bims-camemi Biomed News
on Mitochondrial metabolism in cancer
Issue of 2024–03–24
78 papers selected by
Christian Frezza, Universität zu Köln
  1. SIRT4 loss reprograms intestinal nucleotide metabolism to support proliferation following perturbation of homeostasis.
  2. Knowledge-Based Therapeutics for Tricarboxylic Acid (TCA) Cycle-Deficient Cancers.
  3. The phospholipids cardiolipin and phosphatidylethanolamine differentially regulate MDC biogenesis.
  4. Polyamine-mediated ferroptosis amplification acts as a targetable vulnerability in cancer.
  5. How to let your data shine.
  6. A kinetic dichotomy between mitochondrial and nuclear gene expression processes.
  7. Tracing the Diverse Paths of One-Carbon Metabolism in Cancer and Beyond.
  8. AMPK and insulin control the switch between mitochondrial hitchhiking of Pink1 mRNA and mitophagy in neurons.
  9. Trigonelline is an NAD+ precursor that improves muscle function during ageing and is reduced in human sarcopenia.
  10. Sulfide oxidation promotes hypoxic angiogenesis and neovascularization.
  11. FAM86A methylation of eEF2 links mRNA translation elongation to tumorigenesis.
  12. An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway.
  13. Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy.
  14. A waste product's unexpected role in wasting.
  15. Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver.
  16. Activation of polyamine catabolism promotes glutamine metabolism and creates a targetable vulnerability in lung cancer.
  17. GAS41 modulates ferroptosis by anchoring NRF2 on chromatin.
  18. How the body's cholesterol factory avoids producing too much.
  19. Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability.
  20. Targeting NAD+ Metabolism to Modulate Autoimmunity and Inflammation.
  21. Integrating the response to stressed mitochondria.
  22. Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting transcriptional memory.
  23. Serine synthesis and catabolism in starved lung cancer and primary bronchial epithelial cells.
  24. Up-regulation of cholesterol synthesis by lysosomal defects requires a functional mitochondrial respiratory chain.
  25. Competence for neural crest induction is controlled by hydrostatic pressure through Yap.
  26. Oncogenic KRAS induces arginine auxotrophy and confers a therapeutic vulnerability to SLC7A1 inhibition in non-small cell lung cancer.
  27. Off-target depletion of plasma tryptophan by allosteric inhibitors of BCKDK.
  28. Kynurenine 3-monooxygenase (KMO) limits de novo NAD+ synthesis through dietary tryptophan in renal proximal tubule epithelial cell models.
  29. Mitochondrial Raf1 Regulates Glutamine Catabolism.
  30. Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis.
  31. Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring.
  32. Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes.
  33. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy.
  34. The circadian molecular clock in the suprachiasmatic nucleus is necessary but not sufficient for fear entrainment.
  35. STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma.
  36. Mitochondrial dynamics: Regulating cell metabolism, homoeostasis, health and disease.
  37. Activation of GPR81 by lactate drives tumour-induced cachexia.
  38. A SIFI odyssey: Silencing the stress response amid mitochondrial import blockade to safeguard cell survival.
  39. Disease-associated astrocyte epigenetic memory promotes CNS pathology.
  40. Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.
  41. Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation.
  42. The alanyl-tRNA synthetase AARS1 moonlights as a lactyl-transferase to promote YAP signaling in gastric cancer.
  43. Metabolic regulation of skeletal cell fate and function.
  44. A code within the genetic code.
  45. MCU-independent Ca2+ uptake mediates mitochondrial Ca2+ overload and necrotic cell death in a mouse model of Duchenne muscular dystrophy.
  46. The AMPK-related kinase NUAK1 controls cortical axons branching by locally modulating mitochondrial metabolic functions.
  47. GALDAR: A genetically encoded galactose sensor for visualizing sugar metabolism in vivo.
  48. Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.
  49. Structural determinants of mitochondrial STAT3 targeting and function.
  50. MYC dependency in GLS1 and NAMPT is a therapeutic vulnerability in multiple myeloma.
  51. A fast-acting lipid checkpoint in G1 prevents mitotic defects.
  52. Tubular CPT1A deletion minimally affects aging and chronic kidney injury.
  53. Lac-Phe mediates the effects of metformin on food intake and body weight.
  54. A citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations.
  55. p53 regulates diverse tissue-specific outcomes to endogenous DNA damage in mice.
  56. The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis.
  57. Cellular energy regulates mRNA degradation in a codon-specific manner.
  58. Poly(ADP-ribose) mediates bioenergetic defects and redox imbalance in neurons following oxygen and glucose deprivation.
  59. Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH.
  60. One size does not fit all: Lysosomes exist in biochemically and functionally distinct states.
  61. SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia.
  62. TOR regulates variability of protein synthesis rates.
  63. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.
  64. A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity.
  65. Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance.
  66. Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance.
  67. Intervention with metabolites emulating endogenous cell transitions accelerates muscle regeneration in young and aged mice.
  68. Cancer cells hijack physiological metabolic signals to seed liver metastasis.
  69. Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.
  70. Comprehensive blood metabolomics profiling of Parkinson's disease reveals coordinated alterations in xanthine metabolism.
  71. Uncoupling of behavioral and metabolic 24-h rhythms in reindeer.
  72. Anti-apoptotic MCL-1 promotes long-chain fatty acid oxidation through interaction with ACSL1.
  73. Metformin and feeding increase levels of the appetite-suppressing metabolite Lac-Phe in humans.
  74. Energy balance drives diurnal and nocturnal brain transcriptome rhythms.
  75. Serine metabolism is crucial for cGAS-STING signaling and viral defense control in the gut.
  76. Whittling down the bacterial subspecies that might drive colon cancer.
  77. Multicenter integrated analysis of noncoding CRISPRi screens.
  78. Metformin induces a Lac-Phe gut-brain signalling axis.
  1. Cell Rep. 2024 Mar 19. pii: S2211-1247(24)00303-6. [Epub ahead of print]43(4): 113975
    SIRT4 loss reprograms intestinal nucleotide metabolism to support proliferation following perturbation of homeostasis.
    Sarah A Tucker, Song-Hua Hu, Sejal Vyas, Albert Park, Shakchhi Joshi, Aslihan Inal, Tiffany Lam, Emily Tan, Kevin M Haigis, Marcia C Haigis.
      The intestine is a highly metabolic tissue, but the metabolic programs that influence intestinal crypt proliferation, differentiation, and regeneration are still emerging. Here, we investigate how mitochondrial sirtuin 4 (SIRT4) affects intestinal homeostasis. Intestinal SIRT4 loss promotes cell proliferation in the intestine following ionizing radiation (IR). SIRT4 functions as a tumor suppressor in a mouse model of intestinal cancer, and SIRT4 loss drives dysregulated glutamine and nucleotide metabolism in intestinal adenomas. Intestinal organoids lacking SIRT4 display increased proliferation after IR stress, along with increased glutamine uptake and a shift toward de novo nucleotide biosynthesis over salvage pathways. Inhibition of de novo nucleotide biosynthesis diminishes the growth advantage of SIRT4-deficient organoids after IR stress. This work establishes SIRT4 as a modulator of intestinal metabolism and homeostasis in the setting of DNA-damaging stress.
    Keywords:  CP: Cancer; SIRT4; glutamine; intestinal organoids; irradiation; nucleotide biosynthesis; nucleotide metabolism; sirtuin
    DOI:  https://doi.org/10.1016/j.celrep.2024.113975
  2. Cold Spring Harb Perspect Med. 2024 Mar 19. pii: a041536. [Epub ahead of print]
    Knowledge-Based Therapeutics for Tricarboxylic Acid (TCA) Cycle-Deficient Cancers.
    Daniel Peled, Ruth Casey, Eyal Gottlieb.
      With the foundation pre-laid, research in the new millennium has readily excavated and expanded upon the architectural framework laid out by Otto Warburg's seminal work in a new wave of "westward expansion," ever widening our understanding of cancer metabolism beyond the telescopic vision seen over a century ago. On this path, the unique circuitry of the cancer metabolic program has been elucidated, illuminating mutations of conserved cellular pathways implicated in tumorigenesis. Paramount among these are mutations in tricarboxylic acid cycle enzymes, succinate dehydrogenase, and fumarate hydratase, leading to deleterious accumulations in metabolic intermediates, "oncometabolites," the pilots of the disease process. In this work, we seek to reflect on the advancements in the field in recent years, updating knowledge on the exact biochemical mechanisms at the helm of the tumor, providing rationale for clinical trials currently underway, and anticipating directions for the future on this expansive frontier.
    DOI:  https://doi.org/10.1101/cshperspect.a041536
  3. J Cell Biol. 2024 May 06. pii: e202302069. [Epub ahead of print]223(5):
    The phospholipids cardiolipin and phosphatidylethanolamine differentially regulate MDC biogenesis.
    Tianyao Xiao, Alyssa M English, Zachary N Wilson, J Alan Maschek, James E Cox, Adam L Hughes.
      Cells utilize multiple mechanisms to maintain mitochondrial homeostasis. We recently characterized a pathway that remodels mitochondria in response to metabolic alterations and protein overload stress. This remodeling occurs via the formation of large membranous structures from the mitochondrial outer membrane called mitochondrial-derived compartments (MDCs), which are eventually released from mitochondria and degraded. Here, we conducted a microscopy-based screen in budding yeast to identify factors that regulate MDC formation. We found that two phospholipids, cardiolipin (CL) and phosphatidylethanolamine (PE), differentially regulate MDC biogenesis. CL depletion impairs MDC biogenesis, whereas blocking mitochondrial PE production leads to constitutive MDC formation. Additionally, in response to metabolic MDC activators, cellular and mitochondrial PE declines, and overexpressing mitochondrial PE synthesis enzymes suppress MDC biogenesis. Altogether, our data indicate a requirement for CL in MDC biogenesis and suggest that PE depletion may stimulate MDC formation downstream of MDC-inducing metabolic stress.
    DOI:  https://doi.org/10.1083/jcb.202302069
  4. Nat Commun. 2024 Mar 19. 15(1): 2461
    Polyamine-mediated ferroptosis amplification acts as a targetable vulnerability in cancer.
    Guoshu Bi, Jiaqi Liang, Yunyi Bian, Guangyao Shan, Yiwei Huang, Tao Lu, Huan Zhang, Xing Jin, Zhencong Chen, Mengnan Zhao, Hong Fan, Qun Wang, Boyi Gan, Cheng Zhan.
      Targeting ferroptosis, an iron-dependent form of regulated cell death triggered by the lethal overload of lipid peroxides, in cancer therapy is impeded by our limited understanding of the intersection of tumour's metabolic feature and ferroptosis vulnerability. In the present study, arginine is identified as a ferroptotic promoter using a metabolites library. This effect is mainly achieved through arginine's conversion to polyamines, which exerts their potent ferroptosis-promoting property in an H2O2-dependent manner. Notably, the expression of ornithine decarboxylase 1 (ODC1), the critical enzyme catalysing polyamine synthesis, is significantly activated by the ferroptosis signal--iron overload--through WNT/MYC signalling, as well as the subsequent elevated polyamine synthesis, thus forming a ferroptosis-iron overload-WNT/MYC-ODC1-polyamine-H2O2 positive feedback loop that amplifies ferroptosis. Meanwhile, we notice that ferroptotic cells release enhanced polyamine-containing extracellular vesicles into the microenvironment, thereby further sensitizing neighbouring cells to ferroptosis and accelerating the "spread" of ferroptosis in the tumour region. Besides, polyamine supplementation also sensitizes cancer cells or xenograft tumours to radiotherapy or chemotherapy through inducing ferroptosis. Considering that cancer cells are often characterized by elevated intracellular polyamine pools, our results indicate that polyamine metabolism exposes a targetable vulnerability to ferroptosis and represents an exciting opportunity for therapeutic strategies for cancer.
    DOI:  https://doi.org/10.1038/s41467-024-46776-w
  5. Nat Metab. 2024 Mar 19.
    How to let your data shine.
      
    DOI:  https://doi.org/10.1038/s42255-024-01026-7
  6. Mol Cell. 2024 Mar 14. pii: S1097-2765(24)00170-9. [Epub ahead of print]
    A kinetic dichotomy between mitochondrial and nuclear gene expression processes.
    Erik McShane, Mary Couvillion, Robert Ietswaart, Gyan Prakash, Brendan M Smalec, Iliana Soto, Autum R Baxter-Koenigs, Karine Choquet, L Stirling Churchman.
      Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared with nuclear mRNAs, mt-mRNAs were produced 1,100-fold more, degraded 7-fold faster, and accumulated to 160-fold higher levels. Quantitative modeling and depletion of mitochondrial factors LRPPRC and FASTKD5 identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
    Keywords:  LRPPRC; Leighs disease; RNA life cycle; gene regulation; genetic conflict; metabolic regulation; mitochondrial gene expression; mitochondrial translation; mitonuclear balance; organellular biogenesis; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.028
  7. Cold Spring Harb Perspect Med. 2024 Mar 19. pii: a041533. [Epub ahead of print]
    Tracing the Diverse Paths of One-Carbon Metabolism in Cancer and Beyond.
    Esther W Lim, Christian M Metallo.
      One-carbon (1C) metabolism is a network of biochemical reactions distributed across organelles that delivers folate-activated 1C units to support macromolecule synthesis, methylation, and reductive homeostasis. Fluxes through these pathways are up-regulated in highly proliferative cancer cells, and anti-folates, which target enzymes within the 1C pathway, have long been used in the treatment of cancer. In this work, we review fundamental aspects of 1C metabolism and place it in context with other biosynthetic and redox pathways, such that 1C metabolism acts to bridge pathways across compartments. We further discuss the importance of stable-isotope-tracing techniques combined with mass spectrometry analysis to study 1C metabolism and conclude by highlighting therapeutic approaches that could exploit cancer cells' dependency on 1C metabolism.
    DOI:  https://doi.org/10.1101/cshperspect.a041533
  8. Nat Metab. 2024 Mar 19.
    AMPK and insulin control the switch between mitochondrial hitchhiking of Pink1 mRNA and mitophagy in neurons.
      
    DOI:  https://doi.org/10.1038/s42255-024-01006-x
  9. Nat Metab. 2024 Mar 19.
    Trigonelline is an NAD+ precursor that improves muscle function during ageing and is reduced in human sarcopenia.
    Mathieu Membrez, Eugenia Migliavacca, Stefan Christen, Keisuke Yaku, Jennifer Trieu, Alaina K Lee, Francesco Morandini, Maria Pilar Giner, Jade Stiner, Mikhail V Makarov, Emma S Garratt, Maria F Vasiloglou, Lucie Chanvillard, Emilie Dalbram, Amy M Ehrlich, José Luis Sanchez-Garcia, Carles Canto, Leonidas G Karagounis, Jonas T Treebak, Marie E Migaud, Ramin Heshmat, Farideh Razi, Neerja Karnani, Afshin Ostovar, Farshad Farzadfar, Stacey K H Tay, Matthew J Sanders, Karen A Lillycrop, Keith M Godfrey, Takashi Nakagawa, Sofia Moco, René Koopman, Gordon S Lynch, Vincenzo Sorrentino, Jerome N Feige.
      Mitochondrial dysfunction and low nicotinamide adenine dinucleotide (NAD+) levels are hallmarks of skeletal muscle ageing and sarcopenia1-3, but it is unclear whether these defects result from local changes or can be mediated by systemic or dietary cues. Here we report a functional link between circulating levels of the natural alkaloid trigonelline, which is structurally related to nicotinic acid4, NAD+ levels and muscle health in multiple species. In humans, serum trigonelline levels are reduced with sarcopenia and correlate positively with muscle strength and mitochondrial oxidative phosphorylation in skeletal muscle. Using naturally occurring and isotopically labelled trigonelline, we demonstrate that trigonelline incorporates into the NAD+ pool and increases NAD+ levels in Caenorhabditis elegans, mice and primary myotubes from healthy individuals and individuals with sarcopenia. Mechanistically, trigonelline does not activate GPR109A but is metabolized via the nicotinate phosphoribosyltransferase/Preiss-Handler pathway5,6 across models. In C. elegans, trigonelline improves mitochondrial respiration and biogenesis, reduces age-related muscle wasting and increases lifespan and mobility through an NAD+-dependent mechanism requiring sirtuin. Dietary trigonelline supplementation in male mice enhances muscle strength and prevents fatigue during ageing. Collectively, we identify nutritional supplementation of trigonelline as an NAD+-boosting strategy with therapeutic potential for age-associated muscle decline.
    DOI:  https://doi.org/10.1038/s42255-024-00997-x
  10. Nat Chem Biol. 2024 Mar 20.
    Sulfide oxidation promotes hypoxic angiogenesis and neovascularization.
    Roshan Kumar, Victor Vitvitsky, Apichaya Sethaudom, Rashi Singhal, Sumeet Solanki, Sydney Alibeckoff, Harrison L Hiraki, Hannah N Bell, Anthony Andren, Brendon M Baker, Costas A Lyssiotis, Yatrik M Shah, Ruma Banerjee.
      Angiogenic programming in the vascular endothelium is a tightly regulated process for maintaining tissue homeostasis and is activated in tissue injury and the tumor microenvironment. The metabolic basis of how gas signaling molecules regulate angiogenesis is elusive. Here, we report that hypoxic upregulation of ·NO in endothelial cells reprograms the transsulfuration pathway to increase biogenesis of hydrogen sulfide (H2S), a proangiogenic metabolite. However, decreased H2S oxidation due to sulfide quinone oxidoreductase (SQOR) deficiency synergizes with hypoxia, inducing a reductive shift and limiting endothelial proliferation that is attenuated by dissipation of the mitochondrial NADH pool. Tumor xenografts in whole-body (WBCreSqorfl/fl) and endothelial-specific (VE-cadherinCre-ERT2Sqorfl/fl) Sqor-knockout mice exhibit lower mass and angiogenesis than control mice. WBCreSqorfl/fl mice also exhibit decreased muscle angiogenesis following femoral artery ligation compared to control mice. Collectively, our data reveal the molecular intersections between H2S, O2 and ·NO metabolism and identify SQOR inhibition as a metabolic vulnerability for endothelial cell proliferation and neovascularization.
    DOI:  https://doi.org/10.1038/s41589-024-01583-8
  11. Mol Cell. 2024 Mar 12. pii: S1097-2765(24)00180-1. [Epub ahead of print]
    FAM86A methylation of eEF2 links mRNA translation elongation to tumorigenesis.
    Joel William Francis, Simone Hausmann, Sabeen Ikram, Kunlun Yin, Robert Mealey-Farr, Natasha Mahealani Flores, Annie Truc Trinh, Tourkian Chasan, Julia Thompson, Pawel Karol Mazur, Or Gozani.
      eEF2 post-translational modifications (PTMs) can profoundly affect mRNA translation dynamics. However, the physiologic function of eEF2K525 trimethylation (eEF2K525me3), a PTM catalyzed by the enzyme FAM86A, is unknown. Here, we find that FAM86A methylation of eEF2 regulates nascent elongation to promote protein synthesis and lung adenocarcinoma (LUAD) pathogenesis. The principal physiologic substrate of FAM86A is eEF2, with K525me3 modeled to facilitate productive eEF2-ribosome engagement during translocation. FAM86A depletion in LUAD cells causes 80S monosome accumulation and mRNA translation inhibition. FAM86A is overexpressed in LUAD and eEF2K525me3 levels increase through advancing LUAD disease stages. FAM86A knockdown attenuates LUAD cell proliferation and suppression of the FAM86A-eEF2K525me3 axis inhibits cancer cell and patient-derived LUAD xenograft growth in vivo. Finally, FAM86A ablation strongly attenuates tumor growth and extends survival in KRASG12C-driven LUAD mouse models. Thus, our work uncovers an eEF2 methylation-mediated mRNA translation elongation regulatory node and nominates FAM86A as an etiologic agent in LUAD.
    Keywords:  FAM86A; KRAS; cancer; eEF2; elongation; lung; lysine methylation; mRNA translation; protein synthesis
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.037
  12. Nat Commun. 2024 Mar 21. 15(1): 2517
    An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway.
    Grace Y Liu, Patrick Jouandin, Raymond E Bahng, Norbert Perrimon, David M Sabatini.
      Animals sense and respond to nutrient availability in their environments, a task coordinated in part by the mTOR complex 1 (mTORC1) pathway. mTORC1 regulates growth in response to nutrients and, in mammals, senses specific amino acids through specialized sensors that bind the GATOR1/2 signaling hub. Given that animals can occupy diverse niches, we hypothesized that the pathway might evolve distinct sensors in different metazoan phyla. Whether such customization occurs, and how the mTORC1 pathway might capture new inputs, is unknown. Here, we identify the Drosophila melanogaster protein Unmet expectations (CG11596) as a species-restricted methionine sensor that directly binds the fly GATOR2 complex in a fashion antagonized by S-adenosylmethionine (SAM). We find that in Dipterans GATOR2 rapidly evolved the capacity to bind Unmet and to thereby repurpose a previously independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes to expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise conserved system.
    DOI:  https://doi.org/10.1038/s41467-024-46680-3
  13. Cell Metab. 2024 Mar 13. pii: S1550-4131(24)00061-5. [Epub ahead of print]
    Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy.
    Haikuo Li, Dian Li, Nicolas Ledru, Qiao Xuanyuan, Haojia Wu, Amish Asthana, Lori N Byers, Stefan G Tullius, Giuseppe Orlando, Sushrut S Waikar, Benjamin D Humphreys.
      A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes. We find that the same cell type, including thin limb, thick ascending limb loop of Henle and principal cells, display distinct transcriptomic, chromatin accessibility, and metabolomic signatures, depending on anatomic location. Surveying metabolism-associated gene profiles revealed non-overlapping metabolic signatures between nephron segments and dysregulated lipid metabolism in diseased proximal tubule (PT) cells. Integrating multimodal omics with clinical data identified PLEKHA1 as a disease marker, and its in vitro knockdown increased gene expression in PT differentiation, suggesting possible pathogenic roles. This study highlights previously underrepresented cellular heterogeneity underlying the human kidney anatomy.
    Keywords:  MALDI-MS; SHARE-seq; acute kidney injury; anatomy; chronic kidney disease; lipid metabolism; metabolism; multiomics; single-cell combinatorial indexing; spatial metabolomics
    DOI:  https://doi.org/10.1016/j.cmet.2024.02.015
  14. Nat Metab. 2024 Mar 18.
    A waste product's unexpected role in wasting.
    Jack D Sanford, Marcus D Goncalves.
      
    DOI:  https://doi.org/10.1038/s42255-024-01010-1
  15. Nat Commun. 2024 Mar 18. 15(1): 1878
    Hepatic nutrient and hormone signaling to mTORC1 instructs the postnatal metabolic zonation of the liver.
    Ana Belén Plata-Gómez, Lucía de Prado-Rivas, Alba Sanz, Nerea Deleyto-Seldas, Fernando García, Celia de la Calle Arregui, Camila Silva, Eduardo Caleiras, Osvaldo Graña-Castro, Elena Piñeiro-Yáñez, Joseph Krebs, Luis Leiva-Vega, Javier Muñoz, Ajay Jain, Guadalupe Sabio, Alejo Efeyan.
      The metabolic functions of the liver are spatially organized in a phenomenon called zonation, linked to the differential exposure of portal and central hepatocytes to nutrient-rich blood. The mTORC1 signaling pathway controls cellular metabolism in response to nutrients and insulin fluctuations. Here we show that simultaneous genetic activation of nutrient and hormone signaling to mTORC1 in hepatocytes results in impaired establishment of postnatal metabolic and zonal identity of hepatocytes. Mutant hepatocytes fail to upregulate postnatally the expression of Frizzled receptors 1 and 8, and show reduced Wnt/β-catenin activation. This defect, alongside diminished paracrine Wnt2 ligand expression by endothelial cells, underlies impaired postnatal maturation. Impaired zonation is recapitulated in a model of constant supply of nutrients by parenteral nutrition to piglets. Our work shows the role of hepatocyte sensing of fluctuations in nutrients and hormones for triggering a latent metabolic zonation program.
    DOI:  https://doi.org/10.1038/s41467-024-46032-1
  16. Proc Natl Acad Sci U S A. 2024 Mar 26. 121(13): e2319429121
    Activation of polyamine catabolism promotes glutamine metabolism and creates a targetable vulnerability in lung cancer.
    Xinlu Han, Deyu Wang, Liao Yang, Ning Wang, Jianliang Shen, Jinghan Wang, Lei Zhang, Li Chen, Shenglan Gao, Wei-Xing Zong, Yongbo Wang.
      Polyamines are a class of small polycationic alkylamines that play essential roles in both normal and cancer cell growth. Polyamine metabolism is frequently dysregulated and considered a therapeutic target in cancer. However, targeting polyamine metabolism as monotherapy often exhibits limited efficacy, and the underlying mechanisms are incompletely understood. Here we report that activation of polyamine catabolism promotes glutamine metabolism, leading to a targetable vulnerability in lung cancer. Genetic and pharmacological activation of spermidine/spermine N1-acetyltransferase 1 (SAT1), the rate-limiting enzyme of polyamine catabolism, enhances the conversion of glutamine to glutamate and subsequent glutathione (GSH) synthesis. This metabolic rewiring ameliorates oxidative stress to support lung cancer cell proliferation and survival. Simultaneous glutamine limitation and SAT1 activation result in ROS accumulation, growth inhibition, and cell death. Importantly, pharmacological inhibition of either one of glutamine transport, glutaminase, or GSH biosynthesis in combination with activation of polyamine catabolism synergistically suppresses lung cancer cell growth and xenograft tumor formation. Together, this study unveils a previously unappreciated functional interconnection between polyamine catabolism and glutamine metabolism and establishes cotargeting strategies as potential therapeutics in lung cancer.
    Keywords:  SAT1; glutamine metabolism; lung cancer; polyamine catabolism
    DOI:  https://doi.org/10.1073/pnas.2319429121
  17. Nat Commun. 2024 Mar 21. 15(1): 2531
    GAS41 modulates ferroptosis by anchoring NRF2 on chromatin.
    Zhe Wang, Xin Yang, Delin Chen, Yanqing Liu, Zhiming Li, Shoufu Duan, Zhiguo Zhang, Xuejun Jiang, Brent R Stockwell, Wei Gu.
      YEATS domain-containing protein GAS41 is a histone reader and oncogene. Here, through genome-wide CRISPR-Cas9 screenings, we identify GAS41 as a repressor of ferroptosis. GAS41 interacts with NRF2 and is critical for NRF2 to activate its targets such as SLC7A11 for modulating ferroptosis. By recognizing the H3K27-acetylation (H3K27-ac) marker, GAS41 is recruited to the SLC7A11 promoter, independent of NRF2 binding. By bridging the interaction between NRF2 and the H3K27-ac marker, GAS41 acts as an anchor for NRF2 on chromatin in a promoter-specific manner for transcriptional activation. Moreover, the GAS41-mediated effect on ferroptosis contributes to its oncogenic role in vivo. These data demonstrate that GAS41 is a target for modulating tumor growth through ferroptosis. Our study reveals a mechanism for GAS41-mediated regulation in transcription by anchoring NRF2 on chromatin, and provides a model in which the DNA binding activity on chromatin by transcriptional factors (NRF2) can be directly regulated by histone markers (H3K27-ac).
    DOI:  https://doi.org/10.1038/s41467-024-46857-w
  18. Nature. 2024 Mar 18.
    How the body's cholesterol factory avoids producing too much.
      
    Keywords:  Metabolism
    DOI:  https://doi.org/10.1038/d41586-024-00765-7
  19. Nat Commun. 2024 Mar 16. 15(1): 2377
    Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability.
    Minhui Ye, Yingzhe Fang, Lu Chen, Zemin Song, Qing Bao, Fei Wang, Hao Huang, Jin Xu, Ziwen Wang, Ruijing Xiao, Meng Han, Song Gao, Hudan Liu, Baishan Jiang, Guoliang Qing.
      Tumor cells must rewire nucleotide synthesis to satisfy the demands of unbridled proliferation. Meanwhile, they exhibit augmented reactive oxygen species (ROS) production which paradoxically damages DNA and free deoxy-ribonucleoside triphosphates (dNTPs). How these metabolic processes are integrated to fuel tumorigenesis remains to be investigated. MYC family oncoproteins coordinate nucleotide synthesis and ROS generation to drive the development of numerous cancers. We herein perform a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based functional screen targeting metabolic genes and identified nudix hydrolase 1 (NUDT1) as a MYC-driven dependency. Mechanistically, MYC orchestrates the balance of two metabolic pathways that act in parallel, the NADPH oxidase 4 (NOX4)-ROS pathway and the Polo like kinase 1 (PLK1)-NUDT1 nucleotide-sanitizing pathway. We describe LC-1-40 as a potent, on-target degrader that depletes NUDT1 in vivo. Administration of LC-1-40 elicits excessive nucleotide oxidation, cytotoxicity and therapeutic responses in patient-derived xenografts. Thus, pharmacological targeting of NUDT1 represents an actionable MYC-driven metabolic liability.
    DOI:  https://doi.org/10.1038/s41467-024-46572-6
  20. J Immunol. 2024 Apr 01. 212(7): 1043-1050
    Targeting NAD+ Metabolism to Modulate Autoimmunity and Inflammation.
    Jing Wu, Kim Han, Michael N Sack.
      NAD+ biology is involved in controlling redox balance, functioning as a coenzyme in numerous enzymatic reactions, and is a cofactor for Sirtuin enzymes and a substrate for multiple regulatory enzyme reactions within and outside the cell. At the same time, NAD+ levels are diminished with aging and are consumed during the development of inflammatory and autoimmune diseases linked to aberrant immune activation. Direct NAD+ augmentation via the NAD+ salvage and Priess-Handler pathways is being investigated as a putative therapeutic intervention to improve the healthspan in inflammation-linked diseases. In this review, we survey NAD+ biology and its pivotal roles in the regulation of immunity and inflammation. Furthermore, we discuss emerging studies evaluate NAD+ boosting in murine models and in human diseases, and we highlight areas of research that remain unresolved in understanding the mechanisms of action of these nutritional supplementation strategies.
    DOI:  https://doi.org/10.4049/jimmunol.2300693
  21. Mol Cell. 2024 Mar 21. pii: S1097-2765(24)00168-0. [Epub ahead of print]84(6): 995-997
    Integrating the response to stressed mitochondria.
    Elliot Dine, Richard J Youle.
      Chakrabarty et al.1 demonstrate that phospho-EIF2α (pEIF2α), the translation initiation factor that mediates the integrated stress response (ISR), is necessary and sufficient for the autophagic degradation of mitochondria following the addition of mitochondrial stressors.
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.026
  22. Nat Commun. 2024 Mar 19. 15(1): 2198
    Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting transcriptional memory.
    Daniela Michelatti, Sven Beyes, Chiara Bernardis, Maria Luce Negri, Leonardo Morelli, Naiara Garcia Bediaga, Vittoria Poli, Luca Fagnocchi, Sara Lago, Sarah D'Annunzio, Nicole Cona, Ilaria Gaspardo, Aurora Bianchi, Jovana Jovetic, Matteo Gianesello, Alice Turdo, Caterina D'Accardo, Miriam Gaggianesi, Martina Dori, Mattia Forcato, Giuliano Crispatzu, Alvaro Rada-Iglesias, Maria Soledad Sosa, H T Marc Timmers, Silvio Bicciato, Matilde Todaro, Luca Tiberi, Alessio Zippo.
      Metastasis arises from disseminated tumour cells (DTCs) that are characterized by intrinsic phenotypic plasticity and the capability of seeding to secondary organs. DTCs can remain latent for years before giving rise to symptomatic overt metastasis. In this context, DTCs fluctuate between a quiescent and proliferative state in response to systemic and microenvironmental signals including immune-mediated surveillance. Despite its relevance, how intrinsic mechanisms sustain DTCs plasticity has not been addressed. By interrogating the epigenetic state of metastatic cells, we find that tumour progression is coupled with the activation of oncogenic enhancers that are organized in variable interconnected chromatin domains. This spatial chromatin context leads to the activation of a robust transcriptional response upon repeated exposure to retinoic acid (RA). We show that this adaptive mechanism sustains the quiescence of DTCs through the activation of the master regulator SOX9. Finally, we determine that RA-stimulated transcriptional memory increases the fitness of metastatic cells by supporting the escape of quiescent DTCs from NK-mediated immune surveillance. Overall, these findings highlight the contribution of oncogenic enhancers in establishing transcriptional memories as an adaptive mechanism to reinforce cancer dormancy and immune escape, thus amenable for therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41467-024-46524-0
  23. Cancer Metab. 2024 Mar 21. 12(1): 9
    Serine synthesis and catabolism in starved lung cancer and primary bronchial epithelial cells.
    Theresa Haitzmann, Katharina Schindlmaier, Tobias Frech, Ayusi Mondal, Visnja Bubalo, Barbara Konrad, Gabriele Bluemel, Philipp Stiegler, Stefanie Lackner, Andelko Hrzenjak, Thomas Eichmann, Harald C Köfeler, Katharina Leithner.
      Serine and glycine give rise to important building blocks in proliferating cells. Both amino acids are either synthesized de novo or taken up from the extracellular space. In lung cancer, serine synthesis gene expression is variable, yet, expression of the initial enzyme, phosphoglycerate dehydrogenase (PHGDH), was found to be associated with poor prognosis. While the contribution of de novo synthesis to serine pools has been shown to be enhanced by serine starvation, the impact of glucose deprivation, a commonly found condition in solid cancers is poorly understood. Here, we utilized a stable isotopic tracing approach to assess serine and glycine de novo synthesis and uptake in different lung cancer cell lines and normal bronchial epithelial cells in variable serine, glycine, and glucose conditions. Under low glucose supplementation (0.2 mM, 3-5% of normal plasma levels), serine de novo synthesis was maintained or even activated. As previously reported, also gluconeogenesis supplied carbons from glutamine to serine and glycine under these conditions. Unexpectedly, low glucose treatment consistently enhanced serine to glycine conversion, along with an up-regulation of the mitochondrial one-carbon metabolism enzymes, serine hydroxymethyltransferase (SHMT2) and methylenetetrahydrofolate dehydrogenase (MTHFD2). The relative contribution of de novo synthesis greatly increased in low serine/glycine conditions. In bronchial epithelial cells, adaptations occurred in a similar fashion as in cancer cells, but serine synthesis and serine to glycine conversion, as assessed by label enrichments and gene expression levels, were generally lower than in (PHGDH positive) cancer cells. In summary, we found a variable contribution of glucose or non-glucose carbon sources to serine and glycine and a high adaptability of the downstream one-carbon metabolism pathway to variable glucose supply.
    Keywords:  Glycine; Lung cancer; Metabolism; Serine; Starvation
    DOI:  https://doi.org/10.1186/s40170-024-00337-3
  24. bioRxiv. 2024 Mar 07. pii: 2024.03.06.583589. [Epub ahead of print]
    Up-regulation of cholesterol synthesis by lysosomal defects requires a functional mitochondrial respiratory chain.
    Francesco Agostini, Leonardo Pereyra, Justin Dale, King Faisal Yambire, Silvia Maglioni, Alfonso Schiavi, Natascia Ventura, Ira Milosevic, Nuno Raimundo.
      Mitochondria and lysosomes are two organelles that carry out both signaling and metabolic roles in the cells. Recent evidence has shown that mitochondria and lysosomes are dependent on one another, as primary defects in one cause secondary defects in the other. Nevertheless, the signaling consequences of primary mitochondrial malfunction and of primary lysosomal defects are not similar, despite in both cases there are impairments of mitochondria and of lysosomes. Here, we used RNA sequencing to obtain transcriptomes from cells with primary mitochondrial or lysosomal defects, to identify what are the global cellular consequences that are associated with malfunction of mitochondria or lysosomes. We used these data to determine what are the pathways that are affected by defects in both organelles, which revealed a prominent role for the cholesterol synthesis pathway. This pathway is transcriptionally up-regulated in cellular and mouse models of lysosomal defects and is transcriptionally down-regulated in cellular and mouse models of mitochondrial defects. We identified a role for post-transcriptional regulation of the transcription factor SREBF1, a master regulator of cholesterol and lipid biosynthesis, in models of mitochondrial respiratory chain deficiency. Furthermore, the retention of Ca 2+ in the lysosomes of cells with mitochondrial respiratory chain defects contributes to the differential regulation of the cholesterol synthesis pathway in the mitochondrial and lysosomal defects tested. Finally, we verified in vivo , using models of mitochondria-associated diseases in C. elegans , that normalization of lysosomal Ca 2+ levels results in partial rescue of the developmental arrest induced by the respiratory chain deficiency.
    DOI:  https://doi.org/10.1101/2024.03.06.583589
  25. Nat Cell Biol. 2024 Mar 18.
    Competence for neural crest induction is controlled by hydrostatic pressure through Yap.
    Delan N Alasaadi, Lucas Alvizi, Jonas Hartmann, Namid Stillman, Prachiti Moghe, Takashi Hiiragi, Roberto Mayor.
      Embryonic induction is a key mechanism in development that corresponds to an interaction between a signalling and a responding tissue, causing a change in the direction of differentiation by the responding tissue. Considerable progress has been achieved in identifying inductive signals, yet how tissues control their responsiveness to these signals, known as competence, remains poorly understood. While the role of molecular signals in competence has been studied, how tissue mechanics influence competence remains unexplored. Here we investigate the role of hydrostatic pressure in controlling competence in neural crest cells, an embryonic cell population. We show that neural crest competence decreases concomitantly with an increase in the hydrostatic pressure of the blastocoel, an embryonic cavity in contact with the prospective neural crest. By manipulating hydrostatic pressure in vivo, we show that this increase leads to the inhibition of Yap signalling and impairs Wnt activation in the responding tissue, which would be required for neural crest induction. We further show that hydrostatic pressure controls neural crest induction in amphibian and mouse embryos and in human cells, suggesting a conserved mechanism across vertebrates. Our work sets out how tissue mechanics can interplay with signalling pathways to regulate embryonic competence.
    DOI:  https://doi.org/10.1038/s41556-024-01378-y
  26. Cancer Res. 2024 Mar 19.
    Oncogenic KRAS induces arginine auxotrophy and confers a therapeutic vulnerability to SLC7A1 inhibition in non-small cell lung cancer.
    Xiameng Gai, Yingluo Liu, Xiaojing Lan, Luoyi Chen, Tao Yuan, Jun Xu, Yize Li, Ying Zheng, Yiyang Yan, Liya Yang, Yixian Fu, Shuai Tang, Siyuwei Cao, Xiaoyang Dai, Hong Zhu, Meiyu Geng, Jian Ding, Congying Pu, Min Huang.
      The urea cycle is frequently rewired in cancer cells to meet the metabolic demands of cancer. Elucidation of the underlying mechanism by which oncogenic signaling mediates urea cycle reprogramming could help identify targetable metabolic vulnerabilities. In this study, we discovered that oncogenic activation of KRAS in non-small cell lung cancer (NSCLC) silenced the expression of argininosuccinate synthase 1 (ASS1), a urea cycle enzyme that catalyzes the production of arginine from aspartate and citrulline, and thereby diverted the utilization of aspartate to pyrimidine synthesis to meet the high demand for DNA replication. Specifically, KRAS signaling facilitated a hypo-acetylated state in the promoter region of the ASS1 gene in a histone deacetylase 3 (HDAC3)-dependent manner, which in turn impeded the recruitment of c-MYC for ASS1 transcription. ASS1 suppression in KRAS-mutant NSCLC cells impaired the biosynthesis of arginine and rendered a dependency on the arginine transmembrane transporter SLC7A1 to import extracellular arginine. Depletion of SLC7A1 in both patient-derived organoid and xenograft models inhibited KRAS-driven NSCLC growth. Together, these findings uncover the role of oncogenic KRAS in rewiring urea cycle metabolism and identify SLC7A1-mediated arginine uptake as a therapeutic vulnerability for treating KRAS-mutant NSCLC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-23-2095
  27. bioRxiv. 2024 Mar 10. pii: 2024.03.05.582974. [Epub ahead of print]
    Off-target depletion of plasma tryptophan by allosteric inhibitors of BCKDK.
    Caitlyn E Bowman, Michael D Neinast, Cholsoon Jang, Jiten Patel, Megan C Blair, Emily T Mirek, William O Jonsson, Qingwei Chu, Lauren Merlo, Laura Mandik-Nayak, Tracy G Anthony, Joshua D Rabinowitz, Zolt Arany.
      The activation of branched chain amino acid (BCAA) catabolism has garnered interest as a potential therapeutic approach to improve insulin sensitivity, enhance recovery from heart failure, and blunt tumor growth. Evidence for this interest relies in part on BT2, a small molecule that promotes BCAA oxidation and is protective in mouse models of these pathologies. BT2 and other analogs allosterically inhibit branched chain ketoacid dehydrogenase kinase (BCKDK) to promote BCAA oxidation, which is presumed to underlie the salutary effects of BT2. Potential "off-target" effects of BT2 have not been considered, however. We therefore tested for metabolic off-target effects of BT2 in Bckdk -/- animals. As expected, BT2 failed to activate BCAA oxidation in these animals. Surprisingly, however, BT2 strongly reduced plasma tryptophan levels and promoted catabolism of tryptophan to kynurenine in both control and Bckdk -/- mice. Mechanistic studies revealed that none of the principal tryptophan catabolic or kynurenine-producing/consuming enzymes (TDO, IDO1, IDO2, or KATs) were required for BT2-mediated lowering of plasma tryptophan. Instead, using equilibrium dialysis assays and mice lacking albumin, we show that BT2 avidly binds plasma albumin and displaces tryptophan, releasing it for catabolism. These data confirm that BT2 activates BCAA oxidation via inhibition of BCKDK but also reveal a robust off-target effect on tryptophan metabolism via displacement from serum albumin. The data highlight a potential confounding effect for pharmaceutical compounds that compete for binding with albumin-bound tryptophan.
    DOI:  https://doi.org/10.1101/2024.03.05.582974
  28. Am J Physiol Cell Physiol. 2024 Mar 18.
    Kynurenine 3-monooxygenase (KMO) limits de novo NAD+ synthesis through dietary tryptophan in renal proximal tubule epithelial cell models.
    Yougang Zhai, Jose A Chavez, Katharine E D'Aquino, Rong Meng, Andrea R Nawrocki, Alessandro Pocai, Lifeng Wang, Li-Jun Ma.
      Nicotinamide adenine dinucleotide (NAD+) is a pivotal coenzyme, essential for cellular reactions, metabolism, and mitochondrial function. Depletion of kidney NAD+ levels and reduced de novo NAD+ synthesis through the tryptophan-kynurenine pathway are linked to acute kidney injury (AKI), while augmenting NAD+ shows promise in reducing AKI. We investigated de novo NAD+ biosynthesis using in vitro, ex vivo and in vivo models to understand its role in AKI. 2D cultures of human primary renal proximal tubule epithelial cells (RPTECs) and HK-2 cells showed limited de novo NAD+ synthesis, likely due to low pathway enzyme gene expression. Employing 3D spheroid culture model improved the expression of tubular-specific markers and enzymes involved in de novo NAD+ synthesis. However, de novo NAD+ synthesis remained elusive in the 3D spheroid culture, regardless of injury conditions. Further investigation revealed that 3D cultured cells couldn't metabolize tryptophan (Trp) beyond kynurenine (KYN). Intriguingly, supplementation of 3-hydroxyanthrilinic acid into RPTEC spheroids was readily incorporated into NAD+. In a human precision-cut kidney slice (PCKS) ex vivo model, de novo NAD+ synthesis was limited due to substantially downregulated kynurenine 3-monooxygenase (KMO), which is responsible for KYN to 3-hydroxykynurenine conversion. KMO overexpression in RPTEC 3D spheroids successfully reinstated de novo NAD+ synthesis from Trp. Additionally, in vivo study demonstrated that de novo NAD+ synthesis is intact in the kidney of the healthy adult mice. Our findings highlight disrupted tryptophan-kynurenine NAD+ synthesis in in vitro cellular models and an ex vivo kidney model, primarily attributed to KMO downregulation.
    Keywords:  Kynurenine 3-monooxygenase; de novo NAD+ synthesis; kynurenine pathway; nicotinamide adenine dinucleotide; renal proximal tubule epithelial cell
    DOI:  https://doi.org/10.1152/ajpcell.00445.2023
  29. bioRxiv. 2024 Mar 09. pii: 2024.03.08.581297. [Epub ahead of print]
    Mitochondrial Raf1 Regulates Glutamine Catabolism.
    Ronald L Shanderson, Ian D Ferguson, Zurab Siprashvili, Luca Ducoli, Albert M Li, Weili Miao, Suhas Srinivasan, Mary Grace Velasco, Yang Li, Jiangbin Ye, Paul A Khavari.
      Raf kinases play vital roles in normal mitogenic signaling and cancer, however, the identities of functionally important Raf-proximal proteins throughout the cell are not fully known. Raf1 proximity proteomics/BioID in Raf1-dependent cancer cells unexpectedly identified Raf1-adjacent proteins known to reside in the mitochondrial matrix. Inner-mitochondrial localization of Raf1 was confirmed by mitochondrial purification and super-resolution microscopy. Inside mitochondria, Raf1 associated with glutaminase (GLS) in diverse human cancers and enabled glutaminolysis, an important source of biosynthetic precursors in cancer. These impacts required Raf1 kinase activity and were independent of canonical MAP kinase pathway signaling. Kinase-dead mitochondrial matrix-localized Raf1 impaired glutaminolysis and tumorigenesis in vivo. These data indicate that Raf1 localizes inside mitochondria where it interacts with GLS to engage glutamine catabolism and support tumorigenesis.
    DOI:  https://doi.org/10.1101/2024.03.08.581297
  30. Nat Commun. 2024 Mar 15. 15(1): 2340
    Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis.
    Maryam Ghashghaei, Yilin Liu, James Ettles, Giuseppe Bombaci, Niveditha Ramkumar, Zongmin Liu, Leo Escano, Sandra Spencer Miko, Yerin Kim, Joseph A Waldron, Kim Do, Kyle MacPherson, Katie A Yuen, Thilelli Taibi, Marty Yue, Aaremish Arsalan, Zhen Jin, Glenn Edin, Aly Karsan, Gregg B Morin, Florian Kuchenbauer, Fabiana Perna, Martin Bushell, Ly P Vu.
      Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
    DOI:  https://doi.org/10.1038/s41467-024-46665-2
  31. Cell Rep. 2024 Mar 21. pii: S2211-1247(24)00316-4. [Epub ahead of print]43(4): 113988
    Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring.
    Elena Kuzmin, Toby M Baker, Tom Lesluyes, Jean Monlong, Kento T Abe, Paula P Coelho, Michael Schwartz, Joseph Del Corpo, Dongmei Zou, Genevieve Morin, Alain Pacis, Yang Yang, Constanza Martinez, Jarrett Barber, Hellen Kuasne, Rui Li, Mathieu Bourgey, Anne-Marie Fortier, Peter G Davison, Atilla Omeroglu, Marie-Christine Guiot, Quaid Morris, Claudia L Kleinman, Sidong Huang, Anne-Claude Gingras, Jiannis Ragoussis, Guillaume Bourque, Peter Van Loo, Morag Park.
      The basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and displays consistent large chromosomal deletions. Here, we characterize evolution and maintenance of chromosome 4p (chr4p) loss in basal breast cancer. Analysis of The Cancer Genome Atlas data shows recurrent deletion of chr4p in basal breast cancer. Phylogenetic analysis of a panel of 23 primary tumor/patient-derived xenograft basal breast cancers reveals early evolution of chr4p deletion. Mechanistically we show that chr4p loss is associated with enhanced proliferation. Gene function studies identify an unknown gene, C4orf19, within chr4p, which suppresses proliferation when overexpressed-a member of the PDCD10-GCKIII kinase module we name PGCKA1. Genome-wide pooled overexpression screens using a barcoded library of human open reading frames identify chromosomal regions, including chr4p, that suppress proliferation when overexpressed in a context-dependent manner, implicating network interactions. Together, these results shed light on the early emergence of complex aneuploid karyotypes involving chr4p and adaptive landscapes shaping breast cancer genomes.
    Keywords:  CP: Cancer; CP: Genomics; GCK-III; PDCD10; aneuploidy; basal breast cancer; cancer evolution; chromosomal arm copy number aberrations; chromosome 4p; triple-negative breast cancer
    DOI:  https://doi.org/10.1016/j.celrep.2024.113988
  32. Cell. 2024 Mar 11. pii: S0092-8674(24)00227-7. [Epub ahead of print]
    Contrasting somatic mutation patterns in aging human neurons and oligodendrocytes.
    Javier Ganz, Lovelace J Luquette, Sara Bizzotto, Michael B Miller, Zinan Zhou, Craig L Bohrson, Hu Jin, Antuan V Tran, Vinayak V Viswanadham, Gannon McDonough, Katherine Brown, Yasmine Chahine, Brian Chhouk, Alon Galor, Peter J Park, Christopher A Walsh.
      Characterizing somatic mutations in the brain is important for disentangling the complex mechanisms of aging, yet little is known about mutational patterns in different brain cell types. Here, we performed whole-genome sequencing (WGS) of 86 single oligodendrocytes, 20 mixed glia, and 56 single neurons from neurotypical individuals spanning 0.4-104 years of age and identified >92,000 somatic single-nucleotide variants (sSNVs) and small insertions/deletions (indels). Although both cell types accumulate somatic mutations linearly with age, oligodendrocytes accumulated sSNVs 81% faster than neurons and indels 28% slower than neurons. Correlation of mutations with single-nucleus RNA profiles and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed across the genome similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These stark differences suggest an assortment of active mutagenic processes in oligodendrocytes and neurons.
    Keywords:  aging; brain cancer; brain disorders; glial cells; glioma; gliomagenesis; oligodendrocyte precursor cells; oligodendrocytes; somatic mutations
    DOI:  https://doi.org/10.1016/j.cell.2024.02.025
  33. Nat Immunol. 2024 Mar 19.
    Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy.
    Jonathan H Chen, Linda T Nieman, Maxwell Spurrell, Vjola Jorgji, Liad Elmelech, Peter Richieri, Katherine H Xu, Roopa Madhu, Milan Parikh, Izabella Zamora, Arnav Mehta, Christopher S Nabel, Samuel S Freeman, Joshua D Pirl, Chenyue Lu, Catherine B Meador, Jaimie L Barth, Mustafa Sakhi, Alexander L Tang, Siranush Sarkizova, Colles Price, Nicolas F Fernandez, George Emanuel, Jiang He, Katrina Van Raay, Jason W Reeves, Keren Yizhak, Matan Hofree, Angela Shih, Moshe Sade-Feldman, Genevieve M Boland, Karin Pelka, Martin J Aryee, Mari Mino-Kenudson, Justin F Gainor, Ilya Korsunsky, Nir Hacohen.
      The organization of immune cells in human tumors is not well understood. Immunogenic tumors harbor spatially localized multicellular 'immunity hubs' defined by expression of the T cell-attracting chemokines CXCL10/CXCL11 and abundant T cells. Here, we examined immunity hubs in human pre-immunotherapy lung cancer specimens and found an association with beneficial response to PD-1 blockade. Critically, we discovered the stem-immunity hub, a subtype of immunity hub strongly associated with favorable PD-1-blockade outcome. This hub is distinct from mature tertiary lymphoid structures and is enriched for stem-like TCF7+PD-1+CD8+ T cells, activated CCR7+LAMP3+ dendritic cells and CCL19+ fibroblasts as well as chemokines that organize these cells. Within the stem-immunity hub, we find preferential interactions between CXCL10+ macrophages and TCF7-CD8+ T cells as well as between mature regulatory dendritic cells and TCF7+CD4+ and regulatory T cells. These results provide a picture of the spatial organization of the human intratumoral immune response and its relevance to patient immunotherapy outcomes.
    DOI:  https://doi.org/10.1038/s41590-024-01792-2
  34. Proc Natl Acad Sci U S A. 2024 Mar 26. 121(13): e2316841121
    The circadian molecular clock in the suprachiasmatic nucleus is necessary but not sufficient for fear entrainment.
    Ivana L Bussi, Miriam Ben-Hamo, Luis E Salazar Leon, Leandro P Casiraghi, Victor Y Zhang, Alexandra F Neitz, Jeffrey Lee, Joseph S Takahashi, Jeansok J Kim, Horacio O de la Iglesia.
      We show that nocturnal aversive stimuli presented to mice while they are eating and drinking outside of their safe nest can entrain circadian behaviors, leading to a shift toward daytime activity. We also show that the canonical molecular circadian clock is necessary for fear entrainment and that an intact molecular clockwork in the suprachiasmatic nucleus, the site of the central circadian pacemaker, is necessary but not sufficient to sustain fear entrainment of circadian rhythms. Our results demonstrate that entrainment of a circadian clock by cyclic fearful stimuli can lead to severely mistimed circadian behavior that persists even after the aversive stimulus is removed. Together, our findings support the interpretation that circadian and sleep symptoms associated with fear and anxiety disorders are, in part, the output of a fear-entrained clock, and provide a mechanistic insight into this clock.
    Keywords:  PTSD; circadian; fear; sleep; suprachiasmatic
    DOI:  https://doi.org/10.1073/pnas.2316841121
  35. Cell Rep Med. 2024 Mar 19. pii: S2666-3791(24)00118-6. [Epub ahead of print]5(3): 101472
    STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma.
    Nicole Prutsch, Shuning He, Alla Berezovskaya, Adam D Durbin, Neekesh V Dharia, Kelsey A Maher, Jamie D Matthews, Lucy Hare, Suzanne D Turner, Kimberly Stegmaier, Lukas Kenner, Olaf Merkel, A Thomas Look, Brian J Abraham, Mark W Zimmerman.
      Anaplastic large cell lymphoma (ALCL) is an aggressive, CD30+ T cell lymphoma of children and adults. ALK fusion transcripts or mutations in the JAK-STAT pathway are observed in most ALCL tumors, but the mechanisms underlying tumorigenesis are not fully understood. Here, we show that dysregulated STAT3 in ALCL cooccupies enhancers with master transcription factors BATF3, IRF4, and IKZF1 to form a core regulatory circuit that establishes and maintains the malignant cell state in ALCL. Critical downstream targets of this network in ALCL cells include the protooncogene MYC, which requires active STAT3 to facilitate high levels of MYC transcription. The core autoregulatory transcriptional circuitry activity is reinforced by MYC binding to the enhancer regions associated with STAT3 and each of the core regulatory transcription factors. Thus, activation of STAT3 provides the crucial link between aberrant tyrosine kinase signaling and the core transcriptional machinery that drives tumorigenesis and creates therapeutic vulnerabilities in ALCL.
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101472
  36. Semin Cell Dev Biol. 2024 Mar 19. pii: S1084-9521(24)00023-5. [Epub ahead of print]161-162 20-21
    Mitochondrial dynamics: Regulating cell metabolism, homoeostasis, health and disease.
    Karoline D Raven, Ronan Kapetanovic.
      
    DOI:  https://doi.org/10.1016/j.semcdb.2024.02.002
  37. Nat Metab. 2024 Mar 18.
    Activation of GPR81 by lactate drives tumour-induced cachexia.
    Xidan Liu, Shijin Li, Qionghua Cui, Bujing Guo, Wanqiu Ding, Jie Liu, Li Quan, Xiaochuan Li, Peng Xie, Li Jin, Ye Sheng, Wenxin Chen, Kai Wang, Fanxin Zeng, Yifu Qiu, Changlu Liu, Yan Zhang, Fengxiang Lv, Xinli Hu, Rui-Ping Xiao.
      Cachexia affects 50-80% of patients with cancer and accounts for 20% of cancer-related death, but the underlying mechanism driving cachexia remains elusive. Here we show that circulating lactate levels positively correlate with the degree of body weight loss in male and female patients suffering from cancer cachexia, as well as in clinically relevant mouse models. Lactate infusion per se is sufficient to trigger a cachectic phenotype in tumour-free mice in a dose-dependent manner. Furthermore, we demonstrate that adipose-specific G-protein-coupled receptor (GPR)81 ablation, similarly to global GPR81 deficiency, ameliorates lactate-induced or tumour-induced adipose and muscle wasting in male mice, revealing adipose GPR81 as the major mediator of the catabolic effects of lactate. Mechanistically, lactate/GPR81-induced cachexia occurs independently of the well-established protein kinase A catabolic pathway, but it is mediated by a signalling cascade sequentially activating Gi-Gβγ-RhoA/ROCK1-p38. These findings highlight the therapeutic potential of targeting GPR81 for the treatment of this life-threatening complication of cancer.
    DOI:  https://doi.org/10.1038/s42255-024-01011-0
  38. Mol Cell. 2024 Mar 21. pii: S1097-2765(24)00174-6. [Epub ahead of print]84(6): 1000-1002
    A SIFI odyssey: Silencing the stress response amid mitochondrial import blockade to safeguard cell survival.
    Yuleika G Martinez Castillo, Chantell S Evans.
      In a recent study in Nature, Haakonsen et al.1 identify the SIFI complex as a stress response silencer via its E3 ligase activity to target unimported mitochondrial proteins and stress response components for degradation via the proteasome.
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.034
  39. Nature. 2024 Mar 20.
    Disease-associated astrocyte epigenetic memory promotes CNS pathology.
    Hong-Gyun Lee, Joseph M Rone, Zhaorong Li, Camilo Faust Akl, Seung Won Shin, Joon-Hyuk Lee, Lucas E Flausino, Florian Pernin, Chun-Cheih Chao, Kilian L Kleemann, Lena Srun, Tomer Illouz, Federico Giovannoni, Marc Charabati, Liliana M Sanmarco, Jessica E Kenison, Gavin Piester, Stephanie E J Zandee, Jack P Antel, Veit Rothhammer, Michael A Wheeler, Alexandre Prat, Iain C Clark, Francisco J Quintana.
      Disease-associated astrocyte subsets contribute to the pathology of neurologic diseases, including multiple sclerosis and experimental autoimmune encephalomyelitis1-8 (EAE), an experimental model for multiple sclerosis. However, little is known about the stability of these astrocyte subsets and their ability to integrate past stimulation events. Here we report the identification of an epigenetically controlled memory astrocyte subset that exhibits exacerbated pro-inflammatory responses upon rechallenge. Specifically, using a combination of single-cell RNA sequencing, assay for transposase-accessible chromatin with sequencing, chromatin immunoprecipitation with sequencing, focused interrogation of cells by nucleic acid detection and sequencing, and cell-specific in vivo CRISPR-Cas9-based genetic perturbation studies we established that astrocyte memory is controlled by the metabolic enzyme ATP-citrate lyase (ACLY), which produces acetyl coenzyme A (acetyl-CoA) that is used by histone acetyltransferase p300 to control chromatin accessibility. The number of ACLY+p300+ memory astrocytes is increased in acute and chronic EAE models, and their genetic inactivation ameliorated EAE. We also detected the pro-inflammatory memory phenotype in human astrocytes in vitro; single-cell RNA sequencing and immunohistochemistry studies detected increased numbers of ACLY+p300+ astrocytes in chronic multiple sclerosis lesions. In summary, these studies define an epigenetically controlled memory astrocyte subset that promotes CNS pathology in EAE and, potentially, multiple sclerosis. These findings may guide novel therapeutic approaches for multiple sclerosis and other neurologic diseases.
    DOI:  https://doi.org/10.1038/s41586-024-07187-5
  40. Cell. 2024 Mar 14. pii: S0092-8674(24)00233-2. [Epub ahead of print]
    Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.
    Petra Kukanja, Christoffer M Langseth, Leslie A Rubio Rodríguez-Kirby, Eneritz Agirre, Chao Zheng, Amitha Raman, Chika Yokota, Christophe Avenel, Katarina Tiklová, André O Guerreiro-Cacais, Tomas Olsson, Markus M Hilscher, Mats Nilsson, Gonçalo Castelo-Branco.
      Multiple sclerosis (MS) is a neurological disease characterized by multifocal lesions and smoldering pathology. Although single-cell analyses provided insights into cytopathology, evolving cellular processes underlying MS remain poorly understood. We investigated the cellular dynamics of MS by modeling temporal and regional rates of disease progression in mouse experimental autoimmune encephalomyelitis (EAE). By performing single-cell spatial expression profiling using in situ sequencing (ISS), we annotated disease neighborhoods and found centrifugal evolution of active lesions. We demonstrated that disease-associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course. Single-cell spatial mapping of human archival MS spinal cords confirmed the differential distribution of homeostatic and DA-glia, enabled deconvolution of active and inactive lesions into sub-compartments, and identified new lesion areas. By establishing a spatial resource of mouse and human MS neuropathology at a single-cell resolution, our study unveils the intricate cellular dynamics underlying MS.
    Keywords:  EAE; MS; SERPINA3; Serpina3n; disease-associated glia; experimental autoimmune encephalomyelitis; in situ sequencing; multiple sclerosis; neuroinflammation; neuropathology; single-cell; spatial sequencing
    DOI:  https://doi.org/10.1016/j.cell.2024.02.030
  41. Proc Natl Acad Sci U S A. 2024 Mar 26. 121(13): e2318969121
    Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation.
    Max Brabender, Delfina P Henriques Pereira, Natalia Mrnjavac, Manon Laura Schlikker, Zen-Ichiro Kimura, Jeerus Sucharitakul, Karl Kleinermanns, Harun Tüysüz, Wolfgang Buckel, Martina Preiner, William F Martin.
      Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.
    Keywords:  acetyl CoA pathway; origin of life; origin of metabolism; serpentinization; transition metals
    DOI:  https://doi.org/10.1073/pnas.2318969121
  42. J Clin Invest. 2024 Mar 21. pii: e174587. [Epub ahead of print]
    The alanyl-tRNA synthetase AARS1 moonlights as a lactyl-transferase to promote YAP signaling in gastric cancer.
    Junyi Ju, Hui Zhang, Moubin Lin, Zifeng Yan, Liwei An, Zhifa Cao, Dandan Geng, Jingwu Yue, Yang Tang, Luyang Tian, Fan Chen, Yi Han, Wenjia Wang, Shimin Zhao, Jiao Shi, Zhaocai Zhou.
      Lactylation has been recently identified as a new type of posttranslational modification widely occurring on lysine residues of both histone and non-histone proteins. The acetyl transferase p300 is thought to mediate protein lactylation, yet the cellular concentration of the proposed lactyl-donor, lactyl-coenzyme A is about 1,000 times lower than that of acetyl-CoA, raising the question whether p300 is a genuine lactyl-transferase. Here, we report the Alanyl-tRNA synthetase 1 (AARS1) moonlights as a bona fide lactyl-transferase that directly uses lactate and ATP to catalyze protein lactylation. Among the candidate substrates, we focused on the Hippo pathway that has a well-established role in tumorigenesis. Specifically, AARS1 was found to sense intracellular lactate and translocate into the nucleus to lactylate and activate YAP-TEAD complex; and AARS1 itself was identified as a Hippo target gene that forms a positive feedback loop with YAP-TEAD to promote gastric cancer (GC) cell proliferation. Consistently, the expression of AARS1 was found to be upregulated in GC, and elevated AARS1 expression was found to be associated with poor prognosis for GC patients. Collectively, this work discovered AARS1 with lactyl-transferase activity in vitro and in vivo and revealed how the metabolite lactate is translated into a signal of cell proliferation.
    Keywords:  Cancer; Metabolism
    DOI:  https://doi.org/10.1172/JCI174587
  43. Nat Rev Endocrinol. 2024 Mar 18.
    Metabolic regulation of skeletal cell fate and function.
    Steve Stegen, Geert Carmeliet.
      Bone development and bone remodelling during adult life are highly anabolic processes requiring an adequate supply of oxygen and nutrients. Bone-forming osteoblasts and bone-resorbing osteoclasts interact closely to preserve bone mass and architecture and are often located close to blood vessels. Chondrocytes within the developing growth plate ensure that bone lengthening occurs before puberty, but these cells function in an avascular environment. With ageing, numerous bone marrow adipocytes appear, often with negative effects on bone properties. Many studies have now indicated that skeletal cells have specific metabolic profiles that correspond to the nutritional microenvironment and their stage-specific functions. These metabolic networks provide not only skeletal cells with sufficient energy, but also biosynthetic intermediates that are necessary for proliferation and extracellular matrix synthesis. Moreover, these metabolic pathways control redox homeostasis to avoid oxidative stress and safeguard cell survival. Finally, several intracellular metabolites regulate the activity of epigenetic enzymes and thus control the fate and function of skeletal cells. The metabolic profile of skeletal cells therefore not only reflects their cellular state, but can also drive cellular activity. Insight into skeletal cell metabolism will thus not only advance our understanding of skeletal development and homeostasis, but also of skeletal disorders, such as osteoarthritis, diabetic bone disease and bone malignancies.
    DOI:  https://doi.org/10.1038/s41574-024-00969-x
  44. Nat Rev Mol Cell Biol. 2024 Mar 21.
    A code within the genetic code.
    Susanne Bornelöv.
      
    DOI:  https://doi.org/10.1038/s41580-024-00724-0
  45. Sci Rep. 2024 Mar 21. 14(1): 6751
    MCU-independent Ca2+ uptake mediates mitochondrial Ca2+ overload and necrotic cell death in a mouse model of Duchenne muscular dystrophy.
    Michael J Bround, Eaman Abay, Jiuzhou Huo, Julian R Havens, Allen J York, Donald M Bers, Jeffery D Molkentin.
      Mitochondrial Ca2+ overload can mediate mitochondria-dependent cell death, a major contributor to several human diseases. Indeed, Duchenne muscular dystrophy (MD) is driven by dysfunctional Ca2+ influx across the sarcolemma that causes mitochondrial Ca2+ overload, organelle rupture, and muscle necrosis. The mitochondrial Ca2+ uniporter (MCU) complex is the primary characterized mechanism for acute mitochondrial Ca2+ uptake. One strategy for preventing mitochondrial Ca2+ overload is deletion of the Mcu gene, the pore forming subunit of the MCU-complex. Conversely, enhanced MCU-complex Ca2+ uptake is achieved by deleting the inhibitory Mcub gene. Here we show that myofiber-specific Mcu deletion was not protective in a mouse model of Duchenne MD. Specifically, Mcu gene deletion did not reduce muscle histopathology, did not improve muscle function, and did not prevent mitochondrial Ca2+ overload. Moreover, myofiber specific Mcub gene deletion did not augment Duchenne MD muscle pathology. Interestingly, we observed MCU-independent Ca2+ uptake in dystrophic mitochondria that was sufficient to drive mitochondrial permeability transition pore (MPTP) activation and skeletal muscle necrosis, and this same type of activity was observed in heart, liver, and brain mitochondria. These results demonstrate that mitochondria possess an uncharacterized MCU-independent Ca2+ uptake mechanism that is sufficient to drive MPTP-dependent necrosis in MD in vivo.
    DOI:  https://doi.org/10.1038/s41598-024-57340-3
  46. Nat Commun. 2024 Mar 21. 15(1): 2487
    The AMPK-related kinase NUAK1 controls cortical axons branching by locally modulating mitochondrial metabolic functions.
    Marine Lanfranchi, Sozerko Yandiev, Géraldine Meyer-Dilhet, Salma Ellouze, Martijn Kerkhofs, Raphael Dos Reis, Audrey Garcia, Camille Blondet, Alizée Amar, Anita Kneppers, Hélène Polvèche, Damien Plassard, Marc Foretz, Benoit Viollet, Kei Sakamoto, Rémi Mounier, Cyril F Bourgeois, Olivier Raineteau, Evelyne Goillot, Julien Courchet.
      The cellular mechanisms underlying axonal morphogenesis are essential to the formation of functional neuronal networks. We previously identified the autism-linked kinase NUAK1 as a central regulator of axon branching through the control of mitochondria trafficking. However, (1) the relationship between mitochondrial position, function and axon branching and (2) the downstream effectors whereby NUAK1 regulates axon branching remain unknown. Here, we report that mitochondria recruitment to synaptic boutons supports collateral branches stabilization rather than formation in mouse cortical neurons. NUAK1 deficiency significantly impairs mitochondrial metabolism and axonal ATP concentration, and upregulation of mitochondrial function is sufficient to rescue axonal branching in NUAK1 null neurons in vitro and in vivo. Finally, we found that NUAK1 regulates axon branching through the mitochondria-targeted microprotein BRAWNIN. Our results demonstrate that NUAK1 exerts a dual function during axon branching through its ability to control mitochondrial distribution and metabolic activity.
    DOI:  https://doi.org/10.1038/s41467-024-46146-6
  47. PLoS Biol. 2024 Mar;22(3): e3002549
    GALDAR: A genetically encoded galactose sensor for visualizing sugar metabolism in vivo.
    Uğurcan Sakizli, Tomomi Takano, Sa Kan Yoo.
      Sugar metabolism plays a pivotal role in sustaining life. Its dynamics within organisms is less understood compared to its intracellular metabolism. Galactose, a hexose stereoisomer of glucose, is a monosaccharide transported via the same transporters with glucose. Galactose feeds into glycolysis and regulates protein glycosylation. Defects in galactose metabolism are lethal for animals. Here, by transgenically implementing the yeast galactose sensing system into Drosophila, we developed a genetically encoded sensor, GALDAR, which detects galactose in vivo. Using this heterologous system, we revealed dynamics of galactose metabolism in various tissues. Notably, we discovered that intestinal stem cells do not uptake detectable levels of galactose or glucose. GALDAR elucidates the role for galactokinase in metabolism of galactose and a transition of galactose metabolism during the larval period. This work provides a new system that enables analyses of in vivo sugar metabolism.
    DOI:  https://doi.org/10.1371/journal.pbio.3002549
  48. Nat Biotechnol. 2024 Mar 21.
    Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor-immune hubs.
    Siyu He, Yinuo Jin, Achille Nazaret, Lingting Shi, Xueer Chen, Sham Rampersaud, Bahawar S Dhillon, Izabella Valdez, Lauren E Friend, Joy Linyue Fan, Cameron Y Park, Rachel L Mintz, Yeh-Hsing Lao, David Carrera, Kaylee W Fang, Kaleem Mehdi, Madeline Rohde, José L McFaline-Figueroa, David Blei, Kam W Leong, Alexander Y Rudensky, George Plitas, Elham Azizi.
      Spatially resolved gene expression profiling provides insight into tissue organization and cell-cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell resolution. Current ST analysis methods require single-cell RNA sequencing data as a reference for rigorous interpretation of cell states, mostly do not use associated histology images and are not capable of inferring shared neighborhoods across multiple tissues. Here we present Starfysh, a computational toolbox using a deep generative model that incorporates archetypal analysis and any known cell type markers to characterize known or new tissue-specific cell states without a single-cell reference. Starfysh improves the characterization of spatial dynamics in complex tissues using histology images and enables the comparison of niches as spatial hubs across tissues. Integrative analysis of primary estrogen receptor (ER)-positive breast cancer, triple-negative breast cancer (TNBC) and metaplastic breast cancer (MBC) tissues led to the identification of spatial hubs with patient- and disease-specific cell type compositions and revealed metabolic reprogramming shaping immunosuppressive hubs in aggressive MBC.
    DOI:  https://doi.org/10.1038/s41587-024-02173-8
  49. Mitochondrial Commun. 2024 ;2 1-13
    Structural determinants of mitochondrial STAT3 targeting and function.
    Isabelle J Marié, Tanaya Lahiri, Özlem Önder, Kojo S J Elenitoba-Johnson, David E Levy.
      Signal transducer and activator of transcription (STAT) 3 has been found within mitochondria in addition to its canonical role of shuttling between cytoplasm and nucleus during cytokine signaling. Mitochondrial STAT3 has been implicated in modulation of cellular metabolism, largely through effects on the respiratory electron transport chain. However, the structural requirements underlying mitochondrial targeting and function have remained unclear. Here, we show that mitochondrial STAT3 partitions between mitochondrial compartments defined by differential detergent solubility, suggesting that mitochondrial STAT3 is membrane associated. The majority of STAT3 was found in an SDS soluble fraction copurifying with respiratory chain proteins, including numerous components of the complex I NADH dehydrogenase, while a minor component was found with proteins of the mitochondrial translation machinery. Mitochondrial targeting of STAT3 required the amino-terminal domain, and an internal linker domain motif also directed mitochondrial translocation. However, neither the phosphorylation of serine 727 nor the presence of mitochondrial DNA was required for the mitochondrial localization of STAT3. Two cysteine residues in the STAT3 SH2 domain, which have been previously suggested to be targets for protein palmitoylation, were also not required for mitochondrial translocation, but were required for its function as an enhancer of complex I activity. These structural determinants of STAT3 mitochondrial targeting and function provide potential therapeutic targets for disrupting the activity of mitochondrial STAT3 in diseases such as cancer.
    Keywords:  Electron transport chain; Mitochondrial import; Stat3
    DOI:  https://doi.org/10.1016/j.mitoco.2024.01.001
  50. iScience. 2024 Apr 19. 27(4): 109417
    MYC dependency in GLS1 and NAMPT is a therapeutic vulnerability in multiple myeloma.
    Lama Hasan Bou Issa, Léa Fléchon, William Laine, Aicha Ouelkdite, Silvia Gaggero, Adeline Cozzani, Remi Tilmont, Paul Chauvet, Nicolas Gower, Romanos Sklavenitis-Pistofidis, Carine Brinster, Xavier Thuru, Yasmine Touil, Bruno Quesnel, Suman Mitra, Irene M Ghobrial, Jérôme Kluza, Salomon Manier.
      Multiple myeloma (MM) is an incurable hematological malignancy in which MYC alterations contribute to the malignant phenotype. Nevertheless, MYC lacks therapeutic druggability. Here, we leveraged large-scale loss-of-function screens and conducted a small molecule screen to identify genes and pathways with enhanced essentiality correlated with MYC expression. We reported a specific gene dependency in glutaminase (GLS1), essential for the viability and proliferation of MYC overexpressing cells. Conversely, the analysis of isogenic models, as well as cell lines dataset (CCLE) and patient datasets, revealed GLS1 as a non-oncogenic dependency in MYC-driven cells. We functionally delineated the differential modulation of glutamine to maintain mitochondrial function and cellular biosynthesis in MYC overexpressing cells. Furthermore, we observed that pharmaceutical inhibition of NAMPT selectively affects MYC upregulated cells. We demonstrate the effectiveness of combining GLS1 and NAMPT inhibitors, suggesting that targeting glutaminolysis and NAD synthesis may be a promising strategy to target MYC-driven MM.
    Keywords:  Cancer; Metabolomics; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2024.109417
  51. Nat Commun. 2024 Mar 18. 15(1): 2441
    A fast-acting lipid checkpoint in G1 prevents mitotic defects.
    Marielle S Köberlin, Yilin Fan, Chad Liu, Mingyu Chung, Antonio F M Pinto, Peter K Jackson, Alan Saghatelian, Tobias Meyer.
      Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
    DOI:  https://doi.org/10.1038/s41467-024-46696-9
  52. JCI Insight. 2024 Feb 22. pii: e171961. [Epub ahead of print]9(6):
    Tubular CPT1A deletion minimally affects aging and chronic kidney injury.
    Safaa Hammoud, Alla Ivanova, Yosuke Osaki, Steven Funk, Haichun Yang, Olga Viquez, Rachel Delgado, Dongliang Lu, Melanie Phillips Mignemi, Jane Tonello, Selene Colon, Louise Lantier, David Wasserman, Benjamin D Humphreys, Jeffrey Koenitzer, Justin Kern, Mark de Caestecker, Toren Finkel, Agnes Fogo, Nidia Messias, Irfan J Lodhi, Leslie Gewin.
      Kidney tubules use fatty acid oxidation (FAO) to support their high energetic requirements. Carnitine palmitoyltransferase 1A (CPT1A) is the rate-limiting enzyme for FAO, and it is necessary to transport long-chain fatty acids into mitochondria. To define the role of tubular CPT1A in aging and injury, we generated mice with tubule-specific deletion of Cpt1a (Cpt1aCKO mice), and the mice were either aged for 2 years or injured by aristolochic acid or unilateral ureteral obstruction. Surprisingly, Cpt1aCKO mice had no significant differences in kidney function or fibrosis compared with wild-type mice after aging or chronic injury. Primary tubule cells from aged Cpt1aCKO mice had a modest decrease in palmitate oxidation but retained the ability to metabolize long-chain fatty acids. Very-long-chain fatty acids, exclusively oxidized by peroxisomes, were reduced in kidneys lacking tubular CPT1A, consistent with increased peroxisomal activity. Single-nuclear RNA-Seq showed significantly increased expression of peroxisomal FAO enzymes in proximal tubules of mice lacking tubular CPT1A. These data suggest that peroxisomal FAO may compensate in the absence of CPT1A, and future genetic studies are needed to confirm the role of peroxisomal β-oxidation when mitochondrial FAO is impaired.
    Keywords:  Chronic kidney disease; Fatty acid oxidation; Metabolism; Nephrology
    DOI:  https://doi.org/10.1172/jci.insight.171961
  53. Nat Metab. 2024 Mar 18.
    Lac-Phe mediates the effects of metformin on food intake and body weight.
    Shuke Xiao, Veronica L Li, Xuchao Lyu, Xudong Chen, Wei Wei, Fahim Abbasi, Joshua W Knowles, Alan Sheng-Hwa Tung, Shuliang Deng, Gaurav Tiwari, Xu Shi, Shuning Zheng, Laurie Farrell, Zsu-Zsu Chen, Kent D Taylor, Xiuqing Guo, Mark O Goodarzi, Alexis C Wood, Yii-Der Ida Chen, Leslie A Lange, Stephen S Rich, Jerome I Rotter, Clary B Clish, Usman A Tahir, Robert E Gerszten, Mark D Benson, Jonathan Z Long.
      Metformin is a widely prescribed anti-diabetic medicine that also reduces body weight. There is ongoing debate about the mechanisms that mediate metformin's effects on energy balance. Here, we show that metformin is a powerful pharmacological inducer of the anorexigenic metabolite N-lactoyl-phenylalanine (Lac-Phe) in cells, in mice and two independent human cohorts. Metformin drives Lac-Phe biosynthesis through the inhibition of complex I, increased glycolytic flux and intracellular lactate mass action. Intestinal epithelial CNDP2+ cells, not macrophages, are the principal in vivo source of basal and metformin-inducible Lac-Phe. Genetic ablation of Lac-Phe biosynthesis in male mice renders animals resistant to the effects of metformin on food intake and body weight. Lastly, mediation analyses support a role for Lac-Phe as a downstream effector of metformin's effects on body mass index in participants of a large population-based observational cohort, the Multi-Ethnic Study of Atherosclerosis. Together, these data establish Lac-Phe as a critical mediator of the body weight-lowering effects of metformin.
    DOI:  https://doi.org/10.1038/s42255-024-00999-9
  54. Nat Commun. 2024 Mar 15. 15(1): 2372
    A citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations.
    Hang Zhou, Yiwen Zhang, Christopher P Long, Xuesen Xia, Yanfen Xue, Yanhe Ma, Maciek R Antoniewicz, Yong Tao, Baixue Lin.
      Tricarboxylic acid cycle (TCA cycle) plays an important role for aerobic growth of heterotrophic bacteria. Theoretically, eliminating TCA cycle would decrease carbon dissipation and facilitate chemicals biosynthesis. Here, we construct an E. coli strain without a functional TCA cycle that can serve as a versatile chassis for chemicals biosynthesis. We first use adaptive laboratory evolution to recover aerobic growth in minimal medium of TCA cycle-deficient E. coli. Inactivation of succinate dehydrogenase is a key event in the evolutionary trajectory. Supply of succinyl-CoA is identified as the growth limiting factor. By replacing endogenous succinyl-CoA dependent enzymes, we obtain an optimized TCA cycle-deficient E. coli strain. As a proof of concept, the strain is engineered for high-yield production of four separate products. This work enhances our understanding of the role of the TCA cycle in E. coli metabolism and demonstrates the advantages of using TCA cycle-deficient E. coli strain for biotechnological applications.
    DOI:  https://doi.org/10.1038/s41467-024-46655-4
  55. Nat Commun. 2024 Mar 21. 15(1): 2518
    p53 regulates diverse tissue-specific outcomes to endogenous DNA damage in mice.
    Ross J Hill, Nazareno Bona, Job Smink, Hannah K Webb, Alastair Crisp, Juan I Garaycoechea, Gerry P Crossan.
      DNA repair deficiency can lead to segmental phenotypes in humans and mice, in which certain tissues lose homeostasis while others remain seemingly unaffected. This may be due to different tissues facing varying levels of damage or having different reliance on specific DNA repair pathways. However, we find that the cellular response to DNA damage determines different tissue-specific outcomes. Here, we use a mouse model of the human XPF-ERCC1 progeroid syndrome (XFE) caused by loss of DNA repair. We find that p53, a central regulator of the cellular response to DNA damage, regulates tissue dysfunction in Ercc1-/- mice in different ways. We show that ablation of p53 rescues the loss of hematopoietic stem cells, and has no effect on kidney, germ cell or brain dysfunction, but exacerbates liver pathology and polyploidisation. Mechanistically, we find that p53 ablation led to the loss of cell-cycle regulation in the liver, with reduced p21 expression. Eventually, p16/Cdkn2a expression is induced, serving as a fail-safe brake to proliferation in the absence of the p53-p21 axis. Taken together, our data show that distinct and tissue-specific functions of p53, in response to DNA damage, play a crucial role in regulating tissue-specific phenotypes.
    DOI:  https://doi.org/10.1038/s41467-024-46844-1
  56. Nat Commun. 2024 Mar 18. 15(1): 2009
    The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis.
    Kentaro Ohara, André Figueiredo Rendeiro, Bhavneet Bhinder, Kenneth Wha Eng, Hiranmayi Ravichandran, Duy Nguyen, David Pisapia, Aram Vosoughi, Evan Fernandez, Kyrillus S Shohdy, Jyothi Manohar, Shaham Beg, David Wilkes, Brian D Robinson, Francesca Khani, Rohan Bareja, Scott T Tagawa, Madhu M Ouseph, Andrea Sboner, Olivier Elemento, Bishoy M Faltas, Juan Miguel Mosquera.
      The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are not well understood, and there is a lack of knowledge regarding the genomic and transcriptomic differences between primary and metastatic UTUC. To address these gaps, we integrate whole-exome sequencing, RNA sequencing, and Imaging Mass Cytometry using lanthanide metal-conjugated antibodies of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. We perform a spatially-resolved single-cell analysis of cancer, immune, and stromal cells to understand the evolution of primary to metastatic UTUC. We discover that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature are stable across primary and matched metastatic UTUC. Molecular and immune subtypes are consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single cells. Molecular subtypes at the single-cell level are highly conserved between primary and metastatic UTUC tumors within the same patient.
    DOI:  https://doi.org/10.1038/s41467-024-46320-w
  57. Mol Syst Biol. 2024 Mar 15.
    Cellular energy regulates mRNA degradation in a codon-specific manner.
    Pedro Tomaz da Silva, Yujie Zhang, Evangelos Theodorakis, Laura D Martens, Vicente A Yépez, Vicent Pelechano, Julien Gagneur.
      Codon optimality is a major determinant of mRNA translation and degradation rates. However, whether and through which mechanisms its effects are regulated remains poorly understood. Here we show that codon optimality associates with up to 2-fold change in mRNA stability variations between human tissues, and that its effect is attenuated in tissues with high energy metabolism and amplifies with age. Mathematical modeling and perturbation data through oxygen deprivation and ATP synthesis inhibition reveal that cellular energy variations non-uniformly alter the effect of codon usage. This new mode of codon effect regulation, independent of tRNA regulation, provides a fundamental mechanistic link between cellular energy metabolism and eukaryotic gene expression.
    Keywords:  mRNA Stability; Cellular Energy Metabolism; Tissue-specific Regulation; Codon Usage Bias; Codon Optimality-mediated mRNA Degradation
    DOI:  https://doi.org/10.1038/s44320-024-00026-9
  58. FASEB J. 2024 Mar 31. 38(6): e23556
    Poly(ADP-ribose) mediates bioenergetic defects and redox imbalance in neurons following oxygen and glucose deprivation.
    M Iqbal Hossain, Jun Hee Lee, Jean-Philippe Gagné, Junaid Khan, Guy G Poirier, Peter H King, Valina L Dawson, Ted M Dawson, Shaida A Andrabi.
      PARP-1 over-activation results in cell death via excessive PAR generation in different cell types, including neurons following brain ischemia. Glycolysis, mitochondrial function, and redox balance are key cellular processes altered in brain ischemia. Studies show that PAR generated after PARP-1 over-activation can bind hexokinase-1 (HK-1) and result in glycolytic defects and subsequent mitochondrial dysfunction. HK-1 is the neuronal hexokinase and catalyzes the first reaction of glycolysis, converting glucose to glucose-6-phosphate (G6P), a common substrate for glycolysis, and the pentose phosphate pathway (PPP). PPP is critical in maintaining NADPH and GSH levels via G6P dehydrogenase activity. Therefore, defects in HK-1 will not only decrease cellular bioenergetics but will also cause redox imbalance due to the depletion of GSH. In brain ischemia, whether PAR-mediated inhibition of HK-1 results in bioenergetics defects and redox imbalance is not known. We used oxygen-glucose deprivation (OGD) in mouse cortical neurons to mimic brain ischemia in neuronal cultures and observed that PARP-1 activation via PAR formation alters glycolysis, mitochondrial function, and redox homeostasis in neurons. We used pharmacological inhibition of PARP-1 and adenoviral-mediated overexpression of wild-type HK-1 (wtHK-1) and PAR-binding mutant HK-1 (pbmHK-1). Our data show that PAR inhibition or overexpression of HK-1 significantly improves glycolysis, mitochondrial function, redox homeostasis, and cell survival in mouse cortical neurons exposed to OGD. These results suggest that PAR binding and inhibition of HK-1 during OGD drive bioenergetic defects in neurons due to inhibition of glycolysis and impairment of mitochondrial function.
    Keywords:  DPQ; PAR-binding motif; glycolysis; hexokinase; ischemic stroke; mitochondria; pentose-phosphate pathway; poly(ADP-ribose)
    DOI:  https://doi.org/10.1096/fj.202302559R
  59. Mol Cell. 2024 Mar 14. pii: S1097-2765(24)00172-2. [Epub ahead of print]
    Lysosomal damage sensing and lysophagy initiation by SPG20-ITCH.
    Pinki Gahlot, Bojana Kravic, Giulia Rota, Johannes van den Boom, Sophie Levantovsky, Nina Schulze, Elena Maspero, Simona Polo, Christian Behrends, Hemmo Meyer.
      Cells respond to lysosomal membrane permeabilization by membrane repair or selective macroautophagy of damaged lysosomes, termed lysophagy, but it is not fully understood how this decision is made. Here, we uncover a pathway in human cells that detects lipid bilayer perturbations in the limiting membrane of compromised lysosomes, which fail to be repaired, and then initiates ubiquitin-triggered lysophagy. We find that SPG20 binds the repair factor IST1 on damaged lysosomes and, importantly, integrates that with the detection of damage-associated lipid-packing defects of the lysosomal membrane. Detection occurs via sensory amphipathic helices in SPG20 before rupture of the membrane. If lipid-packing defects are extensive, such as during lipid peroxidation, SPG20 recruits and activates ITCH, which marks the damaged lysosome with lysine-63-linked ubiquitin chains to initiate lysophagy and thus triages the lysosome for destruction. With SPG20 being linked to neurodegeneration, these findings highlight the relevance of a coordinated lysosomal damage response for cellular homeostasis.
    Keywords:  ESCRT; ITCH; Troyer syndrome; lipid sensing; lysophagy; lysosomal membrane permeabilization; lysosomal repair; spartin; spastic paraplegia; ubiquitin
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.029
  60. PLoS Biol. 2024 Mar 22. 22(3): e3002576
    One size does not fit all: Lysosomes exist in biochemically and functionally distinct states.
    Claudio Bussi, Maximiliano G Gutierrez.
      Single-organelle resolution approaches have the potential to advance our knowledge of the heterogeneity of lysosome function. Challenging population-based models, we propose a "lysosome states" concept that links single lysosomes to function.
    DOI:  https://doi.org/10.1371/journal.pbio.3002576
  61. Sci Adv. 2024 Mar 22. 10(12): eadl4018
    SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia.
    Céline Moison, Deanne Gracias, Julie Schmitt, Simon Girard, Jean-François Spinella, Simon Fortier, Isabel Boivin, Rodrigo Mendoza-Sanchez, Bounkham Thavonekham, Tara MacRae, Nadine Mayotte, Eric Bonneil, Mark Wittman, James Carmichael, Réjean Ruel, Pierre Thibault, Josée Hébert, Anne Marinier, Guy Sauvageau.
      In a phenotypical screen of 56 acute myeloid leukemia (AML) patient samples and using a library of 10,000 compounds, we identified a hit with increased sensitivity toward SF3B1-mutated and adverse risk AMLs. Through structure-activity relationship studies, this hit was optimized into a potent, specific, and nongenotoxic molecule called UM4118. We demonstrated that UM4118 acts as a copper ionophore that initiates a mitochondrial-based noncanonical form of cell death known as cuproptosis. CRISPR-Cas9 loss-of-function screen further revealed that iron-sulfur cluster (ISC) deficiency enhances copper-mediated cell death. Specifically, we found that loss of the mitochondrial ISC transporter ABCB7 is synthetic lethal to UM4118. ABCB7 is misspliced and down-regulated in SF3B1-mutated leukemia, creating a vulnerability to copper ionophores. Accordingly, ABCB7 overexpression partially rescued SF3B1-mutated cells to copper overload. Together, our work provides mechanistic insights that link ISC deficiency to cuproptosis, as exemplified by the high sensitivity of SF3B1-mutated AMLs. We thus propose SF3B1 mutations as a biomarker for future copper ionophore-based therapies.
    DOI:  https://doi.org/10.1126/sciadv.adl4018
  62. EMBO J. 2024 Mar 18.
    TOR regulates variability of protein synthesis rates.
    Clovis Basier, Paul Nurse.
      Cellular processes are subject to inherent variability, but the extent to which cells can regulate this variability has received little investigation. Here, we explore the characteristics of the rate of cellular protein synthesis in single cells of the eukaryote fission yeast. Strikingly, this rate is highly variable despite protein synthesis being dependent on hundreds of reactions which might be expected to average out at the overall cellular level. The rate is variable over short time scales, and exhibits homoeostatic behaviour at the population level. Cells can regulate the level of variability through processes involving the TOR pathway, suggesting there is an optimal level of variability conferring a selective advantage. While this could be an example of bet-hedging, but we propose an alternative explanation: regulated 'loose' control of complex processes of overall cellular metabolism such as protein synthesis, may lead to this variability. This could ensure cells are fluid in control and agile in response to changing conditions, and may constitute a novel organisational principle of complex metabolic cellular systems.
    Keywords:  Control; Protein Synthesis; Single-Cell; TOR Pathway; Variability
    DOI:  https://doi.org/10.1038/s44318-024-00075-8
  63. Elife. 2024 Mar 22. pii: RP90579. [Epub ahead of print]12
    Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.
    Wayne Mitchell, Ludger J E Goeminne, Alexander Tyshkovskiy, Sirui Zhang, Julie Y Chen, Joao A Paulo, Kerry A Pierce, Angelina H Choy, Clary B Clish, Steven P Gygi, Vadim N Gladyshev.
      Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges for in vivo applications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear. Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems and warrant further investigation into adapting these approaches for in vivo age reversal.
    Keywords:  aging; biological age; cell biology; mitochondria; mouse; oxidative phosphorylation; reprogramming
    DOI:  https://doi.org/10.7554/eLife.90579
  64. bioRxiv. 2024 Mar 07. pii: 2024.03.05.583623. [Epub ahead of print]
    A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity.
    Eugene V Mosharov, Ayelet M Rosenberg, Anna S Monzel, Corey A Osto, Linsey Stiles, Gorazd B Rosoklija, Andrew J Dwork, Snehal Bindra, Ya Zhang, Masashi Fujita, Madeline B Mariani, Mihran Bakalian, David Sulzer, Philip L De Jager, Vilas Menon, Orian S Shirihai, J John Mann, Mark Underwood, Maura Boldrini, Michel Thiebaut de Schotten, Martin Picard.
      Mitochondrial oxidative phosphorylation (OxPhos) powers brain activity 1,2 , and mitochondrial defects are linked to neurodegenerative and neuropsychiatric disorders 3,4 , underscoring the need to define the brain's molecular energetic landscape 5-10 . To bridge the cognitive neuroscience and cell biology scale gap, we developed a physical voxelization approach to partition a frozen human coronal hemisphere section into 703 voxels comparable to neuroimaging resolution (3×3×3 mm). In each cortical and subcortical brain voxel, we profiled mitochondrial phenotypes including OxPhos enzyme activities, mitochondrial DNA and volume density, and mitochondria-specific respiratory capacity. We show that the human brain contains a diversity of mitochondrial phenotypes driven by both topology and cell types. Compared to white matter, grey matter contains >50% more mitochondria. We show that the more abundant grey matter mitochondria also are biochemically optimized for energy transformation, particularly among recently evolved cortical brain regions. Scaling these data to the whole brain, we created a backward linear regression model integrating several neuroimaging modalities 11 , thereby generating a brain-wide map of mitochondrial distribution and specialization that predicts mitochondrial characteristics in an independent brain region of the same donor brain. This new approach and the resulting MitoBrainMap of mitochondrial phenotypes provide a foundation for exploring the molecular energetic landscape that enables normal brain functions, relating it to neuroimaging data, and defining the subcellular basis for regionalized brain processes relevant to neuropsychiatric and neurodegenerative disorders.
    DOI:  https://doi.org/10.1101/2024.03.05.583623
  65. Cell Rep. 2024 Mar 15. pii: S2211-1247(24)00225-0. [Epub ahead of print]43(3): 113897
    Histone H3.1 is a chromatin-embedded redox sensor triggered by tumor cells developing adaptive phenotypic plasticity and multidrug resistance.
    Flavio R Palma, Diego R Coelho, Kirthi Pulakanti, Marcelo J Sakiyama, Yunping Huang, Fernando T Ogata, Jeanne M Danes, Alison Meyer, Cristina M Furdui, Douglas R Spitz, Ana P Gomes, Benjamin N Gantner, Sridhar Rao, Vadim Backman, Marcelo G Bonini.
      Chromatin structure is regulated through posttranslational modifications of histone variants that modulate transcription. Although highly homologous, histone variants display unique amino acid sequences associated with specific functions. Abnormal incorporation of histone variants contributes to cancer initiation, therapy resistance, and metastasis. This study reports that, among its biologic functions, histone H3.1 serves as a chromatin redox sensor that is engaged by mitochondrial H2O2. In breast cancer cells, the oxidation of H3.1Cys96 promotes its eviction and replacement by H3.3 in specific promoters. We also report that this process facilitates the opening of silenced chromatin domains and transcriptional activation of epithelial-to-mesenchymal genes associated with cell plasticity. Scavenging nuclear H2O2 or amino acid substitution of H3.1(C96S) suppresses plasticity, restores sensitivity to chemotherapy, and induces remission of metastatic lesions. Hence, it appears that increased levels of H2O2 produced by mitochondria of breast cancer cells directly promote redox-regulated H3.1-dependent chromatin remodeling involved in chemoresistance and metastasis.
    Keywords:  CP: Cancer; EMT; H3; ROS; breast cancer; chemoresistance; drug resistance; histone variants; metastasis; redox; thiol oxidation
    DOI:  https://doi.org/10.1016/j.celrep.2024.113897
  66. Proc Natl Acad Sci U S A. 2024 Mar 26. 121(13): e2319055121
    Phenotypic screen of sixty-eight colorectal cancer cell lines identifies CEACAM6 and CEACAM5 as markers of acid resistance.
    Johanna Michl, Bobby White, Stefania Monterisi, Walter F Bodmer, Pawel Swietach.
      Elevated cancer metabolism releases lactic acid and CO2 into the under-perfused tumor microenvironment, resulting in extracellular acidosis. The surviving cancer cells must adapt to this selection pressure; thus, targeting tumor acidosis is a rational therapeutic strategy to manage tumor growth. However, none of the major approved treatments are based explicitly on disrupting acid handling, signaling, or adaptations, possibly because the distinction between acid-sensitive and acid-resistant phenotypes is not clear. Here, we report pH-related phenotypes of sixty-eight colorectal cancer (CRC) cell lines by measuring i) extracellular acidification as a readout of acid production by fermentative metabolism and ii) growth of cell biomass over a range of extracellular pH (pHe) levels as a measure of the acid sensitivity of proliferation. Based on these measurements, CRC cell lines were grouped along two dimensions as "acid-sensitive"/"acid-resistant" versus "low metabolic acid production"/"high metabolic acid production." Strikingly, acid resistance was associated with the expression of CEACAM6 and CEACAM5 genes coding for two related cell-adhesion molecules, and among pH-regulating genes, of CA12. CEACAM5/6 protein levels were strongly induced by acidity, with a further induction under hypoxia in a subset of CRC lines. Lack of CEACAM6 (but not of CEACAM5) reduced cell growth and their ability to differentiate. Finally, CEACAM6 levels were strongly increased in human colorectal cancers from stage II and III patients, compared to matched samples from adjacent normal tissues. Thus, CEACAM6 is a marker of acid-resistant clones in colorectal cancer and a potential motif for targeting therapies to acidic regions within the tumors.
    Keywords:  acidosis; acid–base; metabolism; microenvironment; tumor acidity
    DOI:  https://doi.org/10.1073/pnas.2319055121
  67. Cell Rep Med. 2024 Mar 19. pii: S2666-3791(24)00072-7. [Epub ahead of print]5(3): 101449
    Intervention with metabolites emulating endogenous cell transitions accelerates muscle regeneration in young and aged mice.
    Reyna Hernandez-Benitez, Chao Wang, Lei Shi, Yasuo Ouchi, Cuiqing Zhong, Tomoaki Hishida, Hsin-Kai Liao, Eric A Magill, Sebastian Memczak, Rupa D Soligalla, Chiara Fresia, Fumiyuki Hatanaka, Veronica Lamas, Isabel Guillen, Sanjeeb Sahu, Mako Yamamoto, Yanjiao Shao, Alain Aguirre-Vazquez, Estrella Nuñez Delicado, Pedro Guillen, Concepcion Rodriguez Esteban, Jing Qu, Pradeep Reddy, Steve Horvath, Guang-Hui Liu, Pierre Magistretti, Juan Carlos Izpisua Belmonte.
      Tissue regeneration following an injury requires dynamic cell-state transitions that allow for establishing the cell identities required for the restoration of tissue homeostasis and function. Here, we present a biochemical intervention that induces an intermediate cell state mirroring a transition identified during normal differentiation of myoblasts and other multipotent and pluripotent cells to mature cells. When applied in somatic differentiated cells, the intervention, composed of one-carbon metabolites, reduces some dedifferentiation markers without losing the lineage identity, thus inducing limited reprogramming into a more flexible cell state. Moreover, the intervention enabled accelerated repair after muscle injury in young and aged mice. Overall, our study uncovers a conserved biochemical transitional phase that enhances cellular plasticity in vivo and hints at potential and scalable biochemical interventions of use in regenerative medicine and rejuvenation interventions that may be more tractable than genetic ones.
    Keywords:  histone acetylation; myogenic lineage; one-carbon metabolism; regeneration; reprogramming; small molecules
    DOI:  https://doi.org/10.1016/j.xcrm.2024.101449
  68. Cancer Res. 2024 Mar 19.
    Cancer cells hijack physiological metabolic signals to seed liver metastasis.
    Andres Rettig, Karuna Ganesh.
      Metastasis arises from cancer-cell intrinsic adaptations and permissive tumor microenvironments (TME) that are distinct across different organs. Deciphering the mechanisms underpinning organotropism could provide novel preventive and therapeutic strategies for cancer patients. Rogava and colleagues identified Pip4kc as a driver of liver metastasis, acting by sensitizing cancer cells to insulin-dependent PI3K/AKT signaling, which could be reversed by dual pharmacological inhibition of PI3K and SGLT2 or a ketogenic diet. The study highlights the importance of tumor: microenvironment communication in the context of systemic physiology and points towards potential combination therapies.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-24-0835
  69. Nat Commun. 2024 Mar 20. 15(1): 2358
    Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.
    Zaher ElBeck, Mohammad Bakhtiar Hossain, Humam Siga, Nikolay Oskolkov, Fredrik Karlsson, Julia Lindgren, Anna Walentinsson, Dominique Koppenhöfer, Rebecca Jarvis, Roland Bürli, Tanguy Jamier, Elske Franssen, Mike Firth, Andrea Degasperi, Claus Bendtsen, Robert I Menzies, Katrin Streckfuss-Bömeke, Michael Kohlhaas, Alexander G Nickel, Lars H Lund, Christoph Maack, Ákos Végvári, Christer Betsholtz.
      While excessive production of reactive oxygen species (ROS) is a characteristic hallmark of numerous diseases, clinical approaches that ameliorate oxidative stress have been unsuccessful. Here, utilizing multi-omics, we demonstrate that in cardiomyocytes, mitochondrial isocitrate dehydrogenase (IDH2) constitutes a major antioxidative defense mechanism. Paradoxically reduced expression of IDH2 associated with ventricular eccentric hypertrophy is counterbalanced by an increase in the enzyme activity. We unveil redox-dependent sex dimorphism, and extensive mutual regulation of the antioxidative activities of IDH2 and NRF2 by a feedforward network that involves 2-oxoglutarate and L-2-hydroxyglutarate and mediated in part through unconventional hydroxy-methylation of cytosine residues present in introns. Consequently, conditional targeting of ROS in a murine model of heart failure improves cardiac function in sex- and phenotype-dependent manners. Together, these insights may explain why previous attempts to treat heart failure with antioxidants have been unsuccessful and open new approaches to personalizing and, thereby, improving such treatment.
    DOI:  https://doi.org/10.1038/s41467-024-46384-8
  70. NPJ Parkinsons Dis. 2024 Mar 19. 10(1): 68
    Comprehensive blood metabolomics profiling of Parkinson's disease reveals coordinated alterations in xanthine metabolism.
    NCER-PD Consortium
      Parkinson's disease (PD) is a highly heterogeneous disorder influenced by several environmental and genetic factors. Effective disease-modifying therapies and robust early-stage biomarkers are still lacking, and an improved understanding of the molecular changes in PD could help to reveal new diagnostic markers and pharmaceutical targets. Here, we report results from a cohort-wide blood plasma metabolic profiling of PD patients and controls in the Luxembourg Parkinson's Study to detect disease-associated alterations at the level of systemic cellular process and network alterations. We identified statistically significant changes in both individual metabolite levels and global pathway activities in PD vs. controls and significant correlations with motor impairment scores. As a primary observation when investigating shared molecular sub-network alterations, we detect pronounced and coordinated increased metabolite abundances in xanthine metabolism in de novo patients, which are consistent with previous PD case/control transcriptomics data from an independent cohort in terms of known enzyme-metabolite network relationships. From the integrated metabolomics and transcriptomics network analysis, the enzyme hypoxanthine phosphoribosyltransferase 1 (HPRT1) is determined as a potential key regulator controlling the shared changes in xanthine metabolism and linking them to a mechanism that may contribute to pathological loss of cellular adenosine triphosphate (ATP) in PD. Overall, the investigations revealed significant PD-associated metabolome alterations, including pronounced changes in xanthine metabolism that are mechanistically congruent with alterations observed in independent transcriptomics data. The enzyme HPRT1 may merit further investigation as a main regulator of these network alterations and as a potential therapeutic target to address downstream molecular pathology in PD.
    DOI:  https://doi.org/10.1038/s41531-024-00671-9
  71. Curr Biol. 2024 Mar 14. pii: S0960-9822(24)00254-9. [Epub ahead of print]
    Uncoupling of behavioral and metabolic 24-h rhythms in reindeer.
    Sara A Meier, Melanie Furrer, Nora Nowak, Renato Zenobi, Monica A Sundset, Reto Huber, Steven A Brown, Gabriela Wagner.
      Reindeer in the Arctic seasonally suppress daily circadian patterns of behavior present in most animals.1 In humans and mice, even when all daily behavioral and environmental influences are artificially suppressed, robust endogenous rhythms of metabolism governed by the circadian clock persist and are essential to health.2,3 Disrupted rhythms foster metabolic disorders and weight gain.4 To understand circadian metabolic organization in reindeer, we performed behavioral measurements and untargeted metabolomics from blood plasma samples taken from Eurasian tundra reindeer (Rangifer tarandus tarandus) across 24 h at 2-h intervals in four seasons. Our study confirmed the absence of circadian rhythms of behavior under constant darkness in the Arctic winter and constant daylight in the Arctic summer, as reported by others.1 We detected and measured the intensity of 893 metabolic features in all plasma samples using untargeted ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS). A core group of metabolites (66/893 metabolic features) consistently displayed 24-h rhythmicity. Most metabolites displayed a robust 24-h rhythm in winter and spring but were arrhythmic in summer and fall. Half of all measured metabolites displayed ultradian sleep-wake dependence in summer. Irrespective of the arrhythmic behavior, metabolism is rhythmic (24 h) in seasons of low food availability, potentially favoring energy efficiency. In seasons of food abundance, 24-h rhythmicity in metabolism is drastically reduced, again irrespective of behavioral rhythms, potentially fostering weight gain.
    Keywords:  24-h rhythms; Arctic; NDVIQ3; UPLC-MS; blood metabolomics; caribou; circadian rhythms; metabolism; reindeer; seasonality
    DOI:  https://doi.org/10.1016/j.cub.2024.02.072
  72. Mol Cell. 2024 Mar 11. pii: S1097-2765(24)00176-X. [Epub ahead of print]
    Anti-apoptotic MCL-1 promotes long-chain fatty acid oxidation through interaction with ACSL1.
    Tristen Wright, Meghan E Turnis, Christy R Grace, Xiao Li, Lauren A Brakefield, Yong-Dong Wang, Haiyan Xu, Ewa Kaminska, Leslie K Climer, Tresor O Mukiza, Chi-Lun Chang, Tudor Moldoveanu, Joseph T Opferman.
      MCL-1 is essential for promoting the survival of many normal cell lineages and confers survival and chemoresistance in cancer. Beyond apoptosis regulation, MCL-1 has been linked to modulating mitochondrial metabolism, but the mechanism(s) by which it does so are unclear. Here, we show in tissues and cells that MCL-1 supports essential steps in long-chain (but not short-chain) fatty acid β-oxidation (FAO) through its binding to specific long-chain acyl-coenzyme A (CoA) synthetases of the ACSL family. ACSL1 binds to the BH3-binding hydrophobic groove of MCL-1 through a non-conventional BH3-domain. Perturbation of this interaction, via genetic loss of Mcl1, mutagenesis, or use of selective BH3-mimetic MCL-1 inhibitors, represses long-chain FAO in cells and in mouse livers and hearts. Our findings reveal how anti-apoptotic MCL-1 facilitates mitochondrial metabolism and indicate that disruption of this function may be associated with unanticipated cardiac toxicities of MCL-1 inhibitors in clinical trials.
    Keywords:  MCL-1; acyl-coenzyme A synthetase; apoptosis; fatty acid; metabolism; mitochondria; β-oxidation
    DOI:  https://doi.org/10.1016/j.molcel.2024.02.035
  73. Nat Metab. 2024 Mar 18.
    Metformin and feeding increase levels of the appetite-suppressing metabolite Lac-Phe in humans.
    Barry Scott, Emily A Day, Katie L O'Brien, John Scanlan, Grace Cromwell, Aine Ni Scannail, Marie E McDonnell, David K Finlay, Lydia Lynch.
      Metformin, a widely used first-line treatment for type 2 diabetes (T2D), is known to reduce blood glucose levels and suppress appetite. Here we report a significant elevation of the appetite-suppressing metabolite N-lactoyl phenylalanine (Lac-Phe) in the blood of individuals treated with metformin across seven observational and interventional studies. Furthermore, Lac-Phe levels were found to rise in response to acute metformin administration and post-prandially in patients with T2D or in metabolically healthy volunteers.
    DOI:  https://doi.org/10.1038/s42255-024-01018-7
  74. Cell Rep. 2024 Mar 12. pii: S2211-1247(24)00279-1. [Epub ahead of print] 113951
    Energy balance drives diurnal and nocturnal brain transcriptome rhythms.
    Laura van Rosmalen, Shaunak Deota, Geraldine Maier, Hiep D Le, Terry Lin, Ramesh K Ramasamy, Roelof A Hut, Satchidananda Panda.
      Plasticity in daily timing of activity has been observed in many species, yet the underlying mechanisms driving nocturnality and diurnality are unknown. By regulating how much wheel-running activity will be rewarded with a food pellet, we can manipulate energy balance and switch mice to be nocturnal or diurnal. Here, we present the rhythmic transcriptome of 21 tissues, including 17 brain regions, sampled every 4 h over a 24-h period from nocturnal and diurnal male CBA/CaJ mice. Rhythmic gene expression across tissues comprised different sets of genes with minimal overlap between nocturnal and diurnal mice. We show that non-clock genes in the suprachiasmatic nucleus (SCN) change, and the habenula was most affected. Our results indicate that adaptive flexibility in daily timing of behavior is supported by gene expression dynamics in many tissues and brain regions, especially in the habenula, which suggests a crucial role for the observed nocturnal-diurnal switch.
    Keywords:  CP: Metabolism; CP: Neuroscience; SCN; behavioral plasticity; circadian rhythms; diurnal; habenula; hypothalamus; negative energy balance; nocturnal; running wheel activity; temporal niche switching
    DOI:  https://doi.org/10.1016/j.celrep.2024.113951
  75. iScience. 2024 Mar 15. 27(3): 109173
    Serine metabolism is crucial for cGAS-STING signaling and viral defense control in the gut.
    Björn Becker, Felix Wottawa, Mohamed Bakr, Eric Koncina, Lisa Mayr, Julia Kugler, Guang Yang, Samuel J Windross, Laura Neises, Neha Mishra, Danielle Harris, Florian Tran, Lina Welz, Julian Schwärzler, Zoltán Bánki, Stephanie T Stengel, Go Ito, Christina Krötz, Olivia I Coleman, Christian Jaeger, Dirk Haller, Søren R Paludan, Richard Blumberg, Arthur Kaser, Luka Cicin-Sain, Stefan Schreiber, Timon E Adolph, Elisabeth Letellier, Philip Rosenstiel, Johannes Meiser, Konrad Aden.
      Inflammatory bowel diseases are characterized by the chronic relapsing inflammation of the gastrointestinal tract. While the molecular causality between endoplasmic reticulum (ER) stress and intestinal inflammation is widely accepted, the metabolic consequences of chronic ER stress on the pathophysiology of IBD remain unclear. By using in vitro, in vivo models, and patient datasets, we identified a distinct polarization of the mitochondrial one-carbon metabolism and a fine-tuning of the amino acid uptake in intestinal epithelial cells tailored to support GSH and NADPH metabolism upon ER stress. This metabolic phenotype strongly correlates with IBD severity and therapy response. Mechanistically, we uncover that both chronic ER stress and serine limitation disrupt cGAS-STING signaling, impairing the epithelial response against viral and bacterial infection and fueling experimental enteritis. Consequently, the antioxidant treatment restores STING function and virus control. Collectively, our data highlight the importance of serine metabolism to allow proper cGAS-STING signaling and innate immune responses upon gut inflammation.
    Keywords:  Microbial metabolism; Virology
    DOI:  https://doi.org/10.1016/j.isci.2024.109173
  76. Nature. 2024 Mar 20.
    Whittling down the bacterial subspecies that might drive colon cancer.
    Cynthia L Sears, Jessica Queen.
      
    Keywords:  Cancer; Medical research; Microbiology
    DOI:  https://doi.org/10.1038/d41586-024-00662-z
  77. Nat Methods. 2024 Mar 19.
    Multicenter integrated analysis of noncoding CRISPRi screens.
    David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay-Smith, Benjamin R Doughty, Idan Gabdank, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly.
      The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
    DOI:  https://doi.org/10.1038/s41592-024-02216-7
  78. Nat Metab. 2024 Mar 18.
    Metformin induces a Lac-Phe gut-brain signalling axis.
    Tara TeSlaa.
      
    DOI:  https://doi.org/10.1038/s42255-024-01014-x
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