bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2024–05–26
sixty-one papers selected by
Christian Frezza, Universität zu Köln
  1. Mitochondrial respiratory function is preserved under cysteine starvation via glutathione catabolism in NSCLC.
  2. Illuminating mitochondrial translation through mouse models.
  3. Tryptophan fuels MYC-dependent liver tumorigenesis through indole 3-pyruvate synthesis.
  4. Metabolite profiling of human renal cell carcinoma reveals tissue-origin dominance in nutrient availability.
  5. The OGT-c-Myc-PDK2 axis rewires the TCA cycle and promotes colorectal tumor growth.
  6. Metabolic homeostasis of tissue macrophages across the lifespan.
  7. The microbial metabolite agmatine induces polycystic ovary syndrome in mice.
  8. Weak neuronal glycolysis sustains cognition and organismal fitness.
  9. Mitochondrial DNA release and sensing in innate immune responses.
  10. Glutamate from the microbiome controls host metabolism.
  11. Mitochondria at the crossroads of health and disease.
  12. SDHAF1 confers metabolic resilience to aging hematopoietic stem cells by promoting mitochondrial ATP production.
  13. Up-regulation of cholesterol synthesis by lysosomal defects requires a functional mitochondrial respiratory chain.
  14. Identification of Fasnall as a therapeutically effective Complex I inhibitor.
  15. mTORC1-CTLH E3 ligase regulates the degradation of HMG-CoA synthase 1 through the Pro/N-degron pathway.
  16. Imaging Approaches in Cancer Biology.
  17. Direct Infusion Mass Spectrometry to Rapidly Map Metabolic Flux of Substrates Labeled with Stable Isotopes.
  18. The gluconeogenesis enzyme PCK2 has a non-enzymatic role in proteostasis in endothelial cells.
  19. RNAi screens identify HES4 as a regulator of redox balance supporting pyrimidine synthesis and tumor growth.
  20. Central dogma rates in human mitochondria.
  21. Origins of tissue and cell-type specificity in mitochondrial DNA (mtDNA) disease.
  22. Metabolic coordination between skin epithelium and type 17 immunity sustains chronic skin inflammation.
  23. Intratumoral antigen signaling traps CD8+ T cells to confine exhaustion to the tumor site.
  24. Neuronal hypoglycolysis sustains body health.
  25. Glycolytic enzyme PFKL governs lipolysis by promoting lipid droplet-mitochondria tethering to enhance β-oxidation and tumor cell proliferation.
  26. Coordinating mitochondrial translation with assembly of the OXPHOS complexes.
  27. Mass Spectrometric Analysis of Purine Intermediary Metabolism Indicates Cyanide Induces Purine Catabolism in Rabbits.
  28. Ductal carcinoma in situ develops within clonal fields of mutant cells in morphologically normal ducts.
  29. Decoding the Enigma: Translation Termination in Human Mitochondria.
  30. Elevated Na is a dynamic and reversible modulator of mitochondrial metabolism in the heart.
  31. Mitochondria driven innate immune signaling and inflammation in cancer growth, immune evasion, and therapeutic resistance.
  32. Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
  33. The importance of murine phospho-MLKL-S345 in situ detection for necroptosis assessment in vivo.
  34. A metabolic dependency of EBV can be targeted to hinder B cell transformation.
  35. Immunological Aspects of Cancer Cell Metabolism.
  36. The TWK-26 potassium channel governs nutrient absorption in the C. elegans intestine.
  37. Adding intrinsically disordered proteins to biological ageing clocks.
  38. Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology.
  39. Preserving ester-linked modifications reveals glutamate and aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG.
  40. A mitochondrial carrier transports glycolytic intermediates to link cytosolic and mitochondrial glycolysis in the human gut parasite Blastocystis.
  41. Mitochondrial Phosphopantetheinylation is Required for Oxidative Function.
  42. Molecular and cellular consequences of mitochondrial DNA double-stranded breaks.
  43. The immune response to RNA suppresses nucleic acid synthesis by limiting ribose 5-phosphate.
  44. Cell of origin epigenetic priming determines susceptibility to Tet2 mutation.
  45. Deleting the mitochondrial respiration negative regulator MCJ enhances the efficacy of CD8+ T cell adoptive therapies in pre-clinical studies.
  46. We don't need no inflammation.
  47. Overexpression of PEX14 results in mistargeting to mitochondria, accompanied by organelle fragmentation and clustering in human embryonic kidney cells.
  48. TFAM is an autophagy receptor that limits inflammation by binding to cytoplasmic mitochondrial DNA.
  49. Circadian regulation of macromolecular complex turnover and proteome renewal.
  50. The molecular machinery for maturation of primary mtDNA transcripts.
  51. Fluorescent fatty acid conjugates for live cell imaging of peroxisomes.
  52. Unravelling the complexity of the mitochondrial Ca2+ uniporter: regulation, tissue specificity, and physiological implications.
  53. Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming.
  54. An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions.
  55. Tools for editing the mammalian mitochondrial genome.
  56. ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway.
  57. Visualization of cristae and mtDNA interactions via STED nanoscopy using a low saturation power probe.
  58. Acquisition of epithelial plasticity in human chronic liver disease.
  59. The Evolution of Mouse Models of Cancer: Past, Present, and Future.
  60. Emerging targets in lipid metabolism for cancer therapy.
  61. Polyamines: the pivotal amines in influencing the tumor microenvironment.
  1. Nat Commun. 2024 May 18. 15(1): 4244
    Mitochondrial respiratory function is preserved under cysteine starvation via glutathione catabolism in NSCLC.
    Nathan P Ward, Sang Jun Yoon, Tyce Flynn, Amanda M Sherwood, Maddison A Olley, Juliana Madej, Gina M DeNicola.
      Cysteine metabolism occurs across cellular compartments to support diverse biological functions and prevent the induction of ferroptosis. Though the disruption of cytosolic cysteine metabolism is implicated in this form of cell death, it is unknown whether the substantial cysteine metabolism resident within the mitochondria is similarly pertinent to ferroptosis. Here, we show that despite the rapid depletion of intracellular cysteine upon loss of extracellular cystine, cysteine-dependent synthesis of Fe-S clusters persists in the mitochondria of lung cancer cells. This promotes a retention of respiratory function and a maintenance of the mitochondrial redox state. Under these limiting conditions, we find that glutathione catabolism by CHAC1 supports the mitochondrial cysteine pool to sustain the function of the Fe-S proteins critical to oxidative metabolism. We find that disrupting Fe-S cluster synthesis under cysteine restriction protects against the induction of ferroptosis, suggesting that the preservation of mitochondrial function is antagonistic to survival under starved conditions. Overall, our findings implicate mitochondrial cysteine metabolism in the induction of ferroptosis and reveal a mechanism of mitochondrial resilience in response to nutrient stress.
    DOI:  https://doi.org/10.1038/s41467-024-48695-2
  2. Hum Mol Genet. 2024 May 22. 33(R1): R61-R79
    Illuminating mitochondrial translation through mouse models.
    Laetitia A Hughes, Oliver Rackham, Aleksandra Filipovska.
      Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.
    Keywords:  animal models; gene expression; mitochondria; protein synthesis
    DOI:  https://doi.org/10.1093/hmg/ddae020
  3. Nat Commun. 2024 May 20. 15(1): 4266
    Tryptophan fuels MYC-dependent liver tumorigenesis through indole 3-pyruvate synthesis.
    Niranjan Venkateswaran, Roy Garcia, M Carmen Lafita-Navarro, Yi-Heng Hao, Lizbeth Perez-Castro, Pedro A S Nogueira, Ashley Solmonson, Ilgen Mender, Jessica A Kilgore, Shun Fang, Isabella N Brown, Li Li, Emily Parks, Igor Lopes Dos Santos, Mahima Bhaskar, Jiwoong Kim, Yuemeng Jia, Andrew Lemoff, Nick V Grishin, Lisa Kinch, Lin Xu, Noelle S Williams, Jerry W Shay, Ralph J DeBerardinis, Hao Zhu, Maralice Conacci-Sorrell.
      Cancer cells exhibit distinct metabolic activities and nutritional dependencies compared to normal cells. Thus, characterization of nutrient demands by individual tumor types may identify specific vulnerabilities that can be manipulated to target the destruction of cancer cells. We find that MYC-driven liver tumors rely on augmented tryptophan (Trp) uptake, yet Trp utilization to generate metabolites in the kynurenine (Kyn) pathway is reduced. Depriving MYC-driven tumors of Trp through a No-Trp diet not only prevents tumor growth but also restores the transcriptional profile of normal liver cells. Despite Trp starvation, protein synthesis remains unhindered in liver cancer cells. We define a crucial role for the Trp-derived metabolite indole 3-pyruvate (I3P) in liver tumor growth. I3P supplementation effectively restores the growth of liver cancer cells starved of Trp. These findings suggest that I3P is a potential therapeutic target in MYC-driven cancers. Developing methods to target this metabolite represents a potential avenue for liver cancer treatment.
    DOI:  https://doi.org/10.1038/s41467-024-47868-3
  4. Elife. 2024 May 24. pii: RP95652. [Epub ahead of print]13
    Metabolite profiling of human renal cell carcinoma reveals tissue-origin dominance in nutrient availability.
    Keene L Abbott, Ahmed Ali, Bradley I Reinfeld, Amy Deik, Sonu Subudhi, Madelyn D Landis, Rachel A Hongo, Kirsten L Young, Tenzin Kunchok, Christopher S Nabel, Kayla D Crowder, Johnathan R Kent, Maria Lucia L Madariaga, Rakesh K Jain, Kathryn E Beckermann, Caroline A Lewis, Clary B Clish, Alexander Muir, W Kimryn Rathmell, Jeffrey Rathmell, Matthew G Vander Heiden.
      The tumor microenvironment is a determinant of cancer progression and therapeutic efficacy, with nutrient availability playing an important role. Although it is established that the local abundance of specific nutrients defines the metabolic parameters for tumor growth, the factors guiding nutrient availability in tumor compared to normal tissue and blood remain poorly understood. To define these factors in renal cell carcinoma (RCC), we performed quantitative metabolomic and comprehensive lipidomic analyses of tumor interstitial fluid (TIF), adjacent normal kidney interstitial fluid (KIF), and plasma samples collected from patients. TIF nutrient composition closely resembles KIF, suggesting that tissue-specific factors unrelated to the presence of cancer exert a stronger influence on nutrient levels than tumor-driven alterations. Notably, select metabolite changes consistent with known features of RCC metabolism are found in RCC TIF, while glucose levels in TIF are not depleted to levels that are lower than those found in KIF. These findings inform tissue nutrient dynamics in RCC, highlighting a dominant role of non-cancer-driven tissue factors in shaping nutrient availability in these tumors.
    Keywords:  cancer; cancer biology; human; metabolism; tumor microenvironment
    DOI:  https://doi.org/10.7554/eLife.95652
  5. Cell Death Differ. 2024 May 22.
    The OGT-c-Myc-PDK2 axis rewires the TCA cycle and promotes colorectal tumor growth.
    Huijuan Wang, Jie Sun, Haofan Sun, Yifei Wang, Bingyi Lin, Liming Wu, Weijie Qin, Qiang Zhu, Wen Yi.
      Deregulated glucose metabolism termed the "Warburg effect" is a fundamental feature of cancers, including the colorectal cancer. This is typically characterized with an increased rate of glycolysis, and a concomitant reduced rate of the tricarboxylic acid (TCA) cycle metabolism as compared to the normal cells. How the TCA cycle is manipulated in cancer cells remains unknown. Here, we show that O-linked N-acetylglucosamine (O-GlcNAc) regulates the TCA cycle in colorectal cancer cells. Depletion of OGT, the sole transferase of O-GlcNAc, significantly increases the TCA cycle metabolism in colorectal cancer cells. Mechanistically, OGT-catalyzed O-GlcNAc modification of c-Myc at serine 415 (S415) increases c-Myc stability, which transcriptionally upregulates the expression of pyruvate dehydrogenase kinase 2 (PDK2). PDK2 phosphorylates pyruvate dehydrogenase (PDH) to inhibit the activity of mitochondrial pyruvate dehydrogenase complex, which reduces mitochondrial pyruvate metabolism, suppresses reactive oxygen species production, and promotes xenograft tumor growth. Furthermore, c-Myc S415 glycosylation levels positively correlate with PDK2 expression levels in clinical colorectal tumor tissues. This study highlights the OGT-c-Myc-PDK2 axis as a key mechanism linking oncoprotein activation with deregulated glucose metabolism in colorectal cancer.
    DOI:  https://doi.org/10.1038/s41418-024-01315-4
  6. Trends Endocrinol Metab. 2024 May 18. pii: S1043-2760(24)00111-5. [Epub ahead of print]
    Metabolic homeostasis of tissue macrophages across the lifespan.
    Stefanie K Wculek, Stephan Forisch, Verónica Miguel, David Sancho.
      Macrophages are present in almost all organs. Apart from being immune sentinels, tissue-resident macrophages (TRMs) have organ-specific functions that require a specialized cellular metabolism to maintain homeostasis. In addition, organ-dependent metabolic adaptations of TRMs appear to be fundamentally distinct in homeostasis and in response to a challenge, such as infection or injury. Moreover, TRM function becomes aberrant with advancing age, contributing to inflammaging and organ deterioration, and a metabolic imbalance may underlie TRM immunosenescence. Here, we outline current understanding of the particular metabolic states of TRMs across organs and the relevance for their function. Moreover, we discuss the concomitant aging-related decline in metabolic plasticity and functions of TRMs, highlighting potential novel therapeutic avenues to promote healthy aging.
    Keywords:  aging; macrophage; metabolism; organ homeostasis; tissue residency
    DOI:  https://doi.org/10.1016/j.tem.2024.04.017
  7. Nat Metab. 2024 May 20.
    The microbial metabolite agmatine induces polycystic ovary syndrome in mice.
      
    DOI:  https://doi.org/10.1038/s42255-024-01040-9
  8. Nat Metab. 2024 May 24.
    Weak neuronal glycolysis sustains cognition and organismal fitness.
    Daniel Jimenez-Blasco, Jesús Agulla, Rebeca Lapresa, Marina Garcia-Macia, Veronica Bobo-Jimenez, Dario Garcia-Rodriguez, Israel Manjarres-Raza, Emilio Fernandez, Yannick Jeanson, Spiro Khoury, Jean-Charles Portais, Daniel Padro, Pedro Ramos-Cabrer, Peter Carmeliet, Angeles Almeida, Juan P Bolaños.
      The energy cost of neuronal activity is mainly sustained by glucose1,2. However, in an apparent paradox, neurons modestly metabolize glucose through glycolysis3-6, a circumstance that can be accounted for by the constant degradation of 6-phosphofructo-2-kinase-fructose-2,6-bisphosphatase-3 (PFKFB3)3,7,8, a key glycolysis-promoting enzyme. To evaluate the in vivo physiological importance of this hypoglycolytic metabolism, here we genetically engineered mice with their neurons transformed into active glycolytic cells through Pfkfb3 expression. In vivo molecular, biochemical and metabolic flux analyses of these neurons revealed an accumulation of anomalous mitochondria, complex I disassembly, bioenergetic deficiency and mitochondrial redox stress. Notably, glycolysis-mediated nicotinamide adenine dinucleotide (NAD+) reduction impaired sirtuin-dependent autophagy. Furthermore, these mice displayed cognitive decline and a metabolic syndrome that was mimicked by confining Pfkfb3 expression to hypothalamic neurons. Neuron-specific genetic ablation of mitochondrial redox stress or brain NAD+ restoration corrected these behavioural alterations. Thus, the weak glycolytic nature of neurons is required to sustain higher-order organismal functions.
    DOI:  https://doi.org/10.1038/s42255-024-01049-0
  9. Hum Mol Genet. 2024 May 22. 33(R1): R80-R91
    Mitochondrial DNA release and sensing in innate immune responses.
    Jordyn J VanPortfliet, Cole Chute, Yuanjiu Lei, Timothy E Shutt, A Phillip West.
      Mitochondria are pleiotropic organelles central to an array of cellular pathways including metabolism, signal transduction, and programmed cell death. Mitochondria are also key drivers of mammalian immune responses, functioning as scaffolds for innate immune signaling, governing metabolic switches required for immune cell activation, and releasing agonists that promote inflammation. Mitochondrial DNA (mtDNA) is a potent immunostimulatory agonist, triggering pro-inflammatory and type I interferon responses in a host of mammalian cell types. Here we review recent advances in how mtDNA is detected by nucleic acid sensors of the innate immune system upon release into the cytoplasm and extracellular space. We also discuss how the interplay between mtDNA release and sensing impacts cellular innate immune endpoints relevant to health and disease.
    Keywords:  NLRP3; TLR9; cGAS-STING; inflammation; innate immunity; mitochondria; mitochondrial DNA
    DOI:  https://doi.org/10.1093/hmg/ddae031
  10. Nat Metab. 2024 May 22.
    Glutamate from the microbiome controls host metabolism.
    Gwenola Le Dréan, Hervé M Blottière.
      
    DOI:  https://doi.org/10.1038/s42255-024-01050-7
  11. Cell. 2024 May 23. pii: S0092-8674(24)00463-X. [Epub ahead of print]187(11): 2601-2627
    Mitochondria at the crossroads of health and disease.
    Anu Suomalainen, Jodi Nunnari.
      Mitochondria reside at the crossroads of catabolic and anabolic metabolism-the essence of life. How their structure and function are dynamically tuned in response to tissue-specific needs for energy, growth repair, and renewal is being increasingly understood. Mitochondria respond to intrinsic and extrinsic stresses and can alter cell and organismal function by inducing metabolic signaling within cells and to distal cells and tissues. Here, we review how the centrality of mitochondrial functions manifests in health and a broad spectrum of diseases and aging.
    DOI:  https://doi.org/10.1016/j.cell.2024.04.037
  12. Cell Stem Cell. 2024 May 14. pii: S1934-5909(24)00176-0. [Epub ahead of print]
    SDHAF1 confers metabolic resilience to aging hematopoietic stem cells by promoting mitochondrial ATP production.
    Shintaro Watanuki, Hiroshi Kobayashi, Yuki Sugiura, Masamichi Yamamoto, Daiki Karigane, Kohei Shiroshita, Yuriko Sorimachi, Takayuki Morikawa, Shinya Fujita, Kotaro Shide, Miho Haraguchi, Shinpei Tamaki, Takumi Mikawa, Hiroshi Kondoh, Hiroyasu Nakano, Kenta Sumiyama, Go Nagamatsu, Nobuhito Goda, Shinichiro Okamoto, Ayako Nakamura-Ishizu, Kazuya Shimoda, Makoto Suematsu, Toshio Suda, Keiyo Takubo.
      Aging generally predisposes stem cells to functional decline, impairing tissue homeostasis. Here, we report that hematopoietic stem cells (HSCs) acquire metabolic resilience that promotes cell survival. High-resolution real-time ATP analysis with glucose tracing and metabolic flux analysis revealed that old HSCs reprogram their metabolism to activate the pentose phosphate pathway (PPP), becoming more resistant to oxidative stress and less dependent on glycolytic ATP production at steady state. As a result, old HSCs can survive without glycolysis, adapting to the physiological cytokine environment in bone marrow. Mechanistically, old HSCs enhance mitochondrial complex II metabolism during stress to promote ATP production. Furthermore, increased succinate dehydrogenase assembly factor 1 (SDHAF1) in old HSCs, induced by physiological low-concentration thrombopoietin (TPO) exposure, enables rapid mitochondrial ATP production upon metabolic stress, thereby improving survival. This study provides insight into the acquisition of resilience through metabolic reprogramming in old HSCs and its molecular basis to ameliorate age-related hematopoietic abnormalities.
    Keywords:  SDHAF1; adenosine triphosphate; hematopoietic stem cell; mitochondria; stem cell aging; stem cell metabolism; thrombopoietin
    DOI:  https://doi.org/10.1016/j.stem.2024.04.023
  13. J Biol Chem. 2024 May 21. pii: S0021-9258(24)01904-5. [Epub ahead of print] 107403
    Up-regulation of cholesterol synthesis by lysosomal defects requires a functional mitochondrial respiratory chain.
    Francesco Agostini, Leonardo Pereyra, Justin Dale, King Faisal Yambire, Silvia Maglioni, Alfonso Schiavi, Natascia Ventura, Ira Milosevic, Nuno Raimundo.
      Mitochondria and lysosomes are two organelles that carry out both signaling and metabolic roles in cells. Recent evidence has shown that mitochondria and lysosomes are dependent on one another, as primary defects in one cause secondary defects in the other. Although there are functional impairments in both cases, the signaling consequences of primary mitochondrial dysfunction and lysosomal defects are dissimilar. Here, we used RNA sequencing to obtain transcriptomes from cells with primary mitochondrial or lysosomal defects to identify the global cellular consequences associated with mitochondrial or lysosomal dysfunction. We used these data to determine the pathways affected by defects in both organelles, which revealed a prominent role for the cholesterol synthesis pathway. We observed a transcriptional up-regulated of this pathway in cellular and murine models of lysosomal defects, while it is transcriptionally down-regulated in cellular and murine models of mitochondrial defects. We identified a role for the post-transcriptional regulation of transcription factor SREBF1, a master regulator of cholesterol and lipid biosynthesis, in models of mitochondrial respiratory chain deficiency. Furthermore, we found that retention of Ca2+ in lysosomes of cells with mitochondrial respiratory chain defects contributes to the differential regulation of the cholesterol synthesis pathway in the mitochondrial and lysosomal defects tested. Finally, we verified in vivo, using a model of mitochondria-associated disease in C. elegans, that normalization of lysosomal Ca2+ levels results in partial rescue of the developmental delay induced by the respiratory chain deficiency.
    DOI:  https://doi.org/10.1016/j.jbc.2024.107403
  14. bioRxiv. 2024 May 06. pii: 2024.05.03.592013. [Epub ahead of print]
    Identification of Fasnall as a therapeutically effective Complex I inhibitor.
    Dzmitry Mukha, Jena Dessain, Seamus O'Connor, Katherine Pniewski, Fabrizio Bertolazzi, Jeet Patel, Mary Mullins, Zachary T Schug.
      Proliferating cancer cells actively utilize anabolic processes for biomass production, including de novo biosynthesis of amino acids, nucleotides, and fatty acids. The key enzyme of the fatty acid biosynthesis pathway, fatty acid synthase (FASN), is widely recognized as a promising therapeutic target in cancer and other health conditions 1,2 . Here, we establish a metabolic signature of FASN inhibition using a panel of pharmacological inhibitors (GSK2194069, TVB-2640, TVB-3166, C75, cerulenin, and Fasnall). We find that the activity of commonly used FASN inhibitors is inconsistent with the metabolic signature of FASN inhibition (accumulation of malonate, succinate, malonyl coenzyme A, succinyl coenzyme A, and other metabolic perturbations). Moreover, we show that one of these putative FASN inhibitors, Fasnall, is a respiratory Complex I inhibitor that mimics FASN inhibition through NADH accumulation and consequent depletion of the tricarboxylic acid cycle metabolites. We demonstrate that Fasnall impairs tumor growth in several oxidative phosphorylation-dependent cancer models, including combination therapy-resistant melanoma patient-derived xenografts. Fasnall administration does not reproduce neurological side effects in mice reported for other Complex I inhibitors 3,4 . Our results have significant implications for understanding the FASN role in human health and disease and provide evidence of therapeutic potential for Complex I inhibitors with fast systemic clearance. Our findings also highlight the continuing need for validation of small molecule inhibitors to distinguish high-quality chemical probes and to expand the understanding of their application.
    DOI:  https://doi.org/10.1101/2024.05.03.592013
  15. Mol Cell. 2024 May 20. pii: S1097-2765(24)00393-9. [Epub ahead of print]
    mTORC1-CTLH E3 ligase regulates the degradation of HMG-CoA synthase 1 through the Pro/N-degron pathway.
    Sang Ah Yi, Sara Sepic, Brenda A Schulman, Alban Ordureau, Heeseon An.
      Mammalian target of rapamycin (mTOR) senses changes in nutrient status and stimulates the autophagic process to recycle amino acids. However, the impact of nutrient stress on protein degradation beyond autophagic turnover is incompletely understood. We report that several metabolic enzymes are proteasomal targets regulated by mTOR activity based on comparative proteome degradation analysis. In particular, 3-hydroxy-3-methylglutaryl (HMG)-coenzyme A (CoA) synthase 1 (HMGCS1), the initial enzyme in the mevalonate pathway, exhibits the most significant half-life adaptation. Degradation of HMGCS1 is regulated by the C-terminal to LisH (CTLH) E3 ligase through the Pro/N-degron motif. HMGCS1 is ubiquitylated on two C-terminal lysines during mTORC1 inhibition, and efficient degradation of HMGCS1 in cells requires a muskelin adaptor. Importantly, modulating HMGCS1 abundance has a dose-dependent impact on cell proliferation, which is restored by adding a mevalonate intermediate. Overall, our unbiased degradomics study provides new insights into mTORC1 function in cellular metabolism: mTORC1 regulates the stability of limiting metabolic enzymes through the ubiquitin system.
    Keywords:  CTLH; GID; HMGCS1; degradomics; mTOR; mTORC1; mevalonate pathway; sterol; ubiquitin; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1016/j.molcel.2024.04.026
  16. Cold Spring Harb Perspect Med. 2024 May 21. pii: a041349. [Epub ahead of print]
    Imaging Approaches in Cancer Biology.
    Nirakar Rajbhandari, Emily Diaz, Marcie Kritzik, Tannishtha Reya.
      A majority of cancer research is focused on defining the cellular and molecular basis of cancer cells and the signals that control oncogenic transformation; as a consequence, we know very little about the dynamic behavior of cancer cells in vivo. To begin to view and understand the mechanisms and interactions that control cancer initiation, growth, and metastatic progression and how these processes are influenced by the microenvironment and the signals derived from it, it is essential to develop strategies that allow imaging of the cancer cells in the context of the living microenvironment. Here, we discuss emerging work designed to visualize how cancer cells function within the microenvironment to discover how these interactions act coordinately to enable aberrant growth and to understand how they could be targeted to design new approaches to intercept the disease.
    DOI:  https://doi.org/10.1101/cshperspect.a041349
  17. Metabolites. 2024 Apr 25. pii: 246. [Epub ahead of print]14(5):
    Direct Infusion Mass Spectrometry to Rapidly Map Metabolic Flux of Substrates Labeled with Stable Isotopes.
    Nils W F Meijer, Susan Zwakenberg, Johan Gerrits, Denise Westland, Arif I Ardisasmita, Sabine A Fuchs, Nanda M Verhoeven-Duif, Judith J M Jans, Fried J T Zwartkruis.
      Direct infusion-high-resolution mass spectrometry (DI-HRMS) allows for rapid profiling of complex mixtures of metabolites in blood, cerebrospinal fluid, tissue samples and cultured cells. Here, we present a DI-HRMS method suitable for the rapid determination of metabolic fluxes of isotopically labeled substrates in cultured cells and organoids. We adapted an automated annotation pipeline by selecting labeled adducts that best represent the majority of 13C and/or 15N-labeled glycolytic and tricarboxylic acid cycle intermediates as well as a number of their derivatives. Furthermore, valine, leucine and several of their degradation products were included. We show that DI-HRMS can determine anticipated and unanticipated alterations in metabolic fluxes along these pathways that result from the genetic alteration of single metabolic enzymes, including pyruvate dehydrogenase (PDHA1) and glutaminase (GLS). In addition, it can precisely pinpoint metabolic adaptations to the loss of methylmalonyl-CoA mutase in patient-derived liver organoids. Our results highlight the power of DI-HRMS in combination with stable isotopically labeled compounds as an efficient screening method for fluxomics.
    Keywords:  TCA cycle; direct infusion–high-resolution mass spectrometry; glutaminolysis; glycolysis; isotope tracing; organoids; patient material
    DOI:  https://doi.org/10.3390/metabo14050246
  18. Commun Biol. 2024 May 23. 7(1): 618
    The gluconeogenesis enzyme PCK2 has a non-enzymatic role in proteostasis in endothelial cells.
    Pauline de Zeeuw, Lucas Treps, Melissa García-Caballero, Ulrike Harjes, Joanna Kalucka, Carla De Legher, Katleen Brepoels, Kristel Peeters, Stefan Vinckier, Joris Souffreau, Ann Bouché, Federico Taverna, Jonas Dehairs, Ali Talebi, Bart Ghesquière, Johan Swinnen, Luc Schoonjans, Guy Eelen, Mieke Dewerchin, Peter Carmeliet.
      Endothelial cells (ECs) are highly glycolytic, but whether they generate glycolytic intermediates via gluconeogenesis (GNG) in glucose-deprived conditions remains unknown. Here, we report that glucose-deprived ECs upregulate the GNG enzyme PCK2 and rely on a PCK2-dependent truncated GNG, whereby lactate and glutamine are used for the synthesis of lower glycolytic intermediates that enter the serine and glycerophospholipid biosynthesis pathways, which can play key roles in redox homeostasis and phospholipid synthesis, respectively. Unexpectedly, however, even in normal glucose conditions, and independent of its enzymatic activity, PCK2 silencing perturbs proteostasis, beyond its traditional GNG role. Indeed, PCK2-silenced ECs have an impaired unfolded protein response, leading to accumulation of misfolded proteins, which due to defective proteasomes and impaired autophagy, results in the accumulation of protein aggregates in lysosomes and EC demise. Ultimately, loss of PCK2 in ECs impaired vessel sprouting. This study identifies a role for PCK2 in proteostasis beyond GNG.
    DOI:  https://doi.org/10.1038/s42003-024-06186-6
  19. Nat Struct Mol Biol. 2024 May 20.
    RNAi screens identify HES4 as a regulator of redox balance supporting pyrimidine synthesis and tumor growth.
    Jing He, Aoxue Wang, Qin Zhao, Yejun Zou, Zhuo Zhang, Nannan Sha, Guofang Hou, Bei Zhou, Yi Yang, Tao Chen, Yuzheng Zhao, Yuhui Jiang.
      NADH/NAD+ redox balance is pivotal for cellular metabolism. Systematic identification of NAD(H) redox regulators, although currently lacking, would help uncover unknown effectors critically implicated in the coordination of growth metabolism. In this study, we performed a genome-scale RNA interference (RNAi) screen to globally survey the genes involved in redox modulation and identified the HES family bHLH transcription factor HES4 as a negative regulator of NADH/NAD+ ratio. Functionally, HES4 is shown to be crucial for maintaining mitochondrial electron transport chain (ETC) activity and pyrimidine synthesis. More specifically, HES4 directly represses transcription of SLC44A2 and SDS, thereby inhibiting mitochondrial choline oxidation and cytosolic serine deamination, respectively, which, in turn, ensures coenzyme Q reduction capacity for DHODH-mediated UMP synthesis and serine-derived dTMP production. Accordingly, inhibition of choline oxidation preserves mitochondrial serine catabolism and ETC-coupled redox balance. Furthermore, HES4 protein stability is enhanced under EGFR activation, and increased HES4 levels facilitate EGFR-driven tumor growth and predict poor prognosis of lung adenocarcinoma. These findings illustrate an unidentified mechanism, underlying pyrimidine biosynthesis in the intersection between serine and choline catabolism, and underscore the physiological importance of HES4 in tumor metabolism.
    DOI:  https://doi.org/10.1038/s41594-024-01309-3
  20. Hum Mol Genet. 2024 May 22. 33(R1): R34-R41
    Central dogma rates in human mitochondria.
    Erik McShane, L Stirling Churchman.
      In human cells, the nuclear and mitochondrial genomes engage in a complex interplay to produce dual-encoded oxidative phosphorylation (OXPHOS) complexes. The coordination of these dynamic gene expression processes is essential for producing matched amounts of OXPHOS protein subunits. This review focuses on our current understanding of the mitochondrial central dogma rates, highlighting the striking differences in gene expression rates between mitochondrial and nuclear genes. We synthesize a coherent model of mitochondrial gene expression kinetics, highlighting the emerging principles and emphasizing where more precise measurements would be beneficial. Such an understanding is pivotal for grasping the unique aspects of mitochondrial function and its role in cellular energetics, and it has profound implications for aging, metabolic disorders, and neurodegenerative diseases.
    Keywords:  gene regulation; mitochondrial DNA; mitonuclear balance; oxidative phosphorylation
    DOI:  https://doi.org/10.1093/hmg/ddae036
  21. Hum Mol Genet. 2024 May 22. 33(R1): R3-R11
    Origins of tissue and cell-type specificity in mitochondrial DNA (mtDNA) disease.
    Stephen P Burr, Patrick F Chinnery.
      Mutations of mitochondrial (mt)DNA are a major cause of morbidity and mortality in humans, accounting for approximately two thirds of diagnosed mitochondrial disease. However, despite significant advances in technology since the discovery of the first disease-causing mtDNA mutations in 1988, the comprehensive diagnosis and treatment of mtDNA disease remains challenging. This is partly due to the highly variable clinical presentation linked to tissue-specific vulnerability that determines which organs are affected. Organ involvement can vary between different mtDNA mutations, and also between patients carrying the same disease-causing variant. The clinical features frequently overlap with other non-mitochondrial diseases, both rare and common, adding to the diagnostic challenge. Building on previous findings, recent technological advances have cast further light on the mechanisms which underpin the organ vulnerability in mtDNA diseases, but our understanding is far from complete. In this review we explore the origins, current knowledge, and future directions of research in this area.
    Keywords:  heteroplasmy; mitochondria; mtDNA; single cell
    DOI:  https://doi.org/10.1093/hmg/ddae059
  22. Immunity. 2024 May 14. pii: S1074-7613(24)00227-9. [Epub ahead of print]
    Metabolic coordination between skin epithelium and type 17 immunity sustains chronic skin inflammation.
    Ipsita Subudhi, Piotr Konieczny, Aleksandr Prystupa, Rochelle L Castillo, Erica Sze-Tu, Yue Xing, Daniel Rosenblum, Ilana Reznikov, Ikjot Sidhu, Cynthia Loomis, Catherine P Lu, Niroshana Anandasabapathy, Mayte Suárez-Fariñas, Johann E Gudjonsson, Aristotelis Tsirigos, Jose U Scher, Shruti Naik.
      Inflammatory epithelial diseases are spurred by the concomitant dysregulation of immune and epithelial cells. How these two dysregulated cellular compartments simultaneously sustain their heightened metabolic demands is unclear. Single-cell and spatial transcriptomics (ST), along with immunofluorescence, revealed that hypoxia-inducible factor 1α (HIF1α), downstream of IL-17 signaling, drove psoriatic epithelial remodeling. Blocking HIF1α in human psoriatic lesions ex vivo impaired glycolysis and phenocopied anti-IL-17 therapy. In a murine model of skin inflammation, epidermal-specific loss of HIF1α or its target gene, glucose transporter 1, ameliorated epidermal, immune, vascular, and neuronal pathology. Mechanistically, glycolysis autonomously fueled epithelial pathology and enhanced lactate production, which augmented the γδ T17 cell response. RORγt-driven genetic deletion or pharmacological inhibition of either lactate-producing enzymes or lactate transporters attenuated epithelial pathology and IL-17A expression in vivo. Our findings identify a metabolic hierarchy between epithelial and immune compartments and the consequent coordination of metabolic processes that sustain inflammatory disease.
    Keywords:  HIF1α; epithelium; glycolysis; inflammation; lactate; metabolism; skin; type 17 cells
    DOI:  https://doi.org/10.1016/j.immuni.2024.04.022
  23. Sci Immunol. 2024 May 24. 9(95): eade2094
    Intratumoral antigen signaling traps CD8+ T cells to confine exhaustion to the tumor site.
    Munetomo Takahashi, Tsz Y So, Vitalina Chamberlain-Evans, Robert Hughes, Juan Carlos Yam-Puc, Katarzyna Kania, Michelle Ruhle, Tiffeney Mann, Martijn J Schuijs, Paul Coupland, Dean Naisbitt, Timotheus Y F Halim, Paul A Lyons, Pietro Lio, Rahul Roychoudhuri, Klaus Okkenhaug, David J Adams, Ken G C Smith, Duncan I Jodrell, Michael A Chapman, James E D Thaventhiran.
      Immunotherapy advances have been hindered by difficulties in tracking the behaviors of lymphocytes after antigen signaling. Here, we assessed the behavior of T cells active within tumors through the development of the antigen receptor signaling reporter (AgRSR) mouse, fate-mapping lymphocytes responding to antigens at specific times and locations. Contrary to reports describing the ready egress of T cells out of the tumor, we find that intratumoral antigen signaling traps CD8+ T cells in the tumor. These clonal populations expand and become increasingly exhausted over time. By contrast, antigen-signaled regulatory T cell (Treg) clonal populations readily recirculate out of the tumor. Consequently, intratumoral antigen signaling acts as a gatekeeper to compartmentalize CD8+ T cell responses, even within the same clonotype, thus enabling exhausted T cells to remain confined to a specific tumor tissue site.
    DOI:  https://doi.org/10.1126/sciimmunol.ade2094
  24. Nat Metab. 2024 May 24.
    Neuronal hypoglycolysis sustains body health.
    Beatriz Pardo.
      
    DOI:  https://doi.org/10.1038/s42255-024-01055-2
  25. Nat Metab. 2024 May 21.
    Glycolytic enzyme PFKL governs lipolysis by promoting lipid droplet-mitochondria tethering to enhance β-oxidation and tumor cell proliferation.
    Ying Meng, Dong Guo, Liming Lin, Hong Zhao, Weiting Xu, Shudi Luo, Xiaoming Jiang, Shan Li, Xuxiao He, Rongxuan Zhu, Rongkai Shi, Liwei Xiao, Qingang Wu, Haiyan He, Jingjing Tao, Hongfei Jiang, Zheng Wang, Pengbo Yao, Daqian Xu, Zhimin Lu.
      Lipid droplet tethering with mitochondria for fatty acid oxidation is critical for tumor cells to counteract energy stress. However, the underlying mechanism remains unclear. Here, we demonstrate that glucose deprivation induces phosphorylation of the glycolytic enzyme phosphofructokinase, liver type (PFKL), reducing its activity and favoring its interaction with perilipin 2 (PLIN2). On lipid droplets, PFKL acts as a protein kinase and phosphorylates PLIN2 to promote the binding of PLIN2 to carnitine palmitoyltransferase 1A (CPT1A). This results in the tethering of lipid droplets and mitochondria and the recruitment of adipose triglyceride lipase to the lipid droplet-mitochondria tethering regions to engage lipid mobilization. Interfering with this cascade inhibits tumor cell proliferation, promotes apoptosis and blunts liver tumor growth in male mice. These results reveal that energy stress confers a moonlight function to PFKL as a protein kinase to tether lipid droplets with mitochondria and highlight the crucial role of PFKL in the integrated regulation of glycolysis, lipid metabolism and mitochondrial oxidation.
    DOI:  https://doi.org/10.1038/s42255-024-01047-2
  26. Hum Mol Genet. 2024 May 22. 33(R1): R47-R52
    Coordinating mitochondrial translation with assembly of the OXPHOS complexes.
    Laura S Kremer, Peter Rehling.
      The mitochondrial oxidative phosphorylation (OXPHOS) system produces the majority of energy required by cells. Given the mitochondrion's endosymbiotic origin, the OXPHOS machinery is still under dual genetic control where most OXPHOS subunits are encoded by the nuclear DNA and imported into mitochondria, while a small subset is encoded on the mitochondrion's own genome, the mitochondrial DNA (mtDNA). The nuclear and mtDNA encoded subunits must be expressed and assembled in a highly orchestrated fashion to form a functional OXPHOS system and meanwhile prevent the generation of any harmful assembly intermediates. While several mechanisms have evolved in eukaryotes to achieve such a coordinated expression, this review will focus on how the translation of mtDNA encoded OXPHOS subunits is tailored to OXPHOS assembly.
    Keywords:  Coordination of translation and assembly; Gene expression; Mitochondria; OXPHOS assembly; Oxidative phosphorylation (OXPHOS); Translation
    DOI:  https://doi.org/10.1093/hmg/ddae025
  27. Metabolites. 2024 May 10. pii: 279. [Epub ahead of print]14(5):
    Mass Spectrometric Analysis of Purine Intermediary Metabolism Indicates Cyanide Induces Purine Catabolism in Rabbits.
    Jordan Morningstar, Jangwoen Lee, Sari Mahon, Matthew Brenner, Anjali K Nath.
      Purines are the building blocks of DNA/RNA, energy substrates, and cofactors. Purine metabolites, including ATP, GTP, NADH, and coenzyme A, are essential molecules in diverse biological processes such as energy metabolism, signal transduction, and enzyme activity. When purine levels increase, excess purines are either recycled to synthesize purine metabolites or catabolized to the end product uric acid. Purine catabolism increases during states of low oxygen tension (hypoxia and ischemia), but this metabolic pathway is incompletely understood in the context of histotoxic hypoxia (i.e., inhibition of oxygen utilization despite normal oxygen tension). In rabbits exposed to cyanide-a classical histotoxic hypoxia agent-we demonstrated significant increases in several concordant metabolites in the purine catabolic pathway (including plasma levels of uric acid, xanthosine, xanthine, hypoxanthine, and inosine) via mass spectrometry-based metabolite profiling. Pharmacological inhibition of the purine catabolic pathway with oxypurinol mitigated the deleterious effects of cyanide on skeletal muscle cytochrome c oxidase redox state, measured by non-invasive diffuse optical spectroscopy. Finally, plasma uric acid levels correlated strongly with those of lactic acid, an established clinical biomarker of cyanide exposure, in addition to a tissue biomarker of cyanide exposure (skeletal muscle cytochrome c oxidase redox state). Cumulatively, these findings not only shed light on the in vivo role(s) of cyanide but also have implications in the field of medical countermeasure (MCM) development.
    Keywords:  allopurinol; biomarker; cyanide; cytochrome c oxidase (Complex IV); histotoxic hypoxia; mass spectrometry; nucleoside/nucleotide metabolism; preclinical animal model; purine; uric acid
    DOI:  https://doi.org/10.3390/metabo14050279
  28. J Pathol. 2024 May 23.
    Ductal carcinoma in situ develops within clonal fields of mutant cells in morphologically normal ducts.
    Grand Challenge PRECISION Consortium
      Mutations are abundantly present in tissues of healthy individuals, including the breast epithelium. Yet it remains unknown whether mutant cells directly induce lesion formation or first spread, leading to a field of mutant cells that is predisposed towards lesion formation. To study the clonal and spatial relationships between morphologically normal breast epithelium adjacent to pre-cancerous lesions, we developed a three-dimensional (3D) imaging pipeline combined with spatially resolved genomics on archival, formalin-fixed breast tissue with the non-obligate breast cancer precursor ductal carcinoma in situ (DCIS). Using this 3D image-guided characterization method, we built high-resolution spatial maps of DNA copy number aberration (CNA) profiles within the DCIS lesion and the surrounding normal mammary ducts. We show that the local heterogeneity within a DCIS lesion is limited. However, by mapping the CNA profiles back onto the 3D reconstructed ductal subtree, we find that in eight out of 16 cases the healthy epithelium adjacent to the DCIS lesions has overlapping structural variations with the CNA profile of the DCIS. Together, our study indicates that pre-malignant breast transformations frequently develop within mutant clonal fields of morphologically normal-looking ducts. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
    Keywords:  3D pathology; copy number aberration; ductal carcinoma in situ; field cancerization; pre‐malignant transformation; spatial genomics
    DOI:  https://doi.org/10.1002/path.6289
  29. Hum Mol Genet. 2024 May 22. 33(R1): R42-R46
    Decoding the Enigma: Translation Termination in Human Mitochondria.
    Annika Krüger, Daria Kovalchuk, Dmitrii Shiriaev, Joanna Rorbach.
      Mitochondrial translation is a complex process responsible for the synthesis of essential proteins involved in oxidative phosphorylation, a fundamental pathway for cellular energy production. Central to this process is the termination phase, where dedicated factors play a pivotal role in ensuring accurate and timely protein production. This review provides a comprehensive overview of the current understanding of translation termination in human mitochondria, emphasizing structural features and molecular functions of two mitochondrial termination factors mtRF1 and mtRF1a.
    Keywords:  Mitochondrial translation; mitochondrial translation termination factors; mitoribosomes
    DOI:  https://doi.org/10.1093/hmg/ddae032
  30. Nat Commun. 2024 May 20. 15(1): 4277
    Elevated Na is a dynamic and reversible modulator of mitochondrial metabolism in the heart.
    Yu Jin Chung, Zoe Hoare, Friedrich Baark, Chak Shun Yu, Jia Guo, William Fuller, Richard Southworth, Doerthe M Katschinski, Michael P Murphy, Thomas R Eykyn, Michael J Shattock.
      Elevated intracellular sodium Nai adversely affects mitochondrial metabolism and is a common feature of heart failure. The reversibility of acute Na induced metabolic changes is evaluated in Langendorff perfused rat hearts using the Na/K ATPase inhibitor ouabain and the myosin-uncoupler para-aminoblebbistatin to maintain constant energetic demand. Elevated Nai decreases Gibb's free energy of ATP hydrolysis, increases the TCA cycle intermediates succinate and fumarate, decreases ETC activity at Complexes I, II and III, and causes a redox shift of CoQ to CoQH2, which are all reversed on lowering Nai to baseline levels. Pseudo hypoxia and stabilization of HIF-1α is observed despite normal tissue oxygenation. Inhibition of mitochondrial Na/Ca-exchange with CGP-37517 or treatment with the mitochondrial ROS scavenger MitoQ prevents the metabolic alterations during Nai elevation. Elevated Nai plays a reversible role in the metabolic and functional changes and is a novel therapeutic target to correct metabolic dysfunction in heart failure.
    DOI:  https://doi.org/10.1038/s41467-024-48474-z
  31. Int Rev Cell Mol Biol. 2024 ;pii: S1937-6448(24)00016-9. [Epub ahead of print]386 223-247
    Mitochondria driven innate immune signaling and inflammation in cancer growth, immune evasion, and therapeutic resistance.
    Sanjay Pandey, Vandana Anang, Michelle M Schumacher.
      Mitochondria play an important and multifaceted role in cellular function, catering to the cell's energy and biosynthetic requirements. They modulate apoptosis while responding to diverse extracellular and intracellular stresses including reactive oxygen species (ROS), nutrient and oxygen scarcity, endoplasmic reticulum stress, and signaling via surface death receptors. Integral components of mitochondria, such as mitochondrial DNA (mtDNA), mitochondrial RNA (mtRNA), Adenosine triphosphate (ATP), cardiolipin, and formyl peptides serve as major damage-associated molecular patterns (DAMPs). These molecules activate multiple innate immune pathways both in the cytosol [such as Retionoic Acid-Inducible Gene-1 (RIG-1) and Cyclic GMP-AMP Synthase (cGAS)] and on the cell surface [including Toll-like receptors (TLRs)]. This activation cascade leads to the release of various cytokines, chemokines, interferons, and other inflammatory molecules and oxidative species. The innate immune pathways further induce chronic inflammation in the tumor microenvironment which either promotes survival and proliferation or promotes epithelial to mesenchymal transition (EMT), metastasis and therapeutic resistance in the cancer cell's. Chronic activation of innate inflammatory pathways in tumors also drives immunosuppressive checkpoint expression in the cancer cells and boosts the influx of immune-suppressive populations like Myeloid-Derived Suppressor Cells (MDSCs) and Regulatory T cells (Tregs) in cancer. Thus, sensing of cellular stress by the mitochondria may lead to enhanced tumor growth. In addition to that, the tumor microenvironment also becomes a source of immunosuppressive cytokines. These cytokines exert a debilitating effect on the functioning of immune effector cells, and thus foster immune tolerance and facilitate immune evasion. Here we describe how alteration of the mitochondrial homeostasis and cellular stress drives innate inflammatory pathways in the tumor microenvironment.
    Keywords:  ATP; CGAS; Cardiolipin; Formyl peptides; IFNs; IRF3; Innate immune signaling; MOMP; Mitochondrial DAMPs; MtDNA; MtRNA; NFκB; NLRP3; NLRP3 inflammasome; RIG-1; ROS; STAT3; TLR9
    DOI:  https://doi.org/10.1016/bs.ircmb.2024.01.006
  32. bioRxiv. 2024 May 09. pii: 2024.05.06.592780. [Epub ahead of print]
    Lipid availability influences ferroptosis sensitivity in cancer cells by regulating polyunsaturated fatty acid trafficking.
    Kelly H Sokol, Cameron J Lee, Thomas J Rogers, Althea Waldhart, Abigail E Ellis, Sahithi Madireddy, Samuel R Daniels, Xinyu Ye, Mary Olesnavich, Amy Johnson, Benjamin R Furness, Ryan D Sheldon, Evan C Lien.
      Ferroptosis is a form of cell death caused by lipid peroxidation that is emerging as a target for cancer therapy, highlighting the need to identify factors that govern ferroptosis susceptibility. Lipid peroxidation occurs primarily on phospholipids containing polyunsaturated fatty acids (PUFAs). Here, we show that even though extracellular lipid limitation reduces cellular PUFA levels, lipid-starved cancer cells are paradoxically more sensitive to ferroptosis. Using mass spectrometry-based lipidomics with stable isotope fatty acid labeling, we show that lipid limitation induces a fatty acid trafficking pathway in which PUFAs are liberated from triglycerides to synthesize highly unsaturated PUFAs such as arachidonic acid and adrenic acid. These PUFAs then accumulate in phospholipids, particularly ether phospholipids, to promote ferroptosis sensitivity. Therefore, PUFA levels within cancer cells do not necessarily correlate with ferroptosis susceptibility. Rather, how cancer cells respond to extracellular lipid levels by trafficking PUFAs into proper phospholipid pools dictates their sensitivity to ferroptosis.
    DOI:  https://doi.org/10.1101/2024.05.06.592780
  33. Cell Death Differ. 2024 May 23.
    The importance of murine phospho-MLKL-S345 in situ detection for necroptosis assessment in vivo.
    Konstantinos Kelepouras, Julia Saggau, Ana Beatriz Varanda, Matea Zrilic, Christine Kiefer, Hassan Rakhsh-Khorshid, Ina Lisewski, Iratxe Uranga-Murillo, Maykel Arias, Julian Pardo, Wulf Tonnus, Andreas Linkermann, Alessandro Annibaldi, Henning Walczak, Gianmaria Liccardi.
      Necroptosis is a caspase-independent modality of cell death implicated in many inflammatory pathologies. The execution of this pathway requires the formation of a cytosolic platform that comprises RIPK1 and RIPK3 which, in turn, mediates the phosphorylation of the pseudokinase MLKL (S345 in mouse). The activation of this executioner is followed by its oligomerisation and accumulation at the plasma-membrane where it leads to cell death via plasma-membrane destabilisation and consequent permeabilisation. While the biochemical and cellular characterisation of these events have been amply investigated, the study of necroptosis involvement in vivo in animal models is currently limited to the use of Mlkl-/- or Ripk3-/- mice. Yet, even in many of the models in which the involvement of necroptosis in disease aetiology has been genetically demonstrated, the fundamental in vivo characterisation regarding the question as to which tissue(s) and specific cell type(s) therein is/are affected by the pathogenic necroptotic death are missing. Here, we describe and validate an immunohistochemistry and immunofluorescence-based method to reliably detect the phosphorylation of mouse MLKL at serine 345 (pMLKL-S345). We first validate the method using tissues derived from mice in which Caspase-8 (Casp8) or FADD are specifically deleted from keratinocytes, or intestinal epithelial cells, respectively. We next demonstrate the presence of necroptotic activation in the lungs of SARS-CoV-infected mice and in the skin and spleen of mice bearing a Sharpin inactivating mutation. Finally, we exclude necroptosis occurrence in the intestines of mice subjected to TNF-induced septic shock. Importantly, by directly comparing the staining of pMLKL-345 with that of cleaved Caspase-3 staining in some of these models, we identify spatio-temporal and functional differences between necroptosis and apoptosis supporting a role of RIPK3 in inflammation independently of MLKL versus the role of RIPK3 in activation of necroptosis.
    DOI:  https://doi.org/10.1038/s41418-024-01313-6
  34. Science. 2024 May 23. eadk4898
    A metabolic dependency of EBV can be targeted to hinder B cell transformation.
    Swiss Transplant Cohort Study#
      Following infection of B cells, Epstein Barr virus (EBV) engages host pathways that mediate cell proliferation and transformation, contributing to the propensity of the virus to drive immune dysregulation and lymphomagenesis. We found that the EBV protein EBNA2 initiates NAD de novo biosynthesis by driving expression of the metabolic enzyme IDO1 in infected B cells. Virus-enforced NAD production sustained mitochondrial complex I activity, to match ATP-production with bioenergetic requirements of proliferation and transformation. In transplant patients, IDO1 expression in EBV-infected B cells, and a serum signature of increased IDO1 activity, preceded development of lymphoma. In humanized mice infected with EBV, IDO1 inhibition reduced both viremia and lymphomagenesis. Virus-orchestrated NAD biosynthesis is, thus, a druggable metabolic vulnerability of EBV-driven B cell transformation-opening therapeutic possibilities for EBV-related diseases.
    DOI:  https://doi.org/10.1126/science.adk4898
  35. Int J Mol Sci. 2024 May 13. pii: 5288. [Epub ahead of print]25(10):
    Immunological Aspects of Cancer Cell Metabolism.
    Sisca Ucche, Yoshihiro Hayakawa.
      Cancer cells adeptly manipulate their metabolic processes to evade immune detection, a phenomenon intensifying the complexity of cancer progression and therapy. This review delves into the critical role of cancer cell metabolism in the immune-editing landscape, highlighting how metabolic reprogramming facilitates tumor cells to thrive despite immune surveillance pressures. We explore the dynamic interactions within the tumor microenvironment (TME), where cancer cells not only accelerate their glucose and amino acid metabolism but also induce an immunosuppressive state that hampers effective immune response. Recent findings underscore the metabolic competition between tumor and immune cells, particularly focusing on how this interaction influences the efficacy of emerging immunotherapies. By integrating cutting-edge research on the metabolic pathways of cancer cells, such as the Warburg effect and glutamine addiction, we shed light on potential therapeutic targets. The review proposes that disrupting these metabolic pathways could enhance the response to immunotherapy, offering a dual-pronged strategy to combat tumor growth and immune evasion.
    Keywords:  cancer; immune escape; immune surveillance; metabolism; progression
    DOI:  https://doi.org/10.3390/ijms25105288
  36. bioRxiv. 2024 May 07. pii: 2024.05.06.592787. [Epub ahead of print]
    The TWK-26 potassium channel governs nutrient absorption in the C. elegans intestine.
    Sarah K Torzone, Peter C Breen, Natalie R Cohen, Kaylee N Simmons, Robert H Dowen.
      Ion channels are necessary for proper water and nutrient absorption in the intestine, which supports cellular metabolism and organismal growth. While a role for Na + co-transporters and pumps in intestinal nutrient absorption is well defined, how individual K + uniporters function to maintain ion homeostasis is poorly understood. Using Caenorhabditis elegans , we show that a gain-of-function mutation in twk-26 , which encodes a two-pore domain K + ion channel orthologous to human KCNK3, facilitates nutrient absorption and suppresses the metabolic and developmental defects displayed by impaired intestinal MAP Kinase (MAPK) signaling. Mutations in drl-1 and flr-4, which encode two components of this MAPK pathway, cause severe growth defects, reduced lipid storage, and a dramatic increase in autophagic lysosomes, which mirror dietary restriction phenotypes. Additionally, these MAPK mutants display structural defects of the intestine and an impaired defecation motor program. We find that activation of TWK-26 reverses the dietary restriction-like state of the MAPK mutants by restoring intestinal nutrient absorption without correcting the intestinal bloating or defecation defects. This study provides unique insight into the mechanisms by which intestinal K + ion channels support intestinal metabolic homeostasis.
    DOI:  https://doi.org/10.1101/2024.05.06.592787
  37. Nat Cell Biol. 2024 May 23.
    Adding intrinsically disordered proteins to biological ageing clocks.
    Dorothee Dormann, Edward Anton Lemke.
      Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
    DOI:  https://doi.org/10.1038/s41556-024-01423-w
  38. Cell Chem Biol. 2024 May 17. pii: S2451-9456(24)00178-8. [Epub ahead of print]
    Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology.
    Samskrathi Aravinda Sharma, Sarah Olanrewaju Oladejo, Zheng Kuang.
      Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.
    Keywords:  HDAC; SCFAs; circadian clock; histone modification; immunity; metabolism; metabolites; microbiome
    DOI:  https://doi.org/10.1016/j.chembiol.2024.04.016
  39. Nat Commun. 2024 May 18. 15(1): 4239
    Preserving ester-linked modifications reveals glutamate and aspartate mono-ADP-ribosylation by PARP1 and its reversal by PARG.
    Edoardo José Longarini, Ivan Matić.
      Ester-linked post-translational modifications, including serine and threonine ubiquitination, have gained recognition as important cellular signals. However, their detection remains a significant challenge due to the chemical lability of the ester bond. This is the case even for long-known modifications, such as ADP-ribosylation on aspartate and glutamate, whose role in PARP1 signaling has recently been questioned. Here, we present easily implementable methods for preserving ester-linked modifications. When combined with a specific and sensitive modular antibody and mass spectrometry, these approaches reveal DNA damage-induced aspartate/glutamate mono-ADP-ribosylation. This previously elusive signal represents an initial wave of PARP1 signaling, contrasting with the more enduring nature of serine mono-ADP-ribosylation. Unexpectedly, we show that the poly-ADP-ribose hydrolase PARG is capable of reversing ester-linked mono-ADP-ribosylation in cells. Our methodology enables broad investigations of various ADP-ribosylation writers and, as illustrated here for noncanonical ubiquitination, it paves the way for exploring other emerging ester-linked modifications.
    DOI:  https://doi.org/10.1038/s41467-024-48314-0
  40. Elife. 2024 May 23. pii: RP94187. [Epub ahead of print]13
    A mitochondrial carrier transports glycolytic intermediates to link cytosolic and mitochondrial glycolysis in the human gut parasite Blastocystis.
    Eva Pyrihová, Martin S King, Alannah C King, M Rey Toleco, Mark van der Giezen, Edmund R S Kunji.
      Stramenopiles form a clade of diverse eukaryotic organisms, including multicellular algae, the fish and plant pathogenic oomycetes, such as the potato blight Phytophthora, and the human intestinal protozoan Blastocystis. In most eukaryotes, glycolysis is a strictly cytosolic metabolic pathway that converts glucose to pyruvate, resulting in the production of NADH and ATP (Adenosine triphosphate). In contrast, stramenopiles have a branched glycolysis in which the enzymes of the pay-off phase are located in both the cytosol and the mitochondrial matrix. Here, we identify a mitochondrial carrier in Blastocystis that can transport glycolytic intermediates, such as dihydroxyacetone phosphate and glyceraldehyde-3-phosphate, across the mitochondrial inner membrane, linking the cytosolic and mitochondrial branches of glycolysis. Comparative analyses with the phylogenetically related human mitochondrial oxoglutarate carrier (SLC25A11) and dicarboxylate carrier (SLC25A10) show that the glycolytic intermediate carrier has lost its ability to transport the canonical substrates malate and oxoglutarate. Blastocystis lacks several key components of oxidative phosphorylation required for the generation of mitochondrial ATP, such as complexes III and IV, ATP synthase, and ADP/ATP carriers. The presence of the glycolytic pay-off phase in the mitochondrial matrix generates ATP, which powers energy-requiring processes, such as macromolecular synthesis, as well as NADH, used by mitochondrial complex I to generate a proton motive force to drive the import of proteins and molecules. Given its unique substrate specificity and central role in carbon and energy metabolism, the carrier for glycolytic intermediates identified here represents a specific drug and pesticide target against stramenopile pathogens, which are of great economic importance.
    Keywords:  Blastocystis; E. coli; S. cerevisiae; SLC25 mitochondrial carrier family; biochemistry; chemical biology; evolutionary biology; human; missing transport link; protists; thermostability shift assays; transport assays
    DOI:  https://doi.org/10.7554/eLife.94187
  41. bioRxiv. 2024 May 10. pii: 2024.05.09.592977. [Epub ahead of print]
    Mitochondrial Phosphopantetheinylation is Required for Oxidative Function.
    Pieter R Norden, Riley J Wedan, Jacob Z Longenecker, Samuel E J Preston, Naomi Graber, Olivia Ols, Morgan Canfield, Elizabeth McLaughlin, Sara M Nowinski.
      Sub-cellular compartmentalization of metabolism has important implications for the local production of metabolites and redox co-factors, as well as pathway regulation. 4'-phosphopantetheinyl (4'PP) groups are essential co-factors derived from coenzyme A and added to target proteins in both the cytoplasm and mitochondria by p hospho p antetheinyl transferase (PPTase) enzymes. Mammals express only one PPTase, thought to localize to the cytoplasm: aminoadipate semialdehyde dehydrogenase phosphopantetheinyl transferase (AASDHPPT); raising the question of how mitochondrial proteins are 4'PP-modified. We found that AASDHPPT is required for mitochondrial respiration and oxidative metabolism via the mitochondrial fatty acid synthesis (mtFAS) pathway. Moreover, we discovered that a pool of AASDHPPT localizes to the mitochondrial matrix via an N-terminal mitochondrial targeting sequence contained within the first 13 amino acids of the protein. Our data show that mitochondrial localization of AASDHPPT is required to support mtFAS function, and further identify two variants in Aasdhppt that are likely pathogenic in humans.
    DOI:  https://doi.org/10.1101/2024.05.09.592977
  42. Hum Mol Genet. 2024 May 22. 33(R1): R12-R18
    Molecular and cellular consequences of mitochondrial DNA double-stranded breaks.
    Chenxiao Yu, Samieh Asadian, Marco Tigano.
      Mitochondria are subcellular organelles essential for life. Beyond their role in producing energy, mitochondria govern various physiological mechanisms, encompassing energy generation, metabolic processes, apoptotic events, and immune responses. Mitochondria also contain genetic material that is susceptible to various forms of damage. Mitochondrial double-stranded breaks (DSB) are toxic lesions that the nucleus repairs promptly. Nevertheless, the significance of DSB repair in mammalian mitochondria is controversial. This review presents an updated view of the available research on the consequences of mitochondrial DNA DSB from the molecular to the cellular level. We discuss the crucial function of mitochondrial DNA damage in regulating processes such as senescence, integrated stress response, and innate immunity. Lastly, we discuss the potential role of mitochondrial DNA DSB in mediating the cellular consequences of ionizing radiations, the standard of care in treating solid tumors.
    Keywords:  innate immunity; integrated stress response; mitochondria; mitochondrial DNA; senescence
    DOI:  https://doi.org/10.1093/hmg/ddae048
  43. EMBO J. 2024 May 22.
    The immune response to RNA suppresses nucleic acid synthesis by limiting ribose 5-phosphate.
    Pushpak Bhattacharjee, Die Wang, Dovile Anderson, Joshua N Buckler, Eveline de Geus, Feng Alex Yan, Galina Polekhina, Ralf Schittenhelm, Darren J Creek, Lawrence D Harris, Anthony J Sadler.
      During infection viruses hijack host cell metabolism to promote their replication. Here, analysis of metabolite alterations in macrophages exposed to poly I:C recognises that the antiviral effector Protein Kinase RNA-activated (PKR) suppresses glucose breakdown within the pentose phosphate pathway (PPP). This pathway runs parallel to central glycolysis and is critical to producing NADPH and pentose precursors for nucleotides. Changes in metabolite levels between wild-type and PKR-ablated macrophages show that PKR controls the generation of ribose 5-phosphate, in a manner distinct from its established function in gene expression but dependent on its kinase activity. PKR phosphorylates and inhibits the Ribose 5-Phosphate Isomerase A (RPIA), thereby preventing interconversion of ribulose- to ribose 5-phosphate. This activity preserves redox control but decreases production of ribose 5-phosphate for nucleotide biosynthesis. Accordingly, the PKR-mediated immune response to RNA suppresses nucleic acid production. In line, pharmacological targeting of the PPP during infection decreases the replication of the Herpes simplex virus. These results identify an immune response-mediated control of host cell metabolism and suggest targeting the RPIA as a potential innovative antiviral treatment.
    Keywords:  Antiviral; Immunity; Metabolism; Nucleotide Biosynthesis; PKR (Protein Kinase RNA-Activated); PPP (Pentose Phosphate Pathway); RPIA (Ribose 5-Phosphate Isomerase A)
    DOI:  https://doi.org/10.1038/s44318-024-00100-w
  44. Nat Commun. 2024 May 21. 15(1): 4325
    Cell of origin epigenetic priming determines susceptibility to Tet2 mutation.
    Giulia Schiroli, Vinay Kartha, Fabiana M Duarte, Trine A Kristiansen, Christina Mayerhofer, Rojesh Shrestha, Andrew Earl, Yan Hu, Tristan Tay, Catherine Rhee, Jason D Buenrostro, David T Scadden.
      Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigate how the cell state preceding Tet2 mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we find that the epigenetic features of clones at similar differentiation status are highly heterogeneous and functionally respond differently to Tet2 mutation. Cell differentiation stage also influences Tet2 mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include Sox4 that sensitizes cells to Tet2 inactivation, inducing dedifferentiation, altered metabolism and increasing the in vivo clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.
    DOI:  https://doi.org/10.1038/s41467-024-48508-6
  45. Nat Commun. 2024 May 24. 15(1): 4444
    Deleting the mitochondrial respiration negative regulator MCJ enhances the efficacy of CD8+ T cell adoptive therapies in pre-clinical studies.
    Meng-Han Wu, Felipe Valenca-Pereira, Francesca Cendali, Emily L Giddings, Catherine Pham-Danis, Michael C Yarnell, Amanda J Novak, Tonya M Brunetti, Scott B Thompson, Jorge Henao-Mejia, Richard A Flavell, Angelo D'Alessandro, M Eric Kohler, Mercedes Rincon.
      Mitochondrial respiration is essential for the survival and function of T cells used in adoptive cellular therapies. However, strategies that specifically enhance mitochondrial respiration to promote T cell function remain limited. Here, we investigate methylation-controlled J protein (MCJ), an endogenous negative regulator of mitochondrial complex I expressed in CD8 cells, as a target for improving the efficacy of adoptive T cell therapies. We demonstrate that MCJ inhibits mitochondrial respiration in murine CD8+ CAR-T cells and that deletion of MCJ increases their in vitro and in vivo efficacy against murine B cell leukaemia. Similarly, MCJ deletion in ovalbumin (OVA)-specific CD8+ T cells also increases their efficacy against established OVA-expressing melanoma tumors in vivo. Furthermore, we show for the first time that MCJ is expressed in human CD8 cells and that the level of MCJ expression correlates with the functional activity of CD8+ CAR-T cells. Silencing MCJ expression in human CD8 CAR-T cells increases their mitochondrial metabolism and enhances their anti-tumor activity. Thus, targeting MCJ may represent a potential therapeutic strategy to increase mitochondrial metabolism and improve the efficacy of adoptive T cell therapies.
    DOI:  https://doi.org/10.1038/s41467-024-48653-y
  46. Nat Chem Biol. 2024 May 21.
    We don't need no inflammation.
    Gene Chong.
      
    DOI:  https://doi.org/10.1038/s41589-024-01646-w
  47. Biochim Biophys Acta Mol Cell Res. 2024 May 16. pii: S0167-4889(24)00097-1. [Epub ahead of print]1871(6): 119754
    Overexpression of PEX14 results in mistargeting to mitochondria, accompanied by organelle fragmentation and clustering in human embryonic kidney cells.
    Renate L M Jansen, Rinse de Boer, Eline M F de Lange, Janet Koster, Rifka Vlijm, Hans R Waterham, Ida J van der Klei.
      Peroxisome biogenesis disorders are caused by pathogenic variants in genes involved in biogenesis and maintenance of peroxisomes. However, mitochondria are also often affected in these diseases. Peroxisomal membrane proteins, including PEX14, have been found to mislocalise to mitochondria in cells lacking peroxisomes. Recent studies indicated that this mislocalisation contributes to mitochondrial abnormalities in PEX3-deficient patient fibroblasts cells. Here, we studied whether mitochondrial morphology is also affected in PEX3-deficient HEK293 cells and whether PEX14 mislocalises to mitochondria in these cells. Using high-resolution imaging techniques, we show that although endogenous PEX14 mislocalises to mitochondria, mitochondrial morphology was normal in PEX3-KO HEK293 cells. However, we discovered that overexpression of tagged PEX14 in wild-type HEK293 cells resulted in its mitochondrial localisation, accompanied by altered mitochondrial morphology. Our data indicate that overexpression of tagged PEX14 alone directly or indirectly cause mitochondrial abnormalities in cells containing peroxisomes.
    Keywords:  Microscopy; Mistargeting; Mitochondrial morphology; PEX14; Peroxisomes
    DOI:  https://doi.org/10.1016/j.bbamcr.2024.119754
  48. Nat Cell Biol. 2024 May 23.
    TFAM is an autophagy receptor that limits inflammation by binding to cytoplasmic mitochondrial DNA.
    Hao Liu, Cien Zhen, Jianming Xie, Zhenhuan Luo, Lin Zeng, Guojun Zhao, Shaohua Lu, Haixia Zhuang, Hualin Fan, Xia Li, Zhaojie Liu, Shiyin Lin, Huilin Jiang, Yuqian Chen, Jiahao Cheng, Zhiyu Cao, Keyu Dai, Jinhua Shi, Zhaohua Wang, Yongquan Hu, Tian Meng, Chuchu Zhou, Zhiyuan Han, Huansen Huang, Qinghua Zhou, Pengcheng He, Du Feng.
      When cells are stressed, DNA from energy-producing mitochondria can leak out and drive inflammatory immune responses if not cleared. Cells employ a quality control system called autophagy to specifically degrade damaged components. We discovered that mitochondrial transcription factor A (TFAM)-a protein that binds mitochondrial DNA (mtDNA)-helps to eliminate leaked mtDNA by interacting with the autophagy protein LC3 through an autolysosomal pathway (we term this nucleoid-phagy). TFAM contains a molecular zip code called the LC3 interacting region (LIR) motif that enables this binding. Although mutating TFAM's LIR motif did not affect its normal mitochondrial functions, more mtDNA accumulated in the cell cytoplasm, activating inflammatory signalling pathways. Thus, TFAM mediates autophagic removal of leaked mtDNA to restrict inflammation. Identifying this mechanism advances understanding of how cells exploit autophagy machinery to selectively target and degrade inflammatory mtDNA. These findings could inform research on diseases involving mitochondrial damage and inflammation.
    DOI:  https://doi.org/10.1038/s41556-024-01419-6
  49. EMBO J. 2024 May 22.
    Circadian regulation of macromolecular complex turnover and proteome renewal.
    Estere Seinkmane, Anna Edmondson, Sew Y Peak-Chew, Aiwei Zeng, Nina M Rzechorzek, Nathan R James, James West, Jack Munns, David Cs Wong, Andrew D Beale, John S O'Neill.
      Although costly to maintain, protein homeostasis is indispensable for normal cellular function and long-term health. In mammalian cells and tissues, daily variation in global protein synthesis has been observed, but its utility and consequences for proteome integrity are not fully understood. Using several different pulse-labelling strategies, here we gain direct insight into the relationship between protein synthesis and abundance proteome-wide. We show that protein degradation varies in-phase with protein synthesis, facilitating rhythms in turnover rather than abundance. This results in daily consolidation of proteome renewal whilst minimising changes in composition. Coupled rhythms in synthesis and turnover are especially salient to the assembly of macromolecular protein complexes, particularly the ribosome, the most abundant species of complex in the cell. Daily turnover and proteasomal degradation rhythms render cells and mice more sensitive to proteotoxic stress at specific times of day, potentially contributing to daily rhythms in the efficacy of proteasomal inhibitors against cancer. Our findings suggest that circadian rhythms function to minimise the bioenergetic cost of protein homeostasis through temporal consolidation of protein turnover.
    Keywords:  Circadian; Proteostasis; Ribosome; SILAC
    DOI:  https://doi.org/10.1038/s44318-024-00121-5
  50. Hum Mol Genet. 2024 May 22. 33(R1): R19-R25
    The molecular machinery for maturation of primary mtDNA transcripts.
    Ana Vučković, Christoph Freyer, Anna Wredenberg, Hauke S Hillen.
      Human mitochondria harbour a circular, polyploid genome (mtDNA) encoding 11 messenger RNAs (mRNAs), two ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs). Mitochondrial transcription produces long, polycistronic transcripts that span almost the entire length of the genome, and hence contain all three types of RNAs. The primary transcripts then undergo a number of processing and maturation steps, which constitute key regulatory points of mitochondrial gene expression. The first step of mitochondrial RNA processing consists of the separation of primary transcripts into individual, functional RNA molecules and can occur by two distinct pathways. Both are carried out by dedicated molecular machineries that substantially differ from RNA processing enzymes found elsewhere. As a result, the underlying molecular mechanisms remain poorly understood. Over the last years, genetic, biochemical and structural studies have identified key players involved in both RNA processing pathways and provided the first insights into the underlying mechanisms. Here, we review our current understanding of RNA processing in mammalian mitochondria and provide an outlook on open questions in the field.
    Keywords:  Mitochondria; Mitochondriopathy; RNA; RNA Processing
    DOI:  https://doi.org/10.1093/hmg/ddae023
  51. Nat Commun. 2024 May 21. 15(1): 4314
    Fluorescent fatty acid conjugates for live cell imaging of peroxisomes.
    Daria Korotkova, Anya Borisyuk, Anthony Guihur, Manon Bardyn, Fabien Kuttler, Luc Reymond, Milena Schuhmacher, Triana Amen.
      Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of ether lipids. Consequently, peroxisome dysfunction leads to pediatric-onset neurodegenerative conditions, including Peroxisome Biogenesis Disorders (PBD). Due to the dynamic, tissue-specific, and context-dependent nature of their biogenesis and function, live cell imaging of peroxisomes is essential for studying peroxisome regulation, as well as for the diagnosis of PBD-linked abnormalities. However, the peroxisomal imaging toolkit is lacking in many respects, with no reporters for substrate import, nor cell-permeable probes that could stain dysfunctional peroxisomes. Here we report that the BODIPY-C12 fluorescent fatty acid probe stains functional and dysfunctional peroxisomes in live mammalian cells. We then go on to improve BODIPY-C12, generating peroxisome-specific reagents, PeroxiSPY650 and PeroxiSPY555. These probes combine high peroxisome specificity, bright fluorescence in the red and far-red spectrum, and fast non-cytotoxic staining, making them ideal tools for live cell, whole organism, or tissue imaging of peroxisomes. Finally, we demonstrate that PeroxiSPY enables diagnosis of peroxisome abnormalities in the PBD CRISPR/Cas9 cell models and patient-derived cell lines.
    DOI:  https://doi.org/10.1038/s41467-024-48679-2
  52. Cell Calcium. 2024 May 23. pii: S0143-4160(24)00065-4. [Epub ahead of print]121 102907
    Unravelling the complexity of the mitochondrial Ca2+ uniporter: regulation, tissue specificity, and physiological implications.
    Denis Vecellio Reane, Julian D C Serna, Anna Raffaello.
      Calcium (Ca2+) signalling acts a pleiotropic message within the cell that is decoded by the mitochondria through a sophisticated ion channel known as the Mitochondrial Ca2+ Uniporter (MCU) complex. Under physiological conditions, mitochondrial Ca2+ signalling is crucial for coordinating cell activation with energy production. Conversely, in pathological scenarios, it can determine the fine balance between cell survival and death. Over the last decade, significant progress has been made in understanding the molecular bases of mitochondrial Ca2+ signalling. This began with the elucidation of the MCU channel components and extended to the elucidation of the mechanisms that regulate its activity. Additionally, increasing evidence suggests molecular mechanisms allowing tissue-specific modulation of the MCU complex, tailoring channel activity to the specific needs of different tissues or cell types. This review aims to explore the latest evidence elucidating the regulation of the MCU complex, the molecular factors controlling the tissue-specific properties of the channel, and the physiological and pathological implications of mitochondrial Ca2+ signalling in different tissues.
    Keywords:  Brain; Calcium signalling; Heart; Liver; MCU regulation; Mitochondrial calcium uniporter; Skeletal Muscle; tissue-specific modulation
    DOI:  https://doi.org/10.1016/j.ceca.2024.102907
  53. Elife. 2024 May 22. pii: RP87756. [Epub ahead of print]12
    Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming.
    Corey D Holman, Alexander P Sakers, Ryan P Calhoun, Lan Cheng, Ethan C Fein, Christopher Jacobs, Linus Tsai, Evan D Rosen, Patrick Seale.
      The energy-burning capability of beige adipose tissue is a potential therapeutic tool for reducing obesity and metabolic disease, but this capacity is decreased by aging. Here, we evaluate the impact of aging on the profile and activity of adipocyte stem and progenitor cells (ASPCs) and adipocytes during the beiging process in mice. We found that aging increases the expression of Cd9 and other fibro-inflammatory genes in fibroblastic ASPCs and blocks their differentiation into beige adipocytes. Fibroblastic ASPC populations from young and aged mice were equally competent for beige differentiation in vitro, suggesting that environmental factors suppress adipogenesis in vivo. Examination of adipocytes by single nucleus RNA-sequencing identified compositional and transcriptional differences in adipocyte populations with aging and cold exposure. Notably, cold exposure induced an adipocyte population expressing high levels of de novo lipogenesis (DNL) genes, and this response was severely blunted in aged animals. We further identified Npr3, which encodes the natriuretic peptide clearance receptor, as a marker gene for a subset of white adipocytes and an aging-upregulated gene in adipocytes. In summary, this study indicates that aging blocks beige adipogenesis and dysregulates adipocyte responses to cold exposure and provides a resource for identifying cold and aging-regulated pathways in adipose tissue.
    Keywords:  UCP1; aging; beige adipocyte; beige adipogenesis; cell biology; cold exposure; developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.87756
  54. Dev Cell. 2024 May 21. pii: S1534-5807(24)00271-5. [Epub ahead of print]
    An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions.
    Gea Cereghetti, Vera M Kissling, Lisa M Koch, Alexandra Arm, Claudia C Schmidt, Yannik Thüringer, Nicola Zamboni, Pavel Afanasyev, Miriam Linsenmeier, Cédric Eichmann, Sonja Kroschwald, Jiangtao Zhou, Yiping Cao, Dorota M Pfizenmaier, Thomas Wiegand, Riccardo Cadalbert, Govind Gupta, Daniel Boehringer, Tuomas P J Knowles, Raffaele Mezzenga, Paolo Arosio, Roland Riek, Matthias Peter.
      Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.
    Keywords:  aggregate disassembly; aggregate regulation; amyloid regulation; functional amyloids; isoforms; protein aggregation; pyruvate kinase; reversible amyloids; stress response; stress-induced pH changes
    DOI:  https://doi.org/10.1016/j.devcel.2024.04.018
  55. Hum Mol Genet. 2024 May 22. 33(R1): R92-R99
    Tools for editing the mammalian mitochondrial genome.
    Carlos T Moraes.
      The manipulation of animal mitochondrial genomes has long been a challenge due to the lack of an effective transformation method. With the discovery of specific gene editing enzymes, designed to target pathogenic mitochondrial DNA mutations (often heteroplasmic), the selective removal or modification of mutant variants has become a reality. Because mitochondria cannot efficiently import RNAs, CRISPR has not been the first choice for editing mitochondrial genes. However, the last few years witnessed an explosion in novel and optimized non-CRISPR approaches to promote double-strand breaks or base-edit of mtDNA in vivo. Engineered forms of specific nucleases and cytidine/adenine deaminases form the basis for these techniques. I will review the newest developments that constitute the current toolbox for animal mtDNA gene editing in vivo, bringing these approaches not only to the exploration of mitochondrial function, but also closer to clinical use.
    Keywords:  TALEN technology; base editing; gene modification; genetic enhancements; mitochondrial manipulation
    DOI:  https://doi.org/10.1093/hmg/ddae037
  56. Life Sci Alliance. 2024 Aug;pii: e202402620. [Epub ahead of print]7(8):
    ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway.
    Matteo Veronese, Sebastian Kallabis, Alexander Tobias Kaczmarek, Anushka Das, Lennart Robers, Simon Schumacher, Alessia Lofrano, Susanne Brodesser, Stefan Müller, Kay Hofmann, Marcus Krüger, Elena I Rugarli.
      Complexes of ERLIN1 and ERLIN2 (ER lipid raft-associated 1 and 2) form large ring-like cup-shaped structures on the endoplasmic reticulum (ER) membrane and serve as platforms to bind cholesterol and E3 ubiquitin ligases, potentially defining functional nanodomains. Here, we show that ERLIN scaffolds mediate the interaction between the full-length isoform of TMUB1 (transmembrane and ubiquitin-like domain-containing 1) and RNF170 (RING finger protein 170). We identify a luminal N-terminal conserved region in TMUB1 and RNF170, which is required for this interaction. Three-dimensional modelling shows that this conserved motif binds the stomatin/prohibitin/flotillin/HflKC domain of two adjacent ERLIN subunits at different interfaces. Protein variants that preclude these interactions have been previously linked to hereditary spastic paraplegia. Using omics-based approaches in combination with phenotypic characterization of HeLa cells lacking both ERLINs, we demonstrate a role of ERLIN scaffolds in limiting cholesterol esterification, thereby favouring cholesterol transport from the ER to the Golgi apparatus and regulating Golgi morphology and the secretory pathway.
    DOI:  https://doi.org/10.26508/lsa.202402620
  57. Light Sci Appl. 2024 May 24. 13(1): 116
    Visualization of cristae and mtDNA interactions via STED nanoscopy using a low saturation power probe.
    Wei Ren, Xichuan Ge, Meiqi Li, Jing Sun, Shiyi Li, Shu Gao, Chunyan Shan, Baoxiang Gao, Peng Xi.
      Mitochondria are crucial organelles closely associated with cellular metabolism and function. Mitochondrial DNA (mtDNA) encodes a variety of transcripts and proteins essential for cellular function. However, the interaction between the inner membrane (IM) and mtDNA remains elusive due to the limitations in spatiotemporal resolution offered by conventional microscopy and the absence of suitable in vivo probes specifically targeting the IM. Here, we have developed a novel fluorescence probe called HBmito Crimson, characterized by exceptional photostability, fluorogenicity within lipid membranes, and low saturation power. We successfully achieved over 500 frames of low-power stimulated emission depletion microscopy (STED) imaging to visualize the IM dynamics, with a spatial resolution of 40 nm. By utilizing dual-color imaging of the IM and mtDNA, it has been uncovered that mtDNA tends to habitat at mitochondrial tips or branch points, exhibiting an overall spatially uniform distribution. Notably, the dynamics of mitochondria are intricately associated with the positioning of mtDNA, and fusion consistently occurs in close proximity to mtDNA to minimize pressure during cristae remodeling. In healthy cells, >66% of the mitochondria are Class III (i.e., mitochondria >5 μm or with >12 cristae), while it dropped to <18% in ferroptosis. Mitochondrial dynamics, orchestrated by cristae remodeling, foster the even distribution of mtDNA. Conversely, in conditions of apoptosis and ferroptosis where the cristae structure is compromised, mtDNA distribution becomes irregular. These findings, achieved with unprecedented spatiotemporal resolution, reveal the intricate interplay between cristae and mtDNA and provide insights into the driving forces behind mtDNA distribution.
    DOI:  https://doi.org/10.1038/s41377-024-01463-9
  58. Nature. 2024 May 22.
    Acquisition of epithelial plasticity in human chronic liver disease.
    Christopher Gribben, Vasileios Galanakis, Alexander Calderwood, Eleanor C Williams, Ruben Chazarra-Gil, Miguel Larraz, Carla Frau, Tobias Puengel, Adrien Guillot, Foad J Rouhani, Krishnaa Mahbubani, Edmund Godfrey, Susan E Davies, Emmanouil Athanasiadis, Kourosh Saeb-Parsy, Frank Tacke, Michael Allison, Irina Mohorianu, Ludovic Vallier.
      For many adult human organs, tissue regeneration during chronic disease remains a controversial subject. Regenerative processes are easily observed in animal models, and their underlying mechanisms are becoming well characterized1-4, but technical challenges and ethical aspects are limiting the validation of these results in humans. We decided to address this difficulty with respect to the liver. This organ displays the remarkable ability to regenerate after acute injury, although liver regeneration in the context of recurring injury remains to be fully demonstrated. Here we performed single-nucleus RNA sequencing (snRNA-seq) on 47 liver biopsies from patients with different stages of metabolic dysfunction-associated steatotic liver disease to establish a cellular map of the liver during disease progression. We then combined these single-cell-level data with advanced 3D imaging to reveal profound changes in the liver architecture. Hepatocytes lose their zonation and considerable reorganization of the biliary tree takes place. More importantly, our study uncovers transdifferentiation events that occur between hepatocytes and cholangiocytes without the presence of adult stem cells or developmental progenitor activation. Detailed analyses and functional validations using cholangiocyte organoids confirm the importance of the PI3K-AKT-mTOR pathway in this process, thereby connecting this acquisition of plasticity to insulin signalling. Together, our data indicate that chronic injury creates an environment that induces cellular plasticity in human organs, and understanding the underlying mechanisms of this process could open new therapeutic avenues in the management of chronic diseases.
    DOI:  https://doi.org/10.1038/s41586-024-07465-2
  59. Cold Spring Harb Perspect Med. 2024 May 21. pii: a041736. [Epub ahead of print]
    The Evolution of Mouse Models of Cancer: Past, Present, and Future.
    Cory Abate-Shen, Katerina Politi.
      In the nearly 50 years since the original models of cancer first hit the stage, mouse models have become a major contributor to virtually all aspects of cancer research, and these have evolved well beyond simple transgenic or xenograft models to encompass a wide range of more complex models. As the sophistication of mouse models has increased, an explosion of new technologies has expanded the potential to both further develop and apply these models to address major challenges in cancer research. In the current era, cancer modeling has expanded to include nongermline genetically engineered mouse models (GEMMs), patient-derived models, organoids, and adaptations of the models better suited for cancer immunology research. New technologies that have transformed the field include the application of CRISPR-Cas9-mediated genome editing, in vivo imaging, and single-cell analysis to cancer modeling. Here, we provide a historical perspective on the evolution of mouse models of cancer, focusing on how far we have come in a relatively short time and how new technologies will shape the future development of mouse models of cancer.
    DOI:  https://doi.org/10.1101/cshperspect.a041736
  60. Trends Pharmacol Sci. 2024 May 17. pii: S0165-6147(24)00084-1. [Epub ahead of print]
    Emerging targets in lipid metabolism for cancer therapy.
    Alexander R Terry, Nissim Hay.
      Cancer cells perturb lipid metabolic pathways for a variety of pro-tumorigenic functions, and deregulated cellular metabolism is a hallmark of cancer cells. Although alterations in lipid metabolism in cancer cells have been appreciated for over 20 years, there are no FDA-approved cancer treatments that target lipid-related pathways. Recent advances pertaining to cancer cell fatty acid synthesis (FAS), desaturation, and uptake, microenvironmental and dietary lipids, and lipid metabolism of tumor-infiltrating immune cells have illuminated promising clinical applications for targeting lipid metabolism. This review highlights emerging pathways and targets for tumor lipid metabolism that may soon impact clinical treatment.
    Keywords:  cancer metabolism; fatty acids; lipid metabolism
    DOI:  https://doi.org/10.1016/j.tips.2024.04.007
  61. Discov Oncol. 2024 May 18. 15(1): 173
    Polyamines: the pivotal amines in influencing the tumor microenvironment.
    Cassandra E Holbert, Robert A Casero, Tracy Murray Stewart.
      Cellular proliferation, function and survival is reliant upon maintaining appropriate intracellular polyamine levels. Due to increased metabolic needs, cancer cells elevate their polyamine pools through coordinated metabolism and uptake. High levels of polyamines have been linked to more immunosuppressive tumor microenvironments (TME) as polyamines support the growth and function of many immunosuppressive cell types such as MDSCs, macrophages and regulatory T-cells. As cancer cells and other pro-tumorigenic cell types are highly dependent on polyamines for survival, pharmacological modulation of polyamine metabolism is a promising cancer therapeutic strategy. This review covers the roles of polyamines in various cell types of the TME including both immune and stromal cells, as well as how competition for nutrients, namely polyamine precursors, influences the cellular landscape of the TME. It also details the use of polyamines as biomarkers and the ways in which polyamine depletion can increase the immunogenicity of the TME and reprogram tumors to become more responsive to immunotherapy.
    Keywords:  Amino acid metabolism; Immunotherapy; Polyamine; Tumor microenvironment
    DOI:  https://doi.org/10.1007/s12672-024-01034-9
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