bims-camemi 2023-01-15 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2023–01–15
38 papers selected by
Christian Frezza, Universität zu Köln

Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan.
Targeting succinate metabolism to decrease brain injury upon mechanical thrombectomy treatment of ischemic stroke.
Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth.
OGT controls mammalian cell viability by regulating the proteasome/mTOR/ mitochondrial axis.
Mitochondrial signalling and homeostasis: from cell biology to neurological disease.
GATOR2 rings GATOR1 to speak to mTORC1.
Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria.
Disruption of mitochondrial dynamics triggers muscle inflammation through interorganellar contacts and mitochondrial DNA mislocation.
A central role for regulated protein stability in the control of TFE3 and MITF by nutrients.
Metabolism in stem cell driven leukaemia: parallels between haematopoiesis and immunity.
Metabolites as signalling molecules.
SOD1 is an essential H2S detoxifying enzyme.
Pyruvate dehydrogenase kinase supports macrophage NLRP3 inflammasome activation during acute inflammation.
Long-Chain and Medium-Chain Fatty Acids in Energy Metabolism of Murine Kidney Mitochondria.
OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases.
Overview of Cancer Metabolism and Signaling Transduction.
The mitophagy receptor BNIP3 is critical for the regulation of metabolic homeostasis and mitochondrial function in the nucleus pulposus cells of the intervertebral disc.
The impact of glucose on mitochondria and lifespan is determined by the integrity of proline catabolism in C. elegans.
Tryptophan Metabolism Acts as a New Anti-Ferroptotic Pathway to Mediate Tumor Growth.
Intersection of immune and oncometabolic pathways drives cancer hyperprogression during immunotherapy.
Anti-retroviral treatment with zidovudine alters pyrimidine metabolism, reduces translation, and extends healthy longevity via ATF-4.
Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells.
A critical assessment of the role of creatine in brown adipose tissue thermogenesis.
Strength in diversity: Intra-cellular metabolite sharing enhances longevity.
Targeting TBK1 to overcome resistance to cancer immunotherapy.
Mitochondrial Iron Metabolism: The Crucial Actors in Diseases.
A tale of two pathways: Regulation of proteostasis by UPRmt and MDPs.
An atlas of substrate specificities for the human serine/threonine kinome.
Adaptation to glucose starvation is associated with molecular reorganization of the circadian clock in Neurospora crassa.
The ERAD system is restricted by elevated ceramides.
KDM6A loss triggers an epigenetic switch that disrupts urothelial differentiation and drives cell proliferation in bladder cancer.
Addressing the genetic/nongenetic duality in cancer with systems biology.
RNA splicing dysregulation and the hallmarks of cancer.
p53 engages the cGAS/STING cytosolic DNA sensing pathway for tumor suppression.
IDH2 stabilizes HIF-1α-induced metabolic reprogramming and promotes chemoresistance in urothelial cancer.
Mass Spectrometry Reveals High Levels of Hydrogen Peroxide in Pancreatic Cancer Cells.
ZBTB18 restricts chromatin accessibility and prevents transcriptional adaptations that drive metastasis.
Small molecule agonist of mitochondrial fusion repairs mitochondrial dysfunction.

Cell. 2023 Jan 05. pii: S0092-8674(22)01520-3. [Epub ahead of print]186(1): 63-79.e21

Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan.

Clara Correia-Melo, Stephan Kamrad, Roland Tengölics, Christoph B Messner, Pauline Trebulle, StJohn Townsend, Sreejith Jayasree Varma, Anja Freiwald, Benjamin M Heineike, Kate Campbell, Lucía Herrera-Dominguez, Simran Kaur Aulakh, Lukasz Szyrwiel, Jason S L Yu, Aleksej Zelezniak, Vadim Demichev, Michael Mülleder, Balázs Papp, Mohammad Tauqeer Alam, Markus Ralser.

  Metabolism is deeply intertwined with aging. Effects of metabolic interventions on aging have been explained with intracellular metabolism, growth control, and signaling. Studying chronological aging in yeast, we reveal a so far overlooked metabolic property that influences aging via the exchange of metabolites. We observed that metabolites exported by young cells are re-imported by chronologically aging cells, resulting in cross-generational metabolic interactions. Then, we used self-establishing metabolically cooperating communities (SeMeCo) as a tool to increase metabolite exchange and observed significant lifespan extensions. The longevity of the SeMeCo was attributable to metabolic reconfigurations in methionine consumer cells. These obtained a more glycolytic metabolism and increased the export of protective metabolites that in turn extended the lifespan of cells that supplied them with methionine. Our results establish metabolite exchange interactions as a determinant of cellular aging and show that metabolically cooperating cells can shape the metabolic environment to extend their lifespan.

Keywords:  chronological aging; eukaryotic longevity; metabolic microenvironment; metabolite exchange interactions

DOI:  https://doi.org/10.1016/j.cell.2022.12.007
Redox Biol. 2023 Feb;pii: S2213-2317(23)00001-0. [Epub ahead of print]59 102600

Targeting succinate metabolism to decrease brain injury upon mechanical thrombectomy treatment of ischemic stroke.

Amin Mottahedin, Hiran A Prag, Andreas Dannhorn, Richard Mair, Christina Schmidt, Ming Yang, Annabel Sorby-Adams, Jordan J Lee, Nils Burger, Duvaraka Kulaveerasingam, Margaret M Huang, Stefano Pluchino, Luca Peruzzotti-Jametti, Richard Goodwin, Christian Frezza, Michael P Murphy, Thomas Krieg.

Current treatments for acute ischemic stroke aim to reinstate a normal perfusion in the ischemic territory but can also cause significant ischemia-reperfusion (IR) injury. Previous data in experimental models of stroke show that ischemia leads to the accumulation of succinate, and, upon reperfusion, the accumulated succinate is rapidly oxidized by succinate dehydrogenase (SDH) to drive superoxide production at mitochondrial complex I. Despite this process initiating IR injury and causing further tissue damage, the potential of targeting succinate metabolism to minimize IR injury remains unexplored. Using both quantitative and untargeted high-resolution metabolomics, we show a time-dependent accumulation of succinate in both human and mouse brain exposed to ischemia ex vivo. In a mouse model of ischemic stroke/mechanical thrombectomy mass spectrometry imaging (MSI) shows that succinate accumulation is confined to the ischemic region, and that the accumulated succinate is rapidly oxidized upon reperfusion. Targeting succinate oxidation by systemic infusion of the SDH inhibitor malonate upon reperfusion leads to a dose-dependent decrease in acute brain injury. Together these findings support targeting succinate metabolism upon reperfusion to decrease IR injury as a valuable adjunct to mechanical thrombectomy in ischemic stroke.

DOI: https://doi.org/10.1016/j.redox.2023.102600
Nat Cell Biol. 2023 Jan 12.

Multiplexed screens identify RAS paralogues HRAS and NRAS as suppressors of KRAS-driven lung cancer growth.

Rui Tang, Emily G Shuldiner, Marcus Kelly, Christopher W Murray, Jess D Hebert, Laura Andrejka, Min K Tsai, Nicholas W Hughes, Mitchell I Parker, Hongchen Cai, Yao-Cheng Li, Geoffrey M Wahl, Roland L Dunbrack, Peter K Jackson, Dmitri A Petrov, Monte M Winslow.

Oncogenic KRAS mutations occur in approximately 30% of lung adenocarcinoma. Despite several decades of effort, oncogenic KRAS-driven lung cancer remains difficult to treat, and our understanding of the regulators of RAS signalling is incomplete. Here to uncover the impact of diverse KRAS-interacting proteins on lung cancer growth, we combined multiplexed somatic CRISPR/Cas9-based genome editing in genetically engineered mouse models with tumour barcoding and high-throughput barcode sequencing. Through a series of CRISPR/Cas9 screens in autochthonous lung cancer models, we show that HRAS and NRAS are suppressors of KRASG12D-driven tumour growth in vivo and confirm these effects in oncogenic KRAS-driven human lung cancer cell lines. Mechanistically, RAS paralogues interact with oncogenic KRAS, suppress KRAS-KRAS interactions, and reduce downstream ERK signalling. Furthermore, HRAS and NRAS mutations identified in oncogenic KRAS-driven human tumours partially abolished this effect. By comparing the tumour-suppressive effects of HRAS and NRAS in oncogenic KRAS- and oncogenic BRAF-driven lung cancer models, we confirm that RAS paralogues are specific suppressors of KRAS-driven lung cancer in vivo. Our study outlines a technological avenue to uncover positive and negative regulators of oncogenic KRAS-driven cancer in a multiplexed manner in vivo and highlights the role RAS paralogue imbalance in oncogenic KRAS-driven lung cancer.

DOI: https://doi.org/10.1038/s41556-022-01049-w
Proc Natl Acad Sci U S A. 2023 Jan 17. 120(3): e2218332120

OGT controls mammalian cell viability by regulating the proteasome/mTOR/ mitochondrial axis.

Xiang Li, Xiaojing Yue, Hugo Sepulveda, Rajan A Burt, David A Scott, Steven A Carr, Samuel A Myers, Anjana Rao.

  O-GlcNAc transferase (OGT) modifies serine and threonine residues on nuclear and cytosolic proteins with O-linked N-acetylglucosamine (GlcNAc). OGT is essential for mammalian cell viability, but the underlying mechanisms are still enigmatic. We performed a genome-wide CRISPR-Cas9 screen in mouse embryonic stem cells (mESCs) to identify candidates whose depletion rescued the block in cell proliferation induced by OGT deficiency. We show that the block in cell proliferation in OGT-deficient cells stems from mitochondrial dysfunction secondary to mTOR (mechanistic target of rapamycin) hyperactivation. In normal cells, OGT maintains low mTOR activity and mitochondrial fitness through suppression of proteasome activity; in the absence of OGT, increased proteasome activity results in increased steady-state amino acid levels, which in turn promote mTOR lysosomal translocation and activation, and increased oxidative phosphorylation. mTOR activation in OGT-deficient mESCs was confirmed by an independent phospho-proteomic screen. Our study highlights a unique series of events whereby OGT regulates the proteasome/ mTOR/ mitochondrial axis in a manner that maintains homeostasis of intracellular amino acid levels, mitochondrial fitness, and cell viability. A similar mechanism operates in CD8+ T cells, indicating its generality across mammalian cell types. Manipulating OGT activity may have therapeutic potential in diseases in which this signaling pathway is impaired.

Keywords:  OGT; genome-wide CRISPR/Cas9 screen; mTOR; mitochondrion; proteasome

DOI:  https://doi.org/10.1073/pnas.2218332120
Trends Neurosci. 2023 Jan 10. pii: S0166-2236(22)00239-9. [Epub ahead of print]

Mitochondrial signalling and homeostasis: from cell biology to neurological disease.

Jack J Collier, Monika Oláhová, Thomas G McWilliams, Robert W Taylor.

  Efforts to understand how mitochondrial dysfunction contributes to neurodegeneration have primarily focussed on the role of mitochondria in neuronal energy metabolism. However, progress in understanding the etiological nature of emerging mitochondrial functions has yielded new ideas about the mitochondrial basis of neurological disease. Studies aimed at deciphering how mitochondria signal through interorganellar contacts, vesicular trafficking, and metabolic transmission have revealed that mitochondrial regulation of immunometabolism, cell death, organelle dynamics, and neuroimmune interplay are critical determinants of neural health. Moreover, the homeostatic mechanisms that exist to protect mitochondrial health through turnover via nanoscale proteostasis and lysosomal degradation have become integrated within mitochondrial signalling pathways to support metabolic plasticity and stress responses in the nervous system. This review highlights how these distinct mitochondrial pathways converge to influence neurological health and contribute to disease pathology.

Keywords:  immunity; inflammation; metabolism; mitochondrial-derived vesicles; mitochondria–lysosome axis; quality control

DOI:  https://doi.org/10.1016/j.tins.2022.12.001
Mol Cell. 2023 Jan 05. pii: S1097-2765(22)01168-6. [Epub ahead of print]83(1): 6-8

GATOR2 rings GATOR1 to speak to mTORC1.

Umakant Sahu, Issam Ben-Sahra.

The mechanistic target of rapamycin complex 1 (mTORC1) senses cellular leucine levels through the GATOR1/2-Rag axis. Jiang et al. show that the Ring domains of GATOR2 subunits maintain the integrity of the complex and promote ubiquitination and inhibition of GATOR1, thereby leading to mTORC1 activation.

DOI: https://doi.org/10.1016/j.molcel.2022.12.011
Nucleic Acids Res. 2023 Jan 11. pii: gkac1233. [Epub ahead of print]

Translation initiation of leaderless and polycistronic transcripts in mammalian mitochondria.

Cristina Remes, Anas Khawaja, Sarah F Pearce, Adam M Dinan, Shreekara Gopalakrishna, Miriam Cipullo, Vasileios Kyriakidis, Jingdian Zhang, Xaquin Castro Dopico, Olessya Yukhnovets, Ilian Atanassov, Andrew E Firth, Barry Cooperman, Joanna Rorbach.

The synthesis of mitochondrial OXPHOS complexes is central to cellular metabolism, yet many molecular details of mitochondrial translation remain elusive. It has been commonly held view that translation initiation in human mitochondria proceeded in a manner similar to bacterial systems, with the mitoribosomal small subunit bound to the initiation factors, mtIF2 and mtIF3, along with initiator tRNA and an mRNA. However, unlike in bacteria, most human mitochondrial mRNAs lack 5' leader sequences that can mediate small subunit binding, raising the question of how leaderless mRNAs are recognized by mitoribosomes. By using novel in vitro mitochondrial translation initiation assays, alongside biochemical and genetic characterization of cellular knockouts of mitochondrial translation factors, we describe unique features of translation initiation in human mitochondria. We show that in vitro, leaderless mRNA transcripts can be loaded directly onto assembled 55S mitoribosomes, but not onto the mitoribosomal small subunit (28S), in a manner that requires initiator fMet-tRNAMet binding. In addition, we demonstrate that in human cells and in vitro, mtIF3 activity is not required for translation of leaderless mitochondrial transcripts but is essential for translation of ATP6 in the case of the bicistronic ATP8/ATP6 transcript. Furthermore, we show that mtIF2 is indispensable for mitochondrial protein synthesis. Our results demonstrate an important evolutionary divergence of the mitochondrial translation system and further our fundamental understanding of a process central to eukaryotic metabolism.

DOI: https://doi.org/10.1093/nar/gkac1233
Nat Commun. 2023 Jan 06. 14(1): 108

Disruption of mitochondrial dynamics triggers muscle inflammation through interorganellar contacts and mitochondrial DNA mislocation.

Andrea Irazoki, Isabel Gordaliza-Alaguero, Emma Frank, Nikolaos Nikiforos Giakoumakis, Jordi Seco, Manuel Palacín, Anna Gumà, Lykke Sylow, David Sebastián, Antonio Zorzano.

Some forms of mitochondrial dysfunction induce sterile inflammation through mitochondrial DNA recognition by intracellular DNA sensors. However, the involvement of mitochondrial dynamics in mitigating such processes and their impact on muscle fitness remain unaddressed. Here we report that opposite mitochondrial morphologies induce distinct inflammatory signatures, caused by differential activation of DNA sensors TLR9 or cGAS. In the context of mitochondrial fragmentation, we demonstrate that mitochondria-endosome contacts mediated by the endosomal protein Rab5C are required in TLR9 activation in cells. Skeletal muscle mitochondrial fragmentation promotes TLR9-dependent inflammation, muscle atrophy, reduced physical performance and enhanced IL6 response to exercise, which improved upon chronic anti-inflammatory treatment. Taken together, our data demonstrate that mitochondrial dynamics is key in preventing sterile inflammatory responses, which precede the development of muscle atrophy and impaired physical performance. Thus, we propose the targeting of mitochondrial dynamics as an approach to treating disorders characterized by chronic inflammation and mitochondrial dysfunction.

DOI: https://doi.org/10.1038/s41467-022-35732-1
Mol Cell. 2023 Jan 05. pii: S1097-2765(22)01170-4. [Epub ahead of print]83(1): 57-73.e9

A central role for regulated protein stability in the control of TFE3 and MITF by nutrients.

Christopher Nardone, Brad A Palanski, Daniel C Scott, Richard T Timms, Karl W Barber, Xin Gu, Aoyue Mao, Yumei Leng, Emma V Watson, Brenda A Schulman, Philip A Cole, Stephen J Elledge.

  The TFE3 and MITF master transcription factors maintain metabolic homeostasis by regulating lysosomal, melanocytic, and autophagy genes. Previous studies posited that their cytosolic retention by 14-3-3, mediated by the Rag GTPases-mTORC1, was key for suppressing transcriptional activity in the presence of nutrients. Here, we demonstrate using mammalian cells that regulated protein stability plays a fundamental role in their control. Amino acids promote the recruitment of TFE3 and MITF to the lysosomal surface via the Rag GTPases, activating an evolutionarily conserved phospho-degron and leading to ubiquitination by CUL1β-TrCP and degradation. Elucidation of the minimal functional degron revealed a conserved alpha-helix required for interaction with RagA, illuminating the molecular basis for a severe neurodevelopmental syndrome caused by missense mutations in TFE3 within the RagA-TFE3 interface. Additionally, the phospho-degron is recurrently lost in TFE3 genomic translocations that cause kidney cancer. Therefore, two divergent pathologies converge on the loss of protein stability regulation by nutrients.

Keywords:  MITF; Rag GTPases; TFE3; kidney cancer; lysosomes; mTORC1; neurodevelopment; nutrient-sensing; phospho-degron; ubiquitin; β-TrCP

DOI:  https://doi.org/10.1016/j.molcel.2022.12.013
Blood. 2023 Jan 12. pii: blood.2022018258. [Epub ahead of print]

Metabolism in stem cell driven leukaemia: parallels between haematopoiesis and immunity.

Kevin M Rattigan, Martha M Zarou, Vignir Helgason.

Our understanding of cancer metabolism spans from its role in cellular energetics and supplying the building blocks necessary for proliferation, to maintaining cellular redox and regulating the cellular epigenome and transcriptome. Cancer metabolism, once thought to be solely driven by upregulated glycolysis, is now known to comprise of multiple pathways with great plasticity in response to extrinsic challenges. Furthermore, cancer cells can modify their surrounding niche during disease initiation, maintenance and metastasis, contributing to therapy resistance. Leukaemia is a paradigm model of stem cell driven cancer. Here, we review how leukaemia remodels the niche and rewires its metabolism with particular attention paid to therapy-resistant stem cells. Specifically, we aim to give a global, non-exhaustive overview of key metabolic pathways. By contrasting the metabolic rewiring required by myeloid leukaemic stem cells with that required for haematopoiesis and immune cell function, we highlight the metabolic features they share. This is a critical consideration when contemplating anti-cancer metabolic inhibitor options, especially in the context of anti-cancer immune therapies. Finally, we examine pathways that have not been studied in leukaemia but are critical in solid cancers in the context of metastasis and interaction with new niches. These studies also offer detailed mechanisms that have yet to be investigated in leukaemia. Given that cancer (and normal) cells can meet their energy requirements by not only upregulating metabolic pathways, but also utilising systemically available substrates, we aim to inform how interlinked these metabolic pathways are, both within leukaemic cells and between cancer cells and their niche.

DOI: https://doi.org/10.1182/blood.2022018258
Nat Rev Mol Cell Biol. 2023 Jan 12.

Metabolites as signalling molecules.

Steven Andrew Baker, Jared Rutter.

Traditional views of cellular metabolism imply that it is passively adapted to meet the demands of the cell. It is becoming increasingly clear, however, that metabolites do more than simply supply the substrates for biological processes; they also provide critical signals, either through effects on metabolic pathways or via modulation of other regulatory proteins. Recent investigation has also uncovered novel roles for several metabolites that expand their signalling influence to processes outside metabolism, including nutrient sensing and storage, embryonic development, cell survival and differentiation, and immune activation and cytokine secretion. Together, these studies suggest that, in contrast to the prevailing notion, the biochemistry of a cell is frequently governed by its underlying metabolism rather than vice versa. This important shift in perspective places common metabolites as key regulators of cell phenotype and behaviour. Yet the signalling metabolites, and the cognate targets and transducers through which they signal, are only beginning to be uncovered. In this Review, we discuss the emerging links between metabolism and cellular behaviour. We hope this will inspire further dissection of the mechanisms through which metabolic pathways and intermediates modulate cell function and will suggest possible drug targets for diseases linked to metabolic deregulation.

DOI: https://doi.org/10.1038/s41580-022-00572-w
Proc Natl Acad Sci U S A. 2023 Jan 17. 120(3): e2205044120

SOD1 is an essential H2S detoxifying enzyme.

Christopher H Switzer, Shingo Kasamatsu, Hideshi Ihara, Philip Eaton.

  Although hydrogen sulfide (H2S) is an endogenous signaling molecule with antioxidant properties, it is also cytotoxic by potently inhibiting cytochrome c oxidase and mitochondrial respiration. Paradoxically, the primary route of H2S detoxification is thought to occur inside the mitochondrial matrix via a series of relatively slow enzymatic reactions that are unlikely to compete with its rapid inhibition of cytochrome c oxidase. Therefore, alternative or complementary cellular mechanisms of H2S detoxification are predicted to exist. Here, superoxide dismutase [Cu-Zn] (SOD1) is shown to be an efficient H2S oxidase that has an essential role in limiting cytotoxicity from endogenous and exogenous sulfide. Decreased SOD1 expression resulted in increased sensitivity to H2S toxicity in yeast and human cells, while increased SOD1 expression enhanced tolerance to H2S. SOD1 rapidly converted H2S to sulfate under conditions of limiting sulfide; however, when sulfide was in molar excess, SOD1 catalyzed the formation of per- and polysulfides, which induce cellular thiol oxidation. Furthermore, in SOD1-deficient cells, elevated levels of reactive oxygen species catalyzed sulfide oxidation to per- and polysulfides. These data reveal that a fundamental function of SOD1 is to regulate H2S and related reactive sulfur species.

Keywords:  SOD1; hydrogen sulfide; persulfide; polysulfide; reactive sulfur species

DOI:  https://doi.org/10.1073/pnas.2205044120
Cell Rep. 2023 Jan 09. pii: S2211-1247(22)01842-3. [Epub ahead of print]42(1): 111941

Pyruvate dehydrogenase kinase supports macrophage NLRP3 inflammasome activation during acute inflammation.

Allison K Meyers, Zhan Wang, Wenzheng Han, Qingxia Zhao, Manal Zabalawi, Likun Duan, Juan Liu, Qianyi Zhang, Rajesh K Manne, Felipe Lorenzo, Matthew A Quinn, Qianqian Song, Daping Fan, Hui-Kuan Lin, Cristina M Furdui, Jason W Locasale, Charles E McCall, Xuewei Zhu.

  Activating the macrophage NLRP3 inflammasome can promote excessive inflammation with severe cell and tissue damage and organ dysfunction. Here, we show that pharmacological or genetic inhibition of pyruvate dehydrogenase kinase (PDHK) significantly attenuates NLRP3 inflammasome activation in murine and human macrophages and septic mice by lowering caspase-1 cleavage and interleukin-1β (IL-1β) secretion. Inhibiting PDHK reverses NLRP3 inflammasome-induced metabolic reprogramming, enhances autophagy, promotes mitochondrial fusion over fission, preserves crista ultrastructure, and attenuates mitochondrial reactive oxygen species (ROS) production. The suppressive effect of PDHK inhibition on the NLRP3 inflammasome is independent of its canonical role as a pyruvate dehydrogenase regulator. Our study suggestsa non-canonical role of mitochondrial PDHK in promoting mitochondrial stress and supporting NLRP3 inflammasome activation during acute inflammation.

Keywords:  CP: Immunology; NLRP3 inflammasome; autophagy; cristae; immunometabolism; macrophages; metabolic flux; mitochondria; mitochondrial fission and fusion; pyruvate dehydrogenase kinase; sepsis

DOI:  https://doi.org/10.1016/j.celrep.2022.111941
Int J Mol Sci. 2022 Dec 26. pii: 379. [Epub ahead of print]24(1):

Long-Chain and Medium-Chain Fatty Acids in Energy Metabolism of Murine Kidney Mitochondria.

Alexander V Panov, Vladimir I Mayorov, Anna E Dikalova, Sergey I Dikalov.

  Scientists have long established that fatty acids are the primary substrates for kidney mitochondria. However, to date we still do not know how long-chain and middle-chain fatty acids are oxidized at the mitochondrial level. Our previous research has shown that mitochondria from the heart, brain, and kidney oxidize palmitoylcarnitine at a high rate only in the presence of succinate, glutamate, or pyruvate. In this paper, we report properties of the isolated kidney mitochondria and how malate and succinate affect the oxidation of C16 and C8 acylcarnitines. The isolated kidney mitochondria contain very few endogenous substrates and require malate to oxidize pyruvate, glutamate, and C16 or C8 acylcarnitines. We discovered that with 10 µM of C16 or C8 acylcarnitines, low concentrations of malate (0.2 mM) or succinate (0.5 mM) enhance the States 4 and 3 respiratory rates several times. The highest respiration rates were observed with C16 or C8 acylcarnitines and 5 mM succinate mixtures. Results show that kidney mitochondria, unlike the heart and brain mitochondria, lack the intrinsic inhibition of succinate dehydrogenase. Additionally, results show that the oxidation of fatty acid by the small respirasome's supercomplex generates a high level of CoQH2, and this makes SDH in the presence of succinate reverse the flow of electrons from CoQH2 to reduce fumarate to succinate. Finally, we report evidence that succinate dehydrogenase is a key mitochondrial enzyme that allows fast oxidation of fatty acids and turns the TCA cycle function from the catabolic to the anabolic and anaplerotic metabolic pathways.

Keywords:  beta-oxidation; fatty acids; kidney; kidney mitochondria; octanoylcarnitine; oxidative phosphorylation; palmitoylcarnitine; respirasome; respiration; succinate; succinate dehydrogenase

DOI:  https://doi.org/10.3390/ijms24010379
Commun Biol. 2023 Jan 12. 6(1): 22

OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases.

Gabriel Sturm, Kalpita R Karan, Anna S Monzel, Balaji Santhanam, Tanja Taivassalo, Céline Bris, Sarah A Ware, Marissa Cross, Atif Towheed, Albert Higgins-Chen, Meagan J McManus, Andres Cardenas, Jue Lin, Elissa S Epel, Shamima Rahman, John Vissing, Bruno Grassi, Morgan Levine, Steve Horvath, Ronald G Haller, Guy Lenaers, Douglas C Wallace, Marie-Pierre St-Onge, Saeed Tavazoie, Vincent Procaccio, Brett A Kaufman, Erin L Seifert, Michio Hirano, Martin Picard.

Patients with primary mitochondrial oxidative phosphorylation (OxPhos) defects present with fatigue and multi-system disorders, are often lean, and die prematurely, but the mechanistic basis for this clinical picture remains unclear. By integrating data from 17 cohorts of patients with mitochondrial diseases (n = 690) we find evidence that these disorders increase resting energy expenditure, a state termed hypermetabolism. We examine this phenomenon longitudinally in patient-derived fibroblasts from multiple donors. Genetically or pharmacologically disrupting OxPhos approximately doubles cellular energy expenditure. This cell-autonomous state of hypermetabolism occurs despite near-normal OxPhos coupling efficiency, excluding uncoupling as a general mechanism. Instead, hypermetabolism is associated with mitochondrial DNA instability, activation of the integrated stress response (ISR), and increased extracellular secretion of age-related cytokines and metabokines including GDF15. In parallel, OxPhos defects accelerate telomere erosion and epigenetic aging per cell division, consistent with evidence that excess energy expenditure accelerates biological aging. To explore potential mechanisms for these effects, we generate a longitudinal RNASeq and DNA methylation resource dataset, which reveals conserved, energetically demanding, genome-wide recalibrations. Taken together, these findings highlight the need to understand how OxPhos defects influence the energetic cost of living, and the link between hypermetabolism and aging in cells and patients with mitochondrial diseases.

DOI: https://doi.org/10.1038/s42003-022-04303-x
Int J Mol Sci. 2022 Dec 20. pii: 12. [Epub ahead of print]24(1):

Overview of Cancer Metabolism and Signaling Transduction.

Hee-Suk Chae, Seong-Tshool Hong.

  Despite the remarkable progress in cancer treatment up to now, we are still far from conquering the disease. The most substantial change after the malignant transformation of normal cells into cancer cells is the alteration in their metabolism. Cancer cells reprogram their metabolism to support the elevated energy demand as well as the acquisition and maintenance of their malignancy, even in nutrient-poor environments. The metabolic alterations, even under aerobic conditions, such as the upregulation of the glucose uptake and glycolysis (the Warburg effect), increase the ROS (reactive oxygen species) and glutamine dependence, which are the prominent features of cancer metabolism. Among these metabolic alterations, high glutamine dependency has attracted serious attention in the cancer research community. In addition, the oncogenic signaling pathways of the well-known important genetic mutations play important regulatory roles, either directly or indirectly, in the central carbon metabolism. The identification of the convergent metabolic phenotypes is crucial to the targeting of cancer cells. In this review, we investigate the relationship between cancer metabolism and the signal transduction pathways, and we highlight the recent developments in anti-cancer therapy that target metabolism.

Keywords:  ROS; aerobic glycolysis; anti-cancer drug; cancer; glutamine; metabolism; redox; signal transduction

DOI:  https://doi.org/10.3390/ijms24010012
Autophagy. 2023 Jan 10. 1-23

The mitophagy receptor BNIP3 is critical for the regulation of metabolic homeostasis and mitochondrial function in the nucleus pulposus cells of the intervertebral disc.

Vedavathi Madhu, Miriam Hernandez-Meadows, Paige K Boneski, Yunping Qiu, Anyonya R Guntur, Irwin J Kurland, Ruteja A Barve, Makarand V Risbud.

  The contribution of mitochondria to the metabolic function of hypoxic NP cells has been overlooked. We have shown that NP cells contain networked mitochondria and that mitochondrial translocation of BNIP3 mediates hypoxia-induced mitophagy. However, whether BNIP3 also plays a role in governing mitochondrial function and metabolism in hypoxic NP cells is not known. BNIP3 knockdown altered mitochondrial morphology, and number, and increased mitophagy. Interestingly, BNIP3 deficiency in NP cells reduced glycolytic capacity reflected by lower production of lactate/H+ and lower ATP production rate. Widely targeted metabolic profiling and flux analysis using 1-2-13C-glucose showed that the BNIP3 loss resulted in redirection of glycolytic flux into pentose phosphate and hexosamine biosynthesis as well as pyruvate resulting in increased TCA flux. An overall reduction in one-carbon metabolism was noted suggesting reduced biosynthesis. U13C-glutamine flux analysis showed preservation of glutamine utilization to maintain TCA intermediates. The transcriptomic analysis of the BNIP3-deficient cells showed dysregulation of cellular functions including membrane and cytoskeletal integrity, ECM-growth factor signaling, and protein quality control with an overall increase in themes related to angiogenesis and innate immune response. Importantly, we observed strong thematic similarities with the transcriptome of a subset of human degenerative samples. Last, we noted increased autophagic flux, decreased disc height index and aberrant COL10A1/collagen X expression, signs of early disc degeneration in young adult bnip3 knockout mice. These results suggested that in addition to mitophagy regulation, BNIP3 plays a role in maintaining mitochondrial function and metabolism, and dysregulation of mitochondrial homeostasis could promote disc degeneration.Abbreviations: ECAR extracellular acidification rate; HIF hypoxia inducible factor; MFA metabolic flux analysis; NP nucleus pulposus; OCR oxygen consumption rate; ShBnip3 short-hairpin Bnip3.

Keywords:  BNIP3; disc degeneration; hypoxia; intervertebral disc; metabolism; mitochondria; mitophagy; nucleus pulposus

DOI:  https://doi.org/10.1080/15548627.2022.2162245
J Biol Chem. 2023 Jan 07. pii: S0021-9258(23)00013-3. [Epub ahead of print] 102881

The impact of glucose on mitochondria and lifespan is determined by the integrity of proline catabolism in C. elegans.

Xi Feng, Xinyu Wang, Lei Zhou, Shanshan Pang, Haiqing Tang.

  Mutations in genes involved in mitochondrial proline catabolism lead to the rare genetic disorder hyperprolinemia in humans. We have previously reported that mutations of proline catabolic genes in C. elegans impair mitochondrial homeostasis and shorten lifespan, and that these effects surprisingly occur in a diet type-dependent manner. Therefore, we speculated that a specific dietary component may mitigate the adverse effects of defective proline catabolism. Here, we discovered that high dietary glucose, which is generally detrimental to health, actually improves mitochondrial homeostasis and lifespan in C. elegans with faulty proline catabolism. Mechanistically, defective proline catabolism results in a shift of glucose catabolism towards the pentose phosphate pathway (PPP), which is crucial for cellular redox balance. This shift helps to maintain mitochondrial reactive oxygen species (ROS) homeostasis and to extend lifespan, as suppression of the PPP enzyme GSPD-1 prevents the favorable effects of high glucose. Additionally, we demonstrate that this crosstalk between proline and glucose catabolism is mediated by the transcription factor DAF-16. Altogether, these findings suggest that a glucose-rich diet may be advantageous in certain situations, and might represent a potentially viable treatment strategy for disorders involving impaired proline catabolism.

Keywords:  C. elegans; ROS; glucose metabolism; lifespan; mitochondria; pentose phosphate pathway; proline catabolism

DOI:  https://doi.org/10.1016/j.jbc.2023.102881
Adv Sci (Weinh). 2023 Jan 10. e2204006

Tryptophan Metabolism Acts as a New Anti-Ferroptotic Pathway to Mediate Tumor Growth.

Dong Liu, Chun-Hui Liang, Bin Huang, Xiao Zhuang, Weiwei Cui, Li Yang, Yinghong Yang, Yudan Zhang, Xiaolong Fu, Xiaoju Zhang, Lutao Du, Wei Gu, Xiangdong Wang, Chengqian Yin, Renjie Chai, Bo Chu.

  Emerging evidence reveals that amino acid metabolism plays an important role in ferroptotic cell death. The conversion of methionine to cysteine is well known to protect tumour cells from ferroptosis upon cysteine starvation through transamination. However, whether amino acids-produced metabolites participate in ferroptosis independent of the cysteine pathway is largely unknown. Here, the authors show that the tryptophan metabolites serotonin (5-HT) and 3-hydroxyanthranilic acid (3-HA) remarkably facilitate tumour cells to escape from ferroptosis distinct from cysteine-mediated ferroptosis inhibition. Mechanistically, both 5-HT and 3-HA act as potent radical trapping antioxidants (RTA) to eliminate lipid peroxidation, thereby inhibiting ferroptotic cell death. Monoamine oxidase A (MAOA) markedly abrogates the protective effect of 5-HT via degrading 5-HT. Deficiency of MAOA renders cancer cells resistant to ferroptosis upon 5-HT treatment. Kynureninase (KYNU), which is essential for 3-HA production, confers cells resistant to ferroptotic cell death, whereas 3-hydroxyanthranilate 3,4-dioxygenase (HAAO) significantly blocks 3-HA mediated ferroptosis inhibition by consuming 3-HA. In addition, the expression level of HAAO is positively correlated with lipid peroxidation and clinical outcome. Together, the findings demonstrate that tryptophan metabolism works as a new anti-ferroptotic pathway to promote tumour growth, and targeting this pathway will be a promising therapeutic approach for cancer treatment.

Keywords:  3-HA; 3-hydroxyanthranilate 3,4-dioxygenase (HAAO); 5-HT; ferroptosis; kynureninase (KYNU; monoamine oxidase A (MAOA) ; tryptophan

DOI:  https://doi.org/10.1002/advs.202204006
Cancer Cell. 2023 Jan 03. pii: S1535-6108(22)00594-3. [Epub ahead of print]

Intersection of immune and oncometabolic pathways drives cancer hyperprogression during immunotherapy.

Gaopeng Li, Jae Eun Choi, Ilona Kryczek, Yilun Sun, Peng Liao, Shasha Li, Shuang Wei, Sara Grove, Linda Vatan, Reagan Nelson, Grace Schaefer, Steven G Allen, Kamya Sankar, Leslie A Fecher, Mishal Mendiratta-Lala, Timothy L Frankel, Angel Qin, Jessica J Waninger, Alangoya Tezel, Ajjai Alva, Christopher D Lao, Nithya Ramnath, Marcin Cieslik, Paul W Harms, Michael D Green, Arul M Chinnaiyan, Weiping Zou.

  Immune checkpoint blockade (ICB) can produce durable responses against cancer. We and others have found that a subset of patients experiences paradoxical rapid cancer progression during immunotherapy. It is poorly understood how tumors can accelerate their progression during ICB. In some preclinical models, ICB causes hyperprogressive disease (HPD). While immune exclusion drives resistance to ICB, counterintuitively, patients with HPD and complete response (CR) following ICB manifest comparable levels of tumor-infiltrating CD8+ T cells and interferon γ (IFNγ) gene signature. Interestingly, patients with HPD but not CR exhibit elevated tumoral fibroblast growth factor 2 (FGF2) and β-catenin signaling. In animal models, T cell-derived IFNγ promotes tumor FGF2 signaling, thereby suppressing PKM2 activity and decreasing NAD+, resulting in reduction of SIRT1-mediated β-catenin deacetylation and enhanced β-catenin acetylation, consequently reprograming tumor stemness. Targeting the IFNγ-PKM2-β-catenin axis prevents HPD in preclinical models. Thus, the crosstalk of core immunogenic, metabolic, and oncogenic pathways via the IFNγ-PKM2-β-catenin cascade underlies ICB-associated HPD.

Keywords:  FGF2; IFNγ; PD-L1/PD-1 pathway; T cell immunity; complete response; glycolytic metabolism; hyperprogressive disease; immune checkpoint blockade; oncogenesis; β-catenin

DOI:  https://doi.org/10.1016/j.ccell.2022.12.008
Cell Rep. 2022 Dec 30. pii: S2211-1247(22)01829-0. [Epub ahead of print]42(1): 111928

Anti-retroviral treatment with zidovudine alters pyrimidine metabolism, reduces translation, and extends healthy longevity via ATF-4.

Rebecca L McIntyre, Marte Molenaars, Bauke V Schomakers, Arwen W Gao, Rashmi Kamble, Aldo Jongejan, Michel van Weeghel, André B P van Kuilenburg, Richard Possemato, Riekelt H Houtkooper, Georges E Janssens.

  The human population is aging, and the need for interventions to slow progression of age-related diseases (geroprotective interventions) is growing. Repurposing compounds already used clinically, usually at modified doses, allows rapid implementation of geroprotective pharmaceuticals. Here we find the anti-retroviral nucleoside reverse transcriptase inhibitor (NRTI) zidovudine robustly extends lifespan and health span in C. elegans, independent of electron transport chain impairment or ROS accumulation. Rather, zidovudine treatment modifies pyrimidine metabolism and transcripts related to proteostasis. Testing regulators of mitochondrial stress and proteostasis shows that lifespan extension is dependent on activating transcription factor 4 (ATF-4). ATF-4 regulates longevity induced by mitochondrial stress, specifically communication between mitochondrial and cytosolic translation. Translation is reduced in zidovudine-treated worms, also dependent on ATF-4. Finally, we show ATF-4-dependent lifespan extension induced by didanosine, another NRTI. Altogether, our work elucidates the geroprotective effects of NRTIs such as zidovudine in vivo, via reduction of translation and ATF-4.

Keywords:  ATF-4; CP: Metabolism; CP: Molecular biology; Zidovudine; aging; geroprotector; lifespan; nucleoside reverse transcriptase inhibitor; translation

DOI:  https://doi.org/10.1016/j.celrep.2022.111928
Sci Adv. 2023 Jan 06. 9(1): eade9120

Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells.

Dennis J Hsu, Jenny Gao, Norihiro Yamaguchi, Alexandra Pinzaru, Qiushuang Wu, Nandan Mandayam, Maria Liberti, Søren Heissel, Hanan Alwaseem, Saeed Tavazoie, Sohail F Tavazoie.

Utilization of specific codons varies between organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine limitation-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced an adaptive proteomic shift toward low-arginine codon-containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.

DOI: https://doi.org/10.1126/sciadv.ade9120
Nat Metab. 2023 Jan 09.

A critical assessment of the role of creatine in brown adipose tissue thermogenesis.

David G Nicholls, Martin D Brand.

Brown adipose tissue is specialized for non-shivering thermogenesis, combining lipolysis with an extremely active mitochondrial electron transport chain and a unique regulated uncoupling protein, UCP1, allowing unrestricted respiration. Current excitement focuses on the presence of brown adipose tissue in humans and the possibility that it may contribute to diet-induced thermogenesis, countering obesity and obesity-related disease as well as protecting cardio-metabolic health. In common with other tissues displaying a high, variable respiration, the tissue possesses a creatine pool and mitochondrial and cytosolic creatine kinase isoforms. Genetic and pharmacological manipulation of these components have pleiotropic effects that appear to influence diet- and cold-induced metabolism in vivo and modeled in vitro. These findings have been used to advance the concept of a UCP1-independent diet-induced thermogenic mechanism based on a dissipative hydrolysis of phosphocreatine in beige and brown adipose tissue. Here we review the in vivo and in vitro experimental basis for this hypothesis, and explore alternative explanations. We conclude that there is currently no convincing evidence for a significant futile creatine cycle in these tissues.

DOI: https://doi.org/10.1038/s42255-022-00718-2
Cell. 2023 Jan 05. pii: S0092-8674(22)01525-2. [Epub ahead of print]186(1): 8-9

Strength in diversity: Intra-cellular metabolite sharing enhances longevity.

Dudley W Lamming, Rozalyn M Anderson.

Much of our foundational knowledge of cellular biology comes from studies in budding yeast, often described as a simple unicellular eukaryotic model. In this issue of Cell, Correia-Melo et al. describe an unappreciated feature of yeast biology involving intra-cellular metabolite exchange, where cells adapt and respond as part of a community, and go on to show that sharing of resources linked to methionine metabolism enhances longevity of cooperating cells.

DOI: https://doi.org/10.1016/j.cell.2022.12.012
Nature. 2023 Jan 12.

Targeting TBK1 to overcome resistance to cancer immunotherapy.

Yi Sun, Or-Yam Revach, Seth Anderson, Emily A Kessler, Clara H Wolfe, Anne Jenney, Caitlin E Mills, Emily J Robitschek, Thomas G R Davis, Sarah Kim, Amina Fu, Xiang Ma, Jia Gwee, Payal Tiwari, Peter P Du, Princy Sindurakar, Jun Tian, Arnav Mehta, Alexis M Schneider, Keren Yizhak, Moshe Sade-Feldman, Thomas LaSalle, Tatyana Sharova, Hongyan Xie, Shuming Liu, William A Michaud, Rodrigo Saad-Beretta, Kathleen B Yates, Arvin Iracheta-Vellve, Johan K E Spetz, Xingping Qin, Kristopher A Sarosiek, Gao Zhang, Jong Wook Kim, Mack Y Su, Angelina M Cicerchia, Martin Q Rasmussen, Samuel J Klempner, Dejan Juric, Sara I Pai, David M Miller, Anita Giobbie-Hurder, Jonathan H Chen, Karin Pelka, Dennie T Frederick, Susanna Stinson, Elena Ivanova, Amir R Aref, Cloud P Paweletz, David A Barbie, Debattama R Sen, David E Fisher, Ryan B Corcoran, Nir Hacohen, Peter K Sorger, Keith T Flaherty, Genevieve M Boland, Robert T Manguso, Russell W Jenkins.

Despite the success of PD-1 blockade in melanoma and other cancers, effective treatment strategies to overcome resistance to cancer immunotherapy are lacking1,2. We identified the innate immune kinase TANK-binding kinase 1 (TBK1)3 as a candidate immune evasion gene in a pooled genetic screen4. Using a suite of genetic and pharmacologic tools across multiple experimental model systems, we confirm a role for TBK1 as an immune evasion gene. Targeting TBK1 enhances response to PD-1 blockade by lowering the cytotoxicity threshold to effector cytokines (TNFα/IFNγ). TBK1 inhibition in combination with PD-1 blockade also demonstrated efficacy using patient-derived tumour models, with concordant findings in matched patient-derived organotypic tumour spheroids (PDOTS) and matched patient-derived organoids (PDOs). Tumour cells lacking TBK1 are primed to undergo RIPK- and caspase-dependent cell death in response to TNFα/IFNγ in a JAK/STAT-dependent manner. Taken together, our results demonstrate that targeting TBK1 is a novel and effective strategy to overcome resistance to cancer immunotherapy.

DOI: https://doi.org/10.1038/s41586-023-05704-6
Molecules. 2022 Dec 21. pii: 29. [Epub ahead of print]28(1):

Mitochondrial Iron Metabolism: The Crucial Actors in Diseases.

Geyan Duan, Jianjun Li, Yehui Duan, Changbing Zheng, Qiuping Guo, Fengna Li, Jie Zheng, Jiayi Yu, Peiwen Zhang, Mengliao Wan, Cimin Long.

  Iron is a trace element necessary for cell growth, development, and cellular homeostasis, but insufficient or excessive level of iron is toxic. Intracellularly, sufficient amounts of iron are required for mitochondria (the center of iron utilization) to maintain their normal physiologic function. Iron deficiency impairs mitochondrial metabolism and respiratory activity, while mitochondrial iron overload promotes ROS production during mitochondrial electron transport, thus promoting potential disease development. This review provides an overview of iron homeostasis, mitochondrial iron metabolism, and how mitochondrial iron imbalances-induced mitochondrial dysfunction contribute to diseases.

Keywords:  diseases; iron homeostasis; mitochondrial dysfunction

DOI:  https://doi.org/10.3390/molecules28010029
Curr Opin Neurobiol. 2023 Jan 06. pii: S0959-4388(22)00167-2. [Epub ahead of print]78 102673

A tale of two pathways: Regulation of proteostasis by UPRmt and MDPs.

Angela Johns, Ryo Higuchi-Sanabria, Max A Thorwald, David Vilchez.

Mitochondrial fitness is critical to organismal health and its impairment is associated with aging and age-related diseases. As such, numerous quality control mechanisms exist to preserve mitochondrial stability, including the unfolded protein response of the mitochondria (UPRmt). The UPRmt is a conserved mechanism that drives the transcriptional activation of mitochondrial chaperones, proteases, autophagy (mitophagy), and metabolism to promote restoration of mitochondrial function under stress conditions. UPRmt has direct ramifications in aging, and its activation is often ascribed to improve health whereas its dysfunction tends to correlate with disease. This review pairs a description of the most recent findings within the field of UPRmt with a more poorly understood field: mitochondria-derived peptides (MDPs). Similar to UPRmt, MDPs are microproteins derived from the mitochondria that can impact organismal health and longevity. We then highlight a tantalizing interconnection between UPRmt and MDPs wherein both mechanisms may be efficiently coordinated to maintain organismal health.

DOI: https://doi.org/10.1016/j.conb.2022.102673
Nature. 2023 Jan 11.

An atlas of substrate specificities for the human serine/threonine kinome.

Jared L Johnson, Tomer M Yaron, Emily M Huntsman, Alexander Kerelsky, Junho Song, Amit Regev, Ting-Yu Lin, Katarina Liberatore, Daniel M Cizin, Benjamin M Cohen, Neil Vasan, Yilun Ma, Konstantin Krismer, Jaylissa Torres Robles, Bert van de Kooij, Anne E van Vlimmeren, Nicole Andrée-Busch, Norbert F Käufer, Maxim V Dorovkov, Alexey G Ryazanov, Yuichiro Takagi, Edward R Kastenhuber, Marcus D Goncalves, Benjamin D Hopkins, Olivier Elemento, Dylan J Taatjes, Alexandre Maucuer, Akio Yamashita, Alexei Degterev, Mohamed Uduman, Jingyi Lu, Sean D Landry, Bin Zhang, Ian Cossentino, Rune Linding, John Blenis, Peter V Hornbeck, Benjamin E Turk, Michael B Yaffe, Lewis C Cantley.

Protein phosphorylation is one of the most widespread post-translational modifications in biology1,2. With advances in mass-spectrometry-based phosphoproteomics, 90,000 sites of serine and threonine phosphorylation have so far been identified, and several thousand have been associated with human diseases and biological processes3,4. For the vast majority of phosphorylation events, it is not yet known which of the more than 300 protein serine/threonine (Ser/Thr) kinases encoded in the human genome are responsible3. Here we used synthetic peptide libraries to profile the substrate sequence specificity of 303 Ser/Thr kinases, comprising more than 84% of those predicted to be active in humans. Viewed in its entirety, the substrate specificity of the kinome was substantially more diverse than expected and was driven extensively by negative selectivity. We used our kinome-wide dataset to computationally annotate and identify the kinases capable of phosphorylating every reported phosphorylation site in the human Ser/Thr phosphoproteome. For the small minority of phosphosites for which the putative protein kinases involved have been previously reported, our predictions were in excellent agreement. When this approach was applied to examine the signalling response of tissues and cell lines to hormones, growth factors, targeted inhibitors and environmental or genetic perturbations, it revealed unexpected insights into pathway complexity and compensation. Overall, these studies reveal the intrinsic substrate specificity of the human Ser/Thr kinome, illuminate cellular signalling responses and provide a resource to link phosphorylation events to biological pathways.

DOI: https://doi.org/10.1038/s41586-022-05575-3
Elife. 2023 01 10. pii: e79765. [Epub ahead of print]12

Adaptation to glucose starvation is associated with molecular reorganization of the circadian clock in Neurospora crassa.

Anita Szőke, Orsolya Sárkány, Géza Schermann, Orsolya Kapuy, Axel C R Diernfellner, Michael Brunner, Norbert Gyöngyösi, Krisztina Káldi.

  The circadian clock governs rhythmic cellular functions by driving the expression of a substantial fraction of the genome and thereby significantly contributes to the adaptation to changing environmental conditions. Using the circadian model organism Neurospora crassa, we show that molecular timekeeping is robust even under severe limitation of carbon sources, however, stoichiometry, phosphorylation and subcellular distribution of the key clock components display drastic alterations. Protein kinase A, protein phosphatase 2 A and glycogen synthase kinase are involved in the molecular reorganization of the clock. RNA-seq analysis reveals that the transcriptomic response of metabolism to starvation is highly dependent on the positive clock component WC-1. Moreover, our molecular and phenotypic data indicate that a functional clock facilitates recovery from starvation. We suggest that the molecular clock is a flexible network that allows the organism to maintain rhythmic physiology and preserve fitness even under long-term nutritional stress.

Keywords:  N. crassa; cell biology; chromosomes; circadian rhythm; gene expression; glucose starvation; neurospora; protein kinase A; protein phosphatase 2; transcriptome; white collar complex

DOI:  https://doi.org/10.7554/eLife.79765
Sci Adv. 2023 Jan 13. 9(2): eadd8579

The ERAD system is restricted by elevated ceramides.

Jiwon Hwang, Brian G Peterson, Jeffrey Knupp, Ryan D Baldridge.

Misfolded proteins in the endoplasmic reticulum (ER) are removed through a process known as ER-associated degradation (ERAD). ERAD occurs through an integral membrane protein quality control system that recognizes substrates, retrotranslocates the substrates across the membrane, and ubiquitinates and extracts the substrates from the membrane for degradation at the cytosolic proteasome. While ERAD systems are known to regulate lipid biosynthetic enzymes, the regulation of ERAD systems by the lipid composition of cellular membranes remains unexplored. Here, we report that the ER membrane composition influences ERAD function by incapacitating substrate extraction. Unbiased lipidomic profiling revealed that elevation of specific very-long-chain ceramides leads to a marked increase in the level of ubiquitinated substrates in the ER membrane and concomitantly reduces extracted substrates in the cytoplasm. This work reveals a previously unrecognized mechanism in which ER membrane lipid remodeling changes the activity of ERAD.

DOI: https://doi.org/10.1126/sciadv.add8579
Cancer Res. 2023 Jan 13. pii: CAN-22-1444. [Epub ahead of print]

KDM6A loss triggers an epigenetic switch that disrupts urothelial differentiation and drives cell proliferation in bladder cancer.

Hong Qiu, Vladimir Makarov, Jennifer K Bolzenius, Angela Halstead, Yvonne Parker, Allen Wang, Gopakumar V Iyer, Hannah Wise, Daniel Kim, Varna Thayaparan, Daniel J Lindner, Georges-Pascal Haber, Angela H Ting, Bing Ren, Timothy A Chan, Vivek Arora, David B Solit, Byron H Lee.

Disruption of KDM6A, a histone lysine demethylase, is one of the most common somatic alternations in bladder cancer. Insights into how KDM6A mutations impact the epigenetic landscape to promote carcinogenesis could help reveal potential new treatment approaches. Here, we demonstrated that KDM6A loss triggers an epigenetic switch that disrupts urothelial differentiation and induces a neoplastic state characterized by increased cell proliferation. In bladder cancer cells with intact KDM6A, FOXA1 interacted with KDM6A to activate genes instructing urothelial differentiation. KDM6A-deficient cells displayed simultaneous loss of FOXA1 target binding and genome-wide redistribution of the bZIP transcription factor ATF3, which in turn repressed FOXA1-target genes and activated cell cycle progression genes. Importantly, ATF3 depletion reversed the cell proliferation phenotype induced by KDM6A deficiency. These data establish that KDM6A loss engenders an epigenetic state that drives tumor growth in an ATF3-dependent manner, creating a potentially targetable molecular vulnerability.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-1444
Trends Cancer. 2023 Jan 11. pii: S2405-8033(22)00265-5. [Epub ahead of print]

Addressing the genetic/nongenetic duality in cancer with systems biology.

Prakash Kulkarni, H Steven Wiley, Herbert Levine, Herbert Sauro, Alexander Anderson, Stephen T C Wong, Aaron S Meyer, Puneeth Iyengar, Kevin Corlette, Kristin Swanson, Atish Mohanty, Supriyo Bhattacharya, Amit Patel, Vinay Jain, Ravi Salgia.

The dogma that cancer is a genetic disease is being questioned. Recent findings suggest that genetic/nongenetic duality is necessary for cancer progression. A think tank organized by the Shraman Foundation's Institute for Theoretical Biology compiled key challenges and opportunities that theoreticians, experimentalists, and clinicians can explore from a systems biology perspective to provide a better understanding of the disease as well as help discover new treatment options and therapeutic strategies.

DOI: https://doi.org/10.1016/j.trecan.2022.12.004
Nat Rev Cancer. 2023 Jan 10.

RNA splicing dysregulation and the hallmarks of cancer.

Robert K Bradley, Olga Anczuków.

Dysregulated RNA splicing is a molecular feature that characterizes almost all tumour types. Cancer-associated splicing alterations arise from both recurrent mutations and altered expression of trans-acting factors governing splicing catalysis and regulation. Cancer-associated splicing dysregulation can promote tumorigenesis via diverse mechanisms, contributing to increased cell proliferation, decreased apoptosis, enhanced migration and metastatic potential, resistance to chemotherapy and evasion of immune surveillance. Recent studies have identified specific cancer-associated isoforms that play critical roles in cancer cell transformation and growth and demonstrated the therapeutic benefits of correcting or otherwise antagonizing such cancer-associated mRNA isoforms. Clinical-grade small molecules that modulate or inhibit RNA splicing have similarly been developed as promising anticancer therapeutics. Here, we review splicing alterations characteristic of cancer cell transcriptomes, dysregulated splicing's contributions to tumour initiation and progression, and existing and emerging approaches for targeting splicing for cancer therapy. Finally, we discuss the outstanding questions and challenges that must be addressed to translate these findings into the clinic.

DOI: https://doi.org/10.1038/s41568-022-00541-7
Mol Cell. 2023 Jan 06. pii: S1097-2765(22)01202-3. [Epub ahead of print]

p53 engages the cGAS/STING cytosolic DNA sensing pathway for tumor suppression.

Monisankar Ghosh, Suchandrima Saha, Jinyu Li, David C Montrose, Luis A Martinez.

  Tumor suppression by TP53 involves cell-autonomous and non-cell-autonomous mechanisms. TP53 can suppress tumor growth by modulating immune system functions; however, the mechanistic basis for this activity is not well understood. We report that p53 promotes the degradation of the DNA exonuclease TREX1, resulting in cytosolic dsDNA accumulation. We demonstrate that p53 requires the ubiquitin ligase TRIM24 to induce TREX1 degradation. The cytosolic DNA accumulation resulting from TREX1 degradation activates the cytosolic DNA-sensing cGAS/STING pathway, resulting in induction of type I interferons. TREX1 overexpression sufficed to block p53 activation of the cGAS/STING pathway. p53-mediated induction of type I interferon (IFNB1) is suppressed by cGAS/STING knockout, and p53's tumor suppressor activities are compromised by the loss of signaling through the cGAS/STING pathway. Thus, our study reveals that p53 utilizes the cGAS/STING innate immune system pathway for both cell-intrinsic and cell-extrinsic tumor suppressor activities.

Keywords:  STING; TREX1; cGAS; innate immunity; p53; tumor suppression

DOI:  https://doi.org/10.1016/j.molcel.2022.12.023
EMBO J. 2023 Jan 13. e110620

IDH2 stabilizes HIF-1α-induced metabolic reprogramming and promotes chemoresistance in urothelial cancer.

Keisuke Shigeta, Masanori Hasegawa, Takako Hishiki, Yoshiko Naito, Yuto Baba, Shuji Mikami, Kazuhiro Matsumoto, Ryuichi Mizuno, Akira Miyajima, Eiji Kikuchi, Hideyuki Saya, Takeo Kosaka, Mototsugu Oya.

  Drug resistance contributes to poor therapeutic response in urothelial carcinoma (UC). Metabolomic analysis suggested metabolic reprogramming in gemcitabine-resistant urothelial carcinoma cells, whereby increased aerobic glycolysis and metabolic stimulation of the pentose phosphate pathway (PPP) promoted pyrimidine biosynthesis to increase the production of the gemcitabine competitor deoxycytidine triphosphate (dCTP) that diminishes its therapeutic effect. Furthermore, we observed that gain-of-function of isocitrate dehydrogenase 2 (IDH2) induced reductive glutamine metabolism to stabilize Hif-1α expression and consequently stimulate aerobic glycolysis and PPP bypass in gemcitabine-resistant UC cells. Interestingly, IDH2-mediated metabolic reprogramming also caused cross resistance to CDDP, by elevating the antioxidant defense via increased NADPH and glutathione production. Downregulation or pharmacological suppression of IDH2 restored chemosensitivity. Since the expression of key metabolic enzymes, such as TIGAR, TKT, and CTPS1, were affected by IDH2-mediated metabolic reprogramming and related to poor prognosis in patients, IDH2 might become a new therapeutic target for restoring chemosensitivity in chemo-resistant urothelial carcinoma.

Keywords:  chemoresistance; hypoxia-inducible factor-1α; isocitrate dehydrogenase 2; metabolomic reprogramming; urothelial carcinoma

DOI:  https://doi.org/10.15252/embj.2022110620
Angew Chem Int Ed Engl. 2023 Jan 08.

Mass Spectrometry Reveals High Levels of Hydrogen Peroxide in Pancreatic Cancer Cells.

Qinlei Liu, Wenjie Ge, Sandra Martínez-Jarquín, Yuliang He, Ri Wu, Markus Stoffel, Renato Zenobi.

  Reactive oxygen species (ROS) are critical for many cellular functions, and dysregulation of ROS involves the development of multiple types of tumors, including pancreatic cancer. However, ROS have been grouped into a single biochemical entity for a long time, and the specific roles of certain types of ROS in tumor cells (e.g., pancreatic ductal adenocarcinoma (PDAC)) have not been systematically investigated. In this work, a highly sensitive and accurate mass spectrometry-based method was applied to study PDAC cells of humans and of genetically modified animals. The results show that the oncogenic KRAS mutation promotes the accumulation of hydrogen peroxide (H2O2) rather than superoxide or hydroxyl radicals in pancreatic cancer cells. We further identified that the enriched H2O2 modifies cellular metabolites and promotes the survival of pancreatic cancer cells. These findings highlight the specific roles of H2O2 in pancreatic cancer development, which may provide new directions for pancreatic cancer therapy.

Keywords:  ESI-MS; Reactive oxygen species; hydrogen peroxide; metabolic changes; pancreatic cancer

DOI:  https://doi.org/10.1002/anie.202213703
Sci Adv. 2023 Jan 06. 9(1): eabq3951

ZBTB18 restricts chromatin accessibility and prevents transcriptional adaptations that drive metastasis.

Ruishan Wang, Akshita B Bhatt, Benjamin A Minden-Birkenmaier, Olivia K Travis, Srishti Tiwari, Hong Jia, Wojciech Rosikiewicz, Ophelie Martinot, Eleanor Childs, Robin Loesch, Guenole Tossou, Sophie Jamieson, David Finkelstein, Beisi Xu, Myriam Labelle.

Metastases arise from rare cancer cells that successfully adapt to the diverse microenvironments encountered during dissemination through the bloodstream and colonization of distant tissues. How cancer cells acquire the ability to appropriately respond to microenvironmental stimuli remains largely unexplored. Here, we report an epigenetic pliancy mechanism that allows cancer cells to successfully metastasize. We find that a decline in the activity of the transcriptional repressor ZBTB18 defines metastasis-competent cancer cells in mouse models. Restoration of ZBTB18 activity reduces chromatin accessibility at the promoters of genes that drive metastasis, such as Tgfbr2, and this prevents TGFβ1 pathway activation and consequently reduces cell migration and invasion. Besides repressing the expression of metastatic genes, ZBTB18 also induces widespread chromatin closing, a global epigenetic adaptation previously linked to reduced phenotypic flexibility. Thus, ZBTB18 is a potent chromatin regulator, and the loss of its activity enhances chromatin accessibility and transcriptional adaptations that promote the phenotypic changes required for metastasis.

DOI: https://doi.org/10.1126/sciadv.abq3951
Nat Chem Biol. 2023 Jan 12.

Small molecule agonist of mitochondrial fusion repairs mitochondrial dysfunction.

Yingjie Guo, Huan Zhang, Chen Yan, Birong Shen, Yue Zhang, Xiangyang Guo, Sha Sun, Fan Yu, Jiayun Yan, Ronghe Liu, Qianping Zhang, Di Zhang, Haiyang Liu, Yang Liu, Yaoyao Zhang, Wenlei Li, Jiangyu Qin, He Lv, Zhaoxia Wang, Yun Yuan, Jie-Feng Yang, Ya-Ting Zhong, Song Gao, Bing Zhou, Lei Liu, Deling Kong, Xiaojiang Hao, Junjie Hu, Quan Chen.

Membrane dynamics are important to the integrity and function of mitochondria. Defective mitochondrial fusion underlies the pathogenesis of multiple diseases. The ability to target fusion highlights the potential to fight life-threatening conditions. Here we report a small molecule agonist, S89, that specifically promotes mitochondrial fusion by targeting endogenous MFN1. S89 interacts directly with a loop region in the helix bundle 2 domain of MFN1 to stimulate GTP hydrolysis and vesicle fusion. GTP loading or competition by S89 dislodges the loop from the GTPase domain and unlocks the molecule. S89 restores mitochondrial and cellular defects caused by mitochondrial DNA mutations, oxidative stress inducer paraquat, ferroptosis inducer RSL3 or CMT2A-causing mutations by boosting endogenous MFN1. Strikingly, S89 effectively eliminates ischemia/reperfusion (I/R)-induced mitochondrial damage and protects mouse heart from I/R injury. These results reveal the priming mechanism for MFNs and provide a therapeutic strategy for mitochondrial diseases when additional mitochondrial fusion is beneficial.

DOI: https://doi.org/10.1038/s41589-022-01224-y