an effort to offer new perspectives on how cancer cell fate may be determined by cell death pathway plasticity during early carcinogenesis.
    DOI:  https://doi.org/10.1038/s41420-022-01251-7
  8. Redox Biol. 2022 Nov 19. pii: S2213-2317(22)00305-6. [Epub ahead of print]58 102533
    Mitochondria-originated redox signalling regulates KLF-1 to promote longevity in Caenorhabditis elegans.
    Johannes Cw Hermeling, Marija Herholz, Linda Baumann, Estela Cepeda Cores, Aleksandra Zečić, Thorsten Hoppe, Jan Riemer, Aleksandra Trifunovic.
      Alternations of redox metabolism have been associated with the extension of lifespan in roundworm Caenorhabditis elegans, caused by moderate mitochondrial dysfunction, although the underlying signalling cascades are largely unknown. Previously, we identified transcriptional factor Krüppel-like factor-1 (KLF-1) as the main regulator of cytoprotective longevity-assurance pathways in the C. elegans long-lived mitochondrial mutants. Here, we show that KLF-1 translocation to the nucleus and the activation of the signalling cascade is dependent on the mitochondria-derived hydrogen peroxide (H2O2) produced during late developmental phases where aerobic respiration and somatic mitochondrial biogenesis peak. We further show that mitochondrial-inducible superoxide dismutase-3 (SOD-3), together with voltage-dependent anion channel-1 (VDAC-1), is required for the life-promoting H2O2 signalling that is further regulated by peroxiredoxin-3 (PRDX-3). Increased H2O2 release in the cytoplasm activates the p38 MAPK signalling cascade that induces KLF-1 translocation to the nucleus and the activation of transcription of C. elegans longevity-promoting genes, including cytoprotective cytochrome P450 oxidases. Taken together, our results underline the importance of redox-regulated signalling as the key regulator of longevity-inducing pathways in C. elegans, and position precisely timed mitochondria-derived H2O2 in the middle of it.
    DOI:  https://doi.org/10.1016/j.redox.2022.102533
  9. Development. 2022 Dec 01. pii: dev200870. [Epub ahead of print]149(23):
    Mitochondrial respiration and dynamics of in vivo neural stem cells.
    Stavroula Petridi, Dnyanesh Dubal, Richa Rikhy, Jelle van den Ameele.
      Neural stem cells (NSCs) in the developing and adult brain undergo many different transitions, tightly regulated by extrinsic and intrinsic factors. While the role of signalling pathways and transcription factors is well established, recent evidence has also highlighted mitochondria as central players in NSC behaviour and fate decisions. Many aspects of cellular metabolism and mitochondrial biology change during NSC transitions, interact with signalling pathways and affect the activity of chromatin-modifying enzymes. In this Spotlight, we explore recent in vivo findings, primarily from Drosophila and mammalian model systems, about the role that mitochondrial respiration and morphology play in NSC development and function.
    Keywords:  Mitochondria; Mitochondrial morphology; Neural stem cell; Notch; Oxidative phosphorylation; Reactive oxygen species
    DOI:  https://doi.org/10.1242/dev.200870
  10. Cell Death Differ. 2022 Nov 29.
    Elevated FSP1 protects KRAS-mutated cells from ferroptosis during tumor initiation.
    Fabienne Müller, Jonathan K M Lim, Christina M Bebber, Eric Seidel, Sofya Tishina, Alina Dahlhaus, Jenny Stroh, Julia Beck, Fatma Isil Yapici, Keiko Nakayama, Lucia Torres Fernández, Johannes Brägelmann, Gabriel Leprivier, Silvia von Karstedt.
      Oncogenic KRAS is the key driver oncogene for several of the most aggressive human cancers. One key feature of oncogenic KRAS expression is an early increase in cellular reactive oxygen species (ROS) which promotes cellular transformation if cells manage to escape cell death, mechanisms of which remain incompletely understood. Here, we identify that expression of oncogenic as compared to WT KRAS in isogenic cellular systems renders cells more resistant to ferroptosis, a recently described type of regulated necrosis. Mechanistically, we find that cells with mutant KRAS show a specific lack of ferroptosis-induced lipid peroxidation. Interestingly, KRAS-mutant cells upregulate expression of ferroptosis suppressor protein 1 (FSP1). Indeed, elevated levels of FSP1 in KRAS-mutant cells are responsible for mediating ferroptosis resistance and FSP1 is upregulated as a consequence of MAPK and NRF2 pathway activation downstream of KRAS. Strikingly, FSP1 activity promotes cellular transformation in soft agar and its overexpression is sufficient to promote spheroid growth in 3D in KRAS WT cells. Moreover, FSP1 expression and its activity in ferroptosis inhibition accelerates tumor onset of KRAS WT cells in the absence of oncogenic KRAS in vivo. Consequently, we find that pharmacological induction of ferroptosis in pancreatic organoids derived from the LsL-KRASG12D expressing mouse model is only effective in combination with FSP1 inhibition. Lastly, FSP1 is upregulated in non-small cell lung cancer (NSCLC), colorectal cancer (CRC) and pancreatic ductal adenocarcinoma (PDAC) as compared to the respective normal tissue of origin and correlates with NRF2 expression in PDAC patient datasets. Based on these data, we propose that KRAS-mutant cells must navigate a ferroptosis checkpoint by upregulating FSP1 during tumor establishment. Consequently, ferroptosis-inducing therapy should be combined with FSP1 inhibitors for efficient therapy of KRAS-mutant cancers.
    DOI:  https://doi.org/10.1038/s41418-022-01096-8
  11. Nat Commun. 2022 Dec 01. 13(1): 7400
    PPM1D suppresses p53-dependent transactivation and cell death by inhibiting the Integrated Stress Response.
    Zdenek Andrysik, Kelly D Sullivan, Jeffrey S Kieft, Joaquin M Espinosa.
      The p53 transcription factor is a master regulator of cellular stress responses inhibited by repressors such as MDM2 and the phosphatase PPM1D. Activation of p53 with pharmacological inhibitors of its repressors is being tested in clinical trials for cancer therapy, but efficacy has been limited by poor induction of tumor cell death. We demonstrate that dual inhibition of MDM2 and PPM1D induces apoptosis in multiple cancer cell types via amplification of the p53 transcriptional program through the eIF2α-ATF4 pathway. PPM1D inhibition induces phosphorylation of eIF2α, ATF4 accumulation, and ATF4-dependent enhancement of p53-dependent transactivation upon MDM2 inhibition. Dual inhibition of p53 repressors depletes heme and induces HRI-dependent eIF2α phosphorylation. Pharmacological induction of eIF2α phosphorylation synergizes with MDM2 inhibition to induce cell death and halt tumor growth in mice. These results demonstrate that PPM1D inhibits both the p53 network and the integrated stress response controlled by eIF2α-ATF4, with clear therapeutic implications.
    DOI:  https://doi.org/10.1038/s41467-022-35089-5
  12. Front Cell Dev Biol. 2022 ;10 1049653
    Nicotinamide riboside kinases regulate skeletal muscle fiber-type specification and are rate-limiting for metabolic adaptations during regeneration.
    Tanja Sonntag, Sara Ancel, Sonia Karaz, Paulina Cichosz, Guillaume Jacot, Maria Pilar Giner, José Luis Sanchez-Garcia, Alice Pannérec, Sofia Moco, Vincenzo Sorrentino, Carles Cantó, Jérôme N Feige.
      Nicotinamide riboside kinases (NRKs) control the conversion of dietary Nicotinamide Riboside (NR) to NAD+, but little is known about their contribution to endogenous NAD+ turnover and muscle plasticity during skeletal muscle growth and remodeling. Using NRK1/2 double KO (NRKdKO) mice, we investigated the influence of NRKs on NAD+ metabolism and muscle homeostasis, and on the response to neurogenic muscle atrophy and regeneration following muscle injury. Muscles from NRKdKO animals have altered nicotinamide (NAM) salvage and a decrease in mitochondrial content. In single myonuclei RNAseq of skeletal muscle, NRK2 mRNA expression is restricted to type IIx muscle fibers, and perturbed NAD+ turnover and mitochondrial metabolism shifts the fiber type composition of NRKdKO muscle to fast glycolytic IIB fibers. NRKdKO does not influence muscle atrophy during denervation but alters muscle repair after myofiber injury. During regeneration, muscle stem cells (MuSCs) from NRKdKO animals hyper-proliferate but fail to differentiate. NRKdKO also alters the recovery of NAD+ during muscle regeneration as well as mitochondrial adaptations and extracellular matrix remodeling required for tissue repair. These metabolic perturbations result in a transient delay of muscle regeneration which normalizes during myofiber maturation at late stages of regeneration via over-compensation of anabolic IGF1-Akt signaling. Altogether, we demonstrate that NAD+ synthesis controls mitochondrial metabolism and fiber type composition via NRK1/2 and is rate-limiting for myogenic commitment and mitochondrial maturation during skeletal muscle repair.
    Keywords:  NAD+; NRK; fiber type; mitochondria; muscle regeneration; muscle stem cell (satellite cell); nicotinamide riboside; skeletal muscle
    DOI:  https://doi.org/10.3389/fcell.2022.1049653
  13. PLoS Biol. 2022 Dec 01. 20(12): e3001912
    Inorganic sulfur fixation via a new homocysteine synthase allows yeast cells to cooperatively compensate for methionine auxotrophy.
    Jason S L Yu, Benjamin M Heineike, Johannes Hartl, Simran K Aulakh, Clara Correia-Melo, Andrea Lehmann, Oliver Lemke, Federica Agostini, Cory T Lee, Vadim Demichev, Christoph B Messner, Michael Mülleder, Markus Ralser.
      The assimilation, incorporation, and metabolism of sulfur is a fundamental process across all domains of life, yet how cells deal with varying sulfur availability is not well understood. We studied an unresolved conundrum of sulfur fixation in yeast, in which organosulfur auxotrophy caused by deletion of the homocysteine synthase Met17p is overcome when cells are inoculated at high cell density. In combining the use of self-establishing metabolically cooperating (SeMeCo) communities with proteomic, genetic, and biochemical approaches, we discovered an uncharacterized gene product YLL058Wp, herein named Hydrogen Sulfide Utilizing-1 (HSU1). Hsu1p acts as a homocysteine synthase and allows the cells to substitute for Met17p by reassimilating hydrosulfide ions leaked from met17Δ cells into O-acetyl-homoserine and forming homocysteine. Our results show that cells can cooperate to achieve sulfur fixation, indicating that the collective properties of microbial communities facilitate their basic metabolic capacity to overcome sulfur limitation.
    DOI:  https://doi.org/10.1371/journal.pbio.3001912
  14. Cell Regen. 2022 Dec 01. 11(1): 38
    Mitochondrial fragmentation and ROS signaling in wound response and repair.
    Shiqi Xu, Shiyao Li, Mikael Bjorklund, Suhong Xu.
      Mitochondria are organelles that serve numerous critical cellular functions, including energy production, Ca2+ homeostasis, redox signaling, and metabolism. These functions are intimately linked to mitochondrial morphology, which is highly dynamic and capable of rapid and transient changes to alter cellular functions in response to environmental cues and cellular demands. Mitochondrial morphology and activity are critical for various physiological processes, including wound healing. In mammals, wound healing is a complex process that requires coordinated function of multiple cell types and progresses in partially overlapping but distinct stages: hemostasis and inflammation, cell proliferation and migration, and tissue remodeling. The repair process at the single-cell level forms the basis for wound healing and regeneration in tissues. Recent findings reveal that mitochondria fulfill the intensive energy demand for wound repair and aid wound closure by cytoskeleton remodeling via morphological changes and mitochondrial reactive oxygen species (mtROS) signaling. In this review, we will mainly elucidate how wounding induces changes in mitochondrial morphology and activity and how these changes, in turn, contribute to cellular wound response and repair.
    Keywords:  FZO-1; MFN-1/2; MIRO-1; Membrane repair; Mitochondrial dynamic; Mitochondrial fragmentation; Plasma membrane; Reactive oxygen species
    DOI:  https://doi.org/10.1186/s13619-022-00141-8
  15. Plant Physiol. 2022 Nov 28. pii: kiac541. [Epub ahead of print]
    Mitochondria in photosynthetic cells: Coordinating redox control and energy balance.
    Abir U Igamberdiev, Natalia V Bykova.
      In photosynthetic tissues in the light, the function of energy production is associated primarily with chloroplasts, while mitochondrial metabolism adjusts to balance ATP supply, regulate the reduction level of pyridine nucleotides, and optimize major metabolic fluxes. The tricarboxylic acid cycle in the light transforms into a non-cyclic open structure (hemicycle) maintained primarily by influx of malate and export of citrate to the cytosol. The exchange of malate and citrate forms the basis of feeding redox energy from the chloroplast into the cytosolic pathways. This supports the level of NADPH in different compartments, contributes to the biosynthesis of amino acids, and drives secondary metabolism via the supply of substrates for 2-oxoglutarate dioxygenase and for cytochrome P450-catalyzed monooxygenase reactions. This results in the maintenance of redox and energy balance in photosynthetic plant cells and in the formation of numerous bioactive compounds specific for any particular plant species. The non-coupled mitochondrial respiration operates in coordination with the malate and citrate valves and supports intensive fluxes of respiration and photorespiration. The metabolic system of plants has features associated with remarkable metabolic plasticity of mitochondria that permit the use of energy accumulated in photosynthesis in a way that all anabolic and catabolic pathways become optimized and coordinated.
    Keywords:  2-oxoglutarate dioxygenases; TCA cycle; citrate valve; cytochrome P450; malate valve; photorespiration; plant mitochondria; respiration in the light
    DOI:  https://doi.org/10.1093/plphys/kiac541
  16. Crit Rev Oncol Hematol. 2022 Nov 25. pii: S1040-8428(22)00311-0. [Epub ahead of print] 103887
    Ferroptosis induction via targeting metabolic alterations in head and neck cancer.
    Jaewang Lee, Jong-Lyel Roh.
      Ferroptosis is a newly regulated cell death induced by the accumulation of iron-mediated lipid peroxidation. The alteration of cancer metabolism may contribute to proliferation, metastasis, and treatment resistance in human cancers, implicating the sensitivity to ferroptosis induction. Altered metabolism in cancer cells regulates oxidative stresses and changes metabolism intermediates, contributing to their deregulated growth and proliferation. Cancer metabolic changes toward the elevation of cellular free iron and polyunsaturated fatty acids sensitize cancer cells to lipid peroxidation toxicity tightly linked to ferroptosis. The altered metabolism in cancers can be served as a promising target to reverse cancer therapeutic resistance by ferroptosis induction to selectively kill cancer cells while sparing normal cells. The role of mitochondria and lipid metabolism in inducing ferroptosis in head and neck cancer (HNC) has been elucidated in previous studies. Ferroptosis is receiving attention in cancer research as treating cancers altering cellular metabolism and refractory from conventional therapies. More in-depth studies are needed to develop highly therapeutic drugs and practical methods to induce ferroptosis in diverse cancer cells and tumor microenvironments effectively. Therefore, this review intends to understand the altered metabolism and find new therapeutic possibilities using ferroptosis in HNC.
    Keywords:  Metabolism; ferroptosis; head and neck cancer; lipid peroxidation; mitochondria
    DOI:  https://doi.org/10.1016/j.critrevonc.2022.103887
  17. Sci Adv. 2022 Dec 02. 8(48): eadc9657
    Phosphofructokinase P fine-tunes T regulatory cell metabolism, function, and stability in systemic autoimmunity.
    Marc Scherlinger, Wenliang Pan, Ryo Hisada, Afroditi Boulougoura, Nobuya Yoshida, Milena Vukelic, Masataka Umeda, Suzanne Krishfield, Maria G Tsokos, George C Tsokos.
      Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by defective regulatory T (Treg) cells. Here, we demonstrate that a T cell-specific deletion of calcium/calmodulin-dependent protein kinase 4 (CaMK4) improves disease in B6.lpr lupus-prone mice and expands Treg cells. Mechanistically, CaMK4 phosphorylates the glycolysis rate-limiting enzyme 6-phosphofructokinase, platelet type (PFKP) and promotes aerobic glycolysis, while its end product fructose-1,6-biphosphate suppresses oxidative metabolism. In Treg cells, a CRISPR-Cas9-enabled Pfkp deletion recapitulated the metabolism of Camk4-/- Treg cells and improved their function and stability in vitro and in vivo. In SLE CD4+ T cells, PFKP enzymatic activity correlated with SLE disease activity and pharmacologic inhibition of CaMK4-normalized PFKP activity, leading to enhanced Treg cell function. In conclusion, we provide molecular insights in the defective metabolism and function of Treg cells in SLE and identify PFKP as a target to fine-tune Treg cell metabolism and thereby restore their function.
    DOI:  https://doi.org/10.1126/sciadv.adc9657
  18. iScience. 2022 Dec 22. 25(12): 105610
    Mutation accumulation in mtDNA of cancers resembles mutagenesis in normal stem cells.
    Freek Manders, Jip van Dinter, Ruben van Boxtel.
      Mitochondria are small organelles that play an essential role in the energy production of eukaryotic cells. Defects in their genomes are associated with diseases, such as aging and cancer. Here, we analyzed the mitochondrial genomes of 532 whole-genome sequencing samples from cancers and normal clonally expanded single cells. We show that the mitochondria of normal cells accumulate mutations with age and that most of the mitochondrial mutations found in cancer are the result of healthy mutation accumulation. We also show that the normal HSPCs of patients with leukemia have an increased mitochondrial mutation load. Finally, we show that secondary pediatric cancers and chemotherapy treatments do not impact the mitochondrial mutation load and mtDNA copy numbers of most cells, suggesting that damage to the mitochondrial genome is not a major driver for carcinogenesis. Overall, these findings may contribute to our understanding of mitochondrial genomes and their role in cancer.
    Keywords:  Cancer; Genomics; Stem cells research
    DOI:  https://doi.org/10.1016/j.isci.2022.105610
  19. Cell Rep. 2022 Nov 29. pii: S2211-1247(22)01622-9. [Epub ahead of print]41(9): 111744
    Inhibition of glutaminolysis restores mitochondrial function in senescent stem cells.
    Debanik Choudhury, Na Rong, Izuagie Ikhapoh, Nika Rajabian, Georgios Tseropoulos, Yulun Wu, Pihu Mehrotra, Ramkumar Thiyagarajan, Aref Shahini, Kenneth L Seldeen, Bruce R Troen, Pedro Lei, Stelios T Andreadis.
      Mitochondrial dysfunction, a hallmark of aging, has been associated with the onset of aging phenotypes and age-related diseases. Here, we report that impaired mitochondrial function is associated with increased glutamine catabolism in senescent human mesenchymal stem cells (MSCs) and myofibroblasts derived from patients suffering from Hutchinson-Gilford progeria syndrome. Increased glutaminase (GLS1) activity accompanied by loss of urea transporter SLC14A1 induces urea accumulation, mitochondrial dysfunction, and DNA damage. Conversely, blocking GLS1 activity restores mitochondrial function and leads to amelioration of aging hallmarks. Interestingly, GLS1 expression is regulated through the JNK pathway, as demonstrated by chemical and genetic inhibition. In agreement with our in vitro findings, tissues isolated from aged or progeria mice display increased urea accumulation and GLS1 activity, concomitant with declined mitochondrial function. Inhibition of glutaminolysis in progeria mice improves mitochondrial respiratory chain activity, suggesting that targeting glutaminolysis may be a promising strategy for restoring age-associated loss of mitochondrial function.
    Keywords:  CP: Cell biology; GLS1; Hutchinson-Gilford progeria syndrome; JNK; SLC14A1; aging; glutamine; mitochondria; senescence; urea
    DOI:  https://doi.org/10.1016/j.celrep.2022.111744
  20. Nat Metab. 2022 Nov 28.
    BCAT2-BCKDH metabolon maintains BCAA homeostasis.
    Miao Yin, Qun-Ying Lei.
      
    DOI:  https://doi.org/10.1038/s42255-022-00680-z
  21. EMBO J. 2022 Nov 29. e111389
    The lysosomal Ragulator complex activates NLRP3 inflammasome in vivo via HDAC6.
    Kohei Tsujimoto, Tatsunori Jo, Daiki Nagira, Hachiro Konaka, Jeong Hoon Park, Shin-Ichiro Yoshimura, Akinori Ninomiya, Fuminori Sugihara, Takehiro Hirayama, Eri Itotagawa, Yusei Matsuzaki, Yuki Takaichi, Wataru Aoki, Shotaro Saita, Shuhei Nakamura, Andrea Ballabio, Shigeyuki Nada, Masato Okada, Hyota Takamatsu, Atsushi Kumanogoh.
      The cellular activation of the NLRP3 inflammasome is spatiotemporally orchestrated by various organelles, but whether lysosomes contribute to this process remains unclear. Here, we show the vital role of the lysosomal membrane-tethered Ragulator complex in NLRP3 inflammasome activation. Deficiency of Lamtor1, an essential component of the Ragulator complex, abrogated NLRP3 inflammasome activation in murine macrophages and human monocytic cells. Myeloid-specific Lamtor1-deficient mice showed marked attenuation of NLRP3-associated inflammatory disease severity, including LPS-induced sepsis, alum-induced peritonitis, and monosodium urate (MSU)-induced arthritis. Mechanistically, Lamtor1 interacted with both NLRP3 and histone deacetylase 6 (HDAC6). HDAC6 enhances the interaction between Lamtor1 and NLRP3, resulting in NLRP3 inflammasome activation. DL-all-rac-α-tocopherol, a synthetic form of vitamin E, inhibited the Lamtor1-HDAC6 interaction, resulting in diminished NLRP3 inflammasome activation. Further, DL-all-rac-α-tocopherol alleviated acute gouty arthritis and MSU-induced peritonitis. These results provide novel insights into the role of lysosomes in the activation of NLRP3 inflammasomes by the Ragulator complex.
    Keywords:  HDAC6; NLRP3 inflammasome; Ragulator complex; α-tocopherol
    DOI:  https://doi.org/10.15252/embj.2022111389
  22. Sci Signal. 2022 Nov 29. 15(762): eabo7940
    VPS34-dependent control of apical membrane function of proximal tubule cells and nutrient recovery by the kidney.
    Markus M Rinschen, Jennifer L Harder, Madalina E Carter-Timofte, Luis Zanon Rodriguez, Carmen Mirabelli, Fatih Demir, Naziia Kurmasheva, Suresh K Ramakrishnan, Madlen Kunke, Yifan Tan, Anja Billing, Eileen Dahlke, Alexey A Larionov, Wibke Bechtel-Walz, Ute Aukschun, Marlen Grabbe, Rikke Nielsen, Erik I Christensen, Matthias Kretzler, Tobias B Huber, Christiane E Wobus, David Olagnier, Gary Siuzdak, Florian Grahammer, Franziska Theilig.
      The lipid kinase VPS34 orchestrates autophagy, endocytosis, and metabolism and is implicated in cancer and metabolic disease. The proximal tubule in the kidney is a key metabolic organ that controls reabsorption of nutrients such as fatty acids, amino acids, sugars, and proteins. Here, by combining metabolomics, proteomics, and phosphoproteomics analyses with functional and superresolution imaging assays of mice with an inducible deficiency in proximal tubular cells, we revealed that VPS34 controlled the metabolome of the proximal tubule. In addition to inhibiting pinocytosis and autophagy, VPS34 depletion induced membrane exocytosis and reduced the abundance of the retromer complex necessary for proper membrane recycling and lipid retention, leading to a loss of fuel and biomass. Integration of omics data into a kidney cell metabolomic model demonstrated that VPS34 deficiency increased β-oxidation, reduced gluconeogenesis, and enhanced the use of glutamine for energy consumption. Furthermore, the omics datasets revealed that VPS34 depletion triggered an antiviral response that included a decrease in the abundance of apically localized virus receptors such as ACE2. VPS34 inhibition abrogated SARS-CoV-2 infection in human kidney organoids and cultured proximal tubule cells in a glutamine-dependent manner. Thus, our results demonstrate that VPS34 adjusts endocytosis, nutrient transport, autophagy, and antiviral responses in proximal tubule cells in the kidney.
    DOI:  https://doi.org/10.1126/scisignal.abo7940
  23. J Neurosci Res. 2022 Dec 03.
    Emerging mitochondrial-mediated mechanisms involved in oligodendrocyte development.
    Melanie Gil, Vivian Gama.
      Oligodendrocytes are the myelinating glia of the central nervous system and are generated after oligodendrocyte progenitor cells (OPCs) transition into pre-oligodendrocytes and then into myelinating oligodendrocytes. Myelin is essential for proper signal transmission within the nervous system and axonal metabolic support. Although the intrinsic and extrinsic factors that support the differentiation, survival, integration, and subsequent myelination of appropriate axons have been well investigated, little is known about how mitochondria-related pathways such as mitochondrial dynamics, bioenergetics, and apoptosis finely tune these developmental events. Previous findings suggest that changes to mitochondrial morphology act as an upstream regulatory mechanism of neural stem cell (NSC) fate decisions. Whether a similar mechanism is engaged during OPC differentiation has yet to be elucidated. Maintenance of mitochondrial dynamics is vital for regulating cellular bioenergetics, functional mitochondrial networks, and the ability of cells to distribute mitochondria to subcellular locations, such as the growing processes of oligodendrocytes. Myelination is an energy-consuming event, thus, understanding the interplay between mitochondrial dynamics, metabolism, and apoptosis will provide further insight into mechanisms that mediate oligodendrocyte development in healthy and disease states. Here we will provide a concise overview of oligodendrocyte development and discuss the potential contribution of mitochondrial mitochondrial-mediated mechanisms to oligodendrocyte bioenergetics and development.
    Keywords:  astrocytes; glia; glycolysis; mitochondria; neural precursor cells; neurons; oligodendrocytes; oxidative phosphorylation
    DOI:  https://doi.org/10.1002/jnr.25151
  24. Redox Biol. 2022 Nov 23. pii: S2213-2317(22)00325-1. [Epub ahead of print]58 102553
    The signaling pathways and therapeutic potential of itaconate to alleviate inflammation and oxidative stress in inflammatory diseases.
    Xuan Shi, Huanping Zhou, Juan Wei, Wei Mo, Quanfu Li, Xin Lv.
      Endogenous small molecules are metabolic regulators of cell function. Itaconate is a key molecule that accumulates in cells when the Krebs cycle is disrupted. Itaconate is derived from cis-aconitate decarboxylation by cis-aconitate decarboxylase (ACOD1) in the mitochondrial matrix and is also known as immune-responsive gene 1 (IRG1). Studies have demonstrated that itaconate plays an important role in regulating signal transduction and posttranslational modification through its immunoregulatory activities. Itaconate is also an important bridge among metabolism, inflammation, oxidative stress, and the immune response. This review summarizes the structural characteristics and classical pathways of itaconate, its derivatives, and the compounds that release itaconate. Here, the mechanisms of itaconate action, including its transcriptional regulation of ATF3/IκBζ axis and type I IFN, its protein modification regulation of KEAP1, inflammasome, JAK1/STAT6 pathway, TET2, and TFEB, and succinate dehydrogenase and glycolytic enzyme metabolic action, are presented. Moreover, the roles of itaconate in diseases related to inflammation and oxidative stress induced by autoimmune responses, viruses, sepsis and IRI are discussed in this review. We hope that the information provided in this review will help increase the understanding of cellular immune metabolism and improve the clinical treatment of diseases related to inflammation and oxidative stress.
    Keywords:  Antioxidant therapeutics; COVID-19; IRG1; Inflammation; Itaconate; Metabolism
    DOI:  https://doi.org/10.1016/j.redox.2022.102553
  25. PLoS One. 2022 ;17(12): e0278108
    Kidney tumors associated with germline mutations of FH and SDHB show a CpG island methylator phenotype (CIMP).
    Christopher J Ricketts, J Keith Killian, Cathy D Vocke, Yonghong Wang, Maria J Merino, Paul S Meltzer, W Marston Linehan.
      Germline mutations within the Krebs cycle enzyme genes fumarate hydratase (FH) or succinate dehydrogenase (SDHB, SDHC, SDHD) are associated with an increased risk of aggressive and early metastasizing variants of renal cell carcinoma (RCC). These RCCs express significantly increased levels of intracellular fumarate or succinate that inhibit 2-oxoglutarate-dependent dioxygenases, such as the TET enzymes that regulate DNA methylation. This study evaluated the genome-wide methylation profiles of 34 RCCs from patients with RCC susceptibility syndromes and 11 associated normal samples using the Illumina HumanMethylation450 BeadChip. All the HLRCC (FH mutated) and SDHB-RCC (SDHB mutated) tumors demonstrated a distinct CpG island methylator phenotype (CIMP). HLRCC tumors demonstrated an extensive and relatively uniform level of hypermethylation that showed some correlation with tumor size. SDHB-RCC demonstrated a lesser and more varied pattern of hypermethylation that overlapped in part with the HLRCC hypermethylation. Combined methylation and mRNA expression analysis of the HLRCC tumors demonstrated hypermethylation and transcription downregulation of genes associated with the HIF pathway, HIF3A and CITED4, the WNT pathway, SFRP1, and epithelial-to-mesenchymal transition and MYC expression, OVOL1. These observations were confirmed in the TCGA CIMP-RCC tumors. A selected panel of probes could identify the CIMP tumors and differentiate between HLRCC and SDHB-RCC tumors. This panel accurately detected all CIMP-RCC tumors within the TCGA RCC cohort, identifying them as HLRCC -like, and could potentially be used to create a liquid biopsy-based screening tool. The CIMP signature in these aggressive tumors could provide both a useful biomarker for diagnosis and a target for novel therapies.
    DOI:  https://doi.org/10.1371/journal.pone.0278108
  26. Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2212220119
    Acetyl-CoA-mediated autoacetylation of fatty acid synthase as a metabolic switch of de novo lipogenesis in Drosophila.
    Ting Miao, Jinoh Kim, Ping Kang, Hideji Fujiwara, Fong-Fu Hsu, Hua Bai.
      De novo lipogenesis is a highly regulated metabolic process, which is known to be activated through transcriptional regulation of lipogenic genes, including fatty acid synthase (FASN). Unexpectedly, we find that the expression of FASN protein remains unchanged during Drosophila larval development from the second to the third instar larval stages (L2 to L3) when lipogenesis is hyperactive. Instead, acetylation of FASN is significantly upregulated in fast-growing larvae. We further show that lysine K813 residue is highly acetylated in developing larvae, and its acetylation is required for elevated FASN activity, body fat accumulation, and normal development. Intriguingly, K813 is autoacetylated by acetyl-CoA (AcCoA) in a dosage-dependent manner independent of acetyltransferases. Mechanistically, the autoacetylation of K813 is mediated by a novel P-loop-like motif (N-xx-G-x-A). Lastly, we find that K813 is deacetylated by Sirt1, which brings FASN activity to baseline level. In summary, this work uncovers a previously unappreciated role of FASN acetylation in developmental lipogenesis and a novel mechanism for protein autoacetylation, through which Drosophila larvae control metabolic homeostasis by linking AcCoA, lysine acetylation, and de novo lipogenesis.
    Keywords:  FASN; acetyl-CoA; animal development; autoacetylation; de novo lipogenesis
    DOI:  https://doi.org/10.1073/pnas.2212220119
  27. FEBS J. 2022 Dec 01.
    Pyruvate dehydrogenase phosphatase 1 (PDP1) stimulates HIF activity by supporting histone acetylation under hypoxia.
    Angeliki Karagiota, Amalia Kanoura, Efrosyni Paraskeva, George Simos, Georgia Chachami.
      Cancer cells, when exposed to the hypoxic tumor microenvironment, respond by activating hypoxia-inducible factors (HIFs). HIF-1 mediates extensive metabolic re-programming, and expression of HIF-1α, its oxygen-regulated subunit, is associated with poor prognosis in cancer. Here we analyze the role of pyruvate dehydrogenase phosphatase 1 (PDP1) in the regulation of HIF-1 activity. PDP1 is a key hormone-regulated metabolic enzyme that dephosphorylates and activates pyruvate dehydrogenase (PDH), thereby stimulating conversion of pyruvate into acetyl-CoA. Silencing of PDP1 down-regulated HIF transcriptional activity and the expression of HIF-dependent genes, including that of PDK1, the kinase that phosphorylates and inactivates PDH, opposing the effects of PDP1. Inversely, PDP1 stimulation enhanced HIF activity under hypoxia. Alteration of PDP1 levels or activity did not have an effect on HIF-1α protein levels, nuclear accumulation or interaction with its partners ARNT and NPM1. However, depletion of PDP-1 decreased histone H3 acetylation of HIF-1 target gene promoters and inhibited binding of HIF-1 to the respective hypoxia-response elements (HREs) under hypoxia. Furthermore, the decrease of HIF transcriptional activity upon PDP1 depletion could be reversed by treating the cells with acetate, as an exogenous source of acetyl-CoA, or the histone deacetylase (HDAC) inhibitor trichostatin A. These data suggest that the PDP1/PDH/HIF-1/PDK1 axis is part of a homeostatic loop which, under hypoxia, preserves cellular acetyl-CoA production to a level sufficient to sustain chromatin acetylation and transcription of hypoxia-inducible genes.
    Keywords:  HIF-1α; PDP1; acetyl-CoA; histone acetylation; hypoxia; pyruvate dehydrogenase phosphatase 1
    DOI:  https://doi.org/10.1111/febs.16694
  28. Cell Rep. 2022 Nov 29. pii: S2211-1247(22)01608-4. [Epub ahead of print]41(9): 111730
    Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription.
    Isabel N Goronzy, Sofia A Quinodoz, Joanna W Jachowicz, Noah Ollikainen, Prashant Bhat, Mitchell Guttman.
      Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA & DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments-with multiple active genes simultaneously colocalizing within the same B compartment-and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription.
    Keywords:  AB compartments; CP: Molecular biology; RNA polymerase II transcription; nuclear structure; nucleolus
    DOI:  https://doi.org/10.1016/j.celrep.2022.111730
  29. J Am Coll Cardiol. 2022 Dec 06. pii: S0735-1097(22)07044-9. [Epub ahead of print]80(23): 2220-2223
    Targeting Mitochondrial Calcium Handling to Treat Atrial Fibrillation.
    Niels Voigt, Christoph Maack, Julius Ryan D Pronto.
      
    Keywords:  atrial arrhythmias; atrial fibrillation; calcium; diabetic cardiomyopathy; metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.jacc.2022.09.043
  30. Trends Cell Biol. 2022 Nov 24. pii: S0962-8924(22)00252-5. [Epub ahead of print]
    Cellular functions of cGAS-STING signaling.
    Chen Chen, Pinglong Xu.
      Cyclic GMP-AMP (cGAMP) synthase (cGAS) senses misplaced genomic, mitochondrial, and microbial double-stranded DNA (dsDNA) to synthesize 2'3'-cGAMP that mobilizes stimulator of interferon genes (STING) to unleash innate immune responses, constituting a ubiquitous and effective surveillance system against tissue damage and pathogen invasion. However, imbalanced cGAS-STING signaling tethers considerably in infectious, autoimmune, malignant, fibrotic, and neurodegenerative diseases. Recently, multifaceted roles for cGAS-STING signaling at the cellular scale have emerged; these include autophagy, translation, metabolism homeostasis, cellular condensation, DNA damage repair, senescence, and cell death. These dominances adaptively shape cellular physiologies and impact disease pathogenesis. However, understanding how DNA sensing-initiated responses trigger these diverse cellular processes remains an outstanding challenge. In this review we discuss recent developments of cellular physiological states controlled by cGAS-STING machinery, as well as their disease relevance and underlying mechanisms, canonical or noncanonical. Ultimately, exploiting these cellular functions and mechanisms may represent promising targets for disease therapeutics.
    Keywords:  autophagy; cGAMP; cGAS-STING; condensation; innate immunity; metabolism; organelle; pathogenesis; senescence; translation
    DOI:  https://doi.org/10.1016/j.tcb.2022.11.001
  31. Nat Commun. 2022 Nov 29. 13(1): 7356
    Genetically personalised organ-specific metabolic models in health and disease.
    Carles Foguet, Yu Xu, Scott C Ritchie, Samuel A Lambert, Elodie Persyn, Artika P Nath, Emma E Davenport, David J Roberts, Dirk S Paul, Emanuele Di Angelantonio, John Danesh, Adam S Butterworth, Christopher Yau, Michael Inouye.
      Understanding how genetic variants influence disease risk and complex traits (variant-to-function) is one of the major challenges in human genetics. Here we present a model-driven framework to leverage human genome-scale metabolic networks to define how genetic variants affect biochemical reaction fluxes across major human tissues, including skeletal muscle, adipose, liver, brain and heart. As proof of concept, we build personalised organ-specific metabolic flux models for 524,615 individuals of the INTERVAL and UK Biobank cohorts and perform a fluxome-wide association study (FWAS) to identify 4312 associations between personalised flux values and the concentration of metabolites in blood. Furthermore, we apply FWAS to identify 92 metabolic fluxes associated with the risk of developing coronary artery disease, many of which are linked to processes previously described to play in role in the disease. Our work demonstrates that genetically personalised metabolic models can elucidate the downstream effects of genetic variants on biochemical reactions involved in common human diseases.
    DOI:  https://doi.org/10.1038/s41467-022-35017-7
  32. Adv Sci (Weinh). 2022 Nov 29. e2203718
    STING Suppresses Mitochondrial VDAC2 to Govern RCC Growth Independent of Innate Immunity.
    Zhichuan Zhu, Xin Zhou, Hongwei Du, Erica W Cloer, Jiaming Zhang, Liu Mei, Ying Wang, Xianming Tan, Austin J Hepperla, Jeremy M Simon, Jeanette Gowen Cook, Michael B Major, Gianpietro Dotti, Pengda Liu.
      STING is an innate immune sensor for immune surveillance of viral/bacterial infection and maintenance of an immune-friendly microenvironment to prevent tumorigenesis. However, if and how STING exerts innate immunity-independent function remains elusive. Here, the authors report that STING expression is increased in renal cell carcinoma (RCC) patients and governs tumor growth through non-canonical innate immune signaling involving mitochondrial ROS maintenance and calcium homeostasis. Mitochondrial voltage-dependent anion channel VDAC2 is identified as a new STING binding partner. STING depletion potentiates VDAC2/GRP75-mediated MERC (mitochondria-ER contact) formation to increase mitochondrial ROS/calcium levels, impairs mitochondria function, and suppresses mTORC1/S6K signaling leading to RCC growth retardation. STING interaction with VDAC2 occurs through STING-C88/C91 palmitoylation and inhibiting STING palmitoyl-transferases ZDHHCs by 2-BP significantly impedes RCC cell growth alone or in combination with sorafenib. Together, these studies reveal an innate immunity-independent function of STING in regulating mitochondrial function and growth in RCC, providing a rationale to target the STING/VDAC2 interaction in treating RCC.
    Keywords:  2-BP; STING; VDAC2; innate immunity-independent; mTORC1; mitochondrial homeostasis
    DOI:  https://doi.org/10.1002/advs.202203718
  33. Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2122073119
    Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.
    Ferdinando Insalata, Hanne Hoitzing, Juvid Aryaman, Nick S Jones.
      The expansion of mitochondrial DNA molecules with deletions has been associated with aging, particularly in skeletal muscle fibers; its mechanism has remained unclear for three decades. Previous accounts have assigned a replicative advantage (RA) to mitochondrial DNA containing deletion mutations, but there is also evidence that cells can selectively remove defective mitochondrial DNA. Here we present a spatial model that, without an RA, but instead through a combination of enhanced density for mutants and noise, produces a wave of expanding mutations with speeds consistent with experimental data. A standard model based on RA yields waves that are too fast. We provide a formula that predicts that wave speed drops with copy number, consonant with experimental data. Crucially, our model yields traveling waves of mutants even if mutants are preferentially eliminated. Additionally, we predict that mutant loads observed in single-cell experiments can be produced by de novo mutation rates that are drastically lower than previously thought for neutral models. Given this exemplar of how spatial structure (multiple linked mtDNA populations), noise, and density affect muscle cell aging, we introduce the mechanism of stochastic survival of the densest (SSD), an alternative to RA, that may underpin other evolutionary phenomena.
    Keywords:  aging; biomathematics; evolution; mitochondria; stochastic
    DOI:  https://doi.org/10.1073/pnas.2122073119
  34. Nat Commun. 2022 Dec 01. 13(1): 7404
    Dietary glucosamine overcomes the defects in αβ-T cell ontogeny caused by the loss of de novo hexosamine biosynthesis.
    Guy Werlen, Mei-Ling Li, Luca Tottone, Victoria da Silva-Diz, Xiaoyang Su, Daniel Herranz, Estela Jacinto.
      T cell development requires the coordinated rearrangement of T cell receptor (TCR) gene segments and the expression of either αβ or γδ TCR. However, whether and how de novo synthesis of nutrients contributes to thymocyte commitment to either lineage remains unclear. Here, we find that T cell-specific deficiency in glutamine:fructose-6-phosphate aminotransferase 1 (GFAT1), the rate-limiting enzyme of the de novo hexosamine biosynthesis pathway (dn-HBP), attenuates hexosamine levels, blunts N-glycosylation of TCRβ chains, reduces surface expression of key developmental receptors, thus impairing αβ-T cell ontogeny. GFAT1 deficiency triggers defects in N-glycans, increases the unfolded protein response, and elevates  γδ-T cell numbers despite reducing γδ-TCR diversity. Enhancing TCR expression or PI3K/Akt signaling does not reverse developmental defects. Instead, dietary supplementation with the salvage metabolite, glucosamine, and an α-ketoglutarate analogue partially restores αβ-T cell development in GFAT1T-/- mice, while fully rescuing it in ex vivo fetal thymic organ cultures. Thus, dn-HBP fulfils, while salvage nutrients partially satisfy, the elevated demand for hexosamines during early T cell development.
    DOI:  https://doi.org/10.1038/s41467-022-35014-w
  35. Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2217400119
    Filling gaps in metabolism using hypothetical reactions.
    Feiran Li.
      
    DOI:  https://doi.org/10.1073/pnas.2217400119
  36. Sci Immunol. 2022 Dec 09. 7(78): eade5686
    IL-2 is inactivated by the acidic pH environment of tumors enabling engineering of a pH-selective mutein.
    Silvia Gaggero, Jonathan Martinez-Fabregas, Adeline Cozzani, Paul K Fyfe, Malo Leprohon, Jie Yang, F Emil Thomasen, Hauke Winkelmann, Romain Magnez, Alberto G Conti, Stephan Wilmes, Elizabeth Pohler, Manuel van Gijsel Bonnello, Xavier Thuru, Bruno Quesnel, Fabrice Soncin, Jacob Piehler, Kresten Lindorff-Larsen, Rahul Roychoudhuri, Ignacio Moraga, Suman Mitra.
      Cytokines interact with their receptors in the extracellular space to control immune responses. How the physicochemical properties of the extracellular space influence cytokine signaling is incompletely elucidated. Here, we show that the activity of interleukin-2 (IL-2), a cytokine critical to T cell immunity, is profoundly affected by pH, limiting IL-2 signaling within the acidic environment of tumors. Generation of lactic acid by tumors limits STAT5 activation, effector differentiation, and antitumor immunity by CD8+ T cells and renders high-dose IL-2 therapy poorly effective. Directed evolution enabled selection of a pH-selective IL-2 mutein (Switch-2). Switch-2 binds the IL-2 receptor subunit IL-2Rα with higher affinity, triggers STAT5 activation, and drives CD8+ T cell effector function more potently at acidic pH than at neutral pH. Consequently, high-dose Switch-2 therapy induces potent immune activation and tumor rejection with reduced on-target toxicity in normal tissues. Last, we show that sensitivity to pH is a generalizable property of a diverse range of cytokines with broad relevance to immunity and immunotherapy in healthy and diseased tissues.
    DOI:  https://doi.org/10.1126/sciimmunol.ade5686
  37. Cancer Res. 2022 Dec 02. 82(23): 4322-4324
    A Time and Place for Inhibiting Autophagy.
    Boyi Gan.
      Autophagy is an attractive therapeutic target in cancer. Successful autophagy-focused clinical intervention will require a detailed understanding of when and where autophagy is important during tumorigenesis. In this issue of Cancer Research, Khayati and colleagues use state-of-the-art genetically engineered mouse models to demonstrate that transient systemic inhibition of autophagy can irreversibly impair the growth of established lung tumors with a good tolerability in normal tissues, suggesting a therapeutic strategy for cancer treatment. See related article by Khayati et al., p. 4429.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-3024
  38. Sci Adv. 2022 Dec 02. 8(48): eadc9851
    Stimulation of RAS-dependent ROS signaling extends longevity by modulating a developmental program of global gene expression.
    Robyn Branicky, Ying Wang, Arman Khaki, Ju-Ling Liu, Maximilian Kramer-Drauberg, Siegfried Hekimi.
      We show that elevation of mitochondrial superoxide generation increases Caenorhabditis elegans life span by enhancing a RAS-dependent ROS (reactive oxygen species) signaling pathway (RDRS) that controls the expression of half of the genome as well as animal composition and physiology. RDRS stimulation mimics a program of change in gene expression that is normally observed at the end of postembryonic development. We further show that RDRS is regulated by negative feedback from the superoxide dismutase 1 (SOD-1)-dependent conversion of superoxide into cytoplasmic hydrogen peroxide, which, in turn, acts on a redox-sensitive cysteine (C118) of RAS. Preventing C118 oxidation by replacement with serine, or mimicking oxidation by replacement with aspartic acid, leads to opposite changes in the expression of the same large set of genes that is affected when RDRS is stimulated by mitochondrial superoxide. The identities of these genes suggest that stimulation of the pathway extends life span by boosting turnover and repair while moderating damage from metabolic activity.
    DOI:  https://doi.org/10.1126/sciadv.adc9851
  39. Mol Cell. 2022 Dec 01. pii: S1097-2765(22)01067-X. [Epub ahead of print]82(23): 4407-4409
    D-2HG comes out of its shell: Metabolic effects on the immune environment.
    Juan Manuel Schvartzman, Andrew M Intlekofer.
      A recent study by Notarangelo et al.1 highlights the potential for tumor-derived D-2HG to inhibit neighboring T cell function through a novel mechanism.
    DOI:  https://doi.org/10.1016/j.molcel.2022.11.005
  40. Nat Commun. 2022 Dec 02. 13(1): 7414
    Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation.
    Wei Li, Qi Long, Hao Wu, Yanshuang Zhou, Lifan Duan, Hao Yuan, Yingzhe Ding, Yile Huang, Yi Wu, Jinyu Huang, Delong Liu, Baodan Chen, Jian Zhang, Juntao Qi, Shiwei Du, Linpeng Li, Yang Liu, Zifeng Ruan, Zihuang Liu, Zichao Liu, Yifan Zhao, Jianghuan Lu, Junwei Wang, Wai-Yee Chan, Xingguo Liu.
      Pluripotent stem cells hold great promise in regenerative medicine and developmental biology studies. Mitochondrial metabolites, including tricarboxylic acid (TCA) cycle intermediates, have been reported to play critical roles in pluripotency. Here we show that TCA cycle enzymes including Pdha1, Pcb, Aco2, Cs, Idh3a, Ogdh, Sdha and Mdh2 are translocated to the nucleus during somatic cell reprogramming, primed-to-naive transition and totipotency acquisition. The nuclear-localized TCA cycle enzymes Pdha1, Pcb, Aco2, Cs, Idh3a promote somatic cell reprogramming and primed-to-naive transition. In addition, nuclear-localized TCA cycle enzymes, particularly nuclear-targeted Pdha1, facilitate the 2-cell program in pluripotent stem cells. Mechanistically, nuclear Pdha1 increases the acetyl-CoA and metabolite pool in the nucleus, leading to chromatin remodeling at pluripotency genes by enhancing histone H3 acetylation. Our results reveal an important role of mitochondrial TCA cycle enzymes in the epigenetic regulation of pluripotency that constitutes a mitochondria-to-nucleus retrograde signaling mode in different states of pluripotent acquisition.
    DOI:  https://doi.org/10.1038/s41467-022-35199-0
  41. Nat Genet. 2022 Nov 28.
    Tumor aneuploidy predicts survival following immunotherapy across multiple cancers.
    Liam F Spurr, Ralph R Weichselbaum, Sean P Pitroda.
      Tumor mutational burden (TMB) has emerged as a promising biomarker of immunotherapy response across multiple cancer types; however, clinical outcomes among patients with low TMB tumors are heterogeneous. Herein, we demonstrate that tumor aneuploidy provides independent prognostic value among patients with lower TMB (<80th percentile) tumors treated with immunotherapy. A higher aneuploidy score is associated with poor prognosis following immunotherapy among tumors with low TMB, but not those with high TMB. Importantly, aneuploidy scores can be calculated from existing clinical targeted sequencing infrastructure, facilitating deployment of aneuploidy scores as a clinical biomarker.
    DOI:  https://doi.org/10.1038/s41588-022-01235-4
  42. Science. 2022 Dec 02. 378(6623): 983-989
    Active DNA demethylation promotes cell fate specification and the DNA damage response.
    Dongpeng Wang, Wei Wu, Elsa Callen, Raphael Pavani, Nicholas Zolnerowich, Srikanth Kodali, Dali Zong, Nancy Wong, Santiago Noriega, William J Nathan, Gabriel Matos-Rodrigues, Raj Chari, Michael J Kruhlak, Ferenc Livak, Michael Ward, Keith Caldecott, Bruno Di Stefano, André Nussenzweig.
      Neurons harbor high levels of single-strand DNA breaks (SSBs) that are targeted to neuronal enhancers, but the source of this endogenous damage remains unclear. Using two systems of postmitotic lineage specification-induced pluripotent stem cell-derived neurons and transdifferentiated macrophages-we show that thymidine DNA glycosylase (TDG)-driven excision of methylcytosines oxidized with ten-eleven translocation enzymes (TET) is a source of SSBs. Although macrophage differentiation favors short-patch base excision repair to fill in single-nucleotide gaps, neurons also frequently use the long-patch subpathway. Disrupting this gap-filling process using anti-neoplastic cytosine analogs triggers a DNA damage response and neuronal cell death, which is dependent on TDG. Thus, TET-mediated active DNA demethylation promotes endogenous DNA damage, a process that normally safeguards cell identity but can also provoke neurotoxicity after anticancer treatments.
    DOI:  https://doi.org/10.1126/science.add9838
  43. Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2205789119
    Human cytomegalovirus induces neuronal enolase to support virally mediated metabolic remodeling.
    Isreal Moreno, Irene Rodríguez-Sánchez, Xenia Schafer, Joshua Munger.
      Viruses depend on cellular metabolic resources to supply the energy and biomolecular building blocks necessary for their replication. Human cytomegalovirus (HCMV), a leading cause of birth defects and morbidity in immunosuppressed individuals, induces numerous metabolic activities that are important for productive infection. However, many of the mechanisms through which these metabolic activities are induced and how they contribute to infection are unclear. We find that HCMV infection of fibroblasts induces a neuronal gene signature as well as the expression of several metabolic enzyme isoforms that are typically expressed in other tissue types. Of these, the most substantially induced glycolytic gene was the neuron-specific isoform of enolase 2 (ENO2). Induction of ENO2 expression is important for HCMV-mediated glycolytic activation as well as for the virally induced remodeling of pyrimidine-sugar metabolism, which provides the glycosyl subunits necessary for protein glycosylation. Inhibition of ENO2 expression or activity reduced uridine diphosphate (UDP)-sugar pools, attenuated the accumulation of viral glycoproteins, and induced the accumulation of noninfectious viral particles. In addition, our data indicate that the induction of ENO2 expression depends on the HCMV UL38 protein. Collectively, our data indicate that HCMV infection induces a tissue atypical neuronal glycolytic enzyme to activate glycolysis and UDP-sugar metabolism, increase the accumulation of glycosyl building blocks, and enable the expression of an essential viral glycoprotein and the production of infectious virions.
    Keywords:  enolase; human cytomegalovirus; infection; metabolism; virus
    DOI:  https://doi.org/10.1073/pnas.2205789119
  44. Nature. 2022 Nov 30.
    Ras drives malignancy through stem cell crosstalk with the microenvironment.
    Shaopeng Yuan, Katherine S Stewart, Yihao Yang, Merve Deniz Abdusselamoglu, S Martina Parigi, Tamar Y Feinberg, Karen Tumaneng, Hanseul Yang, John M Levorse, Lisa Polak, David Ng, Elaine Fuchs.
      Squamous cell carcinomas are triggered by marked elevation of RAS-MAPK signalling and progression from benign papilloma to invasive malignancy1-4. At tumour-stromal interfaces, a subset of tumour-initiating progenitors, the cancer stem cells, obtain increased resistance to chemotherapy and immunotherapy along this pathway5,6. The distribution and changes in cancer stem cells during progression from a benign state to invasive squamous cell carcinoma remain unclear. Here we show in mice that, after oncogenic RAS activation, cancer stem cells rewire their gene expression program and trigger self-propelling, aberrant signalling crosstalk with their tissue microenvironment that drives their malignant progression. The non-genetic, dynamic cascade of intercellular exchanges involves downstream pathways that are often mutated in advanced metastatic squamous cell carcinomas with high mutational burden7. Coupling our clonal skin HRASG12V mouse model with single-cell transcriptomics, chromatin landscaping, lentiviral reporters and lineage tracing, we show that aberrant crosstalk between cancer stem cells and their microenvironment triggers angiogenesis and TGFβ signalling, creating conditions that are conducive for hijacking leptin and leptin receptor signalling, which in turn launches downstream phosphoinositide 3-kinase (PI3K)-AKT-mTOR signalling during the benign-to-malignant transition. By functionally examining each step in this pathway, we reveal how dynamic temporal crosstalk with the microenvironment orchestrated by the stem cells profoundly fuels this path to malignancy. These insights suggest broad implications for cancer therapeutics.
    DOI:  https://doi.org/10.1038/s41586-022-05475-6
  45. Nat Metab. 2022 Nov 28.
    Mitochondrial RNA stimulates beige adipocyte development in young mice.
    Anh Cuong Hoang, László Sasi-Szabó, Tibor Pál, Tamás Szabó, Victoria Diedrich, Annika Herwig, Kathrin Landgraf, Antje Körner, Tamás Röszer.
      Childhood obesity is a serious public health crisis and a critical factor that determines future obesity prevalence. Signals affecting adipocyte development in early postnatal life have a strong potential to trigger childhood obesity; however, these signals are still poorly understood. We show here that mitochondrial (mt)RNA efflux stimulates transcription of nuclear-encoded genes for mitobiogenesis and thermogenesis in adipocytes of young mice and human infants. While cytosolic mtRNA is a potential trigger of the interferon (IFN) response, young adipocytes lack such a response to cytosolic mtRNA due to the suppression of IFN regulatory factor (IRF)7 expression by vitamin D receptor signalling. Adult and obese adipocytes, however, strongly express IRF7 and mount an IFN response to cytosolic mtRNA. In turn, suppressing IRF7 expression in adult adipocytes restores mtRNA-induced mitobiogenesis and thermogenesis and eventually mitigates obesity. Retrograde mitochondrion-to-nucleus signalling by mtRNA is thus a mechanism to evoke thermogenic potential during early adipocyte development and to protect against obesity.
    DOI:  https://doi.org/10.1038/s42255-022-00683-w
  46. Nat Commun. 2022 Nov 28. 13(1): 7199
    Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis.
    Yael Aylon, Noa Furth, Giuseppe Mallel, Gilgi Friedlander, Nishanth Belugali Nataraj, Meng Dong, Ori Hassin, Rawan Zoabi, Benjamin Cohen, Vanessa Drendel, Tomer Meir Salame, Saptaparna Mukherjee, Nofar Harpaz, Randy Johnson, Walter E Aulitzky, Yosef Yarden, Efrat Shema, Moshe Oren.
      Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a "basal-like" state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed "basal-like" genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.
    DOI:  https://doi.org/10.1038/s41467-022-34863-9
  47. Cancer Cell. 2022 Nov 30. pii: S1535-6108(22)00552-9. [Epub ahead of print]
    Interferon-dependent SLC14A1+ cancer-associated fibroblasts promote cancer stemness via WNT5A in bladder cancer.
    Zikun Ma, Xiangdong Li, Yize Mao, Chen Wei, Zhuoli Huang, Guibo Li, Jianhua Yin, Xiaoyu Liang, Zhuowei Liu.
      Cancer-associated fibroblasts (CAFs) play a role in response to cancer treatment and patient prognosis. CAFs show phenotypic and functional heterogeneity and differ widely in tumors of different tissue origin. Here, we use single-cell RNA sequencing of bladder cancer (BC) patient samples and report a CAF subpopulation characterized by overexpression of the urea transporter SLC14A1. This population is induced by interferon signaling and confers stemness to BC cells via the WNT5A paracrine pathway. Activation of cGAS-STING signaling in tumor cells drives interferon production, thereby revealing a link between cGAS-STING signaling and SLC14A1+ CAF differentiation. Furthermore, the inhibition of SLC14A1+ CAF formation via targeting of STAT1 or STING sensitizes tumor cells to chemotherapy. More important, BC patients with high proportions of intratumoral SLC14A1+ CAFs show cancer stage-independent poor outcome and a worse response rate to neoadjuvant chemotherapy or immunotherapy.
    Keywords:  bladder cancer; cGAS-STING signaling; cancer associated fibroblasts; fibroblast subtype; interferon signaling; singlel-cell RNA sequencing; tumor immune microenvironment; tumor stemness; wnt/b-catenin
    DOI:  https://doi.org/10.1016/j.ccell.2022.11.005
  48. Elife. 2022 Nov 30. pii: e84279. [Epub ahead of print]11
    An ER phospholipid hydrolase drives ER-associated mitochondrial constriction for fission and fusion.
    Tricia T Nguyen, Gia K Voeltz.
      Mitochondria are dynamic organelles that undergo cycles of fission and fusion at a unified platform defined by endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCSs). These MCSs or nodes co-localize fission and fusion machinery. We set out to identify how ER-associated mitochondrial nodes can regulate both fission and fusion machinery assembly. We have used a promiscuous biotin ligase linked to the fusion machinery, Mfn1, and proteomics to identify an ER membrane protein, ABHD16A, as a major regulator of node formation. In the absence of ABHD16A, fission and fusion machineries fail to recruit to ER-associated mitochondrial nodes and fission and fusion rates are significantly reduced. ABHD16A contains an acyltransferase motif and an α/β hydrolase domain and point mutations in critical residues of these regions fail to rescue the formation of ER-associated mitochondrial hot spots. These data suggest a mechanism whereby ABHD16A functions by altering phospholipid composition at ER-mitochondria MCSs. Our data present the first example of an ER membrane protein that regulates the recruitment of both fission and fusion machineries to mitochondria.
    Keywords:  cell biology; human
    DOI:  https://doi.org/10.7554/eLife.84279
  49. Proc Natl Acad Sci U S A. 2022 Dec 06. 119(49): e2204259119
    Decorating chromatin for enhanced genome editing using CRISPR-Cas9.
    Evelyn Chen, Enrique Lin-Shiao, Marena Trinidad, Mohammad Saffari Doost, David Colognori, Jennifer A Doudna.
      CRISPR-associated (Cas) enzymes have revolutionized biology by enabling RNA-guided genome editing. Homology-directed repair (HDR) in the presence of donor templates is currently the most versatile method to introduce precise edits following CRISPR-Cas-induced double-stranded DNA cuts, but HDR efficiency is generally low relative to end-joining pathways that lead to insertions and deletions (indels). We tested the hypothesis that HDR could be increased using a Cas9 construct fused to PRDM9, a chromatin remodeling factor that deposits histone methylations H3K36me3 and H3K4me3 to mediate homologous recombination in human cells. Our results show that the fusion protein contacts chromatin specifically at the Cas9 cut site in the genome to increase the observed HDR efficiency by threefold and HDR:indel ratio by fivefold compared with that induced by unmodified Cas9. HDR enhancement occurred in multiple cell lines with no increase in off-target genome editing. These findings underscore the importance of chromatin features for the balance between DNA repair mechanisms during CRISPR-Cas genome editing and provide a strategy to increase HDR efficiency.
    Keywords:  CRISPR; chromatin; epigenetics; genome editing
    DOI:  https://doi.org/10.1073/pnas.2204259119
  50. Nat Immunol. 2022 Nov 28.
    Distinct changes in endosomal composition promote NLRP3 inflammasome activation.
    Zhirong Zhang, Rossella Venditti, Li Ran, Zengzhen Liu, Karl Vivot, Annette Schürmann, Juan S Bonifacino, Maria Antonietta De Matteis, Romeo Ricci.
      Inflammasome complexes are pivotal in the innate immune response. The NLR family pyrin domain containing protein 3 (NLRP3) inflammasome is activated in response to a broad variety of cellular stressors. However, a primary and converging sensing mechanism by the NLRP3 receptor initiating inflammasome assembly remains ill defined. Here, we demonstrate that NLRP3 inflammasome activators primarily converge on disruption of endoplasmic reticulum-endosome membrane contact sites (EECS). This defect causes endosomal accumulation of phosphatidylinositol 4-phosphate (PI4P) and a consequent impairment of endosome-to-trans-Golgi network trafficking (ETT), necessary steps for endosomal recruitment of NLRP3 and subsequent inflammasome activation. Lowering endosomal PI4P levels prevents endosomal association of NLRP3 and inhibits inflammasome activation. Disruption of EECS or ETT is sufficient to enhance endosomal PI4P levels, to recruit NLRP3 to endosomes and to potentiate NLRP3 inflammasome activation. Mice with defects in ETT in the myeloid compartment are more susceptible to lipopolysaccharide-induced sepsis. Our study thus identifies a distinct cellular mechanism leading to endosomal NLRP3 recruitment and inflammasome activation.
    DOI:  https://doi.org/10.1038/s41590-022-01355-3
  51. Nat Commun. 2022 Dec 01. 13(1): 7405
    A self-powered ingestible wireless biosensing system for real-time in situ monitoring of gastrointestinal tract metabolites.
    Ernesto De la Paz, Nikhil Harsha Maganti, Alexander Trifonov, Itthipon Jeerapan, Kuldeep Mahato, Lu Yin, Thitaporn Sonsa-Ard, Nicolas Ma, Won Jung, Ryan Burns, Amir Zarrinpar, Joseph Wang, Patrick P Mercier.
      Information related to the diverse and dynamic metabolite composition of the small intestine is crucial for the diagnosis and treatment of various diseases. However, our current understanding of the physiochemical dynamics of metabolic processes within the small intestine is limited due to the lack of in situ access to the intestinal environment. Here, we report a demonstration of a battery-free ingestible biosensing system for monitoring metabolites in the small intestine. As a proof of concept, we monitor the intestinal glucose dynamics on a porcine model. Battery-free operation is achieved through a self-powered glucose biofuel cell/biosensor integrated into a circuit that performs energy harvesting, biosensing, and wireless telemetry via a power-to-frequency conversion scheme using magnetic human body communication. Such long-term biochemical analysis could potentially provide critical information regarding the complex and dynamic small intestine metabolic profiles.
    DOI:  https://doi.org/10.1038/s41467-022-35074-y
  52. Autophagy. 2022 Nov 30.
    The autophagy pathway beyond model organisms: an evolutionary perspective.
    Sidi Zhang, Noboru Mizushima.
      In this issue, we answer a frequently asked question regarding the evolution of the macroautophagy/autophagy pathway.
    Keywords:  Saccharomyces; autophagy; eukaryotes; evolution; question
    DOI:  https://doi.org/10.1080/15548627.2022.2153568
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