bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2024‒08‒04
fifty papers selected by
Christian Frezza, Universität zu Köln
  1. Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy.
  2. Unresolved questions regarding cellular cysteine sources and their possible relationships to ferroptosis.
  3. ASCT2 is a major contributor to serine uptake in cancer cells.
  4. LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.
  5. The Warburg Effect Revisited through Blood and Electron Flow.
  6. Cilia-enriched oxysterol 7β,27-DHC is required for polycystin ion channel activation.
  7. SLC45A4 encodes a mitochondrial putrescine transporter that promotes GABA de novo synthesis.
  8. BMAL1-HIF2α heterodimers contribute to ccRCC.
  9. mTORC1 activity oscillates throughout the cell cycle, promoting mitotic entry and differentially influencing autophagy induction.
  10. Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle.
  11. Epigenetic control of metabolic identity across cell types.
  12. A three-way organelle junction controls PI(4)P metabolism and mitochondrial division.
  13. The ATP-driven extractor ATAD1/Msp1 proof-reads protein translocation into mitochondria.
  14. Single-nucleus transcriptomics identifies separate classes of UCP1 and futile cycle adipocytes.
  15. Organelle-Targeted Laurdans Measure Heterogeneity in Subcellular Membranes and Their Responses to Saturated Lipid Stress.
  16. Etomoxir-carnitine, a novel pharmaco-metabolite of etomoxir, inhibits phospholipases A2 and mitochondrial respiration.
  17. Calcineurin promotes adaptation to chronic stress through two distinct mechanisms.
  18. Iron Chelation Therapy Elicits Innate Immune Control of Metastatic Ovarian Cancer.
  19. Hypoxia-induced cysteine metabolism reprogramming is crucial for the tumorigenesis of colorectal cancer.
  20. Lactate-carried Mitochondrial Energy Overflow.
  21. Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA.
  22. Deubiquitinase USP9x regulates the proline biosynthesis pathway in non-small cell lung cancer.
  23. Remodeling of T-cell mitochondrial metabolism to treat autoimmune diseases.
  24. Impaired fatty acid import or catabolism in macrophages restricts intracellular growth of Mycobacterium tuberculosis.
  25. IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
  26. mTORC2-driven chromatin cGAS mediates chemoresistance through epigenetic reprogramming in colorectal cancer.
  27. The V-ATPase/ATG16L1 axis is controlled by the V1H subunit.
  28. Cancer, metastasis, and the epigenome.
  29. Multi-species genome-wide CRISPR screens identify GPX4 as a conserved suppressor of cold-induced cell death.
  30. MGA deletion leads to Richter's transformation by modulating mitochondrial OXPHOS.
  31. Mutant ARID1A: igniting cancer immunotherapy.
  32. Phosphorylation of PFKL regulates metabolic reprogramming in macrophages following pattern recognition receptor activation.
  33. Copper and iron orchestrate cell-state transitions in cancer and immunity.
  34. Mitochondrial DNA disorders in neuromuscular diseases in diverse populations.
  35. DAP3 promotes mitochondrial activity and tumour progression in hepatocellular carcinoma by regulating MT-ND5 expression.
  36. Chromosomal instability as a driver of cancer progression.
  37. Histone serotonylation regulates ependymoma tumorigenesis.
  38. SMYD5 is a regulator of the mild hypothermia response.
  39. A genome-wide CRISPR/Cas9 screen identifies calreticulin as a selective repressor of ATF6α.
  40. Endogenously produced itaconate negatively regulates innate-driven cytokine production and drives global ubiquitination in human macrophages.
  41. Mitochondria to plasma membrane redox signaling is essential for fatty acid β-oxidation-driven insulin secretion.
  42. Carcinoma-associated mesenchymal stem cells promote ovarian cancer heterogeneity and metastasis through mitochondrial transfer.
  43. Development of an epigenetic clock resistant to changes in immune cell composition.
  44. Stable isotope-resolved metabolomics analyses of metabolic phenotypes reveal variable glutamine metabolism in different patient-derived models of non-small cell lung cancer from a single patient.
  45. SGLT2 inhibitors activate pantothenate kinase in the human heart.
  46. Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.
  47. The membrane transporter SLC25A48 enables transport of choline into human mitochondria.
  48. Daily rhythms in metabolic and locomotor behaviour of prematurely ageing PolgA mice.
  49. Gut microbiota carcinogen metabolism causes distal tissue tumours.
  50. Sestrin2 drives ER-phagy in response to protein misfolding.
  1. Sci Adv. 2024 Aug 02. 10(31): eadp0443
    Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy.
    Sofia Ahola, Lilli A Pazurek, Fiona Mayer, Philipp Lampe, Steffen Hermans, Lore Becker, Oana V Amarie, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabe de Angelis, Dietmar Riedel, Hendrik Nolte, Thomas Langer.
      Mitochondrial fusion and fission accompany adaptive responses to stress and altered metabolic demands. Inner membrane fusion and cristae morphogenesis depends on optic atrophy 1 (Opa1), which is expressed in different isoforms and is cleaved from a membrane-bound, long to a soluble, short form. Here, we have analyzed the physiological role of Opa1 isoforms and Opa1 processing by generating mouse lines expressing only one cleavable Opa1 isoform or a non-cleavable variant thereof. Our results show that expression of a single cleavable or non-cleavable Opa1 isoform preserves embryonic development and the health of adult mice. Opa1 processing is dispensable under metabolic and thermal stress but prolongs life span and protects against mitochondrial cardiomyopathy in OXPHOS-deficient Cox10-/- mice. Mechanistically, loss of Opa1 processing disturbs the balance between mitochondrial biogenesis and mitophagy, suppressing cardiac hypertrophic growth in Cox10-/- hearts. Our results highlight the critical regulatory role of Opa1 processing, mitochondrial dynamics, and metabolism for cardiac hypertrophy.
    DOI:  https://doi.org/10.1126/sciadv.adp0443
  2. Adv Cancer Res. 2024 ;pii: S0065-230X(24)00001-0. [Epub ahead of print]162 1-44
    Unresolved questions regarding cellular cysteine sources and their possible relationships to ferroptosis.
    Elias S J Arnér, Edward E Schmidt.
      Cysteine is required for synthesis of glutathione (GSH), coenzyme A, other sulfur-containing metabolites, and most proteins. In most cells, cysteine comes from extracellular disulfide sources including cystine, glutathione-disulfide, and peptides. The thioredoxin reductase-1 (TrxR1)- or glutathione-disulfide reductase (GSR)-driven enzymatic systems can fuel cystine reduction via thioredoxins, glutaredoxins, or other thioredoxin-fold proteins. Free cystine enters cells thorough the cystine-glutamate antiporter, xCT, but systemically, plasma glutathione-disulfide might predominate as a cystine source. Erastin, inhibiting both xCT and voltage-dependent anion channels, induces ferroptotic cell death, so named because this type of cell death is antagonized by iron-chelators. Many cancer cells seem to be predisposed to ferroptosis, which has been proposed as a targetable cancer liability. Ferroptosis is associated with lipid peroxidation and loss of either glutathione peroxidase-4 (GPX4) or ferroptosis suppressor protein-1 (FSP1), which each prevent accumulation of lipid peroxides. It has been suggested that an xCT inhibition-induced cellular cysteine-deficiency lowers GSH levels, starving GPX4 for reducing power and allowing membrane lipid peroxides to accumulate, thereby causing ferroptosis. Aspects of ferroptosis are however not fully understood and need to be further scrutinized, for example that neither disruption of GSH synthesis, loss of GSH, nor disruption of glutathione disulfide reductase (GSR), triggers ferroptosis in animal models. Here we reevaluate the relationships between Erastin, xCT, GPX4, cellular cysteine and GSH, RSL3 or ML162, and ferroptosis. We conclude that, whereas both Cys and ferroptosis are potential liabilities in cancer, their relationship to each other remains insufficiently understood.
    Keywords:  Cysteine; Cystine; Disulfide reduction; Erastin; Ferroptosis; Glutathione; Glutathione peroxidase 4; Iron; Lipid peroxide; RSL3
    DOI:  https://doi.org/10.1016/bs.acr.2024.04.001
  3. Cell Rep. 2024 Jul 26. pii: S2211-1247(24)00881-7. [Epub ahead of print]43(8): 114552
    ASCT2 is a major contributor to serine uptake in cancer cells.
    Kelly O Conger, Christopher Chidley, Mete Emir Ozgurses, Huiping Zhao, Yumi Kim, Svetlana E Semina, Philippa Burns, Vipin Rawat, Lina Lietuvninkas, Ryan Sheldon, Issam Ben-Sahra, Jonna Frasor, Peter K Sorger, Gina M DeNicola, Jonathan L Coloff.
      The non-essential amino acid serine is a critical nutrient for cancer cells due to its diverse biosynthetic functions. While some tumors can synthesize serine de novo, others are auxotrophic and therefore reliant on serine uptake. Importantly, despite several transporters being known to be capable of transporting serine, the transporters that mediate serine uptake in cancer cells are not known. Here, we characterize the amino acid transporter ASCT2 (SLC1A5) as a major contributor to serine uptake in cancer cells. ASCT2 is well known as a glutamine transporter in cancer, and our work demonstrates that serine and glutamine compete for uptake through ASCT2. We further show that ASCT2-mediated serine uptake is essential for purine nucleotide biosynthesis and that estrogen receptor α (ERα) promotes serine uptake by directly activating SLC1A5 transcription. Collectively, our work defines an additional important role for ASCT2 as a serine transporter in cancer and evaluates ASCT2 as a potential therapeutic target.
    Keywords:  ASCT2; CP: Cancer; ERα; SLC1A5; amino acid uptake; breast cancer; cancer metabolism; diet; purine biosynthesis; serine starvation; serine transporter
    DOI:  https://doi.org/10.1016/j.celrep.2024.114552
  4. Nucleic Acids Res. 2024 Aug 01. pii: gkae662. [Epub ahead of print]
    LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.
    Diana Rubalcava-Gracia, Kristina Bubb, Fredrik Levander, Stephen P Burr, Amelie V August, Patrick F Chinnery, Camilla Koolmeister, Nils-Göran Larsson.
      In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.
    DOI:  https://doi.org/10.1093/nar/gkae662
  5. Cancer Res. 2024 Jul 02. 84(13): 2046-2048
    The Warburg Effect Revisited through Blood and Electron Flow.
    Yahui Wang, Chi V Dang.
      The Warburg effect describes the propensity of many cancers to consume glucose avidly and convert it to lactate in the presence of oxygen. The benefit of the Warburg effect on cancer cells remains enigmatic, particularly because extracellular disposal of incompletely oxidized lactate is wasteful. However, lactate is not discarded from the body, but rather recycled as pyruvate for metabolism through the tricarboxylic acid cycle in oxidative tissues and cells. Hence, tissue and interorgan metabolism play important roles in tumor metabolism. The production of tumor lactate to be recycled elsewhere parallels the Cori cycle, in which lactate produced by muscle activity is shuttled to the liver, where it is converted to pyruvate and subsequently stored as glucose moieties in glycogen. This perspective will consider this organismal contextwhile discussing how glucose is used in tumors. We highlight several key articles published decades ago in Cancer Research that are foundational to our current understanding of cancer biology and metabolism.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-0474
  6. Nat Commun. 2024 Jul 31. 15(1): 6468
    Cilia-enriched oxysterol 7β,27-DHC is required for polycystin ion channel activation.
    Kodaji Ha, Nadine Mundt-Machado, Paola Bisignano, Aide Pinedo, David R Raleigh, Gabriel Loeb, Jeremy F Reiter, Erhu Cao, Markus Delling.
      Polycystin-1 (PC-1) and PC-2 form a heteromeric ion channel complex that is abundantly expressed in primary cilia of renal epithelial cells. This complex functions as a non-selective cation channel, and mutations within the polycystin complex cause autosomal dominant polycystic kidney disease (ADPKD). The spatial and temporal regulation of the polycystin complex within the ciliary membrane remains poorly understood. Using both whole-cell and ciliary patch-clamp recordings, we identify a cilia-enriched oxysterol, 7β,27-dihydroxycholesterol (DHC), that serves as a necessary activator of the polycystin complex. We further identify an oxysterol-binding pocket within PC-2 and showed that mutations within this binding pocket disrupt 7β,27-DHC-dependent polycystin activation. Pharmacologic and genetic inhibition of oxysterol synthesis reduces channel activity in primary cilia. In summary, our findings reveal a regulator of the polycystin complex. This oxysterol-binding pocket in PC-2 may provide a specific target for potential ADPKD therapeutics.
    DOI:  https://doi.org/10.1038/s41467-024-50318-9
  7. bioRxiv. 2024 Jul 24. pii: 2024.07.23.604788. [Epub ahead of print]
    SLC45A4 encodes a mitochondrial putrescine transporter that promotes GABA de novo synthesis.
    Cecilia Colson, Yujue Wang, James Atherton, Xiaoyang Su.
      Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We developed a metabolomic-transcriptomic association analysis, and we found that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrated that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the mitochondrial membrane to facilitate GABA production. Taken together, our results revealed a new biochemical mechanism where SLC45A4 controls GABA production.
    DOI:  https://doi.org/10.1101/2024.07.23.604788
  8. Res Sq. 2024 Jul 16. pii: rs.3.rs-4651047. [Epub ahead of print]
    BMAL1-HIF2α heterodimers contribute to ccRCC.
    Katja A Lamia, Rebecca Mello, Diego Gomez Ceballos, Colby Sandate, Daniel Agudelo, Celine Jouffe, Nina Uhlenhaut, Nicolas Thoma, M Celeste Simon.
      Circadian disruption enhances cancer risk, and many tumors exhibit disordered circadian gene expression. We show rhythmic gene expression is unexpectedly robust in clear cell renal cell carcinoma (ccRCC). Furthermore, the clock gene BMAL1 is higher in ccRCC than in healthy kidneys, unlike in other tumor types. BMAL1 is closely related to ARNT, and we show that BMAL1-HIF2α regulates a subset of HIF2α target genes in ccRCC cells. Depletion of BMAL1 reprograms HIF2α chromatin association and target gene expression and reduces ccRCC growth in culture and in xenografts. Analysis of pre-existing data reveals higher BMAL1 in patient-derived xenografts that are sensitive to growth suppression by a HIF2α antagonist (PT2399). We show that BMAL1-HIF2α is more sensitive than ARNT-HIF2α to suppression by PT2399, and increasing BMAL1 sensitizes 786O cells to growth inhibition by PT2399. Together, these findings indicate that an alternate HIF2α heterodimer containing the circadian partner BMAL1 contributes to HIF2α activity, growth, and sensitivity to HIF2α antagonist drugs in ccRCC cells.
    DOI:  https://doi.org/10.21203/rs.3.rs-4651047/v1
  9. Cell Rep. 2024 Jul 26. pii: S2211-1247(24)00872-6. [Epub ahead of print]43(8): 114543
    mTORC1 activity oscillates throughout the cell cycle, promoting mitotic entry and differentially influencing autophagy induction.
    Jay N Joshi, Ariel D Lerner, Frank Scallo, Alexandra N Grumet, Paul Matteson, James H Millonig, Alexander J Valvezan.
      Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a master metabolic regulator that is active in nearly all proliferating eukaryotic cells; however, it is unclear whether mTORC1 activity changes throughout the cell cycle. We find that mTORC1 activity oscillates from lowest in mitosis/G1 to highest in S/G2. The interphase oscillation is mediated through the TSC complex but is independent of major known regulatory inputs, including Akt and Mek/Erk signaling. By contrast, suppression of mTORC1 activity in mitosis does not require the TSC complex. mTORC1 has long been known to promote progression through G1. We find that mTORC1 also promotes progression through S and G2 and is important for satisfying the Chk1/Wee1-dependent G2/M checkpoint to allow entry into mitosis. We also find that low mTORC1 activity in G1 sensitizes cells to autophagy induction in response to partial mTORC1 inhibition or reduced nutrient levels. Together, these findings demonstrate that mTORC1 is differentially regulated throughout the cell cycle, with important phase-specific consequences for proliferating cells.
    Keywords:  CDK1; CP: Cell biology; G2/M checkpoint; TSC complex; TSC2; autophagy; cell cycle; mTOR; mTORC1; mitosis
    DOI:  https://doi.org/10.1016/j.celrep.2024.114543
  10. Cell Metab. 2024 Jul 24. pii: S1550-4131(24)00273-0. [Epub ahead of print]
    Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle.
    Ariana Vargas-Castillo, Yizhi Sun, Amanda L Smythers, Louisa Grauvogel, Phillip A Dumesic, Margo P Emont, Linus T Tsai, Evan D Rosen, Nathan W Zammit, Sydney M Shaffer, Martha Ordonez, Edward T Chouchani, Steven P Gygi, Tongtong Wang, Anand K Sharma, Miroslav Balaz, Christian Wolfrum, Bruce M Spiegelman.
      Although uncoupling protein 1 (UCP1) is established as a major contributor to adipose thermogenesis, recent data have illustrated an important role for alternative pathways, particularly the futile creatine cycle (FCC). How these pathways co-exist in cells and tissues has not been explored. Beige cell adipogenesis occurs in vivo but has been difficult to model in vitro; here, we describe the development of a murine beige cell line that executes a robust respiratory response, including uncoupled respiration and the FCC. The key FCC enzyme, tissue-nonspecific alkaline phosphatase (TNAP), is localized almost exclusively to mitochondria in these cells. Surprisingly, single-cell cloning from this cell line shows that cells with the highest levels of UCP1 express little TNAP, and cells with the highest expression of TNAP express little UCP1. Immunofluorescence analysis of subcutaneous fat from cold-exposed mice confirms that the highest levels of these critical thermogenic components are expressed in distinct fat cell populations.
    Keywords:  Alpl gene; SV40 large T antigen; TNAP; UCP1; aP2-Prdm16 transgenic mice; functional beige cell line; futile creatine cycle; immortalized beige adipocytes; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2024.07.002
  11. bioRxiv. 2024 Jul 24. pii: 2024.07.24.604914. [Epub ahead of print]
    Epigenetic control of metabolic identity across cell types.
    Maria Pires Pacheco, Déborah Gerard, Riley J Mangan, Alec R Chapman, Dennis Hecker, Manolis Kellis, Marcel H Schulz, Lasse Sinkkonen, Thomas Sauter.
      Constraint-based network modelling is a powerful tool for analysing cellular metabolism at genomic scale. Here, we conducted an integrative analysis of metabolic networks reconstructed from RNA-seq data with paired epigenomic data from the EpiATLAS resource of the International Human Epigenome Consortium (IHEC). Applying a state-of-the-art contextualisation algorithm, we reconstructed metabolic networks across 1,555 samples corresponding to 58 tissues and cell types. Analysis of these networks revealed the distribution of metabolic functionalities across human cell types and provides a compendium of human metabolic activity. This integrative approach allowed us to define, across tissues and cell types, i) reactions that fulfil the basic metabolic processes (core metabolism), and ii) cell type-specific functions (unique metabolism), that shape the metabolic identity of a cell or a tissue. Integration with EpiATLAS-derived cell type-specific gene-level chromatin states and enhancer-gene interactions identified enhancers, transcription factors, and key nodes controlling core and unique metabolism. Transport and first reactions of pathways were enriched for high expression, active chromatin state, and Polycomb-mediated repression in cell types where pathways are inactive, suggesting that key nodes are targets of repression. This integrative analysis forms the basis for identifying regulation points that control metabolic identity in human cells.
    DOI:  https://doi.org/10.1101/2024.07.24.604914
  12. J Cell Biol. 2024 Sep 02. pii: e202407125. [Epub ahead of print]223(9):
    A three-way organelle junction controls PI(4)P metabolism and mitochondrial division.
    York Posor, Volker Haucke.
      Membrane contact sites (MCS) facilitate communication between organelles. Casler et al. (https://doi.org/10.1083/jcb.202308144) show that tripartite MCS between mitochondria, the endoplasmic reticulum (ER), and the plasma membrane (PM) regulate mitochondrial division and the distribution of phosphatidylinositol 4-phosphate [PI(4)P] on the PM.
    DOI:  https://doi.org/10.1083/jcb.202407125
  13. Trends Cell Biol. 2024 Jul 31. pii: S0962-8924(24)00145-4. [Epub ahead of print]
    The ATP-driven extractor ATAD1/Msp1 proof-reads protein translocation into mitochondria.
    Maria Bohnert, Christos Gatsogiannis, Johannes M Herrmann.
      The accumulation of translocation intermediates in the mitochondrial import machinery threatens cellular fitness and is associated with cancer and neurodegeneration. A recent study by Weidberg and colleagues identifies ATAD1 as an ATP-driven extraction machine on the mitochondrial surface that pulls precursors into the cytosol to prevent clogging of mitochondrial import pores.
    Keywords:  AAA protein; cancer; integrated stress response (ISR); mitochondria; protein import; quality control
    DOI:  https://doi.org/10.1016/j.tcb.2024.07.007
  14. Cell Metab. 2024 Jul 26. pii: S1550-4131(24)00276-6. [Epub ahead of print]
    Single-nucleus transcriptomics identifies separate classes of UCP1 and futile cycle adipocytes.
    Tongtong Wang, Anand Kumar Sharma, Chunyan Wu, Claudia Irene Maushart, Adhideb Ghosh, Wu Yang, Patrik Stefanicka, Zuzana Kovanicova, Jozef Ukropec, Jing Zhang, Myrtha Arnold, Manuel Klug, Katrien De Bock, Ulrich Schneider, Cristina Popescu, Bo Zheng, Lianggong Ding, Fen Long, Revati Sumukh Dewal, Caroline Moser, Wenfei Sun, Hua Dong, Martin Takes, Dominique Suelberg, Alexander Mameghani, Antonio Nocito, Christoph Johannes Zech, Alin Chirindel, Damian Wild, Irene A Burger, Michael R Schön, Arne Dietrich, Min Gao, Markus Heine, Yizhi Sun, Ariana Vargas-Castillo, Susanna Søberg, Camilla Scheele, Miroslav Balaz, Matthias Blüher, Matthias Johannes Betz, Bruce M Spiegelman, Christian Wolfrum.
      Adipose tissue can recruit catabolic adipocytes that utilize chemical energy to dissipate heat. This process occurs either by uncoupled respiration through uncoupling protein 1 (UCP1) or by utilizing ATP-dependent futile cycles (FCs). However, it remains unclear how these pathways coexist since both processes rely on the mitochondrial membrane potential. Utilizing single-nucleus RNA sequencing to deconvolute the heterogeneity of subcutaneous adipose tissue in mice and humans, we identify at least 2 distinct subpopulations of beige adipocytes: FC-adipocytes and UCP1-beige adipocytes. Importantly, we demonstrate that the FC-adipocyte subpopulation is highly metabolically active and utilizes FCs to dissipate energy, thus contributing to thermogenesis independent of Ucp1. Furthermore, FC-adipocytes are important drivers of systemic energy homeostasis and linked to glucose metabolism and obesity resistance in humans. Taken together, our findings identify a noncanonical thermogenic adipocyte subpopulation, which could be an important regulator of energy homeostasis in mammals.
    Keywords:  energy homeostasis; futile cycling; human metabolism; single-nucleus RNA sequencing; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2024.07.005
  15. ACS Chem Biol. 2024 Jul 28.
    Organelle-Targeted Laurdans Measure Heterogeneity in Subcellular Membranes and Their Responses to Saturated Lipid Stress.
    Adrian M Wong, Itay Budin.
      Organelles feature characteristic lipid compositions that lead to differences in membrane properties. In cells, membrane ordering and fluidity are commonly measured using the solvatochromic dye Laurdan, whose fluorescence is sensitive to lipid packing. As a general lipophilic dye, Laurdan stains all hydrophobic environments in cells; therefore, it is challenging to characterize membrane properties in specific organelles or assess their responses to pharmacological treatments in intact cells. Here, we describe the synthesis and application of Laurdan-derived probes that read out the membrane packing of individual cellular organelles. The set of organelle-targeted Laurdans (OTL) localizes to the ER, mitochondria, lysosomes, and Golgi compartments with high specificity while retaining the spectral resolution needed to detect biological changes in membrane ordering. We show that ratiometric imaging with OTLs can resolve membrane heterogeneity within organelles as well as changes in lipid packing resulting from inhibition of trafficking or bioenergetic processes. We apply these probes to characterize organelle-specific responses to saturated lipid stress. While the ER and lysosomal membrane fluidity is sensitive to exogenous saturated fatty acids, that of mitochondrial membranes is protected. We then use differences in ER membrane fluidity to sort populations of cells based on their fatty acid diet, highlighting the ability of organelle-localized solvatochromic probes to distinguish between cells based on their metabolic state. These results expand the repertoire of targeted membrane probes and demonstrate their application in interrogating lipid dysregulation.
    DOI:  https://doi.org/10.1021/acschembio.4c00249
  16. J Lipid Res. 2024 Jul 31. pii: S0022-2275(24)00116-0. [Epub ahead of print] 100611
    Etomoxir-carnitine, a novel pharmaco-metabolite of etomoxir, inhibits phospholipases A2 and mitochondrial respiration.
    Sung Ho Moon, Xinping Liu, Christopher M Jenkins, Beverly Gibson Dilthey, Gary J Patti, Richard W Gross.
      Mitochondrial fatty acid oxidation serves as an essential process for cellular survival, differentiation, proliferation, and energy metabolism. Numerous studies have utilized etomoxir (ETO) for the irreversible inhibition of carnitine palmitoylcarnitine transferase 1 (CPT1) which catalyzes the rate-limiting step for mitochondrial long-chain fatty acid β-oxidation to examine the bioenergetic roles of mitochondrial fatty acid metabolism in many tissues in multiple diverse disease states. Herein, we demonstrate that intact mitochondria robustly metabolize etomoxir to etomoxir-carnitine (ETO-carnitine) prior to nearly complete etomoxir-mediated inhibition of CPT1. The novel pharmaco-metabolite, ETO-carnitine, was conclusively identified by accurate mass, fragmentation patterns, and isotopic fine structure. On the basis of these data, ETO-carnitine was successfully differentiated from isobaric structures (e.g., 3-hydroxy-C18:0 carnitine and 3-hydroxy-C18:1 carnitine). Mechanistically, generation of ETO-carnitine from mitochondria required exogenous Mg2+, ATP or ADP, CoASH, and L-carnitine indicating that thioesterification by long-chain acyl-CoA synthetase to form ETO-CoA precedes its conversion to ETO-carnitine by CPT1. CPT1-dependent generation of ETO-carnitine was substantiated by an orthogonal approach using ST1326 (a CPT1 inhibitor) which effectively inhibits mitochondrial ETO-carnitine production. Surprisingly, purified ETO-carnitine potently inhibited calcium-independent PLA2γ and PLA2β as well as mitochondrial respiration independent of CPT1. Robust production and release of ETO-carnitine from HepG2 cells incubated in the presence of ETO was also demonstrated. Collectively, this study identifies the chemical mechanism for the biosynthesis of a novel pharmaco-metabolite of etomoxir, ETO-carnitine, that is generated by CPT1 in mitochondria and likely impacts multiple downstream (non-CPT1 related) enzymes and processes in multiple subcellular compartments.
    Keywords:  Lipidomics; Lipids/Chemistry; Lipolysis and fatty acid metabolism; carnitine palmitoyltransferase (CPT); etomoxir; etomoxir-carnitine; mitochondria; off-target effects; pharmaco-metabolite; phospholipases A(2)
    DOI:  https://doi.org/10.1016/j.jlr.2024.100611
  17. Mol Biol Cell. 2024 Jul 31. mbcE24030122
    Calcineurin promotes adaptation to chronic stress through two distinct mechanisms.
    Mackenzie J Flynn, Nicholas W Harper, Rui Li, Lihua Julie Zhu, Michael J Lee, Jennifer A Benanti.
      Adaptation to environmental stress requires coordination between stress-defense programs and cell cycle progression. The immediate response to many stressors has been well characterized, but how cells survive in challenging environments long-term is unknown. Here, we investigate the role of the stress-activated phosphatase calcineurin (CN) in adaptation to chronic CaCl2 stress in Saccharomyces cerevisiae. We find that prolonged exposure to CaCl2 impairs mitochondrial function and demonstrate that cells respond to this stressor using two CN-dependent mechanisms - one that requires the downstream transcription factor Crz1 and another that is Crz1-independent. Our data indicate that CN maintains cellular fitness by promoting cell cycle progression and preventing CaCl2-induced cell death. When Crz1 is present, transient CN activation suppresses cell death and promotes adaptation despite high levels of mitochondrial loss. However, in the absence of Crz1, prolonged activation of CN prevents mitochondrial loss and further cell death by upregulating glutathione (GSH) biosynthesis genes thereby mitigating damage from reactive oxygen species. These findings illustrate how cells maintain long-term fitness during chronic stress and suggest that CN promotes adaptation in challenging environments by multiple mechanisms.
    DOI:  https://doi.org/10.1091/mbc.E24-03-0122
  18. Cancer Discov. 2024 Jul 29.
    Iron Chelation Therapy Elicits Innate Immune Control of Metastatic Ovarian Cancer.
    Tito A Sandoval, Camilla Salvagno, Chang-Suk Chae, Deepika Awasthi, Paolo Giovanelli, Matias Marin Falco, Sung-Min Hwang, Eli Teran-Cabanillas, Lasse Suominen, Takahiro Yamazaki, Hui-Hsuan Kuo, Jenna E Moyer, M Laura Martin, Jyothi Manohar, Kihwan Kim, Maria A Sierra, Yusibeska Ramos, Chen Tan, Alexander Emmanuelli, Minkyung Song, Diana K Morales, Dmitriy Zamarin, Melissa K Frey, Evelyn Cantillo, Eloise Chapman-Davis, Kevin Holcomb, Christopher E Mason, Lorenzo Galluzzi, Zhen Ni Zhou, Anna Vaharautio, Suzanne M Cloonan, Juan R Cubillos-Ruiz.
      Iron accumulation in tumors contributes to disease progression and chemoresistance. While targeting this process can influence various hallmarks of cancer, the immunomodulatory effects of iron chelation in the tumor microenvironment are unknown. Here, we report that treatment with deferiprone, an FDA-approved iron chelator, unleashes innate immune responses that restrain ovarian cancer. Deferiprone reprogrammed ovarian cancer cells towards an immunostimulatory state characterized by production of type I interferon (IFN) and overexpression of molecules that activate natural killer (NK) cells. Mechanistically, these effects were driven by innate sensing of mitochondrial DNA in the cytosol and concomitant activation of nuclear DNA damage responses triggered upon iron chelation. Deferiprone synergized with chemotherapy and prolonged the survival of mice with ovarian cancer by bolstering type I IFN responses that drove NK cell-dependent control of metastatic disease. Hence, iron chelation may represent an alternative immunotherapeutic strategy for malignancies that are refractory to current T cell-centric modalities.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-1451
  19. Redox Biol. 2024 Jul 26. pii: S2213-2317(24)00264-7. [Epub ahead of print]75 103286
    Hypoxia-induced cysteine metabolism reprogramming is crucial for the tumorigenesis of colorectal cancer.
    Zhang Lin, Shiyi Yang, Qianqian Qiu, Gaoping Cui, Yanhua Zhang, Meilian Yao, Xiangyu Li, Chengkun Chen, Jun Gu, Ting Wang, Peng Yin, Longci Sun, Yujun Hao.
      Metabolic reprogramming is a hallmark of human cancer, and cancer-specific metabolism provides opportunities for cancer diagnosis, prognosis, and treatment. However, the underlying mechanisms by which metabolic pathways affect the initiation and progression of colorectal cancer (CRC) remain largely unknown. Here, we demonstrate that cysteine is highly enriched in colorectal tumors compared to adjacent non-tumor tissues, thereby promoting tumorigenesis of CRC. Synchronously importing both cysteine and cystine in colorectal cancer cells is necessary to maintain intracellular cysteine levels. Hypoxia-induced reactive oxygen species (ROS) and ER stress regulate the co-upregulation of genes encoding cystine transporters (SLC7A11, SLC3A2) and genes encoding cysteine transporters (SLC1A4, SLC1A5) through the transcription factor ATF4. Furthermore, the metabolic flux from cysteine to reduced glutathione (GSH), which is critical to support CRC growth, is increased due to overexpression of glutathione synthetase GSS in CRC. Depletion of cystine/cysteine by recombinant cyst(e)inase effectively inhibits the growth of colorectal tumors by inducing autophagy in colorectal cancer cells through mTOR-ULK signaling axis. This study demonstrates the underlying mechanisms of cysteine metabolism in tumorigenesis of CRC, and evaluates the potential of cysteine metabolism as a biomarker or a therapeutic target for CRC.
    Keywords:  ATF4; Colorectal cancer; Cysteine/cystine; Hypoxia; ROS homeostasis; Transporter genes
    DOI:  https://doi.org/10.1016/j.redox.2024.103286
  20. bioRxiv. 2024 Jul 20. pii: 2024.07.19.604361. [Epub ahead of print]
    Lactate-carried Mitochondrial Energy Overflow.
    Daniela Rauseo, Yasna Contreras-Baeza, Hugo Faurand, Nataly Cárcamo, Raibel Suárez, Alexandra von Faber-Castell, Franco Silva, Valentina Mora-González, Matthias T Wyss, Felipe Baeza-Lehnert, Iván Ruminot, Carlos Alvarez-Navarro, Alejandro San Martín, Bruno Weber, Pamela Y Sandoval, L Felipe Barros.
      We addressed the question of mitochondrial lactate metabolism using genetically-encoded sensors. The organelle was found to contain a dynamic lactate pool that leads to dose- and time-dependent protein lactylation. In neurons, mitochondrial lactate reported blood lactate levels with high fidelity. The exchange of lactate across the inner mitochondrial membrane was found to be mediated by a high affinity H+-coupled transport system involving the mitochondrial pyruvate carrier MPC. Assessment of electron transport chain activity and determination of lactate flux showed that mitochondria are tonic lactate producers, a phenomenon driven by energization and stimulated by hypoxia. We conclude that an overflow mechanism caps the redox level of mitochondria, while saving energy in the form of lactate.
    DOI:  https://doi.org/10.1101/2024.07.19.604361
  21. bioRxiv. 2024 Jul 19. pii: 2024.07.18.604121. [Epub ahead of print]
    Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA.
    Brett T Wisniewski, Laura L Lackner.
      Mitochondria exist as dynamic tubular networks and the morphology of these networks impacts organelle function and cell health. Mitochondrial morphology is maintained in part by the opposing activities of mitochondrial fission and fusion. Mitochondrial fission and fusion are also required to maintain mitochondrial DNA (mtDNA) integrity. In Saccharomyces cerevisiae , the simultaneous inhibition of mitochondrial fission and fusion results in increased mtDNA mutation and the consequent loss of respiratory competence. The mechanism by which fission and fusion maintain mtDNA integrity is not fully understood. Previous work demonstrates that mtDNA is spatially linked to mitochondrial fission sites. Here, we extend this finding using live-cell imaging to localize mtDNA to mitochondrial fusion sites. While mtDNA is present at sites of mitochondrial fission and fusion, mitochondrial fission and fusion rates are not altered in cells lacking mtDNA. Using alleles that alter mitochondrial fission and fusion rates, we find that mtDNA integrity can be maintained in cells with significantly reduced, but balanced, rates of fission and fusion. In addition, we find that increasing mtDNA copy number reduces the loss of respiratory competence in double mitochondrial fission-fusion mutants. Our findings add novel insights into the relationship between mitochondrial dynamics and mtDNA integrity.
    DOI:  https://doi.org/10.1101/2024.07.18.604121
  22. Cell Death Discov. 2024 Jul 29. 10(1): 342
    Deubiquitinase USP9x regulates the proline biosynthesis pathway in non-small cell lung cancer.
    Tina Becirovic, Boxi Zhang, Cecilia Lindskog, Erik Norberg, Helin Vakifahmetoglu-Norberg, Vitaliy O Kaminskyy, Elena Kochetkova.
      Metabolic rewiring has been recognized as a hallmark of malignant transformation, supplying the biosynthetic and energetic demands for rapid cancer cell proliferation and tumor progression. A comprehensive understanding of the regulatory mechanisms governing these metabolic processes is still limited. Here, we identify the deubiquitinase ubiquitin-specific peptidase 9 X-linked (USP9x) as a positive regulator of the proline biosynthesis pathway in non-small cell lung cancer (NSCLC). Our findings demonstrate USP9x directly stabilizes pyrroline-5-carboxylate reductase 3 (PYCR3), a key enzyme in the proline cycle. Disruption of proline biosynthesis by either USP9x or PYCR3 knockdown influences the proline cycle leading to a decreased activity of the connected pentose phosphate pathway and mitochondrial respiration. We show that USP9x is elevated in human cancer tissues and its suppression impairs NSCLC growth in vitro and in vivo. Overall, our study uncovers a novel function of USP9x as a regulator of the proline biosynthesis pathway, which impacts lung cancer growth and progression, and implicates a new potential therapeutic avenue.
    DOI:  https://doi.org/10.1038/s41420-024-02111-2
  23. Autoimmun Rev. 2024 Jul 29. pii: S1568-9972(24)00074-0. [Epub ahead of print] 103583
    Remodeling of T-cell mitochondrial metabolism to treat autoimmune diseases.
    Liyan Lin, Ruyu Ren, Qiao Xiong, Chunfu Zheng, Bin Yang, Huiqing Wang.
      T cells are key drivers of the pathogenesis of autoimmune diseases by producing cytokines, stimulating the generation of autoantibodies, and mediating tissue and cell damage. Distinct mitochondrial metabolic pathways govern the direction of T-cell differentiation and function and rely on specific nutrients and metabolic enzymes. Metabolic substrate uptake and mitochondrial metabolism form the foundational elements for T-cell activation, proliferation, differentiation, and effector function, contributing to the dynamic interplay between immunological signals and mitochondrial metabolism in coordinating adaptive immunity. Perturbations in substrate availability and enzyme activity may impair T-cell immunosuppressive function, fostering autoreactive responses and disrupting immune homeostasis, ultimately contributing to autoimmune disease pathogenesis. A growing body of studies has explored how metabolic processes regulate the function of diverse T-cell subsets in autoimmune diseases such as systemic lupus erythematosus (SLE), multiple sclerosis (MS), autoimmune hepatitis (AIH), inflammatory bowel disease (IBD), and psoriasis. This review describes the coordination of T-cell biology by mitochondrial metabolism, including the electron transport chain (ETC), oxidative phosphorylation, amino acid metabolism, fatty acid metabolism, and one‑carbon metabolism. This study elucidated the intricate crosstalk between mitochondrial metabolic programs, signal transduction pathways, and transcription factors. This review summarizes potential therapeutic targets for T-cell mitochondrial metabolism and signaling in autoimmune diseases, providing insights for future studies.
    Keywords:  Autoimmune diseases; Fatty acid metabolism; Mitochondrial metabolism; OXPHOS; Regulatory T cells; T helper cells; Treatment
    DOI:  https://doi.org/10.1016/j.autrev.2024.103583
  24. bioRxiv. 2024 Jul 23. pii: 2024.07.22.604660. [Epub ahead of print]
    Impaired fatty acid import or catabolism in macrophages restricts intracellular growth of Mycobacterium tuberculosis.
    Nelson V Simwela, Eleni Jaecklein, Christopher M Sassetti, David G Russell.
      Mycobacterium tuberculosis ( Mtb ) infection of macrophages reprograms cellular metabolism to promote lipid retention. While it is clearly known that intracellular Mtb utilize host derived fatty acids and cholesterol to fuel the majority of its metabolic demands, the role of macrophage lipid catabolism on the bacteria's ability to access the intracellular lipid pool remains undefined. We utilized a CRISPR genetic knockdown approach to assess the impact of sequential steps in fatty acid metabolism on the growth of intracellular Mtb . Our analyzes demonstrate that knockdown of lipid import, sequestration and metabolism genes collectively impair the intracellular growth of Mtb in macrophages. We further demonstrate that modulating fatty acid homeostasis in macrophages impairs Mtb replication through diverse pathways like enhancing production of pro-inflammatory cytokines, autophagy, restricting the bacteria access to nutrients and increasing oxidative stress. We also show that impaired macrophage lipid droplet biogenesis is restrictive to intracellular Mtb replication, but increased induction of the same by blockade of downstream fatty acid oxidation fails to rescue Mtb growth. Our work expands our understanding of how host fatty acid homeostasis impacts Mtb growth in the macrophage.Significance: Mycobacterium tuberculosis ( Mtb ) primarily infects macrophages in the lungs. In infected macrophages, Mtb uses host lipids as key carbon sources to maintain infection and survive. In this work, we used a CRISPR-Cas9 gene knockout system in murine macrophages to examine the role of host fatty acid metabolism on the intracellular growth of Mtb . Our work shows that macrophages which cannot either import, store or catabolize fatty acids restrict Mtb growth by both common and divergent anti-microbial mechanisms, including increased glycolysis, increased production of reactive oxygen species, production of pro-inflammatory cytokines, enhanced autophagy and nutrient limitation. Our findings demonstrate that manipulating lipid metabolism in macrophages controls Mtb through multiple other mechanisms, beyond limiting the bacteria's access to nutrients.
    DOI:  https://doi.org/10.1101/2024.07.22.604660
  25. EMBO Rep. 2024 Jul 29.
    IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
    Marco Flores-Mendez, Laura Ohl, Thomas Roule, Yijing Zhou, Jesus A Tintos-Hernández, Kelsey Walsh, Xilma R Ortiz-González, Naiara Akizu.
      Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use mouse models of a childhood neurodegenerative disorder caused by AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that mouse models of AMPD2 deficiency exhibit predominant degeneration of the hippocampal dentate gyrus, despite a general reduction of brain GTP levels. Neurodegeneration-resistant regions accumulate micron-sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis, while these filaments are barely detectable in the hippocampal dentate gyrus. Furthermore, we show that IMPDH2 filament disassembly reduces GTP levels and impairs growth of neural progenitor cells derived from individuals with human AMPD2 deficiency. Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation, opening the possibility of exploring the induction of IMPDH2 assembly as a therapy for neurodegeneration.
    Keywords:  Ampd2; Impdh2 Filaments; Metabolons; Pontocerebellar Hypoplasia; Purine Nucleotides
    DOI:  https://doi.org/10.1038/s44319-024-00218-2
  26. Nat Cell Biol. 2024 Jul 30.
    mTORC2-driven chromatin cGAS mediates chemoresistance through epigenetic reprogramming in colorectal cancer.
    Guoqing Lv, Qian Wang, Lin Lin, Qiao Ye, Xi Li, Qian Zhou, Xiangzhen Kong, Hongxia Deng, Fuping You, Hebing Chen, Song Wu, Lin Yuan.
      Cyclic GMP-AMP synthase (cGAS), a cytosolic DNA sensor that initiates a STING-dependent innate immune response, binds tightly to chromatin, where its catalytic activity is inhibited; however, mechanisms underlying cGAS recruitment to chromatin and functions of chromatin-bound cGAS (ccGAS) remain unclear. Here we show that mTORC2-mediated phosphorylation of human cGAS serine 37 promotes its chromatin localization in colorectal cancer cells, regulating cell growth and drug resistance independently of STING. We discovered that ccGAS recruits the SWI/SNF complex at specific chromatin regions, modifying expression of genes linked to glutaminolysis and DNA replication. Although ccGAS depletion inhibited cell growth, it induced chemoresistance to fluorouracil treatment in vitro and in vivo. Moreover, blocking kidney-type glutaminase, a downstream ccGAS target, overcame chemoresistance caused by ccGAS loss. Thus, ccGAS coordinates colorectal cancer plasticity and acquired chemoresistance through epigenetic patterning. Targeting both mTORC2-ccGAS and glutaminase provides a promising strategy to eliminate quiescent resistant cancer cells.
    DOI:  https://doi.org/10.1038/s41556-024-01473-0
  27. Mol Cell. 2024 Jul 24. pii: S1097-2765(24)00579-3. [Epub ahead of print]
    The V-ATPase/ATG16L1 axis is controlled by the V1H subunit.
    Lewis Timimi, Antoni G Wrobel, George N Chiduza, Sarah L Maslen, Antonio Torres-Méndez, Beatriz Montaner, Colin Davis, Taylor Minckley, Katriona L Hole, Andrea Serio, Michael J Devine, J Mark Skehel, John L Rubinstein, Anne Schreiber, Rupert Beale.
      Defects in organellar acidification indicate compromised or infected compartments. Recruitment of the autophagy-related ATG16L1 complex to pathologically neutralized organelles targets ubiquitin-like ATG8 molecules to perturbed membranes. How this process is coupled to proton gradient disruption is unclear. Here, we reveal that the V1H subunit of the vacuolar ATPase (V-ATPase) proton pump binds directly to ATG16L1. The V1H/ATG16L1 interaction only occurs within fully assembled V-ATPases, allowing ATG16L1 recruitment to be coupled to increased V-ATPase assembly following organelle neutralization. Cells lacking V1H fail to target ATG8s during influenza infection or after activation of the immune receptor stimulator of interferon genes (STING). We identify a loop within V1H that mediates ATG16L1 binding. A neuronal V1H isoform lacks this loop and is associated with attenuated ATG8 targeting in response to ionophores in primary murine and human iPSC-derived neurons. Thus, V1H controls ATG16L1 recruitment following proton gradient dissipation, suggesting that the V-ATPase acts as a cell-intrinsic damage sensor.
    Keywords:  ATG16L1; ATP6V1H; CASM; STING; V-ATPase; VAIL; autophagy; influenza; non-canonical autophagy; vacuolar ATPase
    DOI:  https://doi.org/10.1016/j.molcel.2024.07.003
  28. Mol Cancer. 2024 Aug 02. 23(1): 154
    Cancer, metastasis, and the epigenome.
    Saurav Kiri, Tyrone Ryba.
      Cancer is the second leading cause of death worldwide and disease burden is expected to increase globally throughout the next several decades, with the majority of cancer-related deaths occurring in metastatic disease. Cancers exhibit known hallmarks that endow them with increased survival and proliferative capacities, frequently as a result of de-stabilizing mutations. However, the genomic features that resolve metastatic clones from primary tumors are not yet well-characterized, as no mutational landscape has been identified as predictive of metastasis. Further, many cancers exhibit no known mutation signature. This suggests a larger role for non-mutational genome re-organization in promoting cancer evolution and dissemination. In this review, we highlight current critical needs for understanding cell state transitions and clonal selection advantages for metastatic cancer cells. We examine links between epigenetic states, genome structure, and misregulation of tumor suppressors and oncogenes, and discuss how recent technologies for understanding domain-scale regulation have been leveraged for a more complete picture of oncogenic and metastatic potential.
    Keywords:  Chromatin state; EMT; Epigenetic; Metastasis; Topology; Transcription
    DOI:  https://doi.org/10.1186/s12943-024-02069-w
  29. bioRxiv. 2024 Jul 26. pii: 2024.07.25.605098. [Epub ahead of print]
    Multi-species genome-wide CRISPR screens identify GPX4 as a conserved suppressor of cold-induced cell death.
    Breanna Lam, Kathrin M Kajderowicz, Heather R Keys, Julian M Roessler, Evgeni M Frenkel, Adina Kirkland, Punam Bisht, Mohamed A El-Brolosy, Rudolf Jaenisch, George W Bell, Jonathan S Weissman, Eric C Griffith, Sinisa Hrvatin.
      Cells must adapt to environmental changes to maintain homeostasis. One of the most striking environmental adaptations is entry into hibernation during which core body temperature can decrease from 37°C to as low at 4°C. How mammalian cells, which evolved to optimally function within a narrow range of temperatures, adapt to this profound decrease in temperature remains poorly understood. In this study, we conducted the first genome-scale CRISPR-Cas9 screen in cells derived from Syrian hamster, a facultative hibernator, as well as human cells to investigate the genetic basis of cold tolerance in a hibernator and a non-hibernator in an unbiased manner. Both screens independently revealed glutathione peroxidase 4 (GPX4), a selenium-containing enzyme, and associated proteins as critical for cold tolerance. We utilized genetic and pharmacological approaches to demonstrate that GPX4 is active in the cold and its catalytic activity is required for cold tolerance. Furthermore, we show that the role of GPX4 as a suppressor of cold-induced cell death extends across hibernating species, including 13-lined ground squirrels and greater horseshoe bats, highlighting the evolutionary conservation of this mechanism of cold tolerance. This study identifies GPX4 as a central modulator of mammalian cold tolerance and advances our understanding of the evolved mechanisms by which cells mitigate cold-associated damage-one of the most common challenges faced by cells and organisms in nature.
    DOI:  https://doi.org/10.1101/2024.07.25.605098
  30. Sci Transl Med. 2024 Jul 31. 16(758): eadg7915
    MGA deletion leads to Richter's transformation by modulating mitochondrial OXPHOS.
    Prajish Iyer, Bo Zhang, Tingting Liu, Meiling Jin, Kevyn Hart, Jibin Zhang, Viola Siegert, Marianne Remke, Xuesong Wang, Lei Yu, Joo Song, Girish Venkataraman, Wing C Chan, Zhenyu Jia, Maike Buchner, Tanya Siddiqi, Steven T Rosen, Alexey Danilov, Lili Wang.
      Richter's transformation (RT) is a progression of chronic lymphocytic leukemia (CLL) to aggressive lymphoma. MGA (Max gene associated), a functional MYC suppressor, is mutated at 3% in CLL and 36% in RT. However, genetic models and molecular mechanisms of MGA deletion that drive CLL to RT remain elusive. We established an RT mouse model by knockout of Mga in the Sf3b1/Mdr CLL model using CRISPR-Cas9 to determine the role of Mga in RT. Murine RT cells exhibited mitochondrial aberrations with elevated oxidative phosphorylation (OXPHOS). Through RNA sequencing and functional characterization, we identified Nme1 (nucleoside diphosphate kinase) as an Mga target, which drives RT by modulating OXPHOS. Given that NME1 is also a known MYC target without targetable compounds, we found that concurrent inhibition of MYC and electron transport chain complex II substantially prolongs the survival of RT mice in vivo. Our results suggest that the Mga-Nme1 axis drives murine CLL-to-RT transition via modulating OXPHOS, highlighting a potential therapeutic avenue for RT.
    DOI:  https://doi.org/10.1126/scitranslmed.adg7915
  31. Trends Immunol. 2024 Jul 26. pii: S1471-4906(24)00159-5. [Epub ahead of print]
    Mutant ARID1A: igniting cancer immunotherapy.
    Bujamin H Vokshi, Eneda Toska.
      Maxwell et al. show that ARID1A loss enhances antitumor immunity by triggering a type I IFN response through the cGAS-STING pathway, thereby promoting T cell infiltration and cytotoxicity. These findings highlight SWI/SNF inhibitors as a strategy to augment immunotherapy efficacy by potentially transforming non-responsive tumors into responders and advancing approaches to cancer treatment.
    DOI:  https://doi.org/10.1016/j.it.2024.07.003
  32. Nat Commun. 2024 Jul 31. 15(1): 6438
    Phosphorylation of PFKL regulates metabolic reprogramming in macrophages following pattern recognition receptor activation.
    Meiyue Wang, Heinrich Flaswinkel, Abhinav Joshi, Matteo Napoli, Sergi Masgrau-Alsina, Julia M Kamper, Antonia Henne, Alexander Heinz, Marleen Berouti, Niklas A Schmacke, Karsten Hiller, Elisabeth Kremmer, Benedikt Wefers, Wolfgang Wurst, Markus Sperandio, Jürgen Ruland, Thomas Fröhlich, Veit Hornung.
      Innate immune responses are linked to key metabolic pathways, yet the proximal signaling events that connect these systems remain poorly understood. Here we show that phosphofructokinase 1, liver type (PFKL), a rate-limiting enzyme of glycolysis, is phosphorylated at Ser775 in macrophages following several innate stimuli. This phosphorylation increases the catalytic activity of PFKL, as shown by biochemical assays and glycolysis monitoring in cells expressing phosphorylation-defective PFKL variants. Using a genetic mouse model in which PFKL Ser775 phosphorylation cannot take place, we observe that upon activation, glycolysis in macrophages is lower than in the same cell population of wild-type animals. Consistent with their higher glycolytic activity, wild-type cells have higher levels of HIF1α and IL-1β than PfklS775A/S775A after LPS treatment. In an in vivo inflammation model, PfklS775A/S775A mice show reduced levels of MCP-1 and IL-1β. Our study thus identifies a molecular link between innate immune activation and early induction of glycolysis.
    DOI:  https://doi.org/10.1038/s41467-024-50104-7
  33. Trends Cell Biol. 2024 Jul 29. pii: S0962-8924(24)00143-0. [Epub ahead of print]
    Copper and iron orchestrate cell-state transitions in cancer and immunity.
    Sebastian Müller, Tatiana Cañeque, Stéphanie Solier, Raphaël Rodriguez.
      Whereas genetic mutations can alter cell properties, nongenetic mechanisms can drive rapid and reversible adaptations to changes in their physical environment, a phenomenon termed 'cell-state transition'. Metals, in particular copper and iron, have been shown to be rate-limiting catalysts of cell-state transitions controlling key chemical reactions in mitochondria and the cell nucleus, which govern metabolic and epigenetic changes underlying the acquisition of distinct cell phenotypes. Acquisition of a distinct cell identity, independently of genetic alterations, is an underlying phenomenon of various biological processes, including development, inflammation, erythropoiesis, aging, and cancer. Here, mechanisms that have been uncovered related to the role of these metals in the regulation of cell plasticity are described, illustrating how copper and iron can be exploited for therapeutic intervention.
    Keywords:  cancer; cell-state transition; copper; epigenetics; inflammation; iron; metabolism
    DOI:  https://doi.org/10.1016/j.tcb.2024.07.005
  34. Ann Clin Transl Neurol. 2024 Aug 02.
    Mitochondrial DNA disorders in neuromuscular diseases in diverse populations.
    ICGNMD Consortium
      Neuromuscular features are common in mitochondrial DNA (mtDNA) disorders. The genetic architecture of mtDNA disorders in diverse populations is poorly understood. We analysed mtDNA variants from whole-exome sequencing data in neuromuscular patients from South Africa, Brazil, India, Turkey and Zambia. In 998 individuals, there were two definite diagnoses, two possible diagnoses and eight secondary findings. Surprisingly, common pathogenic mtDNA variants found in people of European ancestry were very rare. Whole-exome or -genome sequencing from undiagnosed patients with neuromuscular symptoms should be re-analysed for mtDNA variants, but the landscape of pathogenic mtDNA variants differs around the world.
    DOI:  https://doi.org/10.1002/acn3.52141
  35. Cell Death Dis. 2024 Jul 29. 15(7): 540
    DAP3 promotes mitochondrial activity and tumour progression in hepatocellular carcinoma by regulating MT-ND5 expression.
    Siyu Tan, Xiao Zhang, Xiaowei Guo, Guoqiang Pan, Lunjie Yan, Ziniu Ding, Ruizhe Li, Dongxu Wang, Yuchuan Yan, Zhaoru Dong, Tao Li.
      Cancer cells often exhibit fragmented mitochondria and dysregulated mitochondrial dynamics, but the underlying mechanism remains elusive. Here, we found that the mitochondrial protein death-associated protein 3 (DAP3) is localized to mitochondria and promotes the progression of hepatocellular carcinoma (HCC) by regulating mitochondrial function. DAP3 can promote the proliferation, migration, and invasion of HCC cells in vitro and in vivo by increasing mitochondrial respiration, inducing the epithelial-mesenchymal transition (EMT), and slowing cellular senescence. Mechanistically, DAP3 can increase mitochondrial complex I activity in HCC cells by regulating the translation and expression of MT-ND5. The phosphorylation of DAP3 at Ser185 mediated by AKT is the key event mediating the mitochondrial localization and function of DAP3 in HCC cells. In addition, the DAP3 expression in HCC samples is inversely correlated with patient survival. Our results revealed a mechanism by which DAP3 promotes mitochondrial function and HCC progression by regulating MT-ND5 translation and expression, indicating that DAP3 may be a therapeutic target for HCC.
    DOI:  https://doi.org/10.1038/s41419-024-06912-2
  36. Nat Rev Genet. 2024 Jul 29.
    Chromosomal instability as a driver of cancer progression.
    Xuelan Chen, Albert S Agustinus, Jun Li, Melody DiBona, Samuel F Bakhoum.
      Chromosomal instability (CIN) refers to an increased propensity of cells to acquire structural and numerical chromosomal abnormalities during cell division, which contributes to tumour genetic heterogeneity. CIN has long been recognized as a hallmark of cancer, and evidence over the past decade has strongly linked CIN to tumour evolution, metastasis, immune evasion and treatment resistance. Until recently, the mechanisms by which CIN propels cancer progression have remained elusive. Beyond the generation of genomic copy number heterogeneity, recent work has unveiled additional tumour-promoting consequences of abnormal chromosome segregation. These mechanisms include complex chromosomal rearrangements, epigenetic reprogramming and the induction of cancer cell-intrinsic inflammation, emphasizing the multifaceted role of CIN in cancer.
    DOI:  https://doi.org/10.1038/s41576-024-00761-7
  37. Nature. 2024 Jul 31.
    Histone serotonylation regulates ependymoma tumorigenesis.
    Hsiao-Chi Chen, Peihao He, Malcolm McDonald, Michael R Williamson, Srinidhi Varadharajan, Brittney Lozzi, Junsung Woo, Dong-Joo Choi, Debosmita Sardar, Emmet Huang-Hobbs, Hua Sun, Siri M Ippagunta, Antrix Jain, Ganesh Rao, Thomas E Merchant, David W Ellison, Jeffrey L Noebels, Kelsey C Bertrand, Stephen C Mack, Benjamin Deneen.
      Bidirectional communication between tumours and neurons has emerged as a key facet of the tumour microenvironment that drives malignancy1,2. Another hallmark feature of cancer is epigenomic dysregulation, in which alterations in gene expression influence cell states and interactions with the tumour microenvironment3. Ependymoma (EPN) is a paediatric brain tumour that relies on epigenomic remodelling to engender malignancy4,5; however, how these epigenetic mechanisms intersect with extrinsic neuronal signalling during EPN tumour progression is unknown. Here we show that the activity of serotonergic neurons regulates EPN tumorigenesis, and that serotonin itself also serves as an activating modification on histones. We found that inhibiting histone serotonylation blocks EPN tumorigenesis and regulates the expression of a core set of developmental transcription factors. High-throughput, in vivo screening of these transcription factors revealed that ETV5 promotes EPN tumorigenesis and functions by enhancing repressive chromatin states. Neuropeptide Y (NPY) is one of the genes repressed by ETV5, and its overexpression suppresses EPN tumour progression and tumour-associated network hyperactivity through synaptic remodelling. Collectively, this study identifies histone serotonylation as a key driver of EPN tumorigenesis, and also reveals how neuronal signalling, neuro-epigenomics and developmental programs are intertwined to drive malignancy in brain cancer.
    DOI:  https://doi.org/10.1038/s41586-024-07751-z
  38. Cell Rep. 2024 Jul 30. pii: S2211-1247(24)00883-0. [Epub ahead of print]43(8): 114554
    SMYD5 is a regulator of the mild hypothermia response.
    Salvor Rafnsdottir, Kijin Jang, Sara Tholl Halldorsdottir, Meghna Vinod, Arnhildur Tomasdottir, Katrin Möller, Katrin Halldorsdottir, Tinna Reynisdottir, Laufey Halla Atladottir, Kristin Elisabet Allison, Kevin Ostacolo, Jin He, Li Zhang, Frances J Northington, Erna Magnusdottir, Raul Chavez-Valdez, Kimberley Jade Anderson, Hans Tomas Bjornsson.
      The mild hypothermia response (MHR) maintains organismal homeostasis during cold exposure and is thought to be critical for the neuroprotection documented with therapeutic hypothermia. To date, little is known about the transcriptional regulation of the MHR. We utilize a forward CRISPR-Cas9 mutagenesis screen to identify the histone lysine methyltransferase SMYD5 as a regulator of the MHR. SMYD5 represses the key MHR gene SP1 at euthermia. This repression correlates with temperature-dependent levels of histone H3 lysine 26 trimethylation (H3K36me3) at the SP1 locus and globally, indicating that the mammalian MHR is regulated at the level of histone modifications. We have identified 37 additional SMYD5-regulated temperature-dependent genes, suggesting a broader MHR-related role for SMYD5. Our study provides an example of how histone modifications integrate environmental cues into the genetic circuitry of mammalian cells and provides insights that may yield therapeutic avenues for neuroprotection after catastrophic events.
    Keywords:  CP: Metabolism; H3K36me3; SP1; cold stress; epigenetics; genetic environmental interaction; histone machinery; histone methylation; hypoxic brain injury; proteasome; repressor
    DOI:  https://doi.org/10.1016/j.celrep.2024.114554
  39. Elife. 2024 Jul 29. pii: RP96979. [Epub ahead of print]13
    A genome-wide CRISPR/Cas9 screen identifies calreticulin as a selective repressor of ATF6α.
    Joanne Tung, Lei Huang, Ginto George, Heather P Harding, David Ron, Adriana Ordonez.
      Activating transcription factor 6 (ATF6) is one of three endoplasmic reticulum (ER) transmembrane stress sensors that mediate the unfolded protein response (UPR). Despite its crucial role in long-term ER stress adaptation, regulation of ATF6 alpha (α) signalling remains poorly understood, possibly because its activation involves ER-to-Golgi and nuclear trafficking. Here, we generated an ATF6α/Inositol-requiring kinase 1 (IRE1) dual UPR reporter CHO-K1 cell line and performed an unbiased genome-wide CRISPR/Cas9 mutagenesis screen to systematically profile genetic factors that specifically contribute to ATF6α signalling in the presence and absence of ER stress. The screen identified both anticipated and new candidate genes that regulate ATF6α activation. Among these, calreticulin (CRT), a key ER luminal chaperone, selectively repressed ATF6α signalling: Cells lacking CRT constitutively activated a BiP::sfGFP ATF6α-dependent reporter, had higher BiP levels and an increased rate of trafficking and processing of ATF6α. Purified CRT interacted with the luminal domain of ATF6α in vitro and the two proteins co-immunoprecipitated from cell lysates. CRT depletion exposed a negative feedback loop implicating ATF6α in repressing IRE1 activity basally and overexpression of CRT reversed this repression. Our findings indicate that CRT, beyond its known role as a chaperone, also serves as an ER repressor of ATF6α to selectively regulate one arm of the UPR.
    Keywords:  ATF6⍺; CHO-K1 cells; CRT; UPR; calreticulin; cell biology; endoplasmic reticulum; genome-wide CRISPR/Cas9 screen; unfolded protein response
    DOI:  https://doi.org/10.7554/eLife.96979
  40. Cell Rep. 2024 Aug 01. pii: S2211-1247(24)00899-4. [Epub ahead of print]43(8): 114570
    Endogenously produced itaconate negatively regulates innate-driven cytokine production and drives global ubiquitination in human macrophages.
    Luke A Bourner, Linda A Chung, Haiyan Long, Anne F McGettrick, Junpeng Xiao, Kenneth Roth, Jade D Bailey, Marie Strickland, Bo Tan, Jason Cunningham, Barry Lutzke, James McGee, Francella J Otero, David C Gemperline, Lin Zhang, Ying C Wang, Michael J Chalmers, Chiao-Wen Yang, Jesus A Gutierrez, Luke A J O'Neill, Frank C Dorsey.
      A wide variety of electrophilic derivatives of itaconate, the Kreb's cycle-derived metabolite, are immunomodulatory, yet these derivatives have overlapping and sometimes contradictory activities. Therefore, we generated a genetic system to interrogate the immunomodulatory functions of endogenously produced itaconate in human macrophages. Endogenous itaconate is driven by multiple innate signals restraining inflammatory cytokine production. Endogenous itaconate directly targets cysteine 13 in IRAK4 (disrupting IRAK4 autophosphorylation and activation), drives the degradation of nuclear factor κB, and modulates global ubiquitination patterns. As a result, cells unable to make itaconate overproduce inflammatory cytokines such as tumor necrosis factor alpha (TNFα), interleukin-6 (IL-6), and IL-1β in response to these innate activators. In contrast, the production of interferon (IFN)β, downstream of LPS, requires the production of itaconate. These data demonstrate that itaconate is a critical arbiter of inflammatory cytokine production downstream of multiple innate signaling pathways, laying the groundwork for the development of itaconate mimetics for the treatment of autoimmunity.
    Keywords:  ACOD1; CP: Immunology; IRAK4; IRG1; MYC; immunometabolism; itaconate; macrophage
    DOI:  https://doi.org/10.1016/j.celrep.2024.114570
  41. Redox Biol. 2024 Jul 23. pii: S2213-2317(24)00261-1. [Epub ahead of print]75 103283
    Mitochondria to plasma membrane redox signaling is essential for fatty acid β-oxidation-driven insulin secretion.
    Martin Jabůrek, Eduardo Klöppel, Pavla Průchová, Oleksandra Mozheitova, Jan Tauber, Hana Engstová, Petr Ježek.
      We asked whether acute redox signaling from mitochondria exists concomitantly to fatty acid- (FA-) stimulated insulin secretion (FASIS) at low glucose by pancreatic β-cells. We show that FA β-oxidation produces superoxide/H2O2, providing: i) mitochondria-to-plasma-membrane redox signaling, closing KATP-channels synergically with elevated ATP (substituting NADPH-oxidase-4-mediated H2O2-signaling upon glucose-stimulated insulin secretion); ii) activation of redox-sensitive phospholipase iPLA2γ/PNPLA8, cleaving mitochondrial FAs, enabling metabotropic GPR40 receptors to amplify insulin secretion (IS). At fasting glucose, palmitic acid stimulated IS in wt mice; palmitic, stearic, lauric, oleic, linoleic, and hexanoic acids also in perifused pancreatic islets (PIs), with suppressed 1st phases in iPLA2γ/PNPLA8-knockout mice/PIs. Extracellular/cytosolic H2O2-monitoring indicated knockout-independent redox signals, blocked by mitochondrial antioxidant SkQ1, etomoxir, CPT1 silencing, and catalase overexpression, all inhibiting FASIS, keeping ATP-sensitive K+-channels open, and diminishing cytosolic [Ca2+]-oscillations. FASIS in mice was a postprandially delayed physiological event. Redox signals of FA β-oxidation are thus documented, reaching the plasma membrane, essentially co-stimulating IS.
    Keywords:  Fatty acid-stimulated insulin secretion; GPR40; Mitochondrial fatty acids; Pancreatic β-cells; Redox signaling; Redox-activated phospholipase iPLA2γ
    DOI:  https://doi.org/10.1016/j.redox.2024.103283
  42. Cell Rep. 2024 Jul 26. pii: S2211-1247(24)00880-5. [Epub ahead of print]43(8): 114551
    Carcinoma-associated mesenchymal stem cells promote ovarian cancer heterogeneity and metastasis through mitochondrial transfer.
    Leonard Frisbie, Catherine Pressimone, Emma Dyer, Roja Baruwal, Geyon Garcia, Claudette St Croix, Simon Watkins, Michael Calderone, Grace Gorecki, Zaineb Javed, Huda I Atiya, Nadine Hempel, Alexander Pearson, Lan G Coffman.
      Ovarian cancer is characterized by early metastatic spread. This study demonstrates that carcinoma-associated mesenchymal stromal cells (CA-MSCs) enhance metastasis by increasing tumor cell heterogeneity through mitochondrial donation. CA-MSC mitochondrial donation preferentially occurs in ovarian cancer cells with low levels of mitochondria ("mito poor"). CA-MSC mitochondrial donation rescues the phenotype of mito poor cells, restoring their proliferative capacity, resistance to chemotherapy, and cellular respiration. Receipt of CA-MSC-derived mitochondria induces tumor cell transcriptional changes leading to the secretion of ANGPTL3, which enhances the proliferation of tumor cells without CA-MSC mitochondria, thus amplifying the impact of mitochondrial transfer. Donated CA-MSC mitochondrial DNA persisted in recipient tumor cells for at least 14 days. CA-MSC mitochondrial donation occurs in vivo, enhancing tumor cell heterogeneity and decreasing mouse survival. Collectively, this work identifies CA-MSC mitochondrial transfer as a critical mediator of ovarian cancer cell survival, heterogeneity, and metastasis and presents a unique therapeutic target in ovarian cancer.
    Keywords:  CP: Cancer; carcinoma-associated mesenchymal stem cells; metastasis; mitochondrial donation; ovarian cancer; oxidative phosphorylation; tumor heterogenity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2024.114551
  43. Commun Biol. 2024 Aug 02. 7(1): 934
    Development of an epigenetic clock resistant to changes in immune cell composition.
    Alan Tomusiak, Ariel Floro, Ritesh Tiwari, Rebeccah Riley, Hiroyuki Matsui, Nicolas Andrews, Herbert G Kasler, Eric Verdin.
      Epigenetic clocks are age predictors that use machine-learning models trained on DNA CpG methylation values to predict chronological or biological age. Increases in predicted epigenetic age relative to chronological age (epigenetic age acceleration) are connected to aging-associated pathologies, and changes in epigenetic age are linked to canonical aging hallmarks. However, epigenetic clocks rely on training data from bulk tissues whose cellular composition changes with age. Here, we found that human naive CD8+ T cells, which decrease in frequency during aging, exhibit an epigenetic age 15-20 years younger than effector memory CD8+ T cells from the same individual. Importantly, homogenous naive T cells isolated from individuals of different ages show a progressive increase in epigenetic age, indicating that current epigenetic clocks measure two independent variables, aging and immune cell composition. To isolate the age-associated cell intrinsic changes, we created an epigenetic clock, the IntrinClock, that did not change among 10 immune cell types tested. IntrinClock shows a robust predicted epigenetic age increase in a model of replicative senescence in vitro and age reversal during OSKM-mediated reprogramming.
    DOI:  https://doi.org/10.1038/s42003-024-06609-4
  44. Metabolomics. 2024 Jul 27. 20(4): 87
    Stable isotope-resolved metabolomics analyses of metabolic phenotypes reveal variable glutamine metabolism in different patient-derived models of non-small cell lung cancer from a single patient.
    Connor J Kinslow, Michael Bousamra Ll, Yihua Cai, Jun Yan, Pawel K Lorkiewicz, Ahmad Al-Attar, Jinlian Tan, Richard M Higashi, Andrew N Lane, Teresa W-M Fan.
      INTRODUCTION: Stable isotope tracers have been increasingly used in preclinical cancer model systems, including cell culture and mouse xenografts, to probe the altered metabolism of a variety of cancers, such as accelerated glycolysis and glutaminolysis and generation of oncometabolites. Comparatively little has been reported on the fidelity of the different preclinical model systems in recapitulating the aberrant metabolism of tumors.OBJECTIVES: We have been developing several different experimental model systems for systems biochemistry analyses of non-small cell lung cancer (NSCLC1) using patient-derived tissues to evaluate appropriate models for metabolic and phenotypic analyses.
    METHODS: To address the issue of fidelity, we have carried out a detailed Stable Isotope-Resolved Metabolomics study of freshly resected tissue slices, mouse patient derived xenografts (PDXs), and cells derived from a single patient using both 13C6-glucose and 13C5,15N2-glutamine tracers.
    RESULTS: Although we found similar glucose metabolism in the three models, glutamine utilization was markedly higher in the isolated cell culture and in cell culture-derived xenografts compared with the primary cancer tissue or direct tissue xenografts (PDX).
    CONCLUSIONS: This suggests that caution is needed in interpreting cancer biochemistry using patient-derived cancer cells in vitro or in xenografts, even at very early passage, and that direct analysis of patient derived tissue slices provides the optimal model for ex vivo metabolomics. Further research is needed to determine the generality of these observations.
    Keywords:  Cancer metabolism; Non-small cell lung cancer; Patient-derived xenografts; Preclinical models; Primary cell culture; Stable isotope-resolved metabolomics
    DOI:  https://doi.org/10.1007/s11306-024-02126-x
  45. bioRxiv. 2024 Jul 27. pii: 2024.07.26.605401. [Epub ahead of print]
    SGLT2 inhibitors activate pantothenate kinase in the human heart.
    Nicholas Forelli, Deborah Eaton, Jiten Patel, Caitlyn E Bowman, Ryo Kawakami, Ivan A Kuznetsov, Kristina Li, Claire Brady, Kenneth Bedi, Yijun Yang, Kaustubh Koya, Emily Megill, Daniel S Kanter, Louis G Smith, Gregory R Bowman, Nathaniel Snyder, Jonathan Edwards, Kenneth Margulies, Zoltan Arany.
      Inhibitors of sodium glucose cotransporter-2 (SGLT2i) demonstrate strong symptomatic and mortality benefits in the treatment of heart failure but appear to do so independently of SGLT2. The relevant pharmacologic target of SGLT2i remains unclear. We show here that SGLT2i directly activate pantothenate kinase 1 (PANK1), the rate-limiting enzyme that initiates the conversion of pantothenate (vitamin B5) to coenzyme-A (CoA), an obligate co-factor for all major pathways of fuel use in the heart. Using stable-isotope infusion studies, we show that SGLT2i promote pantothenate consumption, activate CoA synthesis, rescue decreased levels of CoA in human failing hearts, and broadly stimulate fuel use in ex vivo perfused human cardiac blocks from patients with heart failure. Furthermore, we show that SGLT2i bind to PANK1 directly at physiological concentrations and promote PANK1 enzymatic activity in assays with purified components. Novel in silico dynamic modeling identified the site of SGLT2i binding on PANK1 and indicated a mechanism of activation involving prevention of allosteric inhibition of PANK1 by acyl-CoA species. Finally, we show that inhibition of PANK1 prevents SGLT2i-mediated increased contractility of isolated adult human cardiomyocytes. In summary, we demonstrate robust and specific off-target activation of PANK1 by SGLT2i, promoting CoA synthesis and efficient fuel use in human hearts, providing a likely explanation for the remarkable clinical benefits of SGLT2i.
    DOI:  https://doi.org/10.1101/2024.07.26.605401
  46. bioRxiv. 2024 Jul 19. pii: 2024.07.17.604013. [Epub ahead of print]
    Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.
    Ya-Ting Chang, Benjamin A Barad, Hamidreza Rahmani, Brian M Zid, Danielle A Grotjahn.
      Most of the mitochondria proteome is nuclear-encoded, synthesized by cytoplasmic ribosomes, and targeted to mitochondria post-translationally. However, a subset of mitochondrial-targeted proteins is imported co-translationally, although the molecular mechanisms governing this process remain unclear. We employ cellular cryo-electron tomography to visualize interactions between cytoplasmic ribosomes and mitochondria in Saccharomyces cerevisiae. We use surface morphometrics tools to identify a subset of ribosomes optimally oriented on mitochondrial membranes for protein import. This allows us to establish the first subtomogram average structure of a cytoplasmic ribosome on the surface of the mitochondria in the native cellular context, which showed three distinct connections with the outer mitochondrial membrane surrounding the peptide exit tunnel. Further, this analysis demonstrated that cytoplasmic ribosomes primed for mitochondrial protein import cluster on the outer mitochondrial membrane at sites of local constrictions of the outer and inner mitochondrial membrane. Overall, our study reveals the architecture and the spatial organization of cytoplasmic ribosomes at the mitochondrial surface, providing a native cellular context to define the mechanisms that mediate efficient mitochondrial co-translational protein import.
    DOI:  https://doi.org/10.1101/2024.07.17.604013
  47. Kidney Int. 2024 Jul 29. pii: S0085-2538(24)00526-X. [Epub ahead of print]
    The membrane transporter SLC25A48 enables transport of choline into human mitochondria.
    Suraj Patil, Oleg Borisov, Nora Scherer, Christophe Wirth, Pascal Schlosser, Matthias Wuttke, Sandra Ehret, Luciana Hannibal, Kai-Uwe Eckardt, Carola Hunte, Björn Neubauer, Anna Köttgen, Michael Köttgen.
      Choline has important physiological functions as a precursor for essential cell components, signaling molecules, phospholipids, and the neurotransmitter acetylcholine. Choline is a water-soluble charged molecule requiring transport proteins to cross biological membranes. Although transporters continue to be identified, membrane transport of choline is incompletely understood and knowledge about choline transport into intracellular organelles such as mitochondria remains limited. Here we show that SLC25A48 imports choline into human mitochondria. Human loss-of-function mutations in SLC25A48 show impaired choline transport into mitochondria and are associated with elevated urine and plasma choline levels. Thus, our studies may have implications for understanding and treating conditions related to choline metabolism.
    Keywords:  Choline transport; SLC25A48; deorphanization; mGWAS; mitochondria
    DOI:  https://doi.org/10.1016/j.kint.2024.06.022
  48. FEBS Open Bio. 2024 Jul 28.
    Daily rhythms in metabolic and locomotor behaviour of prematurely ageing PolgA mice.
    Amit Singh, Dilara Yilmaz, Esther Wehrle, Gisela A Kuhn, Ralph Müller.
      Ageing is an inherent and intricate biological process that takes place in living organisms as time progresses. It involves the decline of multiple physiological functions, leading to body structure and overall performance modifications. The ageing process differs among individuals and is influenced by various factors, including lifestyle, environment and genetic makeup. Metabolic changes and reduced locomotor activity are common hallmarks of ageing. Our study focuses on exploring these phenomena in prematurely ageing PolgA(D257A/D257A) mice (also known as PolgA) aged 41-42 weeks, as they closely mimic human ageing. We assess parameters such as oxygen consumption (VO2), carbon dioxide production (VCO2), respiratory exchange ratio (RER) and locomotor activity using a metabolic cage for 4 days and comparing them with age-matched wild-type littermates (WT). Our findings revealed that VO2, VCO2, RER, locomotor activities, water intake and feeding behaviour show a daily rhythm, aligning with roughly a 24-h cycle. We observed that the RER was significantly increased in PolgA mice compared to WT mice during the night-time of the light-dark cycle, suggesting a shift towards a higher reliance on carbohydrate metabolism due to more food intake during the active phase. Additionally, female PolgA mice displayed a distinct phenotype with reduced walking speed, walking distance, body weight and grip strength in comparison to male PolgA and WT mice, indicating an early sign of ageing. Taken together, our research highlights the impact of sex-specific patterns on ageing traits in PolgA mice aged 41-42 weeks, which may be attributable to human ageing phenotypes. The unique genetic composition and accelerated ageing characteristics of PolgA mice make them invaluable in ageing studies, facilitating the investigation of underlying biological mechanisms and the identification of potential therapeutic targets for age-related diseases.
    Keywords:  PolgA mice; ageing; daily rhythm; locomotor activity; metabolic behaviour; phenomaster
    DOI:  https://doi.org/10.1002/2211-5463.13866
  49. Nature. 2024 Jul 31.
    Gut microbiota carcinogen metabolism causes distal tissue tumours.
    Blanka Roje, Boyao Zhang, Eleonora Mastrorilli, Ana Kovačić, Lana Sušak, Ivica Ljubenkov, Elena Ćosić, Katarina Vilović, Antonio Meštrović, Emilija Lozo Vukovac, Viljemka Bučević-Popović, Željko Puljiz, Ivana Karaman, Janoš Terzić, Michael Zimmermann.
      Exposure to environmental pollutants and human microbiome composition are important predisposition factors for tumour development1,2. Similar to drug molecules, pollutants are typically metabolized in the body, which can change their carcinogenic potential and affect tissue distribution through altered toxicokinetics3. Although recent studies demonstrated that human-associated microorganisms can chemically convert a wide range of xenobiotics and influence the profile and tissue exposure of resulting metabolites4,5, the effect of microbial biotransformation on chemical-induced tumour development remains unclear. Here we show that the depletion of the gut microbiota affects the toxicokinetics of nitrosamines, which markedly reduces the development and severity of nitrosamine-induced urinary bladder cancer in mice6,7. We causally linked this carcinogen biotransformation to specific gut bacterial isolates in vitro and in vivo using individualized bacterial culture collections and gnotobiotic mouse models, respectively. We tested gut communities from different human donors to demonstrate that microbial carcinogen metabolism varies between individuals and we showed that this metabolic activity applies to structurally related nitrosamine carcinogens. Altogether, these results indicate that gut microbiota carcinogen metabolism may be a contributing factor for chemical-induced carcinogenesis, which could open avenues to target the microbiome for improved predisposition risk assessment and prevention of cancer.
    DOI:  https://doi.org/10.1038/s41586-024-07754-w
  50. Dev Cell. 2024 Jul 30. pii: S1534-5807(24)00441-6. [Epub ahead of print]
    Sestrin2 drives ER-phagy in response to protein misfolding.
    Chiara De Leonibus, Marianna Maddaluno, Rosa Ferriero, Roberta Besio, Laura Cinque, Pei Jin Lim, Alessandro Palma, Rossella De Cegli, Salvatore Gagliotta, Sandro Montefusco, Maria Iavazzo, Marianne Rohrbach, Cecilia Giunta, Elena Polishchuk, Diego Louis Medina, Diego Di Bernardo, Antonella Forlino, Pasquale Piccolo, Carmine Settembre.
      Protein biogenesis within the endoplasmic reticulum (ER) is crucial for organismal function. Errors during protein folding necessitate the removal of faulty products. ER-associated protein degradation and ER-phagy target misfolded proteins for proteasomal and lysosomal degradation. The mechanisms initiating ER-phagy in response to ER proteostasis defects are not well understood. By studying mouse primary cells and patient samples as a model of ER storage disorders (ERSDs), we show that accumulation of faulty products within the ER triggers a response involving SESTRIN2, a nutrient sensor controlling mTORC1 signaling. SESTRIN2 induction by XBP1 inhibits mTORC1's phosphorylation of TFEB/TFE3, allowing these transcription factors to enter the nucleus and upregulate the ER-phagy receptor FAM134B along with lysosomal genes. This response promotes ER-phagy of misfolded proteins via FAM134B-Calnexin complex. Pharmacological induction of FAM134B improves clearance of misfolded proteins in ERSDs. Our study identifies the interplay between nutrient signaling and ER quality control, suggesting therapeutic strategies for ERSDs.
    Keywords:  ER storage disorders; ER-phagy; FAM134B; TFEB; alpha(1)-antitrypsin Z (alpha(1)-ATZ); autophagy; collagen; endoplasmic reticulum; mTORC1; quality control
    DOI:  https://doi.org/10.1016/j.devcel.2024.07.004
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