bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2024–07–07
sixty papers selected by
Christian Frezza, Universität zu Köln
  1. Bridging lipid metabolism and mitochondrial genome maintenance.
  2. ATP-dependent citrate lyase Drives Left Ventricular Dysfunction by Metabolic Remodeling of the Heart.
  3. From whence it came: Mitochondrial mRNA leaves, a protein returns.
  4. Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer.
  5. Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study.
  6. TRIM2 promotes metabolic adaptation to glutamine deprivation via enhancement of CPT1A activity.
  7. GTPBP8 plays a role in mitoribosome formation in human mitochondria.
  8. Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome.
  9. Mitochondrial genetics through the lens of single-cell multi-omics.
  10. Sample collection time affects microbiome study results.
  11. ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanoma.
  12. E-cadherin Induces Serine Synthesis to Support Progression and Metastasis of Breast Cancer.
  13. Fit for purpose: Selecting the best mitochondrial DNA for the job.
  14. A tandem activity-based sensing and labeling strategy reveals antioxidant response element regulation of labile iron pools.
  15. An organelle tango controls lipid metabolism.
  16. Overexpression of mitochondrial fission or mitochondrial fusion genes enhances resilience and extends longevity.
  17. Beyond fission and fusion-Diving into the mysteries of mitochondrial shape.
  18. The role of BCAA metabolism in metabolic health and disease.
  19. PAQR4 regulates adipocyte function and systemic metabolic health by mediating ceramide levels.
  20. Why cancer risk declines sharply in old age.
  21. The germline coordinates mitokine signaling.
  22. Deuterium MRI of serine metabolism in mouse models of glioblastoma.
  23. Functional multi-organelle units control inflammatory lipid metabolism of macrophages.
  24. Saturation genome editing maps the functional spectrum of pathogenic VHL alleles.
  25. Coenzyme A protects against ferroptosis via CoAlation of thioredoxin reductase 2.
  26. Genetic gear switches drive cancer immune evasion.
  27. Trafficking of mitochondrial double-stranded RNA from mitochondria to the cytosol.
  28. Immune evasion: An imperative and consequence of MYC deregulation.
  29. Interactions of Fatty Acid and Cholesterol Metabolism with Cellular Stress Response Pathways in Cancer.
  30. HuR controls glutaminase RNA metabolism.
  31. Selective nitration of Hsp90 acts as a metabolic switch promoting tumor cell proliferation.
  32. Amyloid formation and depolymerization of tumor suppressor p16INK4a are regulated by a thiol-dependent redox mechanism.
  33. A mitochondrial checkpoint to NF-κB signaling.
  34. The immune and metabolic milieu of the choroid plexus as a potential target in brain protection.
  35. Biological and genetic determinants of glycolysis: Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes.
  36. Physiology of malate dehydrogenase and how dysregulation leads to disease.
  37. Inborn errors of the malate aspartate shuttle - Update on patients and cellular models.
  38. BACH1 inhibits senescence, obesity, and short lifespan by ferroptotic FGF21 secretion.
  39. The history of chromosomal instability in genome doubled tumors.
  40. What's in a @name?
  41. Bioenergetic myths of energy transduction in eukaryotic cells.
  42. Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth.
  43. Neutrophils actively swell to potentiate rapid migration.
  44. Emerging tools and best practices for studying gut microbial community metabolism.
  45. Progestogen-driven B7-H4 contributes to onco-fetal immune tolerance.
  46. MCT1-dependent lactate recycling is a metabolic vulnerability in colorectal cancer cells upon acquired resistance to anti-EGFR targeted therapy.
  47. Asparagine Dependency is a Targetable Metabolic Vulnerability in TP53-Altered Castration-Resistant Prostate Cancer.
  48. Carcinogenesis at single-cell resolution.
  49. Primary cilia formation requires the Leigh syndrome-associated mitochondrial protein NDUFAF2.
  50. Precise measurement of molecular phenotypes with barcode-based CRISPRi systems.
  51. Towards nutrition with precision: unlocking biomarkers as dietary assessment tools.
  52. ER-GUARD: an evolutionarily conserved antioxidant defense system at ER membranes.
  53. Pro-survival signaling regulates lipophagy essential for multiple myeloma resistance to stress-induced death.
  54. Metabolic complexity drives divergence in microbial communities.
  55. Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors.
  56. Atg8/LC3 controls systemic nutrient surplus signaling in flies and humans.
  57. The mitochondrial aspartate/glutamate carrier does not transport GABA.
  58. A genome-wide CRISPR screen reveals that antagonism of glutamine metabolism sensitizes head and neck squamous cell carcinoma to ferroptotic cell death.
  59. Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.
  60. A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction.
  1. J Biol Chem. 2024 Jun 27. pii: S0021-9258(24)01999-9. [Epub ahead of print] 107498
    Bridging lipid metabolism and mitochondrial genome maintenance.
    Casadora Boone, Samantha C Lewis.
      Mitochondria are the nexus of cellular energy metabolism and major signaling hubs that integrate information from within and without the cell to implement cell function. Mitochondria harbor a distinct polyploid genome, mitochondrial DNA (mtDNA), that encodes respiratory chain components required for energy production. MtDNA mutation and depletion have been linked to obesity and metabolic syndrome in humans. At the cellular and subcellular levels, mtDNA synthesis is coordinated by membrane contact sites implicated in lipid transfer from the endoplasmic reticulum, tying genome maintenance to lipid storage and homeostasis. Here, we examine the relationship between mtDNA and lipid trafficking, the influence of lipotoxicity on mtDNA integrity, and how lipid metabolism may be disrupted in primary mtDNA disease.
    Keywords:  Mitochondria; lipid metabolism; lipotoxicity; mitochondrial DNA (mtDNA); mitochondrial metabolism
    DOI:  https://doi.org/10.1016/j.jbc.2024.107498
  2. bioRxiv. 2024 Jun 21. pii: 2024.06.21.600099. [Epub ahead of print]
    ATP-dependent citrate lyase Drives Left Ventricular Dysfunction by Metabolic Remodeling of the Heart.
    Shijie Liu, Seth T Gammon, Lin Tan, Yaqi Gao, Kyoungmin Kim, Ian K Williamson, Janet Pham, Angela Davidian, Radhika Khanna, Benjamin D Gould, Rebecca Salazar, Heidi Vitrac, An Dinh, Evan C Lien, Francisca N de L Vitorino, Joanna M Gongora, Sara A Martinez, Czer S C Lawrence, Evan P Kransdorf, David Leffer, Blake Hanson, Benjamin A Garcia, Matthew G Vander Heiden, Philip L Lorenzi, Heinrich Taegtmeyer, David Piwnica-Worms, James F Martin, Anja Karlstaedt.
       Background: Metabolic remodeling is a hallmark of the failing heart. Oncometabolic stress during cancer increases the activity and abundance of the ATP-dependent citrate lyase (ACL, Acly ), which promotes histone acetylation and cardiac adaptation. ACL is critical for the de novo synthesis of lipids, but how these metabolic alterations contribute to cardiac structural and functional changes remains unclear.
    Methods: We utilized human heart tissue samples from healthy donor hearts and patients with hypertrophic cardiomyopathy. Further, we used CRISPR/Cas9 gene editing to inactivate Acly in cardiomyocytes of MyH6-Cas9 mice. In vivo, positron emission tomography and ex vivo stable isotope tracer labeling were used to quantify metabolic flux changes in response to the loss of ACL. We conducted a multi-omics analysis using RNA-sequencing and mass spectrometry-based metabolomics and proteomics. Experimental data were integrated into computational modeling using the metabolic network CardioNet to identify significantly dysregulated metabolic processes at a systems level.
    Results: Here, we show that in mice, ACL drives metabolic adaptation in the heart to sustain contractile function, histone acetylation, and lipid modulation. Notably, we show that loss of ACL increases glucose oxidation while maintaining fatty acid oxidation. Ex vivo isotope tracing experiments revealed a reduced efflux of glucose-derived citrate from the mitochondria into the cytosol, confirming that citrate is required for reductive metabolism in the heart. We demonstrate that YAP inactivation facilitates ACL deficiency. Computational flux analysis and integrative multi-omics analysis indicate that loss of ACL induces alternative isocitrate dehydrogenase 1 flux to compensate.
    Conclusions: This study mechanistically delineates how cardiac metabolism compensates for suppressed citrate metabolism in response to ACL loss and uncovers metabolic vulnerabilities in the heart.
    DOI:  https://doi.org/10.1101/2024.06.21.600099
  3. Cell Metab. 2024 Jul 02. pii: S1550-4131(24)00227-4. [Epub ahead of print]36(7): 1433-1435
    From whence it came: Mitochondrial mRNA leaves, a protein returns.
    Kevin A Janssen, Angela Song.
      Small peptides have previously been reported to be encoded in mitochondrial rRNA and translated by cytosolic ribosomes. In this issue of Cell Metabolism, Hu et al. use mass spectrometry to identify a cytosolically translated protein, encoded instead in mitochondrial mRNA, that is surprisingly targeted back into the mitochondrial matrix.
    DOI:  https://doi.org/10.1016/j.cmet.2024.06.002
  4. Nat Genet. 2024 Jul 03.
    Homopolymer switches mediate adaptive mutability in mismatch repair-deficient colorectal cancer.
    Hamzeh Kayhanian, William Cross, Suzanne E M van der Horst, Panagiotis Barmpoutis, Eszter Lakatos, Giulio Caravagna, Luis Zapata, Arne Van Hoeck, Sjors Middelkamp, Kevin Litchfield, Christopher Steele, William Waddingham, Dominic Patel, Salvatore Milite, Chen Jin, Ann-Marie Baker, Daniel C Alexander, Khurum Khan, Daniel Hochhauser, Marco Novelli, Benjamin Werner, Ruben van Boxtel, Joris H Hageman, Julian R Buissant des Amorie, Josep Linares, Marjolijn J L Ligtenberg, Iris D Nagtegaal, Miangela M Laclé, Leon M G Moons, Lodewijk A A Brosens, Nischalan Pillay, Andrea Sottoriva, Trevor A Graham, Manuel Rodriguez-Justo, Kai-Keen Shiu, Hugo J G Snippert, Marnix Jansen.
      Mismatch repair (MMR)-deficient cancer evolves through the stepwise erosion of coding homopolymers in target genes. Curiously, the MMR genes MutS homolog 6 (MSH6) and MutS homolog 3 (MSH3) also contain coding homopolymers, and these are frequent mutational targets in MMR-deficient cancers. The impact of incremental MMR mutations on MMR-deficient cancer evolution is unknown. Here we show that microsatellite instability modulates DNA repair by toggling hypermutable mononucleotide homopolymer runs in MSH6 and MSH3 through stochastic frameshift switching. Spontaneous mutation and reversion modulate subclonal mutation rate, mutation bias and HLA and neoantigen diversity. Patient-derived organoids corroborate these observations and show that MMR homopolymer sequences drift back into reading frame in the absence of immune selection, suggesting a fitness cost of elevated mutation rates. Combined experimental and simulation studies demonstrate that subclonal immune selection favors incremental MMR mutations. Overall, our data demonstrate that MMR-deficient colorectal cancers fuel intratumor heterogeneity by adapting subclonal mutation rate and diversity to immune selection.
    DOI:  https://doi.org/10.1038/s41588-024-01777-9
  5. bioRxiv. 2024 Jun 22. pii: 2024.06.18.599628. [Epub ahead of print]
    Perturbations in mitochondrial metabolism associated with defective cardiolipin biosynthesis: An in-organello real-time NMR study.
    Antonio J Rua, Wayne Mitchell, Steven M Claypool, Nathan N Alder, Andrei T Alexandrescu.
      Mitochondria are central to cellular metabolism; hence, their dysfunction contributes to a wide array of human diseases including cancer, cardiopathy, neurodegeneration, and heritable pathologies such as Barth syndrome. Cardiolipin, the signature phospholipid of the mitochondrion promotes proper cristae morphology, bioenergetic functions, and directly affects metabolic reactions carried out in mitochondrial membranes. To match tissue-specific metabolic demands, cardiolipin typically undergoes an acyl tail remodeling process with the final step carried out by the phospholipid-lysophospholipid transacylase tafazzin. Mutations in the tafazzin gene are the primary cause of Barth syndrome. Here, we investigated how defects in cardiolipin biosynthesis and remodeling impact metabolic flux through the tricarboxylic acid cycle and associated pathways in yeast. Nuclear magnetic resonance was used to monitor in real-time the metabolic fate of 13 C 3 -pyruvate in isolated mitochondria from three isogenic yeast strains. We compared mitochondria from a wild-type strain to mitochondria from a Δ taz1 strain that lacks tafazzin and contains lower amounts of unremodeled cardiolipin, and mitochondria from a Δ crd1 strain that lacks cardiolipin synthase and cannot synthesize cardiolipin. We found that the 13 C-label from the pyruvate substrate was distributed through about twelve metabolites. Several of the identified metabolites were specific to yeast pathways, including branched chain amino acids and fusel alcohol synthesis. Most metabolites showed similar kinetics amongst the different strains but mevalonate and α-ketoglutarate, as well as the NAD+/NADH couple measured in separate nuclear magnetic resonance experiments, showed pronounced differences. Taken together, the results show that cardiolipin remodeling influences pyruvate metabolism, tricarboxylic acid cycle flux, and the levels of mitochondrial nucleotides.
    DOI:  https://doi.org/10.1101/2024.06.18.599628
  6. FEBS J. 2024 Jul 01.
    TRIM2 promotes metabolic adaptation to glutamine deprivation via enhancement of CPT1A activity.
    Kaimin Liao, Kaiyue Liu, Zhongyu Wang, Kailiang Zhao, Yide Mei.
      Cancer cells undergo metabolic adaptation to promote their survival and growth under energy stress conditions, yet the underlying mechanisms remain largely unclear. Here, we report that tripartite motif-containing protein 2 (TRIM2) is upregulated in response to glutamine deprivation by the transcription factor cyclic AMP-dependent transcription factor (ATF4). TRIM2 is shown to specifically interact with carnitine O-palmitoyltransferase 1 (CPT1A), a rate-limiting enzyme of fatty acid oxidation. Via this interaction, TRIM2 enhances the enzymatic activity of CPT1A, thereby regulating intracellular lipid levels and protecting cells from glutamine deprivation-induced apoptosis. Furthermore, TRIM2 is able to promote both in vitro cell proliferation and in vivo xenograft tumor growth via CPT1A. Together, these findings establish TRIM2 as an important regulator of the metabolic adaptation of cancer cells to glutamine deprivation and implicate TRIM2 as a potential therapeutic target for cancer.
    Keywords:  CPT1A; TRIM2; glutamine deprivation; metabolic adaptation
    DOI:  https://doi.org/10.1111/febs.17218
  7. Nat Commun. 2024 Jul 05. 15(1): 5664
    GTPBP8 plays a role in mitoribosome formation in human mitochondria.
    Miriam Cipullo, Genís Valentín Gesé, Shreekara Gopalakrishna, Annika Krueger, Vivian Lobo, Maria A Pirozhkova, James Marks, Petra Páleníková, Dmitrii Shiriaev, Yong Liu, Jelena Misic, Yu Cai, Minh Duc Nguyen, Abubakar Abdelbagi, Xinping Li, Michal Minczuk, Markus Hafner, Daniel Benhalevy, Aishe A Sarshad, Ilian Atanassov, B Martin Hällberg, Joanna Rorbach.
      Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.
    DOI:  https://doi.org/10.1038/s41467-024-50011-x
  8. Sci Adv. 2024 Jul 05. 10(27): eadh9613
    Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome.
    Kouki Abe, Brian Maunze, Pedro-Avila Lopez, Jessica Xu, Nefertiti Muhammad, Guang-Yu Yang, David Katz, Yaping Liu, Shannon M Lauberth.
      Downstream-of-gene (DoG) transcripts are an emerging class of noncoding RNAs. However, it remains largely unknown how DoG RNA production is regulated and whether alterations in DoG RNA signatures exist in major cancers. Here, through transcriptomic analyses of matched tumors and nonneoplastic tissues and cancer cell lines, we reveal a comprehensive catalog of DoG RNA signatures. Through separate lines of evidence, we support the biological importance of DoG RNAs in carcinogenesis. First, we show tissue-specific and stage-specific differential expression of DoG RNAs in tumors versus paired normal tissues with their respective host genes involved in tumor-promoting versus tumor-suppressor pathways. Second, we identify that differential DoG RNA expression is associated with poor patient survival. Third, we identify that DoG RNA induction is a consequence of treating colon cancer cells with the topoisomerase I (TOP1) poison camptothecin and following TOP1 depletion. Our results underlie the significance of DoG RNAs and TOP1-dependent regulation of DoG RNAs in diversifying and modulating the cancer transcriptome.
    DOI:  https://doi.org/10.1126/sciadv.adh9613
  9. Nat Genet. 2024 Jul 01.
    Mitochondrial genetics through the lens of single-cell multi-omics.
    Lena Nitsch, Caleb A Lareau, Leif S Ludwig.
      Mitochondria carry their own genetic information encoding for a subset of protein-coding genes and translational machinery essential for cellular respiration and metabolism. Despite its small size, the mitochondrial genome, its natural genetic variation and molecular phenotypes have been challenging to study using bulk sequencing approaches, due to its variation in cellular copy number, non-Mendelian modes of inheritance and propensity for mutations. Here we highlight emerging strategies designed to capture mitochondrial genetic variation across individual cells for lineage tracing and studying mitochondrial genetics in primary human cells and clinical specimens. We review recent advances surrounding single-cell mitochondrial genome sequencing and its integration with functional genomic readouts, including leveraging somatic mitochondrial DNA mutations as clonal markers that can resolve cellular population dynamics in complex human tissues. Finally, we discuss how single-cell whole mitochondrial genome sequencing approaches can be utilized to investigate mitochondrial genetics and its contribution to cellular heterogeneity and disease.
    DOI:  https://doi.org/10.1038/s41588-024-01794-8
  10. Nat Metab. 2024 Jul 01.
    Sample collection time affects microbiome study results.
      
    DOI:  https://doi.org/10.1038/s42255-024-01077-w
  11. Cell Rep. 2024 Jul 02. pii: S2211-1247(24)00735-6. [Epub ahead of print]43(7): 114406
    ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanoma.
    Yuting Lu, Jana Travnickova, Mihaly Badonyi, Florian Rambow, Andrea Coates, Zaid Khan, Jair Marques, Laura C Murphy, Pablo Garcia-Martinez, Richard Marais, Pakavarin Louphrasitthiphol, Alex H Y Chan, Christopher J Schofield, Alex von Kriegsheim, Joseph A Marsh, Valeria Pavet, Owen J Sansom, Robert S Illingworth, E Elizabeth Patton.
      Cancer cellular heterogeneity and therapy resistance arise substantially from metabolic and transcriptional adaptations, but how these are interconnected is poorly understood. Here, we show that, in melanoma, the cancer stem cell marker aldehyde dehydrogenase 1A3 (ALDH1A3) forms an enzymatic partnership with acetyl-coenzyme A (CoA) synthetase 2 (ACSS2) in the nucleus to couple high glucose metabolic flux with acetyl-histone H3 modification of neural crest (NC) lineage and glucose metabolism genes. Importantly, we show that acetaldehyde is a metabolite source for acetyl-histone H3 modification in an ALDH1A3-dependent manner, providing a physiologic function for this highly volatile and toxic metabolite. In a zebrafish melanoma residual disease model, an ALDH1-high subpopulation emerges following BRAF inhibitor treatment, and targeting these with an ALDH1 suicide inhibitor, nifuroxazide, delays or prevents BRAF inhibitor drug-resistant relapse. Our work reveals that the ALDH1A3-ACSS2 couple directly coordinates nuclear acetaldehyde-acetyl-CoA metabolism with specific chromatin-based gene regulation and represents a potential therapeutic vulnerability in melanoma.
    Keywords:  ACSS2; ALDH1A3; CP: Cancer; CP: Metabolism; Nifuroxazide; TFAP2B; acetaldehyde; melanoma; neural crest stem cell; pyruvate metabolism; residual disease
    DOI:  https://doi.org/10.1016/j.celrep.2024.114406
  12. Cancer Res. 2024 Jul 03.
    E-cadherin Induces Serine Synthesis to Support Progression and Metastasis of Breast Cancer.
    Geonhui Lee, Claudia Wong, Anna Cho, Junior J West, Ashleigh J Crawford, Gabriella C Russo, Bishwa Ranjan Si, Jungwoo Kim, Lauren Hoffner, Cholsoon Jang, Moonjung Jung, Robert D Leone, Konstantinos Konstantopoulos, Andrew J Ewald, Denis Wirtz, Sangmoo Jeong.
      The loss of E-cadherin, an epithelial cell adhesion molecule, has been implicated in metastasis by mediating the epithelial-mesenchymal transition (EMT), which promotes invasion and migration of cancer cells. However, recent studies have demonstrated that E-cadherin supports the survival and proliferation of metastatic cancer cells. Here, we identified a metabolic role for E-cadherin in breast cancer by upregulating the de novo serine synthesis pathway (SSP). The upregulated SSP provided metabolic precursors for biosynthesis and resistance to oxidative stress, enabling E-cadherin+ breast cancer cells to achieve faster tumor growth and enhanced metastases. Inhibition of PHGDH, a rate-limiting enzyme in the SSP, significantly and specifically hampered proliferation of E-cadherin+ breast cancer cells and rendered them vulnerable to oxidative stress, inhibiting their metastatic potential. These findings reveal that E-cadherin reprograms cellular metabolism, promoting tumor growth and metastasis of breast cancers.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-23-3082
  13. Cell Metab. 2024 Jul 02. pii: S1550-4131(24)00236-5. [Epub ahead of print]36(7): 1436-1438
    Fit for purpose: Selecting the best mitochondrial DNA for the job.
    Sarah J Pickett, Robert W Taylor, Robert McFarland.
      The factors determining levels of pathogenic mitochondrial DNA in cells and tissues are critical to disease pathology but remain poorly understood and contentious. In Nature, Kotrys et al. published a single-cell-based analysis casting fresh light on this thorny problem and introduced a powerful new investigative tool.
    DOI:  https://doi.org/10.1016/j.cmet.2024.06.011
  14. Proc Natl Acad Sci U S A. 2024 Jul 09. 121(28): e2401579121
    A tandem activity-based sensing and labeling strategy reveals antioxidant response element regulation of labile iron pools.
    Aidan T Pezacki, Ryan L Gonciarz, Toshitaka Okamura, Carson D Matier, Laura Torrente, Ke Cheng, Sophia G Miller, Martina Ralle, Nathan P Ward, Gina M DeNicola, Adam R Renslo, Christopher J Chang.
      Iron is an essential element for life owing to its ability to participate in a diverse array of oxidation-reduction reactions. However, misregulation of iron-dependent redox cycling can also produce oxidative stress, contributing to cell growth, proliferation, and death pathways underlying aging, cancer, neurodegeneration, and metabolic diseases. Fluorescent probes that selectively monitor loosely bound Fe(II) ions, termed the labile iron pool, are potentially powerful tools for studies of this metal nutrient; however, the dynamic spatiotemporal nature and potent fluorescence quenching capacity of these bioavailable metal stores pose challenges for their detection. Here, we report a tandem activity-based sensing and labeling strategy that enables imaging of labile iron pools in live cells through enhancement in cellular retention. Iron green-1 fluoromethyl (IG1-FM) reacts selectively with Fe(II) using an endoperoxide trigger to release a quinone methide dye for subsequent attachment to proximal biological nucleophiles, providing a permanent fluorescent stain at sites of elevated labile iron. IG1-FM imaging reveals that degradation of the major iron storage protein ferritin through ferritinophagy expands the labile iron pool, while activation of nuclear factor-erythroid 2-related factor 2 (NRF2) antioxidant response elements (AREs) depletes it. We further show that lung cancer cells with heightened NRF2 activation, and thus lower basal labile iron, have reduced viability when treated with an iron chelator. By connecting labile iron pools and NRF2-ARE activity to a druggable metal-dependent vulnerability in cancer, this work provides a starting point for broader investigations into the roles of transition metal and antioxidant signaling pathways in health and disease.
    Keywords:  activity-based sensing; antioxidant regulation; cancer metabolism; fluorescent iron probe; transition metal signaling
    DOI:  https://doi.org/10.1073/pnas.2401579121
  15. Nat Cell Biol. 2024 Jul 05.
    An organelle tango controls lipid metabolism.
    Johannes Pilic, Tatjana Kleele.
      
    DOI:  https://doi.org/10.1038/s41556-024-01441-8
  16. Aging Cell. 2024 Jul 02. e14262
    Overexpression of mitochondrial fission or mitochondrial fusion genes enhances resilience and extends longevity.
    Annika Traa, Allison Keil, Abdelrahman AlOkda, Suleima Jacob-Tomas, Aura A Tamez González, Shusen Zhu, Zenith Rudich, Jeremy M Van Raamsdonk.
      The dynamicity of the mitochondrial network is crucial for meeting the ever-changing metabolic and energy needs of the cell. Mitochondrial fission promotes the degradation and distribution of mitochondria, while mitochondrial fusion maintains mitochondrial function through the complementation of mitochondrial components. Previously, we have reported that mitochondrial networks are tubular, interconnected, and well-organized in young, healthy C. elegans, but become fragmented and disorganized with advancing age and in models of age-associated neurodegenerative disease. In this work, we examine the effects of increasing mitochondrial fission or mitochondrial fusion capacity by ubiquitously overexpressing the mitochondrial fission gene drp-1 or the mitochondrial fusion genes fzo-1 and eat-3, individually or in combination. We then measured mitochondrial function, mitochondrial network morphology, physiologic rates, stress resistance, and lifespan. Surprisingly, we found that overexpression of either mitochondrial fission or fusion machinery both resulted in an increase in mitochondrial fragmentation. Similarly, both mitochondrial fission and mitochondrial fusion overexpression strains have extended lifespans and increased stress resistance, which in the case of the mitochondrial fusion overexpression strains appears to be at least partially due to the upregulation of multiple pathways of cellular resilience in these strains. Overall, our work demonstrates that increasing the expression of mitochondrial fission or fusion genes extends lifespan and improves biological resilience without promoting the maintenance of a youthful mitochondrial network morphology. This work highlights the importance of the mitochondria for both resilience and longevity.
    Keywords:   C. elegans ; aging; biological resilience; genetics; lifespan; mitochondria; mitochondrial fission; mitochondrial fusion
    DOI:  https://doi.org/10.1111/acel.14262
  17. PLoS Biol. 2024 Jul;22(7): e3002671
    Beyond fission and fusion-Diving into the mysteries of mitochondrial shape.
    Noga Preminger, Maya Schuldiner.
      Mitochondrial shape and network formation have been primarily associated with the well-established processes of fission and fusion. However, recent research has unveiled an intricate and multifaceted landscape of mitochondrial morphology that extends far beyond the conventional fission-fusion paradigm. These less-explored dimensions harbor numerous unresolved mysteries. This review navigates through diverse processes influencing mitochondrial shape and network formation, highlighting the intriguing complexities and gaps in our understanding of mitochondrial architecture. The exploration encompasses various scales, from biophysical principles governing membrane dynamics to molecular machineries shaping mitochondria, presenting a roadmap for future research in this evolving field.
    DOI:  https://doi.org/10.1371/journal.pbio.3002671
  18. Exp Mol Med. 2024 Jul 02.
    The role of BCAA metabolism in metabolic health and disease.
    Byeong Hun Choi, Seunghoon Hyun, Seung-Hoi Koo.
      It has long been postulated that dietary restriction is beneficial for ensuring longevity and extending the health span of mammals, including humans. In particular, a reduction in protein consumption has been shown to be specifically linked to the beneficial effect of dietary restriction on metabolic disorders, presumably by reducing the activity of the mechanistic target of rapamycin complex (mTORC) 1 and the reciprocal activation of AMP-activated protein kinase (AMPK) and sirtuin pathways. Although it is widely used as a dietary supplement to delay the aging process in humans, recent evidence suggests that branched-chain amino acids (BCAAs) might be a major cause of the deteriorating effect of a protein diet on aging and related disorders. In this review, we delineate the regulation of metabolic pathways for BCAAs at the tissue-specific level and summarize recent findings regarding the role of BCAAs in the control of metabolic health and disease in mammals.
    DOI:  https://doi.org/10.1038/s12276-024-01263-6
  19. Nat Metab. 2024 Jul 03.
    PAQR4 regulates adipocyte function and systemic metabolic health by mediating ceramide levels.
    Qingzhang Zhu, Shiuhwei Chen, Jan-Bernd Funcke, Leon G Straub, Qian Lin, Shangang Zhao, Chanmin Joung, Zhuzhen Zhang, Dae-Seok Kim, Na Li, Christy M Gliniak, Charlotte Lee, Alberto Cebrian-Serrano, Line Pedersen, Nils Halberg, Ruth Gordillo, Christine M Kusminski, Philipp E Scherer.
      PAQR4 is an orphan receptor in the PAQR family with an unknown function in metabolism. Here, we identify a critical role of PAQR4 in maintaining adipose tissue function and whole-body metabolic health. We demonstrate that expression of Paqr4 specifically in adipocytes, in an inducible and reversible fashion, leads to partial lipodystrophy, hyperglycaemia and hyperinsulinaemia, which is ameliorated by wild-type adipose tissue transplants or leptin treatment. By contrast, deletion of Paqr4 in adipocytes improves healthy adipose remodelling and glucose homoeostasis in diet-induced obesity. Mechanistically, PAQR4 regulates ceramide levels by mediating the stability of ceramide synthases (CERS2 and CERS5) and, thus, their activities. Overactivation of the PQAR4-CERS axis causes ceramide accumulation and impairs adipose tissue function through suppressing adipogenesis and triggering adipocyte de-differentiation. Blocking de novo ceramide biosynthesis rescues PAQR4-induced metabolic defects. Collectively, our findings suggest a critical function of PAQR4 in regulating cellular ceramide homoeostasis and targeting PAQR4 offers an approach for the treatment of metabolic disorders.
    DOI:  https://doi.org/10.1038/s42255-024-01078-9
  20. Nature. 2024 Jul 02.
    Why cancer risk declines sharply in old age.
    Heidi Ledford.
      
    Keywords:  Ageing; Cancer; Transcriptomics
    DOI:  https://doi.org/10.1038/d41586-024-02107-z
  21. Cell. 2024 Jun 26. pii: S0092-8674(24)00650-0. [Epub ahead of print]
    The germline coordinates mitokine signaling.
    Koning Shen, Jenni Durieux, Cesar G Mena, Brant M Webster, C Kimberly Tsui, Hanlin Zhang, Larry Joe, Kristen M Berendzen, Andrew Dillin.
      The ability of mitochondria to coordinate stress responses across tissues is critical for health. In C. elegans, neurons experiencing mitochondrial stress elicit an inter-tissue signaling pathway through the release of mitokine signals, such as serotonin or the Wnt ligand EGL-20, which activate the mitochondrial unfolded protein response (UPRMT) in the periphery to promote organismal health and lifespan. We find that germline mitochondria play a surprising role in neuron-to-periphery UPRMT signaling. Specifically, we find that germline mitochondria signal downstream of neuronal mitokines, Wnt and serotonin, and upstream of lipid metabolic pathways in the periphery to regulate UPRMT activation. We also find that the germline tissue itself is essential for UPRMT signaling. We propose that the germline has a central signaling role in coordinating mitochondrial stress responses across tissues, and germline mitochondria play a defining role in this coordination because of their inherent roles in germline integrity and inter-tissue signaling.
    Keywords:  C. elegans; aging; germline; lipids; mitochondria; mtUPR; proteostasis; stress response
    DOI:  https://doi.org/10.1016/j.cell.2024.06.010
  22. Magn Reson Med. 2024 Jun 30.
    Deuterium MRI of serine metabolism in mouse models of glioblastoma.
    Friederike Hesse, Jacob Low, Jianbo Cao, Flaviu Bulat, Felix Kreis, Alan J Wright, Kevin M Brindle.
       PURPOSE: Serine is a major source of one-carbon units needed for the synthesis of nucleotides and the production of intramitochondrial nicotinamide adenine dinucleotide phosphate (NADPH), and it plays an important role in cancer cell proliferation. The aim of this study was to develop a deuterium (2H) MRS imaging method for imaging tumor serine metabolism.
    METHODS: Sequential (2H) spectra and spectroscopic images were used to monitor the metabolism of [2,3,3-2H3]serine in patient-derived glioblastoma cells in vitro and in tumors obtained by their orthotopic implantation in mouse brain.
    RESULTS: [14,14-2H2] 5,10-methylene-tetrahydrofolate, [2H]glycine, [2H]formate, and labeled water were detected in cell suspensions and water labeling in spectroscopic images of tumors. Studies in cells and tumors with variable mitochondrial content and inhibitor studies in cells demonstrated that most of the labeled serine was metabolized in the mitochondria. Water labeling in the cell suspensions was correlated with formate labeling; therefore, water labeling observed in tumors could be used to provide a surrogate measure of flux in the pathway of one-carbon metabolism in vivo.
    CONCLUSION: The method has the potential to be used clinically to select patients for treatment with inhibitors of one-carbon metabolism and subsequently to detect their early responses to such treatment.
    Keywords:  folate cycle; one‐carbon metabolism; serine; tumor
    DOI:  https://doi.org/10.1002/mrm.30198
  23. Nat Cell Biol. 2024 Jul 05.
    Functional multi-organelle units control inflammatory lipid metabolism of macrophages.
    Julia A Zimmermann, Kerstin Lucht, Manuel Stecher, Chahat Badhan, Katharina M Glaser, Maximilian W Epple, Lena R Koch, Ward Deboutte, Thomas Manke, Klaus Ebnet, Frauke Brinkmann, Olesja Fehler, Thomas Vogl, Ev-Marie Schuster, Anna Bremser, Joerg M Buescher, Angelika S Rambold.
      Eukaryotic cells contain several membrane-separated organelles to compartmentalize distinct metabolic reactions. However, it has remained unclear how these organelle systems are coordinated when cells adapt metabolic pathways to support their development, survival or effector functions. Here we present OrgaPlexing, a multi-spectral organelle imaging approach for the comprehensive mapping of six key metabolic organelles and their interactions. We use this analysis on macrophages, immune cells that undergo rapid metabolic switches upon sensing bacterial and inflammatory stimuli. Our results identify lipid droplets (LDs) as primary inflammatory responder organelle, which forms three- and four-way interactions with other organelles. While clusters with endoplasmic reticulum (ER) and mitochondria (mitochondria-ER-LD unit) help supply fatty acids for LD growth, the additional recruitment of peroxisomes (mitochondria-ER-peroxisome-LD unit) supports fatty acid efflux from LDs. Interference with individual components of these units has direct functional consequences for inflammatory lipid mediator synthesis. Together, we show that macrophages form functional multi-organellar units to support metabolic adaptation and provide an experimental strategy to identify organelle-metabolic signalling hubs.
    DOI:  https://doi.org/10.1038/s41556-024-01457-0
  24. Nat Genet. 2024 Jul 05.
    Saturation genome editing maps the functional spectrum of pathogenic VHL alleles.
    Megan Buckley, Chloé Terwagne, Athina Ganner, Laura Cubitt, Reid Brewer, Dong-Kyu Kim, Christina M Kajba, Nicole Forrester, Phoebe Dace, Joachim De Jonghe, Scott T C Shepherd, Chelsea Sawyer, Mairead McEwen, Sven Diederichs, Elke Neumann-Haefelin, Samra Turajlic, Evgueni A Ivakine, Gregory M Findlay.
      To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and to accurately quantify their functional effects. A gene exemplifying the challenge of variant interpretation is the von Hippel-Lindautumor suppressor (VHL). VHL encodes an E3 ubiquitin ligase that regulates the cellular response to hypoxia. Germline pathogenic variants in VHL predispose patients to tumors including clear cell renal cell carcinoma (ccRCC) and pheochromocytoma, and somatic VHL mutations are frequently observed in sporadic renal cancer. Here we optimize and apply saturation genome editing to assay nearly all possible single-nucleotide variants (SNVs) across VHL's coding sequence. To delineate mechanisms, we quantify mRNA dosage effects and compare functional effects in isogenic cell lines. Function scores for 2,268 VHL SNVs identify a core set of pathogenic alleles driving ccRCC with perfect accuracy, inform differential risk across tumor types and reveal new mechanisms by which variants impact function. These results have immediate utility for classifying VHL variants encountered clinically and illustrate how precise functional measurements can resolve pleiotropic and dosage-dependent genotype-phenotype relationships across complete genes.
    DOI:  https://doi.org/10.1038/s41588-024-01800-z
  25. Res Sq. 2024 Jun 18. pii: rs.3.rs-4522617. [Epub ahead of print]
    Coenzyme A protects against ferroptosis via CoAlation of thioredoxin reductase 2.
    Jen-Tsan Chi, Chao Chieh Lin, Yi-Tzu Lin, Ssu-Yu Chen, Yasaman Setayeshpour, Yubin Chen, Denise Dunn, Erik Soderblom, Guo-Fang Zhang, Valeriy Filonenko, Suh Young Jeong, Scott Floyd, Susan Hayflick, Ivan Gout.
      The Cystine-xCT transporter-Glutathione (GSH)-GPX4 axis is the canonical pathway to protect against ferroptosis. While not required for ferroptosis-inducing compounds (FINs) targeting GPX4, FINs targeting the xCT transporter require mitochondria and its lipid peroxidation to trigger ferroptosis. However, the mechanism underlying the difference between these FINs is still unknown. Given that cysteine is also required for coenzyme A (CoA) biosynthesis, here we show that CoA supplementation specifically prevents ferroptosis induced by xCT inhibitors but not GPX4 inhibitors. We find that, auranofin, a thioredoxin reductase inhibitor, abolishes the protective effect of CoA. We also find that CoA availability determines the enzymatic activity of thioredoxin reductase, but not thioredoxin. Importantly, the mitochondrial thioredoxin system, but not the cytosolic thioredoxin system, determines CoA-mediated ferroptosis inhibition. Our data show that the CoA regulates the in vitro enzymatic activity of mitochondrial thioredoxin reductase (TXNRD2) by covalently modifying the thiol group of cysteine (CoAlation) on Cys-483. Replacing Cys-483 with alanine on TXNRD2 abolishes its in vitro enzymatic activity and ability to protect cells from ferroptosis. Targeting xCT to limit cysteine import and, therefore, CoA biosynthesis reduced CoAlation on TXNRD2, an effect that was rescued by CoA supplementation. Furthermore, the fibroblasts from patients with disrupted CoA metabolism demonstrate increased mitochondrial lipid peroxidation. In organotypic brain slice cultures, inhibition of CoA biosynthesis leads to an oxidized thioredoxin system, mitochondrial lipid peroxidation, and loss in cell viability, which were all rescued by ferrostatin-1. These findings identify CoA-mediated post-translation modification to regulate the thioredoxin system as an alternative ferroptosis protection pathway with potential clinical relevance for patients with disrupted CoA metabolism.
    DOI:  https://doi.org/10.21203/rs.3.rs-4522617/v1
  26. Nat Genet. 2024 Jul 03.
    Genetic gear switches drive cancer immune evasion.
      
    DOI:  https://doi.org/10.1038/s41588-024-01778-8
  27. Life Sci Alliance. 2024 Sep;pii: e202302396. [Epub ahead of print]7(9):
    Trafficking of mitochondrial double-stranded RNA from mitochondria to the cytosol.
    Matthew R Krieger, Melania Abrahamian, Kevin L He, Sean Atamdede, Hesamedin Hakimjavadi, Milica Momcilovic, Dejerianne Ostrow, Simran Ds Maggo, Yik Pui Tsang, Xiaowu Gai, Guillaume F Chanfreau, David B Shackelford, Michael A Teitell, Carla M Koehler.
      In addition to mitochondrial DNA, mitochondrial double-stranded RNA (mtdsRNA) is exported from mitochondria. However, specific channels for RNA transport have not been demonstrated. Here, we begin to characterize channel candidates for mtdsRNA export from the mitochondrial matrix to the cytosol. Down-regulation of SUV3 resulted in the accumulation of mtdsRNAs in the matrix, whereas down-regulation of PNPase resulted in the export of mtdsRNAs to the cytosol. Targeting experiments show that PNPase functions in both the intermembrane space and matrix. Strand-specific sequencing of the double-stranded RNA confirms the mitochondrial origin. Inhibiting or down-regulating outer membrane proteins VDAC1/2 and BAK/BAX or inner membrane proteins PHB1/2 strongly attenuated the export of mtdsRNAs to the cytosol. The cytosolic mtdsRNAs subsequently localized to large granules containing the stress protein TIA-1 and activated the type 1 interferon stress response pathway. Abundant mtdsRNAs were detected in a subset of non-small-cell lung cancer cell lines that were glycolytic, indicating relevance in cancer biology. Thus, we propose that mtdsRNA is a new damage-associated molecular pattern that is exported from mitochondria in a regulated manner.
    DOI:  https://doi.org/10.26508/lsa.202302396
  28. Mol Oncol. 2024 Jul 02.
    Immune evasion: An imperative and consequence of MYC deregulation.
    Bastian Krenz, Jongkuen Lee, Toshitha Kannan, Martin Eilers.
      MYC has been implicated in the pathogenesis of a wide range of human tumors and has been described for many years as a transcription factor that regulates genes with pleiotropic functions to promote tumorigenic growth. However, despite extensive efforts to identify specific target genes of MYC that alone could be responsible for promoting tumorigenesis, the field is yet to reach a consensus whether this is the crucial function of MYC. Recent work shifts the view on MYC's function from being a gene-specific transcription factor to an essential stress resilience factor. In highly proliferating cells, MYC preserves cell integrity by promoting DNA repair at core promoters, protecting stalled replication forks, and/or preventing transcription-replication conflicts. Furthermore, an increasing body of evidence demonstrates that MYC not only promotes tumorigenesis by driving cell-autonomous growth, but also enables tumors to evade the host's immune system. In this review, we summarize our current understanding of how MYC impairs antitumor immunity and why this function is evolutionarily hard-wired to the biology of the MYC protein family. We show why the cell-autonomous and immune evasive functions of MYC are mutually dependent and discuss ways to target MYC proteins in cancer therapy.
    Keywords:  MYC; MYC inhibition; immune checkpoints; immune evasion; immunotherapy; stress resilience; tumor metabolism
    DOI:  https://doi.org/10.1002/1878-0261.13695
  29. Cold Spring Harb Perspect Med. 2024 Jul 01. pii: a041548. [Epub ahead of print]
    Interactions of Fatty Acid and Cholesterol Metabolism with Cellular Stress Response Pathways in Cancer.
    Alina M Winkelkotte, Kamal Al-Shami, Adriano B Chaves-Filho, Felix C E Vogel, Almut Schulze.
      Lipids have essential functions as structural components of cellular membranes, as efficient energy storage molecules, and as precursors of signaling mediators. While deregulated glucose and amino acid metabolism in cancer have received substantial attention, the roles of lipids in the metabolic reprogramming of cancer cells are less well understood. However, since the first description of de novo fatty acid biosynthesis in cancer tissues almost 70 years ago, numerous studies have investigated the complex functions of altered lipid metabolism in cancer. Here, we will summarize the mechanisms by which oncogenic signaling pathways regulate fatty acid and cholesterol metabolism to drive rapid proliferation and protect cancer cells from environmental stress. The review also discusses the role of fatty acid metabolism in metabolic plasticity required for the adaptation to changing microenvironments during cancer progression and the connections between fatty acid and cholesterol metabolism and ferroptosis.
    DOI:  https://doi.org/10.1101/cshperspect.a041548
  30. Nat Commun. 2024 Jul 04. 15(1): 5620
    HuR controls glutaminase RNA metabolism.
    Douglas Adamoski, Larissa M Dos Reis, Ana Carolina Paschoalini Mafra, Felipe Corrêa-da-Silva, Pedro Manoel Mendes de Moraes-Vieira, Ioana Berindan-Neagoe, George A Calin, Sandra Martha Gomes Dias.
      Glutaminase (GLS) is directly related to cell growth and tumor progression, making it a target for cancer treatment. The RNA-binding protein HuR (encoded by the ELAVL1 gene) influences mRNA stability and alternative splicing. Overexpression of ELAVL1 is common in several cancers, including breast cancer. Here we show that HuR regulates GLS mRNA alternative splicing and isoform translation/stability in breast cancer. Elevated ELAVL1 expression correlates with high levels of the glutaminase isoforms C (GAC) and kidney-type (KGA), which are associated with poor patient prognosis. Knocking down ELAVL1 reduces KGA and increases GAC levels, enhances glutamine anaplerosis into the TCA cycle, and drives cells towards glutamine dependence. Furthermore, we show that combining chemical inhibition of GLS with ELAVL1 silencing synergistically decreases breast cancer cell growth and invasion. These findings suggest that dual inhibition of GLS and HuR offers a therapeutic strategy for breast cancer treatment.
    DOI:  https://doi.org/10.1038/s41467-024-49874-x
  31. Redox Biol. 2024 Jun 19. pii: S2213-2317(24)00227-1. [Epub ahead of print]75 103249
    Selective nitration of Hsp90 acts as a metabolic switch promoting tumor cell proliferation.
    Isabelle E Logan, Kyle T Nguyen, Tilottama Chatterjee, Bhagyashree Manivannan, Ngozi P Paul, Sharon R Kim, Evelyn M Sixta, Lydia P Bastian, Carrie Marean-Reardon, Matthias A Karajannis, Cristina Fernández-Valle, Alvaro G Estevez, Maria Clara Franco.
      Tumors develop in an oxidative environment characterized by peroxynitrite production and downstream protein tyrosine (Y) nitration. We showed that tyrosine nitration supports schwannoma cell proliferation and regulates cell metabolism in the inheritable tumor disorder NF2-related Schwannomatosis (NF2-SWN). Here, we identified the chaperone Heat shock protein 90 (Hsp90) as the first nitrated protein that acts as a metabolic switch to promote schwannoma cell proliferation. Doubling the endogenous levels of nitrated Hsp90 in schwannoma cells or supplementing nitrated Hsp90 into normal Schwann cells increased their proliferation. Metabolically, nitration on either Y33 or Y56 conferred Hsp90 distinct functions; nitration at Y33 (Hsp90NY33) down-regulated mitochondrial oxidative phosphorylation, while nitration at Y56 (Hsp90NY56) increased glycolysis by activating the purinergic receptor P2X7 in both schwannoma and normal Schwann cells. Hsp90NY33 and Hsp90NY56 showed differential subcellular and spatial distribution corresponding with their metabolic and proliferative functions in schwannoma three-dimensional cell culture models. Collectively, these results underscore the role of tyrosine nitration as a post-translational modification regulating critical cellular processes. Nitrated proteins, particularly nitrated Hsp90, emerge as a novel category of tumor-directed therapeutic targets.
    Keywords:  Cell metabolism; Hsp90; Neurofibromatosis; P2X7 receptor; Tumor; Tyrosine nitration
    DOI:  https://doi.org/10.1016/j.redox.2024.103249
  32. Nat Commun. 2024 Jul 01. 15(1): 5535
    Amyloid formation and depolymerization of tumor suppressor p16INK4a are regulated by a thiol-dependent redox mechanism.
    Sarah G Heath, Shelby G Gray, Emilie M Hamzah, Karina M O'Connor, Stephanie M Bozonet, Alex D Botha, Pierre de Cordovez, Nicholas J Magon, Jennifer D Naughton, Dylan L W Goldsmith, Abigail J Schwartfeger, Margaret Sunde, Alexander K Buell, Vanessa K Morris, Christoph Göbl.
      The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.
    DOI:  https://doi.org/10.1038/s41467-024-49581-7
  33. Cell Death Dis. 2024 Jul 03. 15(7): 477
    A mitochondrial checkpoint to NF-κB signaling.
    Emma Guilbaud, Lorenzo Galluzzi.
      Mitochondrial dysfunction can elicit multiple inflammatory pathways, especially when apoptotic caspases are inhibited. Such an inflammatory program is negatively regulated by the autophagic disposal of permeabilized mitochondria. Recent data demonstrate that the ubiquitination of mitochondrial proteins is essential for NEMO-driven NF-kB activation downstream of mitochondrial permeabilization.
    DOI:  https://doi.org/10.1038/s41419-024-06868-3
  34. Trends Neurosci. 2024 Jun 29. pii: S0166-2236(24)00090-0. [Epub ahead of print]
    The immune and metabolic milieu of the choroid plexus as a potential target in brain protection.
    Afroditi Tsitsou-Kampeli, Stefano Suzzi, Michal Schwartz.
      The brain's choroid plexus (CP), which operates as an anatomical and functional 'checkpoint', regulates the communication between brain and periphery and contributes to the maintenance of healthy brain homeostasis throughout life. Evidence from mouse models and humans reveals a link between loss of CP checkpoint properties and dysregulation of the CP immune milieu as a conserved feature across diverse neurological conditions. In particular, we suggest that an imbalance between different immune signals at the CP, including CD4+ T cell-derived cytokines, type-I interferon, and complement components, can perpetuate brain inflammation and cognitive deterioration in aging and neurodegeneration. Furthermore, we highlight the role of CP metabolism in controlling CP inflammation, and propose that targeting molecules that regulate CP metabolism could be effective in safeguarding brain function.
    Keywords:  T cells; aging; checkpoint; inflammation; interferon; metabolism; neurodegeneration
    DOI:  https://doi.org/10.1016/j.tins.2024.05.010
  35. Cell Metab. 2024 Jun 27. pii: S1550-4131(24)00232-8. [Epub ahead of print]
    Biological and genetic determinants of glycolysis: Phosphofructokinase isoforms boost energy status of stored red blood cells and transfusion outcomes.
    Travis Nemkov, Daniel Stephenson, Eric J Earley, Gregory R Keele, Ariel Hay, Alicia Key, Zachary B Haiman, Christopher Erickson, Monika Dzieciatkowska, Julie A Reisz, Amy Moore, Mars Stone, Xutao Deng, Steven Kleinman, Steven L Spitalnik, Eldad A Hod, Krystalyn E Hudson, Kirk C Hansen, Bernhard O Palsson, Gary A Churchill, Nareg Roubinian, Philip J Norris, Michael P Busch, James C Zimring, Grier P Page, Angelo D'Alessandro.
      Mature red blood cells (RBCs) lack mitochondria and thus exclusively rely on glycolysis to generate adenosine triphosphate (ATP) during aging in vivo or storage in blood banks. Here, we leveraged 13,029 volunteers from the Recipient Epidemiology and Donor Evaluation Study to identify associations between end-of-storage levels of glycolytic metabolites and donor age, sex, and ancestry-specific genetic polymorphisms in regions encoding phosphofructokinase 1, platelet (detected in mature RBCs); hexokinase 1 (HK1); and ADP-ribosyl cyclase 1 and 2 (CD38/BST1). Gene-metabolite associations were validated in fresh and stored RBCs from 525 Diversity Outbred mice and via multi-omics characterization of 1,929 samples from 643 human RBC units during storage. ATP and hypoxanthine (HYPX) levels-and the genetic traits linked to them-were associated with hemolysis in vitro and in vivo, both in healthy autologous transfusion recipients and in 5,816 critically ill patients receiving heterologous transfusions, suggesting their potential as markers to improve transfusion outcomes.
    Keywords:  ATP; Embden-Meyerhof-Parnas; blood; diversity outbred; erythrocyte; genetic ancestry; hemolysis; lactate; mQTL; population study
    DOI:  https://doi.org/10.1016/j.cmet.2024.06.007
  36. Essays Biochem. 2024 Jul 04. pii: EBC20230085. [Epub ahead of print]
    Physiology of malate dehydrogenase and how dysregulation leads to disease.
    Amy D Parente, Danielle E Bolland, Kathryn L Huisinga, Joseph J Provost.
      Malate dehydrogenase (MDH) is pivotal in mammalian tissue metabolism, participating in various pathways beyond its classical roles and highlighting its adaptability to cellular demands. This enzyme is involved in maintaining redox balance, lipid synthesis, and glutamine metabolism and supports rapidly proliferating cells' energetic and biosynthetic needs. The involvement of MDH in glutamine metabolism underlines its significance in cell physiology. In contrast, its contribution to lipid metabolism highlights its role in essential biosynthetic processes necessary for cell maintenance and proliferation. The enzyme's regulatory mechanisms, such as post-translational modifications, underscore its complexity and importance in metabolic regulation, positioning MDH as a potential target in metabolic dysregulation. Furthermore, the association of MDH with various pathologies, including cancer and neurological disorders, suggests its involvement in disease progression. The overexpression of MDH isoforms MDH1 and MDH2 in cancers like breast, prostate, and pancreatic ductal adenocarcinoma, alongside structural modifications, implies their critical role in the metabolic adaptation of tumor cells. Additionally, mutations in MDH2 linked to pheochromocytomas, paragangliomas, and other metabolic diseases emphasize MDH's role in metabolic homeostasis. This review spotlights MDH's potential as a biomarker and therapeutic target, advocating for further research into its multifunctional roles and regulatory mechanisms in health and disease.
    Keywords:  MDH; OAA; TCA; disease; malate dehydrogenase; metabolism
    DOI:  https://doi.org/10.1042/EBC20230085
  37. Mol Genet Metab. 2024 Jun 24. pii: S1096-7192(24)00404-9. [Epub ahead of print]142(4): 108520
    Inborn errors of the malate aspartate shuttle - Update on patients and cellular models.
    Jasmine Koch, Melissa H Broeks, Matthias Gautschi, Judith Jans, Alexander Laemmle.
      The malate aspartate shuttle (MAS) plays a pivotal role in transporting cytosolic reducing equivalents - electrons - into the mitochondria for energy conversion at the electron transport chain (ETC) and in the process of oxidative phosphorylation. The MAS consists of two pairs of cytosolic and mitochondrial isoenzymes (malate dehydrogenases 1 and 2; and glutamate oxaloacetate transaminases 1 and 2) and two transporters (malate-2-oxoglutarate carrier and aspartate glutamate carrier (AGC), the latter of which has two tissue-dependent isoforms AGC1 and AGC2). While the inner mitochondrial membrane is impermeable to NADH, the MAS forms one of the main routes for mitochondrial electron uptake by promoting uptake of malate. Inherited bi-allelic pathogenic variants in five of the seven components of the MAS have been described hitherto and cause a wide spectrum of symptoms including early-onset epileptic encephalopathy. This review provides an overview of reported patients suffering from MAS deficiencies. In addition, we give an overview of diagnostic procedures and research performed on patient-derived cellular models and tissues. Current cellular models are briefly discussed and novel ways to achieve a better understanding of MAS deficiencies are highlighted.
    DOI:  https://doi.org/10.1016/j.ymgme.2024.108520
  38. Cell Rep. 2024 Jun 27. pii: S2211-1247(24)00731-9. [Epub ahead of print]43(7): 114403
    BACH1 inhibits senescence, obesity, and short lifespan by ferroptotic FGF21 secretion.
    Hironari Nishizawa, Mitsuyo Matsumoto, Mie Yamanaka, Riko Irikura, Kazuma Nakajima, Keisuke Tada, Yoshiaki Nakayama, Morichika Konishi, Nobuyuki Itoh, Ryo Funayama, Keiko Nakayama, Kazuhiko Igarashi.
      Ferroptosis is a type of regulated cell death characterized by iron-dependent lipid peroxidation. A model cell system is constructed to induce ferroptosis by re-expressing the transcription factor BACH1, a potent ferroptosis inducer, in immortalized mouse embryonic fibroblasts (iMEFs). The transfer of the culture supernatant from ferroptotic iMEFs activates the proliferation of hepatoma cells and other fibroblasts and suppresses cellular senescence-like features. The BACH1-dependent secretion of the longevity factor FGF21 is increased in ferroptotic iMEFs. The anti-senescent effects of the culture supernatant from these iMEFs are abrogated by Fgf21 knockout. BACH1 activates the transcription of Fgf21 by promoting ferroptotic stress and increases FGF21 protein expression by suppressing its autophagic degradation through transcriptional Sqstm1 and Lamp2 repression. The BACH1-induced ferroptotic FGF21 secretion suppresses obesity in high-fat diet-fed mice and the short lifespan of progeria mice. The inhibition of these aging-related phenotypes can be physiologically significant regarding ferroptosis.
    Keywords:  BACH1; CP: Metabolism; DAMPs; FGF21; aging; cell death; cellular senescence; ferroptosis; longevity; obesity; α-klotho
    DOI:  https://doi.org/10.1016/j.celrep.2024.114403
  39. Cancer Discov. 2024 Jul 01.
    The history of chromosomal instability in genome doubled tumors.
    Toby M Baker, Siqi Lai, Andrew R Lynch, Tom Lesluyes, Haixi Yan, Huw A Ogilvie, Annelien Verfaillie, Stefan Dentro, Amy L Bowes, Nischalan Pillay, Adrienne M Flanagan, Charles Swanton, Paul T Spellman, Maxime Tarabichi, Peter Van Loo.
      Tumors frequently display high chromosomal instability and contain multiple copies of genomic regions. Here, we describe GRITIC, a generic method for timing genomic gains leading to complex copy number states, using single-sample bulk whole-genome sequencing data. By applying GRITIC to 6,091 tumors, we found that non-parsimonious evolution is frequent in the formation of complex copy number states in genome-doubled tumors. We measured chromosomal instability before and after genome duplication in human tumors and found that late genome doubling was followed by an increase in the rate of copy number gain. Copy number gains often accumulate as punctuated bursts, commonly after genome doubling. We infer that genome duplications typically affect the landscape of copy number losses, while only minimally impacting copy number gains. In summary, GRITIC is a novel copy number gain timing framework that permits the analysis of copy number evolution in chromosomally unstable tumors.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-1249
  40. EMBO Rep. 2024 Jul 01.
    What's in a @name?
    Howy Jacobs.
      
    DOI:  https://doi.org/10.1038/s44319-024-00194-7
  41. Front Mol Biosci. 2024 ;11 1402910
    Bioenergetic myths of energy transduction in eukaryotic cells.
    Guy C Brown.
      The study of energy transduction in eukaryotic cells has been divided between Bioenergetics and Physiology, reflecting and contributing to a variety of Bioenergetic myths considered here: 1) ATP production = energy production, 2) energy transduction is confined to mitochondria (plus glycolysis and chloroplasts), 3) mitochondria only produce heat when required, 4) glycolysis is inefficient compared to mitochondria, and 5) mitochondria are the main source of reactive oxygen species (ROS) in cells. These myths constitute a 'mitocentric' view of the cell that is wrong or unbalanced. In reality, mitochondria are the main site of energy dissipation and heat production in cells, and this is an essential function of mitochondria in mammals. Energy transduction and ROS production occur throughout the cell, particularly the cytosol and plasma membrane, and all cell membranes act as two-dimensional energy conduits. Glycolysis is efficient, and produces less heat per ATP than mitochondria, which might explain its increased use in muscle and cancer cells.
    Keywords:  Warburg effect; bioenergetics; cancer; cell metabolism; energetics; glycolysis; mitochondria; oxidative stress
    DOI:  https://doi.org/10.3389/fmolb.2024.1402910
  42. Cancer Discov. 2024 Jul 03.
    Oncogenic KRAS-dependent stromal interleukin-33 directs the pancreatic microenvironment to promote tumor growth.
    Katelyn L Donahue, Hannah R Watkoske, Padma Kadiyala, Wenting Du, Kristee Brown, Michael K Scales, Ahmed M Elhossiny, Carlos E Espinoza, Emily L Lasse Opsahl, Brian D Griffith, Yukang Wen, Lei Sun, Ashley Velez-Delgado, Nur M Renollet, Jacqueline Morales, Nicholas M Nedzesky, Rachael K Baliira, Rosa E Menjivar, Paola I Medina-Cabrera, Arvind Rao, Benjamin Allen, Jiaqi Shi, Timothy L Frankel, Eileen S Carpenter, Filip Bednar, Yaqing Zhang, Marina Pasca di Magliano.
      Pancreatic cancer is characterized by an extensive fibroinflammatory microenvironment. During carcinogenesis, normal stromal cells are converted to cytokine-high cancer associated fibroblasts (CAFs). The mechanisms underlying this conversion, including regulation and function of fibroblast-derived cytokines, are poorly understood. Thus, efforts to target CAFs therapeutically have so far failed. Here, we show that signals from epithelial cells expressing oncogenic KRAS -a hallmark pancreatic cancer mutation- activate fibroblast autocrine signaling, which drives expression of the cytokine interleukin-33 (IL-33). Stromal IL-33 expression remains high and dependent on epithelial KRAS throughout carcinogenesis; in turn, environmental stress induces IL-33 secretion. Using compartment-specific IL-33 knockout mice, we observed that lack of stromal IL-33 leads to profound reprogramming of multiple components of the pancreatic tumor microenvironment, including CAFs, myeloid cells and lymphocytes. Notably, loss of stromal IL-33 leads to an increase in CD8+ T cell infiltration and activation, and, ultimately, reduced tumor growth.
    DOI:  https://doi.org/10.1158/2159-8290.CD-24-0100
  43. Elife. 2024 Jul 02. pii: RP90551. [Epub ahead of print]12
    Neutrophils actively swell to potentiate rapid migration.
    Tamas L Nagy, Evelyn Strickland, Orion D Weiner.
      While the involvement of actin polymerization in cell migration is well-established, much less is known about the role of transmembrane water flow in cell motility. Here, we investigate the role of water influx in a prototypical migrating cell, the neutrophil, which undergoes rapid, directed movement to sites of injury, and infection. Chemoattractant exposure both increases cell volume and potentiates migration, but the causal link between these processes are not known. We combine single-cell volume measurements and a genome-wide CRISPR screen to identify the regulators of chemoattractant-induced neutrophil swelling, including NHE1, AE2, PI3K-gamma, and CA2. Through NHE1 inhibition in primary human neutrophils, we show that cell swelling is both necessary and sufficient for the potentiation of migration following chemoattractant stimulation. Our data demonstrate that chemoattractant-driven cell swelling complements cytoskeletal rearrangements to enhance migration speed.
    Keywords:  cell biology; cell migration; cell size; cell volume; human; neutrophil; physical forces; physics of living systems
    DOI:  https://doi.org/10.7554/eLife.90551
  44. Nat Metab. 2024 Jul 03.
    Emerging tools and best practices for studying gut microbial community metabolism.
    Cecilia Noecker, Peter J Turnbaugh.
      The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.
    DOI:  https://doi.org/10.1038/s42255-024-01074-z
  45. Cell. 2024 Jun 28. pii: S0092-8674(24)00652-4. [Epub ahead of print]
    Progestogen-driven B7-H4 contributes to onco-fetal immune tolerance.
    Jiali Yu, Yijian Yan, Shasha Li, Ying Xu, Abhijit Parolia, Syed Rizvi, Weichao Wang, Yiwen Zhai, Rongxin Xiao, Xiong Li, Peng Liao, Jiajia Zhou, Karolina Okla, Heng Lin, Xun Lin, Sara Grove, Shuang Wei, Linda Vatan, Jiantao Hu, Justyna Szumilo, Jan Kotarski, Zachary T Freeman, Stephanie Skala, Max Wicha, Kathleen R Cho, Arul M Chinnaiyan, Samantha Schon, Fei Wen, Ilona Kryczek, Shaomeng Wang, Lieping Chen, Weiping Zou.
      Immune tolerance mechanisms are shared in cancer and pregnancy. Through cross-analyzing single-cell RNA-sequencing data from multiple human cancer types and the maternal-fetal interface, we found B7-H4 (VTCN1) is an onco-fetal immune tolerance checkpoint. We showed that genetic deficiency of B7-H4 resulted in immune activation and fetal resorption in allogeneic pregnancy models. Analogously, B7-H4 contributed to MPA/DMBA-induced breast cancer progression, accompanied by CD8+ T cell exhaustion. Female hormone screening revealed that progesterone stimulated B7-H4 expression in placental and breast cancer cells. Mechanistically, progesterone receptor (PR) bound to a newly identified -58 kb enhancer, thereby mediating B7-H4 transcription via the PR-P300-BRD4 axis. PR antagonist or BRD4 degrader potentiated immunotherapy in a murine B7-H4+ breast cancer model. Thus, our work unravels a mechanistic and biological connection of a female sex hormone (progesterone) to onco-fetal immune tolerance via B7-H4 and suggests that the PR-P300-BRD4 axis is targetable for treating B7-H4+ cancer.
    Keywords:  B7-H4; BRD4; T cell exhaustion; cancer; enhancer; immune checkpoint; immunotherapy; onco-fetal immune tolerance; pregnancy; progesterone
    DOI:  https://doi.org/10.1016/j.cell.2024.06.012
  46. Cancer Lett. 2024 Jul 02. pii: S0304-3835(24)00486-5. [Epub ahead of print] 217091
    MCT1-dependent lactate recycling is a metabolic vulnerability in colorectal cancer cells upon acquired resistance to anti-EGFR targeted therapy.
    Elena Richiardone, Rim Al Roumi, Fanny Lardinois, Maria Virginia Giolito, Jérôme Ambroise, Romain Boidot, Bernhard Drotleff, Bart Ghesquière, Akeila Bellahcène, Alberto Bardelli, Sabrina Arena, Cyril Corbet.
      Despite the implementation of personalized medicine, patients with metastatic CRC (mCRC) still have a dismal overall survival due to the frequent occurrence of acquired resistance mechanisms thereby leading to clinical relapse. Understanding molecular mechanisms that support acquired resistance to anti-EGFR targeted therapy in mCRC is therefore clinically relevant and key to improving patient outcomes. Here, we observe distinct metabolic changes between cetuximab-resistant CRC cell populations, with in particular an increased glycolytic activity in KRAS-mutant cetuximab-resistant CRC cells (LIM1215 and OXCO2) but not in KRAS-amplified resistant DiFi cells. We show that cetuximab-resistant LIM1215 and OXCO2 cells have the capacity to recycle glycolysis-derived lactate to sustain their growth capacity. This is associated with an upregulation of the lactate importer MCT1 at both transcript and protein levels. Pharmacological inhibition of MCT1, with AR-C155858, reduces the uptake and oxidation of lactate and impairs growth capacity in cetuximab-resistant LIM1215 cells both in vitro and in vivo. This study identifies MCT1-dependent lactate utilization as a clinically actionable, metabolic vulnerability to overcome KRAS-mutant-mediated acquired resistance to anti-EGFR therapy in CRC.
    Keywords:  Colorectal cancer; KRAS; cetuximab; lactate; metabolism; monocarboxylate transporter; therapy resistance
    DOI:  https://doi.org/10.1016/j.canlet.2024.217091
  47. Cancer Res. 2024 Jul 03.
    Asparagine Dependency is a Targetable Metabolic Vulnerability in TP53-Altered Castration-Resistant Prostate Cancer.
    Young A Yoo, Songhua Quan, William Yang, Qianyu Guo, Yara Rodríguez, Zachary R Chalmers, Mary F Dufficy, Barbara Lackie, Vinay Sagar, Kenji Unno, Mihai I Truica, Navdeep S Chandel, Sarki A Abdulkadir.
      The TP53 tumor suppressor is frequently altered in lethal, castration-resistant prostate cancer (CRPC). However, to date there are no effective treatments that specifically target TP53 alterations. Using transcriptomic and metabolomic analyses, we showed here that TP53-altered prostate cancer (PCa) exhibits an increased dependency on asparagine and overexpresses asparagine synthetase (ASNS), the enzyme catalyzing the synthesis of asparagine. Mechanistically, loss or mutation of TP53 transcriptionally activated ASNS expression, directly as well as via mTORC1-mediated ATF4 induction, driving de novo asparagine biosynthesis to support CRPC growth. TP53-altered CRPC cells were sensitive to asparagine restriction by knockdown of ASNS or L-asparaginase treatment to deplete the intracellular and extracellular sources of asparagine, respectively, and cell viability was rescued by asparagine addition. Notably, pharmacological inhibition of intracellular asparagine biosynthesis using a glutaminase inhibitor and depletion of extracellular asparagine with L-asparaginase significantly reduced asparagine production and effectively impaired CRPC growth. This study highlights the significance of ASNS-mediated metabolic adaptation as a synthetic vulnerability in CRPC with TP53 alterations, providing a rationale for targeting asparagine production to treat these lethal prostate cancers.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-23-2910
  48. Nat Rev Cancer. 2024 Jul 04.
    Carcinogenesis at single-cell resolution.
    Daniela Senft.
      
    DOI:  https://doi.org/10.1038/s41568-024-00722-6
  49. J Clin Invest. 2024 Jul 01. pii: e175560. [Epub ahead of print]134(13):
    Primary cilia formation requires the Leigh syndrome-associated mitochondrial protein NDUFAF2.
    Chien-Hui Lo, Zhiquan Liu, Siyu Chen, Frank Lin, Andrew R Berneshawi, Charles Q Yu, Euna B Koo, Tia J Kowal, Ke Ning, Yang Hu, Won-Jing Wang, Y Joyce Liao, Yang Sun.
      Mitochondria-related neurodegenerative diseases have been implicated in the disruption of primary cilia function. Mutation in an intrinsic mitochondrial complex I component NDUFAF2 has been identified in Leigh syndrome, a severe inherited mitochondriopathy. Mutations in ARMC9, which encodes a basal body protein, cause Joubert syndrome, a ciliopathy with defects in the brain, kidney, and eye. Here, we report a mechanistic link between mitochondria metabolism and primary cilia signaling. We discovered that loss of NDUFAF2 caused both mitochondrial and ciliary defects in vitro and in vivo and identified NDUFAF2 as a binding partner for ARMC9. We also found that NDUFAF2 was both necessary and sufficient for cilia formation and that exogenous expression of NDUFAF2 rescued the ciliary and mitochondrial defects observed in cells from patients with known ARMC9 deficiency. NAD+ supplementation restored mitochondrial and ciliary dysfunction in ARMC9-deficient cells and zebrafish and ameliorated the ocular motility and motor deficits of a patient with ARMC9 deficiency. The present results provide a compelling mechanistic link, supported by evidence from human studies, between primary cilia and mitochondrial signaling. Importantly, our findings have significant implications for the development of therapeutic approaches targeting ciliopathies.
    Keywords:  Cell biology; Neurodegeneration; Neurological disorders; Ophthalmology; Retinopathy
    DOI:  https://doi.org/10.1172/JCI175560
  50. bioRxiv. 2024 Jun 22. pii: 2024.06.21.600132. [Epub ahead of print]
    Precise measurement of molecular phenotypes with barcode-based CRISPRi systems.
    Joseph H Lobel, Nicholas T Ingolia.
      Genome-wide CRISPR-Cas9 screens have untangled regulatory networks and revealed the genetic underpinnings of diverse biological processes. Their success relies on experimental designs that interrogate specific molecular phenotypes and distinguish key regulators from background effects. Here, we realize these goals with a generalizable platform for CRISPR interference with barcoded expression reporter sequencing (CiBER-seq) that dramatically improves the sensitivity and scope of genome-wide screens. We systematically address technical factors that distort phenotypic measurements by normalizing expression reporters against closely-matched control promoters, integrated together into the genome at single copy. To test our ability to capture post-transcriptional and post-translational regulation through sequencing, we screened for genes that affected nonsense-mediated mRNA decay and Doa10-mediated cytosolic protein decay. Our optimized CiBER-seq screens accurately capture the known components of well-studied RNA and protein quality control pathways with minimal background. These results demonstrate the precision and versatility of CiBER-seq for dissecting the genetic networks controlling cellular behaviors.
    DOI:  https://doi.org/10.1101/2024.06.21.600132
  51. Nat Metab. 2024 Jul 02.
    Towards nutrition with precision: unlocking biomarkers as dietary assessment tools.
    Cătălina Cuparencu, Tuğçe Bulmuş-Tüccar, Jan Stanstrup, Giorgia La Barbera, Henrik M Roager, Lars O Dragsted.
      Precision nutrition requires precise tools to monitor dietary habits. Yet current dietary assessment instruments are subjective, limiting our understanding of the causal relationships between diet and health. Biomarkers of food intake (BFIs) hold promise to increase the objectivity and accuracy of dietary assessment, enabling adjustment for compliance and misreporting. Here, we update current concepts and provide a comprehensive overview of BFIs measured in urine and blood. We rank BFIs based on a four-level utility scale to guide selection and identify combinations of BFIs that specifically reflect complex food intakes, making them applicable as dietary instruments. We discuss the main challenges in biomarker development and illustrate key solutions for the application of BFIs in human studies, highlighting different strategies for selecting and combining BFIs to support specific study designs. Finally, we present a roadmap for BFI development and implementation to leverage current knowledge and enable precision in nutrition research.
    DOI:  https://doi.org/10.1038/s42255-024-01067-y
  52. bioRxiv. 2024 Jun 20. pii: 2024.06.19.599784. [Epub ahead of print]
    ER-GUARD: an evolutionarily conserved antioxidant defense system at ER membranes.
    Zhijian Ji, Taruna Pandey, Henry de Belly, Bingying Wang, Orion D Weiner, Yao Tang, Shouhong Guang, Thomas D Goddard, Dengke K Ma.
      Oxidative protein folding in the endoplasmic reticulum (ER) is essential for all eukaryotic cells yet generates hydrogen peroxide (H2O2), a reactive oxygen species (ROS). The ER-transmembrane protein that provides reducing equivalents to ER and guards the cytosol for antioxidant defense remains unidentified. Here we combine AlphaFold2-based and functional reporter screens in C. elegans to identify a previously uncharacterized and evolutionarily conserved protein ERGU-1 that fulfills these roles. Deleting C. elegans ERGU-1 causes excessive H2O2 and transcriptional gene up-regulation through SKN-1, homolog of mammalian antioxidant master regulator NRF2. ERGU-1 deficiency also impairs organismal reproduction and behaviors. Both C. elegans and human ERGU-1 proteins localize to ER membranes and form network reticulum structures. We name this system ER-GUARD, Endoplasmic Reticulum Guardian Aegis of Redox Defense. Human and Drosophila homologs of ERGU-1 can rescue C. elegans mutant phenotypes, demonstrating evolutionarily ancient and conserved functions. Together, our results reveal an ER-membrane-specific protein machinery and defense-net system ER-GUARD for peroxide detoxification and suggest a previously unknown but conserved pathway for antioxidant defense in animal cells.
    DOI:  https://doi.org/10.1101/2024.06.19.599784
  53. Cell Rep. 2024 Jul 03. pii: S2211-1247(24)00774-5. [Epub ahead of print]43(7): 114445
    Pro-survival signaling regulates lipophagy essential for multiple myeloma resistance to stress-induced death.
    Peng Peng, Colin Chavel, Wensheng Liu, Louise M Carlson, Sha Cao, Adam Utley, Scott H Olejniczak, Kelvin P Lee.
      Pro-survival metabolic adaptations to stress in tumorigenesis remain less well defined. We find that multiple myeloma (MM) is unexpectedly dependent on beta-oxidation of long-chain fatty acids (FAs) for survival under both basal and stress conditions. However, under stress conditions, a second pro-survival signal is required to sustain FA oxidation (FAO). We previously found that CD28 is expressed on MM cells and transduces a significant pro-survival/chemotherapy resistance signal. We now find that CD28 signaling regulates autophagy/lipophagy that involves activation of the Ca2+→AMPK→ULK1 axis and regulates the translation of ATG5 through HuR, resulting in sustained lipophagy, increased FAO, and enhanced MM survival. Conversely, blocking autophagy/lipophagy sensitizes MM to chemotherapy in vivo. Our findings link a pro-survival signal to FA availability needed to sustain the FAO required for cancer cell survival under stress conditions and identify lipophagy as a therapeutic target to overcome treatment resistance in MM.
    Keywords:  CD28; CP: Cancer; CP: Metabolism; autophagy; fatty acid metabolism; fatty acid oxidation; lipid droplets; lipophagy; multiple myeloma; pro-survival regulation
    DOI:  https://doi.org/10.1016/j.celrep.2024.114445
  54. Nat Ecol Evol. 2024 Jul 02.
    Metabolic complexity drives divergence in microbial communities.
    Michael R Silverstein, Jennifer M Bhatnagar, Daniel Segrè.
      Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.
    DOI:  https://doi.org/10.1038/s41559-024-02440-6
  55. Nat Commun. 2024 Jul 04. 15(1): 5611
    Non-homologous end joining shapes the genomic rearrangement landscape of chromothripsis from mitotic errors.
    Qing Hu, Jose Espejo Valle-Inclán, Rashmi Dahiya, Alison Guyer, Alice Mazzagatti, Elizabeth G Maurais, Justin L Engel, Huiming Lu, Anthony J Davis, Isidro Cortés-Ciriano, Peter Ly.
      Mitotic errors generate micronuclei entrapping mis-segregated chromosomes, which are susceptible to catastrophic fragmentation through chromothripsis. The reassembly of fragmented chromosomes by error-prone DNA double-strand break (DSB) repair generates diverse genomic rearrangements associated with human diseases. How specific repair pathways recognize and process these lesions remains poorly understood. Here we use CRISPR/Cas9 to systematically inactivate distinct DSB repair pathways and interrogate the rearrangement landscape of fragmented chromosomes. Deletion of canonical non-homologous end joining (NHEJ) components substantially reduces complex rearrangements and shifts the rearrangement landscape toward simple alterations without the characteristic patterns of chromothripsis. Following reincorporation into the nucleus, fragmented chromosomes localize within sub-nuclear micronuclei bodies (MN bodies) and undergo ligation by NHEJ within a single cell cycle. In the absence of NHEJ, chromosome fragments are rarely engaged by alternative end-joining or recombination-based mechanisms, resulting in delayed repair kinetics, persistent 53BP1-labeled MN bodies, and cell cycle arrest. Thus, we provide evidence supporting NHEJ as the exclusive DSB repair pathway generating complex rearrangements from mitotic errors.
    DOI:  https://doi.org/10.1038/s41467-024-49985-5
  56. Curr Biol. 2024 Jun 26. pii: S0960-9822(24)00757-7. [Epub ahead of print]
    Atg8/LC3 controls systemic nutrient surplus signaling in flies and humans.
    Aditi Madan, Kevin P Kelly, Patrick Bahk, Camille E Sullivan, Michelle E Poling, Ava E Brent, Mroj Alassaf, Julien Dubrulle, Akhila Rajan.
      Organisms experience constant nutritional flux. Mechanisms at the interface of opposing nutritional states-scarcity and surplus-enable organismal energy homeostasis. Contingent on nutritional stores, adipocytes secrete adipokines, such as the fat hormone leptin, to signal nutrient status to the central brain. Increased leptin secretion underlies metabolic dysregulation during common obesity, but the molecular mechanisms regulating leptin secretion from human adipocytes are poorly understood. Here, we report that Atg8/LC3 family proteins, best known for their role in autophagy during nutrient scarcity, play an evolutionarily conserved role during nutrient surplus by promoting adipokine secretion. We show that in a well-fed state, Atg8/LC3 promotes the secretion of the Drosophila functional leptin ortholog unpaired 2 (Upd2) and leptin from human adipocytes. Proteomic analyses reveal that LC3 directs leptin to a secretory pathway in human cells. We identified LC3-dependent extracellular vesicle (EV) loading and secretion (LDELS) as a required step for leptin release, highlighting a unique secretory route adopted by leptin in human adipocytes. In Drosophila, mutations to Upd2's Atg8 interaction motif (AIM) result in constitutive adipokine retention. Atg8-mediated Upd2 retention alters lipid storage and hunger response and rewires the bulk organismal transcriptome in a manner conducive to starvation survival. Thus, Atg8/LC3's bidirectional role in nutrient sensing-conveying nutrient surplus and responding to nutrient deprivation-enables organisms to manage nutrient flux effectively. We posit that decoding how bidirectional molecular switches-such as Atg8/LC3-operate at the nexus of nutritional scarcity and surplus will inform therapeutic strategies to tackle chronic metabolic disorders.
    Keywords:  Upd2; adipokine; autophagy independent; exosomes; leptin; obesity; satiety; starvation resilience; unconventional secretion
    DOI:  https://doi.org/10.1016/j.cub.2024.06.005
  57. Biochim Biophys Acta Bioenerg. 2024 Jun 28. pii: S0005-2728(24)00457-2. [Epub ahead of print]1865(4): 149487
    The mitochondrial aspartate/glutamate carrier does not transport GABA.
    Vito Porcelli, Serena Barile, Loredana Capobianco, Simona Nicole Barile, Ruggiero Gorgoglione, Giuseppe Fiermonte, Barbara Monti, Francesco Massimo Lasorsa, Luigi Palmieri.
      ɣ-aminobutyric acid (GABA) is a four‑carbon amino acid acting as the main inhibitory transmitter in the invertebrate and vertebrate nervous systems. The metabolism of GABA is well compartmentalized in the cell and the uptake of cytosolic GABA into the mitochondrial matrix is required for its degradation. A previous study carried out in the fruit fly Drosophila melanogaster indicated that the mitochondrial aspartate/glutamate carrier (AGC) is responsible for mitochondrial GABA accumulation. Here, we investigated the transport of GABA catalysed by the human and D. melanogaster AGC proteins through a well-established method for the study of the substrate specificity and the kinetic parameters of the mitochondrial carriers. In this experimental system, the D. melanogaster spliced AGC isoforms (Aralar1-PA and Aralar1-PE) and the human AGC isoforms (AGC1/aralar1 and AGC2/citrin) are unable to transport GABA both in homo- and in hetero-exchange with either glutamate or aspartate, i.e. the canonical substrates of AGC. Moreover, GABA has no inhibitory effect on the exchange activities catalysed by the investigated AGCs. Our data demonstrate that AGC does not transport GABA and the molecular identity of the GABA transporter in human and D. melanogaster mitochondria remains unknown.
    Keywords:  AGC; Aralar; Citrin; GABA; Mitochondrial carriers
    DOI:  https://doi.org/10.1016/j.bbabio.2024.149487
  58. Cancer Lett. 2024 Jul 02. pii: S0304-3835(24)00484-1. [Epub ahead of print] 217089
    A genome-wide CRISPR screen reveals that antagonism of glutamine metabolism sensitizes head and neck squamous cell carcinoma to ferroptotic cell death.
    Michael M Allevato, Sally Trinh, Keiichi Koshizuka, Daniela Nachmanson, Thien-Tu C Nguyen, Yumi Yokoyama, Xingyu Wu, Allen Andres, Zhiyong Wang, Jeramie Watrous, Alfredo A Molinolo, Prashant Mali, Olivier Harismendy, Mohit Jain, Robert Wild, J Silvio Gutkind.
      Glutamine is a conditionally essential amino acid for the growth and survival of rapidly proliferating cancer cells. Many cancers are addicted to glutamine, and as a result, targeting glutamine metabolism has been explored clinically as a therapeutic approach. Glutamine-catalyzing enzymes are highly expressed in primary and metastatic head and neck squamous cell carcinoma (HNSCC). However, the nature of the glutamine-associated pathways in this aggressive cancer type has not been elucidated. Here, we explored the therapeutic potential of a broad glutamine antagonist, DRP-104 (sirpiglenastat), in HNSCC tumors and aimed at shedding light on glutamine-dependent pathways in this disease. We observed a potent antitumoral effect of sirpiglenastat in HPV- and HPV+ HNSCC xenografts. We conducted a whole-genome CRISPR screen and metabolomics analyses to identify mechanisms of sensitivity and resistance to glutamine metabolism blockade. These approaches revealed that glutamine metabolism blockade results in the rapid buildup of polyunsaturated fatty acids (PUFAs) via autophagy nutrient-sensing pathways. Finally, our analysis demonstrated that GPX4 mediates the protection of HNSCC cells from accumulating toxic lipid peroxides; hence, glutamine blockade sensitizes HNSCC cells to ferroptosis cell death upon GPX4 inhibition. These findings demonstrate the therapeutic potential of sirpiglenastat in HNSCC and establish a novel link between glutamine metabolism and ferroptosis, which may be uniquely translated into targeted glutamine-ferroptosis combination therapies.
    Keywords:  Glutamine; autophagy; ferroptosis; head and neck squamous cell carcinoma; poly-unsaturated fatty acids; precision medicine; targeted therapy
    DOI:  https://doi.org/10.1016/j.canlet.2024.217089
  59. Mol Cell. 2024 Jun 27. pii: S1097-2765(24)00511-2. [Epub ahead of print]
    Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.
    Robert Ietswaart, Brendan M Smalec, Albert Xu, Karine Choquet, Erik McShane, Ziad Mohamoud Jowhar, Chantal K Guegler, Autum R Baxter-Koenigs, Emma R West, Becky Xu Hua Fu, Luke Gilbert, Stephen N Floor, L Stirling Churchman.
      Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.
    Keywords:  DDX3X; RNA dynamics; RNA flow; RNA-binding proteins; kinetic modeling; nuclear RNA degradation; nuclear export; poly(A) tails; subcellular TimeLapse-seq; translation
    DOI:  https://doi.org/10.1016/j.molcel.2024.06.008
  60. J Cell Biol. 2024 Sep 02. pii: e202311126. [Epub ahead of print]223(9):
    A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction.
    Xiao Li, Rico Gamuyao, Ming-Lun Wu, Woo Jung Cho, Sharon V King, R A Petersen, Daniel R Stabley, Caleb Lindow, Leslie K Climer, Abbas Shirinifard, Francesca Ferrara, Robert E Throm, Camenzind G Robinson, Yiwang Zhou, Alexandre F Carisey, Alison G Tebo, Chi-Lun Chang.
      Contact sites between lipid droplets and other organelles are essential for cellular lipid and energy homeostasis upon metabolic demands. Detection of these contact sites at the nanometer scale over time in living cells is challenging. We developed a tool kit for detecting contact sites based on fluorogen-activated bimolecular complementation at CONtact sites, FABCON, using a reversible, low-affinity split fluorescent protein, splitFAST. FABCON labels contact sites with minimal perturbation to organelle interaction. Via FABCON, we quantitatively demonstrated that endoplasmic reticulum (ER)- and mitochondria (mito)-lipid droplet contact sites are dynamic foci in distinct metabolic conditions, such as during lipid droplet biogenesis and consumption. An automated analysis pipeline further classified individual contact sites into distinct subgroups based on size, likely reflecting differential regulation and function. Moreover, FABCON is generalizable to visualize a repertoire of organelle contact sites including ER-mito. Altogether, FABCON reveals insights into the dynamic regulation of lipid droplet-organelle contact sites and generates new hypotheses for further mechanistical interrogation during metabolic regulation.
    DOI:  https://doi.org/10.1083/jcb.202311126
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