bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2021‒04‒18
fifty-four papers selected by
Christian Frezza,

  1. A naturally occurring mutation in ATP synthase subunit c is associated with increased damage following hypoxia/reoxygenation in STEMI patients.
  2. A guide to interrogating immunometabolism.
  3. AMPK signaling and its targeting in cancer progression and treatment.
  4. The functional roles of TCA cycle metabolites in cancer.
  5. AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity.
  6. Metabolic impact of pathogenic variants in the mitochondrial glutamyl-tRNA synthetase EARS2.
  7. Depletion of mitochondrial inorganic polyphosphate (polyP) in mammalian cells causes metabolic shift from oxidative phosphorylation to glycolysis.
  8. Metabolic flexibility determines human NK cell functional fate in the tumor microenvironment.
  9. Mitochondrial membrane tension governs fission.
  10. Mitochondrial hydrogen peroxide positively regulates neuropeptide secretion during diet-induced activation of the oxidative stress response.
  11. TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia.
  12. Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.
  13. The Roles of 2-Hydroxyglutarate.
  14. Mitochondrial biogenesis in developing astrocytes regulates astrocyte maturation and synapse formation.
  15. Ferroptotic cell death triggered by conjugated linolenic acids is mediated by ACSL1.
  16. A methionine-Mettl3-N6-methyladenosine axis promotes polycystic kidney disease.
  17. Lactic Acid Fermentation Is Required for NLRP3 Inflammasome Activation.
  18. Elevated Asparagine Biosynthesis Drives Brain Tumor Stem Cell Metabolic Plasticity and Resistance to Oxidative Stress.
  19. An energetics perspective on geroscience: mitochondrial protonmotive force and aging.
  20. Towards a new WHO classification of renal cell tumor: what the clinician needs to know-a narrative review.
  21. CFTR chloride channel activity modulates the mitochondrial morphology in cultured epithelial cells.
  22. The function of glutaredoxin GRXS15 is required for lipoyl-dependent dehydrogenases in mitochondria.
  23. A membrane arm of mitochondrial complex I sufficient to promote respirasome formation.
  24. NMR-Based Serum and Urine Metabolomic Profile Reveals Suppression of Mitochondrial Pathways in Experimental Sepsis-Associated Acute Kidney Injury.
  25. Brd4-bound enhancers drive cell-intrinsic sex differences in glioblastoma.
  26. CRL4AMBRA1 is a master regulator of D-type cyclins.
  27. The interplay between DNA and histone methylation: molecular mechanisms and disease implications.
  28. Oncogenic KRAS recruits an expansive transcriptional network through mutant p53 to drive pancreatic cancer metastasis.
  29. Kog1/Raptor mediates metabolic rewiring during nutrient limitation by controlling SNF1/AMPK activity.
  30. P53 regulates cellular redox state, ferroptosis and metabolism.
  31. Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation.
  32. Glucose makes Treg lose their temper.
  33. Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1.
  34. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics.
  35. Spatiotemporal regulation of hydrogen sulfide signaling in the kidney.
  36. Dietary spermidine improves cognitive function.
  37. Inositol treatment inhibits medulloblastoma through suppression of epigenetic-driven metabolic adaptation.
  38. SOD1 regulates ribosome biogenesis in KRAS mutant non-small cell lung cancer.
  39. eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction.
  40. Role of LncRNAs in regulating cancer amino acid metabolism.
  41. Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets.
  42. ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER.
  43. Organelle degradation in the lens by PLAAT phospholipases.
  44. An in vitro tumorigenesis model based on live-cell-generated oxygen and nutrient gradients.
  45. Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes.
  46. Parkin-independent mitophagy via Drp1-mediated outer membrane severing and inner membrane ubiquitination.
  47. Age-induced metabolic reprogramming underlies cancer progression.
  48. Mitochondrial OMA1 and OPA1 as Gatekeepers of Organellar Structure/Function and Cellular Stress Response.
  49. Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer.
  50. NLRP3 as a sensor of metabolism gone awry.
  51. The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.
  52. Pancreatic stellate cells regulate branched-chain amino acid metabolism in pancreatic cancer.
  53. Clocking cancer: the circadian clock as a target in cancer therapy.
  54. A note on the power per mitochondrion and the number of associated active ATP synthases.
  1. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00297-7. [Epub ahead of print]35(2): 108983
    A naturally occurring mutation in ATP synthase subunit c is associated with increased damage following hypoxia/reoxygenation in STEMI patients.
    Giampaolo Morciano, Gaia Pedriali, Massimo Bonora, Rita Pavasini, Elisa Mikus, Simone Calvi, Matteo Bovolenta, Magdalena Lebiedzinska-Arciszewska, Mirko Pinotti, Alberto Albertini, Mariusz R Wieckowski, Carlotta Giorgi, Roberto Ferrari, Lorenzo Galluzzi, Gianluca Campo, Paolo Pinton.
      Preclinical models of ischemia/reperfusion injury (RI) demonstrate the deleterious effects of permeability transition pore complex (PTPC) opening in the first minutes upon revascularization of the occluded vessel. The ATP synthase c subunit (Csub) influences PTPC activity in cells, thus impacting tissue injury. A conserved glycine-rich domain in Csub is classified as critical because, when mutated, it modifies ATP synthase properties, protein interaction with the mitochondrial calcium (Ca2+) uniporter complex, and the conductance of the PTPC. Here, we document the role of a naturally occurring mutation in the Csub-encoding ATP5G1 gene at the G87 position found in two ST-segment elevation myocardial infarction (STEMI) patients and how PTPC opening is related to RI in patients affected by the same disease. We report a link between the expression of ATP5G1G87E and the response to hypoxia/reoxygenation of human cardiomyocytes, which worsen when compared to those expressing the wild-type protein, and a positive correlation between PTPC and RI.
    Keywords:  ATP synthase; PTP; STEMI patients; cardiovascular diseases; glycine-rich domain; ischemia; mitochondria; reperfusion injury; subunit c
    DOI:  https://doi.org/10.1016/j.celrep.2021.108983
  2. Nat Rev Immunol. 2021 Apr 15.
    A guide to interrogating immunometabolism.
    Kelsey Voss, Hanna S Hong, Jackie E Bader, Ayaka Sugiura, Costas A Lyssiotis, Jeffrey C Rathmell.
      The metabolic charts memorized in early biochemistry courses, and then later forgotten, have come back to haunt many immunologists with new recognition of the importance of these pathways. Metabolites and the activity of metabolic pathways drive energy production, macromolecule synthesis, intracellular signalling, post-translational modifications and cell survival. Immunologists who identify a metabolic phenotype in their system are often left wondering where to begin and what does it mean? Here, we provide a framework for navigating and selecting the appropriate biochemical techniques to explore immunometabolism. We offer recommendations for initial approaches to develop and test metabolic hypotheses and how to avoid common mistakes. We then discuss how to take things to the next level with metabolomic approaches, such as isotope tracing and genetic approaches. By proposing strategies and evaluating the strengths and weaknesses of different methodologies, we aim to provide insight, note important considerations and discuss ways to avoid common misconceptions. Furthermore, we highlight recent studies demonstrating the power of these metabolic approaches to uncover the role of metabolism in immunology. By following the framework in this Review, neophytes and seasoned investigators alike can venture into the emerging realm of cellular metabolism and immunity with confidence and rigour.
    DOI:  https://doi.org/10.1038/s41577-021-00529-8
  3. Semin Cancer Biol. 2021 Apr 13. pii: S1044-579X(21)00107-3. [Epub ahead of print]
    AMPK signaling and its targeting in cancer progression and treatment.
    Che-Chia Hsu, Danni Peng, Zhen Cai, Hui-Kuan Lin.
      The intrinsic mechanisms sensing the imbalance of energy in cells are pivotal for cell survival under various environmental insults. AMP-activated protein kinase (AMPK) serves as a central guardian maintaining energy homeostasis by orchestrating diverse cellular processes, such as lipogenesis, glycolysis, TCA cycle, cell cycle progression and mitochondrial dynamics. Given that AMPK plays an essential role in the maintenance of energy balance and metabolism, managing AMPK activation is considered as a promising strategy for the treatment of metabolic disorders such as type 2 diabetes and obesity. Since AMPK has been attributed to aberrant activation of metabolic pathways, mitochondrial dynamics and functions, and epigenetic regulation, which are hallmarks of cancer, targeting AMPK may open up a new avenue for cancer therapies. Although AMPK is previously thought to be involved in tumor suppression, several recent studies have unraveled its tumor promoting activity. The double-edged sword characteristics for AMPK as a tumor suppressor or an oncogene are determined by distinct cellular contexts. In this review, we will summarize recent progress in dissecting the upstream regulators and downstream effectors for AMPK, discuss the distinct roles of AMPK in cancer regulation and finally offer potential strategies with AMPK targeting in cancer therapy.
    Keywords:  AMPK; Cancer; glucose deprivation; metabolism; mitocondrial; phosphorylation
    DOI:  https://doi.org/10.1016/j.semcancer.2021.04.006
  4. Oncogene. 2021 Apr 16.
    The functional roles of TCA cycle metabolites in cancer.
    Joseph Eniafe, Shuai Jiang.
      The tricarboxylic acid cycle (TCA cycle) has been known for decades as a hub for generating cellular energy and precursors for biosynthetic pathways. Several cancers harbor mutations that affect the integrity of this cycle, mostly at the levels of isocitrate dehydrogenase (IDH), succinate dehydrogenase (SDH), and fumarate hydratase (FH). This results in dysregulation in the production of TCA cycle metabolites and is probably implicated in cancer initiation. By modulating cellular activities, including metabolism and signaling, TCA cycle intermediates are able to impact the processes of cancer development and progression. In this review, we discuss the functional roles of the TCA cycle intermediates in suppressing or promoting the progression of cancers. A further understanding of TCA metabolites' roles and molecular mechanisms in oncogenesis would prompt developing novel metabolite-based cancer therapy in the future.
    DOI:  https://doi.org/10.1038/s41388-020-01639-8
  5. Nature. 2021 Apr 14.
    AMBRA1 regulates cyclin D to guard S-phase entry and genomic integrity.
    Emiliano Maiani, Giacomo Milletti, Francesca Nazio, Søs Grønbæk Holdgaard, Jirina Bartkova, Salvatore Rizza, Valentina Cianfanelli, Mar Lorente, Daniele Simoneschi, Miriam Di Marco, Pasquale D'Acunzo, Luca Di Leo, Rikke Rasmussen, Costanza Montagna, Marilena Raciti, Cristiano De Stefanis, Estibaliz Gabicagogeascoa, Gergely Rona, Nélida Salvador, Emanuela Pupo, Joanna Maria Merchut-Maya, Colin J Daniel, Marianna Carinci, Valeriana Cesarini, Alfie O'sullivan, Yeon-Tae Jeong, Matteo Bordi, Francesco Russo, Silvia Campello, Angela Gallo, Giuseppe Filomeni, Letizia Lanzetti, Rosalie C Sears, Petra Hamerlik, Armando Bartolazzi, Robert E Hynds, David R Pearce, Charles Swanton, Michele Pagano, Guillermo Velasco, Elena Papaleo, Daniela De Zio, Apolinar Maya-Mendoza, Franco Locatelli, Jiri Bartek, Francesco Cecconi.
      Mammalian development, adult tissue homeostasis and the avoidance of severe diseases including cancer require a properly orchestrated cell cycle, as well as error-free genome maintenance. The key cell-fate decision to replicate the genome is controlled by two major signalling pathways that act in parallel-the MYC pathway and the cyclin D-cyclin-dependent kinase (CDK)-retinoblastoma protein (RB) pathway1,2. Both MYC and the cyclin D-CDK-RB axis are commonly deregulated in cancer, and this is associated with increased genomic instability. The autophagic tumour-suppressor protein AMBRA1 has been linked to the control of cell proliferation, but the underlying molecular mechanisms remain poorly understood. Here we show that AMBRA1 is an upstream master regulator of the transition from G1 to S phase and thereby prevents replication stress. Using a combination of cell and molecular approaches and in vivo models, we reveal that AMBRA1 regulates the abundance of D-type cyclins by mediating their degradation. Furthermore, by controlling the transition from G1 to S phase, AMBRA1 helps to maintain genomic integrity during DNA replication, which counteracts developmental abnormalities and tumour growth. Finally, we identify the CHK1 kinase as a potential therapeutic target in AMBRA1-deficient tumours. These results advance our understanding of the control of replication-phase entry and genomic integrity, and identify the AMBRA1-cyclin D pathway as a crucial cell-cycle-regulatory mechanism that is deeply interconnected with genomic stability in embryonic development and tumorigenesis.
    DOI:  https://doi.org/10.1038/s41586-021-03422-5
  6. J Inherit Metab Dis. 2021 Apr 14.
    Metabolic impact of pathogenic variants in the mitochondrial glutamyl-tRNA synthetase EARS2.
    Min Ni, Lauren Friedrich, Chunxiao Pan, Hieu Vu, Jimin Pei, Bookyung Ko, Ling Cai, Ashley Solmonson, Chendong Yang, Kimberly M Nugent, Nick V Grishin, Chao Xing, Elizabeth Roeder, Ralph J DeBerardinis.
      Glutamyl-tRNA synthetase 2 (encoded by EARS2) is a mitochondrial aminoacyl-tRNA synthetase required to translate the 13 subunits of the electron transport chain encoded by the mitochondrial DNA. Pathogenic EARS2 variants cause combined oxidative phosphorylation deficiency, subtype 12 (COXPD12), an autosomal recessive disorder involving lactic acidosis, intellectual disability and other features of mitochondrial compromise. Patients with EARS2 deficiency present with variable phenotypes ranging from neonatal lethality to a mitigated disease with clinical improvement in early childhood. Here, we report a neonate homozygous for a rare pathogenic variant in EARS2 (c.949G>T; p.G317C). Metabolomics in primary fibroblasts from this patient revealed expected abnormalities in TCA cycle metabolites, as well as numerous changes in purine, pyrimidine and fatty acid metabolism. To examine genotype-phenotype correlations in COXPD12, we compared the metabolic impact of reconstituting these fibroblasts with wild-type EARS2 vs. four additional EARS2 variants from COXPD12 patients with varying clinical severity. Metabolomics identified a group of signature metabolites, mostly from the TCA cycle and amino acid metabolism, that discriminate between EARS2 variants causing relatively mild and severe COXPD12. Taken together, these findings indicate that metabolomics in patient-derived fibroblasts may help establish genotype-phenotype correlations in EARS2 deficiency and likely other mitochondrial disorders. This article is protected by copyright. All rights reserved.
    Keywords:  EARS2; Mitochondria; genotype-phenotype correlation; inborn errors of metabolism; lactic acidosis; metabolomics
    DOI:  https://doi.org/10.1002/jimd.12387
  7. Biochem J. 2021 Apr 12. pii: BCJ20200975. [Epub ahead of print]
    Depletion of mitochondrial inorganic polyphosphate (polyP) in mammalian cells causes metabolic shift from oxidative phosphorylation to glycolysis.
    Maria E Solesio, Lihan Xie, Brendan McIntyre, Mathew Ellenberger, Erna Mitaishvili, Siddharth Bhadra-Lobo, Lisa F Bettcher, Jason N Bazil, Daniel Raftery, Ursula Jakob, Evgeny V Pavlov.
      Inorganic polyphosphate (polyP) is a linear polymer composed of up to a few hundred orthophosphates linked together by high-energy phosphoanhydride bonds, identical to those found in ATP. In mammalian mitochondria, polyP has been implicated in multiple processes, including energy metabolism, ion channels function, and the regulation of calcium signaling. However, the specific mechanisms of all these effects of polyP within the organelle remain poorly understood. The central goal of this study was to investigate how mitochondrial polyP participates in the regulation of the mammalian cellular energy metabolism. To accomplish this, we created HEK293 cells depleted of mitochondrial polyP, through the stable expression of the polyP hydrolyzing enzyme (scPPX). We found that these cells have significantly reduced rates of oxidative phosphorylation (OXPHOS), while their rates of glycolysis were elevated. Consistent with this, metabolomics assays confirmed increased levels of metabolites involved in glycolysis in these cells, compared with the wild-type samples. At the same time, key respiratory parameters of the isolated mitochondria were unchanged, suggesting that respiratory chain activity is not affected by the lack of mitochondrial polyP. However, we detected that mitochondria from cells that lack mitochondrial polyP are more fragmented when compared with those from wild-type cells. Based on these results, we propose that mitochondrial polyP plays an important role as a regulator of the metabolic switch between OXPHOS and glycolysis.
    Keywords:  glycolysis; inorganic polyphosphates; mitochondrial bioenergetics; oxidative phosphorylation; polyP
    DOI:  https://doi.org/10.1042/BCJ20200975
  8. Cell Metab. 2021 Apr 10. pii: S1550-4131(21)00130-3. [Epub ahead of print]
    Metabolic flexibility determines human NK cell functional fate in the tumor microenvironment.
    Sophie M Poznanski, Kanwaldeep Singh, Tyrah M Ritchie, Jennifer A Aguiar, Isabella Y Fan, Ana L Portillo, Eduardo A Rojas, Fatemeh Vahedi, Abdullah El-Sayes, Sansi Xing, Martin Butcher, Yu Lu, Andrew C Doxey, Jonathan D Schertzer, Hal W Hirte, Ali A Ashkar.
      NK cells are central to anti-tumor immunity and recently showed efficacy for treating hematologic malignancies. However, their dysfunction in the hostile tumor microenvironment remains a pivotal barrier for cancer immunotherapies against solid tumors. Using cancer patient samples and proteomics, we found that human NK cell dysfunction in the tumor microenvironment is due to suppression of glucose metabolism via lipid peroxidation-associated oxidative stress. Activation of the Nrf2 antioxidant pathway restored NK cell metabolism and function and resulted in greater anti-tumor activity in vivo. Strikingly, expanded NK cells reprogrammed with complete metabolic substrate flexibility not only sustained metabolic fitness but paradoxically augmented their tumor killing in the tumor microenvironment and in response to nutrient deprivation. Our results uncover that metabolic flexibility enables a cytotoxic immune cell to exploit the metabolic hostility of tumors for their advantage, addressing a critical hurdle for cancer immunotherapy.
    Keywords:  NK cell metabolism; NK cells; Warburg effect; adoptive cell therapy; cancer immunotherapy; glucose metabolism; immunometabolism; metabolic flexibility; oxidative stress; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cmet.2021.03.023
  9. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00261-8. [Epub ahead of print]35(2): 108947
    Mitochondrial membrane tension governs fission.
    Dora Mahecic, Lina Carlini, Tatjana Kleele, Adai Colom, Antoine Goujon, Stefan Matile, Aurélien Roux, Suliana Manley.
      During mitochondrial fission, key molecular and cellular factors assemble on the outer mitochondrial membrane, where they coordinate to generate constriction. Constriction sites can eventually divide or reverse upon disassembly of the machinery. However, a role for membrane tension in mitochondrial fission, although speculated, has remained undefined. We capture the dynamics of constricting mitochondria in mammalian cells using live-cell structured illumination microscopy (SIM). By analyzing the diameters of tubules that emerge from mitochondria and implementing a fluorescence lifetime-based mitochondrial membrane tension sensor, we discover that mitochondria are indeed under tension. Under perturbations that reduce mitochondrial tension, constrictions initiate at the same rate, but are less likely to divide. We propose a model based on our estimates of mitochondrial membrane tension and bending energy in living cells which accounts for the observed probability distribution for mitochondrial constrictions to divide.
    Keywords:  fluorescence lifetime; fluorescent tension sensor; membrane tension; microtubules; mitochondrial division; mitochondrial dynamics; super-resolution microscopy
    DOI:  https://doi.org/10.1016/j.celrep.2021.108947
  10. Nat Commun. 2021 Apr 16. 12(1): 2304
    Mitochondrial hydrogen peroxide positively regulates neuropeptide secretion during diet-induced activation of the oxidative stress response.
    Qi Jia, Derek Sieburth.
      Mitochondria play a pivotal role in the generation of signals coupling metabolism with neurotransmitter release, but a role for mitochondrial-produced ROS in regulating neurosecretion has not been described. Here we show that endogenously produced hydrogen peroxide originating from axonal mitochondria (mtH2O2) functions as a signaling cue to selectively regulate the secretion of a FMRFamide-related neuropeptide (FLP-1) from a pair of interneurons (AIY) in C. elegans. We show that pharmacological or genetic manipulations that increase mtH2O2 levels lead to increased FLP-1 secretion that is dependent upon ROS dismutation, mitochondrial calcium influx, and cysteine sulfenylation of the calcium-independent PKC family member PKC-1. mtH2O2-induced FLP-1 secretion activates the oxidative stress response transcription factor SKN-1/Nrf2 in distal tissues and protects animals from ROS-mediated toxicity. mtH2O2 levels in AIY neurons, FLP-1 secretion and SKN-1 activity are rapidly and reversibly regulated by exposing animals to different bacterial food sources. These results reveal a previously unreported role for mtH2O2 in linking diet-induced changes in mitochondrial homeostasis with neuropeptide secretion.
    DOI:  https://doi.org/10.1038/s41467-021-22561-x
  11. Blood Cancer Discov. 2021 Mar;2(2): 162-185
    TFEB links MYC signaling to epigenetic control of myeloid differentiation and acute myeloid leukemia.
    Seongseok Yun, Nicole D Vincelette, Xiaoqing Yu, Gregory W Watson, Mario R Fernandez, Chunying Yang, Taro Hitosugi, Chia-Ho Cheng, Audrey R Freischel, Ling Zhang, Weimin Li, Hsinan Hou, Franz X Schaub, Alexis R Vedder, Ling Cen, Kathy L McGraw, Jungwon Moon, Daniel J Murphy, Andrea Ballabio, Scott H Kaufmann, Anders E Berglund, John L Cleveland.
      MYC oncoproteins regulate transcription of genes directing cell proliferation, metabolism and tumorigenesis. A variety of alterations drive MYC expression in acute myeloid leukemia (AML) and enforced MYC expression in hematopoietic progenitors is sufficient to induce AML. Here we report that AML and myeloid progenitor cell growth and survival rely on MYC-directed suppression of Transcription Factor EB (TFEB), a master regulator of the autophagy-lysosome pathway. Notably, although originally identified as an oncogene, TFEB functions as a tumor suppressor in AML, where it provokes AML cell differentiation and death. These responses reflect TFEB control of myeloid epigenetic programs, by inducing expression of isocitrate dehydrogenase-1 (IDH1) and IDH2, resulting in global hydroxylation of 5-methycytosine. Finally, activating the TFEB-IDH1/IDH2-TET2 axis is revealed as a targetable vulnerability in AML. Thus, epigenetic control by a MYC-TFEB circuit dictates myeloid cell fate and is essential for maintenance of AML.
    DOI:  https://doi.org/10.1158/2643-3230.bcd-20-0029
  12. Mol Cell. 2021 Apr 10. pii: S1097-2765(21)00143-X. [Epub ahead of print]
    Loss of LUC7L2 and U1 snRNP subunits shifts energy metabolism from glycolysis to OXPHOS.
    Alexis A Jourdain, Bridget E Begg, Eran Mick, Hardik Shah, Sarah E Calvo, Owen S Skinner, Rohit Sharma, Steven M Blue, Gene W Yeo, Christopher B Burge, Vamsi K Mootha.
      Oxidative phosphorylation (OXPHOS) and glycolysis are the two major pathways for ATP production. The reliance on each varies across tissues and cell states, and can influence susceptibility to disease. At present, the full set of molecular mechanisms governing the relative expression and balance of these two pathways is unknown. Here, we focus on genes whose loss leads to an increase in OXPHOS activity. Unexpectedly, this class of genes is enriched for components of the pre-mRNA splicing machinery, in particular for subunits of the U1 snRNP. Among them, we show that LUC7L2 represses OXPHOS and promotes glycolysis by multiple mechanisms, including (1) splicing of the glycolytic enzyme PFKM to suppress glycogen synthesis, (2) splicing of the cystine/glutamate antiporter SLC7A11 (xCT) to suppress glutamate oxidation, and (3) secondary repression of mitochondrial respiratory supercomplex formation. Our results connect LUC7L2 expression and, more generally, the U1 snRNP to cellular energy metabolism.
    Keywords:  7q-; LUC7; MDS; Tarui disease; cancer; ferroptosis; myelodysplastic syndrome; phosphofructokinase; spliceosome; system X(c)(−)
    DOI:  https://doi.org/10.1016/j.molcel.2021.02.033
  13. Front Cell Dev Biol. 2021 ;9 651317
    The Roles of 2-Hydroxyglutarate.
    Xin Du, Hai Hu.
      2-Hydroxyglutarate (2-HG) is structurally similar to α-ketoglutarate (α-KG), which is an intermediate product of the tricarboxylic acid (TCA) cycle; it can be generated by reducing the ketone group of α-KG to a hydroxyl group. The significant role that 2-HG plays has been certified in the pathophysiology of 2-hydroxyglutaric aciduria (2HGA), tumors harboring mutant isocitrate dehydrogenase 1/2 (IDH1/2mt), and in clear cell renal cell carcinoma (ccRCC). It is taken as an oncometabolite, raising much attention on its oncogenic mechanism. In recent years, 2-HG has been verified to accumulate in the context of hypoxia or acidic pH, and there are also researches confirming the vital role that 2-HG plays in the fate decision of immune cells. Therefore, 2-HG not only participates in tumorigenesis. This text will also summarize 2-HG's identities besides being an oncometabolite and will discuss their enlightenment for future research and clinical treatment.
    Keywords:  2-Hydroxyglutarate; epigenetics; immunology; isocitrate dehydrogenase; metabolism
    DOI:  https://doi.org/10.3389/fcell.2021.651317
  14. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00266-7. [Epub ahead of print]35(2): 108952
    Mitochondrial biogenesis in developing astrocytes regulates astrocyte maturation and synapse formation.
    Tamara Zehnder, Francesco Petrelli, Jennifer Romanos, Eva C De Oliveira Figueiredo, Tommy L Lewis, Nicole Déglon, Franck Polleux, Mirko Santello, Paola Bezzi.
      The mechanisms controlling the post-natal maturation of astrocytes play a crucial role in ensuring correct synaptogenesis. We show that mitochondrial biogenesis in developing astrocytes is necessary for coordinating post-natal astrocyte maturation and synaptogenesis. The astrocytic mitochondrial biogenesis depends on the transient upregulation of metabolic regulator peroxisome proliferator-activated receptor gamma (PPARγ) co-activator 1α (PGC-1α), which is controlled by metabotropic glutamate receptor 5 (mGluR5). At tissue level, the loss or downregulation of astrocytic PGC-1α sustains astrocyte proliferation, dampens astrocyte morphogenesis, and impairs the formation and function of neighboring synapses, whereas its genetic re-expression is sufficient to restore the mitochondria compartment and correct astroglial and synaptic defects. Our findings show that the developmental enhancement of mitochondrial biogenesis in astrocytes is a critical mechanism controlling astrocyte maturation and supporting synaptogenesis, thus suggesting that astrocytic mitochondria may be a therapeutic target in the case of neurodevelopmental and psychiatric disorders characterized by impaired synaptogenesis.
    Keywords:  PGC-1α; astrocyte; mGluR5; mitochondria
    DOI:  https://doi.org/10.1016/j.celrep.2021.108952
  15. Nat Commun. 2021 04 14. 12(1): 2244
    Ferroptotic cell death triggered by conjugated linolenic acids is mediated by ACSL1.
    Alexander Beatty, Tanu Singh, Yulia Y Tyurina, Vladimir A Tyurin, Svetlana Samovich, Emmanuelle Nicolas, Kristen Maslar, Yan Zhou, Kathy Q Cai, Yinfei Tan, Sebastian Doll, Marcus Conrad, Aravind Subramanian, Hülya Bayır, Valerian E Kagan, Ulrike Rennefahrt, Jeffrey R Peterson.
      Ferroptosis is associated with lipid hydroperoxides generated by the oxidation of polyunsaturated acyl chains. Lipid hydroperoxides are reduced by glutathione peroxidase 4 (GPX4) and GPX4 inhibitors induce ferroptosis. However, the therapeutic potential of triggering ferroptosis in cancer cells with polyunsaturated fatty acids is unknown. Here, we identify conjugated linoleates including α-eleostearic acid (αESA) as ferroptosis inducers. αESA does not alter GPX4 activity but is incorporated into cellular lipids and promotes lipid peroxidation and cell death in diverse cancer cell types. αESA-triggered death is mediated by acyl-CoA synthetase long-chain isoform 1, which promotes αESA incorporation into neutral lipids including triacylglycerols. Interfering with triacylglycerol biosynthesis suppresses ferroptosis triggered by αESA but not by GPX4 inhibition. Oral administration of tung oil, naturally rich in αESA, to mice limits tumor growth and metastasis with transcriptional changes consistent with ferroptosis. Overall, these findings illuminate a potential approach to ferroptosis, complementary to GPX4 inhibition.
    DOI:  https://doi.org/10.1038/s41467-021-22471-y
  16. Cell Metab. 2021 Apr 09. pii: S1550-4131(21)00131-5. [Epub ahead of print]
    A methionine-Mettl3-N6-methyladenosine axis promotes polycystic kidney disease.
    Harini Ramalingam, Sonu Kashyap, Patricia Cobo-Stark, Andrea Flaten, Chun-Mien Chang, Sachin Hajarnis, Kyaw Zaw Hein, Jorgo Lika, Gina M Warner, Jair M Espindola-Netto, Ashwani Kumar, Mohammed Kanchwala, Chao Xing, Eduardo N Chini, Vishal Patel.
      Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenic disorder marked by numerous progressively enlarging kidney cysts. Mettl3, a methyltransferase that catalyzes the abundant N6-methyladenosine (m6A) RNA modification, is implicated in development, but its role in most diseases is unknown. Here, we show that Mettl3 and m6A levels are increased in mouse and human ADPKD samples and that kidney-specific transgenic Mettl3 expression produces tubular cysts. Conversely, Mettl3 deletion in three orthologous ADPKD mouse models slows cyst growth. Interestingly, methionine and S-adenosylmethionine (SAM) levels are also elevated in ADPKD models. Moreover, methionine and SAM induce Mettl3 expression and aggravate ex vivo cyst growth, whereas dietary methionine restriction attenuates mouse ADPKD. Finally, Mettl3 activates the cyst-promoting c-Myc and cAMP pathways through enhanced c-Myc and Avpr2 mRNA m6A modification and translation. Thus, Mettl3 promotes ADPKD and links methionine utilization to epitranscriptomic activation of proliferation and cyst growth.
    Keywords:  AVPR2; METTL3; N(6)-methyladenosine; S-adenosylmethionine; c-Myc; m6A mRNA methylation; mRNA translation; methionine; polycystic kidney disease
    DOI:  https://doi.org/10.1016/j.cmet.2021.03.024
  17. Front Immunol. 2021 ;12 630380
    Lactic Acid Fermentation Is Required for NLRP3 Inflammasome Activation.
    Hsin-Chung Lin, Yu-Jen Chen, Yau-Huei Wei, Hsin-An Lin, Chien-Chou Chen, Tze-Fan Liu, Yi-Lin Hsieh, Kuo-Yang Huang, Kuan-Hung Lin, Hsueh-Hsiao Wang, Lih-Chyang Chen.
      Activation of the Nod-like receptor 3 (NLRP3) inflammasome is important for activation of innate immune responses, but improper and excessive activation can cause inflammatory disease. We previously showed that glycolysis, a metabolic pathway that converts glucose into pyruvate, is essential for NLRP3 inflammasome activation in macrophages. Here, we investigated the role of metabolic pathways downstream glycolysis - lactic acid fermentation and pyruvate oxidation-in activation of the NLRP3 inflammasome. Using pharmacological or genetic approaches, we show that decreasing lactic acid fermentation by inhibiting lactate dehydrogenase reduced caspase-1 activation and IL-1β maturation in response to various NLRP3 inflammasome agonists such as nigericin, ATP, monosodium urate (MSU) crystals, or alum, indicating that lactic acid fermentation is required for NLRP3 inflammasome activation. Inhibition of lactate dehydrogenase with GSK2837808A reduced lactate production and activity of the NLRP3 inflammasome regulator, phosphorylated protein kinase R (PKR), but did not reduce the common trigger of NLRP3 inflammasome, potassium efflux, or reactive oxygen species (ROS) production. By contrast, decreasing the activity of pyruvate oxidation by depletion of either mitochondrial pyruvate carrier 2 (MPC2) or pyruvate dehydrogenase E1 subunit alpha 1 (PDHA1) enhanced NLRP3 inflammasome activation, suggesting that inhibition of mitochondrial pyruvate transport enhanced lactic acid fermentation. Moreover, treatment with GSK2837808A reduced MSU-mediated peritonitis in mice, a disease model used for studying the consequences of NLRP3 inflammasome activation. Our results suggest that lactic acid fermentation is important for NLRP3 inflammasome activation, while pyruvate oxidation is not. Thus, reprograming pyruvate metabolism in mitochondria and in the cytoplasm should be considered as a novel strategy for the treatment of NLRP3 inflammasome-associated diseases.
    Keywords:  NLRP3 inflammasome; glycolysis; inflammation; lactic acid fermentation; pyruvate oxidation
    DOI:  https://doi.org/10.3389/fimmu.2021.630380
  18. Mol Cancer Res. 2021 Apr 16. pii: molcanres.0086.2020. [Epub ahead of print]
    Elevated Asparagine Biosynthesis Drives Brain Tumor Stem Cell Metabolic Plasticity and Resistance to Oxidative Stress.
    Tom M Thomas, Ken Miyaguchi, Lincoln A Edwards, Hongqiang Wang, Hassen Wollebo, Li Aiguo, Ramachandran Murali, Yizhou Wang, Daniel Braas, Justin S Michael, Allen Andres, Miqin Zhang, Kamel Khalili, Roberta A Gottlieb, J Manuel Perez, John S Yu.
      Asparagine synthetase (ASNS) is a gene on the long arm of chromosome 7 that is copy number amplified in the majority of glioblastomas. ASNS copy number amplification is associated with a significantly decreased survival. Using patient-derived glioma stem cells (GSCs), we showed significant metabolic alterations occur in gliomas when perturbing the expression of asparagine synthetase, which is not merely restricted to amino acid homeostasis. ASNS-high GSCs maintained a slower basal metabolic profile yet readily shifted to a greatly increased capacity for glycolysis and oxidative phosphorylation when needed. This led ASNS-high cells to a greater ability to proliferate and spread into brain tissue. Finally, we demonstrate that these changes confer resistance to cellular stress, notably oxidative stress, through adaptive redox homeostasis which led to radiation resistance. Furthermore, ASNS overexpression led to modifications of the one-carbon metabolism to promote a more antioxidant tumor environment revealing a metabolic vulnerability that may be therapeutically exploited. Implications: This study reveals a new role for ASNS in metabolic control and redox homeostasis in glioma stem cells and proposes a new treatment strategy that attempts to exploit one vulnerable metabolic node within the larger multilayered tumor network.
    DOI:  https://doi.org/10.1158/1541-7786.MCR-20-0086
  19. Geroscience. 2021 Apr 17.
    An energetics perspective on geroscience: mitochondrial protonmotive force and aging.
    Brandon J Berry, Matt Kaeberlein.
      Mitochondria are organelles that provide energy to cells through ATP production. Mitochondrial dysfunction has long been postulated to mediate cellular declines that drive biological aging. Many well-characterized hallmarks of aging may involve underlying energetic defects that stem from loss of mitochondrial function with age. Why and how mitochondrial function declines with age is an open question and one that has been difficult to answer. Mitochondria are powered by an electrochemical gradient across the inner mitochondrial membrane known as the protonmotive force (PMF). This gradient decreases with age in several experimental models. However, it is unclear if a diminished PMF is a cause or a consequence of aging. Herein, we briefly review and define mitochondrial function, we summarize how PMF changes with age in several models, and we highlight recent studies that implicate PMF in aging biology. We also identify barriers that must be addressed for the field to progress. Emerging technology permits more precise in vivo study of mitochondria that will allow better understanding of cause and effect in metabolic models of aging. Once cause and effect can be discerned more precisely, energetics approaches to combat aging may be developed to prevent or reverse functional decline.
    Keywords:  AMPK; Autophagy; Membrane potential; Metabolism; mTOR
    DOI:  https://doi.org/10.1007/s11357-021-00365-7
  20. Transl Androl Urol. 2021 Mar;10(3): 1506-1520
    Towards a new WHO classification of renal cell tumor: what the clinician needs to know-a narrative review.
    Alessia Cimadamore, Liang Cheng, Marina Scarpelli, Francesco Massari, Veronica Mollica, Matteo Santoni, Antonio Lopez-Beltran, Rodolfo Montironi, Holger Moch.
      In 1952, renal cell carcinomas had been divided into 2 categories-clear cell or granular cell-depending upon their cytoplasmic staining characteristics. In the following years, the inventory of renal epithelial tumors has expanded by the addition of tumors named by their architectural pattern (i.e., papillary RCC, tubulocystic RCC), anatomic location (i.e., collecting duct carcinoma, renal medullary carcinoma), associated diseases (i.e., acquired cystic disease-associated RCCs). With the extensive application of molecular diagnostic techniques, it becomes possible to detect genetic distinctions between various types of renal neoplasm and discover new entities, otherwise misdiagnosed or diagnosed as unclassified RCC. Some tumors such as ALK rearrangement-associated RCC, MiT family translocation renal carcinomas, SDH-deficient renal cancer or FH-deficient RCC, are defined by their molecular characteristics. The most recent World Health Organization (WHO) classification of renal neoplasms account for more than 50 entities and provisional entities. New entities might be included in the upcoming WHO classification. The aim of this review is to summarise and discuss the newly acquired data and evidence on the clinical, pathological, molecular features and on the prognosis of new RCC entities, which will hopefully increase the awareness and the acceptance of these entities among clinicians and improve prognostication for individual patients.
    Keywords:  Renal cell carcinoma; Von Hippel-Lindau gene (VHL); anaplastic lymphoma kinase (ALK); classification; clear cell RCC; emerging entities; fumarate hydratase (FH); molecular pathology; non-clear cells RCC; succinate dehydrogenase (SDH)
    DOI:  https://doi.org/10.21037/tau-20-1150
  21. Int J Biochem Cell Biol. 2021 Apr 09. pii: S1357-2725(21)00060-1. [Epub ahead of print] 105976
    CFTR chloride channel activity modulates the mitochondrial morphology in cultured epithelial cells.
    Rocío García, Camila Falduti, Raquel Jara, Mariángeles Clauzure, María M Massip-Copiz, María de Los Ángeles Aguilar, Tomás A Santa-Coloma, Ángel G Valdivieso.
      The impairment of the CFTR channel activity, a cAMP-activated chloride (Cl-) channel responsible for cystic fibrosis (CF), has been associated with a variety of mitochondrial alterations such as modified gene expression, impairment in oxidative phosphorylation, increased reactive oxygen species (ROS), and a disbalance in calcium homeostasis. The mechanisms by which these processes occur in CF are not fully understood. Previously, we demonstrated a reduced MTND4 expression and a failure in the mitochondrial complex I (mCx-I) activity in CF cells. Here we hypothesized that the activity of CFTR might modulate the mitochondrial fission/fusion balance, explaining the decreased mCx-I. The mitochondrial morphology and the levels of mitochondrial dynamic proteins MFN1 and DRP1 were analysed in IB3-1 CF cells, and S9 (IB3-1 expressing wt-CFTR), and C38 (IB3-1 expressing a truncated functional CFTR) cells. The mitochondrial morphology of IB3-1 cells compared to S9 and C38 cells showed that the impaired CFTR activity induced a fragmented mitochondrial network with increased rounded mitochondria and shorter branches. Similar results were obtained by using the CFTR pharmacological inhibitors CFTR(inh)-172 and GlyH101 on C38 cells. These morphological changes were accompanied by modifications in the levels of the mitochondrial dynamic proteins MFN1, DRP1, and p(616)-DRP1. IB3-1 CF cells treated with Mdivi-1, an inhibitor of the mitochondrial fission, restored the mCx-I activity to values similar to those seen in S9 and C38 cells. These results suggest that the mitochondrial fission/fusion balance is regulated by the CFTR activity and might be a potential target to treat the impaired mCx-I activity in CF.
    Keywords:  CFTR; Cystic fibrosis; DRP1; MFN1; Mdivi-1; Mitochondrial dynamics
    DOI:  https://doi.org/10.1016/j.biocel.2021.105976
  22. Plant Physiol. 2021 Apr 15. pii: kiab172. [Epub ahead of print]
    The function of glutaredoxin GRXS15 is required for lipoyl-dependent dehydrogenases in mitochondria.
    Anna Moseler, Inga Kruse, Andrew E Maclean, Luca Pedroletti, Marina Franceschetti, Stephan Wagner, Regina Wehler, Katrin Fischer-Schrader, Gernot Poschet, Markus Wirtz, Peter Dörmann, Tatjana M Hildebrandt, Rüdiger Hell, Markus Schwarzländer, Janneke Balk, Andreas J Meyer.
      Iron-sulfur (Fe-S) clusters are ubiquitous cofactors in all life and are used in a wide array of diverse biological processes, including electron transfer chains and several metabolic pathways. Biosynthesis machineries for Fe-S clusters exist in plastids, the cytosol and mitochondria. A single monothiol glutaredoxin (GRX) is involved in Fe-S cluster assembly in mitochondria of yeast and mammals. In plants, the role of the mitochondrial homologue GRXS15 has only partially been characterized. Arabidopsis (Arabidopsis thaliana) grxs15 null mutants are not viable, but mutants complemented with the variant GRXS15 K83A develop with a dwarf phenotype similar to the knockdown line GRXS15amiR. In an in-depth metabolic analysis of the variant and knockdown GRXS15 lines, we show that most Fe-S cluster-dependent processes are not affected, including biotin biosynthesis, molybdenum cofactor biosynthesis, the electron transport chain and aconitase in the TCA cycle. Instead, we observed an increase in most TCA cycle intermediates and amino acids, especially pyruvate, glycine and branched-chain amino acids (BCAAs). Additionally, we found an accumulation of branched-chain α-keto acids (BCKAs), the first degradation products resulting from transamination of BCAAs. In wild-type plants, pyruvate, glycine and BCKAs are all metabolized through decarboxylation by mitochondrial lipoyl cofactor-dependent dehydrogenase complexes. These enzyme complexes are very abundant, comprising a major sink for lipoyl cofactor. Because biosynthesis of lipoyl cofactor depends on continuous Fe-S cluster supply to lipoyl synthase, this could explain why lipoyl cofactor-dependent processes are most sensitive to restricted Fe-S supply in grxs15 mutants.
    DOI:  https://doi.org/10.1093/plphys/kiab172
  23. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00277-1. [Epub ahead of print]35(2): 108963
    A membrane arm of mitochondrial complex I sufficient to promote respirasome formation.
    Hezhi Fang, Xianglai Ye, Jie Xie, Yuanyuan Li, Haiyan Li, Xinzhu Bao, Yue Yang, Zifan Lin, Manli Jia, Qing Han, Jingjing Zhu, Xueyun Li, Qiongya Zhao, Yanling Yang, Jianxin Lyu.
      The assembly pathways of mitochondrial respirasome (supercomplex I+III2+IV) are not fully understood. Here, we show that an early sub-complex I assembly, rather than holo-complex I, is sufficient to initiate mitochondrial respirasome assembly. We find that a distal part of the membrane arm of complex I (PD-a module) is a scaffold for the incorporation of complexes III and IV to form a respirasome subcomplex. Depletion of PD-a, rather than other complex I modules, decreases the steady-state levels of complexes III and IV. Both HEK293T cells lacking TIMMDC1 and patient-derived cells with disease-causing mutations in TIMMDC1 showed accumulation of this respirasome subcomplex. This suggests that TIMMDC1, previously known as a complex-I assembly factor, may function as a respirasome assembly factor. Collectively, we provide a detailed, cooperative assembly model in which most complex-I subunits are added to the respirasome subcomplex in the lateral stages of respirasome assembly.
    Keywords:  Leigh syndrome; TIMMDC1; cooperative assembly; mitochondrial respirasome; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.celrep.2021.108963
  24. Am J Physiol Renal Physiol. 2021 Apr 12.
    NMR-Based Serum and Urine Metabolomic Profile Reveals Suppression of Mitochondrial Pathways in Experimental Sepsis-Associated Acute Kidney Injury.
    Stephen Wade Standage, Shenyuan Xu, Lauren Brown, Qing Ma, Adeleine Koterba, Patrick Lahni, Prasad Devarajan, Michael A Kennedy.
      Sepsis-associated acute kidney injury (SA-AKI) is a significant problem in the critically ill that causes increased death. Emerging understanding of this disease implicates metabolic dysfunction in its pathophysiology. This study sought to identify specific metabolic pathways amenable to potential therapeutic intervention. Using a murine model of sepsis, blood and tissue samples were collected for assessment of systemic inflammation, kidney function, and renal injury. Nuclear magnetic resonance (NMR)-based metabolomics quantified dozens of metabolites in serum and urine which were subsequently submitted to pathway analysis. Kidney tissue gene expression analysis confirmed implicated pathways. Septic mice had elevated circulating levels of inflammatory cytokines and increased levels of blood urea nitrogen and creatinine, indicating both systemic inflammation and poor kidney function. Renal tissue showed only mild histologic evidence of injury in sepsis. NMR metabolomic analysis identified the involvement of mitochondrial pathways associated with branched-chain amino acid (BCAA) metabolism, fatty acid oxidation, and de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis in SA-AKI. Renal cortical gene expression of enzymes associated with those pathways was predominantly suppressed. Similar to humans, septic mice demonstrate renal dysfunction without significant tissue disruption, pointing to metabolic derangement as an important contributor to SA-AKI pathophysiology. Metabolism of BCAAs and fatty acids and NAD+ synthesis, which all center on mitochondrial function, appear to be suppressed. Developing interventions to activate these pathways may provide new therapeutic opportunities for SA-AKI.
    Keywords:  acute kidney injury; metabolic profiling; metabolomics; nuclear magnetic resonance; sepsis
    DOI:  https://doi.org/10.1152/ajprenal.00582.2020
  25. Proc Natl Acad Sci U S A. 2021 Apr 20. pii: e2017148118. [Epub ahead of print]118(16):
    Brd4-bound enhancers drive cell-intrinsic sex differences in glioblastoma.
    Najla Kfoury, Zongtai Qi, Briana C Prager, Michael N Wilkinson, Lauren Broestl, Kristopher C Berrett, Arnav Moudgil, Sumithra Sankararaman, Xuhua Chen, Jason Gertz, Jeremy N Rich, Robi D Mitra, Joshua B Rubin.
      Sex can be an important determinant of cancer phenotype, and exploring sex-biased tumor biology holds promise for identifying novel therapeutic targets and new approaches to cancer treatment. In an established isogenic murine model of glioblastoma (GBM), we discovered correlated transcriptome-wide sex differences in gene expression, H3K27ac marks, large Brd4-bound enhancer usage, and Brd4 localization to Myc and p53 genomic binding sites. These sex-biased gene expression patterns were also evident in human glioblastoma stem cells (GSCs). These observations led us to hypothesize that Brd4-bound enhancers might underlie sex differences in stem cell function and tumorigenicity in GBM. We found that male and female GBM cells exhibited sex-specific responses to pharmacological or genetic inhibition of Brd4. Brd4 knockdown or pharmacologic inhibition decreased male GBM cell clonogenicity and in vivo tumorigenesis while increasing both in female GBM cells. These results were validated in male and female patient-derived GBM cell lines. Furthermore, analysis of the Cancer Therapeutic Response Portal of human GBM samples segregated by sex revealed that male GBM cells are significantly more sensitive to BET (bromodomain and extraterminal) inhibitors than are female cells. Thus, Brd4 activity is revealed to drive sex differences in stem cell and tumorigenic phenotypes, which can be abrogated by sex-specific responses to BET inhibition. This has important implications for the clinical evaluation and use of BET inhibitors.
    Keywords:  BET inhibitors; Brd4-bound enhancers; glioblastoma; sex differences; sex-specific transcriptional programs
    DOI:  https://doi.org/10.1073/pnas.2017148118
  26. Nature. 2021 Apr 14.
    CRL4AMBRA1 is a master regulator of D-type cyclins.
    Daniele Simoneschi, Gergely Rona, Nan Zhou, Yeon-Tae Jeong, Shaowen Jiang, Giacomo Milletti, Arnaldo A Arbini, Alfie O'Sullivan, Andrew A Wang, Sorasicha Nithikasem, Sarah Keegan, Yik Siu, Valentina Cianfanelli, Emiliano Maiani, Francesca Nazio, Francesco Cecconi, Francesco Boccalatte, David Fenyö, Drew R Jones, Luca Busino, Michele Pagano.
      D-type cyclins are central regulators of the cell division cycle and are among the most frequently deregulated therapeutic targets in human cancer1, but the mechanisms that regulate their turnover are still being debated2,3. Here, by combining biochemical and genetics studies in somatic cells, we identify CRL4AMBRA1 (also known as CRL4DCAF3) as the ubiquitin ligase that targets all three D-type cyclins for degradation. During development, loss of Ambra1 induces the accumulation of D-type cyclins and retinoblastoma (RB) hyperphosphorylation and hyperproliferation, and results in defects of the nervous system that are reduced by treating pregnant mice with the FDA-approved CDK4 and CDK6 (CDK4/6) inhibitor abemaciclib. Moreover, AMBRA1 acts as a tumour suppressor in mouse models and low AMBRA1 mRNA levels are predictive of poor survival in cancer patients. Cancer hotspot mutations in D-type cyclins abrogate their binding to AMBRA1 and induce their stabilization. Finally, a whole-genome, CRISPR-Cas9 screen identified AMBRA1 as a regulator of the response to CDK4/6 inhibition. Loss of AMBRA1 reduces sensitivity to CDK4/6 inhibitors by promoting the formation of complexes of D-type cyclins with CDK2. Collectively, our results reveal the molecular mechanism that controls the stability of D-type cyclins during cell-cycle progression, in development and in human cancer, and implicate AMBRA1 as a critical regulator of the RB pathway.
    DOI:  https://doi.org/10.1038/s41586-021-03445-y
  27. EMBO Rep. 2021 Apr 12. e51803
    The interplay between DNA and histone methylation: molecular mechanisms and disease implications.
    Yinglu Li, Xiao Chen, Chao Lu.
      Methylation of cytosine in CpG dinucleotides and histone lysine and arginine residues is a chromatin modification that critically contributes to the regulation of genome integrity, replication, and accessibility. A strong correlation exists between the genome-wide distribution of DNA and histone methylation, suggesting an intimate relationship between these epigenetic marks. Indeed, accumulating literature reveals complex mechanisms underlying the molecular crosstalk between DNA and histone methylation. These in vitro and in vivo discoveries are further supported by the finding that genes encoding DNA- and histone-modifying enzymes are often mutated in overlapping human diseases. Here, we summarize recent advances in understanding how DNA and histone methylation cooperate to maintain the cellular epigenomic landscape. We will also discuss the potential implication of these insights for understanding the etiology of, and developing biomarkers and therapies for, human congenital disorders and cancers that are driven by chromatin abnormalities.
    Keywords:  DNA methylation; cancer; chromatin; developmental disorder; histone methylation
    DOI:  https://doi.org/10.15252/embr.202051803
  28. Cancer Discov. 2021 Apr 10. pii: candisc.1228.2020. [Epub ahead of print]
    Oncogenic KRAS recruits an expansive transcriptional network through mutant p53 to drive pancreatic cancer metastasis.
    Michael P Kim, Xinqun Li, Jenying Deng, Yun Zhang, Bingbing Dai, Kendra L Allton, Tara G Hughes, Christian Siangco, Jithesh J Augustine, Ya'an Kang, Joy M McDaniel, Shunbin Xiong, Eugene J Koay, Florencia McAllister, Christopher A Bristow, Timothy P Heffernan, Anirban Maitra, Bin Liu, Michelle C Barton, Amanda R Wasylishen, Jason B Fleming, Guillermina Lozano.
      Pancreatic ductal adenocarcinoma (PDAC) is almost uniformly fatal and characterized by early metastasis. Oncogenic KRAS mutations prevail in 95% of PDAC tumors and co-occur with genetic alterations in the TP53 tumor suppressor in nearly 70% of patients. Most TP53 alterations are missense mutations that exhibit gain-of-function phenotypes that include increased invasiveness and metastasis yet the extent of direct cooperation between KRAS effectors and mutant p53 remains largely undefined. We show that oncogenic KRAS effectors activate cyclic AMP responsive element binding protein 1 (CREB1) to allow physical interactions with mutant p53 that hyperactivate multiple pro-metastatic transcriptional networks. Specifically, mutant p53 and CREB1 upregulate the pro-metastatic, pioneer transcription factor, FOXA1, activating its transcriptional network while promoting Wnt/B-catenin signaling, together driving PDAC metastasis. Pharmacologic CREB1 inhibition dramatically reduced FOXA1 and B-catenin expression and dampened PDAC metastasis, identifying a new therapeutic strategy to disrupt cooperation between oncogenic KRAS and mutant p53 to mitigate metastasis.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1228
  29. Sci Adv. 2021 Apr;pii: eabe5544. [Epub ahead of print]7(16):
    Kog1/Raptor mediates metabolic rewiring during nutrient limitation by controlling SNF1/AMPK activity.
    Zeenat Rashida, Rajalakshmi Srinivasan, Meghana Cyanam, Sunil Laxman.
      In changing environments, cells modulate resource budgeting through distinct metabolic routes to control growth. Accordingly, the TORC1 and SNF1/AMPK pathways operate contrastingly in nutrient replete or limited environments to maintain homeostasis. The functions of TORC1 under glucose and amino acid limitation are relatively unknown. We identified a modified form of the yeast TORC1 component Kog1/Raptor, which exhibits delayed growth exclusively during glucose and amino acid limitations. Using this, we found a necessary function for Kog1 in these conditions where TORC1 kinase activity is undetectable. Metabolic flux and transcriptome analysis revealed that Kog1 controls SNF1-dependent carbon flux apportioning between glutamate/amino acid biosynthesis and gluconeogenesis. Kog1 regulates SNF1/AMPK activity and outputs and mediates a rapamycin-independent activation of the SNF1 targets Mig1 and Cat8. This enables effective glucose derepression, gluconeogenesis activation, and carbon allocation through different pathways. Therefore, Kog1 centrally regulates metabolic homeostasis and carbon utilization during nutrient limitation by managing SNF1 activity.
    DOI:  https://doi.org/10.1126/sciadv.abe5544
  30. Mol Cell Oncol. 2021 ;8(2): 1877076
    P53 regulates cellular redox state, ferroptosis and metabolism.
    Julia I-Ju Leu, Maureen E Murphy, Donna L George.
      The tumor protein P53 (TP53, or p53) has complex and at times seemingly contradictory roles in the regulation of metabolism and ferroptosis sensitivity. We find that the actions of p53 influence the redox state, which can trigger changes in redox-sensitive proteins, thereby modifying metabolic processes and response to ferroptosis.
    Keywords:  Ferroptosis; cysteine modification; metabolism; p53; redox signaling
    DOI:  https://doi.org/10.1080/23723556.2021.1877076
  31. EMBO Mol Med. 2021 Apr 14. e13258
    Neurodegenerative VPS41 variants inhibit HOPS function and mTORC1-dependent TFEB/TFE3 regulation.
    Reini E N van der Welle, Rebekah Jobling, Christian Burns, Paolo Sanza, Jan A van der Beek, Alfonso Fasano, Lan Chen, Fried J Zwartkruis, Susan Zwakenberg, Edward F Griffin, Corlinda Ten Brink, Tineke Veenendaal, Nalan Liv, Conny M A van Ravenswaaij-Arts, Henny H Lemmink, Rolph Pfundt, Susan Blaser, Carolina Sepulveda, Andres M Lozano, Grace Yoon, Teresa Santiago-Sim, Cedric S Asensio, Guy A Caldwell, Kim A Caldwell, David Chitayat, Judith Klumperman.
      Vacuolar protein sorting 41 (VPS41) is as part of the Homotypic fusion and Protein Sorting (HOPS) complex required for lysosomal fusion events and, independent of HOPS, for regulated secretion. Here, we report three patients with compound heterozygous mutations in VPS41 (VPS41S285P and VPS41R662 * ; VPS41c.1423-2A>G and VPS41R662 * ) displaying neurodegeneration with ataxia and dystonia. Cellular consequences were investigated in patient fibroblasts and VPS41-depleted HeLa cells. All mutants prevented formation of a functional HOPS complex, causing delayed lysosomal delivery of endocytic and autophagic cargo. By contrast, VPS41S285P enabled regulated secretion. Strikingly, loss of VPS41 function caused a cytosolic redistribution of mTORC1, continuous nuclear localization of Transcription Factor E3 (TFE3), enhanced levels of LC3II, and a reduced autophagic response to nutrient starvation. Phosphorylation of mTORC1 substrates S6K1 and 4EBP1 was not affected. In a C. elegans model of Parkinson's disease, co-expression of VPS41S285P /VPS41R662 * abolished the neuroprotective function of VPS41 against α-synuclein aggregates. We conclude that the VPS41 variants specifically abrogate HOPS function, which interferes with the TFEB/TFE3 axis of mTORC1 signaling, and cause a neurodegenerative disease.
    Keywords:  Autophagy; HOPS complex; TFEB/TFE3; lysosome-associated disorder; mTORC1
    DOI:  https://doi.org/10.15252/emmm.202013258
  32. Cancer Cell. 2021 Apr 12. pii: S1535-6108(21)00159-8. [Epub ahead of print]39(4): 460-462
    Glucose makes Treg lose their temper.
    Matteo Villa, David O'Sullivan, Erika L Pearce.
      Competition for glucose regulates the balance between cancer and immune responses. New findings published in Nature show that regulatory T cells (Treg) shape their metabolism to avoid glucose competition, thus maintaining their stability and sustaining tumor progression. This research suggests hijacking the "eating habits" of Treg could improve cancer therapy.
    DOI:  https://doi.org/10.1016/j.ccell.2021.03.001
  33. Nat Commun. 2021 04 12. 12(1): 2176
    Protein kinase A controls the hexosamine pathway by tuning the feedback inhibition of GFAT-1.
    Sabine Ruegenberg, Felix A M C Mayr, Ilian Atanassov, Ulrich Baumann, Martin S Denzel.
      The hexosamine pathway (HP) is a key anabolic pathway whose product uridine 5'-diphospho-N-acetyl-D-glucosamine (UDP-GlcNAc) is an essential precursor for glycosylation processes in mammals. It modulates the ER stress response and HP activation extends lifespan in Caenorhabditis elegans. The highly conserved glutamine fructose-6-phosphate amidotransferase 1 (GFAT-1) is the rate-limiting HP enzyme. GFAT-1 activity is modulated by UDP-GlcNAc feedback inhibition and via phosphorylation by protein kinase A (PKA). Molecular consequences of GFAT-1 phosphorylation, however, remain poorly understood. Here, we identify the GFAT-1 R203H substitution that elevates UDP-GlcNAc levels in C. elegans. In human GFAT-1, the R203H substitution interferes with UDP-GlcNAc inhibition and with PKA-mediated Ser205 phosphorylation. Our data indicate that phosphorylation affects the interactions of the two GFAT-1 domains to control catalytic activity. Notably, Ser205 phosphorylation has two discernible effects: it lowers baseline GFAT-1 activity and abolishes UDP-GlcNAc feedback inhibition. PKA controls the HP by uncoupling the metabolic feedback loop of GFAT-1.
    DOI:  https://doi.org/10.1038/s41467-021-22320-y
  34. J Pharm Biomed Anal. 2021 Mar 19. pii: S0731-7085(21)00143-6. [Epub ahead of print]199 114031
    Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics.
    Sinem Nalbantoglu, Abdullah Karadag.
      Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
    Keywords:  Integrative multiomics; Metabolite; Metabolomics; Oncometabolite; PTMs; Proteomics; Reprogramming cancer metabolism; Systems biology
    DOI:  https://doi.org/10.1016/j.jpba.2021.114031
  35. Redox Biol. 2021 Apr 02. pii: S2213-2317(21)00109-9. [Epub ahead of print]43 101961
    Spatiotemporal regulation of hydrogen sulfide signaling in the kidney.
    Maurits Roorda, Jan Lj Miljkovic, Harry van Goor, Robert H Henning, Hjalmar R Bouma.
      Hydrogen sulfide (H2S) has long been recognized as a putrid, toxic gas. However, as a result of intensive biochemical research in the past two decades, H2S is now considered to be the third gasotransmitter alongside nitric oxide (NO) and carbon monoxide (CO) in mammalian systems. H2S-producing enzymes are expressed in all organs, playing an important role in their physiology. In the kidney, H2S is a critical regulator of vascular and cellular function, although the mechanisms that affect (sub)cellular levels of H2S are not precisely understood. H2S modulates systemic and renal blood flow, glomerular filtration rate and the renin-angiotensin axis through direct inhibition of nitric oxide synthesis. Further, H2S affects cellular function by modulating protein activity via post-translational protein modification: a process termed persulfidation. Persulfidation modulates protein activity, protein localization and protein-protein interactions. Additionally, acute kidney injury (AKI) due to mitochondrial dysfunction, which occurs during hypoxia or ischemia-reperfusion (IR), is attenuated by H2S. H2S enhances ATP production, prevents damage due to free radicals and regulates endoplasmic reticulum stress during IR. In this review, we discuss current insights in the (sub)cellular regulation of H2S anabolism, retention and catabolism, with relevance to spatiotemporal regulation of renal H2S levels. Together, H2S is a versatile gasotransmitter with pleiotropic effects on renal function and offers protection against AKI. Unraveling the mechanisms that modulate (sub)cellular signaling of H2S not only expands fundamental insight in the regulation of functional effects mediated by H2S, but can also provide novel therapeutic targets to prevent kidney injury due to hypoxic or ischemic injury.
    Keywords:  Gasotransmitter; Hydrogen sulfide; Hypoxia; Ischemia-reperfusion injury; Kidney; Persulfidation
    DOI:  https://doi.org/10.1016/j.redox.2021.101961
  36. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00299-0. [Epub ahead of print]35(2): 108985
    Dietary spermidine improves cognitive function.
    Sabrina Schroeder, Sebastian J Hofer, Andreas Zimmermann, Raimund Pechlaner, Christopher Dammbrueck, Tobias Pendl, G Mark Marcello, Viktoria Pogatschnigg, Martina Bergmann, Melanie Müller, Verena Gschiel, Selena Ristic, Jelena Tadic, Keiko Iwata, Gesa Richter, Aitak Farzi, Muammer Üçal, Ute Schäfer, Michael Poglitsch, Philipp Royer, Ronald Mekis, Marlene Agreiter, Regine C Tölle, Péter Sótonyi, Johann Willeit, Barbara Mairhofer, Helga Niederkofler, Irmgard Pallhuber, Gregorio Rungger, Herbert Tilg, Michaela Defrancesco, Josef Marksteiner, Frank Sinner, Christoph Magnes, Thomas R Pieber, Peter Holzer, Guido Kroemer, Didac Carmona-Gutierrez, Luca Scorrano, Jörn Dengjel, Tobias Madl, Simon Sedej, Stephan J Sigrist, Bence Rácz, Stefan Kiechl, Tobias Eisenberg, Frank Madeo.
      Decreased cognitive performance is a hallmark of brain aging, but the underlying mechanisms and potential therapeutic avenues remain poorly understood. Recent studies have revealed health-protective and lifespan-extending effects of dietary spermidine, a natural autophagy-promoting polyamine. Here, we show that dietary spermidine passes the blood-brain barrier in mice and increases hippocampal eIF5A hypusination and mitochondrial function. Spermidine feeding in aged mice affects behavior in homecage environment tasks, improves spatial learning, and increases hippocampal respiratory competence. In a Drosophila aging model, spermidine boosts mitochondrial respiratory capacity, an effect that requires the autophagy regulator Atg7 and the mitophagy mediators Parkin and Pink1. Neuron-specific Pink1 knockdown abolishes spermidine-induced improvement of olfactory associative learning. This suggests that the maintenance of mitochondrial and autophagic function is essential for enhanced cognition by spermidine feeding. Finally, we show large-scale prospective data linking higher dietary spermidine intake with a reduced risk for cognitive impairment in humans.
    Keywords:  Pink1; aging; autophagy; cognitive function; dietary spermidine; memory; mitochondria; mitophagy
    DOI:  https://doi.org/10.1016/j.celrep.2021.108985
  37. Nat Commun. 2021 04 12. 12(1): 2148
    Inositol treatment inhibits medulloblastoma through suppression of epigenetic-driven metabolic adaptation.
    Sara Badodi, Nicola Pomella, Xinyu Zhang, Gabriel Rosser, John Whittingham, Maria Victoria Niklison-Chirou, Yau Mun Lim, Sebastian Brandner, Gillian Morrison, Steven M Pollard, Christopher D Bennett, Steven C Clifford, Andrew Peet, M Albert Basson, Silvia Marino.
      Deregulation of chromatin modifiers plays an essential role in the pathogenesis of medulloblastoma, the most common paediatric malignant brain tumour. Here, we identify a BMI1-dependent sensitivity to deregulation of inositol metabolism in a proportion of medulloblastoma. We demonstrate mTOR pathway activation and metabolic adaptation specifically in medulloblastoma of the molecular subgroup G4 characterised by a BMI1High;CHD7Low signature and show this can be counteracted by IP6 treatment. Finally, we demonstrate that IP6 synergises with cisplatin to enhance its cytotoxicity in vitro and extends survival in a pre-clinical BMI1High;CHD7Low xenograft model.
    DOI:  https://doi.org/10.1038/s41467-021-22379-7
  38. Nat Commun. 2021 04 15. 12(1): 2259
    SOD1 regulates ribosome biogenesis in KRAS mutant non-small cell lung cancer.
    Xiaowen Wang, Hong Zhang, Russell Sapio, Jun Yang, Justin Wong, Xin Zhang, Jessie Y Guo, Sharon Pine, Holly Van Remmen, Hong Li, Eileen White, Chen Liu, Megerditch Kiledjian, Dimitri G Pestov, X F Steven Zheng.
      SOD1 is known as the major cytoplasmic superoxide dismutase and an anticancer target. However, the role of SOD1 in cancer is not fully understood. Herein we describe the generation of an inducible Sod1 knockout in KRAS-driven NSCLC mouse model. Sod1 knockout markedly reduces tumor burden in vivo and blocks growth of KRAS mutant NSCLC cells in vitro. Intriguingly, SOD1 is enriched in the nucleus and notably in the nucleolus of NSCLC cells. The nuclear and nucleolar, not cytoplasmic, form of SOD1 is essential for lung cancer cell proliferation. Moreover, SOD1 interacts with PeBoW complex and controls its assembly necessary for pre-60S ribosomal subunit maturation. Mechanistically, SOD1 regulates co-localization of PeBoW with and processing of pre-rRNA, and maturation of cytoplasmic 60S ribosomal subunits in KRAS mutant lung cancer cells. Collectively, our study unravels a nuclear SOD1 function essential for ribosome biogenesis and proliferation in KRAS-driven lung cancer.
    DOI:  https://doi.org/10.1038/s41467-021-22480-x
  39. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00255-2. [Epub ahead of print]35(2): 108941
    eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction.
    YongTian Liang, Chengji Piao, Christine B Beuschel, David Toppe, Laxmikanth Kollipara, Boris Bogdanow, Marta Maglione, Janine Lützkendorf, Jason Chun Kit See, Sheng Huang, Tim O F Conrad, Ulrich Kintscher, Frank Madeo, Fan Liu, Albert Sickmann, Stephan J Sigrist.
      Mitochondrial function declines during brain aging and is suspected to play a key role in age-induced cognitive decline and neurodegeneration. Supplementing levels of spermidine, a body-endogenous metabolite, has been shown to promote mitochondrial respiration and delay aspects of brain aging. Spermidine serves as the amino-butyl group donor for the synthesis of hypusine (Nε-[4-amino-2-hydroxybutyl]-lysine) at a specific lysine residue of the eukaryotic translation initiation factor 5A (eIF5A). Here, we show that in the Drosophila brain, hypusinated eIF5A levels decline with age but can be boosted by dietary spermidine. Several genetic regimes of attenuating eIF5A hypusination all similarly affect brain mitochondrial respiration resembling age-typical mitochondrial decay and also provoke a premature aging of locomotion and memory formation in adult Drosophilae. eIF5A hypusination, conserved through all eukaryotes as an obviously critical effector of spermidine, might thus be an important diagnostic and therapeutic avenue in aspects of brain aging provoked by mitochondrial decline.
    Keywords:  CG8005; brain aging; deoxyhypusine synthase; eIF5A; eIF5A hypusination; learning and memory; locomotion; longevity; mitochondrial respiration; spermidine
    DOI:  https://doi.org/10.1016/j.celrep.2021.108941
  40. Cancer Cell Int. 2021 Apr 13. 21(1): 209
    Role of LncRNAs in regulating cancer amino acid metabolism.
    Yuhong Guo, Bin Lv, Renfeng Liu, Zhengzai Dai, Feifei Zhang, Yiping Liang, Bo Yu, Duo Zeng, Xiao-Bin Lv, Zhiping Zhang.
      The metabolic change of tumor cells is an extremely complicated process that involves the intersection and integration of various signal pathways. Compared with normal tissues, cancer cells show distinguished metabolic characteristics called metabolic reprogramming, which has been considered as a sign of cancer occurrence. With the deepening of tumor research in recent years, people gradually found that amino acid metabolism played crucial roles in cancer progression. Long non-coding RNAs (lncRNAs), which are implicated in many important biological processes, were firstly discovered dysregulating in cancer tissues and participating in extensive regulation of tumorigenesis. This review focuses on the reprogramming of amino acid metabolism in cancers and how lncRNAs participate in the regulatory network by interacting with other macromolecular substances. Understanding the functions of lncRNA in amino acid reprogramming in tumors might provide a new vision on the mechanisms of tumorigenesis and the development of new approaches for cancer therapy.
    Keywords:  Amino acid; Cancer; Glutamine; Metabolism; lncRNA
    DOI:  https://doi.org/10.1186/s12935-021-01926-8
  41. Nat Commun. 2021 04 15. 12(1): 2277
    Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets.
    Zhen Miao, Michael S Balzer, Ziyuan Ma, Hongbo Liu, Junnan Wu, Rojesh Shrestha, Tamas Aranyi, Amy Kwan, Ayano Kondo, Marco Pontoglio, Junhyong Kim, Mingyao Li, Klaus H Kaestner, Katalin Susztak.
      Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development.
    DOI:  https://doi.org/10.1038/s41467-021-22266-1
  42. Cell. 2021 Apr 13. pii: S0092-8674(21)00366-4. [Epub ahead of print]
    ER-to-Golgi protein delivery through an interwoven, tubular network extending from ER.
    Aubrey V Weigel, Chi-Lun Chang, Gleb Shtengel, C Shan Xu, David P Hoffman, Melanie Freeman, Nirmala Iyer, Jesse Aaron, Satya Khuon, John Bogovic, Wei Qiu, Harald F Hess, Jennifer Lippincott-Schwartz.
      Cellular versatility depends on accurate trafficking of diverse proteins to their organellar destinations. For the secretory pathway (followed by approximately 30% of all proteins), the physical nature of the vessel conducting the first portage (endoplasmic reticulum [ER] to Golgi apparatus) is unclear. We provide a dynamic 3D view of early secretory compartments in mammalian cells with isotropic resolution and precise protein localization using whole-cell, focused ion beam scanning electron microscopy with cryo-structured illumination microscopy and live-cell synchronized cargo release approaches. Rather than vesicles alone, the ER spawns an elaborate, interwoven tubular network of contiguous lipid bilayers (ER exit site) for protein export. This receptacle is capable of extending microns along microtubules while still connected to the ER by a thin neck. COPII localizes to this neck region and dynamically regulates cargo entry from the ER, while COPI acts more distally, escorting the detached, accelerating tubular entity on its way to joining the Golgi apparatus through microtubule-directed movement.
    Keywords:  COPI; COPII; cholesterol; correlative light and electron microscopy; endoplasmic reticulum exit sites; endoplasmic reticulum to Golgi transport intermediate; focused ion beam-scanning electron microscopy; membrane trafficking; retention using selective hook system; secretory pathway
    DOI:  https://doi.org/10.1016/j.cell.2021.03.035
  43. Nature. 2021 Apr 14.
    Organelle degradation in the lens by PLAAT phospholipases.
    Hideaki Morishita, Tomoya Eguchi, Satoshi Tsukamoto, Yuriko Sakamaki, Satoru Takahashi, Chieko Saito, Ikuko Koyama-Honda, Noboru Mizushima.
      The eye lens of vertebrates is composed of fibre cells in which all membrane-bound organelles undergo degradation during terminal differentiation to form an organelle-free zone1. The mechanism that underlies this large-scale organelle degradation remains largely unknown, although it has previously been shown to be independent of macroautophagy2,3. Here we report that phospholipases in the PLAAT (phospholipase A/acyltransferase, also known as HRASLS) family-Plaat1 (also known as Hrasls) in zebrafish and PLAAT3 (also known as HRASLS3, PLA2G16, H-rev107 or AdPLA) in mice4-6-are essential for the degradation of lens organelles such as mitochondria, the endoplasmic reticulum and lysosomes. Plaat1 and PLAAT3 translocate from the cytosol to various organelles immediately before organelle degradation, in a process that requires their C-terminal transmembrane domain. The translocation of Plaat1 to organelles depends on the differentiation of fibre cells and damage to organelle membranes, both of which are mediated by Hsf4. After the translocation of Plaat1 or PLAAT3 to membranes, the phospholipase induces extensive organelle rupture that is followed by complete degradation. Organelle degradation by PLAAT-family phospholipases is essential for achieving an optimal transparency and refractive function of the lens. These findings expand our understanding of intracellular organelle degradation and provide insights into the mechanism by which vertebrates acquired transparent lenses.
    DOI:  https://doi.org/10.1038/s41586-021-03439-w
  44. Commun Biol. 2021 Apr 15. 4(1): 477
    An in vitro tumorigenesis model based on live-cell-generated oxygen and nutrient gradients.
    Anne C Gilmore, Sarah J Flaherty, Veena Somasundaram, David A Scheiblin, Stephen J Lockett, David A Wink, William F Heinz.
      The tumor microenvironment (TME) is multi-cellular, spatially heterogenous, and contains cell-generated gradients of soluble molecules. Current cell-based model systems lack this complexity or are difficult to interrogate microscopically. We present a 2D live-cell chamber that approximates the TME and demonstrate that breast cancer cells and macrophages generate hypoxic and nutrient gradients, self-organize, and have spatially varying phenotypes along the gradients, leading to new insights into tumorigenesis.
    DOI:  https://doi.org/10.1038/s42003-021-01954-0
  45. Bioessays. 2021 Apr 16. e2000256
    Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes.
    Michael Brandeis.
      I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check.
    Keywords:  endosymbiosis; eukaryogenesis; evolution of sex; meiosis; mitochondrial DNA
    DOI:  https://doi.org/10.1002/bies.202000256
  46. J Cell Biol. 2021 Jun 07. pii: e202006043. [Epub ahead of print]220(6):
    Parkin-independent mitophagy via Drp1-mediated outer membrane severing and inner membrane ubiquitination.
    Yumiko Oshima, Etienne Cartier, Liron Boyman, Nicolas Verhoeven, Brian M Polster, Weiliang Huang, Maureen Kane, W Jonathan Lederer, Mariusz Karbowski.
      Here, we report that acute reduction in mitochondrial translation fidelity (MTF) causes ubiquitination of the inner mitochondrial membrane (IMM) proteins, including TRAP1 and CPOX, which occurs selectively in mitochondria with a severed outer mitochondrial membrane (OMM). Ubiquitinated IMM recruits the autophagy machinery. Inhibiting autophagy leads to increased accumulation of mitochondria with severed OMM and ubiquitinated IMM. This process occurs downstream of the accumulation of cytochrome c/CPOX in a subset of mitochondria heterogeneously distributed throughout the cell ("mosaic distribution"). Formation of mosaic mitochondria, OMM severing, and IMM ubiquitination require active mitochondrial translation and mitochondrial fission, but not the proapoptotic proteins Bax and Bak. In contrast, in Parkin-overexpressing cells, MTF reduction does not lead to the severing of the OMM or IMM ubiquitination, but it does induce Drp1-independent ubiquitination of the OMM. Furthermore, high-cytochrome c/CPOX mitochondria are preferentially targeted by Parkin, indicating that in the context of reduced MTF, they are mitophagy intermediates regardless of Parkin expression. In sum, Parkin-deficient cells adapt to mitochondrial proteotoxicity through a Drp1-mediated mechanism that involves the severing of the OMM and autophagy targeting ubiquitinated IMM proteins.
    DOI:  https://doi.org/10.1083/jcb.202006043
  47. Mol Cell Oncol. 2021 ;8(2): 1876506
    Age-induced metabolic reprogramming underlies cancer progression.
    Didem Ilter, Ana P Gomes.
      Aging is a main risk factor for cancer. Using human serum we demonstrated that tumor progression and metastases occur, at least in part, as a manifestation of global metabolic deregulation of the aged host. This shows that the role of aging in cancer goes far beyond increased exposure time to mutagens; the aging process coordinates various aspects required for malignancy.
    Keywords:  Aging; metabolism; metastasis
    DOI:  https://doi.org/10.1080/23723556.2021.1876506
  48. Front Cell Dev Biol. 2021 ;9 626117
    Mitochondrial OMA1 and OPA1 as Gatekeepers of Organellar Structure/Function and Cellular Stress Response.
    Robert Gilkerson, Patrick De La Torre, Shaynah St Vallier.
      Mammalian mitochondria are emerging as a critical stress-responsive contributor to cellular life/death and developmental outcomes. Maintained as an organellar network distributed throughout the cell, mitochondria respond to cellular stimuli and stresses through highly sensitive structural dynamics, particularly in energetically demanding cell settings such as cardiac and muscle tissues. Fusion allows individual mitochondria to form an interconnected reticular network, while fission divides the network into a collection of vesicular organelles. Crucially, optic atrophy-1 (OPA1) directly links mitochondrial structure and bioenergetic function: when the transmembrane potential across the inner membrane (ΔΨm) is intact, long L-OPA1 isoforms carry out fusion of the mitochondrial inner membrane. When ΔΨm is lost, L-OPA1 is cleaved to short, fusion-inactive S-OPA1 isoforms by the stress-sensitive OMA1 metalloprotease, causing the mitochondrial network to collapse to a fragmented population of organelles. This proteolytic mechanism provides sensitive regulation of organellar structure/function but also engages directly with apoptotic factors as a major mechanism of mitochondrial participation in cellular stress response. Furthermore, emerging evidence suggests that this proteolytic mechanism may have critical importance for cell developmental programs, particularly in cardiac, neuronal, and stem cell settings. OMA1's role as a key mitochondrial stress-sensitive protease motivates exciting new questions regarding its mechanistic regulation and interactions, as well as its broader importance through involvement in apoptotic, stress response, and developmental pathways.
    Keywords:  OMA1; OPA1; apoptosis; development; mitochondria
    DOI:  https://doi.org/10.3389/fcell.2021.626117
  49. Cell Rep. 2021 Apr 13. pii: S2211-1247(21)00304-1. [Epub ahead of print]35(2): 108990
    Stabilized epithelial phenotype of cancer cells in primary tumors leads to increased colonization of liver metastasis in pancreatic cancer.
    Julienne L Carstens, Sujuan Yang, Pedro Correa de Sampaio, Xiaofeng Zheng, Souptik Barua, Kathleen M McAndrews, Arvind Rao, Jared K Burks, Andrew D Rhim, Raghu Kalluri.
      Pancreatic ductal adenocarcinoma (PDAC) is therapeutically recalcitrant and metastatic. Partial epithelial to mesenchymal transition (EMT) is associated with metastasis; however, a causal connection needs further unraveling. Here, we use single-cell RNA sequencing and genetic mouse models to identify the functional roles of partial EMT and epithelial stabilization in PDAC growth and metastasis. A global EMT expression signature identifies ∼50 cancer cell clusters spanning the epithelial-mesenchymal continuum in both human and murine PDACs. The combined genetic suppression of Snail and Twist results in PDAC epithelial stabilization and increased liver metastasis. Genetic deletion of Zeb1 in PDAC cells also leads to liver metastasis associated with cancer cell epithelial stabilization. We demonstrate that epithelial stabilization leads to the enhanced collective migration of cancer cells and modulation of the immune microenvironment, which likely contribute to efficient liver colonization. Our study provides insights into the diverse mechanisms of metastasis in pancreatic cancer and potential therapeutic targets.
    Keywords:  Snail; Twist; Zeb1; collective migration; epithelial-to-mesenchymal transition; immune modulation; metastasis; mouse models; pancreatic cancer; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.celrep.2021.108990
  50. Curr Opin Biotechnol. 2021 Apr 12. pii: S0958-1669(21)00054-9. [Epub ahead of print]68 300-309
    NLRP3 as a sensor of metabolism gone awry.
    Emilia Neuwirt, Oliver Gorka, Benedikt S Saller, Christina J Groß, Tobias Madl, Olaf Groß.
      The NLRP3 inflammasome is an important player in innate immunity and pathogenic inflammation. Numerous studies have implicated it in sensing endogenous danger signals, yet the precise mechanisms remain unknown. Here, we review the current knowledge on the organismal and cellular metabolic triggers engaging NLRP3, and the mechanisms involved in integrating the diverse signals.
    DOI:  https://doi.org/10.1016/j.copbio.2021.03.009
  51. Nature. 2021 Apr 14.
    The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D.
    Andrea C Chaikovsky, Chuan Li, Edwin E Jeng, Samuel Loebell, Myung Chang Lee, Christopher W Murray, Ran Cheng, Janos Demeter, Danielle L Swaney, Si-Han Chen, Billy W Newton, Jeffrey R Johnson, Alexandros P Drainas, Yan Ting Shue, Jose A Seoane, Preethi Srinivasan, Andy He, Akihiro Yoshida, Susan Q Hipkins, Edel McCrea, Carson D Poltorack, Nevan J Krogan, J Alan Diehl, Christina Kong, Peter K Jackson, Christina Curtis, Dmitri A Petrov, Michael C Bassik, Monte M Winslow, Julien Sage.
      The initiation of cell division integrates a large number of intra- and extracellular inputs. D-type cyclins (hereafter, cyclin D) couple these inputs to the initiation of DNA replication1. Increased levels of cyclin D promote cell division by activating cyclin-dependent kinases 4 and 6 (hereafter, CDK4/6), which in turn phosphorylate and inactivate the retinoblastoma tumour suppressor. Accordingly, increased levels and activity of cyclin D-CDK4/6 complexes are strongly linked to unchecked cell proliferation and cancer2,3. However, the mechanisms that regulate levels of cyclin D are incompletely understood4,5. Here we show that autophagy and beclin 1 regulator 1 (AMBRA1) is the main regulator of the degradation of cyclin D. We identified AMBRA1 in a genome-wide screen to investigate the genetic basis of  the response to CDK4/6 inhibition. Loss of AMBRA1 results in high levels of cyclin D in cells and in mice, which promotes proliferation and decreases sensitivity to CDK4/6 inhibition. Mechanistically, AMBRA1 mediates ubiquitylation and proteasomal degradation of cyclin D as a substrate receptor for the cullin 4 E3 ligase complex. Loss of AMBRA1 enhances the growth of lung adenocarcinoma in a mouse model, and low levels of AMBRA1 correlate with worse survival in patients with lung adenocarcinoma. Thus, AMBRA1 regulates cellular levels of cyclin D, and contributes to cancer development and the response of cancer cells to CDK4/6 inhibitors.
    DOI:  https://doi.org/10.1038/s41586-021-03474-7
  52. Ann Transl Med. 2021 Mar;9(5): 417
    Pancreatic stellate cells regulate branched-chain amino acid metabolism in pancreatic cancer.
    Wenna Jiang, Lu Qiao, Yawei Han, Aimin Zhang, Haohua An, Jiawei Xiao, Li Ren.
      Background: Pancreatic ductal adenocarcinoma (PDAC) is the most lethal malignancy: it has a 5-year survival rate of less than 9%. Although surgical resection is an effective treatment for PDAC, only a small number of patients can have their tumors surgically removed. Thus, an urgent need to find new therapeutic targets for PDAC exists. Understanding the molecular mechanism of PDAC development is essential for the treatment of this malignancy. This research aimed to study the mechanisms of pancreatic stellate cells (PSCs), which regulate branched-chain amino acid (BCAA) metabolism in PDAC.Methods: Differentially expressed proteins were detected via nanoliquid chromatography coupled to mass spectrometry (nano-LC-MS/MS). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment methods were used to find the valine-leucine-isoleucine (BCAA) degradation pathway. The levels of BCAAs in the sera and tissues of patients with PDAC were measured by using nuclear magnetic resonance (NMR). The functions of BCAA concentrations and the effects of activated pancreatic stellate cells (aPSCs) were also evaluated by performing Cell Counting Kit-8, colony formation, and wound healing assays.
    Results: A total of 1,519 proteins with significantly differential expression were discovered in PDAC and adjacent tissues by using nano-LC-MS/MS. KEGG pathway enrichment analysis identified the BCAA degradation pathway. The content of BCAA in PDAC clinical samples was up-regulated. However, the addition of different concentrations of BCAA to PDAC cell culture medium failed to promote the proliferation and migration of PDAC cells. Given that analysis based on The Cancer Genome Atlas database showed that the number of aPSCs gradually increased with the progression of PDAC, the effects of aPSCs on PDAC cells were explored. After coculture with aPSCs, PDAC cell proliferation showed a significant increase, and the proteins involved in the BCAA degradation pathway in PDAC cells had also changed.
    Conclusions: aPSCs could regulate BCAA metabolism to enhance the progression of PDAC, indicating that the regulation of BCAA metabolism may serve as a new therapeutic direction for PDAC.
    Keywords:  Pancreatic stellate cells (PSCs); branched-chain amino acid metabolism; pancreatic cancer
    DOI:  https://doi.org/10.21037/atm-21-761
  53. Oncogene. 2021 Apr 12.
    Clocking cancer: the circadian clock as a target in cancer therapy.
    Francesca Battaglin, Priscilla Chan, Yuanzhong Pan, Shivani Soni, Meng Qu, Erin R Spiller, Sofi Castanon, Evanthia T Roussos Torres, Shannon M Mumenthaler, Steve A Kay, Heinz-Josef Lenz.
      Disruption of the cellular pathway modulating endogenous 24-h rhythms, referred to as "the circadian clock", has been recently proven to be associated with cancer risk, development, and progression. This pathway operates through a complex network of transcription-translation feedback loops generated by a set of interplaying proteins. The expression of core circadian clock genes is frequently dysregulated in human tumors; however, the specific effects and underlying mechanisms seem to vary depending on the cancer types and are not fully understood. In addition, specific oncogenes may differentially induce the dysregulation of the circadian clock in tumors. Pharmacological modulation of clock components has been shown to result in specific lethality in certain types of cancer cells, and thus holds great promise as a novel anti-cancer therapeutic approach. Here we present an overview of the rationale and current evidence for targeting the clock in cancer treatment.
    DOI:  https://doi.org/10.1038/s41388-021-01778-6
  54. Phys Biol. 2021 Apr 14.
    A note on the power per mitochondrion and the number of associated active ATP synthases.
    Peyman Fahimi, Cherif Matta.
      Recent experiments and thermodynamic arguments suggest that mitochondrial temperatures are higher than those of the cytoplasm. A "hot mitochondrion" calls for a closer examination of the energy balance that endows it with these claimed elevated temperatures. As a first step in this effort, we present here a semi-quantitative bookkeeping whereby, in one stroke, a formula is proposed that yields the rate of heat production in a typical mitochondrion and a formula for estimating the number of active ATP synthase molecules per mitochondrion. Scaling laws are shown to determine the number of active ATP synthase molecules in a mitochondrion and mitochondrial rate of heat production. Mitochondrial population of active ATP synthases and mitochondrial rate of heat production appear, both, to scale with cell volume. Four heterotrophic protozoa cell types are considered in this study. The studied cells, selected to cover a wide range of sizes (volumes) from ca. 100 μm3 to 1 million μm3, are estimated to exhibit a power per mitochondrion ranging from ca. 1 pW to 0.03 pW. The corresponding number of active ATP synthases per mitochondrion in these cells ranges from 5,000 to just about a hundred.
    Keywords:  Allometric power laws; Cellular volumes; Mitochondrial heat production; Mitochondrial thermodynamics; Number of ATP synthase molecules; Scaling laws
    DOI:  https://doi.org/10.1088/1478-3975/abf7d9
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