bims-camemi 2022-12-11 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2022–12–11
forty-two papers selected by
Christian Frezza, Universität zu Köln

Mitochondrial RNA stimulates heat production in young adipocytes to reduce obesity.
NAD precursors cycle between host tissues and the gut microbiome.
Not so neutral lipids: Metabolic regulation of the pre-metastatic niche.
A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome.
PHGDH and cancer: new job for an old enzyme!
The NAD+ precursor NMN activates dSarm to trigger axon degeneration in Drosophila.
Distinct effects of intracellular vs. extracellular acidic pH on the cardiac metabolome during ischemia and reperfusion.
Mitochondrial cristae architecture protects against mtDNA release and inflammation.
DJ-1 promotes energy balance by regulating both mitochondrial and autophagic homeostasis.
Plant-cell machinery for making metabolites transferred to mammalian cells.
Hypoxic activation of PFKFB4 in breast tumor microenvironment shapes metabolic and cellular plasticity to accentuate metastatic competence.
Age-associated remodeling of T cell immunity and metabolism.
OLA1 Phosphorylation Governs the Mitochondrial Bioenergetic Function of Pulmonary Vascular Cells.
The circadian clock influences T cell responses to vaccination by regulating dendritic cell antigen processing.
Glycolytic flux-signaling controls mouse embryo mesoderm development.
The role of cholesterol and mitochondrial bioenergetics in activation of the inflammasome in IBD.
Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells.
Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features.
EIF4A inhibition targets bioenergetic homeostasis in AML MOLM-14 cells in vitro and in vivo and synergizes with cytarabine and venetoclax.
Crosstalk between pro-survival sphingolipid metabolism and complement signaling induces inflammasome-mediated tumor metastasis.
Contribution of metabolic abnormalities to acute myeloid leukemia pathogenesis.
Lipolysis-derived linoleic acid drives beige fat progenitor cell proliferation.
PINK1-mediated mitophagy promotes oxidative phosphorylation and redox homeostasis to induce drug-tolerant persister cancer cells.
The role of the tryptophan-NAD + pathway in a mouse model of severe malnutrition induced liver dysfunction.
A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations.
Ammonia detoxification promotes CD8+ T cell memory development by urea and citrulline cycles.
Uncoupling of energy production.
Xenotopic expression of alternative oxidase (AOX) to study mechanisms of mitochondrial disease.
ER-associated RNA silencing promotes ER quality control.
Mitochondria need their sleep: Sleep-wake cycling and the role of redox, bioenergetics, and temperature regulation, involving cysteine-mediated redox signaling, uncoupling proteins, and substrate cycles.
Cancer cell-derived type I interferons instruct tumor monocyte polarization.
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.
Nitric oxide regulation of cellular metabolism: Adaptive tuning of cellular energy.
Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
Mitochondrial succinate dehydrogenase function is essential for sperm motility and male fertility.
Inner mitochondrial membrane structure and fusion dynamics are altered in senescent human iPSC-derived and primary rat cardiomyocytes.
Proteogenomic characterization of MiT family translocation renal cell carcinoma.
Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.
IFITM proteins assist cellular uptake of diverse linked chemotypes.
Spatial biology of cancer evolution.
Elevated methionine flux drives pyroptosis evasion in persister cancer cells.
Deoxyribonucleoside triphosphate pools in mammalian cells are expandable upon DNA damage.

Nat Metab. 2022 Dec 06.

Mitochondrial RNA stimulates heat production in young adipocytes to reduce obesity.

DOI: https://doi.org/10.1038/s42255-022-00686-7
Cell Metab. 2022 Dec 06. pii: S1550-4131(22)00495-8. [Epub ahead of print]34(12): 1947-1959.e5

NAD precursors cycle between host tissues and the gut microbiome.

Karthikeyani Chellappa, Melanie R McReynolds, Wenyun Lu, Xianfeng Zeng, Mikhail Makarov, Faisal Hayat, Sarmistha Mukherjee, Yashaswini R Bhat, Siddharth R Lingala, Rafaella T Shima, Hélène C Descamps, Timothy Cox, Lixin Ji, Connor Jankowski, Qingwei Chu, Shawn M Davidson, Christoph A Thaiss, Marie E Migaud, Joshua D Rabinowitz, Joseph A Baur.

  Nicotinamide adenine dinucleotide (NAD) is an essential redox cofactor in mammals and microbes. Here we use isotope tracing to investigate the precursors supporting NAD synthesis in the gut microbiome of mice. We find that dietary NAD precursors are absorbed in the proximal part of the gastrointestinal tract and not available to microbes in the distal gut. Instead, circulating host nicotinamide enters the gut lumen and supports microbial NAD synthesis. The microbiome converts host-derived nicotinamide into nicotinic acid, which is used for NAD synthesis in host tissues and maintains circulating nicotinic acid levels even in the absence of dietary consumption. Moreover, the main route from oral nicotinamide riboside, a widely used nutraceutical, to host NAD is via conversion into nicotinic acid by the gut microbiome. Thus, we establish the capacity for circulating host micronutrients to feed the gut microbiome, and in turn be transformed in a manner that enhances host metabolic flexibility.

Keywords:  NAD; flux; gastrointestinal; microbe; microbiome; mononucleotide; niacin; nicotinamide; nicotinic acid; riboside

DOI:  https://doi.org/10.1016/j.cmet.2022.11.004
Cell Metab. 2022 Dec 06. pii: S1550-4131(22)00498-3. [Epub ahead of print]34(12): 1899-1900

Not so neutral lipids: Metabolic regulation of the pre-metastatic niche.

Joshua D Schoenfeld, Santosha A Vardhana.

How primary tumors alter distant tissue sites to facilitate seeding and metastasis remains unclear. In this issue, Gong et al. demonstrate that IL-1β-dependent lipid accumulation in lung mesenchymal cells supports both tumor growth and NK cell dysfunction, facilitating lung metastasis of primary breast tumors.

DOI: https://doi.org/10.1016/j.cmet.2022.11.007
Nat Biomed Eng. 2022 Dec 05.

A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome.

Pedro Silva-Pinheiro, Christian D Mutti, Lindsey Van Haute, Christopher A Powell, Pavel A Nash, Keira Turner, Michal Minczuk.

The development of curative treatments for mitochondrial diseases, which are often caused by mutations in mitochondrial DNA (mtDNA) that impair energy metabolism and other aspects of cellular homoeostasis, is hindered by an incomplete understanding of the underlying biology and a scarcity of cellular and animal models. Here we report the design and application of a library of double-stranded-DNA deaminase-derived cytosine base editors optimized for the precise ablation of every mtDNA protein-coding gene in the mouse mitochondrial genome. We used the library, which we named MitoKO, to produce near-homoplasmic knockout cells in vitro and to generate a mouse knockout with high heteroplasmy levels and no off-target edits. MitoKO should facilitate systematic and comprehensive investigations of mtDNA-related pathways and their impact on organismal homoeostasis, and aid the generation of clinically meaningful in vivo models of mtDNA dysfunction.

DOI: https://doi.org/10.1038/s41551-022-00968-1
EMBO J. 2022 Dec 07. e113068

PHGDH and cancer: new job for an old enzyme!

Duygu Kuzuoglu-Ozturk.

How do cancer cells bolster their energy metabolism under conditions of stress? Recent work by Shu et al (2022) unveils a novel, non-canonical function of the de novo serine synthesis pathway enzyme phosphoglycerate dehydrogenase (PHGDH) as a regulator of mitochondrial translation and tumor progression in liver cancer.

DOI: https://doi.org/10.15252/embj.2022113068
Elife. 2022 Dec 07. pii: e80245. [Epub ahead of print]11

The NAD+ precursor NMN activates dSarm to trigger axon degeneration in Drosophila.

Arnau Llobet Rosell, Maria Paglione, Jonathan Gilley, Magdalena Kocia, Giulia Perillo, Massimiliano Gasparrini, Lucia Cialabrini, Nadia Raffaelli, Carlo Angeletti, Giuseppe Orsomando, Pei-Hsuan Wu, Michael P Coleman, Andrea Loreto, Lukas Jakob Neukomm.

  Axon degeneration contributes to the disruption of neuronal circuit function in diseased and injured nervous systems. Severed axons degenerate following the activation of an evolutionarily conserved signaling pathway, which culminates in the activation of SARM1 in mammals to execute the pathological depletion of the metabolite NAD+. SARM1 NADase activity is activated by the NAD+ precursor nicotinamide mononucleotide (NMN). In mammals, keeping NMN levels low potently preserves axons after injury. However, it remains unclear whether NMN is also a key mediator of axon degeneration and dSarm activation in flies. Here, we demonstrate that lowering NMN levels in Drosophila through the expression of a newly generated prokaryotic NMN-Deamidase (NMN-D) preserves severed axons for months and keeps them circuit-integrated for weeks. NMN-D alters the NAD+ metabolic flux by lowering NMN, while NAD+ remains unchanged in vivo. Increased NMN synthesis, by the expression of mouse nicotinamide phosphoribosyltransferase (mNAMPT), leads to faster axon degeneration after injury. We also show that NMN-induced activation of dSarm mediates axon degeneration in vivo. Finally, NMN-D delays neurodegeneration caused by loss of the sole NMN-consuming and NAD+-synthesizing enzyme dNmnat. Our results reveal a critical role for NMN in neurodegeneration in the fly, which extends beyond axonal injury. The potent neuroprotection by reducing NMN levels is similar to the interference with other essential mediators of axon degeneration in Drosophila.

Keywords:  D. melanogaster; cell biology; neuroscience

DOI:  https://doi.org/10.7554/eLife.80245
J Mol Cell Cardiol. 2022 Dec 05. pii: S0022-2828(22)00568-5. [Epub ahead of print]174 101-114

Distinct effects of intracellular vs. extracellular acidic pH on the cardiac metabolome during ischemia and reperfusion.

Alexander S Milliken, Jessica H Ciesla, Sergiy M Nadtochiy, Paul S Brookes.

  Tissue ischemia results in intracellular pH (pHIN) acidification, and while metabolism is a known driver of acidic pHIN, less is known about how acidic pHIN regulates metabolism. Furthermore, acidic extracellular (pHEX) during early reperfusion confers cardioprotection, but how this impacts metabolism is unclear. Herein we employed LCMS based targeted metabolomics to analyze perfused mouse hearts exposed to: (i) control perfusion, (ii) hypoxia, (iii) ischemia, (iv) enforced acidic pHIN, (v) control reperfusion, and (vi) acidic pHEX (6.8) reperfusion. Surprisingly little overlap was seen between metabolic changes induced by hypoxia, ischemia, and acidic pHIN. Acidic pHIN elevated metabolites in the top half of glycolysis, and enhanced glutathione redox state. Meanwhile, acidic pHEX reperfusion induced substantial metabolic changes in addition to those seen in control reperfusion. This included elevated metabolites in the top half of glycolysis, prevention of purine nucleotide loss, and an enhancement in glutathione redox state. These data led to hypotheses regarding potential roles for methylglyoxal inhibiting the mitochondrial permeability transition pore, and for acidic inhibition of ecto-5'-nucleotidase, as potential mediators of cardioprotection by acidic pHEX reperfusion. However, neither hypothesis was supported by subsequent experiments. In contrast, analysis of cardiac effluents revealed complex effects of pHEX on metabolite transport, suggesting that mildly acidic pHEX may enhance succinate release during reperfusion. Overall, each intervention had distinct and overlapping metabolic effects, suggesting acidic pH is an independent metabolic regulator regardless which side of the cell membrane it is imposed.

Keywords:  Acidosis; Hypoxia; Ischemia; Metabolism; Purines; pH

DOI:  https://doi.org/10.1016/j.yjmcc.2022.11.008
Cell Rep. 2022 Dec 06. pii: S2211-1247(22)01657-6. [Epub ahead of print]41(10): 111774

Mitochondrial cristae architecture protects against mtDNA release and inflammation.

Baiyu He, Huatong Yu, Shanshan Liu, Huayun Wan, Song Fu, Siqi Liu, Jun Yang, Zihan Zhang, Huanwei Huang, Qi Li, Fengchao Wang, Zhaodi Jiang, Qinghua Liu, Hui Jiang.

  Mitochondrial damage causes mitochondrial DNA (mtDNA) release to activate the type I interferon (IFN-I) response via the cGAS-STING pathway. mtDNA-induced inflammation promotes autoimmune- and aging-related degenerative disorders. However, the global picture of inflammation-inducing mitochondrial damages remains obscure. Here, we have performed a mitochondria-targeted CRISPR knockout screen for regulators of the IFN-I response. Strikingly, our screen reveals dozens of hits enriched with key regulators of cristae architecture, including phospholipid cardiolipin and protein complexes such as OPA1, mitochondrial contact site and cristae organization (MICOS), sorting and assembly machinery (SAM), mitochondrial intermembrane space bridging (MIB), prohibitin (PHB), and the F1Fo-ATP synthase. Disrupting these cristae organizers consistently induces mtDNA release and the STING-dependent IFN-I response. Furthermore, knocking out MTX2, a subunit of the SAM complex whose null mutations cause progeria in humans, induces a robust STING-dependent IFN-I response in mouse liver. Taken together, beyond revealing the central role of cristae architecture to prevent mtDNA release and inflammation, our results mechanistically link mitochondrial cristae disorganization and inflammation, two emerging hallmarks of aging and aging-related degenerative diseases.

Keywords:  CP: Cell biology; CP: Molecular biology; MICOS; Metaxin2; OPA1; SAM; cGAS-STING; cristae architecture; inflammation; mtDNA release; type I interferon response

DOI:  https://doi.org/10.1016/j.celrep.2022.111774
Neurobiol Dis. 2022 Dec 05. pii: S0969-9961(22)00333-3. [Epub ahead of print]176 105941

DJ-1 promotes energy balance by regulating both mitochondrial and autophagic homeostasis.

Federica De Lazzari, Francesco Agostini, Nicoletta Plotegher, Michele Sandre, Elisa Greggio, Aram Megighian, Luigi Bubacco, Federica Sandrelli, Alexander J Whitworth, Marco Bisaglia.

  The protein DJ-1 is mutated in rare familial forms of recessive Parkinson's disease and in parkinsonism accompanied by amyotrophic lateral sclerosis symptoms and dementia. DJ-1 is considered a multitasking protein able to confer protection under various conditions of stress. However, the precise cellular function still remains elusive. In the present work, we evaluated fruit flies lacking the expression of the DJ-1 homolog dj-1β as compared to control aged-matched individuals. Behavioral evaluations included lifespan, locomotion in an open field arena, sensitivity to oxidative insults, and resistance to starvation. Molecular analyses were carried out by analyzing the mitochondrial morphology and functionality, and the autophagic response. We demonstrated that dj-1β null mutant flies are hypoactive and display higher sensitivity to oxidative insults and food deprivation. Analysis of mitochondrial homeostasis revealed that loss of dj-1β leads to larger and more circular mitochondria, characterized by impaired complex-I-linked respiration while preserving ATP production capacity. Additionally, dj-1β null mutant flies present an impaired autophagic response, which is suppressed by treatment with the antioxidant molecule N-Acetyl-L-Cysteine. Overall, our data point to a mechanism whereby DJ-1 plays a critical role in the maintenance of energy homeostasis, by sustaining mitochondrial homeostasis and affecting the autophagic flux through the maintenance of the cellular redox state. In light of the involvement of DJ-1 in neurodegenerative diseases and considering that neurons are highly energy-demanding cells, particularly sensitive to redox stress, our study sheds light on a key role of DJ-1 in the maintenance of cellular homeostasis.

Keywords:  Autophagy; DJ-1; Energy balance; Mitochondria; Redox homeostasis

DOI:  https://doi.org/10.1016/j.nbd.2022.105941
Nature. 2022 Dec 07.

Plant-cell machinery for making metabolites transferred to mammalian cells.



Keywords:  Biomaterials; Biotechnology; Metabolism; Regeneration

DOI:  https://doi.org/10.1038/d41586-022-03629-0
Cell Rep. 2022 Dec 06. pii: S2211-1247(22)01639-4. [Epub ahead of print]41(10): 111756

Hypoxic activation of PFKFB4 in breast tumor microenvironment shapes metabolic and cellular plasticity to accentuate metastatic competence.

Tao Dai, Spencer R Rosario, Eriko Katsuta, Abhisha Sawant Dessai, Emily J Paterson, Aaron T Novickis, Eduardo Cortes Gomez, Bokai Zhu, Song Liu, Hai Wang, Scott I Abrams, Mukund Seshadri, Wiam Bshara, Subhamoy Dasgupta.

  Cancer cells encounter a hostile tumor microenvironment (TME), and their adaptations to metabolic stresses determine metastatic competence. Here, we show that the metabolic enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase-4 (PFKFB4) is induced in hypoxic tumors acquiring metabolic plasticity and invasive phenotype. In mouse models of breast cancer, genetic ablation of PFKFB4 significantly delays distant organ metastasis, reducing local lymph node invasion by suppressing expression of invasive gene signature including integrin β3. Photoacoustic imaging followed by metabolomics analyses of hypoxic tumors show that PFKFB4 drives metabolic flexibility, enabling rapid detoxification of reactive oxygen species favoring survival under selective pressure. Mechanistically, hypoxic induction triggers nuclear translocation of PFKFB4 accentuating non-canonical transcriptional activation of HIF-1α, and breast cancer patients with increased nuclear PFKFB4 in their tumors are found to be significantly associated with poor prognosis. Our findings imply that PFKFB4 induction is crucial for tumor cell adaptation in the hypoxic TME that determines metastatic competence.

Keywords:  CP: Cancer; CP: Metabolism; breast cancer; hypoxia; metabolism; metastasis; redox; stress; transcription; tumor microenvironment

DOI:  https://doi.org/10.1016/j.celrep.2022.111756
Cell Metab. 2022 Nov 29. pii: S1550-4131(22)00496-X. [Epub ahead of print]

Age-associated remodeling of T cell immunity and metabolism.

SeongJun Han, Peter Georgiev, Alison E Ringel, Arlene H Sharpe, Marcia C Haigis.

  Aging results in remodeling of T cell immunity and is associated with poor clinical outcomes in age-related diseases such as cancer. Among the hallmarks of aging, changes in host and cellular metabolism critically affect the development, maintenance, and function of T cells. Although metabolic perturbations impact anti-tumor T cell responses, the link between age-associated metabolic dysfunction and anti-tumor immunity remains unclear. In this review, we summarize recent advances in our understanding of aged T cell metabolism, with a focus on the bioenergetic and immunologic features of T cell subsets unique to the aging process. We also survey insights into mechanisms of metabolic T cell dysfunction in aging and discuss the impacts of aging on the efficacy of cancer immunotherapy. As the average life expectancy continues to increase, understanding the interplay between age-related metabolic reprogramming and maladaptive T cell immunity will be instrumental for the development of therapeutic strategies for older patients.

Keywords:  T cells; aging; cancer; immunity; immunotherapy; metabolism; mitochondria

DOI:  https://doi.org/10.1016/j.cmet.2022.11.005
Am J Respir Cell Mol Biol. 2022 Dec 08.

OLA1 Phosphorylation Governs the Mitochondrial Bioenergetic Function of Pulmonary Vascular Cells.

Paul Sidlowski, Amanda Czerwinski, Yong Liu, Pengyuan Liu, Ru-Jeng Teng, Suresh Kumar, Clive Wells, Kirkwood Pritchard, Girija G Konduri, Adeleye J Afolayan.

  Mitochondrial function and metabolic homeostasis are integral to cardiovascular function and influence how vascular cells respond to stress. However, little is known regarding how mitochondrial redox control mechanisms and metabolic regulation interact in the developing lungs. Here we show that human Obg-like ATPase-1 (OLA1) couples redox signals to the metabolic response pathway by activating metabolic gene transcription in the nucleus. We observed that OLA1 phosphorylation at Ser232/Tyr236 triggers its translocation from the cytoplasm/mitochondria into the nucleus. Subsequent phosphorylation of OLA1 at Thr325 effectively changes its biochemical function from ATPase to GTPase, promoting the expression of genes involved in the mitochondrial bioenergetic function. This process is regulated by extracellular-regulated kinases (ERK1/2), which were restrained by protein phosphatases 1A (PP1A) when stress abated. Knockdowns of ERK1 or OLA1 mutated to a phosphoresistant T325A mutant blocked its nuclear translocation, compromised the expression of nuclear-encoded mitochondrial genes, and as a consequence, led to cellular energy depletion. Moreover, the lungs of OLA1 knockout mice have fewer numbers of mitochondria, lower cellular ATP levels, and higher lactate levels. The ensuing mitochondrial metabolic dysfunction resulted in abnormal behaviors of pulmonary vascular cells and significant vascular remodeling. Our findings demonstrate that OLA1 is an important component of the mitochondrial retrograde communication pathways that couple stress signals with metabolic genes in the nucleus. Thus, phosphorylation-dependent nuclear OLA1 localization that governs cellular energy metabolism is critical to cardiovascular function.

Keywords:  OLA1; mitochondrial energy metabolism; phosphorylation; pulmonary hypertension; pulmonary vascular cells

DOI:  https://doi.org/10.1165/rcmb.2022-0186OC
Nat Commun. 2022 Dec 05. 13(1): 7217

The circadian clock influences T cell responses to vaccination by regulating dendritic cell antigen processing.

Mariana P Cervantes-Silva, Richard G Carroll, Mieszko M Wilk, Diana Moreira, Cloe A Payet, James R O'Siorain, Shannon L Cox, Lauren E Fagan, Paula A Klavina, Yan He, Tabea Drewinski, Alan McGinley, Sharleen M Buel, George A Timmons, James O Early, Roger J S Preston, Jennifer M Hurley, David K Finlay, Ingmar Schoen, F Javier Sánchez-García, Kingston H G Mills, Annie M Curtis.

Dendritic cells play a key role in processing and presenting antigens to naïve T cells to prime adaptive immunity. Circadian rhythms are known to regulate many aspects of immunity; however, the role of circadian rhythms in dendritic cell function is still unclear. Here, we show greater T cell responses when mice are immunised in the middle of their rest versus their active phase. We find a circadian rhythm in antigen processing that correlates with rhythms in both mitochondrial morphology and metabolism, dependent on the molecular clock gene, Bmal1. Using Mdivi-1, a compound that promotes mitochondrial fusion, we are able to rescue the circadian deficit in antigen processing and mechanistically link mitochondrial morphology and antigen processing. Furthermore, we find that circadian changes in mitochondrial Ca2+ are central to the circadian regulation of antigen processing. Our results indicate that rhythmic changes in mitochondrial calcium, which are associated with changes in mitochondrial morphology, regulate antigen processing.

DOI: https://doi.org/10.1038/s41467-022-34897-z
Elife. 2022 Dec 05. pii: e83299. [Epub ahead of print]11

Glycolytic flux-signaling controls mouse embryo mesoderm development.

Hidenobu Miyazawa, Marteinn T Snaebjornsson, Nicole Prior, Eleni Kafkia, Henrik M Hammarén, Nobuko Tsuchida-Straeten, Kiran R Patil, Martin Beck, Alexander Aulehla.

  How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Overexpression of cytoPFKFB3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPFKFB3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.

Keywords:  developmental biology; mouse

DOI:  https://doi.org/10.7554/eLife.83299
Front Immunol. 2022 ;13 1028953

The role of cholesterol and mitochondrial bioenergetics in activation of the inflammasome in IBD.

Jessica Astorga, Naschla Gasaly, Karen Dubois-Camacho, Marjorie De la Fuente, Glauben Landskron, Klaas Nico Faber, Félix A Urra, Marcela A Hermoso.

  Inflammatory Bowel Disease (IBD) is characterized by a loss of intestinal barrier function caused by an aberrant interaction between the immune response and the gut microbiota. In IBD, imbalance in cholesterol homeostasis and mitochondrial bioenergetics have been identified as essential events for activating the inflammasome-mediated response. Mitochondrial alterations, such as reduced respiratory complex activities and reduced production of tricarboxylic acid (TCA) cycle intermediates (e.g., citric acid, fumarate, isocitric acid, malate, pyruvate, and succinate) have been described in in vitro and clinical studies. Under inflammatory conditions, mitochondrial architecture in intestinal epithelial cells is dysmorphic, with cristae destruction and high dynamin-related protein 1 (DRP1)-dependent fission. Likewise, these alterations in mitochondrial morphology and bioenergetics promote metabolic shifts towards glycolysis and down-regulation of antioxidant Nuclear erythroid 2-related factor 2 (Nrf2)/Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) signaling. Although the mechanisms underlying the mitochondrial dysfunction during mucosal inflammation are not fully understood at present, metabolic intermediates and cholesterol may act as signals activating the NLRP3 inflammasome in IBD. Notably, dietary phytochemicals exhibit protective effects against cholesterol imbalance and mitochondrial function alterations to maintain gastrointestinal mucosal renewal in vitro and in vivo conditions. Here, we discuss the role of cholesterol and mitochondrial metabolism in IBD, highlighting the therapeutic potential of dietary phytochemicals, restoring intestinal metabolism and function.

Keywords:  IBD - inflammatory bowel disease; NLRP3 inflammasome; diet phytochemicals; inflammasome; intracellular cholesterol accumulation; mitochondrial dysfunction

DOI:  https://doi.org/10.3389/fimmu.2022.1028953
Cell Syst. 2022 Dec 01. pii: S2405-4712(22)00462-8. [Epub ahead of print]

Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells.

Kshitiz, Junaid Afzal, Yasir Suhail, Hao Chang, Maimon E Hubbi, Archer Hamidzadeh, Ruchi Goyal, Yamin Liu, Peng Sun, Stefania Nicoli, Chi V Dang, Andre Levchenko.

  Response to hypoxia is a highly regulated process, but little is known about single-cell responses to hypoxic conditions. Using fluorescent reporters of hypoxia response factor-1α (HIF-1α) activity in various cancer cell lines and patient-derived cancer cells, we show that hypoxic responses in individual cancer cells can be highly dynamic and variable. These responses fall into three classes, including oscillatory activity. We identify a molecular mechanism that can account for all three response classes, implicating reactive-oxygen-species-dependent chaperone-mediated autophagy of HIF-1α in a subset of cells. Furthermore, we show that oscillatory response is modulated by the abundance of extracellular lactate in a quorum-sensing-like mechanism. We show that oscillatory HIF-1α activity rescues hypoxia-mediated inhibition of cell division and causes broad suppression of genes downregulated in cancers and activation of genes upregulated in many cancers, suggesting a mechanism for aggressive growth in a subset of hypoxic tumor cells.

Keywords:  HIF; ROS; Warburg and reverse Warburg effect; cancer microenvironment; chaperone-mediated autophagy; hypoxia; hypoxic oscillations; lactate; quorum sensing; reactive oxygen species

DOI:  https://doi.org/10.1016/j.cels.2022.11.003
Nat Commun. 2022 Dec 07. 13(1): 7551

Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features.

Dustin J Flanagan, Raheleh Amirkhah, David F Vincent, Nuray Gundaz, Pauline Gentaz, Patrizia Cammareri, Aoife J McCooey, Amy M B McCorry, Natalie C Fisher, Hayley L Davis, Rachel A Ridgway, Jeroen Lohuis, Joshua D G Leach, Rene Jackstadt, Kathryn Gilroy, Elisa Mariella, Colin Nixon, William Clark, Ann Hedley, Elke K Markert, Douglas Strathdee, Laurent Bartholin, Keara L Redmond, Emma M Kerr, Daniel B Longley, Fiona Ginty, Sanghee Cho, Helen G Coleman, Maurice B Loughrey, Alberto Bardelli, Timothy S Maughan, Andrew D Campbell, Mark Lawler, Simon J Leedham, Simon T Barry, Gareth J Inman, Jacco van Rheenen, Philip D Dunne, Owen J Sansom.

The pro-tumourigenic role of epithelial TGFβ signalling in colorectal cancer (CRC) is controversial. Here, we identify a cohort of born to be bad early-stage (T1) colorectal tumours, with aggressive features and a propensity to disseminate early, that are characterised by high epithelial cell-intrinsic TGFβ signalling. In the presence of concurrent Apc and Kras mutations, activation of epithelial TGFβ signalling rampantly accelerates tumourigenesis and share transcriptional signatures with those of the born to be bad T1 human tumours and predicts recurrence in stage II CRC. Mechanistically, epithelial TGFβ signalling induces a growth-promoting EGFR-signalling module that synergises with mutant APC and KRAS to drive MAPK signalling that re-sensitise tumour cells to MEK and/or EGFR inhibitors. Together, we identify epithelial TGFβ signalling both as a determinant of early dissemination and a potential therapeutic vulnerability of CRC's with born to be bad traits.

DOI: https://doi.org/10.1038/s41467-022-35134-3
J Exp Clin Cancer Res. 2022 Dec 09. 41(1): 340

EIF4A inhibition targets bioenergetic homeostasis in AML MOLM-14 cells in vitro and in vivo and synergizes with cytarabine and venetoclax.

Katie Fooks, Gabriela Galicia-Vazquez, Victor Gife, Alejandro Schcolnik-Cabrera, Zaynab Nouhi, William W L Poon, Vincent Luo, Ryan N Rys, Raquel Aloyz, Alexandre Orthwein, Nathalie A Johnson, Laura Hulea, Francois E Mercier.

   BACKGROUND: Acute myeloid leukemia (AML) is an aggressive hematological cancer resulting from uncontrolled proliferation of differentiation-blocked myeloid cells. Seventy percent of AML patients are currently not cured with available treatments, highlighting the need of novel therapeutic strategies. A promising target in AML is the mammalian target of rapamycin complex 1 (mTORC1). Clinical inhibition of mTORC1 is limited by its reactivation through compensatory and regulatory feedback loops. Here, we explored a strategy to curtail these drawbacks through inhibition of an important effector of the mTORC1signaling pathway, the eukaryotic initiation factor 4A (eIF4A).
METHODS: We tested the anti-leukemic effect of a potent and specific eIF4A inhibitor (eIF4Ai), CR-1-31-B, in combination with cytosine arabinoside (araC) or the BCL2 inhibitor venetoclax. We utilized the MOLM-14 human AML cell line to model chemoresistant disease both in vitro and in vivo. In eIF4Ai-treated cells, we assessed for changes in survival, apoptotic priming, de novo protein synthesis, targeted intracellular metabolite content, bioenergetic profile, mitochondrial reactive oxygen species (mtROS) and mitochondrial membrane potential (MMP).
RESULTS: eIF4Ai exhibits anti-leukemia activity in vivo while sparing non-malignant myeloid cells. In vitro, eIF4Ai synergizes with two therapeutic agents in AML, araC and venetoclax. EIF4Ai reduces mitochondrial membrane potential (MMP) and the rate of ATP synthesis from mitochondrial respiration and glycolysis. Furthermore, eIF4i enhanced apoptotic priming while reducing the expression levels of the antiapoptotic factors BCL2, BCL-XL and MCL1. Concomitantly, eIF4Ai decreases intracellular levels of specific metabolic intermediates of the tricarboxylic acid cycle (TCA cycle) and glucose metabolism, while enhancing mtROS. In vitro redox stress contributes to eIF4Ai cytotoxicity, as treatment with a ROS scavenger partially rescued the viability of eIF4A inhibition.
CONCLUSIONS: We discovered that chemoresistant MOLM-14 cells rely on eIF4A-dependent cap translation for survival in vitro and in vivo. EIF4A drives an intrinsic metabolic program sustaining bioenergetic and redox homeostasis and regulates the expression of anti-apoptotic proteins. Overall, our work suggests that eIF4A-dependent cap translation contributes to adaptive processes involved in resistance to relevant therapeutic agents in AML.

Keywords:  AML; BCL-XL; BCL2; Bioenergetics; MCL1; Metabolism; ROS; Venetoclax; araC; eIF4A; mTORC1

DOI:  https://doi.org/10.1186/s13046-022-02542-8
Cell Rep. 2022 Dec 06. pii: S2211-1247(22)01620-5. [Epub ahead of print]41(10): 111742

Crosstalk between pro-survival sphingolipid metabolism and complement signaling induces inflammasome-mediated tumor metastasis.

Alhaji H Janneh, Mohamed Faisal Kassir, F Cansu Atilgan, Han Gyul Lee, Megan Sheridan, Natalia Oleinik, Zdzislaw Szulc, Christina Voelkel-Johnson, Hung Nguyen, Hong Li, Yuri K Peterson, Elisabetta Marangoni, Ozge Saatci, Ozgur Sahin, Michael Lilly, Carl Atkinson, Stephen Tomlinson, Shikhar Mehrotra, Besim Ogretmen.

  Crosstalk between metabolic and signaling events that induce tumor metastasis remains elusive. Here, we determine how oncogenic sphingosine 1-phosphate (S1P) metabolism induces intracellular C3 complement activation to enhance migration/metastasis. We demonstrate that increased S1P metabolism activates C3 complement processing through S1P receptor 1 (S1PR1). S1P/S1PR1-activated intracellular C3b-α'2 is associated with PPIL1 through glutamic acid 156 (E156) and aspartic acid 111 (D111) residues, resulting in NLRP3/inflammasome induction. Inactivation mutations of S1PR1 to prevent S1P signaling or mutations of C3b-α'2 to prevent its association with PPIL1 attenuate inflammasome activation and reduce lung colonization/metastasis in mice. Also, activation of the S1PR1/C3/PPIL1/NLRP3 axis is highly associated with human metastatic melanoma tissues and patient-derived xenografts. Moreover, targeting S1PR1/C3/PPIL1/NLRP3 signaling using molecular, genetic, and pharmacologic tools prevents lung colonization/metastasis of various murine cancer cell lines using WT and C3a-receptor1 knockout (C3aR1-/-) mice. These data provide strategies for treating high-grade/metastatic tumors by targeting the S1PR1/C3/inflammasome axis.

Keywords:  CP: Cancer; CP: Metabolism; S1P; S1P receptor 1; S1PR1; complement signaling; inflammasome; metastasis; sphingolipids; sphingosine 1-phosphate

DOI:  https://doi.org/10.1016/j.celrep.2022.111742
Trends Cell Biol. 2022 Dec 05. pii: S0962-8924(22)00255-0. [Epub ahead of print]

Contribution of metabolic abnormalities to acute myeloid leukemia pathogenesis.

Grace Egan, Aaron D Schimmer.

  Acute myeloid leukemia (AML) is a malignant disease of myeloid precursors. Somatic mutations have long been accepted as drivers of this malignancy. Over the past decade, unique mitochondrial and metabolic dependencies of AML and AML stem cells have been identified, including a reliance on oxidative phosphorylation. More recently, metabolic enzymes have demonstrated noncanonical roles in regulating gene expression in AML, controlling cell differentiation and stemness. These mitochondrial and metabolic adaptations occur independent of underlying genomic abnormalities and contribute to chemoresistance and relapse. In this opinion article, we discuss the current understanding of AML pathogenesis and whether mitochondrial and metabolic abnormalities drive leukemogenesis or are a non-contributory phenotype.

Keywords:  acute myeloid leukemia; metabolism; mitochondria; oxidative phosphorylation; pathogenesis

DOI:  https://doi.org/10.1016/j.tcb.2022.11.004
Dev Cell. 2022 Dec 05. pii: S1534-5807(22)00788-2. [Epub ahead of print]57(23): 2623-2637.e8

Lipolysis-derived linoleic acid drives beige fat progenitor cell proliferation.

Ichitaro Abe, Yasuo Oguri, Anthony R P Verkerke, Lauar B Monteiro, Carly M Knuth, Christopher Auger, Yunping Qiu, Gregory P Westcott, Saverio Cinti, Kosaku Shinoda, Marc G Jeschke, Shingo Kajimura.

  De novo beige adipocyte biogenesis involves the proliferation of progenitor cells in white adipose tissue (WAT); however, what regulates this process remains unclear. Here, we report that in mouse models but also in human tissues, WAT lipolysis-derived linoleic acid triggers beige progenitor cell proliferation following cold acclimation, β3-adrenoceptor activation, and burn injury. A subset of adipocyte progenitors, as marked by cell surface markers PDGFRα or Sca1 and CD81, harbored cristae-rich mitochondria and actively imported linoleic acid via a fatty acid transporter CD36. Linoleic acid not only was oxidized as fuel in the mitochondria but also was utilized for the synthesis of arachidonic acid-derived signaling entities such as prostaglandin D2. Oral supplementation of linoleic acid was sufficient to stimulate beige progenitor cell proliferation, even under thermoneutral conditions, in a CD36-dependent manner. Together, this study provides mechanistic insights into how diverse pathophysiological stimuli, such as cold and burn injury, promote de novo beige fat biogenesis.

Keywords:  adipose tissue development; beige adipocytes; bioenergetics; brown adipose tissue; lipolysis; metabolic disease; progenitor cells; white adipose tissue

DOI:  https://doi.org/10.1016/j.devcel.2022.11.007
Cancer Res. 2022 Dec 08. pii: CAN-22-2370. [Epub ahead of print]

PINK1-mediated mitophagy promotes oxidative phosphorylation and redox homeostasis to induce drug-tolerant persister cancer cells.

Yun Li, Hengxing Chen, Xuan Xie, Bing Yang, Xiaojuan Wang, Jingyuan Zhang, Tian Qiao, Jiao Guan, Yuntan Qiu, Yong-Xin Huang, Duanqing Tian, Xinyi Yao, Daning Lu, H Phillip Koeffler, Yin Zhang, Dong Yin.

The drug-tolerant persister (DTP) state enables cancer cells to evade cytotoxic stress from anti-cancer therapy. However, the mechanisms governing DTP generation remain poorly understood. Here, we observed that lung adenocarcinoma (LUAD) cells and organoids entered a quiescent DTP state to survive MAPK inhibitor treatment. DTP cells following MAPK inhibition underwent a metabolic switch from glycolysis to oxidative phosphorylation (OXPHOS). PTEN-induced kinase 1 (PINK1), a serine/threonine kinase that initiates mitophagy, was upregulated to maintain mitochondrial homeostasis during DTP generation. PINK1-mediated mitophagy supported DTP cell survival and contributed to poor prognosis. Mechanistically, MAPK pathway inhibition resulted in MYC-dependent transcriptional upregulation of PINK1, leading to mitophagy activation. Mitophagy inhibition using either clinically applicable chloroquine or depletion of PINK1 eradicated drug tolerance and allowed complete response to MAPK inhibitors. This study uncovers PINK1-mediated mitophagy as a novel tumor protective mechanism for DTP generation, providing a therapeutic opportunity to eradicate DTP and achieve complete responses.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2370
Nat Commun. 2022 Dec 08. 13(1): 7576

The role of the tryptophan-NAD + pathway in a mouse model of severe malnutrition induced liver dysfunction.

Guanlan Hu, Catriona Ling, Lijun Chi, Mehakpreet K Thind, Samuel Furse, Albert Koulman, Jonathan R Swann, Dorothy Lee, Marjolein M Calon, Celine Bourdon, Christian J Versloot, Barbara M Bakker, Gerard Bryan Gonzales, Peter K Kim, Robert H J Bandsma.

Mortality in children with severe malnutrition is strongly related to signs of metabolic dysfunction, such as hypoglycemia. Lower circulating tryptophan levels in children with severe malnutrition suggest a possible disturbance in the tryptophan-nicotinamide adenine dinucleotide (TRP-NAD+) pathway and subsequently in NAD+ dependent metabolism regulator sirtuin1 (SIRT1). Here we show that severe malnutrition in weanling mice, induced by 2-weeks of low protein diet feeding from weaning, leads to an impaired TRP-NAD+ pathway with decreased NAD+ levels and affects hepatic mitochondrial turnover and function. We demonstrate that stimulating the TRP-NAD+ pathway with NAD+ precursors improves hepatic mitochondrial and overall metabolic function through SIRT1 modulation. Activating SIRT1 is sufficient to induce improvement in metabolic functions. Our findings indicate that modulating the TRP-NAD+ pathway can improve liver metabolic function in a mouse model of severe malnutrition. These results could lead to the development of new interventions for children with severe malnutrition.

DOI: https://doi.org/10.1038/s41467-022-35317-y
Sci Data. 2022 Dec 03. 9(1): 751

A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations.

Gabriel Sturm, Anna S Monzel, Kalpita R Karan, Jeremy Michelson, Sarah A Ware, Andres Cardenas, Jue Lin, Céline Bris, Balaji Santhanam, Michael P Murphy, Morgan E Levine, Steve Horvath, Daniel W Belsky, Shuang Wang, Vincent Procaccio, Brett A Kaufman, Michio Hirano, Martin Picard.

Aging is a process of progressive change. To develop biological models of aging, longitudinal datasets with high temporal resolution are needed. Here we report a multi-omics longitudinal dataset for cultured primary human fibroblasts measured across their replicative lifespans. Fibroblasts were sourced from both healthy donors (n = 6) and individuals with lifespan-shortening mitochondrial disease (n = 3). The dataset includes cytological, bioenergetic, DNA methylation, gene expression, secreted proteins, mitochondrial DNA copy number and mutations, cell-free DNA, telomere length, and whole-genome sequencing data. This dataset enables the bridging of mechanistic processes of aging as outlined by the "hallmarks of aging", with the descriptive characterization of aging such as epigenetic age clocks. Here we focus on bridging the gap for the hallmark mitochondrial metabolism. Our dataset includes measurement of healthy cells, and cells subjected to over a dozen experimental manipulations targeting oxidative phosphorylation (OxPhos), glycolysis, and glucocorticoid signaling, among others. These experiments provide opportunities to test how cellular energetics affect the biology of cellular aging. All data are publicly available at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/.

DOI: https://doi.org/10.1038/s41597-022-01852-y
Nat Immunol. 2022 Dec 05.

Ammonia detoxification promotes CD8+ T cell memory development by urea and citrulline cycles.

Ke Tang, Huafeng Zhang, Jinghui Deng, Dianheng Wang, Shichuan Liu, Shuya Lu, Qingfa Cui, Chen Chen, Jincheng Liu, Zhuoshun Yang, Yonggang Li, Jie Chen, Jiadi Lv, Jingwei Ma, Bo Huang.

Amino acid metabolism is essential for cell survival, while the byproduct ammonia is toxic and can injure cellular longevity. Here we show that CD8+ memory T (TM) cells mobilize the carbamoyl phosphate (CP) metabolic pathway to clear ammonia, thus promoting memory development. CD8+ TM cells use β-hydroxybutyrylation to upregulate CP synthetase 1 and trigger the CP metabolic cascade to form arginine in the cytosol. This cytosolic arginine is then translocated into the mitochondria where it is split by arginase 2 to urea and ornithine. Cytosolic arginine is also converted to nitric oxide and citrulline by nitric oxide synthases. Thus, both the urea and citrulline cycles are employed by CD8+ T cells to clear ammonia and enable memory development. This ammonia clearance machinery might be targeted to improve T cell-based cancer immunotherapies.

DOI: https://doi.org/10.1038/s41590-022-01365-1
Cell Metab. 2022 Dec 06. pii: S1550-4131(22)00499-5. [Epub ahead of print]34(12): 1901-1903

Uncoupling of energy production.

Yi Shiau Ng, Doug M Turnbull.

Mitochondrial genetic diseases are a very diverse group of conditions. A recent report by Mootha and colleagues in NEJM describes the underlying genetic defect and clinical findings in monozygotic twins with uncoupling of ATP production.

DOI: https://doi.org/10.1016/j.cmet.2022.11.008
Biochim Biophys Acta Bioenerg. 2022 Dec 05. pii: S0005-2728(22)00417-0. [Epub ahead of print] 148947

Xenotopic expression of alternative oxidase (AOX) to study mechanisms of mitochondrial disease.

Carlo Viscomi, Anthony L Moore, Massimo Zeviani, Marten Szibor.

  The mitochondrial respiratory chain or electron transport chain (ETC) facilitates redox reactions which ultimately lead to the reduction of oxygen to water (respiration). Energy released by this process is used to establish a proton electrochemical gradient which drives ATP formation (oxidative phosphorylation, OXPHOS). It also plays an important role in vital processes beyond ATP formation and cellular metabolism, such as heat production, redox and ion homeostasis. Dysfunction of the ETC can thus impair cellular and organismal viability and is thought to be the underlying cause of a heterogeneous group of so-called mitochondrial diseases. Plants, yeasts, and many lower organisms, but not insects and vertebrates, possess an enzymatic mechanism that confers resistance to respiratory stress conditions, i.e. the alternative oxidase (AOX). Even in cells that naturally lack AOX, it is autonomously imported into the mitochondrial compartment upon xenotopic expression, where it refolds and becomes catalytically engaged when the cytochrome segment of the ETC is blocked. AOX was therefore proposed as a tool to study disease etiologies. To this end, AOX has been xenotopically expressed in mammalian cells and disease models of the fruit fly and mouse. Surprisingly, AOX showed remarkable rescue effects in some cases, whilst in others it had no effect or even exacerbated a condition. Here we summarize what has been learnt from the use of AOX in various disease models and discuss issues which still need to be addressed in order to understand the role of the ETC in health and disease.

Keywords:  Alternative oxidase; Disease models; Mitochondria; Mitochondrial disease; Mouse; Xenogene

DOI:  https://doi.org/10.1016/j.bbabio.2022.148947
Nat Cell Biol. 2022 Dec;24(12): 1714-1725

ER-associated RNA silencing promotes ER quality control.

Sotirios Efstathiou, Franziska Ottens, Lena-Sophie Schütter, Sonia Ravanelli, Nikolaos Charmpilas, Aljona Gutschmidt, Jérémie Le Pen, Niels H Gehring, Eric A Miska, Jorge Bouças, Thorsten Hoppe.

The endoplasmic reticulum (ER) coordinates mRNA translation and processing of secreted and endomembrane proteins. ER-associated degradation (ERAD) prevents the accumulation of misfolded proteins in the ER, but the physiological regulation of this process remains poorly characterized. Here, in a genetic screen using an ERAD model substrate in Caenorhabditis elegans, we identified an anti-viral RNA interference pathway, referred to as ER-associated RNA silencing (ERAS), which acts together with ERAD to preserve ER homeostasis and function. Induced by ER stress, ERAS is mediated by the Argonaute protein RDE-1/AGO2, is conserved in mammals and promotes ER-associated RNA turnover. ERAS and ERAD are complementary, as simultaneous inactivation of both quality-control pathways leads to increased ER stress, reduced protein quality control and impaired intestinal integrity. Collectively, our findings indicate that ER homeostasis and organismal health are protected by synergistic functions of ERAS and ERAD.

DOI: https://doi.org/10.1038/s41556-022-01025-4
Free Radic Biol Med. 2022 Nov 30. pii: S0891-5849(22)01013-9. [Epub ahead of print]

Mitochondria need their sleep: Sleep-wake cycling and the role of redox, bioenergetics, and temperature regulation, involving cysteine-mediated redox signaling, uncoupling proteins, and substrate cycles.

Richard B Richardson, Ryan J Mailloux.

  There is a dearth of evidence-based reports linking the generation of free radicals and associated redox modifications with other major physiological changes of the sleep-wake cycle. To address this shortcoming, we examine and hypothesize that circadian/ultradian interaction of the redoxome, bioenergetics, and thermal signaling strongly regulate the differential activities of the sleep-wake cycle. Post-translational modifications of proteins by reversible cysteine oxoforms, S-glutathionylation and S-nitrosylation, are shown to play a major role regulating mitochondrial reactive oxygen species production, protein synthesis, respiration, and metabolomics. Protein synthesis and nuclear DNA repair are maximized during the wake state, whereas the redoxome is restored and mitochondrial protection is maximized during sleep. Hence, our analysis of redox/bioenergetics/temperature cycling indicates that the wake phase is more restorative and protective to the nucleus, whereas sleep is more restorative and protective to mitochondria. The redox/bioenergetics/temperature regulatory hypothesis adds to the understanding of mitochondrial respiratory uncoupling, substrate or futile cycling control, sudden infant death syndrome, torpor and hibernation and space radiation effects. Similarly, the hypothesis clarifies how the oscillatory redox/bioenergetics/temperature-regulated sleep-wake states, when perturbed by mitochondrial interactome disturbances, contribute to aging and the pathogenesis of diseases of the metabolism and cerebral nervous system.

Keywords:  Circadian; Mitochondria; Nuclear; Oxidative stress; Redoxome; S-glutathionylation; S-nitrosylation; Sleep; Substrate cycles; Uncoupling

DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.11.036
Cell Rep. 2022 Dec 06. pii: S2211-1247(22)01652-7. [Epub ahead of print]41(10): 111769

Cancer cell-derived type I interferons instruct tumor monocyte polarization.

Dylan Kwart, Jing He, Subhashini Srivatsan, Clarissa Lett, Jacquelynn Golubov, Erin M Oswald, Patrick Poon, Xuan Ye, Janelle Waite, Arielle Glatman Zaretsky, Sokol Haxhinasto, Elsa Au-Yeung, Namita T Gupta, Joyce Chiu, Christina Adler, Samvitha Cherravuru, Evangelia Malahias, Nicole Negron, Kathryn Lanza, Angel Coppola, Min Ni, Hang Song, Yi Wei, Gurinder S Atwal, Lynn Macdonald, Nicole Stokes Oristian, William Poueymirou, Vladimir Jankovic, Matthew Fury, Israel Lowy, Andrew J Murphy, Matthew A Sleeman, Bei Wang, Dimitris Skokos.

  Monocytes are highly plastic immune cells that modulate antitumor immunity. Therefore, identifying factors that regulate tumor monocyte functions is critical for developing effective immunotherapies. Here, we determine that endogenous cancer cell-derived type I interferons (IFNs) control monocyte functional polarization. Guided by single-cell transcriptomic profiling of human and mouse tumors, we devise a strategy to distinguish and separate immunostimulatory from immunosuppressive tumor monocytes by surface CD88 and Sca-1 expression. Leveraging this approach, we show that cGAS-STING-regulated cancer cell-derived IFNs polarize immunostimulatory monocytes associated with anti-PD-1 immunotherapy response in mice. We also demonstrate that immunosuppressive monocytes convert into immunostimulatory monocytes upon cancer cell-intrinsic cGAS-STING activation. Consistently, we find that human cancer cells can produce type I IFNs that polarize monocytes, and our immunostimulatory monocyte gene signature is enriched in patient tumors that respond to anti-PD-1 immunotherapy. Our work exposes a role for cancer cell-derived IFNs in licensing monocyte functions that influence immunotherapy outcomes.

Keywords:  CP: Cancer; MDSCs; STING; cGAS; cancer immunology; immune checkpoint blockade; innate immunity; macrophages; monocytes; tumor microenvironment; type I interferon

DOI:  https://doi.org/10.1016/j.celrep.2022.111769
Nat Genet. 2022 Dec;54(12): 1881-1894

The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.

Ilon Liu, Li Jiang, Erik R Samuelsson, Sergio Marco Salas, Alexander Beck, Olivia A Hack, Daeun Jeong, McKenzie L Shaw, Bernhard Englinger, Jenna LaBelle, Hafsa M Mire, Sibylle Madlener, Lisa Mayr, Michael A Quezada, Maria Trissal, Eshini Panditharatna, Kati J Ernst, Jayne Vogelzang, Taylor A Gatesman, Matthew E Halbert, Hana Palova, Petra Pokorna, Jaroslav Sterba, Ondrej Slaby, Rene Geyeregger, Aaron Diaz, Izac J Findlay, Matthew D Dun, Adam Resnick, Mario L Suvà, David T W Jones, Sameer Agnihotri, Jessica Svedlund, Carl Koschmann, Christine Haberler, Thomas Czech, Irene Slavc, Jennifer A Cotter, Keith L Ligon, Sanda Alexandrescu, W K Alfred Yung, Isabel Arrillaga-Romany, Johannes Gojo, Michelle Monje, Mats Nilsson, Mariella G Filbin.

Histone 3 lysine27-to-methionine (H3-K27M) mutations most frequently occur in diffuse midline gliomas (DMGs) of the childhood pons but are also increasingly recognized in adults. Their potential heterogeneity at different ages and midline locations is vastly understudied. Here, through dissecting the single-cell transcriptomic, epigenomic and spatial architectures of a comprehensive cohort of patient H3-K27M DMGs, we delineate how age and anatomical location shape glioma cell-intrinsic and -extrinsic features in light of the shared driver mutation. We show that stem-like oligodendroglial precursor-like cells, present across all clinico-anatomical groups, display varying levels of maturation dependent on location. We reveal a previously underappreciated relationship between mesenchymal cancer cell states and age, linked to age-dependent differences in the immune microenvironment. Further, we resolve the spatial organization of H3-K27M DMG cell populations and identify a mitotic oligodendroglial-lineage niche. Collectively, our study provides a powerful framework for rational modeling and therapeutic interventions.

DOI: https://doi.org/10.1038/s41588-022-01236-3
Nitric Oxide. 2022 Dec 02. pii: S1089-8603(22)00125-2. [Epub ahead of print]

Nitric oxide regulation of cellular metabolism: Adaptive tuning of cellular energy.

Gregory Pappas, Melissa L Wilkinson, Andrew J Gow.

  Nitric oxide can interact with a wide range of proteins including many that are involved in metabolism. In this review we have summarized the effects of NO on glycolysis, fatty acid metabolism, the TCA cycle, and oxidative phosphorylation with reference to skeletal muscle. Low to moderate NO concentrations upregulate glucose and fatty acid oxidation, while higher NO concentrations shift cellular reliance toward a fully glycolytic phenotype. Moderate NO production directly inhibits pyruvate dehydrogenase activity, reducing glucose-derived carbon entry into the TCA cycle and subsequently increasing anaploretic reactions. NO directly inhibits aconitase activity, increasing reliance on glutamine for continued energy production. At higher or prolonged NO exposure, citrate accumulation can inhibit multiple ATP-producing pathways. Reduced TCA flux slows NADH/FADH entry into the ETC. NO can also inhibit the ETC directly, further limiting oxidative phosphorylation. Moderate NO production improves mitochondrial efficiency while improving O2 utilization increasing whole-body energy production. Long-term bioenergetic capacity may be increased because of NO-derived ROS, which participate in adaptive cellular redox signaling through AMPK, PCG1-α, HIF-1, and NF-κB. However, prolonged exposure or high concentrations of NO can result in membrane depolarization and opening of the MPT. In this way NO may serve as a biochemical rheostat matching energy supply with demand for optimal respiratory function.

Keywords:  Cellular respiration; Exercise; Glycolysis; Metabolism; Mitochondria; Nitric oxide

DOI:  https://doi.org/10.1016/j.niox.2022.11.006
Elife. 2022 Dec 08. pii: e77460. [Epub ahead of print]11

Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.

Yuzuru Itoh, Vivek Singh, Anas Khawaja, Andreas Naschberger, Minh Duc Nguyen, Joanna Rorbach, Alexey Amunts.

  The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.

Keywords:  Fe–S cluster; aging; antibiotics; human; mitochondria; mitoribosome; molecular biophysics; structural biology; translation

DOI:  https://doi.org/10.7554/eLife.77460
iScience. 2022 Dec 22. 25(12): 105573

Mitochondrial succinate dehydrogenase function is essential for sperm motility and male fertility.

Rachel M Woodhouse, Natalya Frolows, Guoqiang Wang, Azelle Hawdon, Edmund Heng Kin Wong, Linda C Dansereau, Yingying Su, Liam D Adair, Elizabeth J New, Ashleigh M Philp, Wei Kang Tan, Andrew Philp, Alyson Ashe.

  Mitochondrial health is crucial to sperm quality and male fertility, but the precise role of mitochondria in sperm function remains unclear. SDHA is a component of the succinate dehydrogenase (SDH) complex and plays a critical role in mitochondria. In humans, SDH activity is positively correlated with sperm quality, and mutations in SDHA are associated with Leigh Syndrome. Here we report that the C. elegans SDHA orthologue SDHA-2 is essential for male fertility: sdha-2 mutants produce dramatically fewer offspring due to defective sperm activation and motility, have hyperfused sperm mitochondria, and disrupted redox balance. Similar sperm motility defects in sdha-1 and icl-1 mutant animals suggest an imbalance in metabolites may underlie the fertility defect. Our results demonstrate a role for SDHA-2 in sperm motility and male reproductive health and establish an animal model of SDH deficiency-associated infertility.

Keywords:  Biological sciences; biochemistry; cell biology; molecular biology

DOI:  https://doi.org/10.1016/j.isci.2022.105573
Biochim Biophys Acta Bioenerg. 2022 Dec 06. pii: S0005-2728(22)00419-4. [Epub ahead of print] 148949

Inner mitochondrial membrane structure and fusion dynamics are altered in senescent human iPSC-derived and primary rat cardiomyocytes.

Silke Morris, Isidora Molina-Riquelme, Gonzalo Barrientos, Francisco Bravo, Geraldine Aedo, Wileidy Gómez, Daniel Lagos, Hugo Verdejo, Stefan Peischard, Guiscard Seebohm, Olympia Ekaterini Psathaki, Verónica Eisner, Karin B Busch.

  Dysfunction of the aging heart is a major cause of death in the human population. Amongst other tasks, mitochondria are pivotal to supply the working heart with ATP. The mitochondrial inner membrane (IMM) ultrastructure is tailored to meet these demands and to provide nano-compartments for specific tasks. Thus, function and morphology are closely coupled. Senescent cardiomyocytes from the mouse heart display alterations of the inner mitochondrial membrane. To study the relation between inner mitochondrial membrane architecture, dynamics and function is hardly possible in living organisms. Here, we present two cardiomyocyte senescence cell models that allow in cellular studies of mitochondrial performance. We show that doxorubicin treatment transforms human iPSC-derived cardiomyocytes and rat neonatal cardiomyocytes in an aged phenotype. The treated cardiomyocytes display double-strand breaks in the nDNA, have β-galactosidase activity, possess enlarged nuclei, and show p21 upregulation. Most importantly, they also display a compromised inner mitochondrial structure. This prompted us to test whether the dynamics of the inner membrane was also altered. We found that the exchange of IMM components after organelle fusion was faster in doxorubicin-treated cells than in control cells, with no change in mitochondrial fusion dynamics at the meso-scale. Such altered IMM morphology and dynamics may have important implications for local OXPHOS protein organization, exchange of damaged components, and eventually the mitochondrial bioenergetics function of the aged cardiomyocyte.

Keywords:  Cardiomyocytes; Cristae structure; Doxorubicin; Inner mitochondrial membrane dynamics; Mitochondrial fusion and fission dynamics; Senescence

DOI:  https://doi.org/10.1016/j.bbabio.2022.148949
Nat Commun. 2022 Dec 05. 13(1): 7494

Proteogenomic characterization of MiT family translocation renal cell carcinoma.

Yuanyuan Qu, Xiaohui Wu, Aihetaimujiang Anwaier, Jinwen Feng, Wenhao Xu, Xiaoru Pei, Yu Zhu, Yang Liu, Lin Bai, Guojian Yang, Xi Tian, Jiaqi Su, Guo-Hai Shi, Da-Long Cao, Fujiang Xu, Yue Wang, Hua-Lei Gan, Shujuan Ni, Meng-Hong Sun, Jian-Yuan Zhao, Hailiang Zhang, Dingwei Ye, Chen Ding.

Microphthalmia transcription factor (MiT) family translocation renal cell carcinoma (tRCC) is a rare type of kidney cancer, which is not well characterized. Here we show the comprehensive proteogenomic analysis of tRCC tumors and normal adjacent tissues to elucidate the molecular landscape of this disease. Our study reveals that defective DNA repair plays an important role in tRCC carcinogenesis and progression. Metabolic processes are markedly dysregulated at both the mRNA and protein levels. Proteomic and phosphoproteome data identify mTOR signaling pathway as a potential therapeutic target. Moreover, molecular subtyping and immune infiltration analysis characterize the inter-tumoral heterogeneity of tRCC. Multi-omic integration reveals the dysregulation of cellular processes affected by genomic alterations, including oxidative phosphorylation, autophagy, transcription factor activity, and proteasome function. This study represents a comprehensive proteogenomic analysis of tRCC, providing valuable insights into its biological mechanisms, disease diagnosis, and prognostication.

DOI: https://doi.org/10.1038/s41467-022-34460-w
Cancer Res. 2022 Dec 05. pii: canres.0275.2022-1-24 21:38:02.347. [Epub ahead of print]

Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models.

Livius Penter, Elisa Ten Hacken, Jackson Southard, Caleb Lareau, Leif S Ludwig, Shuqiang Li, Donna S Neuberg, Kenneth J Livak, Catherine J Wu.

Murine models are indispensable tools for functional genomic studies and preclinical testing of novel therapeutic approaches. Mitochondrial single-cell assay for transposase-accessible chromatin (mtscATAC-seq) enables the dissection of cellular heterogeneity and clonal dynamics by capturing chromatin accessibility, copy number variations (CNV), and mitochondrial DNA (mtDNA) mutations, yet its applicability to murine studies remains unexplored. By leveraging mtscATAC-seq in novel chronic lymphocytic leukemia and Richter syndrome mouse models, we report the detection of mtDNA mutations, particularly in highly proliferative murine cells, alongside CNV and chromatin state changes indicative of clonal evolution upon secondary transplant. This study thus demonstrates the feasibility and utility of multi-modal single-cell and natural barcoding approaches to characterize murine cancer models.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-0275
Science. 2022 Dec 09. 378(6624): 1097-1104

IFITM proteins assist cellular uptake of diverse linked chemotypes.

Kevin Lou, Douglas R Wassarman, Tangpo Yang, YiTing Paung, Ziyang Zhang, Thomas A O'Loughlin, Megan K Moore, Regina K Egan, Patricia Greninger, Cyril H Benes, Markus A Seeliger, Jack Taunton, Luke A Gilbert, Kevan M Shokat.

The search for cell-permeable drugs has conventionally focused on low-molecular weight (MW), nonpolar, rigid chemical structures. However, emerging therapeutic strategies break traditional drug design rules by employing flexibly linked chemical entities composed of more than one ligand. Using complementary genome-scale chemical-genetic approaches we identified an endogenous chemical uptake pathway involving interferon-induced transmembrane proteins (IFITMs) that modulates the cell permeability of a prototypical biopic inhibitor of MTOR (RapaLink-1, MW: 1784 g/mol). We devised additional linked inhibitors targeting BCR-ABL1 (DasatiLink-1, MW: 1518 g/mol) and EIF4A1 (BisRoc-1, MW: 1466 g/mol), uptake of which was facilitated by IFITMs. We also found that IFITMs moderately assisted some proteolysis-targeting chimeras and examined the physicochemical requirements for involvement of this uptake pathway.

DOI: https://doi.org/10.1126/science.abl5829
Nat Rev Genet. 2022 Dec 09.

Spatial biology of cancer evolution.

Zaira Seferbekova, Artem Lomakin, Lucy R Yates, Moritz Gerstung.

The natural history of cancers can be understood through the lens of evolution given that the driving forces of cancer development are mutation and selection of fitter clones. Cancer growth and progression are spatial processes that involve the breakdown of normal tissue organization, invasion and metastasis. For these reasons, spatial patterns are an integral part of histological tumour grading and staging as they measure the progression from normal to malignant disease. Furthermore, tumour cells are part of an ecosystem of tumour cells and their surrounding tumour microenvironment. A range of new spatial genomic, transcriptomic and proteomic technologies offers new avenues for the study of cancer evolution with great molecular and spatial detail. These methods enable precise characterizations of the tumour microenvironment, cellular interactions therein and micro-anatomical structures. In conjunction with spatial genomics, it emerges that tumours and microenvironments co-evolve, which helps explain observable patterns of heterogeneity and offers new routes for therapeutic interventions.

DOI: https://doi.org/10.1038/s41576-022-00553-x
Cancer Res. 2022 Dec 08. pii: CAN-22-1002. [Epub ahead of print]

Elevated methionine flux drives pyroptosis evasion in persister cancer cells.

Asmaa El-Kenawi, Anders Berglund, Veronica Estrella, Yonghong Zhang, Min Liu, Ryan M Putney, Sean Yoder, Joseph Johnson, Joel Brown, Robert Gatenby.

Induction of cell death represents a primary goal of most anti-cancer treatments. Despite the efficacy of such approaches, a small population of "persisters" develop evasion strategies to therapy-induced cell death. While previous studies have identified mechanisms of resistance to apoptosis, the mechanisms by which persisters dampen other forms of cell death, such as pyroptosis, remain to be elucidated. Pyroptosis is a form of inflammatory cell death that involves formation of membrane pores, ion gradient imbalance, water inflow and membrane rupture. Herein, we investigate mechanisms by which cancer persisters resist pyroptosis, survive, then proliferate in the presence of tyrosine kinase inhibitors (TKI). Lung, prostate and esophageal cancer persister cells remaining after treatments exhibited several hallmarks indicative of pyroptosis resistance. The inflammatory attributes of persisters included chronic activation of inflammasome, STING, and type I interferons. Comprehensive metabolomic characterization uncovered that TKI-induced pyroptotic persisters display high methionine consumption and excessive taurine production. Elevated methionine flux or exogenous taurine preserved plasma membrane integrity via osmolyte-mediated effects. Increased dependency on methionine flux decreased the level of one carbon metabolism intermediate S-(5'-adenosyl)-L-homocysteine, a determinant of cell methylation capacity. The consequent increase in methylation potential induced DNA hypermethylation of genes regulating metal ion balance and intrinsic immune response. This enabled thwarting TKI resistance by using the hypomethylating agent decitabine. In summary, the evolution of resistance to pyroptosis can occur via a stepwise process of physical acclimation and epigenetic changes without existing or recurrent mutations. .

DOI: https://doi.org/10.1158/0008-5472.CAN-22-1002
Cell Metab. 2022 Dec 06. pii: S1550-4131(22)00497-1. [Epub ahead of print]34(12): 1897-1898

Deoxyribonucleoside triphosphate pools in mammalian cells are expandable upon DNA damage.

Rui Liu, Qianming Chen.

The rapid increase of dNTP pools in mammalian cells upon DNA damage has been previously documented. Alterations in protein modifications or interactions can rapidly modulate the activity and protein stability of mammalian RNR, and activation of PRPS1/2-dependent generation of PRPP enhances the production of the indispensable ribose sugar for nucleotide biosynthesis.

DOI: https://doi.org/10.1016/j.cmet.2022.11.006