bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2023–03–26
forty-nine papers selected by
Christian Frezza, Universität zu Köln
  1. Beyond the matrix: structural and physiological advancements in mitochondrial calcium signaling.
  2. p53 regulates the mitochondrial immune checkpoint.
  3. Targeting the mevalonate pathway suppresses ARID1A-inactivated cancers by promoting pyroptosis.
  4. SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin secreting cells.
  5. Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation.
  6. Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions.
  7. Leaked genomic and mitochondrial DNA contribute to the host response to noroviruses in a STING-dependent manner.
  8. The structural flexibility of MAD1 facilitates the assembly of the Mitotic Checkpoint Complex.
  9. Increased mitochondrial Ca2+ contributes to health decline with age and Duchene muscular dystrophy in C. elegans.
  10. Reprogramming of tissue metabolism during cancer metastasis.
  11. H2O2 transit through the mitochondrial intermembrane space promotes tumor cell growth in vitro and in vivo.
  12. Histone deacetylase 6 inhibition exploits selective metabolic vulnerabilities in LKB1 mutant, KRAS driven non-small cell lung cancer.
  13. Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.
  14. Sphingolipid desaturase DEGS1 is essential for mitochondria-associated membrane integrity.
  15. Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report.
  16. Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging.
  17. Inhibition of nucleotide biosynthesis disrupts lipid accumulation and adipogenesis.
  18. A quantitative fluorescence-based approach to study mitochondrial protein import.
  19. Nrf2 regulates glucose uptake and metabolism in neurons and astrocytes.
  20. Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state.
  21. Loss of respiratory complex I subunit NDUFB10 affects complex I assembly and supercomplex formation.
  22. Astrocytic OxPhos: more than just energy production.
  23. Alpha-ketoglutarate as a potent regulator for lifespan and healthspan: Evidences and perspectives.
  24. Nitric oxide regulates metabolism in murine stress erythroid progenitors to promote recovery during inflammatory anemia.
  25. Molecular and metabolic heterogeneity of astrocytes and microglia.
  26. DAB2IP is a bifunctional tumor suppressor that regulates wildtype RAS and inflammatory cascades in KRAS mutant colon cancer.
  27. Assessment of the Peroxisomal Redox State in Living Cells Using NADPH- and NAD+/NADH-Specific Fluorescent Protein Sensors.
  28. Defects in lipid homeostasis reflect the function of TANGO2 in phospholipid and neutral lipid metabolism.
  29. The DREAM complex functions as conserved master regulator of somatic DNA-repair capacities.
  30. Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.
  31. Cancer cells remodel nuclear actin filaments to resist chemotherapy.
  32. Proximity-Ligation Assay to Detect Peroxisome-Organelle Interaction.
  33. The lactate dehydrogenase (LDH) isoenzyme spectrum enables optimally controlling T cell glycolysis and differentiation.
  34. m6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis.
  35. RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer.
  36. Redox metabolism maintains the leukemogenic capacity and drug resistance of AML cells.
  37. Tetracycline-dependent inhibition of mitoribosome protein elongation in mitochondrial disease mutant cells suppresses IRE1α to promote cell survival.
  38. Co-option of epidermal cells enables touch sensing.
  39. Loss of fatty acid degradation by astrocytic mitochondria triggers neuroinflammation and neurodegeneration.
  40. Thymidine nucleotide metabolism controls human telomere length.
  41. Diseases of Hereditary Renal Cell Cancers.
  42. Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA ubiquitination.
  43. Bucket lists must be completed during cell death.
  44. Saturated fatty acids dampen the immunogenicity of cancer by suppressing STING.
  45. Lipid hydroperoxides promote sarcopenia through carbonyl stress.
  46. Beyond the Genetic Code: A Tissue Code?
  47. Synchronization of the circadian clock to the environment tracked in real time.
  48. Breast tumors interfere with endothelial TRAIL at the premetastatic niche to promote cancer cell seeding.
  49. Mitochondrial function declines with age within individuals but is not linked to the pattern of growth or mortality risk in zebra finch.
  1. Biochem Soc Trans. 2023 Mar 24. pii: BST20220317. [Epub ahead of print]
    Beyond the matrix: structural and physiological advancements in mitochondrial calcium signaling.
    Melissa J S MacEwen, Yasemin Sancak.
      Mitochondrial calcium (Ca2+) signaling has long been known to regulate diverse cellular functions, ranging from ATP production via oxidative phosphorylation, to cytoplasmic Ca2+ signaling to apoptosis. Central to mitochondrial Ca2+ signaling is the mitochondrial Ca2+ uniporter complex (MCUC) which enables Ca2+ flux from the cytosol into the mitochondrial matrix. Several pivotal discoveries over the past 15 years have clarified the identity of the proteins comprising MCUC. Here, we provide an overview of the literature on mitochondrial Ca2+ biology and highlight recent findings on the high-resolution structure, dynamic regulation, and new functions of MCUC, with an emphasis on publications from the last five years. We discuss the importance of these findings for human health and the therapeutic potential of targeting mitochondrial Ca2+ signaling.
    Keywords:  calcium signaling; mitochondria; mitochondrial calcium uniporter; mitochondrial signaling
    DOI:  https://doi.org/10.1042/BST20220317
  2. Trends Immunol. 2023 Mar 16. pii: S1471-4906(23)00045-5. [Epub ahead of print]
    p53 regulates the mitochondrial immune checkpoint.
    Claire Vanpouille-Box, Lorenzo Galluzzi.
      Mitochondrial outer membrane permeabilization (MOMP) is crucial for the cytosolic accumulation of mitochondrial DNA (mtDNA) species that are required to jumpstart innate and adaptive immunity. Recent data reported by Ghosh et al. suggest that tumor protein p53 regulates MOMP-dependent type I interferon (IFN) production, not only via MOMP-promoting effects, but also by directing mtDNA-degrading exonucleases to proteasomal processing.
    Keywords:  BAX; BCL2; DNA-damage response; TRIM24; apoptosis
    DOI:  https://doi.org/10.1016/j.it.2023.03.001
  3. Cancer Cell. 2023 Mar 16. pii: S1535-6108(23)00050-8. [Epub ahead of print]
    Targeting the mevalonate pathway suppresses ARID1A-inactivated cancers by promoting pyroptosis.
    Wei Zhou, Heng Liu, Zhe Yuan, Joseph Zundell, Martina Towers, Jianhuang Lin, Simona Lombardi, Hao Nie, Brennah Murphy, Tyler Yang, Chen Wang, Liping Liao, Aaron R Goldman, Toshitha Kannan, Andrew V Kossenkov, Ronny Drapkin, Luis J Montaner, Daniel T Claiborne, Nan Zhang, Shuai Wu, Rugang Zhang.
      ARID1A, encoding a subunit of the SWI/SNF complex, is mutated in ∼50% of clear cell ovarian carcinoma (OCCC) cases. Here we show that inhibition of the mevalonate pathway synergizes with immune checkpoint blockade (ICB) by driving inflammasome-regulated immunomodulating pyroptosis in ARID1A-inactivated OCCCs. SWI/SNF inactivation downregulates the rate-limiting enzymes in the mevalonate pathway such as HMGCR and HMGCS1, which creates a dependence on the residual activity of the pathway in ARID1A-inactivated cells. Inhibitors of the mevalonate pathway such as simvastatin suppresses the growth of ARID1A mutant, but not wild-type, OCCCs. In addition, simvastatin synergizes with anti-PD-L1 antibody in a genetic OCCC mouse model driven by conditional Arid1a inactivation and in a humanized immunocompetent ARID1A mutant patient-derived OCCC mouse model. Our data indicate that inhibition of the mevalonate pathway simultaneously suppresses tumor cell growth and boosts antitumor immunity by promoting pyroptosis, which synergizes with ICB in suppressing ARID1A-mutated cancers.
    Keywords:  ARID1A; Pyroptosis; SWI/SNF; anti-PD-L1; humanized mouse model; immune checkpoint blockade; inflammasome; mevalonate pathway; ovarian cancer; statin
    DOI:  https://doi.org/10.1016/j.ccell.2023.03.002
  4. J Cell Sci. 2023 Mar 21. pii: jcs.260049. [Epub ahead of print]
    SLC25A46 promotes mitochondrial fission and mediates resistance to lipotoxic stress in INS-1E insulin secreting cells.
    Jaime Santo-Domingo, Steve Lassueur, Antonio Núñez Galindo, Pilar Alvarez-Illera, Silvia Romero-Sanz, Elena Caldero-Escudero, Sergio de la Fuente, Loïc Dayon, Andreas Wiederkehr.
      Glucose sensing in pancreatic beta-cells depends on oxidative phosphorylation and mitochondria-derived signals that promote insulin secretion. Using mass spectrometry-based phosphoproteomics to search for down-stream effectors of glucose dependent signal transduction in INS-1E insulinoma cells, we identified the outer mitochondrial membrane protein SLC25A46. Under resting glucose concentrations, SLC25A46 was phosphorylated on a pair of threonine residues (T44/T45) and was dephosphorylated in response to glucose-induced calcium signals. Overexpression of SLC25A46 in INS-1E cells caused complete mitochondrial fragmentation, resulting in a mild mitochondrial defect associated with lowered glucose-induced insulin secretion. In contrast, inactivation of the SLC25A46 gene resulted in dramatic mitochondrial hyperfusion but without affecting respiratory activity or insulin secretion. Consequently, SLC25A46 is not essential for metabolism-secretion coupling under normal nutrient conditions. Importantly, insulin secreting cells lacking SLC25A46 had an exacerbated sensitivity to lipotoxic conditions undergoing massive apoptosis when exposed to palmitate. Therefore, in addition to its role in mitochondrial dynamics, SLC25A46 plays a role in preventing mitochondria-induced apoptosis in INS-E cells exposed to nutrient stress. By protecting mitochondria, SLC25A46 may help to maintain beta-cell mass essential for blood glucose control.
    Keywords:  Beta-cell; Mitochondria; Mitochondrial dynamics
    DOI:  https://doi.org/10.1242/jcs.260049
  5. bioRxiv. 2023 Mar 10. pii: 2023.03.08.531724. [Epub ahead of print]
    Sirtuin3 ensures the metabolic plasticity of neurotransmission during glucose deprivation.
    Anupama Tiwari, Arsalan Hashemiaghdam, Marissa A Laramie, Dario Maschi, Tristaan Haddad, Marion I Stunault, Carmen Bergom, Ali Javaheri, Vitaly Klyachko, Ghazaleh Ashrafi.
      Neurotransmission is an energetically expensive process that underlies cognition. During intense electrical activity or dietary restrictions, glucose levels in the brain plummet, forcing neurons to utilize alternative fuels. However, the molecular mechanisms of neuronal metabolic plasticity remain poorly understood. Here, we demonstrate that glucose-deprived neurons activate the CREB and PGC1α transcriptional program that induces the expression of the mitochondrial deacetylase Sirtuin 3 (Sirt3) both in vitro and in vivo . We show that Sirt3 localizes to axonal mitochondria and stimulates mitochondrial oxidative capacity in hippocampal nerve terminals. Sirt3 plays an essential role in sustaining synaptic transmission in the absence of glucose by powering the retrieval of synaptic vesicles after release. These results demonstrate that the transcriptional induction of Sirt3 ensures the metabolic plasticity of synaptic transmission.
    Highlights: Glucose deprivation drives transcriptional reprogramming of neuronal metabolism via CREB and PGC1α. Glucose or food deprivation trigger the neuronal expression of mitochondrial deacetylase sirtuin 3 (Sirt3) both in vitro and in vivo . Sirt3 stimulates oxidative ATP synthesis in nerve terminals.Sirt3 sustains the synaptic vesicle cycle in the absence of glucose.
    DOI:  https://doi.org/10.1101/2023.03.08.531724
  6. PLoS Comput Biol. 2023 Mar 23. 19(3): e1010953
    Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions.
    Robert C Glastad, Iain G Johnston.
      Mitochondria are highly dynamic organelles, containing vital populations of mitochondrial DNA (mtDNA) distributed throughout the cell. Mitochondria form diverse physical structures in different cells, from cell-wide reticulated networks to fragmented individual organelles. These physical structures are known to influence the genetic makeup of mtDNA populations between cell divisions, but their influence on the inheritance of mtDNA at divisions remains less understood. Here, we use statistical and computational models of mtDNA content inside and outside the reticulated network to quantify how mitochondrial network structure can control the variances of inherited mtDNA copy number and mutant load. We assess the use of moment-based approximations to describe heteroplasmy variance and identify several cases where such an approach has shortcomings. We show that biased inclusion of one mtDNA type in the network can substantially increase heteroplasmy variance (acting as a genetic bottleneck), and controlled distribution of network mass and mtDNA through the cell can conversely reduce heteroplasmy variance below a binomial inheritance picture. Network structure also allows the generation of heteroplasmy variance while controlling copy number inheritance to sub-binomial levels, reconciling several observations from the experimental literature. Overall, different network structures and mtDNA arrangements within them can control the variances of key variables to suit a palette of different inheritance priorities.
    DOI:  https://doi.org/10.1371/journal.pcbi.1010953
  7. Cell Rep. 2023 Mar 20. pii: S2211-1247(23)00190-0. [Epub ahead of print]42(3): 112179
    Leaked genomic and mitochondrial DNA contribute to the host response to noroviruses in a STING-dependent manner.
    Aminu S Jahun, Frederic Sorgeloos, Yasmin Chaudhry, Sabastine E Arthur, Myra Hosmillo, Iliana Georgana, Rhys Izuagbe, Ian G Goodfellow.
      The cGAS-STING pathway is central to the interferon response against DNA viruses. However, recent studies are increasingly demonstrating its role in the restriction of some RNA viruses. Here, we show that the cGAS-STING pathway also contributes to the interferon response against noroviruses, currently the commonest causes of infectious gastroenteritis worldwide. We show a significant reduction in interferon-β induction and a corresponding increase in viral replication in norovirus-infected cells after deletion of STING, cGAS, or IFI16. Further, we find that immunostimulatory host genome-derived DNA and mitochondrial DNA accumulate in the cytosol of norovirus-infected cells. Lastly, overexpression of the viral NS4 protein is sufficient to drive the accumulation of cytosolic DNA. Together, our data find a role for cGAS, IFI16, and STING in the restriction of noroviruses and show the utility of host genomic DNA as a damage-associated molecular pattern in cells infected with an RNA virus.
    Keywords:  CP: Immunology; CP: Molecular biology; DNA leakage; IFI16; NS4; STING; VF1; cGAS; cytosolic DNA; genomic DNA; interferon response; mitochondrial DNA; norovirus; p204
    DOI:  https://doi.org/10.1016/j.celrep.2023.112179
  8. Nat Commun. 2023 Mar 18. 14(1): 1529
    The structural flexibility of MAD1 facilitates the assembly of the Mitotic Checkpoint Complex.
    Chu Chen, Valentina Piano, Amal Alex, Simon J Y Han, Pim J Huis In 't Veld, Babhrubahan Roy, Daniel Fergle, Andrea Musacchio, Ajit P Joglekar.
      The spindle assembly checkpoint (SAC) safeguards the genome during cell division by generating an effector molecule known as the Mitotic Checkpoint Complex (MCC). The MCC comprises two subcomplexes: BUBR1:BUB3 and CDC20:MAD2, and the formation of CDC20:MAD2 is the rate-limiting step during MCC assembly. Recent studies show that the rate of CDC20:MAD2 formation is significantly accelerated by the cooperative binding of CDC20 to the SAC proteins MAD1 and BUB1. However, the molecular basis for this acceleration is not fully understood. Here, we demonstrate that the structural flexibility of MAD1 at a conserved hinge near the C-terminus is essential for catalytic MCC assembly. This MAD1 hinge enables the MAD1:MAD2 complex to assume a folded conformation in vivo. Importantly, truncating the hinge reduces the rate of MCC assembly in vitro and SAC signaling in vivo. Conversely, mutations that preserve hinge flexibility retain SAC signaling, indicating that the structural flexibility of the hinge, rather than a specific amino acid sequence, is important for SAC signaling. We summarize these observations as the 'knitting model' that explains how the folded conformation of MAD1:MAD2 promotes CDC20:MAD2 assembly.
    DOI:  https://doi.org/10.1038/s41467-023-37235-z
  9. FASEB J. 2023 Apr;37(4): e22851
    Increased mitochondrial Ca2+ contributes to health decline with age and Duchene muscular dystrophy in C. elegans.
    Atsushi Higashitani, Mika Teranishi, Yui Nakagawa, Yukou Itoh, Surabhi Sudevan, Nathaniel J Szewczyk, Yukihiko Kubota, Takaaki Abe, Takeshi Kobayashi.
      Sarcopenia is a geriatric syndrome characterized by an age-related decline in skeletal muscle mass and strength. Here, we show that suppression of mitochondrial calcium uniporter (MCU)-mediated Ca2+ influx into mitochondria in the body wall muscles of the nematode Caenorhabditis elegans improved the sarcopenic phenotypes, blunting movement and mitochondrial structural and functional decline with age. We found that normally aged muscle cells exhibited elevated resting mitochondrial Ca2+ levels and increased mitophagy to eliminate damaged mitochondria. Similar to aging muscle, we found that suppressing MCU function in muscular dystrophy improved movement via reducing elevated resting mitochondrial Ca2+ levels. Taken together, our results reveal that elevated resting mitochondrial Ca2+ levels contribute to muscle decline with age and muscular dystrophy. Further, modulation of MCU activity may act as a potential pharmacological target in various conditions involving muscle loss.
    Keywords:  MCU; aging; calcium; dystrophy; mitophagy; sarcopenia
    DOI:  https://doi.org/10.1096/fj.202201489RR
  10. Trends Cancer. 2023 Mar 17. pii: S2405-8033(23)00028-6. [Epub ahead of print]
    Reprogramming of tissue metabolism during cancer metastasis.
    Koelina Ganguly, Alec C Kimmelman.
      Cancer is a systemic disease that involves malignant cell-intrinsic and -extrinsic metabolic adaptations. Most studies have tended to focus on elucidating the metabolic vulnerabilities in the primary tumor microenvironment, leaving the metastatic microenvironment less explored. In this opinion article, we discuss the current understanding of the metabolic crosstalk between the cancer cells and the tumor microenvironment, both at local and systemic levels. We explore the possible influence of the primary tumor secretome to metabolically and epigenetically rewire the nonmalignant distant organs during prometastatic niche formation and successful metastatic colonization by the cancer cells. In an attempt to understand the process of prometastatic niche formation, we have speculated how cancer may hijack the inherent regenerative propensity of tissue parenchyma during metastatic colonization.
    Keywords:  metabolism; metastasis; prometastatic niche; stroma; tissue regeneration; wound response
    DOI:  https://doi.org/10.1016/j.trecan.2023.02.005
  11. J Biol Chem. 2023 Mar 17. pii: S0021-9258(23)00266-1. [Epub ahead of print] 104624
    H2O2 transit through the mitochondrial intermembrane space promotes tumor cell growth in vitro and in vivo.
    SimranS Sabharwal, V Joseph Dudley, Charlène Landwerlin, PaulT Schumacker.
      Cancer cells experience increased levels of oxidant stress as a consequence of oncogene activation, nucleotide biosynthesis, and growth factor receptor signaling. Mitochondria contribute to this redox stress by generating reactive oxygen species (ROS) along the electron transport chain (ETC), which are released to the matrix and the intermembrane space (IMS). Assessing the contribution of mitochondrial ROS in cancer cells is technically difficult, as ETC inhibitors can increase or decrease ROS generation, while they also block oxidative phosphorylation and ATP synthesis. Mitochondria-targeted antioxidant compounds can scavenge ROS in the matrix compartment, but do not act on ROS released to the intermembrane space. We assessed the importance of mitochondrial ROS for tumor cell proliferation, survival, and for tumor xenograft growth by stably expressing a hydrogen peroxide (H2O2) scavenger, peroxiredoxin-5, in the mitochondrial IMS (IMS-Prdx5) in 143B osteosarcoma and HCT116 colorectal cancer cell lines. IMS-Prdx5 attenuates hypoxia-induced ROS signaling as assessed independently in cytosol and IMS, HIF-1α stabilization and activity, and cellular proliferation under normoxic and hypoxic culture conditions. It also suppressed tumor growth in vivo. Stable expression of non-degradable HIF-1α only partially rescued proliferation in IMS-Prdx5-expressing cells, indicating that mitochondrial H2O2 signaling contributes to tumor cell proliferation and survival through HIF-dependent and HIF-independent mechanisms.
    Keywords:  Hypoxia-Inducible Factor-1; Reactive oxygen species; cancer; mitochondrial intermembrane space; peroxiredoxin-5; redox signaling
    DOI:  https://doi.org/10.1016/j.jbc.2023.104624
  12. J Thorac Oncol. 2023 Mar 21. pii: S1556-0864(23)00197-1. [Epub ahead of print]
    Histone deacetylase 6 inhibition exploits selective metabolic vulnerabilities in LKB1 mutant, KRAS driven non-small cell lung cancer.
    Hua Zhang, Christopher S Nabel, Dezhi Li, Ruth Í O'Connor, Caroline R Crosby, Sarah M Chang, Yuan Hao, Robyn Stanley, Soumyadip Sahu, Daniel S Levin, Ting Chen, Sittinon Tang, Hsin-Yi Huang, Mary Meynardie, Janaye Stephens, Fiona Sherman, Alison Chafitz, Naoise Costelloe, Daniel A Rodrigues, Hilda Fogarty, Miranda G Kiernan, Fiona Cronin, Eleni Papadopoulos, Magdalena Ploszaj, Vajira Weerasekara, Jiehui Deng, Patrick Kiely, Nabeel Bardeesy, Matthew G Vander Heiden, Triona Ni Chonghaile, Catríona M Dowling, Kwok-Kin Wong.
       INTRODUCTION: In KRAS-mutant non-small lung cancer (NSCLC), co-occurring alterations in LKB1 confer a negative prognosis compared to other mutations such as TP53. LKB1 is a tumor suppressor that coordinates several signaling pathways in response to energetic stress. Our recent work on pharmacologic and genetical inhibition of HDAC6 demonstrated impaired activity of numerous enzymes involved in glycolysis. Based on these prior findings, we explored the therapeutic window for HDAC6 inhibition in metabolically-active KRAS-mutant lung tumors.
    EXPERIMENTAL DESIGN: Using cell lines derived from mouse autochthonous tumors bearing the KRAS/LKB1 (KL) and KRAS/TP53 (KP) mutant genotypes to control for confounding germline and somatic mutations in human models, we characterize the metabolic phenotypes at baseline and in response to HDAC6 inhibition. The impact of HDAC6 inhibition was measured on cancer cell growth in vitro and on tumor growth in vivo.
    RESULTS: Surprisingly, KL-mutant cells demonstrated reduced levels of redox-sensitive cofactors at baseline. This associated with increased sensitivity to pharmacologic HDAC6 inhibition with ACY-1215 and blunted ability to increase compensatory metabolism and buffer oxidative stress. Seeking synergistic metabolic combination treatments, we found enhanced cell killing and anti-tumor efficacy with glutaminase inhibition in KL lung cancer models in vitro and in vivo.
    CONCLUSIONS: Exploring the differential metabolism of KL and KP mutant NSCLC, we identified decreased metabolic reserve in KL mutant tumors. HDAC6 inhibition exploited a therapeutic window in KL NSCLC based on a diminished ability to compensate for impaired glycolysis, nominating a novel strategy for treatment of KRAS-mutant NSCLC with co-occurring LKB1 mutations.
    Keywords:  HDAC6; KRAS; LKB1; TP53; glutaminase inhibition; glycolysis; non-small cell lung cancer; oxidative stress
    DOI:  https://doi.org/10.1016/j.jtho.2023.03.014
  13. Nature. 2023 Mar 22.
    Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.
    Alexander Mühleip, Rasmus Kock Flygaard, Rozbeh Baradaran, Outi Haapanen, Thomas Gruhl, Victor Tobiasson, Amandine Maréchal, Vivek Sharma, Alexey Amunts.
      Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane1. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III2-IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.
    DOI:  https://doi.org/10.1038/s41586-023-05817-y
  14. J Clin Invest. 2023 Mar 23. pii: e162957. [Epub ahead of print]
    Sphingolipid desaturase DEGS1 is essential for mitochondria-associated membrane integrity.
    Laura Planas-Serra, Nathalie Launay, Leire Goicoechea, Bénédicte Heron, Cristina Jou, Natalia Juliá-Palacios, Montserrat Ruiz, Stéphane Fourcade, Carlos Casasnovas, Carolina De La Torre, Antoinette Gelot, Maria Marsal, Pablo Loza-Alvarez, Àngels García-Cazorla, Ali Fatemi, Isidre Ferrer, Manuel Portero-Otin, Estela Area-Gómez, Aurora Pujol.
      Sphingolipids function as membrane constituents and signaling molecules, with crucial roles in human diseases, from neurodevelopmental to cancer, best exemplified in the inborn errors of sphingolipid metabolism in lysosomes. The dihydroceramide desaturase DEGS1 acts in the last step of a sector of the sphingolipid pathway, de novo ceramide biosynthesis. Defects in DEGS1 cause the recently described hypomyelinating leukodystrophy-18 (HLD18, OMIM #618404). Here, we reveal that DEGS1 is a mitochondria-associated endoplasmic reticulum membrane (MAM)-resident enzyme, refining previous reports locating DEGS1 at the endoplasmic reticulum only. Using patient fibroblasts, multi-omics and enzymatic assays, we show that DEGS1 deficiency disrupts the main core functions of the MAM: i) mitochondrial dynamics, with a hyperfused mitochondrial network associated with decreased activation of dynamin-related protein 1; ii) cholesterol metabolism, with impaired sterol O-acyltransferase activity and decreased cholesteryl esters; iii) phospholipid metabolism, with increased phosphatidic acid and phosphatidylserine and decreased phosphatidylethanolamine; iv) biogenesis of lipid droplets, with increased size and numbers. Moreover, we detected increased mitochondrial superoxide species production in fibroblasts and mitochondrial respiration impairment in patient muscle biopsy tissues. Our findings shed light on the pathophysiology of HLD18 and broaden our understanding of the role of sphingolipid metabolism in MAMs function.
    Keywords:  Bioenergetics; Demyelinating disorders; Lipid rafts; Metabolism; Neuroscience
    DOI:  https://doi.org/10.1172/JCI162957
  15. Ann N Y Acad Sci. 2023 Mar 24.
    Immunometabolism at the crossroads of obesity and cancer-a Keystone Symposia report.
    Jennifer Cable, Jeffrey C Rathmell, Erika L Pearce, Ping-Chih Ho, Marcia C Haigis, Murad R Mamedov, Meng-Ju Wu, Susan M Kaech, Lydia Lynch, Mark A Febbraio, Sagar P Bapat, Hanna S Hong, Weiping Zou, Yasmine Belkaid, Zuri A Sullivan, Andrea Keller, Stefanie K Wculek, Douglas R Green, Catherine Postic, Ido Amit, Salvador Aznar Benitah, Russell G Jones, Miguel Reina-Campos, Santiago Valle Torres, Semir Beyaz, Donal Brennan, Luke A J O'Neill, Rachel J Perry, Dirk Brenner.
      Immunometabolism considers the relationship between metabolism and immunity. Typically, researchers focus on either the metabolic pathways within immune cells that affect their function or the impact of immune cells on systemic metabolism. A more holistic approach that considers both these viewpoints is needed. On September 5-8, 2022, experts in the field of immunometabolism met for the Keystone symposium "Immunometabolism at the Crossroads of Obesity and Cancer" to present recent research across the field of immunometabolism, with the setting of obesity and cancer as an ideal example of the complex interplay between metabolism, immunity, and cancer. Speakers highlighted new insights on the metabolic links between tumor cells and immune cells, with a focus on leveraging unique metabolic vulnerabilities of different cell types in the tumor microenvironment as therapeutic targets and demonstrated the effects of diet, the microbiome, and obesity on immune system function and cancer pathogenesis and therapy. Finally, speakers presented new technologies to interrogate the immune system and uncover novel metabolic pathways important for immunity.
    Keywords:  cancer; immunity; immunometabolism; immunotherapy; metabolism; obesity
    DOI:  https://doi.org/10.1111/nyas.14976
  16. bioRxiv. 2023 Mar 08. pii: 2023.03.06.531392. [Epub ahead of print]
    Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging.
    Isabel M Serrano, Misa Hirose, Clint Valentine, Sharie Austin, Elizabeth Schmidt, Gabriel Pratt, Lindsey Williams, Jesse Salk, Saleh Ibrahim, Peter H Sudmant.
      Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here, we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mt-genome in different tissues throughout aging. We used ultra-sensitive Duplex Sequencing to profile ∼2.5 million mt-genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloging ∼1.2 million mitochondrial somatic mutations. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the Light Strand Origin of Replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared to primates with a surfeit of reactive oxygen species-associated G>T/C>A mutations and that somatic mutations in protein coding genes exhibit strong signatures of positive selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that "re-align" mito-nuclear ancestry within an organism's lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.
    DOI:  https://doi.org/10.1101/2023.03.06.531392
  17. J Biol Chem. 2023 Mar 22. pii: S0021-9258(23)00277-6. [Epub ahead of print] 104635
    Inhibition of nucleotide biosynthesis disrupts lipid accumulation and adipogenesis.
    Abhijit B Shinde, Elizabeth R Nunn, Genesis A Wilson, Mathew T Chvasta, Julia A Pinette, Jacob W Myers, Sun H Peck, Jessica B Spinelli, Elma Zaganjor.
      Energy balance and nutrient availability are key determinants of cellular decisions to remain quiescent, proliferate or differentiate into a mature cell. After assessing its environmental state, the cell must rewire its metabolism to support distinct cellular outcomes. Mechanistically, how metabolites regulate cell fate decisions is poorly understood. We used adipogenesis as our model system to ascertain the role of metabolism in differentiation. We isolated adipose tissue stromal vascular fraction (SVF) cells and profiled metabolites before and after adipogenic differentiation to identify metabolic signatures associated with these distinct cellular states. We found that differentiation alters nucleotide accumulation. Furthermore, inhibition of nucleotide biosynthesis prevented lipid storage within adipocytes and downregulated the expression of lipogenic factors. In contrast to proliferating cells, in which mTORC1 is activated by purine accumulation, mTORC1 signaling was unaffected by purine levels in differentiating adipocytes. Rather, our data indicated that purines regulate transcriptional activators of adipogenesis, PPARγ and C/EBPα to promote differentiation. Although de novo nucleotide biosynthesis has mainly been studied in proliferation, our study points to its requirement in adipocyte differentiation.
    Keywords:  adipocytes; adipogenesis; lipid droplets; metabolism; nucleotides; purine; pyrimidine
    DOI:  https://doi.org/10.1016/j.jbc.2023.104635
  18. EMBO Rep. 2023 Mar 20. e55760
    A quantitative fluorescence-based approach to study mitochondrial protein import.
    Naintara Jain, Ridhima Gomkale, Olaf Bernhard, Peter Rehling, Luis Daniel Cruz-Zaragoza.
      Mitochondria play central roles in cellular energy production and metabolism. Most proteins required to carry out these functions are synthesized in the cytosol and imported into mitochondria. A growing number of metabolic disorders arising from mitochondrial dysfunction can be traced to errors in mitochondrial protein import. The mechanisms underlying the import of precursor proteins are commonly studied using radioactively labeled precursor proteins imported into purified mitochondria. Here, we establish a fluorescence-based import assay to analyze protein import into mitochondria. We show that fluorescently labeled precursors enable import analysis with similar sensitivity to those using radioactive precursors, yet they provide the advantage of quantifying import with picomole resolution. We adapted the import assay to a 96-well plate format allowing for fast analysis in a screening-compatible format. Moreover, we show that fluorescently labeled precursors can be used to monitor the assembly of the F1 F0 ATP synthase in purified mitochondria. Thus, we provide a sensitive fluorescence-based import assay that enables quantitative and fast import analysis.
    Keywords:  fluorescent precursor; in vitro import; mitochondria; presequence pathway; protein import
    DOI:  https://doi.org/10.15252/embr.202255760
  19. Redox Biol. 2023 Mar 14. pii: S2213-2317(23)00073-3. [Epub ahead of print]62 102672
    Nrf2 regulates glucose uptake and metabolism in neurons and astrocytes.
    Noemí Esteras, Thomas S Blacker, Evgeny A Zherebtsov, Olga A Stelmashuk, Ying Zhang, W Christian Wigley, Michael R Duchen, Albena T Dinkova-Kostova, Andrey Y Abramov.
      The transcription factor Nrf2 and its repressor Keap1 mediate cell stress adaptation by inducing expression of genes regulating cellular detoxification, antioxidant defence and energy metabolism. Energy production and antioxidant defence employ NADH and NADPH respectively as essential metabolic cofactors; both are generated in distinct pathways of glucose metabolism, and both pathways are enhanced by Nrf2 activation. Here, we examined the role of Nrf2 on glucose distribution and the interrelation between NADH production in energy metabolism and NADPH homeostasis using glio-neuronal cultures isolated from wild-type, Nrf2-knockout and Keap1-knockdown mice. Employing advanced microscopy imaging of single live cells, including multiphoton fluorescence lifetime imaging microscopy (FLIM) to discriminate between NADH and NADPH, we found that Nrf2 activation increases glucose uptake into neurons and astrocytes. Glucose consumption is prioritized in brain cells for mitochondrial NADH and energy production, with a smaller contribution to NADPH synthesis in the pentose phosphate pathway for redox reactions. As Nrf2 is suppressed during neuronal development, this strategy leaves neurons reliant on astrocytic Nrf2 to maintain redox balance and energy homeostasis.
    Keywords:  Astrocytes; Brain; Glucose metabolism; Mitochondria; NADH; NADPH; Neurons; Nrf2
    DOI:  https://doi.org/10.1016/j.redox.2023.102672
  20. Elife. 2023 Mar 23. pii: e84415. [Epub ahead of print]12
    Resting mitochondrial complex I from Drosophila melanogaster adopts a helix-locked state.
    Abhilash Padavannil, Anjaneyulu Murari, Shauna-Kay Rhooms, Edward Owusu-Ansah, James A Letts.
      Respiratory complex I is a proton-pumping oxidoreductase key to bioenergetic metabolism. Biochemical studies have found a divide in the behavior of complex I in metazoans that aligns with the evolutionary split between Protostomia and Deuterostomia. Complex I from Deuterostomia including mammals can adopt a biochemically defined off-pathway 'deactive' state, whereas complex I from Protostomia cannot. The presence of off-pathway states complicates the interpretation of structural results and has led to considerable mechanistic debate. Here, we report the structure of mitochondrial complex I from the thoracic muscles of the model protostome Drosophila melanogaster. We show that although D. melanogaster complex I (Dm-CI) does not have a NEM-sensitive deactive state, it does show slow activation kinetics indicative of an off-pathway resting state. The resting-state structure of Dm-CI from the thoracic muscle reveals multiple conformations. We identify a helix-locked state in which an N-terminal α-helix on the NDUFS4 subunit wedges between the peripheral and membrane arms. Comparison of the Dm-CI structure and conformational states to those observed in bacteria, yeast, and mammals provides insight into the roles of subunits across organisms, explains why the Dm-CI off-pathway resting state is NEM insensitive, and raises questions regarding current mechanistic models of complex I turnover.
    Keywords:  complex I; drosophila melanogaster; electron transport chain; mitochondria; molecular biophysics; respiration; single particle cryoEM; structural biology
    DOI:  https://doi.org/10.7554/eLife.84415
  21. Biol Chem. 2023 Mar 24.
    Loss of respiratory complex I subunit NDUFB10 affects complex I assembly and supercomplex formation.
    Tasnim Arroum, Marie-Theres Borowski, Nico Marx, Frank Schmelter, Martin Scholz, Olympia Ekaterini Psathaki, Michael Hippler, José Antonio Enriquez, Karin B Busch.
      The orchestrated activity of the mitochondrial respiratory or electron transport chain (ETC) and ATP synthase convert reduction power (NADH, FADH2) into ATP, the cell's energy currency in a process named oxidative phosphorylation (OXPHOS). Three out of the four ETC complexes are found in supramolecular assemblies: complex I, III, and IV form the respiratory supercomplexes (SC). The plasticity model suggests that SC formation is a form of adaptation to changing conditions such as energy supply, redox state, and stress. Complex I, the NADH-dehydrogenase, is part of the largest supercomplex (CI + CIII2 + CIVn). Here, we demonstrate the role of NDUFB10, a subunit of the membrane arm of complex I, in complex I and supercomplex assembly on the one hand and bioenergetics function on the other. NDUFB10 knockout was correlated with a decrease of SCAF1, a supercomplex assembly factor, and a reduction of respiration and mitochondrial membrane potential. This likely is due to loss of proton pumping since the CI P P -module is downregulated and the P D -module is completely abolished in NDUFB10 knock outs.
    Keywords:  NDUFB10; OXPHOS; complex I; mitochondria; respiratory chain supercomplexes
    DOI:  https://doi.org/10.1515/hsz-2022-0309
  22. Nat Metab. 2023 Mar 23.
    Astrocytic OxPhos: more than just energy production.
    Luis F Rubio-Atonal, Maria S Ioannou.
      
    DOI:  https://doi.org/10.1038/s42255-023-00755-5
  23. Exp Gerontol. 2023 Mar 20. pii: S0531-5565(23)00075-X. [Epub ahead of print]175 112154
    Alpha-ketoglutarate as a potent regulator for lifespan and healthspan: Evidences and perspectives.
    Saghi Hakimi Naeini, Laleh Mavaddatiyan, Zahra Rashid Kalkhoran, Soroush Taherkhani, Mahmood Talkhabi.
      Aging is a natural process that determined by a functional decline in cells and tissues as organisms are growing old, resulting in an increase at risk of disease and death. To this end, many efforts have been made to control aging and increase lifespan and healthspan. These efforts have led to the discovery of several anti-aging drugs and compounds such as rapamycin and metformin. Recently, alpha-ketoglutarate (AKG) has been introduced as a potential anti-aging metabolite that can control several functions in organisms, thereby increases longevity and improves healthspan. Unlike other synthetic anti-aging drugs, AKG is one of the metabolites of the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, and synthesized in the body. It plays a crucial role in the cell energy metabolism, amino acid/protein synthesis, epigenetic regulation, stemness and differentiation, fertility and reproductive health, and cancer cell behaviors. AKG exerts its effects through different mechanisms such as inhibiting mTOR and ATP-synthase, modulating DNA and histone demethylation and reducing ROS formation. Herein, we summarize the recent findings of AKG-related lifespan and healthspan studies and discuss AKG associated cell and molecular mechanisms involved in increasing longevity, improving reproduction, and modulating stem cells and cancer cells behavior. We also discuss the promises and limitations of AKG for delaying aging and other potential applications.
    Keywords:  ATP synthesis; Aging; Alpha-ketoglutarate; DNA methylation; Healthspan; Lifespan; mTOR
    DOI:  https://doi.org/10.1016/j.exger.2023.112154
  24. bioRxiv. 2023 Mar 11. pii: 2023.03.11.532207. [Epub ahead of print]
    Nitric oxide regulates metabolism in murine stress erythroid progenitors to promote recovery during inflammatory anemia.
    Baiye Ruan, Yuanting Chen, Sara Trimidal, Imhoi Koo, Fenghua Qian, Jingwei Cai, John Mcguigan, Molly A Hall, Andrew D Patterson, K Sandeep Prabhu, Robert F Paulson.
      Inflammation skews bone marrow hematopoiesis increasing the production of myeloid effector cells at the expense of steady-state erythropoiesis. A compensatory stress erythropoiesis response is induced to maintain homeostasis until inflammation is resolved. In contrast to steady-state erythroid progenitors, stress erythroid progenitors (SEPs) utilize signals induced by inflammatory stimuli. However, the mechanistic basis for this is not clear. Here we reveal a nitric oxide (NO)-dependent regulatory network underlying two stages of stress erythropoiesis, namely proliferation, and the transition to differentiation. In the proliferative stage, immature SEPs and cells in the niche increased expression of inducible nitric oxide synthase ( Nos2 or iNOS ) to generate NO. Increased NO rewires SEP metabolism to increase anabolic pathways, which drive the biosynthesis of nucleotides, amino acids and other intermediates needed for cell division. This NO-dependent metabolism promotes cell proliferation while also inhibiting erythroid differentiation leading to the amplification of a large population of non-committed progenitors. The transition of these progenitors to differentiation is mediated by the activation of nuclear factor erythroid 2-related factor 2 (Nfe2l2 or Nrf2). Nrf2 acts as an anti-inflammatory regulator that decreases NO production, which removes the NO-dependent erythroid inhibition and allows for differentiation. These data provide a paradigm for how alterations in metabolism allow inflammatory signals to amplify immature progenitors prior to differentiation.
    Key points: Nitric-oxide (NO) dependent signaling favors an anabolic metabolism that promotes proliferation and inhibits differentiation.Activation of Nfe2l2 (Nrf2) decreases NO production allowing erythroid differentiation.
    DOI:  https://doi.org/10.1101/2023.03.11.532207
  25. Cell Metab. 2023 Mar 17. pii: S1550-4131(23)00084-0. [Epub ahead of print]
    Molecular and metabolic heterogeneity of astrocytes and microglia.
    Philip Hasel, William H Aisenberg, F Chris Bennett, Shane A Liddelow.
      Astrocytes and microglia are central players in a myriad of processes in the healthy and diseased brain, ranging from metabolism to immunity. The crosstalk between these two cell types contributes to pathology in many if not all neuroinflammatory and neurodegenerative diseases. Recent advancements in integrative multimodal sequencing techniques have begun to highlight how heterogeneous both cell types are and the importance of metabolism to their regulation. We discuss here the transcriptomic, metabolic, and functional heterogeneity of astrocytes and microglia and highlight their interaction in health and disease.
    DOI:  https://doi.org/10.1016/j.cmet.2023.03.006
  26. Cancer Res. 2023 Mar 20. pii: CAN-22-0370. [Epub ahead of print]
    DAB2IP is a bifunctional tumor suppressor that regulates wildtype RAS and inflammatory cascades in KRAS mutant colon cancer.
    Abigail L Miller, Naiara Perurena, Alycia Gardner, Toshinori Hinoue, Patrick Loi, Peter W Laird, Karen Cichowski.
      The DAB2IP tumor suppressor encodes a RAS GTPase-activating protein (RASGAP). Accordingly, DAB2IP has been shown to be mutated or suppressed in tumor types that typically lack RAS mutations. However, here we report that DAB2IP is mutated or selectively silenced in the vast majority of KRAS and BRAF mutant CRCs. In this setting, DAB2IP loss promoted tumor development by activating wild-type H- and NRAS proteins, which was surprisingly required to achieve robust activation of RAS effector pathways in KRAS-mutant tumors. DAB2IP loss also triggered production of inflammatory mediators and the recruitment of pro-tumorigenic macrophages in vivo. Importantly, tumor growth was suppressed by depleting macrophages or inhibiting cytokine/inflammatory mediator expression with a JAK/TBK1 inhibitor. In human tumors DAB2IP was lost at early stages of tumor development, and its depletion was associated with an enrichment of macrophage and inflammatory signatures. Together, these findings demonstrate that DAB2IP restrains the activation of the RAS pathway and inflammatory cascades in the colon and that its loss represents a common and unappreciated mechanism for amplifying these two critical oncogenic signals in colorectal cancer.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0370
  27. Methods Mol Biol. 2023 ;2643 183-197
    Assessment of the Peroxisomal Redox State in Living Cells Using NADPH- and NAD+/NADH-Specific Fluorescent Protein Sensors.
    Cláudio F Costa, Hongli Li, Mohamed A F Hussein, Yi Yang, Celien Lismont, Marc Fransen.
      The pyridine nucleotides NAD(H) and NADP(H) are key molecules in cellular metabolism, and measuring their levels and oxidation states with spatiotemporal precision is of great value in biomedical research. Traditional methods to assess the redox state of these metabolites are intrusive and prohibit live-cell quantifications. This obstacle was surpassed by the development of genetically encoded fluorescent biosensors enabling dynamic measurements with subcellular resolution in living cells. Here, we provide step-by-step protocols to monitor the intraperoxisomal NADPH levels and NAD+/NADH redox state in cellulo by using targeted variants of iNAP1 and SoNar, respectively.
    Keywords:  Fluorescent biosensors; Live-cell imaging; NAD(H); NADP(H); Peroxisomes; Redox state; SoNar; iNAP
    DOI:  https://doi.org/10.1007/978-1-0716-3048-8_13
  28. Elife. 2023 Mar 24. pii: e85345. [Epub ahead of print]12
    Defects in lipid homeostasis reflect the function of TANGO2 in phospholipid and neutral lipid metabolism.
    Agustin Leonardo Lujan, Ombretta Foresti, Conor Sugden, Nathalie Brouwers, Alex Mateo Farre, Alessio Vignoli, Mahshid Azamian, Alicia Turner, Jose Wojnacki, Vivek Malhotra.
      We show that TANGO2 in mammalian cells localizes predominantly to mitochondria and partially at mitochondria sites juxtaposed to lipid droplets (LDs) and the endoplasmic reticulum. HepG2 cells and fibroblasts of patients lacking TANGO2 exhibit enlarged LDs. Quantitative lipidomics revealed a marked increase in lysophosphatidic acid (LPA) and a concomitant decrease in its biosynthetic precursor phosphatidic acid (PA). These changes were exacerbated in nutrient-starved cells. Based on our data, we suggest that TANGO2 function is linked to acyl-CoA metabolism, which is necessary for the acylation of LPA to generate PA. The defect in acyl-CoA availability impacts the metabolism of many other fatty acids, generates high levels of reactive oxygen (ROS), and promotes lipid peroxidation. We suggest that the increased size of LDs is a combination of enrichment in peroxidized lipids and a defect in their catabolism. Our findings help explain the physiological consequence of mutations in TANGO2 that induce acute metabolic crises, including rhabdomyolysis, cardiomyopathy, and cardiac arrhythmias, often leading to fatality upon starvation and stress.
    Keywords:  cell biology; human
    DOI:  https://doi.org/10.7554/eLife.85345
  29. Nat Struct Mol Biol. 2023 Mar 23.
    The DREAM complex functions as conserved master regulator of somatic DNA-repair capacities.
    Arturo Bujarrabal-Dueso, Georg Sendtner, David H Meyer, Georgia Chatzinikolaou, Kalliopi Stratigi, George A Garinis, Björn Schumacher.
      The DNA-repair capacity in somatic cells is limited compared with that in germ cells. It has remained unknown whether not only lesion-type-specific, but overall repair capacities could be improved. Here we show that the DREAM repressor complex curbs the DNA-repair capacities in somatic tissues of Caenorhabditis elegans. Mutations in the DREAM complex induce germline-like expression patterns of multiple mechanisms of DNA repair in the soma. Consequently, DREAM mutants confer resistance to a wide range of DNA-damage types during development and aging. Similarly, inhibition of the DREAM complex in human cells boosts DNA-repair gene expression and resistance to distinct DNA-damage types. DREAM inhibition leads to decreased DNA damage and prevents photoreceptor loss in progeroid Ercc1-/- mice. We show that the DREAM complex transcriptionally represses essentially all DNA-repair systems and thus operates as a highly conserved master regulator of the somatic limitation of DNA-repair capacities.
    DOI:  https://doi.org/10.1038/s41594-023-00942-8
  30. Mol Syst Biol. 2023 Mar 21. e11443
    Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.
    Shivani Nanda, Marc-Antoine Jacques, Wen Wang, Chad L Myers, L Safak Yilmaz, Albertha Jm Walhout.
      Metabolism is controlled to ensure organismal development and homeostasis. Several mechanisms regulate metabolism, including allosteric control and transcriptional regulation of metabolic enzymes and transporters. So far, metabolism regulation has mostly been described for individual genes and pathways, and the extent of transcriptional regulation of the entire metabolic network remains largely unknown. Here, we find that three-quarters of all metabolic genes are transcriptionally regulated in the nematode Caenorhabditis elegans. We find that many annotated metabolic pathways are coexpressed, and we use gene expression data and the iCEL1314 metabolic network model to define coregulated subpathways in an unbiased manner. Using a large gene expression compendium, we determine the conditions where subpathways exhibit strong coexpression. Finally, we develop "WormClust," a web application that enables a gene-by-gene query of genes to view their association with metabolic (sub)-pathways. Overall, this study sheds light on the ubiquity of transcriptional regulation of metabolism and provides a blueprint for similar studies in other organisms, including humans.
    Keywords:  gene regulation; metabolic network model; metabolism; systems biology; transcription
    DOI:  https://doi.org/10.15252/msb.202211443
  31. Nature. 2023 Mar 22.
    Cancer cells remodel nuclear actin filaments to resist chemotherapy.
    Stephanie Panier.
      
    Keywords:  Cancer; Medical research
    DOI:  https://doi.org/10.1038/d41586-023-00801-y
  32. Methods Mol Biol. 2023 ;2643 135-148
    Proximity-Ligation Assay to Detect Peroxisome-Organelle Interaction.
    Maki Kamoshita, Michael Schrader.
      Peroxisomes are essential organelles in mammals, which contribute to cellular lipid metabolism and redox homeostasis. They do not function as isolated entities but cooperate and interact with other subcellular organelles, in particular the endoplasmic reticulum, mitochondria, and lipid droplets. Those interactions are often mediated by membrane contact sites. Tether proteins at those sites bring the organelles in close proximity to facilitate metabolite and lipid transfer as well as organelle communication. There is great interest in the investigation of the physiological functions of peroxisome-organelle contacts and how they are regulated. Here, we present an antibody- and fluorescence-based proximity ligation approach used successfully in our laboratory for the detection and quantification of peroxisome-organelle interactions in cultured mammalian cells.
    Keywords:  Cell culture; Immunofluorescence; Membrane contact sites; Organelle interaction; Peroxisome; Proximity ligation; Transfection
    DOI:  https://doi.org/10.1007/978-1-0716-3048-8_10
  33. Sci Adv. 2023 Mar 24. 9(12): eadd9554
    The lactate dehydrogenase (LDH) isoenzyme spectrum enables optimally controlling T cell glycolysis and differentiation.
    Xuyong Chen, Lingling Liu, Siwen Kang, Jn Rashida Gnanaprakasam, Ruoning Wang.
      Isoenzyme divergence is a prevalent mechanism governing tissue-specific and developmental stage-specific metabolism in mammals. The lactate dehydrogenase (LDH) isoenzyme spectrum reflects the tissue-specific metabolic status. We found that three tetrameric isoenzymes composed of LDHA and LDHB (LDH-3/4/5) comprise the LDH spectrum in T cells. Genetically deleting LDHA or LDHB altered the isoenzyme spectrum by removing all heterotetramers and leaving T cells with LDH-1 (the homotetramer of LDHB) or LDH-5 (the homotetramer of LDHA), respectively. Accordingly, deleting LDHA suppressed glycolysis, cell proliferation, and differentiation. Unexpectedly, deleting LDHB enhanced glycolysis but suppressed T cell differentiation, indicating that an optimal zone of glycolytic activity is required to maintain cell fitness. Mechanistically, the LDH isoenzyme spectrum imposed by LDHA and LDHB is necessary to optimize glycolysis to maintain a balanced nicotinamide adenine dinucleotide/nicotinamide adenine dinucleotide hydrogen pool. Our results suggest that the LDH isoenzyme spectrum enables "Goldilocks levels" of glycolytic and redox activity to control T cell differentiation.
    DOI:  https://doi.org/10.1126/sciadv.add9554
  34. Mol Cell. 2023 Mar 08. pii: S1097-2765(23)00151-X. [Epub ahead of print]
    m6A-driven SF3B1 translation control steers splicing to direct genome integrity and leukemogenesis.
    Maciej Cieśla, Phuong Cao Thi Ngoc, Sowndarya Muthukumar, Gabriele Todisco, Magdalena Madej, Helena Fritz, Marios Dimitriou, Danny Incarnato, Eva Hellström-Lindberg, Cristian Bellodi.
      SF3B1 is the most mutated splicing factor (SF) in myelodysplastic syndromes (MDSs), which are clonal hematopoietic disorders with variable risk of leukemic transformation. Although tumorigenic SF3B1 mutations have been extensively characterized, the role of "non-mutated" wild-type SF3B1 in cancer remains largely unresolved. Here, we identify a conserved epitranscriptomic program that steers SF3B1 levels to counteract leukemogenesis. Our analysis of human and murine pre-leukemic MDS cells reveals dynamic regulation of SF3B1 protein abundance, which affects MDS-to-leukemia progression in vivo. Mechanistically, ALKBH5-driven 5' UTR m6A demethylation fine-tunes SF3B1 translation directing splicing of central DNA repair and epigenetic regulators during transformation. This impacts genome stability and leukemia progression in vivo, supporting an integrative analysis in humans that SF3B1 molecular signatures may predict mutational variability and poor prognosis. These findings highlight a post-transcriptional gene expression nexus that unveils unanticipated SF3B1-dependent cancer vulnerabilities.
    Keywords:  ALKBH5; MYC; SF3B1; acute myeloid leukemia; alternative splicing; genome integrity; m(6)A; myelodysplastic syndromes; p53; translation
    DOI:  https://doi.org/10.1016/j.molcel.2023.02.024
  35. Nature. 2023 Mar 22.
    RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer.
    Amina Jbara, Kuan-Ting Lin, Chani Stossel, Zahava Siegfried, Haya Shqerat, Adi Amar-Schwartz, Ela Elyada, Maxim Mogilevsky, Maria Raitses-Gurevich, Jared L Johnson, Tomer M Yaron, Ofek Ovadia, Gun Ho Jang, Miri Danan-Gotthold, Lewis C Cantley, Erez Y Levanon, Steven Gallinger, Adrian R Krainer, Talia Golan, Rotem Karni.
      Pancreatic ductal adenocarcinoma (PDA) is characterized by aggressive local invasion and metastatic spread, leading to high lethality. Although driver gene mutations during PDA progression are conserved, no specific mutation is correlated with the dissemination of metastases1-3. Here we analysed RNA splicing data of a large cohort of primary and metastatic PDA tumours to identify differentially spliced events that correlate with PDA progression. De novo motif analysis of these events detected enrichment of motifs with high similarity to the RBFOX2 motif. Overexpression of RBFOX2 in a patient-derived xenograft (PDX) metastatic PDA cell line drastically reduced the metastatic potential of these cells in vitro and in vivo, whereas depletion of RBFOX2 in primary pancreatic tumour cell lines increased the metastatic potential of these cells. These findings support the role of RBFOX2 as a potent metastatic suppressor in PDA. RNA-sequencing and splicing analysis of RBFOX2 target genes revealed enrichment of genes in the RHO GTPase pathways, suggesting a role of RBFOX2 splicing activity in cytoskeletal organization and focal adhesion formation. Modulation of RBFOX2-regulated splicing events, such as via myosin phosphatase RHO-interacting protein (MPRIP), is associated with PDA metastases, altered cytoskeletal organization and the induction of focal adhesion formation. Our results implicate the splicing-regulatory function of RBFOX2 as a tumour suppressor in PDA and suggest a therapeutic approach for metastatic PDA.
    DOI:  https://doi.org/10.1038/s41586-023-05820-3
  36. Proc Natl Acad Sci U S A. 2023 Mar 28. 120(13): e2210796120
    Redox metabolism maintains the leukemogenic capacity and drug resistance of AML cells.
    Dan Huang, Changcheng Zhang, Ming Xiao, Xie Li, Weicai Chen, Yu Jiang, Yamin Yuan, Yaping Zhang, Yejun Zou, Lei Deng, Yang Wang, Yuying Sun, Wenping Dong, Zhuo Zhang, Li Xie, Zhuo Yu, Chiqi Chen, Ligen Liu, Jing Wang, Yi Yang, Jie Yang, Yuzheng Zhao, Junke Zheng.
      Rewiring of redox metabolism has a profound impact on tumor development, but how the cellular heterogeneity of redox balance affects leukemogenesis remains unknown. To precisely characterize the dynamic change in redox metabolism in vivo, we developed a bright genetically encoded biosensor for H2O2 (named HyPerion) and tracked the redox state of leukemic cells in situ in a transgenic sensor mouse. A H2O2-low (HyPerion-low) subset of acute myeloid leukemia (AML) cells was enriched with leukemia-initiating cells, which were endowed with high colony-forming ability, potent drug resistance, endosteal rather than vascular localization, and short survival. Significantly high expression of malic enzymes, including ME1/3, accounted for nicotinamide adenine dinucleotide phosphate (NADPH) production and the subsequent low abundance of H2O2. Deletion of malic enzymes decreased the population size of leukemia-initiating cells and impaired their leukemogenic capacity and drug resistance. In summary, by establishing an in vivo redox monitoring tool at single-cell resolution, this work reveals a critical role of redox metabolism in leukemogenesis and a potential therapeutic target.
    Keywords:  AML; H2O2 biosensor; drug resistance; leukemia-initiating cells; redox metabolism
    DOI:  https://doi.org/10.1073/pnas.2210796120
  37. bioRxiv. 2023 Mar 09. pii: 2023.03.09.531795. [Epub ahead of print]
    Tetracycline-dependent inhibition of mitoribosome protein elongation in mitochondrial disease mutant cells suppresses IRE1α to promote cell survival.
    Conor T Ronayne, Christopher F Bennett, Elizabeth A Perry, Noa Kantorovic, Pere Puigserver.
      Mitochondrial diseases are a group of disorders defined by defects in oxidative phosphorylation caused by nuclear- or mitochondrial-encoded gene mutations. A main cellular phenotype of mitochondrial disease mutations are redox imbalances and inflammatory signaling underlying pathogenic signatures of these patients. Depending on the type of mitochondrial mutation, certain mechanisms can efficiently rescue cell death vulnerability. One method is the inhibition of mitochondrial translation elongation using tetracyclines, potent suppressors of cell death in mitochondrial disease mutant cells. However, the mechanisms whereby tetracyclines promote cell survival are unknown. Here, we show that in mitochondrial mutant disease cells, tetracycline-mediated inhibition of mitoribosome elongation promotes survival through suppression of the ER stress IRE1α protein. Tetracyclines increased levels of the splitting factor MALSU1 (Mitochondrial Assembly of Ribosomal Large Subunit 1) at the mitochondria with recruitment to the mitochondrial ribosome (mitoribosome) large subunit. MALSU1, but not other quality control factors, was required for tetracycline-induced cell survival in mitochondrial disease mutant cells during glucose starvation. In these cells, nutrient stress induced cell death through IRE1α activation associated with a strong protein loading in the ER lumen. Notably, tetracyclines rescued cell death through suppression of IRE1α oligomerization and activity. Consistent with MALSU1 requirement, MALSU1 deficient mitochondrial mutant cells were sensitive to glucose-deprivation and exhibited increased ER stress and activation of IRE1α that was not reversed by tetracyclines. These studies show that inhibition of mitoribosome elongation signals to the ER to promote survival, establishing a new interorganelle communication between the mitoribosome and ER with implications in basic mechanisms of cell survival and treatment of mitochondrial diseases.
    Significance Statement: Mitochondrial diseases are a rare and heterogenous class of diseases that result from mutations in mitochondrial genes. Currently, there are no curative therapies due to a lack of mechanistic insights into pathological transformation and signaling. Our lab has discovered that the class of mitochondrial ribosome targeting antibiotics, tetracyclines, promote survival and fitness in models of mitochondrial disease, establishing a new paradigm of cell survival under nutrient stress conditions. In the current study, we present mechanistic insights into tetracyclines ability to rescue mitochondrial disease cells, detailing an interorganelle communication between mitochondrial protein translation and the unfolded protein response during endoplasmic reticulum stress.
    DOI:  https://doi.org/10.1101/2023.03.09.531795
  38. Nat Cell Biol. 2023 Mar 23.
    Co-option of epidermal cells enables touch sensing.
    Federica Mangione, Joshua Titlow, Catherine Maclachlan, Michel Gho, Ilan Davis, Lucy Collinson, Nicolas Tapon.
      The epidermis is equipped with specialized mechanosensory organs that enable the detection of tactile stimuli. Here, by examining the differentiation of the tactile bristles, mechanosensory organs decorating the Drosophila adult epidermis, we show that neighbouring epidermal cells are essential for touch perception. Each mechanosensory bristle signals to the surrounding epidermis to co-opt a single epidermal cell, which we named the F-Cell. Once specified, the F-Cell adopts a specialized morphology to ensheath each bristle. Functional assays reveal that adult mechanosensory bristles require association with the epidermal F-Cell for touch sensing. Our findings underscore the importance of resident epidermal cells in the assembly of functional touch-sensitive organs.
    DOI:  https://doi.org/10.1038/s41556-023-01110-2
  39. Nat Metab. 2023 Mar 23.
    Loss of fatty acid degradation by astrocytic mitochondria triggers neuroinflammation and neurodegeneration.
    Yashi Mi, Guoyuan Qi, Francesca Vitali, Yuan Shang, Adam C Raikes, Tian Wang, Yan Jin, Roberta D Brinton, Haiwei Gu, Fei Yin.
      Astrocytes provide key neuronal support, and their phenotypic transformation is implicated in neurodegenerative diseases. Metabolically, astrocytes possess low mitochondrial oxidative phosphorylation (OxPhos) activity, but its pathophysiological role in neurodegeneration remains unclear. Here, we show that the brain critically depends on astrocytic OxPhos to degrade fatty acids (FAs) and maintain lipid homeostasis. Aberrant astrocytic OxPhos induces lipid droplet (LD) accumulation followed by neurodegeneration that recapitulates key features of Alzheimer's disease (AD), including synaptic loss, neuroinflammation, demyelination and cognitive impairment. Mechanistically, when FA load overwhelms astrocytic OxPhos capacity, elevated acetyl-CoA levels induce astrocyte reactivity by enhancing STAT3 acetylation and activation. Intercellularly, lipid-laden reactive astrocytes stimulate neuronal FA oxidation and oxidative stress, activate microglia through IL-3 signalling, and inhibit the biosynthesis of FAs and phospholipids required for myelin replenishment. Along with LD accumulation and impaired FA degradation manifested in an AD mouse model, we reveal a lipid-centric, AD-resembling mechanism by which astrocytic mitochondrial dysfunction progressively induces neuroinflammation and neurodegeneration.
    DOI:  https://doi.org/10.1038/s42255-023-00756-4
  40. Nat Genet. 2023 Mar 23.
    Thymidine nucleotide metabolism controls human telomere length.
    William Mannherz, Suneet Agarwal.
      Telomere length in humans is associated with lifespan and severe diseases, yet the genetic determinants of telomere length remain incompletely defined. Here we performed genome-wide CRISPR-Cas9 functional telomere length screening and identified thymidine (dT) nucleotide metabolism as a limiting factor in human telomere maintenance. Targeted genetic disruption using CRISPR-Cas9 revealed multiple telomere length control points across the thymidine nucleotide metabolism pathway: decreasing dT nucleotide salvage via deletion of the gene encoding nuclear thymidine kinase (TK1) or de novo production by knockout of the thymidylate synthase gene (TYMS) decreased telomere length, whereas inactivation of the deoxynucleoside triphosphohydrolase-encoding gene SAMHD1 lengthened telomeres. Remarkably, supplementation with dT alone drove robust telomere elongation by telomerase in cells, and thymidine triphosphate stimulated telomerase activity in a substrate-independent manner in vitro. In induced pluripotent stem cells derived from patients with genetic telomere biology disorders, dT supplementation or inhibition of SAMHD1 promoted telomere restoration. Our results demonstrate a critical role of thymidine metabolism in controlling human telomerase and telomere length, which may be therapeutically actionable in patients with fatal degenerative diseases.
    DOI:  https://doi.org/10.1038/s41588-023-01339-5
  41. Urol Clin North Am. 2023 May;pii: S0094-0143(23)00010-1. [Epub ahead of print]50(2): 205-215
    Diseases of Hereditary Renal Cell Cancers.
    Othon Iliopoulos.
      Germline mutations in tumor suppressor genes and oncogenes lead to hereditary renal cell carcinoma (HRCC) diseases, characterized by a high risk of RCC and extrarenal manifestations. Patients of young age, those with a family history of RCC, and/or those with a personal and family history of HRCC-related extrarenal manifestations should be referred for germline testing. Identification of a germline mutation will allow for testing of family members at risk, as well as personalized surveillance programs to detect the early onset of HRCC-related lesions. The latter allows for more targeted and therefore more effective therapy and better preservation of renal parenchyma.
    Keywords:  Birt–Hogg–Dubé (BHD); Folliculin; Fumarate hydratase (FH); Germline mutations; Hereditary kidney cancers; Hereditary leiomyomatosis and renal cell carcinoma (HLRCC); Succinate dehydrogenase (SDH); Von Hippel–Lindau (VHL)
    DOI:  https://doi.org/10.1016/j.ucl.2023.01.010
  42. Cell Rep. 2023 Mar 23. pii: S2211-1247(23)00307-8. [Epub ahead of print]42(4): 112296
    Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA ubiquitination.
    Yi-Chang Wang, Andrew A Kelso, Adak Karamafrooz, Yi-Hsuan Chen, Wei-Kai Chen, Chun-Ting Cheng, Yue Qi, Long Gu, Linda Malkas, Angelo Taglialatela, Hsing-Jien Kung, George-Lucian Moldovan, Alberto Ciccia, Jeremy M Stark, David K Ann.
      The arginine dependency of cancer cells creates metabolic vulnerability. In this study, we examine the impact of arginine availability on DNA replication and genotoxicity resistance. Using DNA combing assays, we find that limiting extracellular arginine results in the arrest of cancer cells at S phase and a slowing or stalling of DNA replication. The translation of new histone H4 is arginine dependent and influences DNA replication. Increased proliferating cell nuclear antigen (PCNA) occupancy and helicase-like transcription factor (HLTF)-catalyzed PCNA K63-linked polyubiquitination protect arginine-starved cells from DNA damage. Arginine-deprived cancer cells display tolerance to genotoxicity in a PCNA K63-linked polyubiquitination-dependent manner. Our findings highlight the crucial role of extracellular arginine in nutrient-regulated DNA replication and provide potential avenues for the development of cancer treatments.
    Keywords:  CP: Molecular biology; HLTF; K63-linked polyubiquitination; PCNA; S phase; arginine; genotoxin resistance; histone H4; replication stress; translation
    DOI:  https://doi.org/10.1016/j.celrep.2023.112296
  43. Trends Cell Biol. 2023 Mar 22. pii: S0962-8924(23)00040-5. [Epub ahead of print]
    Bucket lists must be completed during cell death.
    Kengo Nozaki, Edward A Miao.
      Regulated cell death occurs in many forms, including apoptosis, pyroptosis, necroptosis, and NETosis. Most obviously, the purpose of these pathways is to kill the cell. However, many cells need to complete a set of effector programs before they die, which we define as a cellular 'bucket list'. These effector programs are specific to the cell type, and mode and circumstances of death. For example, intestinal epithelial cells need to complete the process of extrusion before they die. Cells use regulatory mechanisms to temporarily prolong their life, including endosomal sorting complex required for transport (ESCRT)- and acid sphingomyelinase (ASM)-driven membrane repair. These allow cells to complete their bucket lists before they die.
    Keywords:  ESCRT; acid sphingomyelinase; caspase-7; cell death; gasdermin; membrane repair
    DOI:  https://doi.org/10.1016/j.tcb.2023.02.008
  44. Cell Rep. 2023 Mar 22. pii: S2211-1247(23)00314-5. [Epub ahead of print]42(4): 112303
    Saturated fatty acids dampen the immunogenicity of cancer by suppressing STING.
    Blake R Heath, Wang Gong, Hülya F Taner, Luke Broses, Kohei Okuyama, Wanqing Cheng, Max Jin, Zackary R Fitzsimonds, Andriana Manousidaki, Yuesong Wu, Shaoping Zhang, Haitao Wen, Steven B Chinn, Eric Bartee, Yuying Xie, James J Moon, Yu Leo Lei.
      Oncogenes destabilize STING in epithelial cell-derived cancer cells, such as head and neck squamous cell carcinomas (HNSCCs), to promote immune escape. Despite the abundance of tumor-infiltrating myeloid cells, HNSCC presents notable resistance to STING stimulation. Here, we show how saturated fatty acids in the microenvironment dampen tumor response to STING stimulation. Using single-cell analysis, we found that obesity creates an IFN-I-deprived tumor microenvironment with a massive expansion of suppressive myeloid cell clusters and contraction of effector T cells. Saturated fatty acids, but not unsaturated fatty acids, potently inhibit the STING-IFN-I pathway in HNSCC cells. Myeloid cells from obese mice show dampened responses to STING stimulation and are more suppressive of T cell activation. In agreement, obese hosts exhibited increased tumor burden and lower responsiveness to STING agonist. As a mechanism, saturated fatty acids induce the expression of NLRC3, depletion of which results in a T cell inflamed tumor microenvironment and IFN-I-dependent tumor control.
    Keywords:  CP: Cancer; CP: Immunology; NLRC3; STING; head and neck cancer; immunogenicity; innate immunity; metabolism; obesity; saturated fatty acids; type-I interferon
    DOI:  https://doi.org/10.1016/j.celrep.2023.112303
  45. Elife. 2023 Mar 23. pii: e85289. [Epub ahead of print]12
    Lipid hydroperoxides promote sarcopenia through carbonyl stress.
    Hiroaki Eshima, Justin L Shahtout, Piyarat Siripoksup, MacKenzie J Pearson, Ziad S Mahmassani, Patrick J Ferrara, Alexis W Lyons, John Alan Maschek, Alek D Peterlin, Anthony R P Verkerke, Jordan M Johnson, Anahy Salcedo, Jonathan J Petrocelli, Edwin R Miranda, Ethan J Anderson, Sihem Boudina, Qitao Ran, James E Cox, Micah J Drummond, Katsuhiko Funai.
      Reactive oxygen species (ROS) accumulation is a cardinal feature of skeletal muscle atrophy. ROS refers to a collection of radical molecules whose cellular signals are vast, and it is unclear which downstream consequences of ROS are responsible for the loss of muscle mass and strength. Here we show that lipid hydroperoxides (LOOH) are increased with age and disuse, and the accumulation of LOOH by deletion of glutathione peroxidase 4 (GPx4) is sufficient to augment muscle atrophy. LOOH promoted atrophy in a lysosomal-dependent, proteasomal-independent manner. In young and old mice, genetic and pharmacologic neutralization of LOOH or their secondary reactive lipid aldehydes robustly prevented muscle atrophy and weakness, indicating that LOOH-derived carbonyl stress mediates age- and disuse-induced muscle dysfunction. Our findings provide novel insights for the role of LOOH in sarcopenia including a therapeutic implication by pharmacologic suppression.
    Keywords:  cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.85289
  46. bioRxiv. 2023 Mar 06. pii: 2023.03.05.531161. [Epub ahead of print]
    Beyond the Genetic Code: A Tissue Code?
    Bruce M Boman, Thien-Nam Dinh, Keith Decker, Brooks Emerick, Shirin Modarai, Lynn Opdenaker, Jeremy Z Fields, Christopher Raymond, Gilberto Schleiniger.
      The genetic code determines how the precise amino acid sequence of proteins is specified by genomic information in cells. But what specifies the precise histologic organization of cells in plant and animal tissues is unclear. We now hypothesize that another code, the tissue code , exists at an even higher level of complexity which determines how tissue organization is dynamically maintained. Accordingly, we modeled spatial and temporal asymmetries of cell division and established that five simple mathematical laws ("the tissue code") convey a set of biological rules that maintain the specific organization and continuous self-renewal dynamics of cells in tissues. These laws might even help us understand wound healing, and how tissue disorganization leads to birth defects and tissue pathology like cancer.
    DOI:  https://doi.org/10.1101/2023.03.05.531161
  47. Proc Natl Acad Sci U S A. 2023 Mar 28. 120(13): e2221453120
    Synchronization of the circadian clock to the environment tracked in real time.
    Mingxu Fang, Archana G Chavan, Andy LiWang, Susan S Golden.
      The circadian system of the cyanobacterium Synechococcus elongatus PCC 7942 relies on a three-protein nanomachine (KaiA, KaiB, and KaiC) that undergoes an oscillatory phosphorylation cycle with a period of ~24 h. This core oscillator can be reconstituted in vitro and is used to study the molecular mechanisms of circadian timekeeping and entrainment. Previous studies showed that two key metabolic changes that occur in cells during the transition into darkness, changes in the ATP/ADP ratio and redox status of the quinone pool, are cues that entrain the circadian clock. By changing the ATP/ADP ratio or adding oxidized quinone, one can shift the phase of the phosphorylation cycle of the core oscillator in vitro. However, the in vitro oscillator cannot explain gene expression patterns because the simple mixture lacks the output components that connect the clock to genes. Recently, a high-throughput in vitro system termed the in vitro clock (IVC) that contains both the core oscillator and the output components was developed. Here, we used IVC reactions and performed massively parallel experiments to study entrainment, the synchronization of the clock with the environment, in the presence of output components. Our results indicate that the IVC better explains the in vivo clock-resetting phenotypes of wild-type and mutant strains and that the output components are deeply engaged with the core oscillator, affecting the way input signals entrain the core pacemaker. These findings blur the line between input and output pathways and support our previous demonstration that key output components are fundamental parts of the clock.
    Keywords:  Circadian clock; Circadian phase resetting; Cyanobacteria; KaiC; Real-time monitoring
    DOI:  https://doi.org/10.1073/pnas.2221453120
  48. Sci Adv. 2023 Mar 22. 9(12): eadd5028
    Breast tumors interfere with endothelial TRAIL at the premetastatic niche to promote cancer cell seeding.
    Carla Riera-Domingo, Eduarda Leite-Gomes, Iris Charatsidou, Peihua Zhao, Giovanna Carrá, Federica Cappellesso, Larissa Mourao, Maxim De Schepper, Dana Liu, Jens Serneels, Mohamad-Gabriel Alameh, Vladimir V Shuvaev, Tatjana Geukens, Edoardo Isnaldi, Hans Prenen, Drew Weissman, Vladimir R Muzykantov, Stefaan Soenen, Christine Desmedt, Colinda L G J Scheele, Anna Sablina, Mario Di Matteo, Rosa Martín-Pérez, Massimiliano Mazzone.
      Endothelial cells (ECs) grant access of disseminated cancer cells to distant organs. However, the molecular players regulating the activation of quiescent ECs at the premetastatic niche (PMN) remain elusive. Here, we find that ECs at the PMN coexpress tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and its cognate death receptor 5 (DR5). Unexpectedly, endothelial TRAIL interacts intracellularly with DR5 to prevent its signaling and preserve a quiescent vascular phenotype. In absence of endothelial TRAIL, DR5 activation induces EC death and nuclear factor κB/p38-dependent EC stickiness, compromising vascular integrity and promoting myeloid cell infiltration, breast cancer cell adhesion, and metastasis. Consistently, both down-regulation of endothelial TRAIL at the PMN by proangiogenic tumor-secreted factors and the presence of the endogenous TRAIL inhibitors decoy receptor 1 (DcR1) and DcR2 favor metastasis. This study discloses an intracrine mechanism whereby TRAIL blocks DR5 signaling in quiescent endothelia, acting as gatekeeper of the vascular barrier that is corrupted by the tumor during cancer cell dissemination.
    DOI:  https://doi.org/10.1126/sciadv.add5028
  49. Aging Cell. 2023 Mar 20. e13822
    Mitochondrial function declines with age within individuals but is not linked to the pattern of growth or mortality risk in zebra finch.
    Pablo Salmón, Neal J Dawson, Caroline Millet, Colin Selman, Pat Monaghan.
      Mitochondrial dysfunction is considered a highly conserved hallmark of ageing. However, most of the studies in both model and non-model organisms are cross-sectional in design; therefore, little is known, at the individual level, on how mitochondrial function changes with age, its link to early developmental conditions or its relationship with survival. Here we manipulated the postnatal growth in zebra finches (Taeniopygia guttata) via dietary modification that induced accelerated growth without changing adult body size. In the same individuals, we examined blood cells mitochondrial functioning (mainly erythrocytes) when they were young (ca. 36 weeks) and again in mid-aged (ca. 91 weeks) adulthood. Mitochondrial function was strongly influenced by age but not by postnatal growth conditions. Across all groups, within individual ROUTINE respiration, OXPHOS and OXPHOS coupling efficiency significantly declined with age, while LEAK respiration increased. However, we found no link between mitochondrial function and the probability of survival into relatively old age (ca. 4 years). Our results suggest that the association between accelerated growth and reduced longevity, evident in this as in other species, is not attributable to age-related changes in any of the measured mitochondrial function traits.
    Keywords:  ageing; avian models; mitochondria; red blood cells; senescence; survival
    DOI:  https://doi.org/10.1111/acel.13822
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